{"entity": "journal", "iuid": "e3ecf5f7f29840a1a64a01c388850719", "timestamp": "2026-07-10T20:01:34.639Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Sci%20Rep.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Sci%20Rep"}}, "title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "publications_count": 382, "publications": [{"entity": "publication", "iuid": "5d45f88c5d364945a3debc7f75535c9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d45f88c5d364945a3debc7f75535c9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d45f88c5d364945a3debc7f75535c9d"}}, "title": "Disrupting Notch signalling by a small molecule inhibiting dihydroorotate dehydrogenase activity.", "authors": [{"family": "Braune", "given": "Eike-Benjamin", "initials": "EB", "orcid": "0009-0003-1019-8137", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca99d2f589348cfad6c2bfc8a641558.json"}}, {"family": "Wienke", "given": "Dirk", "initials": "D"}, {"family": "Seshire", "given": "Anita", "initials": "A"}, {"family": "Heinrich", "given": "Timo", "initials": "T"}, {"family": "Haraldsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-0743-7830", "researcher": {"href": "https://publications.scilifelab.se/researcher/42031e3e48ba47f896b74bfb733cdeff.json"}}, {"family": "Lain", "given": "Sonia", "initials": "S"}, {"family": "Lendahl", "given": "Urban", "initials": "U", "orcid": "0000-0001-9543-8141", "researcher": {"href": "https://publications.scilifelab.se/researcher/c61e35bb0bfc40e2968aa758873ee27a.json"}}], "type": "journal article", "published": "2026-06-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "The Notch signalling pathway is highly evolutionarily conserved and regulates differentiation and homeostasis in most organs. Given the critical role of Notch signalling for normal development, dysregulated Notch signalling is frequently linked to pathogenesis of disease and cancer. Hence, developing Notch-targeting therapeutics is warranted but has been challenging and Notch inhibitors have not yet reached broad clinical use. In this report, we identify potential Notch inhibitors, using a novel cell-based Notch reporter system for unbiased screening of compounds reducing Notch signalling. A library of 37,966 small organic compounds was screened for inhibitor candidates, followed by a counter screen to eliminate \u03b3-secretase inhibitor-like compounds and an orthogonal screen based on the role of Notch signalling in myogenic differentiation. This triage led to the identification of five Notch inhibitor candidate hits with different chemical backbones and unrelated to previous Notch antagonists. One candidate hit proved to be a DHODH inhibitor, and we also provide evidence that a well-established DHODH inhibitor is a highly potent Notch inhibitor. In conclusion, our data support the notion that DHODH inhibition may be an interesting avenue to explore for the development of novel Notch inhibitors.", "doi": "10.1038/s41598-026-55679-3", "pmid": "42251101", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-026-55679-3"}, {"db": "pmc", "key": "PMC13242511"}], "notes": [], "created": "2026-07-01T07:50:22.727Z", "modified": "2026-07-06T20:10:32.090Z"}, {"entity": "publication", "iuid": "9bafa70241894ebcab4e2bf9d0640d40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40"}}, "title": "Comparing DNA metabarcoding with light microscopy to identify eukaryotic phytoplankton in the Baltic Sea, Kattegat and Skagerrak", "authors": [{"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B", "orcid": "0000-0002-7524-3504", "researcher": {"href": "https://publications.scilifelab.se/researcher/44722b5ece5b420bb59fdb749833f443.json"}}, {"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}], "type": "journal-article", "published": "2026-05-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Marine phytoplankton monitoring has long relied on microscopy, but DNA metabarcoding has recently emerged as a complementary approach. This study assessed the applicability of DNA metabarcoding of the 18S ribosomal RNA gene in marine monitoring and compared its results with conventional microscopy. We analyzed data from 232 surface water samples from 17 monitoring stations in the Baltic Sea, Kattegat, and Skagerrak. Metabarcoding detected more orders, genera, and species than microscopy, with a 43% overlap in the most common genera identified by both methods. Despite attempts to normalize sequence reads to spike-in DNA or DNA concentrations, the correlations between abundances derived from the two methods were weak, though varied considerably between taxonomic groups and geographical areas. Correlations were consistently stronger when using carbon and biovolume concentrations than cell abundances. Our results highlight the potential of metabarcoding to expand biodiversity assessments and advance our understanding of microbial biodiversity in marine ecosystems. As a complement to microscopy, it can enhance existing monitoring efforts. Future improvements in reference database completeness, adoption of long-read sequencing technologies, and better characterization of gene copy number variability per cell are needed to further extend the applicability of metabarcoding for quantitative analyses.", "doi": "10.1038/s41598-026-48838-z", "pmid": "42156811", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13190673"}, {"db": "pii", "key": "10.1038/s41598-026-48838-z"}], "notes": [], "created": "2026-06-08T17:17:40.513Z", "modified": "2026-07-04T18:59:51.656Z"}, {"entity": "publication", "iuid": "15e539643f51433caa47680271e70979", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15e539643f51433caa47680271e70979.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15e539643f51433caa47680271e70979"}}, "title": "Limosilactobacillus reuteri metabolites modulate immune pathways and intestinal barrier repair after 5 fluorouracil exposure.", "authors": [{"family": "Lasaviciute", "given": "Gintare", "initials": "G"}, {"family": "L\u00f3pez Plana", "given": "Marta", "initials": "M"}, {"family": "Sundberg \u00d6rtegren", "given": "Sofia", "initials": "S"}, {"family": "Telli", "given": "Sevasteia", "initials": "S"}, {"family": "Kourmoulakis", "given": "Symeon", "initials": "S"}, {"family": "Ermann Lundberg", "given": "Ludwig", "initials": "L", "orcid": "0000-0001-5983-1771", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb47fe370d24b30b505f75583167a9f.json"}}, {"family": "Lidberg", "given": "Kenny", "initials": "K"}, {"family": "Peiris", "given": "Oshadi", "initials": "O"}, {"family": "Sinha", "given": "Indranil", "initials": "I", "orcid": "0000-0002-2513-5927", "researcher": {"href": "https://publications.scilifelab.se/researcher/970cda1bb71d4ae1b36cc5628023f7d4.json"}}, {"family": "Jonsson", "given": "Ann-Beth", "initials": "AB"}, {"family": "Roos", "given": "Stefan", "initials": "S", "orcid": "0000-0002-1606-1794", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab7209c1ebe40d8bdcc73f99fb44b29.json"}}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Mata Forsberg", "given": "Manuel", "initials": "M", "orcid": "0009-0008-3711-9722", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1120ae12e54a829e523e983c5ea0d2.json"}}, {"family": "Sverremark-Ekstr\u00f6m", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2026-04-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Antimetabolites such as 5 fluorouracil are known to induce inflammation in the gut and oral cavity, underscoring the need for strategies that mitigate chemotherapy-associated toxicity. The aim of this study was to determine whether secreted components from the probiotic bacterium Limosilactobacillus reuteri DSM 17938, specifically cell-free supernatant, exopolysaccharides, and extracellular membrane vesicles, can support epithelial barrier recovery following 5 fluorouracil-induced injury. Exposure to 5 fluorouracil impaired viability, metabolic activity, and barrier integrity, and shifted the functional responses of Caco-2 cells toward increased inflammation. Stimulation with exopolysaccharides after removal of 5 fluorouracil significantly improved barrier integrity in both enterocyte-like Caco-2 cells and primary human intestinal epithelial cells, while paradoxically inducing an inflammatory protein profile in the enterocyte-like cells. Transcriptomic analysis revealed that exopolysaccharides modulate gene programs associated with extracellular matrix organization and structural remodelling. Furthermore, cell-free supernatant, membrane vesicles, and exopolysaccharides differentially influenced monocyte polarization pathways when monocytes were cultured with supernatant from 5 fluorouracil-exposed Caco-2 cells. Together, these findings demonstrate that bacterial metabolites such as exopolysaccharides influence intestinal barrier recovery upon inflammation and activate immune cell recruitment that could have consequences for the intestinal epithelial integrity during inflammation.", "doi": "10.1038/s41598-026-45524-y", "pmid": "41927663", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13049081"}, {"db": "pii", "key": "10.1038/s41598-026-45524-y"}], "notes": [], "created": "2026-04-10T12:45:16.030Z", "modified": "2026-05-04T07:55:34.771Z"}, {"entity": "publication", "iuid": "4841e395d0f541e6b7f8203d0fa258c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4841e395d0f541e6b7f8203d0fa258c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4841e395d0f541e6b7f8203d0fa258c0"}}, "title": "Medical facemask waste alters detritus decomposition and fungal communities in a freshwater pond.", "authors": [{"family": "Kong", "given": "Ze Hui", "initials": "ZH"}, {"family": "Stangl", "given": "Martina", "initials": "M"}, {"family": "Oester", "given": "Rebecca", "initials": "R"}, {"family": "Rehnstam", "given": "Svante", "initials": "S"}, {"family": "Futter", "given": "Martyn", "initials": "M"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Bundschuh", "given": "Mirco", "initials": "M"}, {"family": "Mckie", "given": "Brendan G", "initials": "BG"}], "type": "journal article", "published": "2026-03-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Plastic pollution is an ongoing issue in freshwater ecosystems, including that generated from the spike in disposable facemask use during the COVID-19 pandemic. The degradation products of such plastic waste, including plastic leachate compounds and generation of microplastics, have the potential to affect freshwater ecosystem structure and function. We investigated the effects of facemask-derived polypropylene particles of different sizes and their leachates on fungal communities and detritus decomposition in a pond. We further investigated effects of the presence of wood shavings, used to represent a naturally-occurring, highly refractory, organic reference material. Over five weeks, leaf litter mass loss and cotton cellulose tensile strength loss were quantified weekly, and fungal biomass, community composition, and functional gene abundance at two time points. Wood shavings reduced leaf decomposition (-4.4%) relative to controls, while plastics increased decomposition of labile cotton cellulose (+ 6.6%), with the strongest effect from unleached microplastics (+ 22.7%). After 21 days, litter-associated fungal biomass was reduced by the presence of wood shavings (-20.1%) and plastics (-8.6%). Fungal communities differed between wood- and control treatments, and varied widely under plastic exposure. Our findings highlight size- and leachate-dependent effects of facemask-derived plastic particles on freshwater fungal communities and ecosystem functions, which largely contrasted with those of wood.\n\nThe online version contains supplementary material available at 10.1038/s41598-026-45795-5.", "doi": "10.1038/s41598-026-45795-5", "pmid": "41912744", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13039742"}, {"db": "pii", "key": "10.1038/s41598-026-45795-5"}], "notes": [], "created": "2026-06-01T08:43:00.886Z", "modified": "2026-06-01T08:43:00.918Z"}, {"entity": "publication", "iuid": "51ab6bef0c294812a1af87272c18bba2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51ab6bef0c294812a1af87272c18bba2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51ab6bef0c294812a1af87272c18bba2"}}, "title": "Genetic predisposition to coffee consumption and the association with the early risk of atherosclerosis.", "authors": [{"family": "Qiao", "given": "Xiangyu", "initials": "X"}, {"family": "Toma", "given": "Vanessa William", "initials": "VW"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Herraiz-Adillo", "given": "\u00c1ngel", "initials": "\u00c1"}, {"family": "S\u00f6derholm", "given": "Simon", "initials": "S"}, {"family": "Berglind", "given": "Daniel", "initials": "D"}, {"family": "Calling", "given": "Susanna", "initials": "S"}, {"family": "Daka", "given": "Bledar", "initials": "B"}, {"family": "Martinell", "given": "Mats", "initials": "M"}, {"family": "Bergman", "given": "Frida", "initials": "F"}, {"family": "Henriksson", "given": "Pontus", "initials": "P"}, {"family": "Ghafouri", "given": "Bijar", "initials": "B"}, {"family": "Ulander", "given": "Martin", "initials": "M"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ"}, {"family": "Cant\u00f9", "given": "Claudio", "initials": "C"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Iredahl", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2026-03-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "The cardiovascular effects of coffee consumption remain debated, particularly regarding early-stage subclinical atherosclerosis. This study investigated the association between coffee intake, genetic predisposition, and the risk of subclinical coronary and carotid atherosclerosis in 24,835 participants from the Swedish CArdioPulmonary bioImage Study (SCAPIS). Coffee intake was assessed via self-reported questionnaires. Atherosclerosis was assessed via segment involvement score (SIS), coronary artery calcium score (CACS) and carotid plaque. Observational analysis showed no significant association between coffee consumption and SIS, CACS, or carotid plaques. However, both one-sample and two-sample (SCAPIS and UK Biobank) Mendelian randomization (MR) analyses showed an association between genetic predisposition to higher coffee consumption and increased SIS. Stratification analyses further explored differences in genetic associations across varying coffee consumption levels. Among individuals consuming coffee more than twice daily, two coffee consumption-associated single nucleotide polymorphisms (SNPs) in AHR and CYP1A1/CYP1A2 were correlated with SIS. Integrative metabolomics and proteomics analyses identified lipid-related metabolites (triglycerides, phospholipids, free cholesterol) and inflammation-related proteins (DLK1, IL1RL2, CCL17) associated with the genetic proxy of coffee consumption. These findings suggest that genetically influenced coffee consumption may be associated with coronary atherosclerosis risk in frequent coffee drinkers, although the underlying biological basis remains to be clarified.", "doi": "10.1038/s41598-026-44122-2", "pmid": "41865070", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13009213"}, {"db": "pii", "key": "10.1038/s41598-026-44122-2"}], "notes": [], "created": "2026-06-01T08:45:44.894Z", "modified": "2026-06-01T08:45:44.897Z"}, {"entity": "publication", "iuid": "999289be0c1e406bb30bd4b40e7a2f00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00"}}, "title": "Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost", "authors": [{"family": "Selvatici", "given": "Sofia", "initials": "S"}, {"family": "Jin", "given": "Chenyu", "initials": "C"}, {"family": "Zazula", "given": "Grant", "initials": "G", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Moots", "given": "Hannah M", "initials": "HM", "orcid": "0000-0002-6637-6321", "researcher": {"href": "https://publications.scilifelab.se/researcher/5105354f578c480ba144061ffbb49bf5.json"}}, {"family": "Sharif", "given": "Bilal", "initials": "B"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Parducci", "given": "Laura", "initials": "L", "orcid": "0000-0003-1956-4757", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed4c737e2c7c4266b598a89aa2116a91.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}], "type": "journal-article", "published": "2026-03-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "We identified a 3000-year-old specimen from the Traditional Territory of the Tr'ond\u00ebk Hw\u00ebch'in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as \"Ts'ey\" in the H\u00e4n language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.", "doi": "10.1038/s41598-026-44540-2", "pmid": "41845022", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996357"}, {"db": "pii", "key": "10.1038/s41598-026-44540-2"}], "notes": [], "created": "2026-03-23T13:18:35.892Z", "modified": "2026-03-24T09:12:30.461Z"}, {"entity": "publication", "iuid": "d029c59777c84c9bad57d48f2ef1f8a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d029c59777c84c9bad57d48f2ef1f8a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d029c59777c84c9bad57d48f2ef1f8a0"}}, "title": "Efficacy of mebendazole in the spontaneous NZBxNZWF1 animal model of systemic lupus erythematosus.", "authors": [{"family": "Eloranta", "given": "M L", "initials": "ML"}, {"family": "Nygren", "given": "P", "initials": "P"}, {"family": "Larsson", "given": "R", "initials": "R"}, {"family": "Loskog", "given": "A", "initials": "A"}, {"family": "Woodworth", "given": "N", "initials": "N"}, {"family": "Hultqvist", "given": "M", "initials": "M"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gravenfors", "given": "Ylva", "initials": "Y"}, {"family": "R\u00f6nnblom", "given": "L", "initials": "L"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}], "type": "journal article", "published": "2026-02-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "pages": "6357", "issn-l": "2045-2322"}, "abstract": "Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a complex etiology involving both innate and adaptive immune dysregulation. Among several perturbed signaling pathways, decreased ERK activity in CD4\u207a T-cells has been linked to DNA hypomethylation and aberrant gene expression in SLE. Mebendazole (MBZ), an anti-helminthic drug with a well-established safety profile, has shown immunomodulatory effects in preclinical studies, including activation of the MEK/ERK pathway and inhibition of MAPK14 (p38), a known driver of inflammation. To evaluate the therapeutic potential of MBZ in SLE, we tested its efficacy in NZBxNZWF1 mice, a spontaneous and well-characterized SLE model. MBZ treatment resulted in reduced proteinuria, lower anti-dsDNA antibody levels, and diminished glomerular IgG deposition, both in preventive and therapeutic settings. Exploratory in vitro data suggest that MBZ may also influence ERK signaling in B cells, while the mechanistic basis of these effects remains to be clarified. Our findings demonstrate robust phenotypic improvements and support further investigation of MBZ as a repositioned candidate for SLE.\n\nThe online version contains supplementary material available at 10.1038/s41598-026-37930-z.", "doi": "10.1038/s41598-026-37930-z", "pmid": "41680254", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12905218"}, {"db": "pii", "key": "10.1038/s41598-026-37930-z"}], "notes": [], "created": "2026-05-14T20:14:52.517Z", "modified": "2026-05-14T20:14:52.521Z"}, {"entity": "publication", "iuid": "0b5071faf9e94295890d2321eea1b81a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b5071faf9e94295890d2321eea1b81a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b5071faf9e94295890d2321eea1b81a"}}, "title": "Metabolic interactions between bacterial co-isolates from catheter-associated urinary tract infections", "authors": [{"family": "Sokol", "given": "Dmytro", "initials": "D"}, {"family": "Rzhepishevska", "given": "Olena", "initials": "O", "orcid": "0000-0002-7912-7447", "researcher": {"href": "https://publications.scilifelab.se/researcher/53216ecce7934eb3a4beedb82f318fc5.json"}}, {"family": "Marynova", "given": "Iryna", "initials": "I"}, {"family": "Monsen", "given": "Tor", "initials": "T"}, {"family": "Antti", "given": "Henrik", "initials": "H"}, {"family": "Ramstedt", "given": "Madeleine", "initials": "M", "orcid": "0000-0003-2646-8501", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0fb139ad40341fd85e4ba6fe39eb7fe.json"}}], "type": "journal-article", "published": "2026-01-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "pages": "2061", "issn-l": "2045-2322"}, "abstract": "Catheter-associated urinary tract infections (CAUTI) are complex infections often involving multi-species bacteria. Escherichia coli is frequently an early coloniser. Subsequent colonisation by Pseudomonas aeruginosa and coexistence mechanisms between the two strains within urethral catheters is not yet fully understood. In this study, metabolic adaptations between co-isolated clinical E. coli and P. aeruginosa strains were investigated. It was found that P. aeruginosa outgrew E. coli in artificial urine medium (AUM), whereas E. coli dominated in culture broth such as Iso-sensitest. No evidence of direct antagonism was observed. Metabolite analyses revealed distinct metabolite patterns indicating cross-feeding and metabolic adaptations. In AUM, stress-response metabolites were elevated. Additionally, E. coli appeared to experience Fe-limitation in AUM, while the same was not observed for P. aeruginosa. The results highlight the influence of nutrient conditions on processes within mixed biofilms.\n\nThe online version contains supplementary material available at 10.1038/s41598-025-33855-1.", "doi": "10.1038/s41598-025-33855-1", "pmid": "41535363", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12808099"}, {"db": "pii", "key": "10.1038/s41598-025-33855-1"}], "notes": [], "created": "2026-02-23T09:04:21.178Z", "modified": "2026-03-24T09:14:47.860Z"}, {"entity": "publication", "iuid": "85c5bdfdbc81457e81767eab223261e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3"}}, "title": "Diagnostic and prognostic biomarkers associated with histotype in advanced epithelial ovarian cancer.", "authors": [{"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Swenson", "given": "Hugo", "initials": "H"}, {"family": "Werner", "given": "Lucas", "initials": "L"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Mateoiu", "given": "Constantina", "initials": "C"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Dahm-K\u00e4hler", "given": "Pernilla", "initials": "P"}, {"family": "Saed", "given": "Ghassan", "initials": "G"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2025-10-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "37171", "issn-l": "2045-2322"}, "abstract": "Despite advances in cancer treatments, epithelial ovarian cancer (EOC) remains the leading cause of death among gynecologic cancers. EOC is stratified into five main histopathological subtypes: high-grade serous carcinoma (HGSC), low-grade serous carcinoma (LGSC), endometrioid carcinoma (EC), clear cell carcinoma (CCC), and mucinous carcinoma (MC). However, personalized treatment strategies and reliable biomarkers for all histotypes remain elusive. Building on our previous work with early-stage EOC, we aim to explore diagnostic and prognostic biomarkers in advanced-stage EOC, updated to the latest World Health Organization classification guidelines from 2020, using comprehensive transcriptomic profiling from total RNA sequencing of 146 EOCs. Differential expression analysis identified top 9 histotype-specific gene panels for HGSC, CCC, MC, and EC, including S100A1 (HGSC), ARID3A (CCC), LGALS4 (MC), and PAX9 (EC). We also identified gene candidates associated with overall survival and disease-specific survival, reflecting both favorable (e.g., OTOF, EEF1E1-BLOC1S5, and STAC3) and unfavorable (e.g., SMOC1, GDPGP1, EPRS1) clinical outcome. Additionally, enrichment analysis revealed tumor progression-related pathways unique to each histotype, offering insights into the molecular mechanisms underlying disease progression and potential therapeutic targets. These findings provide valuable insights into the molecular landscape of advanced-stage EOC, paving the way for more effective diagnostic and prognostic tools across diverse histotypes.", "doi": "10.1038/s41598-025-24938-0", "pmid": "41131133", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550092"}, {"db": "pii", "key": "10.1038/s41598-025-24938-0"}], "notes": [], "created": "2025-11-07T07:25:02.175Z", "modified": "2025-11-28T10:47:09.805Z"}, {"entity": "publication", "iuid": "76bc40380dd544cdaf4932e9eb027c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/76bc40380dd544cdaf4932e9eb027c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/76bc40380dd544cdaf4932e9eb027c93"}}, "title": "Distribution of photosensitive fagopyrin in buckwheat flowers and its potential biological relevance.", "authors": [{"family": "Horny\u00e1k", "given": "Marta", "initials": "M"}, {"family": "Kula-Maximenko", "given": "Monika", "initials": "M"}, {"family": "Miszalski", "given": "Zbigniew", "initials": "Z"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U"}, {"family": "Slazak", "given": "Blazej", "initials": "B"}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "36279", "issn-l": "2045-2322"}, "abstract": "Fagopyrum esculentum (Moench) is a valuable pseudo-cereal valued for its highly nutritious, gluten-free seeds. Despite being recognized as a 21st -century superfood, buckwheat remains non-competitive in seed yield compared to common cereals. Low productivity is mainly caused by abnormalities in female gametophyte development and frequent flower and embryo abortion. Buckwheat flowers accumulate high levels of phototoxic fagopyrin (FAG), whose physiological role remains unclear. FAG and its precursor (PFAG) are light-sensitive compounds with absorbance spectra in the green-yellow range (549-593 nm, peak at 590 nm), which makes their accumulation potentially responsive to light conditions. To address this, plants were cultivated under different light spectra, and the content of FAG and PFAG was analyzed in distinct floral organs (stamen, pistil, petal, and receptacle) using LC-MS, with their spatial distribution assessed by the MALDI-MS imaging. Pistil showed statistically the highest FAG and PFAG contents, while petals contained the lowest levels. A high density of FAG surrounding the ovary indicates a potential role in the reproductive part. Moreover, negative correlations were detected between flower production and FAG levels in the receptacles and pistils under specific light treatments. These results suggest that FAG may influence flower production and female gametophyte development, linking light environment to reproductive success in buckwheat.", "doi": "10.1038/s41598-025-20116-4", "pmid": "41102249", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12533014"}, {"db": "pii", "key": "10.1038/s41598-025-20116-4"}], "notes": [], "created": "2025-11-21T09:46:16.328Z", "modified": "2025-11-21T09:46:16.332Z"}, {"entity": "publication", "iuid": "afb960cb22864dd38a6d8ae590cc4341", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afb960cb22864dd38a6d8ae590cc4341.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afb960cb22864dd38a6d8ae590cc4341"}}, "title": "Evaluating cell-specific gene expression using single-cell and single-nuclei RNA-sequencing data from human pancreatic islets of the same donors.", "authors": [{"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Ofori", "given": "Jones K", "initials": "JK", "orcid": "0000-0001-6484-1544", "researcher": {"href": "https://publications.scilifelab.se/researcher/31b7b1843fd94a99b488eaf653c6385b.json"}}, {"family": "Wierup", "given": "Nils", "initials": "N"}, {"family": "Bacos", "given": "Karl", "initials": "K", "orcid": "0000-0002-2461-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/527a271d23de48f8937b489c43e9da1b.json"}}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "36133", "issn-l": "2045-2322"}, "abstract": "Single-cell and single-nuclei RNA-sequencing (scRNA-seq and snRNA-seq) analyze cell-specific transcriptomes. However, only snRNA-seq applies to frozen biobanked samples. For human pancreatic islets, marker genes and reference-based cell type annotation methods are mainly from scRNA-seq datasets and may not be suitable for snRNA-seq. We compared human islet scRNA-seq and snRNA-seq data from the same donors (N = 4) and evaluated annotation methods by studying cell type composition and gene detection, and identified novel marker genes. We compared cell type annotations: (1) manual annotation based on identified marker genes, (2) reference-based annotation using Azimuth's scRNA-seq pancreasref dataset, or (3) Seurat's label transfer from the Human Pancreas Analysis Program (HPAP) scRNA-seq dataset. ScRNA-seq and snRNA-seq identified the same cell types, but predicted cell type proportions differed. Cell type proportion-differences between annotation methods were larger for snRNA-seq. Reference-based annotations generated higher cell type prediction and mapping scores for scRNA-seq than snRNA-seq. Manual annotation identified the novel snRNA-seq markers DOCK10, KIRREL3 (beta cells), STK32B (alpha cells), MECOM, AC007368.1 (acinar cells), LAMC2 and SLC28A3 (ductal cells), which improve snRNA-seq-based annotation. We confirmed ZNF385D as a snRNA-seq beta cell marker and ZNF385D silencing reduced insulin secretion. In conclusion, this study discovered novel snRNA-seq cell type marker genes in human pancreatic islets, and highlights the need for tailored snRNA-seq annotation strategies.", "doi": "10.1038/s41598-025-21595-1", "pmid": "41102292", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12533216"}, {"db": "pii", "key": "10.1038/s41598-025-21595-1"}], "notes": [], "created": "2025-10-30T13:58:54.553Z", "modified": "2025-11-13T17:36:11.555Z"}, {"entity": "publication", "iuid": "8ed54f29f33f4ce39d346fdb35295c92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92"}}, "title": "Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.", "authors": [{"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S", "orcid": "0000-0001-5877-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/baea894b3ac14408a7492df2fc6c796e.json"}}, {"family": "Granstr\u00f6m", "given": "Anna L\u00f6f", "initials": "AL", "orcid": "0000-0003-2169-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c08d2119eca4e67936cd5b5d2dc47d3.json"}}, {"family": "Kiasat", "given": "Ali", "initials": "A", "orcid": "0000-0001-5568-3265", "researcher": {"href": "https://publications.scilifelab.se/researcher/f92cb577648943a2a09efe76787545c4.json"}}, {"family": "Ahlstr\u00f6m", "given": "Gustav", "initials": "G"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/6538b950bbd440e3aa32435d23c98074.json"}}, {"family": "Rautiainen", "given": "Susanne", "initials": "S", "orcid": "0000-0001-7193-6082", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb22af02cdd04e80b1a0809b163ad56e.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Andersson", "given": "Fredrik O", "initials": "FO"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications.scilifelab.se/researcher/17bed8be7a9c46b5a94147b80fd58e82.json"}}, {"family": "Gustafsson", "given": "Ulf O", "initials": "UO", "orcid": "0000-0001-9549-061X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4302890c32a24317aa1d0f6807c4458e.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "35039", "issn-l": "2045-2322"}, "abstract": "Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.", "doi": "10.1038/s41598-025-18106-7", "pmid": "41062543", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508173"}, {"db": "pii", "key": "10.1038/s41598-025-18106-7"}], "notes": [], "created": "2025-11-07T15:05:48.239Z", "modified": "2025-11-07T15:05:53.602Z"}, {"entity": "publication", "iuid": "379697221e864158b23905f98efc1f8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/379697221e864158b23905f98efc1f8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/379697221e864158b23905f98efc1f8a"}}, "title": "Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A"}, {"family": "Pacheco-Valenciana", "given": "Armando", "initials": "A"}, {"family": "Milke", "given": "Felix", "initials": "F"}, {"family": "Dharamshi", "given": "Jennah E", "initials": "JE"}, {"family": "Hampel", "given": "Justyna J", "initials": "JJ"}, {"family": "Damashek", "given": "Julian", "initials": "J"}, {"family": "Wienhausen", "given": "Gerrit", "initials": "G"}, {"family": "Rodriguez-R", "given": "Luis Miguel", "initials": "LM"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "34482", "issn-l": "2045-2322"}, "abstract": "Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.", "doi": "10.1038/s41598-025-22383-7", "pmid": "41044404", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12495000"}, {"db": "pii", "key": "10.1038/s41598-025-22383-7"}], "notes": [], "created": "2025-11-19T07:34:55.667Z", "modified": "2025-11-28T10:47:04.484Z"}, {"entity": "publication", "iuid": "5030ff3ac322493db0bee8969ebf9d14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5030ff3ac322493db0bee8969ebf9d14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5030ff3ac322493db0bee8969ebf9d14"}}, "title": "Reliable on-treatment prognostication and target identification with a customized assay for circulating tumor DNA in patients with newly diagnosed pancreatic cancer.", "authors": [{"family": "Petersson", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-5574-9217", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f02e97bd25493c993d1a2568935885.json"}}, {"family": "Svensson", "given": "Maja", "initials": "M"}, {"family": "Hau", "given": "Sofie Olsson", "initials": "SO"}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3610-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/1369ca149def47a8abb8abb90b23ca66.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Chattopadhyay", "given": "Subhayan", "initials": "S", "orcid": "0000-0002-8599-2971", "researcher": {"href": "https://publications.scilifelab.se/researcher/78358668578b4661bed1f6a37365fae4.json"}}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Heidenblad", "given": "Markus", "initials": "M", "orcid": "0000-0002-0668-2263", "researcher": {"href": "https://publications.scilifelab.se/researcher/b49a0816fc794c27a25b34731e8ca7bf.json"}}, {"family": "Leandersson", "given": "Karin", "initials": "K", "orcid": "0000-0001-8254-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/4736923f382845c2990efb251340bfb4.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K", "orcid": "0000-0003-2257-5000", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b7c5c8216d943d2b344d9de5622770b.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "34481", "issn-l": "2045-2322"}, "abstract": "The vast majority of patients with pancreatic cancer present with unresectable disease and precision medicine is lagging behind. Circulating tumor DNA (ctDNA) has emerged as a promising tool, both as a proxy for tumor burden and for capturing tumor heterogeneity, but optimal gene panels and prognostic cutoffs remain to be determined. Herein, we applied ultra-deep ctDNA sequencing using a customized panel targeting 23 genes and six frequently altered chromosomes on plasma samples obtained before, during and after chemotherapy from 60 patients enrolled in a prospective clinical study. At baseline, positive versus negative ctDNA was not prognostic, neither in the adjuvant nor in the palliative setting, but in palliative patients, an independent prognostic cutoff could be calculated from the absolute number of mutated DNA molecules. Median overall survival was 3.7 months in the ctDNAhigh compared to 11.9 months in the ctDNAlow group (p < 0.0001), and the cutoff remained prognostic at one and three months. Moreover, relevant genetic alterations were highly concordant in ctDNA and paired tumor tissue. These findings demonstrate the potential clinical utility of a customized and focused gene panel for prognostication and target identification over time in patients with newly diagnosed pancreatic cancer, in particular in the palliative setting.ClinicalTrials.gov number: NCT03724994.", "doi": "10.1038/s41598-025-22369-5", "pmid": "41044171", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Clinical Genomics Lund": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12494785"}, {"db": "pii", "key": "10.1038/s41598-025-22369-5"}, {"db": "ClinicalTrials.gov", "key": "NCT03724994"}], "notes": [], "created": "2025-10-16T17:14:10.829Z", "modified": "2025-11-18T20:46:37.775Z"}, {"entity": "publication", "iuid": "d1f8810655e14e5896912d1b996ed6a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1f8810655e14e5896912d1b996ed6a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1f8810655e14e5896912d1b996ed6a7"}}, "title": "Immune-coagulation dynamics in severe COVID-19 revealed by autoantibody profiling and multi-omics integration.", "authors": [{"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Cederholm", "given": "Axel", "initials": "A", "orcid": "0009-0006-5973-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2dffb2fd8e446d6a72c765602b97291.json"}}, {"family": "Rezene", "given": "Sefanit", "initials": "S"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M", "orcid": "0000-0003-0050-704X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65dc88b917274bc595daed855b63abab.json"}}, {"family": "Nordqvist", "given": "Hampus", "initials": "H"}, {"family": "Treutiger", "given": "Carl Johan", "initials": "CJ"}, {"family": "Lira-Junior", "given": "Ronaldo", "initials": "R"}, {"family": "Landegren", "given": "Nils", "initials": "N", "orcid": "0000-0002-6163-9540", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ceacb17b7448709f9bfcd593bec1e2.json"}}, {"family": "Gupta", "given": "Soham", "initials": "S", "orcid": "0000-0003-1136-3010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbd430437164ba38676d7b94e2189ab.json"}}], "type": "journal article", "published": "2025-09-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "32149", "issn-l": "2045-2322"}, "abstract": "Severe COVID-19 is characterized by immune-coagulation dysregulation, yet the contribution of related autoantibodies remains poorly understood. We investigated relationships between plasma autoantibody reactivities, whole-blood transcriptomics, plasma proteomics, and clinical laboratory parameters in a cohort of hospitalized COVID-19 patients. Transcriptomic analysis revealed that 42 curated coagulation and complement cascade genes were upregulated in severe cases compared to healthy controls, with 15 genes, including CR1L, ELANE, ITGA2B, ITGB3, VWF, TFPI, PROS1, MMRN1, and SELP (> 1.2 log2 fold-change), also significantly different from mild cases. Autoantibody profiling against eight coagulation-related proteins (ADAMTS13, Factor V, Protein S, SERPINC1, Apo-H, PROC1, Prothrombin, and PF4) showed reactivities below positivity thresholds across all groups. Using an exploratory approach, in severe cases, subthreshold autoantibody candidates (FDR < 0.25) showed negative correlation trends with select gene expressions and inflammatory markers (Factor V with IL-6 and CXCL10), suggesting potential disease-specific immunomodulatory associations. In contrast, while mild cases exhibited stronger gene-protein correlations, they showed limited associations with antigen reactivities or clinical laboratory parameters. Additionally, no correlations were observed between autoantibodies and platelet-counts or Fibrin-D-dimer levels. Age-associated increases in antigen reactivities were noted in severe disease, implying a role for immunosenescence. These findings support further investigation into the role of subthreshold autoantibody candidates in thromboinflammatory COVID-19 pathogenesis.", "doi": "10.1038/s41598-025-17054-6", "pmid": "40890263", "labels": {"Autoimmunity and Serology Profiling": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12402181"}, {"db": "pii", "key": "10.1038/s41598-025-17054-6"}], "notes": [], "created": "2025-09-10T08:19:37.842Z", "modified": "2025-11-25T19:21:42.478Z"}, {"entity": "publication", "iuid": "a820631626024f32811c8031777bf540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540"}}, "title": "Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation.", "authors": [{"family": "Atienza P\u00e1rraga", "given": "Alba", "initials": "A"}, {"family": "Nylund", "given": "Patrick", "initials": "P", "orcid": "0000-0002-1274-4010", "researcher": {"href": "https://publications.scilifelab.se/researcher/683976ea3c094b198998dabb0d433f4b.json"}}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Garrido-Zabala", "given": "Berta", "initials": "B"}, {"family": "Tziola", "given": "Stefania Iliana", "initials": "SI"}, {"family": "Vasquez", "given": "Louella", "initials": "L", "orcid": "0000-0002-5758-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479eadb09d44ece8523730e1e0fd0b1.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69051a0275c442c8c0d5621b4000929.json"}}, {"family": "Raykova", "given": "Doroteya", "initials": "D", "orcid": "0000-0001-6452-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a81c40491e349178167f148f2351875.json"}}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Ma", "given": "Anqi", "initials": "A", "orcid": "0000-0002-9293-4753", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c70ee5b7bd4136a74d7605ec7b1614.json"}}, {"family": "Jin", "given": "Jian", "initials": "J", "orcid": "0000-0002-3774-1609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed488bfe2c024a6b874b3b964ce80b97.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 Ignacio", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "\u00d6berg", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3609-1197", "researcher": {"href": "https://publications.scilifelab.se/researcher/c68243c8cc754cdb8b380db120f3b771.json"}}, {"family": "De Bruyne", "given": "Elke", "initials": "E", "orcid": "0000-0003-4012-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2715df4e920432c9723d8fdf4ff897b.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Jernberg Wiklund", "given": "Helena", "initials": "H"}, {"family": "Kalushkova", "given": "Antonia", "initials": "A", "orcid": "0000-0003-4535-506X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df89c7522b7b4af3b3cef8555380fe8c.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "31568"}, "abstract": "Comprehensive epigenomic studies in multiple myeloma (MM) that unravel the connections between major epigenetic regulators, their intertwined collaboration and the potential of combinatorial targeting remain limited. Utilizing ChIP-seq, ATAC-seq, RNA-seq, and DNA methylation (DNAme) data, we generated whole-genome chromatin annotations from normal plasma cells and MM patients, revealing epigenomic re-configuration affecting downstream genes involved in tumour growth and survival. Primary MM samples showed global DNA hypomethylation but site-specific hypermethylation was observed at transcription start sites, promoters, and enhancers. Moreover, increased deposition of H3K27me3 was observed in clinically relevant functional chromatin clusters. Combined EZH2 and DNMTs inhibition resulted in extensive epigenomic alterations activating apoptosis and cell cycle genes, leading to increased G2/M arrest and apoptosis in MM cell lines. Our findings provide novel insights into the role of epigenetic gene silencing in MM tumorigenesis and the interplay between the Polycomb repressive complex 2 and DNAme.\r\n\r\nThe online version contains supplementary material available at 10.1038/s41598-025-17093-z.", "doi": "10.1038/s41598-025-17093-z", "pmid": "40866476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12391466"}, {"db": "pii", "key": "10.1038/s41598-025-17093-z"}], "notes": [], "created": "2025-09-08T07:11:30.283Z", "modified": "2025-10-06T12:40:33.288Z"}, {"entity": "publication", "iuid": "6631db4df635414dbbbe505ccbd190ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6631db4df635414dbbbe505ccbd190ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6631db4df635414dbbbe505ccbd190ce"}}, "title": "Discovery of tumour indicating morphological changes in benign prostate biopsies through AI.", "authors": [{"family": "Chelebian", "given": "Eduard", "initials": "E"}, {"family": "Avenel", "given": "Christophe", "initials": "C"}, {"family": "J\u00e4remo", "given": "Helena", "initials": "H"}, {"family": "Andersson", "given": "Pernilla", "initials": "P"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}], "type": "journal article", "published": "2025-08-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "30770", "issn-l": "2045-2322"}, "abstract": "Diagnostic needle biopsies that miss clinically significant prostate cancer (PCa) often sample benign tissue near hidden cancers. Such benign samples might still display subtle morphological signs of cancer elsewhere in the prostate. This study examined if artificial intelligence (AI) could detect these morphological clues in benign biopsies from men with elevated prostate-specific antigen (PSA) levels to predict subsequent diagnosis of clinically significant PCa within 30 months. We analysed biopsies from 232 men initially diagnosed as benign, matched for age, diagnosis year, and PSA levels-half were later diagnosed with PCa, while the rest remained cancer-free for at least eight years. The AI model accurately predicted future PCa diagnosis from initial benign biopsies (AUC = 0.82), highlighting patterns such as changes in stromal collagen and altered glandular epithelial cells. This demonstrates that AI analysis of routine haematoxylin-eosin biopsy sections can detect subtle signs indicating clinically significant PCa before it becomes histologically apparent. Such morphological patterns shed light on the broader tissue alterations induced by prostate cancer, even in benign tissue, potentially enhancing early detection and clinical decision-making.", "doi": "10.1038/s41598-025-15105-6", "pmid": "40841408", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12370971"}, {"db": "pii", "key": "10.1038/s41598-025-15105-6"}], "notes": [], "created": "2025-11-25T12:52:52.168Z", "modified": "2025-11-25T12:52:52.171Z"}, {"entity": "publication", "iuid": "8731474c0874412e8ff9f33c698c18a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8731474c0874412e8ff9f33c698c18a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8731474c0874412e8ff9f33c698c18a1"}}, "title": "Profiling of the microRNA transcriptome in feline whole blood.", "authors": [{"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-1116-0141", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d12e64d2d740669ec499319b66c22e.json"}}, {"family": "Han\u00e5s", "given": "Sofia", "initials": "S"}, {"family": "Holst", "given": "Bodil S", "initials": "BS"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "H\u00f6glund", "given": "Katja", "initials": "K"}, {"family": "Tidholm", "given": "Anna", "initials": "A"}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6617-0454", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b19ecb541c4d13a685b574390e8104.json"}}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-3402-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e1779188e20402294f12861a8232e71.json"}}], "type": "journal article", "published": "2025-07-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "27962", "issn-l": "2045-2322"}, "abstract": "Circulating microRNAs (miRNAs) are potential biomarkers for numerous diseases. Characterization of the whole blood (WB) miRNA-transcriptome (miRNome) in cats is lacking, which limits the potential use of miRNAs as biomarkers for diseases such as feline cardiovascular disease. The aims of the present study were to profile and evaluate circulating miRNAs in feline WB by high-throughput sequencing of the total miRNome in WB from twelve domestic mixed breed (DOM) and Norwegian Forest (NFO) cats stringently diagnosed with or without preclinical hypertrophic cardiomyopathy (HCM). A total of 459 mature miRNAs were identified in feline WB, of which 40 were potential novel feline miRNAs. A majority, 85.3%, of the miRNAs showed sequence similarity with human miRNAs. An effect of breed was found, with up to thirteen WB miRNAs being differentially abundant between breeds. The majority of the significant breed-specific miRNAs in feline WB could be associated with regulation of haematopoietic cells. One miRNA, miR-204-5p, was potentially associated with preclinical HCM in NFO cats, but the results need to be confirmed in a larger and sex-unbiased cohort. In conclusion, here we used miRNome-sequencing to identify hundreds of circulating miRNAs in feline WB. Breed should be considered when evaluating the miRNome in feline WB.", "doi": "10.1038/s41598-025-09478-x", "pmid": "40745193", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12313912"}, {"db": "pii", "key": "10.1038/s41598-025-09478-x"}], "notes": [], "created": "2025-09-05T08:24:52.249Z", "modified": "2025-09-09T13:12:41.462Z"}, {"entity": "publication", "iuid": "d5108740da8e45ba8da2b5476a7d0993", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5108740da8e45ba8da2b5476a7d0993.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5108740da8e45ba8da2b5476a7d0993"}}, "title": "Poincare guided geometric UNet for left atrial epicardial adipose tissue segmentation in Dixon MRI images.", "authors": [{"family": "Firouznia", "given": "Marjan", "initials": "M"}, {"family": "Ylip\u00e4\u00e4", "given": "Erik", "initials": "E"}, {"family": "Henningsson", "given": "Markus", "initials": "M"}, {"family": "Carlh\u00e4ll", "given": "Carl-Johan", "initials": "CJ"}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "25549", "issn-l": "2045-2322"}, "abstract": "Epicardial Adipose Tissue (EAT) is a recognized risk factor for cardiovascular diseases and plays a pivotal role in the pathophysiology of Atrial Fibrillation (AF). Accurate automatic segmentation of the EAT around the Left Atrium (LA) from Magnetic Resonance Imaging (MRI) data remains challenging. While Convolutional Neural Networks excel at multi-scale feature extraction using stacked convolutions, they struggle to capture long-range self-similarity and hierarchical relationships, which are essential in medical image segmentation. In this study, we present and validate PoinUNet, a deep learning model that integrates a Poincar\u00e9 embedding layer into a 3D UNet to enhance LA wall and fat segmentation from Dixon MRI data. By using hyperbolic space learning, PoinUNet captures complex LA and EAT relationships and addresses class imbalance and fat geometry challenges using a new loss function. Sixty-six participants, including forty-eight AF patients, were scanned at 1.5T. The first network identified fat regions, while the second utilized Poincar\u00e9 embeddings and convolutional layers for precise segmentation, enhanced by fat fraction maps. PoinUNet achieved a Dice Similarity Coefficient of 0.87 and a Hausdorff distance of 9.42 on the test set. This performance surpasses state-of-the-art methods, providing accurate quantification of the LA wall and LA EAT.", "doi": "10.1038/s41598-025-10110-1", "pmid": "40664735", "labels": {"AIDA Data Hub": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12263985"}, {"db": "pii", "key": "10.1038/s41598-025-10110-1"}], "notes": [], "created": "2025-11-25T13:12:40.133Z", "modified": "2025-11-25T13:12:40.136Z"}, {"entity": "publication", "iuid": "4bfa745c2a514b2c8a47ec6ffc073c31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bfa745c2a514b2c8a47ec6ffc073c31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bfa745c2a514b2c8a47ec6ffc073c31"}}, "title": "Novel insights on remnant stomach following Roux-en-Y gastric bypass surgery based on histological evaluation and quantitative proteomics analysis.", "authors": [{"family": "Larson", "given": "Carl I W", "initials": "CIW"}, {"family": "F\u00e4ndriks", "given": "Lars", "initials": "L"}, {"family": "Casselbrant", "given": "Anna", "initials": "A"}, {"family": "Wallenius", "given": "Ville", "initials": "V"}], "type": "journal article", "published": "2025-07-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "25243", "issn-l": "2045-2322"}, "abstract": "Patients undergoing weight-reducing Roux-en-Y gastric bypass (RYGB) have immediate positive effects on metabolic health, including type 2 diabetes (T2D). Refeeding via the secluded stomach, either by a gastrotube or after gastro-gastric fistulation result in T2D relapse and weight regain. The stomach therefore seems to play an active role in metabolism. To explore histological and protein expression changes in the gastric mucosa before compared to after RYGB. Perioperatively, biopsies were taken in a non-paired manner from the stomach (fundus, corpus, antrum) in patients undergoing Sleeve Gastrectomy (SG) and patients > 8 months postoperatively after RYGB by balloon-enteroscopy. The included SG and RYGB patients did not display any obvious mucosal or luminal pathology during surgery or the balloon-enteroscopies. The gastric biopsies both at perioperatively and postoperatively were prepared f\u00f6r histological evaluation and for quantitative (comparative) non-targeted proteomics. The results were compared by Volcano plots, Principal Component Analysis and STRING functional protein association networks. Histologically the gastric mucosa looked normal in biopsies from all the different parts of the postoperative bypassed stomach with no clear differences compared to the perioperative samples. The perioperative biopsies generally contained significantly higher amounts of proteins involved in fatty acid metabolism, oxidative phosphorylation and ATP metabolic processes, citric acid cycle and the respiratory chain. Postoperative biopsies instead showed overall increased quantities of proteins associated with ribosomes, RNA-metabolic processes, the mitotic cycle and pancreatic secretion. The results provide novel insights into the mucosal proteome-changes in the secluded stomach following RYGB.", "doi": "10.1038/s41598-025-10114-x", "pmid": "40652086", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12255712"}, {"db": "pii", "key": "10.1038/s41598-025-10114-x"}], "notes": [], "created": "2025-10-23T11:13:55.730Z", "modified": "2025-10-23T11:13:55.738Z"}, {"entity": "publication", "iuid": "237bc9b3ceaf4af580a4097b4ee55e08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/237bc9b3ceaf4af580a4097b4ee55e08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/237bc9b3ceaf4af580a4097b4ee55e08"}}, "title": "Cerebrospinal fluid protein profiling of inflammatory and neurobiological markers in Lyme neuroborreliosis.", "authors": [{"family": "Haglund", "given": "Sofie", "initials": "S"}, {"family": "Gyllemark", "given": "Paula", "initials": "P"}, {"family": "Forsberg", "given": "Pia", "initials": "P"}, {"family": "Brudin", "given": "Lars", "initials": "L"}, {"family": "Tjernberg", "given": "Ivar", "initials": "I"}, {"family": "Henningsson", "given": "Anna J", "initials": "AJ"}], "type": "journal article", "published": "2025-06-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "20190", "issn-l": "2045-2322"}, "abstract": "Lyme neuroborreliosis (LNB) is the most common form of disseminated Lyme borreliosis in Europe and North America. There are limitations in existing LNB diagnostics and a lack of reliable objective markers for disease-course. Here, extensive protein profiling with two panels of 184 proteins, was done in the search for new clinically useful diagnostic and prognostic candidate biomarkers. Cerebrospinal fluid (CSF) was collected from patients with definite LNB (n = 13) at the time of diagnosis before initiating antibiotic treatment, and at a follow-up one month later. When symptoms were evaluated at a six-month follow-up, six patients had recovered with no persistent symptoms (NPS), and seven experienced delayed recovery with persistent post-treatment symptoms (PS). Orthopedic patients (n = 60) served as controls. With the panels used, no protein biomarkers able to differentiate between PS and NPS were identified. However, from a diagnostic perspective, we identified multiple proteins that were differentially expressed between LNB and controls. The majority of them were downregulated following antibiotic treatment, at the one-month follow-up. IL10, TNF, and CCL8 were considered examples of potentially useful candidate biomarkers in both the early diagnostics and in monitoring of treatment response. These markers merit further investigation to understand their utility in relation to other neurological manifestations.", "doi": "10.1038/s41598-025-06146-y", "pmid": "40542080", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12181437"}, {"db": "pii", "key": "10.1038/s41598-025-06146-y"}], "notes": [], "created": "2025-11-25T19:22:23.103Z", "modified": "2025-11-25T19:22:23.107Z"}, {"entity": "publication", "iuid": "f61af6cf5a7c4a2389ab8f8d63c905f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f61af6cf5a7c4a2389ab8f8d63c905f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f61af6cf5a7c4a2389ab8f8d63c905f2"}}, "title": "Metagenomic biodiversity assessment within an offshore wind farm.", "authors": [{"family": "Serivichyaswat", "given": "Phanu Theodore", "initials": "PT"}, {"family": "Scholte", "given": "Thijs", "initials": "T"}, {"family": "Wilms", "given": "Tim", "initials": "T"}, {"family": "Stranddorf", "given": "Liv", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2025-05-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "16786", "issn-l": "2045-2322"}, "abstract": "Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.", "doi": "10.1038/s41598-025-01541-x", "pmid": "40368948", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12078662"}, {"db": "pii", "key": "10.1038/s41598-025-01541-x"}], "notes": [], "created": "2025-11-28T10:46:59.450Z", "modified": "2025-11-28T10:46:59.453Z"}, {"entity": "publication", "iuid": "784df73e8dc84ac78534a0c33e5aec03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/784df73e8dc84ac78534a0c33e5aec03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/784df73e8dc84ac78534a0c33e5aec03"}}, "title": "Cytoskeletal alterations in neuronal cells implicate Toxoplasma gondii secretory machinery and host microRNA-containing extracellular vesicles.", "authors": [{"family": "Mazza", "given": "Thomas", "initials": "T"}, {"family": "Aslanzadeh", "given": "Morteza", "initials": "M"}, {"family": "Berentsen", "given": "L\u00efse", "initials": "L"}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Barragan", "given": "Antonio", "initials": "A", "orcid": "0000-0001-7746-9964", "researcher": {"href": "https://publications.scilifelab.se/researcher/4eefb95f00db42e3891769f384269c6c.json"}}], "type": "journal article", "published": "2025-04-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "12606", "issn-l": "2045-2322"}, "abstract": "The widespread protozoan Toxoplasma gondii chronically infects neural tissue in vertebrates and is linked to various neurological and neuropsychiatric disorders in humans. However, its effects on sparsely infected neurons and on broader neural circuits remain elusive. Our study reveals that T. gondii infection disrupts cytoskeletal dynamics in SH-SY5Y neuronal cells and primary cortical neurons. Infected neuronal cells undergo significant cytomorphological changes, including retraction of dendritic extensions and alterations in microtubule and F-actin networks, across both parasite genotypes I and II. These cytoskeletal alterations were notably diminished in cells exposed to T. gondii mutants with impaired secretion via the MYR translocon, and were independent of intraneuronal parasite replication. Moreover, a bystander effect was observed, with supernatants from T. gondii-challenged cells inducing similar cytoskeletal changes in uninfected cells. Analyses of extracellular vesicles (EVs) in supernatants revealed differential expression of host microRNAs in response to infection, most notably the upregulation of miR-221-3p, a microRNA not previously associated with T. gondii. The data indicate that unidentified parasite-derived effector(s) secreted via the MYR translocon, in conjunction with MYR-independently induced EV-associated host microRNAs, mediate cytoskeletal alterations in both infected and bystander neuronal cells. The findings provide new insights into molecular mechanisms by which T. gondii infection may disrupt neural networks, shedding light on its potential role in neuronal dysregulation.", "doi": "10.1038/s41598-025-96298-8", "pmid": "40221584", "labels": {"NGI Short read": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Other": "Collaborative", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11993698"}, {"db": "pii", "key": "10.1038/s41598-025-96298-8"}], "notes": [], "created": "2025-06-03T09:17:07.614Z", "modified": "2025-06-03T09:17:07.717Z"}, {"entity": "publication", "iuid": "9e856a21e11244789a7890b2151f1617", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e856a21e11244789a7890b2151f1617.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e856a21e11244789a7890b2151f1617"}}, "title": "A red fluorescent lifeact marker to study actin morphology in podocytes.", "authors": [{"family": "Wiesner", "given": "Eva", "initials": "E"}, {"family": "Binz-Lotter", "given": "Julia", "initials": "J"}, {"family": "Tr\u00f6der", "given": "Simon E", "initials": "SE"}, {"family": "Unnersj\u00f6-Jess", "given": "David", "initials": "D"}, {"family": "Rutkowski", "given": "Nelli", "initials": "N"}, {"family": "Zevnik", "given": "Branko", "initials": "B"}, {"family": "Schermer", "given": "Bernhard", "initials": "B"}, {"family": "Benzing", "given": "Thomas", "initials": "T"}, {"family": "Wedlich-S\u00f6ldner", "given": "Roland", "initials": "R"}, {"family": "Hackl", "given": "Matthias J", "initials": "MJ"}], "type": "journal article", "published": "2025-04-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "12386", "issn-l": "2045-2322"}, "abstract": "F-actin is a major component of the cellular cytoskeleton, responsible for maintaining cell shape, enabling movement and facilitating intracellular transport. In the kidney, glomerular podocytes are highly dependent on their actin cytoskeleton shaping their unique foot processes. Hereditary mutations in actin-binding proteins cause focal segmental glomerulosclerosis, while other organs remain largely unaffected. So far, actin visualization in podocytes has been limited to electron microscopy or indirect immunofluorescent labeling of actin-binding proteins. However, the short F-actin-binding peptide Lifeact enables researchers to study actin dynamics in vitro and in vivo with minimal interference with actin metabolism. Here we introduce a new mouse model with conditional expression of a Lifeact.mScarlet-I fusion protein providing red labeling of actin. Cre recombinase-mediated activity allows cell-specific and mosaic expression in podocytes, enabling selective labeling of individual cells to contrast with non-expressing neighboring cells. Transgenic mice are born healthy and young animals display no kidney-related phenotype. By intravital imaging and super-resolution microscopy, we show subcellular localization of actin to the foot processes in a resolution previously only obtainable by electron microscopy. Our novel mouse line provides the opportunity to study the actin cytoskeleton in podocytes and other cell types by intravital imaging and other conventional light microscopy techniques.", "doi": "10.1038/s41598-025-96822-w", "pmid": "40216917", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11992033"}, {"db": "pii", "key": "10.1038/s41598-025-96822-w"}], "notes": [], "created": "2025-04-18T09:49:47.683Z", "modified": "2025-04-18T09:49:47.688Z"}, {"entity": "publication", "iuid": "0a472783b44b468ea76f2796c228b8f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a472783b44b468ea76f2796c228b8f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a472783b44b468ea76f2796c228b8f4"}}, "title": "Comparison of the proteomic landscape in experimental ischemia reperfusion with versus without ischemic preconditioning.", "authors": [{"family": "Kakaei", "given": "Yalda", "initials": "Y"}, {"family": "Hussain", "given": "Shafaat", "initials": "S"}, {"family": "Elmahdy", "given": "Ahmed", "initials": "A"}, {"family": "Berger", "given": "Evelin", "initials": "E"}, {"family": "Shekka Espinosa", "given": "Aaron", "initials": "A"}, {"family": "Sevastianova", "given": "Valentyna", "initials": "V"}, {"family": "Sheybani", "given": "Zahra", "initials": "Z"}, {"family": "Al-Awar", "given": "Amin", "initials": "A"}, {"family": "Kalani", "given": "Mana", "initials": "M"}, {"family": "Jha", "given": "Sandeep", "initials": "S"}, {"family": "Zulfaj", "given": "Ermir", "initials": "E"}, {"family": "Nejat", "given": "Amirali", "initials": "A"}, {"family": "Jha", "given": "Abhishek", "initials": "A"}, {"family": "Pylova", "given": "Tetiana", "initials": "T"}, {"family": "Krasnikova", "given": "Maryna", "initials": "M"}, {"family": "Andersson", "given": "Erik Axel", "initials": "EA"}, {"family": "Silva", "given": "Vagner Ramon Rodrigues", "initials": "VRR"}, {"family": "Omerovic", "given": "Elmir", "initials": "E"}, {"family": "Redfors", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2025-04-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "11836", "issn-l": "2045-2322"}, "abstract": "Myocardial ischemic preconditioning (IPC) enhances myocardial resilience to ischemic injury. Myocardial stunning is a transient, reversible dysfunction, while necrosis involves irreversible cell death. The relationship between IPC, stunning, and necrosis is not well understood, requiring further molecular investigation. This study aimed to investigate the proteomic changes associated with IPC, focusing on its relationship with myocardial stunning and necrosis. A novel 13.5-minute ischemia-reperfusion (I/R) rat model was specifically chosen to induce myocardial stunning, providing a unique approach to assess IPC effects in this context. Rats underwent either IPC with two 5-minute ischemia/reperfusion cycles followed by a 13.5-minute ischemic period or the procedure without IPC (no ischemic preconditioning, NIPC). Myocardial samples were collected at early (T1) and 4-hour post-reperfusion (T2) time points for proteomic analysis. Protein levels were quantified by differential labeling using TMTpro reagents, and subsequent liquid chromatography-mass spectrometry. IPC induced upregulation of proteins involved in endocytosis and Fc gamma R-mediated phagocytosis pathways at T1, while downregulating proteins related to tissue remodeling, immune response, and coagulation at T2. Conversely, NIPC exhibited upregulation of proteins associated with tissue damage and inflammation. IPC rats demonstrated enhanced leukocyte migration, complement activation, and immune response between T1 and T2. Consistent proteomic changes were observed between T1 and T2 in IPC vs. NIPC groups, and common alterations between IPC T2 vs. T1 and NIPC T2 vs. T1 comparisons underline shared pathways in cardiac complement and coagulation cascades. Our study reveals distinct proteomic changes induced by IPC in the context of myocardial stunning and necrosis. IPC activates early protective pathways, attenuates tissue damage and inflammation, and preserves myocardial function. These findings underscore IPC's reparative potential and identify myocardial stunning as an important, transient adaptation, which may have implications for supportive clinical management in I/R.", "doi": "10.1038/s41598-025-90735-4", "pmid": "40195349", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11976975"}, {"db": "pii", "key": "10.1038/s41598-025-90735-4"}], "notes": [], "created": "2025-10-23T11:18:47.789Z", "modified": "2025-10-23T11:18:47.794Z"}, {"entity": "publication", "iuid": "a624b6ccad7b449fa079200d5b4a545f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f"}}, "title": "Genetic influence of a STAU2 frameshift mutation and RELN regulatory elements on performance in Icelandic horses.", "authors": [{"family": "Sigur\u00f0ard\u00f3ttir", "given": "Hei\u00f0r\u00fan", "initials": "H"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Rhodin", "given": "Marie", "initials": "M"}, {"family": "Albertsd\u00f3ttir", "given": "Elsa", "initials": "E"}, {"family": "Kristjansson", "given": "Thorvaldur", "initials": "T"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2025-04-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "11641", "issn-l": "2045-2322"}, "abstract": "Selection for performance in horse breeding benefits from precise genetic insights at a molecular level, but knowledge remains limited. This study used whole-genome sequences of 39 elite and non-elite Icelandic horses to identify candidate causal variants linked to previously identified haplotypes in the STAU2 and RELN genes affecting pace and other gaits. A frameshift variant in linkage disequilibrium with the previously identified haplotypes in the STAU2 gene (r2 = 0.85) was identified within a predicted STAU2 transcript. This variant alters the amino acid sequence and introduces a premature stop codon but does not appear harmful or disease-causing and is potentially unique to equine biology. A large portion of the RELN haplotype overlapped with an H3K27me3 modification mark, suggesting a regulatory role of this region. Despite the small sample size, the RELN haplotype's effects were validated for t\u00f6lt, trot, and canter/gallop. Additionally, the RELN haplotype significantly influenced the age at which horses were presented for breeding field tests, indicating a potential role of the region in precocity and trainability. Functional experiments are needed to further investigate the regions' influences on biological processes and their potential impact on horse performance.", "doi": "10.1038/s41598-025-95593-8", "pmid": "40185812", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11971302"}, {"db": "pii", "key": "10.1038/s41598-025-95593-8"}], "notes": [], "created": "2025-11-07T07:27:05.828Z", "modified": "2025-11-14T11:07:06.654Z"}, {"entity": "publication", "iuid": "85c57e4cdd15436f887cf31addb56758", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85c57e4cdd15436f887cf31addb56758.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85c57e4cdd15436f887cf31addb56758"}}, "title": "Immunological and structural evaluation of the intranasally administrated CVB1 whole-virus and VLP vaccines.", "authors": [{"family": "Soppela", "given": "Saana", "initials": "S"}, {"family": "Plavec", "given": "Zlatka", "initials": "Z"}, {"family": "Gr\u00f6hn", "given": "Stina", "initials": "S"}, {"family": "Mustonen", "given": "Iiris", "initials": "I"}, {"family": "Jartti", "given": "Minne", "initials": "M"}, {"family": "Oikarinen", "given": "Sami", "initials": "S"}, {"family": "Laajala", "given": "Mira", "initials": "M"}, {"family": "Marjom\u00e4ki", "given": "Varpu", "initials": "V"}, {"family": "Butcher", "given": "Sarah J", "initials": "SJ"}, {"family": "Hankaniemi", "given": "Minna M", "initials": "MM"}], "type": "journal article", "published": "2025-03-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "10198", "issn-l": "2045-2322"}, "abstract": "Coxsackievirus B1 (CVB1) is a common cause of acute and chronic myocarditis, cardiomyopathy, and meningitis. CVBs replicate in mucosal membranes. Therefore, vaccines inducing robust mucosal immune responses are needed. We investigated the immunogenicity of virus-like particles (VLP) and inactivated virus vaccines for CVB1, administered to mice either subcutaneously or intranasally, formulated with and without commercial and an experimental adjuvant. In this study, epigallocatechin-3-gallate (EGCG) was used both as a potential adjuvant and as an inactivating agent. EGCG adjuvanted CVB1-VLP enhanced immunogenicity via the parenteral route, but not intranasally. EGCG-adjuvanted and non-adjuvanted CVB1-VLPs triggered an immune response after intranasal administration, although the response remained weak. Intranasal administration of formalin-inactivated virus elicited robust CVB1-specific humoral, cellular, and mucosal immune responses, but after EGCG-inactivation, the mucosal antibody response was lower than after formalin-inactivation. To identify the link between structure and mucosal immunogenicity, we solved the structures of CVB1-VLP and formalin-inactivated CVB1 virus at resolutions ranging from 2.15 to 4.1 \u00c5. The structural difference between VLP and formalin-inactivated CVB1 was the presence of the genome and cross-linked amino acid residues in the formalin-inactivated virus. Formalin-inactivated CVB1 vaccine shows promise for mucosal immunizations and the structural data supports the development of next-generation VLP-vaccines in the future.", "doi": "10.1038/s41598-025-94656-0", "pmid": "40133550", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11937443"}, {"db": "pii", "key": "10.1038/s41598-025-94656-0"}], "notes": [], "created": "2025-11-13T09:34:00.598Z", "modified": "2025-11-13T09:34:00.602Z"}, {"entity": "publication", "iuid": "631321ade8c64aee894b30aeb0022924", "links": {"self": {"href": "https://publications.scilifelab.se/publication/631321ade8c64aee894b30aeb0022924.json"}, "display": {"href": "https://publications.scilifelab.se/publication/631321ade8c64aee894b30aeb0022924"}}, "title": "Insights into metabolic changes during epidermal differentiation as revealed by multiphoton microscopy with fluorescence lifetime imaging.", "authors": [{"family": "Malak", "given": "Monika", "initials": "M"}, {"family": "Qian", "given": "Chen", "initials": "C"}, {"family": "James", "given": "Jeemol", "initials": "J"}, {"family": "Nair", "given": "Syam", "initials": "S"}, {"family": "Grantham", "given": "Julie", "initials": "J"}, {"family": "Ericson", "given": "Marica B", "initials": "MB"}], "type": "journal article", "published": "2025-02-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "6377", "issn-l": "2045-2322"}, "abstract": "Rapid developments in the field of organotypic cultures have generated a growing need for effective and non-invasive methods for quality control during tissue development. In this study, we correlate metabolic changes with epidermal differentiation and demonstrate that multiphoton microscopy with fluorescence lifetime imaging (MPM-FLIM) can be applied to monitor epidermal differentiation of keratinocytes with respect to proliferative and differentiated states. In a 2D keratinocyte tissue culture model, increased expression of differentiation markers keratin-1 and keratin-10 was induced with calcium supplementation. An accompanying shift from glycolysis to mitochondrial respiration was detected in metabolic flux assays. Analysis of MPM-FLIM images acquired at 750 nm and 900 nm excitation revealed a decreased relative fraction of intracellular NADH and FAD after high calcium treatment, consistent with increased oxidative phosphorylation. Epidermal differentiation could be monitored over a 96 h period. Discrimination analysis based on k-means clustering generated clusters that correlated well with the duration of high Ca2+ treatment, suggesting that MPM-FLIM can provide useful parameters for monitoring keratinocyte differentiation.", "doi": "10.1038/s41598-025-90101-4", "pmid": "39984626", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11845624"}, {"db": "pii", "key": "10.1038/s41598-025-90101-4"}], "notes": [], "created": "2025-11-05T13:54:13.831Z", "modified": "2025-11-05T13:54:13.868Z"}, {"entity": "publication", "iuid": "031dd715561244629454ed59ab2b7d5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/031dd715561244629454ed59ab2b7d5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/031dd715561244629454ed59ab2b7d5c"}}, "title": "The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice.", "authors": [{"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Lawenius", "given": "Lina", "initials": "L"}, {"family": "Jiang", "given": "Yiwen", "initials": "Y"}, {"family": "Horkeby", "given": "Karin", "initials": "K"}, {"family": "Wu", "given": "Jianyao", "initials": "J"}, {"family": "Nilsson", "given": "Karin H", "initials": "KH"}, {"family": "Koskela", "given": "Antti", "initials": "A"}, {"family": "Tuukkanen", "given": "Juha", "initials": "J"}, {"family": "Mov\u00e9rare-Skrtic", "given": "Sofia", "initials": "S"}, {"family": "Henning", "given": "Petra", "initials": "P"}, {"family": "Sj\u00f6gren", "given": "Klara", "initials": "K"}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "6182", "issn-l": "2045-2322"}, "abstract": "Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p \u2264 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.", "doi": "10.1038/s41598-025-91056-2", "pmid": "39979617", "labels": {"Clinical Genomics": "Service", "Clinical Genomics Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11842756"}, {"db": "pii", "key": "10.1038/s41598-025-91056-2"}], "notes": [], "created": "2025-07-08T13:56:17.822Z", "modified": "2025-11-04T11:37:45.596Z"}, {"entity": "publication", "iuid": "41afeeccb52b4070923d6c4d9c505ea1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41afeeccb52b4070923d6c4d9c505ea1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41afeeccb52b4070923d6c4d9c505ea1"}}, "title": "Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic.", "authors": [{"family": "Plascencia", "given": "Alan God\u00ednez", "initials": "AG"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "S\u00e1nchez-Quinto", "given": "Federico", "initials": "F"}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "6161", "issn-l": "2045-2322"}, "abstract": "Computational HLA typing has surged as a cost-effective strategy to uncover questions regarding the evolution of the HLA system, enabling immunogenic characterization from ancient DNA (aDNA) data. Nevertheless, it remains to be seen whether these methods are suitable for analyzing aDNA generated without target-enrichment. To investigate this, we evaluated the performance of five HLA typing tools using present-day data with simulated profiles typical of aDNA, as well as from high-coverage aDNA genomes downsampled at different read depths. We found that characterization of Class I genes at the first field resolution is feasible at read depths as low as 2x, where it retains an accuracy of \u2248 80%. Next, we used this insight to characterize HLA evolution in Europe from 154 ancient genomes by detecting allele frequency changes throughout distinct prehistoric European populations. We observed important shifts in alleles associated with infectious and autoimmune diseases, most of which are found by contrasting the HLA landscape of Neolithic Farmers to that of present-day. Interestingly, several of these observations are in line with findings that have been previously reported by target-enrichment-based studies. Our results highlight the feasibility of applying HLA typing on shotgun aDNA data to examine the evolution of this loci during important transitions.", "doi": "10.1038/s41598-024-82449-w", "pmid": "39979344", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11842861"}, {"db": "pii", "key": "10.1038/s41598-024-82449-w"}], "notes": [], "created": "2025-11-28T10:46:54.368Z", "modified": "2025-11-28T10:46:54.377Z"}, {"entity": "publication", "iuid": "67fe70a7254545e7b2be4a509f5ff479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479"}}, "title": "Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.", "authors": [{"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Mujica", "given": "Endrina", "initials": "E"}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Jenseit", "given": "Anne", "initials": "A"}, {"family": "Evcimen", "given": "Bade", "initials": "B"}, {"family": "Metzendorf", "given": "Christoph", "initials": "C"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Loos", "given": "Ruth Jf", "initials": "RJ"}, {"family": "Vienberg", "given": "Sara Gry", "initials": "SG"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "5408"}, "abstract": "Hundreds of loci have been robustly associated with obesity-related traits, but functional characterization of candidate genes remains a bottleneck. Aiming to systematically characterize candidate genes for a role in accumulation of lipids in adipocytes and other cardiometabolic traits, we developed a pipeline using CRISPR/Cas9, non-invasive, semi-automated fluorescence imaging and deep learning-based image analysis in live zebrafish larvae. Results from a dietary intervention show that 5 days of overfeeding is sufficient to increase the odds of lipid accumulation in adipocytes by 10 days post-fertilization (dpf, n = 275). However, subsequent experiments show that across 12 to 16 established obesity genes, 10 dpf is too early to detect an effect of CRISPR/Cas9-induced mutations on lipid accumulation in adipocytes (n = 1014), and effects on food intake at 8 dpf (n = 1127) are inconsistent with earlier results from mammals. Despite this, we observe effects of CRISPR/Cas9-induced mutations on ectopic accumulation of lipids in the vasculature (sh2b1 and sim1b) and liver (bdnf); as well as on body size (pcsk1, pomca, irs1); whole-body LDLc and/or total cholesterol content (irs2b and sh2b1); and pancreatic beta cell traits and/or glucose content (pcsk1, pomca, and sim1a). Taken together, our results illustrate that CRISPR/Cas9- and image-based experiments in zebrafish larvae can highlight direct effects of obesity genes on cardiometabolic traits, unconfounded by their - not yet apparent - effect on excess adiposity.", "doi": "10.1038/s41598-025-89823-2", "pmid": "39948378", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11825957"}, {"db": "pii", "key": "10.1038/s41598-025-89823-2"}], "notes": [], "created": "2025-09-08T11:37:27.351Z", "modified": "2025-11-28T10:47:20.122Z"}, {"entity": "publication", "iuid": "e0831ab011e349ca8730591503d89f54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0831ab011e349ca8730591503d89f54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0831ab011e349ca8730591503d89f54"}}, "title": "Characterization of the genomic landscape of canine diffuse large B-cell lymphoma reveals recurrent H3K27M mutations linked to progression-free survival.", "authors": [{"family": "van der Heiden", "given": "Anna Darlene", "initials": "AD"}, {"family": "Pensch", "given": "Raphaela", "initials": "R"}, {"family": "Agger", "given": "Sophie", "initials": "S"}, {"family": "Gardner", "given": "Heather L", "initials": "HL"}, {"family": "Hendricks", "given": "William", "initials": "W"}, {"family": "Zismann", "given": "Victoria", "initials": "V"}, {"family": "Wong", "given": "Shukmei", "initials": "S"}, {"family": "Briones", "given": "Natalia", "initials": "N"}, {"family": "Turner", "given": "Bryce", "initials": "B"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K"}, {"family": "London", "given": "Cheryl", "initials": "C"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Arendt", "given": "Maja Louise", "initials": "ML"}], "type": "journal article", "published": "2025-02-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4724", "issn-l": "2045-2322"}, "abstract": "Diffuse large B-cell lymphoma (DLBCL) is an aggressive hematopoietic neoplasm that affects humans as well as dogs. While previous studies on canine DLBCL (cDLBCL) have significantly advanced our understanding of the disease, the majority of this research has relied on whole-exome sequencing, which is limited in its ability to detect copy number aberrations and other genomic changes beyond coding regions. Furthermore, many of these studies lack sufficient clinical follow-up data, making it difficult to draw meaningful associations between genetic variants and patient outcomes. Our study aimed to characterize the mutational landscape of cDLBCL using whole-genome sequencing of matched tumor-normal samples obtained from a cohort of 43 dogs previously enrolled in a clinical trial for which longitudinal follow-up was available. We focused on identifying genes that were significantly or recurrently mutated with coding point mutations, copy number aberrations, and their associations with patient outcomes. We identified 26 recurrently mutated genes, 18 copy number gains, and 8 copy number losses. Consistent with prior studies, the most commonly mutated genes included TRAF3, FBXW7, POT1, TP53, SETD2, DDX3X and TBL1XR1. The most prominent copy number gain occurred on chromosome 13, overlapping key oncogenes such as MYC and KIT, while the most frequent deletion was a focal loss on chromosome 26, encompassing IGL, PRAME, GNAZ, RAB36, RSPH14, and ZNF280B. Notably, our set of recurrently mutated genes was significantly enriched with genes involved in epigenetic regulation. In particular, we identified hotspot mutations in two histone genes, H3C8, and LOC119877878, resulting in H3K27M alterations predicted to dysregulate gene expression. Finally, a survival analysis revealed that H3K27M mutations in H3C8 were associated with increased hazard ratios for progression-free survival. No copy number aberrations were associated with survival. These findings underscore the critical role of epigenetic dysregulation in cDLBCL and affirm the dog as a relevant large animal model for interrogating the biological activity of novel histone-modifying treatment strategies.", "doi": "10.1038/s41598-025-89245-0", "pmid": "39922874", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11807134"}, {"db": "pii", "key": "10.1038/s41598-025-89245-0"}], "notes": [], "created": "2025-11-28T10:47:15.103Z", "modified": "2025-11-28T10:47:15.106Z"}, {"entity": "publication", "iuid": "ae26270a2c64410591f4cbb23c632b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69"}}, "title": "In vivo regulation of the monocyte phenotype by Mycobacterium marinum and the ESX-1 type VII secretion system.", "authors": [{"family": "Munke", "given": "Kristina", "initials": "K"}, {"family": "Wulff", "given": "Line", "initials": "L"}, {"family": "Lienard", "given": "Julia", "initials": "J"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "Agace", "given": "William W", "initials": "WW"}], "type": "journal article", "published": "2025-02-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4545", "issn-l": "2045-2322"}, "abstract": "Pathogenic mycobacteria require the conserved ESX-1 type VII secretion system to cause disease. In a murine Mycobacterium marinum infection model we previously demonstrated that infiltrating monocytes and neutrophils represent the major bacteria-harbouring cell populations in infected tissue. In the current study we use this model, in combination with scRNA sequencing, to assess the impact of M. marinum infection on the transcriptional profile of infiltrating Ly6C\u207aMHCII\u207a monocytes in vivo. Our findings demonstrate that infection of infiltrating monocytes with M. marinum alters their cytokine expression profile, induces glycolytic metabolism, hypoxia-mediated signaling, nitric oxide synthesis, tissue remodeling, and suppresses responsiveness to IFN\u03b3. We further show that the transcriptional response of bystander monocytes is influenced by ESX-1-dependent mechanisms, including a reduced responsiveness to IFN\u03b3. These findings suggest that mycobacterial infection has pleiotropic effects on monocyte phenotype, with potential implications in bacterial growth restriction and granuloma formation.", "doi": "10.1038/s41598-025-88212-z", "pmid": "39915532", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11802795"}, {"db": "pii", "key": "10.1038/s41598-025-88212-z"}], "notes": [], "created": "2025-09-08T11:29:57.395Z", "modified": "2025-09-08T11:29:57.400Z"}, {"entity": "publication", "iuid": "05dfc96807f64f37a3917f85f1198b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e"}}, "title": "Whole genome sequencing in early onset advanced heart failure.", "authors": [{"family": "Linn\u00e9r", "given": "Erik", "initials": "E", "orcid": "0009-0004-6961-8957", "researcher": {"href": "https://publications.scilifelab.se/researcher/666959db0ed3435ab374dcbd50cb9925.json"}}, {"family": "Czuba", "given": "Tomasz", "initials": "T"}, {"family": "Gidl\u00f6f", "given": "Olof", "initials": "O", "orcid": "0000-0002-7402-3139", "researcher": {"href": "https://publications.scilifelab.se/researcher/83f5453e507041b995e0d69a74540c24.json"}}, {"family": "Lundgren", "given": "Jakob", "initials": "J", "orcid": "0000-0001-9338-2906", "researcher": {"href": "https://publications.scilifelab.se/researcher/c929a6ea1c6f4975ad0ec84da3a32f5e.json"}}, {"family": "Bollano", "given": "Entela", "initials": "E", "orcid": "0000-0003-3341-2434", "researcher": {"href": "https://publications.scilifelab.se/researcher/f486393025c0406bbf6c397b7d1b6f05.json"}}, {"family": "Hellberg", "given": "Maria", "initials": "M"}, {"family": "Celik", "given": "Selvi", "initials": "S", "orcid": "0000-0001-7032-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da057ac725d4fb0bdbaddbc06a8ea64.json"}}, {"family": "Pimpalwar", "given": "Neha", "initials": "N"}, {"family": "Rentzsch", "given": "Philipp", "initials": "P", "orcid": "0000-0002-0413-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/372fb956b5634de493dd639dae9e8158.json"}}, {"family": "Martorella", "given": "Molly", "initials": "M", "orcid": "0000-0002-3306-6650", "researcher": {"href": "https://publications.scilifelab.se/researcher/64e0f833822b463b9736178d9a25c861.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Melander", "given": "Olle", "initials": "O", "orcid": "0000-0002-2581-484X", "researcher": {"href": "https://publications.scilifelab.se/researcher/868a7e41aa054097a85575aa1d9658cc.json"}}, {"family": "Albinsson", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6936-3967", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac577769c2d44ac7bd8ccc28f69045de.json"}}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4961-9704", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5ee559ab58458197bab1d119a50824.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Jeppsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-2356-2295", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec361c8c3f84b25a44213af77f4ac31.json"}}, {"family": "Lumbers", "given": "R Thomas", "initials": "RT", "orcid": "0000-0002-9077-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53e4d6591db481f881ec6046d54535b.json"}}, {"family": "Shah", "given": "Sonia", "initials": "S", "orcid": "0000-0001-5860-4526", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6a8568b3cae476199b27818eeb19e4d.json"}}, {"family": "Nilsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-6860-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/c07e3381e15b4806b77d1b575e4ddca2.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications.scilifelab.se/researcher/85de5f6926c94fbd96bbc9428b6a384f.json"}}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T", "orcid": "0000-0002-7746-8109", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f81f8a2e6f4f11ad4504746492fc41.json"}}, {"family": "Levin", "given": "Malin", "initials": "M", "orcid": "0000-0003-1069-5275", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d251e6a73fb49bcbd930f7ec8bd274c.json"}}, {"family": "Ehrencrona", "given": "Hans", "initials": "H", "orcid": "0000-0002-5589-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b89608a8ce941c3b9911630b4ff9720.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG", "orcid": "0000-0001-6285-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e50df6bb7f4194a52546dbd5652e84.json"}}], "type": "journal article", "published": "2025-02-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4306", "issn-l": "2045-2322"}, "abstract": "The genetic contributions to early onset heart failure (HF) are incompletely understood. Genetic testing in advanced HF patients undergoing heart transplantation (HTx) may yield clinical benefits, but data is limited. We performed deep-coverage whole genome sequencing (WGS) in 102 Swedish HTx recipients. Gene lists were compiled through a systematic literature review. Variants were prioritized for pathogenicity and classified manually. We also compared polygenic HF risk scores to a population-based cohort. We found a pathogenic (LP/P) variant in 34 individuals (34%). Testing yield was highest in hypertrophic (63% LP/P carriers), dilated (40%) and arrhythmogenic right ventricular (33%) cardiomyopathy and lower in ischemic cardiomyopathy (10%). A family history was more common in LP/P variant carriers than in non-carriers but was present in less than half of carriers (44% vs 13%, P < 0.001), whereas age was similar. Polygenic risk scores were similar in HTx recipients and the population cohort. In conclusion, we observed a high prevalence of pathogenic cardiomyopathy gene variants in individuals with early-onset advanced HF, which could not accurately be ruled out by family history and age. In contrast, we did not observe higher polygenic risk scores in early onset advanced HF cases than in the general population.", "doi": "10.1038/s41598-025-88465-8", "pmid": "39910139", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11799378"}, {"db": "pii", "key": "10.1038/s41598-025-88465-8"}], "notes": [], "created": "2025-02-11T07:01:17.258Z", "modified": "2025-02-11T07:01:20.425Z"}, {"entity": "publication", "iuid": "ce8b106b6f714fb9af54bf212eb1a45f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce8b106b6f714fb9af54bf212eb1a45f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce8b106b6f714fb9af54bf212eb1a45f"}}, "title": "Dissociable genetic influences on eye movements during abstract versus naturalistic social scene viewing in infancy.", "authors": [{"family": "Portugal", "given": "Ana Maria", "initials": "AM"}, {"family": "Taylor", "given": "Mark J", "initials": "MJ"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}, {"family": "Ronald", "given": "Angelica", "initials": "A"}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4100", "issn-l": "2045-2322"}, "abstract": "Eye-movement metrics like fixation location and duration are increasingly being used in infancy research. We tested whether fixation durations during meaningful social stimulus viewing involve common or different familial influences than fixation durations during viewing of abstract stimulus. We analysed the duration of fixations, and the allocation of fixations to face and motion, from 536 dizygotic and monozygotic 5-month-old twins in: naturalistic scenes including low- and high-level social features, and abstract scenes only having low-level features. We observed significant genetic influences in both conditions (h2naturalistic = 0.30, 95% confidence interval (CI) 0.14 to 0.44; h2abstract = 0.25, 95% CI 0.09 to 0.39), while shared environmental influences were negligible. Although some genetic influences were shared between the two conditions, unique genetic factors were linked to naturalistic scene viewing, indicating that fixation durations index different phenomena dependent on the context. Heritability for face looking was moderate (h2 = 0.19, 95% CI 0.03 to 0.34), and no familial influences were found for motion looking. Exploratory polygenic score analyses revealed no significant associations with fixation measures. This study underscores the dissociable genetic influences on infants' visual exploration of abstract versus naturalistic stimuli and the importance of considering context when interpreting eye-tracking data.", "doi": "10.1038/s41598-024-83557-3", "pmid": "39900629", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11791049"}, {"db": "pii", "key": "10.1038/s41598-024-83557-3"}], "notes": [], "created": "2025-09-08T11:34:00.982Z", "modified": "2025-11-14T11:07:01.444Z"}, {"entity": "publication", "iuid": "f1a9c58aaeef4132b2cdec07c05109a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a9c58aaeef4132b2cdec07c05109a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a9c58aaeef4132b2cdec07c05109a4"}}, "title": "Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity.", "authors": [{"family": "Cougnoux", "given": "Antony", "initials": "A"}, {"family": "Mahmoud", "given": "Loay", "initials": "L"}, {"family": "Johnsson", "given": "Per A", "initials": "PA"}, {"family": "Eroglu", "given": "Alper", "initials": "A"}, {"family": "Gsell", "given": "Louise", "initials": "L"}, {"family": "Rosenbauer", "given": "Jakob", "initials": "J"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "Hausser", "given": "Jean", "initials": "J"}], "type": "journal article", "published": "2025-01-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "3811", "issn-l": "2045-2322"}, "abstract": "Combining 3D cultures such as tumor spheroids and organoids with spatial omics holds great potential for tissue biology and cancer research. Yet, this potential is presently limited by technical and financial challenges of spatial omics methods and 3D cultures. To address this, we combine dye diffusion, the Smart-seq3xpress protocol for deep single-cell gene expression profiling, and dedicated probabilistic inference methods into diffusion Smart-seq3 (Smart-seq3D), to reveal the transcriptome of single cells along with their position along the core-periphery axis of spheroids. Applying Smart-seq3D to triple-negative breast tumor spheroids identifies thousands of spatial genes and reveals continuous, ungated spatial gene expression. Spatial gene and pathway expression patterns suggest biologies specific to spheroid regions, which we validate by immunostainings and pharmacological interventions. We use the Smart-seq3D data to test evolutionary principles of spatial tumor heterogeneity. Finally, we characterize aspects of tumor heterogeneity captured by 3D spheroids that are missing from 2D cultures but found in tumors in vivo. Smart-seq3D can offer a cost-efficient approach to explore how cells adapt their transcriptome to different micro-environments, reveal spatial determinants of drug resistance and could serve to characterize spatial interactions between cancer and stromal/immune cells in 3D co-cultures.", "doi": "10.1038/s41598-024-83989-x", "pmid": "39885179", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11782488"}, {"db": "pii", "key": "10.1038/s41598-024-83989-x"}], "notes": [], "created": "2025-04-07T08:46:18.744Z", "modified": "2025-04-07T08:46:18.749Z"}, {"entity": "publication", "iuid": "fdd85dd6bc6544c9abccb2e0a6b9a4fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdd85dd6bc6544c9abccb2e0a6b9a4fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdd85dd6bc6544c9abccb2e0a6b9a4fa"}}, "title": "Modulation of biological activities in adipose derived stem cells by histone deacetylation.", "authors": [{"family": "Abdallah", "given": "Sallam", "initials": "S"}, {"family": "Tabebi", "given": "Mouna", "initials": "M", "orcid": "0000-0002-2873-161X", "researcher": {"href": "https://publications.scilifelab.se/researcher/285705c043f34b55826e7f33ab36a875.json"}}, {"family": "Qanadilo", "given": "Sawsan", "initials": "S"}, {"family": "Ali", "given": "Neserin", "initials": "N"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "D'Arcy", "given": "P\u00e1draig", "initials": "P"}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Sjoberg", "given": "Folke", "initials": "F"}, {"family": "Elmasry", "given": "Moustafa", "initials": "M"}, {"family": "El-Serafi", "given": "Ahmed", "initials": "A"}], "type": "journal article", "published": "2025-01-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "3629"}, "abstract": "Difficult-to-heal wounds management accounts for about 4% of healthcare costs, highlighting the need for innovative solutions. Extracellular signals drive cell proliferation during tissue regeneration, while epigenetic mechanisms regulate stem cell homeostasis, differentiation, and skin repair. Exploring epigenetic regulation in adipose-derived stem cells (ADSCs) holds promise for improving skin injury treatments. We investigated the effects of histone deacetylase inhibitor (SAHA) on ADSCs to better understand its cellular and molecular impacts. ADSCs were treated with SAHA for 72 h, showing no change in cell viability at the studied concentrations. However, the expression of histone deacetylase decreased at 1000 nM, while the cell proliferation marker Ki-67 increased after SAHA treatment, as confirmed by immunofluorescence. CCND1 gene expression increased, whereas protein expression of the proliferating cell nuclear antigen (PCNA) decreased. Cell cycle analysis showed an increase in G2 phase in SAHA-treated cells. Microarray analysis revealed 74 upregulated and 40 downregulated differentially expressed genes, including upregulation of P53 targets, CDKN1A and MDM2. Proteomic analysis identified 631 upregulated and 823 downregulated proteins compared to the vehicle. Pathway enrichment analysis showed cell cycle, ATP-dependent chromatin remodeling and DNA processes were among the affected pathways. This study suggests SAHA modulates ADSCs' biological processes, highlighting its potential for skin regeneration.", "doi": "10.1038/s41598-024-84652-1", "pmid": "39880862", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-024-84652-1"}, {"db": "pmc", "key": "PMC11779964"}], "notes": [], "created": "2025-01-31T10:37:54.632Z", "modified": "2025-03-24T08:23:01.425Z"}, {"entity": "publication", "iuid": "e91f3d289b5744af8e560cfea7c0910e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e91f3d289b5744af8e560cfea7c0910e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e91f3d289b5744af8e560cfea7c0910e"}}, "title": "A de novo, mosaic and complex chromosome 21 rearrangement causes APP triplication and familial autosomal dominant early onset Alzheimer disease.", "authors": [{"family": "Ehn", "given": "Emma", "initials": "E"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Laffita-Mesa", "given": "Jose M", "initials": "JM"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0003-4503-4717", "researcher": {"href": "https://publications.scilifelab.se/researcher/481958db26a2433ea8d5cc786c3b2bca.json"}}, {"family": "Schoumans", "given": "Jacqueline", "initials": "J"}, {"family": "Portaankorva", "given": "Anne M", "initials": "AM"}, {"family": "Viitanen", "given": "Matti", "initials": "M"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Graff", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9949-2951", "researcher": {"href": "https://publications.scilifelab.se/researcher/3faadb7b187046b090d947f85d8c4dd1.json"}}], "type": "journal article", "published": "2025-01-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "2912", "issn-l": "2045-2322"}, "abstract": "Copy number variation (CNV) of the amyloid-\u03b2 precursor protein gene (APP) is a known cause of autosomal dominant Alzheimer disease (ADAD), but de novo genetic variants causing ADAD are rare. We report a mother and daughter with neuropathologically confirmed definite Alzheimer disease (AD) and extensive cerebral amyloid angiopathy (CAA). Copy number analysis identified an increased number of APP copies and genome sequencing (GS) revealed the underlying complex genomic rearrangement (CGR) including a triplication of APP with two unique breakpoint junctions (BPJs). The mosaic state in the mother had likely occurred de novo. Digital droplet PCR (ddPCR) on 42 different tissues, including 17 different brain regions, showed the derivative chromosome at varying mosaic levels (20-96%) in the mother who had symptom onset at age 58 years. In contrast, the derivative chromosome was present in all analyzed cells in the daughter whose symptom onset was at 34 years. This study reveals the architecture of a de novo CGR causing APP triplication and ADAD with a striking difference in age at onset between the fully heterozygous daughter compared to the mosaic mother. The GS analysis identified the complexity of the CGR illustrating its usefulness in identifying structural variants (SVs) in neurodegenerative disorders.", "doi": "10.1038/s41598-025-86645-0", "pmid": "39849058", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11759332"}, {"db": "pii", "key": "10.1038/s41598-025-86645-0"}], "notes": [], "created": "2025-01-30T10:52:39.932Z", "modified": "2025-11-18T20:45:12.186Z"}, {"entity": "publication", "iuid": "626dde82bebd4d8bb7880ecc0a2237e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0"}}, "title": "Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.", "authors": [{"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boger", "given": "Mathias Franzen", "initials": "MF"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Burgener", "given": "Adam D", "initials": "AD"}, {"family": "Bradley", "given": "Frideborg", "initials": "F", "orcid": "0000-0003-3006-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d51eaeb949e94bd39ab3605d495dc647.json"}}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Fowke", "given": "Keith", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "1014"}, "abstract": "The injectable contraceptive, depot medroxyprogesterone acetate (DMPA), is associated with compromised cervical mucosal barriers. High-resolution spatial transcriptomics is applied here to reveal the spatial localization of these altered molecular markers. Ectocervical tissue samples from Kenyan sex workers using DMPA, or non-hormonal contraceptives, underwent spatial transcriptomics and gene set enrichment analyses. Integrated systemic estradiol levels and bulk tissue gene expression data from a larger cohort enhanced the study's scope. Unsupervised clustering unveiled four epithelial and seven submucosal layers, showcasing spatially restricted and diverse functional epithelial responses, and a less structured submucosal spatial ordering. DMPA associated with mucosal-wide immunoglobulin gene upregulation, verified by CD20+ B-cell immunostaining, and upregulated immune markers adjacent to the basal membrane. Downregulated genes represented spatially restricted disrupted epithelial barrier integrity and submucosal extracellular matrix dysfunction. The transcriptional profile was associated with markers of estrogen regulation. Collectively, our findings reveal estrogen-modulated distinct ectocervical transcriptional profiles associated with DMPA usage. While upregulation of immunoglobulin genes occurs throughout the mucosa, activation of innate immune responses and dysregulation of barrier integrity markers are spatially restricted. These results extend previous analyses using bulk transcriptomics and provide insights into the molecular landscape influenced by DMPA, shedding light on contraceptive effects and health implications.", "doi": "10.1038/s41598-024-83775-9", "pmid": "39762272", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11704007"}, {"db": "pii", "key": "10.1038/s41598-024-83775-9"}], "notes": [], "created": "2025-01-23T12:51:23.407Z", "modified": "2025-11-19T08:36:34.197Z"}, {"entity": "publication", "iuid": "13600136596f4b84869a1e2d85c6a40e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13600136596f4b84869a1e2d85c6a40e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13600136596f4b84869a1e2d85c6a40e"}}, "title": "Multi-omics analysis detail a submicroscopic inv(15)(q14q15) generating fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency.", "authors": [{"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Soller", "given": "Maria Johansson", "initials": "MJ"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-12-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "30343", "issn-l": "2045-2322"}, "abstract": "Inversions are balanced structural variants that often remain undetected in genetic diagnostics. We present a female proband with a de novo Chromosome 15 paracentric inversion, disrupting MEIS2 and NUSAP1. The inversion was detected by short-read genome sequencing and confirmed with adaptive long-read sequencing. The breakpoint junction analysis revealed a 96 bp (bp) deletion and an 18 bp insertion in the two junctions, suggesting that the rearrangement arose through a replicative error. Transcriptome sequencing of cultured fibroblasts revealed normal MEIS2 levels and 0.61-fold decreased expression of NUSAP1. Furthermore, three fusion transcripts were detected and confirmed by Sanger sequencing. Heterozygous loss of MEIS2 (MIM# 600987) is associated with a cleft palate, heart malformations, and intellectual impairment, which overlap with the clinical symptoms observed in the proband. The observed fusion transcripts are likely non-functional, and MEIS2 haploinsufficiency is the likely disease causative mechanism. Altogether, this study's findings illustrate the importance of including inversions in rare disease diagnostic testing and highlight the value of long read sequencing for the validation and characterization of such variants.", "doi": "10.1038/s41598-024-81507-7", "pmid": "39639090", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11621304"}, {"db": "pii", "key": "10.1038/s41598-024-81507-7"}], "notes": [], "created": "2025-01-02T10:32:21.284Z", "modified": "2025-11-18T20:49:45.019Z"}, {"entity": "publication", "iuid": "0892eae30e2345098adbee303745503a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0892eae30e2345098adbee303745503a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0892eae30e2345098adbee303745503a"}}, "title": "Systemic inflammatory response in colorectal cancer is associated with tumour mismatch repair and impaired survival.", "authors": [{"family": "Hjortborg", "given": "Mats", "initials": "M"}, {"family": "Edin", "given": "Sofia", "initials": "S"}, {"family": "B\u00f6ckelman", "given": "Camilla", "initials": "C"}, {"family": "Kaprio", "given": "Tuomas", "initials": "T"}, {"family": "Li", "given": "Xingru", "initials": "X"}, {"family": "Gkekas", "given": "Ioannis", "initials": "I"}, {"family": "Hagstr\u00f6m", "given": "Jaana", "initials": "J"}, {"family": "Strig\u00e5rd", "given": "Karin", "initials": "K"}, {"family": "Haglund", "given": "Caj", "initials": "C"}, {"family": "Gunnarsson", "given": "Ulf", "initials": "U"}, {"family": "Palmqvist", "given": "Richard", "initials": "R"}], "type": "journal article", "published": "2024-11-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "29738", "issn-l": "2045-2322"}, "abstract": "The systemic inflammatory response (SIR), defined as elevated levels of circulating C-reactive protein (CRP), is an important predictor of impaired survival in colorectal cancer. The aim of this study was to explore the prognostic role of SIR and its association with tumour mismatch repair status and the immune response. Immune activity profiles of mononuclear cells isolated from CRC tissues and blood in the U-CAN exploration cohort (n = 69), were analysed by flow cytometry. In the U-CAN validation cohort (n = 257), T-helper cells (T-bet+), cytotoxic T cells (CD8+), regulatory T cells (FoxP3+), B cells (CD20+), and macrophages (CD68+) were analysed by multispectral imaging. Microsatellite instability was determined using five mononucleotide-repeat microsatellite markers. Patients with high CRP levels (> 10 mg/l) were significantly more often diagnosed with high-grade tumours and tumours exhibiting microsatellite instability. However, some patients with high CRP levels were found to have microsatellite-stable tumours. Furthermore, high CRP levels were associated with specific tumour immune traits including an augmented macrophage response and were significantly linked to poorer cancer-specific survival, particularly in patients with microsatellite-stable tumours. In conclusion, our findings suggest an interplay between SIR and mismatch repair status in CRC prognosis which needs to be further explored.", "doi": "10.1038/s41598-024-80803-6", "pmid": "39613865", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11607405"}, {"db": "pii", "key": "10.1038/s41598-024-80803-6"}], "notes": [], "created": "2025-11-25T19:20:24.421Z", "modified": "2025-11-25T19:20:24.438Z"}, {"entity": "publication", "iuid": "80fde0e59021465788e7dc10ee840965", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80fde0e59021465788e7dc10ee840965.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80fde0e59021465788e7dc10ee840965"}}, "title": "Altered O-Glycans in stimulated whole saliva from patients with primary Sj\u00f6gren's syndrome and non-pSS sicca.", "authors": [{"family": "Kamounah", "given": "Sarah", "initials": "S"}, {"family": "Thomsson", "given": "Kristina A", "initials": "KA"}, {"family": "S\u00f8rensen", "given": "Christiane Elisabeth", "initials": "CE"}, {"family": "Bennett", "given": "Eric Paul", "initials": "EP"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Pedersen", "given": "Anne Marie Lynge", "initials": "AML"}], "type": "journal article", "published": "2024-11-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "29377", "issn-l": "2045-2322"}, "abstract": "To investigate if salivary O-linked glycans are altered in primary Sj\u00f6gren's syndrome (pSS), and thus contributing to explain symptoms of oral dryness, and an impaired oral mucosal barrier function leading to changes in microbial metabolism and colonization by both pathogenic and commensal microorganisms and increased prevalence of oral diseases. O-linked oligosaccharides from stimulated whole saliva (SWS) samples from 24 patients with pSS, 38 patients with non-pSS sicca, and 23 healthy controls were analyzed using liquid chromatography mass spectrometer (LC-MS). Non-fractionated reduced and alkylated saliva was dot-blotted to PVDF-membrane and O-linked oligosaccharides were released using reductive beta-elimination. The 50 most abundant glycans were identified and their intensity compared for each sample, reflecting the relative abundance of individual monosaccharide residues. Comparison of the compositions of O-glycans in SWS samples revealed higher relative levels of sialic acid (NeuAc) and lower levels of neutral amino-monosaccharides (HexNAc) in pSS and non-pSS sicca patients than in the healthy controls. MS2 fragmentation analysis of salivary O-glycans suggests that altered sulfation, fucosylation, sialylation and distribution of core types may all contribute to the observed alteration, directly or indirectly. Additionally, the short disaccharide sialyl-Tn was most abundant in the saliva samples from patients with pSS. Our findings indicate that the salivary mucin-type O-glycan profile is altered in pSS, reflecting a dysfunction of the post-translational modification of salivary mucins leading to rheological changes of saliva, oral dryness symptoms, and impaired oral mucosal barrier function. The pathophysiological significance of the aberrant O-glycosylation needs further elucidation.", "doi": "10.1038/s41598-024-79473-1", "pmid": "39592783", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11599585"}, {"db": "pii", "key": "10.1038/s41598-024-79473-1"}], "notes": [], "created": "2025-10-23T13:28:33.430Z", "modified": "2025-10-23T13:28:33.436Z"}, {"entity": "publication", "iuid": "f2e19341e7de45c59fd7c018899e6346", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2e19341e7de45c59fd7c018899e6346.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2e19341e7de45c59fd7c018899e6346"}}, "title": "Sirtuin inhibitors reduce intracellular growth of M. tuberculosis in human macrophages via modulation of host cell immunity.", "authors": [{"family": "Kalsum", "given": "Sadaf", "initials": "S"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Loreti", "given": "Marco Giulio", "initials": "MG"}, {"family": "Andersson", "given": "Blanka", "initials": "B"}, {"family": "Danielson", "given": "Eva", "initials": "E"}, {"family": "Lerm", "given": "Maria", "initials": "M", "orcid": "0000-0002-5092-9892", "researcher": {"href": "https://publications.scilifelab.se/researcher/6645c25a513f4bb8a24d11fd80c1b23d.json"}}, {"family": "Brighenti", "given": "Susanna", "initials": "S"}], "type": "journal article", "published": "2024-11-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "28150", "issn-l": "2045-2322"}, "abstract": "Host-directed therapies aiming to strengthen the body's immune system, represent an underexplored opportunity to improve treatment of tuberculosis (TB). We have previously shown in Mycobacterium tuberculosis (Mtb)-infection models and clinical trials that treatment with the histone deacetylase (HDAC) inhibitor, phenylbutyrate (PBA), can restore Mtb-induced impairment of antimicrobial responses and improve clinical outcomes in pulmonary TB. In this study, we evaluated the efficacy of different groups of HDAC inhibitors to reduce Mtb growth in human immune cells. A panel of 21 selected HDAC inhibitors with different specificities that are known to modulate infection or inflammation was tested using high-content live-cell imaging and analysis. Monocyte-derived macrophages or bulk peripheral blood cells (PBMCs) were infected with the green fluorescent protein (GFP)-expressing Mtb strains H37Ra or H37Rv and treated with HDAC inhibitors in the micromolar range in parallel with a combination of the first-line antibiotics, rifampicin, and isoniazid. Host cell viability in HDAC inhibitor treated cell cultures was monitored with Cytotox-red. Seven HDAC inhibitors were identified that reduced Mtb growth in macrophages > 45-75% compared to average 40% for PBA. The most effective compounds were inhibitors of the class III HDAC proteins, the sirtuins. While these compounds may exhibit their effects by improving macrophage function, one of the sirtuin inhibitors, tenovin, was also highly effective in extracellular killing of Mtb bacilli. Antimicrobial synergy testing using checkerboard assays revealed additive effects between selected sirtuin inhibitors and subinhibitory concentrations of rifampicin or isoniazid. A customized macrophage RNA array including 23 genes associated with cytokines, chemokines and inflammation, suggested that Mtb-infected macrophages are differentially modulated by the sirtuin inhibitors as compared to PBA. Altogether, these results demonstrated that sirtuin inhibitors may be further explored as promising host-directed compounds to support immune functions and reduce intracellular growth of Mtb in human cells.", "doi": "10.1038/s41598-024-79136-1", "pmid": "39548210", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11568201"}, {"db": "pii", "key": "10.1038/s41598-024-79136-1"}], "notes": [], "created": "2024-12-02T15:26:25.458Z", "modified": "2025-10-17T13:04:27.024Z"}, {"entity": "publication", "iuid": "8c3d196aac004a68ab004f9c14f4ad36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c3d196aac004a68ab004f9c14f4ad36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c3d196aac004a68ab004f9c14f4ad36"}}, "title": "Impact of thermal seed treatment on spermosphere microbiome, metabolome and viability of winter wheat.", "authors": [{"family": "Karlsson", "given": "Maria E", "initials": "ME"}, {"family": "Forsberg", "given": "Gustaf", "initials": "G"}, {"family": "Rosberg", "given": "Anna Karin", "initials": "AK"}, {"family": "Thaning", "given": "Christian", "initials": "C"}, {"family": "Alsanius", "given": "Beatrix", "initials": "B"}], "type": "journal article", "published": "2024-11-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "27197", "issn-l": "2045-2322"}, "abstract": "Thermal seed treatment can be used as an alternative method to prevent infection by seed-borne diseases, but exposure duration and temperature during thermal treatment are important to maintain high seed viability and emergence whilst decreasing infection rate. A method for predicting suitable treatment parameters to maintain viability and eliminate seed-borne pathogens is therefore needed. Seeds of winter wheat were subjected to thermal treatment at four levels of intensity and pre-treatments with or without imbibition. Treatment impact was measured by metabolome analysis using LC-MS and GC-MS, analysis of spermosphere bacterial and fungal metagenomes using Illumina MiSeq, and detection of presence of Fusarium spp. and Microdochium spp. using ddPCR. The results showed that moderate treatment intensity reduced signs of infection and increased seedling emergence. In imbibed samples, myo-inositol concentration and myo-inositol: glucose ratio were positively correlated with treatment intensity, whereas concentrations of glucose and citric acid were negatively correlated. No correlations were found for non-imbibed samples. Imbibition had a large significant impact on microbial community composition of the wheat spermosphere. Imbibition of wheat seeds prior to thermal treatment altered wheat spermosphere microbiota. The concentration of myo-inositol, potentially in combination with glucose, could be a candidate predictor for suitable thermal treatment intensity of wheat seeds.", "doi": "10.1038/s41598-024-78575-0", "pmid": "39516585", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11549219"}, {"db": "pii", "key": "10.1038/s41598-024-78575-0"}], "notes": [], "created": "2024-11-26T10:43:25.633Z", "modified": "2025-10-17T13:03:12.786Z"}, {"entity": "publication", "iuid": "5a04bb7c654544609c10639696a8b1d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a04bb7c654544609c10639696a8b1d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a04bb7c654544609c10639696a8b1d8"}}, "title": "Autoantibodies to protein S may explain rare cases of coagulopathy following COVID-19 vaccination.", "authors": [{"family": "Yalcinkaya", "given": "Ahmet", "initials": "A"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M"}, {"family": "Cederholm", "given": "Axel", "initials": "A"}, {"family": "G\u00fcner", "given": "Almira", "initials": "A"}, {"family": "Rietrae", "given": "Isabel", "initials": "I"}, {"family": "Mildner", "given": "Hedvig", "initials": "H"}, {"family": "Behere", "given": "Anish", "initials": "A"}, {"family": "Eriksson", "given": "Oskar", "initials": "O"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Landegren", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2024-10-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "24512", "issn-l": "2045-2322"}, "abstract": "While Coronavirus disease 2019 (COVID-19) vaccines have proven to be both effective and generally safe, rare but severe adverse events following immunization (AEFIs) are described. Autoantibodies to platelet factor-4 are associated with catastrophic thrombotic AEFIs, but comprehensive investigations of other autoantibodies are lacking. We aimed to detect and describe autoantibodies targeting coagulation-related proteins in a population-wide cohort (SWEDEGENE) including AEFIs attributed to COVID-19 vaccines in Sweden. Subjects were recruited from December 2020 to October 2022 and were stratified based on diagnosis and COVID-19 exposure. Screening was carried out in two phases, with a multiplex bead-based assay in the first subset (until September 2021) and with targeted assays for the second (until October 2022). Positivity was defined based on absolute, relative, and biological/technical thresholds. Patients with coagulation-related AEFIs were older and the Vaxzevria vaccine was overrepresented in this group. Two cases had antiphospholipid antibodies but none had PF4 antibodies. We identified six positives for protein S autoantibodies. Protein S concentrations were negatively correlated with autoantibody response in patients with immunoreactivity and functional analysis revealed low protein S activity in three subjects. Our population-wide analysis reveals cases with autoantibodies against protein S which possibly underlie coagulopathic AEFIs.", "doi": "10.1038/s41598-024-75514-x", "pmid": "39424883", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11489816"}, {"db": "pii", "key": "10.1038/s41598-024-75514-x"}], "notes": [], "created": "2024-11-07T12:54:49.632Z", "modified": "2024-11-07T12:54:49.642Z"}, {"entity": "publication", "iuid": "f1a9d262eed546358b98560bcbaa52d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a9d262eed546358b98560bcbaa52d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a9d262eed546358b98560bcbaa52d7"}}, "title": "Estrogen-stimulated uropathogenic E. coli mediate enhanced neutrophil responses.", "authors": [{"family": "Pettersson", "given": "Carolina", "initials": "C"}, {"family": "Wu", "given": "Rongrong", "initials": "R"}, {"family": "Demirel", "given": "Isak", "initials": "I"}], "type": "journal article", "published": "2024-10-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "23030", "issn-l": "2045-2322"}, "abstract": "Urinary tract infection (UTI) is one of the most common bacterial infections worldwide and the most common cause is uropathogenic Escherichia coli (UPEC). Current research is mostly focused on how UPEC affects host factors, whereas the effect of host factors on UPEC is less studied. Our previous studies have shown that estrogen alters UPEC virulence. However, the effect of this altered UPEC virulence on neutrophils is unknown. The aim of the present study was to investigate how the altered UPEC virulence mediated by estrogen modulates neutrophil responses. We found that estradiol-stimulated CFT073 increased neutrophil phagocytosis, NETs formation and intracellular ROS production. We observed that the total ROS production from neutrophils was reduced by estradiol-stimulated CFT073. We also found that estradiol-stimulated CFT073 induced less cytotoxicity in neutrophils. Additionally, we found that several cytokines and chemokines like IL-8, IL-1\u03b2, CXCL6, MCP-1 and MCP-4 were increased upon estradiol-stimulated CFT073 infection. In conclusion, this study demonstrates that the estrogen-mediated alterations to UPEC virulence modulates neutrophil responses, most likely in a host-beneficial manner.", "doi": "10.1038/s41598-024-74863-x", "pmid": "39362931", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11449900"}, {"db": "pii", "key": "10.1038/s41598-024-74863-x"}], "notes": [], "created": "2024-11-27T22:19:57.087Z", "modified": "2024-11-27T22:19:57.098Z"}, {"entity": "publication", "iuid": "72adce29e0fe45cc9fd0b0f06d8a238b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72adce29e0fe45cc9fd0b0f06d8a238b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72adce29e0fe45cc9fd0b0f06d8a238b"}}, "title": "Cancer associated variant enrichment CAVE, a gene agnostic approach to identify low burden variants in chronic lymphocytic leukemia.", "authors": [{"family": "Yaacov", "given": "Adar", "initials": "A"}, {"family": "Lazarian", "given": "Gregory", "initials": "G"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Westr\u00f6m", "given": "Simone", "initials": "S"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P"}, {"family": "Imache", "given": "Samia", "initials": "S"}, {"family": "Lefebvre", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Cymbalista", "given": "Florence", "initials": "F"}, {"family": "Baran-Marszak", "given": "Fanny", "initials": "F"}, {"family": "Rosenberg", "given": "Shai", "initials": "S"}, {"family": "Soussi", "given": "Thierry", "initials": "T"}], "type": "journal article", "published": "2024-09-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "21962", "issn-l": "2045-2322"}, "abstract": "Intratumoral heterogeneity is an important clinical challenge because low burden clones expressing specific genetic alterations drive therapeutic resistance mechanisms. We have developed CAVE (cancer-associated variant enrichment), a gene-agnostic computational tool to identify specific enrichment of low-burden cancer driver variants in next-generation sequencing (NGS) data. For this study, CAVE was applied to TP53 in chronic lymphocytic leukemia (CLL) as a cancer model. Indeed, as TP53 mutations are part of treatment decision-making algorithms and low-burden variants are frequent, there is a need to distinguish true variants from background noise. Recommendations have been published for reliable calling of low-VAF variants of TP53 in CLL and the assessment of the background noise for each platform is essential for the quality of the testing. CAVE is able to detect specific enrichment of low-burden variants starting at variant allele frequencies (VAFs) as low as 0.3%. In silico TP53 dependent and independent analyses confirmed the true driver nature of all these variants. Orthogonal validation using either ddPCR or NGS analyses of follow-up samples confirmed variant identification. CAVE can be easily deployed in any cancer-related NGS workflow to detect the enrichment of low-burden variants of clinical interest.", "doi": "10.1038/s41598-024-73027-1", "pmid": "39304718", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11415367"}, {"db": "pii", "key": "10.1038/s41598-024-73027-1"}], "notes": [], "created": "2024-11-22T09:06:54.214Z", "modified": "2024-11-22T09:06:54.222Z"}, {"entity": "publication", "iuid": "b3f38948268a40c1a82bfcc788171bfa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3f38948268a40c1a82bfcc788171bfa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3f38948268a40c1a82bfcc788171bfa"}}, "title": "Monitoring SARS-CoV-2 IgA, IgM and IgG antibodies in dried blood and saliva samples using antibody proximity extension assays (AbPEA).", "authors": [{"family": "Wang", "given": "Mengqi", "initials": "M"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Cortabarr\u00eda Fernandez", "given": "Matilde", "initials": "M"}, {"family": "D\u00edaz Codina", "given": "Roger", "initials": "R"}, {"family": "Sterky", "given": "Fredrik H", "initials": "FH"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Zhao", "given": "Hongxing", "initials": "H"}], "type": "journal article", "published": "2024-09-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "21655", "issn-l": "2045-2322"}, "abstract": "Using a modified proximity extension assay, total and immunoglobulin (Ig) class-specific anti-SARS-CoV-2 antibodies were sensitively and conveniently detected directly from \u00f81.2 mm discs cut from dried blood and saliva spots (DBS and DSS) without the need for elution. For total Ig detection, antigen probes were prepared by conjugating recombinant spike protein subunit 1 (S1-RBD) to a pair of oligonucleotides. To detect isotype-specific antibody reactivity, one antigen probe was replaced with oligonucleotide-conjugated antibodies specific for antibody isotypes. Binding of pairs of oligonucleotide-conjugated probes to antibodies in patient samples brings oligonucleotides in proximity. An added DNA polymerase uses a transient hybridization between the oligonucleotides to prime synthesis of a DNA strand, which serves as a DNA amplicon that is quantified by real-time PCR. The S1-RBD-specific IgG, IgM, and IgA antibodies in DBS samples collected over the course of a first and second vaccination exhibited kinetics consistent with previous reports. Both DBS and DSS collected from 42 individuals in the autumn of 2023 showed significant level of total S1-RBD antibodies with a correlation of R = 0.70. However, levels in DSS were generally 10 to 100-fold lower than in DBS. Anti-S1-RBD IgG and IgA in DSS demonstrated a correlation of R = 0.6.", "doi": "10.1038/s41598-024-72453-5", "pmid": "39289450", "labels": {"Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11408710"}, {"db": "pii", "key": "10.1038/s41598-024-72453-5"}], "notes": [], "created": "2024-11-27T22:30:28.522Z", "modified": "2024-11-27T22:30:28.529Z"}, {"entity": "publication", "iuid": "cc0dc021cd52477eadcc7e7cf07b0128", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc0dc021cd52477eadcc7e7cf07b0128.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc0dc021cd52477eadcc7e7cf07b0128"}}, "title": "Blood based metabolic markers of glioma from pre-diagnosis to surgery.", "authors": [{"family": "L\u00f6ding", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-9228-0625", "researcher": {"href": "https://publications.scilifelab.se/researcher/14cb4391b5614a4892baf3113e1e010d.json"}}, {"family": "Antti", "given": "Henrik", "initials": "H"}, {"family": "Sj\u00f6berg", "given": "Rickard L", "initials": "RL"}, {"family": "Melin", "given": "Beatrice", "initials": "B"}, {"family": "Bj\u00f6rkblom", "given": "Benny", "initials": "B", "orcid": "0000-0001-9347-5790", "researcher": {"href": "https://publications.scilifelab.se/researcher/acf29b039dfc496fb33c0cf7cb1d587c.json"}}], "type": "journal article", "published": "2024-09-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "20680", "issn-l": "2045-2322"}, "abstract": "Gliomas are highly complex and metabolically active brain tumors associated with poor prognosis. Recent reports have found altered levels of blood metabolites during early tumor development, suggesting that tumor development could be detected several years before clinical manifestation. In this study, we performed metabolite analyses of blood samples collected from healthy controls and future glioma patients, up to eight years before glioma diagnosis, and on the day of glioma surgery. We discovered that metabolites related to early glioma development were associated with an increased energy turnover, as highlighted by elevated levels of TCA-related metabolites such as fumarate, malate, lactate and pyruvate in pre-diagnostic cases. We also found that metabolites related to glioma progression at surgery were primarily high levels of amino acids and metabolites of amino acid catabolism, with elevated levels of 11 amino acids and two branched-chain alpha-ketoacids, ketoleucine and ketoisoleucine. High amino acid turnover in glioma tumor tissue is currently utilized for PET imaging, diagnosis and delineation of tumor margins. By examining blood-based metabolic progression patterns towards disease onset, we demonstrate that this high amino acid turnover is also detectable in a simple blood sample. These findings provide additional insight of metabolic alterations during glioma development and progression.", "doi": "10.1038/s41598-024-71375-6", "pmid": "39237693", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11377417"}, {"db": "pii", "key": "10.1038/s41598-024-71375-6"}], "notes": [], "created": "2024-11-26T10:43:35.450Z", "modified": "2025-10-17T13:03:13.052Z"}, {"entity": "publication", "iuid": "caacd24708a649b79c654cf4fd2151a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/caacd24708a649b79c654cf4fd2151a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/caacd24708a649b79c654cf4fd2151a1"}}, "title": "Soil volatilomics uncovers tight linkage between soybean presence and soil omics profiles in agricultural fields.", "authors": [{"family": "Kuchikata", "given": "Hikari", "initials": "H"}, {"family": "Sano", "given": "Mizuki", "initials": "M"}, {"family": "Fujiwara", "given": "Fuki", "initials": "F"}, {"family": "Murashima", "given": "Kazuki", "initials": "K"}, {"family": "Kumaishi", "given": "Kie", "initials": "K"}, {"family": "Narukawa", "given": "Megumi", "initials": "M"}, {"family": "Nose", "given": "Yui", "initials": "Y"}, {"family": "Kobayashi", "given": "Makoto", "initials": "M"}, {"family": "Hamamoto", "given": "Shoichiro", "initials": "S"}, {"family": "Kobayashi", "given": "Natsuko I", "initials": "NI"}, {"family": "Sugiyama", "given": "Akifumi", "initials": "A"}, {"family": "Nihei", "given": "Naoto", "initials": "N"}, {"family": "Ichihashi", "given": "Yasunori", "initials": "Y"}, {"family": "Kusano", "given": "Miyako", "initials": "M"}], "type": "journal article", "published": "2024-09-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "20541", "issn-l": "2045-2322"}, "abstract": "Securing a stable food supply and achieving sustainable agricultural production are essential for mitigating future food insecurity. Soil metabolomics is a promising tool for capturing soil status, which is a critical issue for future sustainable food security. This study aims to provide deeper insights into the status of soybean-grown fields under varying soil conditions over three years by employing comprehensive soil volatile organic compound (VOC) profiling, also known as soil volatilomics. Profiling identified approximately 200 peaks in agricultural fields. The soil of soybean-presented plots exhibited markedly higher VOC levels than those of non-soybean plots during the flowering season. Pentanoic acid, 2,2,4-trimethyl-3-carboxyisopropyl, isobutyl ester, a discriminative soil VOC, was identified through multivariate data analysis as a distinctively present VOC in fields with or without soybean plants during the flowering period. Soil VOC profiles exhibited strong correlations with soil-related omics datasets (soil ionome, microbiome, metabolome, and physics) and no significant correlations with root microbiome and rhizosphere chemicals. These findings indicate that soil VOC profiles could serve as a valuable indicator for assessing soil status, thereby supporting efforts to ensure future global food security.", "doi": "10.1038/s41598-024-70873-x", "pmid": "39232061", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11375131"}, {"db": "pii", "key": "10.1038/s41598-024-70873-x"}], "notes": [], "created": "2025-11-18T12:06:31.446Z", "modified": "2025-11-18T12:06:31.464Z"}, {"entity": "publication", "iuid": "4756ff74b4e14f04b6e4d2147352389e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4756ff74b4e14f04b6e4d2147352389e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4756ff74b4e14f04b6e4d2147352389e"}}, "title": "The involvement of cyclotides in the heavy metal tolerance of Viola spp.", "authors": [{"family": "Sychta", "given": "Klaudia", "initials": "K"}, {"family": "S\u0142omka", "given": "Aneta", "initials": "A"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "Samardakiewicz", "given": "S\u0142awomir", "initials": "S"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U"}, {"family": "Slazak", "given": "Blazej", "initials": "B"}], "type": "journal article", "published": "2024-08-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "19306", "issn-l": "2045-2322"}, "abstract": "The Violaceae family is rich in metal-tolerant species and species producing cyclic peptides (cyclotides) that are linked to the resistance to biotic factors. Plants that inhabit areas polluted with heavy metals have developed various mechanisms of tolerance. To test the role of cyclotides in protection against abiotic factors, including heavy metals, cell suspension cultures of Viola species/genotypes (V. lutea ssp. westfalica, V. tricolor, V. arvensis, and V. uliginosa), representing different levels of tolerance to heavy metals (from the most tolerant-MET to the least tolerant populations/species-NMET), were used. The relative abundances of the cyclotides in the control, untreated cell suspensions of all the selected species/genotypes, and cells treated with Zn or Pb (200 \u00b5M or 2000 \u00b5M) for 24 h or 72 h were determined via MALDI-MS. Transmission electron microscopy with X-ray microanalysis was used to detect putative co-localization of the cyclotides with Zn or Pb in the cells of V. tricolor treated with the highest concentration of heavy metals for 72 h. Cyclotide biosynthesis was dependent on the type of heavy metal and its concentration, time of treatment, plant species, and population type (MET vs. NMET). It was positively correlated with the level of tolerance of particular Viola species. The increased production of cyclotides was observed in the cells of metallophyte species, mostly in Zn-treated cells. The nonmetallophyte-V. uliginosa presented a decrease in the production of cyclotides independent of the dose and duration of the metal treatment. Cyclotides co-localized with Pb more evidently than with Zn, suggesting that cyclotides have heavy metal affinity. V. lutea ssp. westfalica transcriptome mining yielded 100 cyclotide sequences, 16 known and 84 novel named viwe 1-84. These findings support the hypothesis that cyclotides are involved in certain mechanisms of plant tolerance to heavy metals.", "doi": "10.1038/s41598-024-69018-x", "pmid": "39164283", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11336087"}, {"db": "pii", "key": "10.1038/s41598-024-69018-x"}], "notes": [], "created": "2024-11-20T10:35:54.631Z", "modified": "2024-11-20T10:37:37.738Z"}, {"entity": "publication", "iuid": "69d3c968e92644688b9b1341bc588cc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69d3c968e92644688b9b1341bc588cc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69d3c968e92644688b9b1341bc588cc9"}}, "title": "Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species.", "authors": [{"family": "Fetsiukh", "given": "Anastasiia", "initials": "A"}, {"family": "Pall", "given": "Taavi", "initials": "T"}, {"family": "Timmusk", "given": "Salme", "initials": "S"}], "type": "journal article", "published": "2024-08-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "18806", "issn-l": "2045-2322"}, "abstract": "Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed.", "doi": "10.1038/s41598-024-68123-1", "pmid": "39138231", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11322436"}, {"db": "pii", "key": "10.1038/s41598-024-68123-1"}], "notes": [], "created": "2024-10-21T11:17:11.546Z", "modified": "2024-10-21T11:17:11.551Z"}, {"entity": "publication", "iuid": "b25674a18c78498ba39b13ddb7fc9246", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b25674a18c78498ba39b13ddb7fc9246.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b25674a18c78498ba39b13ddb7fc9246"}}, "title": "Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.", "authors": [{"family": "Salgkamis", "given": "Dimitrios", "initials": "D"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Hartman", "given": "Johan", "initials": "J"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T"}, {"family": "Matikas", "given": "Alexios", "initials": "A"}, {"family": "Zerdes", "given": "Ioannis", "initials": "I"}], "type": "journal article", "published": "2024-08-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "18275", "issn-l": "2045-2322"}, "abstract": "Formalin-fixed paraffin-embedded (FFPE) tissue represents a valuable source for translational cancer research. However, the widespread application of various downstream methods remains challenging. Here, we aimed to assess the feasibility of a genomic and gene expression analysis workflow using FFPE breast cancer (BC) tissue. We conducted a systematic literature review for the assessment of concordance between FFPE and fresh-frozen matched tissue samples derived from patients with BC for DNA and RNA downstream applications. The analytical performance of three different nucleic acid extraction kits on FFPE BC clinical samples was compared. We also applied a newly developed targeted DNA Next-Generation Sequencing (NGS) 370-gene panel and the nCounter BC360\u00ae platform on simultaneously extracted DNA and RNA, respectively, using FFPE tissue from a phase II clinical trial. Of the 3701 initial search results, 40 articles were included in the systematic review. High degree of concordance was observed in various downstream application platforms. Moreover, the performance of simultaneous DNA/RNA extraction kit was demonstrated with targeted DNA NGS and gene expression profiling. Exclusion of variants below 5% variant allele frequency was essential to overcome FFPE-induced artefacts. Targeted genomic analyses were feasible in simultaneously extracted DNA/RNA from FFPE material, providing insights for their implementation in clinical trials/cohorts.", "doi": "10.1038/s41598-024-69285-8", "pmid": "39107471", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11303707"}, {"db": "pii", "key": "10.1038/s41598-024-69285-8"}], "notes": [], "created": "2024-11-20T20:03:06.171Z", "modified": "2024-11-20T20:03:06.219Z"}, {"entity": "publication", "iuid": "083d4ea1eab4440d9429b817a041e0e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/083d4ea1eab4440d9429b817a041e0e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/083d4ea1eab4440d9429b817a041e0e9"}}, "title": "Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV.", "authors": [{"family": "Narayanan", "given": "Aswathy", "initials": "A"}, {"family": "Kieri", "given": "Oscar", "initials": "O"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Ghorbani", "given": "Mahin", "initials": "M"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Ray", "given": "Shilpa", "initials": "S"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}], "type": "journal article", "published": "2024-08-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "17820", "issn-l": "2045-2322"}, "abstract": "The gut and oral microbiome is altered in people living with HIV (PLWH). While antiretroviral treatment (ART) is pivotal in restoring immune function in PLWH, several studies have identified an association between specific antiretrovirals, particularly integrase inhibitors (INSTI), and weight gain. In our study, we explored the differences in the oral and gut microbiota of PLWH under different ART regimens, and its correlation to Body Mass Index (BMI). Fecal and salivary samples were collected from PLWH (n = 69) and healthy controls (HC, n = 80). We performed taxonomy analysis to determine the microbial composition and relationship between microbial abundance and ART regimens, BMI, CD4+T-cell count, CD4/CD8 ratio, and ART duration. PLWH showed significantly lower richness compared to HC in both the oral and gut environment. The gut microbiome composition of INSTI-treated individuals was enriched with Faecalibacterium and Bifidobacterium, whereas non-nucleotide reverse transcriptase inhibitor (NNRTI)-treated individuals were enriched with Gordonibacter, Megasphaera, and Staphylococcus. In the oral microenvironment, Veillonella was significantly more abundant in INSTI-treated individuals and Fusobacterium and Alloprevotella in the NNRTI-treated individuals. Furthermore, Bifidobacterium and Dorea were enriched in gut milieu of PLWH with high BMI. Collectively, our findings identify distinct microbial profiles, which are associated with different ART regimens and BMI in PLWH on successful ART, thereby highlighting significant effects of specific antiretrovirals on the microbiome.", "doi": "10.1038/s41598-024-68479-4", "pmid": "39090139", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11294597"}, {"db": "pii", "key": "10.1038/s41598-024-68479-4"}], "notes": [], "created": "2024-11-15T09:06:45.594Z", "modified": "2024-11-25T10:21:34.231Z"}, {"entity": "publication", "iuid": "e31905d9133149d288cf5eacb904181a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e31905d9133149d288cf5eacb904181a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e31905d9133149d288cf5eacb904181a"}}, "title": "The interaction of genetics and physical activity in the pathogenesis of metabolic dysfunction associated liver disease.", "authors": [{"family": "Frostdahl", "given": "Hanna", "initials": "H"}, {"family": "Ahmad", "given": "Nouman", "initials": "N"}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Mora", "given": "Andr\u00e9s Mart\u00ednez", "initials": "AM"}, {"family": "Langner", "given": "Taro", "initials": "T"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Kullberg", "given": "Joel", "initials": "J"}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H"}, {"family": "Brooke", "given": "Hannah L", "initials": "HL"}, {"family": "Ahmad", "given": "Shafqat", "initials": "S"}], "type": "journal article", "published": "2024-08-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "17817", "issn-l": "2045-2322"}, "abstract": "Genetic variants associated with increased liver fat and volume have been reported, but whether physical activity (PA) can attenuate the impact of genetic susceptibility to these traits is poorly understood. We aimed to investigate whether higher PA modify genetic impact on liver-related traits in the UK Biobank cohort. PA was self-reported, while magnetic resonance images were used to estimate liver fat (n = 27,243) and liver volume (n = 24,752). Metabolic dysfunction-associated liver disease (MASLD) and chronic liver disease (CLD) were diagnosed using ICD-9 and ICD-10 codes. Ten liver fat and eleven liver volume-associated genetic variants were selected and unweighted genetic-risk scores for liver fat (GRSLF) and liver volume (GRSLV) were computed. Linear regression analyses were performed to explore interactions between GRSLF/ GRSLV and PA in relation to liver-related traits. Association between GRSLF and liver fat was not different among lower (\u03b2 = 0.063, 95% CI 0.041-0.084) versus higher PA individuals (\u03b2 = 0.065, 95% CI 0.054-0.077, pinteraction = 0.62). The association between the GRSLV and liver volume was not different across different PA groups (pinteraction = 0.71). Similarly, PA did not modify the effect of GRSLF and GRSLV on MASLD or CLD. Our findings show that physical activity and genetic susceptibility to liver-related phenotypes seem to act independently, benefiting all individuals regardless of genetic risk.", "doi": "10.1038/s41598-024-68271-4", "pmid": "39090170", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11294342"}, {"db": "pii", "key": "10.1038/s41598-024-68271-4"}], "notes": [], "created": "2024-11-25T10:21:29.134Z", "modified": "2024-11-25T10:21:29.138Z"}, {"entity": "publication", "iuid": "cb40d036f76546bcaf773bb135db83a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb40d036f76546bcaf773bb135db83a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb40d036f76546bcaf773bb135db83a3"}}, "title": "The rate of W chromosome degeneration across multiple avian neo-sex chromosomes.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Downing", "given": "Philip A", "initials": "PA", "orcid": "0000-0002-5286-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e004ff0660ee411cb310ab108f29c171.json"}}, {"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2024-07-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "16548", "issn-l": "2045-2322"}, "abstract": "When sex chromosomes evolve recombination suppression, the sex-limited chromosome (Y/W) commonly degenerate by losing functional genes. The rate of Y/W degeneration is believed to slow down over time as the most essential genes are maintained by purifying selection, but supporting data are scarce especially for ZW systems. Here, we study W degeneration in Sylvioidea songbirds where multiple autosomal translocations to the sex chromosomes, and multiple recombination suppression events causing separate evolutionary strata, have occurred during the last ~ 28.1-4.5 million years (Myr). We show that the translocated regions have maintained 68.3-97.7% of their original gene content, compared to only 4.2% on the much older ancestral W chromosome. By mapping W gene losses onto a dated phylogeny, we estimate an average gene loss rate of 1.0% per Myr, with only moderate variation between four independent lineages. Consistent with previous studies, evolutionarily constrained and haploinsufficient genes were preferentially maintained on W. However, the gene loss rate did not show any consistent association with strata age or with the number of W genes at strata formation. Our study provides a unique account on the pace of W gene loss and reinforces the significance of purifying selection in maintaining essential genes on sex chromosomes.", "doi": "10.1038/s41598-024-66470-7", "pmid": "39020011", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11255319"}, {"db": "pii", "key": "10.1038/s41598-024-66470-7"}], "notes": [], "created": "2024-10-21T11:21:49.931Z", "modified": "2024-11-25T10:21:24.059Z"}, {"entity": "publication", "iuid": "bad3049be34a4216813b014d4dc962e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bad3049be34a4216813b014d4dc962e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bad3049be34a4216813b014d4dc962e2"}}, "title": "Evaluating regression and probabilistic methods for ECG-based electrolyte prediction.", "authors": [{"family": "von Bachmann", "given": "Philipp", "initials": "P"}, {"family": "Gedon", "given": "Daniel", "initials": "D"}, {"family": "Gustafsson", "given": "Fredrik K", "initials": "FK"}, {"family": "Ribeiro", "given": "Ant\u00f4nio H", "initials": "AH"}, {"family": "Lampa", "given": "Erik", "initials": "E"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Sch\u00f6n", "given": "Thomas B", "initials": "TB"}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "15273", "issn-l": "2045-2322"}, "abstract": "Imbalances in electrolyte concentrations can have severe consequences, but accurate and accessible measurements could improve patient outcomes. The current measurement method based on blood tests is accurate but invasive and time-consuming and is often unavailable for example in remote locations or an ambulance setting. In this paper, we explore the use of deep neural networks (DNNs) for regression tasks to accurately predict continuous electrolyte concentrations from electrocardiograms (ECGs), a quick and widely adopted tool. We analyze our DNN models on a novel dataset of over 290,000 ECGs across four major electrolytes and compare their performance with traditional machine learning models. For improved understanding, we also study the full spectrum from continuous predictions to a binary classification of extreme concentration levels. Finally, we investigate probabilistic regression approaches and explore uncertainty estimates for enhanced clinical usefulness. Our results show that DNNs outperform traditional models but model performance varies significantly across different electrolytes. While discretization leads to good classification performance, it does not address the original problem of continuous concentration level prediction. Probabilistic regression has practical potential, but our uncertainty estimates are not perfectly calibrated. Our study is therefore a first step towards developing an accurate and reliable ECG-based method for electrolyte concentration level prediction-a method with high potential impact within multiple clinical scenarios.", "doi": "10.1038/s41598-024-65223-w", "pmid": "38961109", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11222546"}, {"db": "pii", "key": "10.1038/s41598-024-65223-w"}], "notes": [], "created": "2024-11-25T10:21:19.045Z", "modified": "2024-11-25T10:21:19.049Z"}, {"entity": "publication", "iuid": "71bc285bc319470d9958c5404641f2a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71bc285bc319470d9958c5404641f2a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71bc285bc319470d9958c5404641f2a3"}}, "title": "Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.", "authors": [{"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2024-06-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "14637", "issn-l": "2045-2322"}, "abstract": "Type 2 diabetes (T2D) is the fastest growing non-infectious disease worldwide. Impaired insulin secretion from pancreatic beta-cells is a hallmark of T2D, but the mechanisms behind this defect are insufficiently characterized. Integrating multiple layers of biomedical information, such as different Omics, may allow more accurate understanding of complex diseases such as T2D. Our aim was to explore and use Machine Learning to integrate multiple sources of biological/molecular information (multiOmics), in our case RNA-sequening, DNA methylation, SNP and phenotypic data from islet donors with T2D and non-diabetic controls. We exploited Machine Learning to perform multiOmics integration of DNA methylation, expression, SNPs, and phenotypes from pancreatic islets of 110 individuals, with ~ 30% being T2D cases. DNA methylation was analyzed using Infinium MethylationEPIC array, expression was analyzed using RNA-sequencing, and SNPs were analyzed using HumanOmniExpress arrays. Supervised linear multiOmics integration via DIABLO based on Partial Least Squares (PLS) achieved an accuracy of 91 \u00b1 15% of T2D prediction with an area under the curve of 0.96 \u00b1 0.08 on the test dataset after cross-validation. Biomarkers identified by this multiOmics integration, including SACS and TXNIP DNA methylation, OPRD1 and RHOT1 expression and a SNP annotated to ANO1, provide novel insights into the interplay between different biological mechanisms contributing to T2D. This Machine Learning approach of multiOmics cross-sectional data from human pancreatic islets achieved a promising accuracy of T2D prediction, which may potentially find broad applications in clinical diagnostics. In addition, it delivered novel candidate biomarkers for T2D and links between them across the different Omics.", "doi": "10.1038/s41598-024-64846-3", "pmid": "38918439", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11199577"}, {"db": "pii", "key": "10.1038/s41598-024-64846-3"}], "notes": [], "created": "2024-10-21T11:11:23.000Z", "modified": "2024-11-08T13:48:34.777Z"}, {"entity": "publication", "iuid": "3af9d90fbc974bc7a0a702085de9014d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3af9d90fbc974bc7a0a702085de9014d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3af9d90fbc974bc7a0a702085de9014d"}}, "title": "Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane.", "authors": [{"family": "Gonz\u00e1lez-L\u00f3pez", "given": "Adri\u00e1n", "initials": "A"}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD"}, {"family": "Koripella", "given": "Ravi Kiran", "initials": "RK"}, {"family": "Cain", "given": "Brett N", "initials": "BN"}, {"family": "Chavez", "given": "Martin Garcia", "initials": "MG"}, {"family": "Hergenrother", "given": "Paul J", "initials": "PJ"}, {"family": "Sanyal", "given": "Suparna", "initials": "S"}, {"family": "Selmer", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2024-06-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "14253", "issn-l": "2045-2322"}, "abstract": "The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 \u00c5 resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 \u00c5 resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target.", "doi": "10.1038/s41598-024-64868-x", "pmid": "38902339", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11190147"}, {"db": "pii", "key": "10.1038/s41598-024-64868-x"}], "notes": [], "created": "2024-10-08T09:35:37.331Z", "modified": "2025-10-29T15:01:08.155Z"}, {"entity": "publication", "iuid": "9716f3138ad84b71861f8fa3d241d1d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9716f3138ad84b71861f8fa3d241d1d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9716f3138ad84b71861f8fa3d241d1d6"}}, "title": "Hearing loss and its association with the proteome of perilymph, cerebrospinal fluid, and tumor tissue in patients with vestibular schwannoma.", "authors": [{"family": "Edvardsson Rasmussen", "given": "Jesper", "initials": "J"}, {"family": "Li", "given": "Peng", "initials": "P"}, {"family": "Laurell", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Per Olof", "initials": "PO"}], "type": "journal article", "published": "2024-06-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "14118", "issn-l": "2045-2322"}, "abstract": "This study examined the association between hearing loss in sporadic vestibular schwannoma patients and the proteome of perilymph (PL), cerebrospinal fluid (CSF), and vestibular schwannoma. Intraoperative sampling of PL and of CSF, and biopsy of vestibular schwannoma tissue, was performed in 32, 32, and 20 patients with vestibular schwannoma, respectively. Perilymph and CSF in three patients with meningioma and normal hearing were also sampled. The proteomes were identified by liquid chromatography coupled to high-resolution tandem mass spectrometry. Preoperative hearing function of the patients was evaluated with pure tone audiometry, with mean values at frequencies of 500, 1000, 2000, and 4000 Hz (PTA4) in the tumor-affected ear used to delineate three hearing groups. Analysis of the PL samples revealed significant upregulation of complement factor H-related protein 2 (CFHR2) in patients with severe to profound hearing loss after false discovery rate correction. Pathway analysis of biofunctions revealed higher activation scores in the severe/profound hearing loss group of leukocyte migration, viral infection, and migration of cells in PL. Upregulation of CFHR2 and activation of these pathways indicate chronic inflammation in the cochlea of vestibular schwannoma patients with severe to profound hearing loss compared with patients with normal hearing or mild hearing loss.", "doi": "10.1038/s41598-024-64352-6", "pmid": "38898156", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11187212"}, {"db": "pii", "key": "10.1038/s41598-024-64352-6"}], "notes": [], "created": "2024-11-12T19:33:28.441Z", "modified": "2024-11-12T19:33:28.448Z"}, {"entity": "publication", "iuid": "9fd0cd5c795f411f840ee9eeab721e36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fd0cd5c795f411f840ee9eeab721e36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fd0cd5c795f411f840ee9eeab721e36"}}, "title": "Long-term impact of digital media on brain development in children.", "authors": [{"family": "Nivins", "given": "Samson", "initials": "S"}, {"family": "Sauce", "given": "Bruno", "initials": "B"}, {"family": "Liebherr", "given": "Magnus", "initials": "M"}, {"family": "Judd", "given": "Nicholas", "initials": "N"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}], "type": "journal article", "published": "2024-06-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "13030", "issn-l": "2045-2322"}, "abstract": "Digital media (DM) takes an increasingly large part of children's time, yet the long-term effect on brain development remains unclear. We investigated how individual effects of DM use (i.e., using social media, playing video games, or watching television/videos) on the development of the cortex (i.e., global cortical surface area), striatum, and cerebellum in children over 4 years, accounting for both socioeconomic status and genetic predisposition. We used a prospective, multicentre, longitudinal cohort of children from the Adolescent Brain and Cognitive Development Study, aged 9.9 years when entering the study, and who were followed for 4 years. Annually, children reported their DM usage through the Youth Screen Time Survey and underwent brain magnetic resonance imaging scans every 2 years. Quadratic-mixed effect modelling was used to investigate the relationship between individual DM usage and brain development. We found that individual DM usage did not alter the development of cortex or striatum volumes. However, high social media usage was associated with a statistically significant change in the developmental trajectory of cerebellum volumes, and the accumulated effect of high-vs-low social media users on cerebellum volumes over 4 years was only \u03b2 = - 0.03, which was considered insignificant. Nevertheless, the developmental trend for heavy social media users was accelerated at later time points. This calls for further studies and longer follow-ups on the impact of social media on brain development.", "doi": "10.1038/s41598-024-63566-y", "pmid": "38844772", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11156852"}, {"db": "pii", "key": "10.1038/s41598-024-63566-y"}], "notes": [], "created": "2024-11-12T20:54:57.860Z", "modified": "2024-11-12T20:54:57.872Z"}, {"entity": "publication", "iuid": "1421a942772b4129b65b2b69595dc105", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1421a942772b4129b65b2b69595dc105.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1421a942772b4129b65b2b69595dc105"}}, "title": "PIK3CA mutations in endocrine-resistant breast cancer.", "authors": [{"family": "Schagerholm", "given": "Caroline", "initials": "C"}, {"family": "Robertson", "given": "Stephanie", "initials": "S"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Hartman", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2024-05-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "12542", "issn-l": "2045-2322"}, "abstract": "Around 75% of breast cancer (BC) patients have tumors expressing the predictive biomarker estrogen receptor \u03b1 (ER) and are offered endocrine therapy. One-third eventually develop endocrine resistance, a majority with retained ER expression. Mutations in the phosphatidylinositol bisphosphate 3-kinase (PI3K) catalytic subunit encoded by PIK3CA is a proposed resistance mechanism and a pharmacological target in the clinical setting. Here we explore the frequency of PIK3CA mutations in endocrine-resistant BC before and during treatment and correlate to clinical features. Patients with ER-positive (ER +), human epidermal growth factor receptor 2 (HER2)-negative primary BC with an ER + relapse within 5 years of ongoing endocrine therapy were retrospectively assessed. Tissue was collected from primary tumors (n = 58), relapse tumors (n = 54), and tumor-free lymph nodes (germline controls, n = 62). Extracted DNA was analyzed through panel sequencing. Somatic mutations were observed in 50% (31/62) of the patients, of which 29% occurred outside hotspot regions. The presence of PIK3CA mutations was significantly associated with nodal involvement and mutations were more frequent in relapse than primary tumors. Our study shows the different PIK3CA mutations in endocrine-resistant BC and their fluctuations during therapy. These results may aid investigations of response prediction, facilitating research deciphering the mechanisms of endocrine resistance.", "doi": "10.1038/s41598-024-62664-1", "pmid": "38822093", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11143214"}, {"db": "pii", "key": "10.1038/s41598-024-62664-1"}], "notes": [], "created": "2024-07-01T10:48:55.362Z", "modified": "2024-07-01T10:48:55.372Z"}, {"entity": "publication", "iuid": "bb9a2d13371b46089d479f0a3063d8ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb9a2d13371b46089d479f0a3063d8ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb9a2d13371b46089d479f0a3063d8ad"}}, "title": "Quantifying combined effects of colistin and ciprofloxacin against Escherichia coli in an in silico pharmacokinetic-pharmacodynamic model.", "authors": [{"family": "Zhao", "given": "Chenyan", "initials": "C"}, {"family": "Kristoffersson", "given": "Anders N", "initials": "AN"}, {"family": "Khan", "given": "David D", "initials": "DD"}, {"family": "Lagerb\u00e4ck", "given": "Pernilla", "initials": "P"}, {"family": "Lustig", "given": "Ulrika", "initials": "U"}, {"family": "Cao", "given": "Sha", "initials": "S"}, {"family": "Annerstedt", "given": "Charlotte", "initials": "C"}, {"family": "Cars", "given": "Otto", "initials": "O"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Hughes", "given": "Diarmaid", "initials": "D"}, {"family": "Nielsen", "given": "Elisabet I", "initials": "EI"}, {"family": "Friberg", "given": "Lena E", "initials": "LE"}], "type": "journal article", "published": "2024-05-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "11706", "issn-l": "2045-2322"}, "abstract": "Co-administering a low dose of colistin (CST) with ciprofloxacin (CIP) may improve the antibacterial effect against resistant Escherichia coli, offering an acceptable benefit-risk balance. This study aimed to quantify the interaction between ciprofloxacin and colistin in an in silico pharmacokinetic-pharmacodynamic model from in vitro static time-kill experiments (using strains with minimum inhibitory concentrations, MICCIP 0.023-1 mg/L and MICCST 0.5-0.75 mg/L). It was also sought to demonstrate an approach of simulating concentrations at the site of infection with population pharmacokinetic and whole-body physiologically based pharmacokinetic models to explore the clinical value of the combination when facing more resistant strains (using extrapolated strains with lower susceptibility). The combined effect in the final model was described as the sum of individual drug effects with a change in drug potency: for ciprofloxacin, concentration at half maximum killing rate (EC50) in combination was 160% of the EC50 in monodrug experiments, while for colistin, the change in EC50 was strain-dependent from 54.1% to 119%. The benefit of co-administrating a lower-than-commonly-administrated colistin dose with ciprofloxacin in terms of drug effect in comparison to either monotherapy was predicted in simulated bloodstream infections and pyelonephritis. The study illustrates the value of pharmacokinetic-pharmacodynamic modelling and simulation in streamlining rational development of antibiotic combinations.", "doi": "10.1038/s41598-024-61518-0", "pmid": "38778123", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11111785"}, {"db": "pii", "key": "10.1038/s41598-024-61518-0"}], "notes": [], "created": "2024-11-25T10:21:14.010Z", "modified": "2024-11-25T10:21:14.013Z"}, {"entity": "publication", "iuid": "d6234b6e336845bfaf21a038c009dabd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6234b6e336845bfaf21a038c009dabd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6234b6e336845bfaf21a038c009dabd"}}, "title": "The Gly82Ser polymorphism in the receptor for advanced glycation endproducts increases the risk for coronary events in the general population.", "authors": [{"family": "Grauen Larsen", "given": "Helena", "initials": "H"}, {"family": "Sun", "given": "Jiangming", "initials": "J"}, {"family": "Sj\u00f6gren", "given": "Marketa", "initials": "M"}, {"family": "Born\u00e9", "given": "Yan", "initials": "Y"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Goncalves", "given": "Isabel", "initials": "I"}, {"family": "Nilsson", "given": "Jan", "initials": "J"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Schiopu", "given": "Alexandru", "initials": "A"}], "type": "journal article", "published": "2024-05-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "11567", "issn-l": "2045-2322"}, "abstract": "The receptor for advanced glycation endproducts (RAGE) has pro-inflammatory and pro-atherogenic effects. Low plasma levels of soluble RAGE (sRAGE), a decoy receptor for RAGE ligands, have been associated with increased risk for major adverse coronary events (MACE) in the general population. We performed a genome-wide association study to identify genetic determinants of plasma sRAGE in 4338 individuals from the cardiovascular arm of the Malm\u00f6 Diet and Cancer study (MDC-CV). Further, we explored the associations between these genetic variants, incident first-time MACE and mortality in 24,640 unrelated individuals of European ancestry from the MDC cohort. The minor alleles of four single nucleotide polymorphisms (SNPs): rs2070600, rs204993, rs116653040, and rs7306778 were independently associated with lower plasma sRAGE. The minor T (vs. C) allele of rs2070600 was associated with increased risk for MACE [HR 1.13 95% CI (1.02-1.25), P = 0.016]. Neither SNP was associated with mortality. This is the largest study to demonstrate a link between a genetic sRAGE determinant and CV risk. Only rs2070600, which enhances RAGE function by inducing a Gly82Ser polymorphism in the ligand-binding domain, was associated with MACE. The lack of associations with incident MACE for the other sRAGE-lowering SNPs suggests that this functional RAGE modification is central for the observed relationship.", "doi": "10.1038/s41598-024-62385-5", "pmid": "38773223", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11109115"}, {"db": "pii", "key": "10.1038/s41598-024-62385-5"}], "notes": [], "created": "2024-11-27T22:22:31.609Z", "modified": "2024-11-27T22:22:31.630Z"}, {"entity": "publication", "iuid": "a0c0acf600de4866b5133701a7e87eb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0c0acf600de4866b5133701a7e87eb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0c0acf600de4866b5133701a7e87eb5"}}, "title": "TMAO enhances TNF-\u03b1 mediated fibrosis and release of inflammatory mediators from renal fibroblasts.", "authors": [{"family": "Stefania", "given": "Kapetanaki", "initials": "K"}, {"family": "Ashok", "given": "Kumawat Kumar", "initials": "KK"}, {"family": "Geena", "given": "Paramel Varghese", "initials": "PV"}, {"family": "Katarina", "given": "Persson", "initials": "P"}, {"family": "Isak", "given": "Demirel", "initials": "D"}], "type": "journal article", "published": "2024-04-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "9070", "issn-l": "2045-2322"}, "abstract": "Trimethylamine-N-oxide (TMAO) is a gut microbiota-derived metabolite and TNF-\u03b1 is proinflammatory cytokine, both known to be associated with renal inflammation, fibrosis and chronic kidney disease. However, today there are no data showing the combined effect of TMAO and TNF-\u03b1 on renal fibrosis-and inflammation. The aim of this study was to investigate whether TMAO can enhance the inflammatory and fibrotic effects of TNF-\u03b1 on renal fibroblasts. We found that the combination of TNF-\u03b1 and TMAO synergistically increased fibronectin release and total collagen production from renal fibroblasts. The combination of TMAO and TNF-\u03b1 also promoted increased cell proliferation. Both renal proliferation and collagen production were mediated through Akt/mTOR/ERK signaling. We also found that TMAO enhanced TNF-\u03b1 mediated renal inflammation by inducing the release of several cytokines (IL-6, LAP TGF-beta-1), chemokines (CXCL-6, MCP-3), inflammatory-and growth mediators (VEGFA, CD40, HGF) from renal fibroblasts. In conclusion, we showed that TMAO can enhance TNF-\u03b1 mediated renal fibrosis and release of inflammatory mediators from renal fibroblasts in vitro. Our results can promote further research evaluating the combined effect of TMAO and inflammatory mediators on the development of kidney disease.", "doi": "10.1038/s41598-024-58084-w", "pmid": "38643262", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11032383"}, {"db": "pii", "key": "10.1038/s41598-024-58084-w"}], "notes": [], "created": "2024-11-27T22:23:39.656Z", "modified": "2024-11-27T22:23:39.661Z"}, {"entity": "publication", "iuid": "73186db56e264ccba504d9a715c478d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73186db56e264ccba504d9a715c478d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73186db56e264ccba504d9a715c478d9"}}, "title": "Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.", "authors": [{"family": "Ten Berk de Boer", "given": "Esmee", "initials": "E"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-04-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "9000", "issn-l": "2045-2322"}, "abstract": "Long-read genome sequencing (lrGS) is a promising method in genetic diagnostics. Here we investigate the potential of lrGS to detect a disease-associated chromosomal translocation between 17p13 and the 19 centromere. We constructed two sets of phased and non-phased de novo assemblies; (i) based on lrGS only and (ii) hybrid assemblies combining lrGS with optical mapping using lrGS reads with a median coverage of 34X. Variant calling detected both structural variants (SVs) and small variants and the accuracy of the small variant calling was compared with those called with short-read genome sequencing (srGS). The de novo and hybrid assemblies had high quality and contiguity with N50 of 62.85 Mb, enabling a near telomere to telomere assembly with less than a 100 contigs per haplotype. Notably, we successfully identified the centromeric breakpoint of the translocation. A concordance of 92% was observed when comparing small variant calling between srGS and lrGS. In summary, our findings underscore the remarkable potential of lrGS as a comprehensive and accurate solution for the analysis of SVs and small variants. Thus, lrGS could replace a large battery of genetic tests that were used for the diagnosis of a single symptomatic translocation carrier, highlighting the potential of lrGS in the realm of digital karyotyping.", "doi": "10.1038/s41598-024-59683-3", "pmid": "38637641", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11026446"}, {"db": "pii", "key": "10.1038/s41598-024-59683-3"}], "notes": [], "created": "2024-04-26T08:52:09.946Z", "modified": "2024-11-25T10:21:08.824Z"}, {"entity": "publication", "iuid": "0885ec9c38e64c2f8cf9d3d8eb45ec51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0885ec9c38e64c2f8cf9d3d8eb45ec51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0885ec9c38e64c2f8cf9d3d8eb45ec51"}}, "title": "Cardiac biopsies reveal differences in transcriptomics between left and right ventricle in patients with or without diagnostic signs of heart failure.", "authors": [{"family": "Frisk", "given": "Christoffer", "initials": "C"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Walentinsson", "given": "Anna", "initials": "A"}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Hage", "given": "Camilla", "initials": "C"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Maret", "given": "Eva", "initials": "E"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Persson", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2024-03-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "5811", "issn-l": "2045-2322"}, "abstract": "New or mild heart failure (HF) is mainly caused by left ventricular dysfunction. We hypothesised that gene expression differ between the left (LV) and right ventricle (RV) and secondly by type of LV dysfunction. We compared gene expression through myocardial biopsies from LV and RV of patients undergoing elective coronary bypass surgery (CABG). Patients were categorised based on LV ejection fraction (EF), diastolic function and NT-proBNP into pEF (preserved; LVEF \u2265 45%), rEF (reduced; LVEF < 45%) or normal LV function. Principal component analysis of gene expression displayed two clusters corresponding to LV and RV. Up-regulated genes in LV included natriuretic peptides NPPA and NPPB, transcription factors/coactivators STAT4 and VGLL2, ion channel related HCN2 and LRRC38 associated with cardiac muscle contraction, cytoskeleton, and cellular component movement. Patients with pEF phenotype versus normal differed in gene expression predominantly in LV, supporting that diastolic dysfunction and structural changes reflect early LV disease in pEF. DKK2 was overexpressed in LV of HFpEF phenotype, potentially leading to lower expression levels of \u03b2-catenin, \u03b1-SMA (smooth muscle actin), and enhanced apoptosis, and could be a possible factor in the development of HFpEF. CXCL14 was down-regulated in both pEF and rEF, and may play a role to promote development of HF.", "doi": "10.1038/s41598-024-56025-1", "pmid": "38461325", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10924960"}, {"db": "pii", "key": "10.1038/s41598-024-56025-1"}], "notes": [], "created": "2024-03-14T11:07:07.576Z", "modified": "2024-11-25T10:20:58.292Z"}, {"entity": "publication", "iuid": "3450b7c1f75249119cccdb958020c5dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3450b7c1f75249119cccdb958020c5dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3450b7c1f75249119cccdb958020c5dc"}}, "title": "Identification of microbial pathogens in Neolithic Scandinavian humans.", "authors": [{"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Mirabello", "given": "Claudio", "initials": "C"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "Jorgensen", "given": "Roger", "initials": "R"}, {"family": "Skar", "given": "Birgitte", "initials": "B"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2024-03-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "14", "issue": "1", "pages": "5630"}, "abstract": "With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.", "doi": "10.1038/s41598-024-56096-0", "pmid": "38453993", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10920878"}, {"db": "pii", "key": "10.1038/s41598-024-56096-0"}], "notes": [], "created": "2024-03-14T11:09:30.525Z", "modified": "2024-11-25T10:21:03.650Z"}, {"entity": "publication", "iuid": "c00414cd923a4f9e9a0751b4edc7a150", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c00414cd923a4f9e9a0751b4edc7a150.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c00414cd923a4f9e9a0751b4edc7a150"}}, "title": "Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist.", "authors": [{"family": "Rengefors", "given": "Karin", "initials": "K"}, {"family": "Annenkova", "given": "Nataliia", "initials": "N"}, {"family": "Wallenius", "given": "Joel", "initials": "J"}, {"family": "Svensson", "given": "Marie", "initials": "M"}, {"family": "Kremp", "given": "Anke", "initials": "A"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2024-02-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "4986", "issn-l": "2045-2322"}, "abstract": "Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.", "doi": "10.1038/s41598-024-55362-5", "pmid": "38424140", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10904836"}, {"db": "pii", "key": "10.1038/s41598-024-55362-5"}], "notes": [], "created": "2024-03-06T13:04:42.545Z", "modified": "2024-11-25T10:20:53.163Z"}, {"entity": "publication", "iuid": "9670731db7d94785b128f5d9454c7b1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9670731db7d94785b128f5d9454c7b1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9670731db7d94785b128f5d9454c7b1e"}}, "title": "Differential gene expression in two consecutive pregnancies between same sex siblings and implications on maternal constraint.", "authors": [{"family": "Kallak", "given": "Theodora Kunovac", "initials": "TK"}, {"family": "Serapio", "given": "Solveig", "initials": "S"}, {"family": "Visser", "given": "Nadja", "initials": "N"}, {"family": "Lager", "given": "Susanne", "initials": "S"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}, {"family": "Ahlsson", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2024-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "4210", "issn-l": "2045-2322"}, "abstract": "The objective of this study was to investigate how placental gene expression differs in two consecutive pregnancies in same sex siblings, and its possible association with the \"maternal constraint\" hypothesis. Material was gathered from the BASIC study (Biological, Affect, Stress, Imaging, and Cognition in Pregnancy and the Puerperium), a population based prospective study that was started in 2009 in Uppsala. Over 900 specimens of placenta biopsies were collected and out of these 10 women gave birth twice, to the same sex child, and were included in this study. The total RNA was isolated and prepared from frozen villous tissue from the placenta and further analyzed by use of Ion AmpliSeq Human Transcriptome Gene Expression kit. A total of 234 genes differed significantly between the first and second pregnancy placentas, when adjusting for delivery mode, maternal BMI and gestational age. Of special interest was the down-regulated group of genes in the second pregnancy. Exemplified by Pentraxin 3, SRY-Box Transcription Factor 9, and Serum Amyloid A1, which all were associated with biological processes involved in the immune system and inflammation. Further, protein-protein interaction analysis visualized them as hub genes interacting with several of the other differentially expressed genes. How these altered gene expressions affect maternal constraint during pregnancy needs further validation in lager study cohorts and also future validation in functional assays.", "doi": "10.1038/s41598-024-54724-3", "pmid": "38378837", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10879170"}, {"db": "pii", "key": "10.1038/s41598-024-54724-3"}], "notes": [], "created": "2024-11-12T17:42:40.329Z", "modified": "2024-11-25T10:20:47.752Z"}, {"entity": "publication", "iuid": "d53efd169d754ccca5fd70684c689438", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d53efd169d754ccca5fd70684c689438.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d53efd169d754ccca5fd70684c689438"}}, "title": "Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.", "authors": [{"family": "Hold", "given": "Katharina", "initials": "K"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC"}, {"family": "Le Moullec", "given": "Mathilde", "initials": "M"}, {"family": "Bieker", "given": "Vanessa C", "initials": "VC"}, {"family": "Ellegaard", "given": "Martin R", "initials": "MR"}, {"family": "Rasmussen", "given": "Jacob A", "initials": "JA"}, {"family": "Kellner", "given": "Fabian L", "initials": "FL"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}, {"family": "Yannic", "given": "Glenn", "initials": "G"}, {"family": "R\u00f8ed", "given": "Knut H", "initials": "KH"}, {"family": "Hansen", "given": "Brage B", "initials": "BB"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}], "type": "journal article", "published": "2024-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "14", "issue": "1", "pages": "4143"}, "abstract": "Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.", "doi": "10.1038/s41598-024-54296-2", "pmid": "38374421", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10876933"}, {"db": "pii", "key": "10.1038/s41598-024-54296-2"}], "notes": [], "created": "2024-03-14T11:11:17.523Z", "modified": "2024-11-25T10:20:42.576Z"}, {"entity": "publication", "iuid": "7fbb4159eeef44e6ae1681e36879d476", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fbb4159eeef44e6ae1681e36879d476.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fbb4159eeef44e6ae1681e36879d476"}}, "title": "Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants.", "authors": [{"family": "Viktorsson", "given": "Charlotte", "initials": "C"}, {"family": "Portugal", "given": "Ana Maria", "initials": "AM"}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}], "type": "journal article", "published": "2024-02-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "3668", "issn-l": "2045-2322"}, "abstract": "A tendency to look at the left side of faces from the observer's point of view has been found in older children and adults, but it is not known when this face-specific left gaze bias develops and what factors may influence individual differences in gaze lateralization. Therefore, the aims of this study were to estimate gaze lateralization during face observation and to more broadly estimate lateralization tendencies across a wider set of social and non-social stimuli, in early infancy. In addition, we aimed to estimate the influence of genetic and environmental factors on lateralization of gaze. We studied gaze lateralization in 592 5-month-old twins (282 females, 330 monozygotic twins) by recording their gaze while viewing faces and two other types of stimuli that consisted of either collections of dots (non-social stimuli) or faces interspersed with objects (mixed stimuli). A right gaze bias was found when viewing faces, and this measure was moderately heritable (A = 0.38, 95% CI 0.24; 0.50). A left gaze bias was observed in the non-social condition, while a right gaze bias was found in the mixed condition, suggesting that there is no general left gaze bias at this age. Genetic influence on individual differences in gaze lateralization was only found for the tendency to look at the right versus left side of faces, suggesting genetic specificity of lateralized gaze when viewing faces.", "doi": "10.1038/s41598-024-54373-6", "pmid": "38351309", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10864339"}, {"db": "pii", "key": "10.1038/s41598-024-54373-6"}], "notes": [], "created": "2024-03-21T12:10:13.155Z", "modified": "2024-03-21T12:10:13.169Z"}, {"entity": "publication", "iuid": "652ef4bf70e84b36b7d9aa8a86e01efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/652ef4bf70e84b36b7d9aa8a86e01efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/652ef4bf70e84b36b7d9aa8a86e01efa"}}, "title": "Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo).", "authors": [{"family": "Chondrelli", "given": "Niki", "initials": "N"}, {"family": "Kuehn", "given": "Emily", "initials": "E"}, {"family": "Meurling", "given": "Sara", "initials": "S"}, {"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2024-01-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "2495", "issn-l": "2045-2322"}, "abstract": "Batrachochytrium dendrobatidis (Bd) is a fungal pathogen that has decimated amphibian populations worldwide for several decades. We examined the changes in gene expression in response to Bd infection in two populations of the common toad, Bufo bufo, in a laboratory experiment. We collected B. bufo eggs in southern and northern Sweden, and infected the laboratory-raised metamorphs with two strains of the global panzoonotic lineage Bd-GPL. Differential expression analysis showed significant differences between infected and control individuals in both liver and skin. The skin samples showed no discernible differences in gene expression between the two strains used, while liver samples were differentiated by strain, with one of the strains eliciting no immune response from infected toads. Immune system genes were overexpressed in skin samples from surviving infected individuals, while in liver samples the pattern was more diffuse. Splitting samples by population revealed a stronger immune response in northern individuals. Differences in transcriptional regulation between populations are particularly relevant to study in Swedish amphibians, which may have experienced varying exposure to Bd. Earlier exposure to this pathogen and subsequent adaptation or selection pressure may contribute to the survival of some populations over others, while standing genetic diversity in different populations may also affect the infection outcome.", "doi": "10.1038/s41598-024-52975-8", "pmid": "38291226", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10828426"}, {"db": "pii", "key": "10.1038/s41598-024-52975-8"}], "notes": [], "created": "2024-03-21T09:01:24.203Z", "modified": "2025-01-02T10:35:06.385Z"}, {"entity": "publication", "iuid": "02ca4d46df3c4e73b9e068dd236e5d2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02ca4d46df3c4e73b9e068dd236e5d2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02ca4d46df3c4e73b9e068dd236e5d2a"}}, "title": "Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk.", "authors": [{"family": "Bod\u00e9n", "given": "Stina", "initials": "S", "orcid": "0000-0002-8958-975X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dcfadb86b8040499a7af3c4a744d3b2.json"}}, {"family": "Zheng", "given": "Rui", "initials": "R"}, {"family": "Ribbenstedt", "given": "Anton", "initials": "A"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Harlid", "given": "Sophia", "initials": "S", "orcid": "0000-0001-8540-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a824f2687b460890ae6d9ef40d97c9.json"}}, {"family": "Vidman", "given": "Linda", "initials": "L"}, {"family": "Gunter", "given": "Marc J", "initials": "MJ"}, {"family": "Winkvist", "given": "Anna", "initials": "A", "orcid": "0000-0001-9122-7240", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34ca937891145e190390ae9418d2243.json"}}, {"family": "Johansson", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-9227-8434", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee3e20587b664a42a880870f1648160a.json"}}, {"family": "Van Guelpen", "given": "Bethany", "initials": "B", "orcid": "0000-0002-9692-101X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ea901d796bc4f3fbc53f930c5021118.json"}}, {"family": "Brunius", "given": "Carl", "initials": "C"}], "type": "journal article", "published": "2024-01-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "2244", "issn-l": "2045-2322"}, "abstract": "We investigated data-driven and hypothesis-driven dietary patterns and their association to plasma metabolite profiles and subsequent colorectal cancer (CRC) risk in 680 CRC cases and individually matched controls. Dietary patterns were identified from combined exploratory/confirmatory factor analysis. We assessed association to LC-MS metabolic profiles by random forest regression and to CRC risk by multivariable conditional logistic regression. Principal component analysis was used on metabolite features selected to reflect dietary exposures. Component scores were associated to CRC risk and dietary exposures using partial Spearman correlation. We identified 12 data-driven dietary patterns, of which a breakfast food pattern showed an inverse association with CRC risk (OR per standard deviation increase 0.89, 95% CI 0.80-1.00, p = 0.04). This pattern was also inversely associated with risk of distal colon cancer (0.75, 0.61-0.96, p = 0.01) and was more pronounced in women (0.69, 0.49-0.96, p = 0.03). Associations between meat, fast-food, fruit soup/rice patterns and CRC risk were modified by tumor location in women. Alcohol as well as fruit and vegetables associated with metabolite profiles (Q2 0.22 and 0.26, respectively). One metabolite reflecting alcohol intake associated with increased CRC risk, whereas three metabolites reflecting fiber, wholegrain, and fruit and vegetables associated with decreased CRC risk.", "doi": "10.1038/s41598-023-50567-6", "pmid": "38278865", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10817924"}, {"db": "pii", "key": "10.1038/s41598-023-50567-6"}], "notes": [], "created": "2024-11-25T10:20:32.223Z", "modified": "2024-11-27T15:34:24.513Z"}, {"entity": "publication", "iuid": "50f17519fbe44f2eb49fdc91933ee0ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50f17519fbe44f2eb49fdc91933ee0ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50f17519fbe44f2eb49fdc91933ee0ee"}}, "title": "Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.", "authors": [{"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "Damlien", "given": "Hege", "initials": "H"}, {"family": "Manninen", "given": "Mikael A", "initials": "MA"}, {"family": "Nordqvist", "given": "Bengt", "initials": "B"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Lindberg", "given": "A Michael", "initials": "AM"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Persson", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Aravena", "given": "Andr\u00e9s", "initials": "A"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "case reports", "published": "2024-01-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "22125"}, "abstract": "Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.", "doi": "10.1038/s41598-023-48762-6", "pmid": "38238372", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10796427"}, {"db": "pii", "key": "10.1038/s41598-023-48762-6"}], "notes": [], "created": "2024-01-19T06:32:34.876Z", "modified": "2024-11-25T10:20:27.063Z"}, {"entity": "publication", "iuid": "1103e19dc8b74508a72dbc8bf2f53fc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1103e19dc8b74508a72dbc8bf2f53fc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1103e19dc8b74508a72dbc8bf2f53fc1"}}, "title": "Elevated circulating adiponectin levels do not prevent anxiety-like behavior in a PCOS-like mouse model.", "authors": [{"family": "Samad", "given": "Manisha", "initials": "M"}, {"family": "Ek", "given": "Joakim", "initials": "J"}, {"family": "B\u00f6rchers", "given": "Stina", "initials": "S"}, {"family": "Krieger", "given": "Jean-Philippe", "initials": "JP", "orcid": "0000-0003-1913-4466", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1105ccfff044340856418ab78e3baa8.json"}}, {"family": "Stener-Victorin", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-3424-1502", "researcher": {"href": "https://publications.scilifelab.se/researcher/b56343efabb34afa9baecef059417a3a.json"}}, {"family": "Skibicka", "given": "Karolina P", "initials": "KP"}, {"family": "Asterholm", "given": "Ingrid Wernstedt", "initials": "IW", "orcid": "0000-0002-0755-5784", "researcher": {"href": "https://publications.scilifelab.se/researcher/45e1e47469f942fe8392109ca802f78c.json"}}, {"family": "Benrick", "given": "Anna", "initials": "A", "orcid": "0000-0003-4616-6789", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b2939d573c04f0abc063ac18e97bd40.json"}}], "type": "journal article", "published": "2024-01-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "563", "issn-l": "2045-2322"}, "abstract": "Polycystic ovary syndrome (PCOS) is associated with symptoms of moderate to severe anxiety and depression. Hyperandrogenism is a key feature together with lower levels of the adipocyte hormone adiponectin. Androgen exposure leads to anxiety-like behavior in female offspring while adiponectin is reported to be anxiolytic. Here we test the hypothesis that elevated adiponectin levels protect against the development of androgen-induced anxiety-like behavior. Pregnant mice overexpressing adiponectin (APNtg) and wildtypes were injected with vehicle or dihydrotestosterone to induce prenatal androgenization (PNA) in the offspring. Metabolic profiling and behavioral tests were performed in 4-month-old female offspring. PNA offspring spent more time in the closed arms of the elevated plus maze, indicating anxiety-like behavior. Intriguingly, neither maternal nor offspring adiponectin overexpression prevented an anxiety-like behavior in PNA-exposed offspring. However, adiponectin overexpression in dams had metabolic imprinting effects, shown as lower fat mass and glucose levels in their offspring. While serum adiponectin levels were elevated in APNtg mice, cerebrospinal fluid levels were similar between genotypes. Adiponectin overexpression improved metabolic functions but did not elicit anxiolytic effects in PNA-exposed offspring. These observations might be attributed to increased circulating but unchanged cerebrospinal fluid adiponectin levels in APNtg mice. Thus, increased adiponectin levels in the brain are likely needed to stimulate anxiolytic effects.", "doi": "10.1038/s41598-023-50503-8", "pmid": "38177175", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10766608"}, {"db": "pii", "key": "10.1038/s41598-023-50503-8"}], "notes": [], "created": "2024-09-15T11:36:54.305Z", "modified": "2024-09-15T11:36:55.162Z"}, {"entity": "publication", "iuid": "12e49eee38b34480aa21925cdd7fa0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12e49eee38b34480aa21925cdd7fa0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12e49eee38b34480aa21925cdd7fa0e5"}}, "title": "The functional and molecular impact of triamcinolone acetonide on primary human bone marrow mesenchymal stem cells.", "authors": [{"family": "Kumlin", "given": "Maritha", "initials": "M"}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J"}, {"family": "Cai", "given": "Huan", "initials": "H"}, {"family": "Leonard", "given": "Elory", "initials": "E"}, {"family": "Fell\u00e4nder-Tsai", "given": "Li", "initials": "L"}, {"family": "Qian", "given": "Hong", "initials": "H"}], "type": "journal article", "published": "2023-12-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "21787", "issn-l": "2045-2322"}, "abstract": "Traumatic or degenerative joint pain is abundant in the population. Symptom relief by intra- and periarticular glucocorticoid administration is frequently used, however may have potentially devastating effects, changing the normal healing process of the joint. Mesenchymal stem cells (MSCs) are important for wound-healing processes due to their multipotency in regenerating osteoblasts, chondrocytes and adipocytes but also have immunomodulatory properties. The aim of this study was to investigate the impact of triamcinolone acetonide (TA) a common glucocorticoid administrated intra- and periarticularly, on human bone marrow derived MSC viability, functionality, multi-lineage differentiation and transcriptomic output. We found that TA treatment induced apoptosis and promoted adipogenesis while impairing chondrogenesis of MSCs. RNA sequencing indicated that TA modulated the inflammatory response of MSCs, which may have an impact on the immunologic environment where the inflammatory phase is a physiological part of the natural healing process. These data indicate that triamcinolone acetonide should be used with consideration bearing the patient's outcome in mind, with the intention to optimize joint recovery and homeostasis.", "doi": "10.1038/s41598-023-48448-z", "pmid": "38066109", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10709330"}, {"db": "pii", "key": "10.1038/s41598-023-48448-z"}], "notes": [], "created": "2024-01-02T13:27:30.002Z", "modified": "2024-01-02T13:27:30.006Z"}, {"entity": "publication", "iuid": "d839b4f76f8f43aa9477e6790297fb62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d839b4f76f8f43aa9477e6790297fb62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d839b4f76f8f43aa9477e6790297fb62"}}, "title": "Using trials of caloric restriction and bariatric surgery to explore the effects of body mass index on the circulating proteome.", "authors": [{"family": "Goudswaard", "given": "Lucy J", "initials": "LJ"}, {"family": "Smith", "given": "Madeleine L", "initials": "ML"}, {"family": "Hughes", "given": "David A", "initials": "DA"}, {"family": "Taylor", "given": "Roy", "initials": "R"}, {"family": "Lean", "given": "Michael", "initials": "M"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Welsh", "given": "Paul", "initials": "P"}, {"family": "McConnachie", "given": "Alex", "initials": "A"}, {"family": "Blazeby", "given": "Jane M", "initials": "JM"}, {"family": "Rogers", "given": "Chris A", "initials": "CA"}, {"family": "Suhre", "given": "Karsten", "initials": "K"}, {"family": "Zaghlool", "given": "Shaza B", "initials": "SB"}, {"family": "Hers", "given": "Ingeborg", "initials": "I"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Corbin", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2023-11-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "21077"}, "abstract": "Thousands of proteins circulate in the bloodstream; identifying those which associate with weight and intervention-induced weight loss may help explain mechanisms of diseases associated with adiposity. We aimed to identify consistent protein signatures of weight loss across independent studies capturing changes in body mass index (BMI). We analysed proteomic data from studies implementing caloric restriction (Diabetes Remission Clinical trial) and bariatric surgery (By-Band-Sleeve), using SomaLogic and Olink Explore1536 technologies, respectively. Linear mixed models were used to estimate the effect of the interventions on circulating proteins. Twenty-three proteins were altered in a consistent direction after both bariatric surgery and caloric restriction, suggesting that these proteins are modulated by weight change, independent of intervention type. We also integrated Mendelian randomisation (MR) estimates of the effect of BMI on proteins measured by SomaLogic from a UK blood donor cohort as a third line of causal evidence. These MR estimates provided further corroborative evidence for a role of BMI in regulating the levels of six proteins including alcohol dehydrogenase-4, nogo receptor and interleukin-1 receptor antagonist protein. These results indicate the importance of triangulation in interrogating causal relationships; further study into the role of proteins modulated by weight in disease is now warranted.", "doi": "10.1038/s41598-023-47030-x", "pmid": "38030643", "labels": {"Affinity Proteomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Proteomics": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10686974"}, {"db": "pii", "key": "10.1038/s41598-023-47030-x"}], "notes": [], "created": "2024-11-27T16:10:08.369Z", "modified": "2024-11-27T19:28:55.863Z"}, {"entity": "publication", "iuid": "f9e3a5e951614a658cd8e2a15c554f57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9e3a5e951614a658cd8e2a15c554f57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9e3a5e951614a658cd8e2a15c554f57"}}, "title": "Selection, characterization and in vivo evaluation of novel CD44v6-targeting antibodies for targeted molecular radiotherapy.", "authors": [{"family": "Mortensen", "given": "A C L", "initials": "ACL"}, {"family": "Berglund", "given": "H", "initials": "H"}, {"family": "Segerstr\u00f6m", "given": "L", "initials": "L"}, {"family": "Walle", "given": "M", "initials": "M"}, {"family": "Hofstr\u00f6m", "given": "C", "initials": "C"}, {"family": "Persson", "given": "H", "initials": "H"}, {"family": "Nygren", "given": "P-\u00c5", "initials": "P"}, {"family": "Nilvebrant", "given": "J", "initials": "J"}, {"family": "Frejd", "given": "F Y", "initials": "FY"}, {"family": "Nestor", "given": "M", "initials": "M"}], "type": "journal article", "published": "2023-11-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "20648"}, "abstract": "Molecular radiotherapy combines the advantages of systemic administration of highly specific antibodies or peptides and the localized potency of ionizing radiation. A potential target for molecular radiotherapy is the cell surface antigen CD44v6, which is overexpressed in numerous cancers, with limited expression in normal tissues. The aim of the present study was to generate and characterize a panel of human anti-CD44v6 antibodies and identify a suitable candidate for future use in molecular radiotherapy of CD44v6-expressing cancers. Binders were first isolated from large synthetic phage display libraries containing human scFv and Fab antibody fragments. The antibodies were extensively analyzed through in vitro investigations of binding kinetics, affinity, off-target binding, and cell binding. Lead candidates were further subjected to in vivo biodistribution studies in mice bearing anaplastic thyroid cancer xenografts that express high levels of CD44v6. Additionally, antigen-dependent tumor uptake of the lead candidate was verified in additional xenograft models with varying levels of target expression. Interestingly, although only small differences were observed among the top antibody candidates in vitro, significant differences in tumor uptake and retention were uncovered in in vivo experiments. A high-affinity anti-CD44v6 lead drug candidate was identified, mAb UU-40, which exhibited favorable target binding properties and in vivo distribution. In conclusion, a panel of human anti-CD44v6 antibodies was successfully generated and characterized in this study. Through comprehensive evaluation, mAb UU-40 was identified as a promising lead candidate for future molecular radiotherapy of CD44v6-expressing cancers due to its high affinity, excellent target binding properties, and desirable in vivo distribution characteristics.", "doi": "10.1038/s41598-023-47891-2", "pmid": "38001360", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10673843"}, {"db": "pii", "key": "10.1038/s41598-023-47891-2"}], "notes": [], "created": "2024-01-16T15:12:05.359Z", "modified": "2025-10-17T13:05:07.459Z"}, {"entity": "publication", "iuid": "f8aa1479eff8415b950c15e1654bdec9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8aa1479eff8415b950c15e1654bdec9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8aa1479eff8415b950c15e1654bdec9"}}, "title": "Dysregulations in hemostasis, metabolism, immune response, and angiogenesis in post-acute COVID-19 syndrome with and without postural orthostatic tachycardia syndrome: a multi-omic profiling study.", "authors": [{"family": "Mahdi", "given": "Ali", "initials": "A"}, {"family": "Zhao", "given": "Allan", "initials": "A"}, {"family": "Fredengren", "given": "Emelie", "initials": "E"}, {"family": "Fedorowski", "given": "Artur", "initials": "A"}, {"family": "Braunschweig", "given": "Frieder", "initials": "F"}, {"family": "Nygren-Bonnier", "given": "Malin", "initials": "M"}, {"family": "Runold", "given": "Michael", "initials": "M"}, {"family": "Bruchfeld", "given": "Judith", "initials": "J"}, {"family": "Nickander", "given": "Jannike", "initials": "J"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}, {"family": "Checa", "given": "Antonio", "initials": "A"}, {"family": "Desta", "given": "Liyew", "initials": "L"}, {"family": "Pernow", "given": "John", "initials": "J"}, {"family": "St\u00e5hlberg", "given": "Marcus", "initials": "M"}], "type": "journal article", "published": "2023-11-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "20230"}, "abstract": "Post-acute COVID-19 (PACS) are associated with cardiovascular dysfunction, especially postural orthostatic tachycardia syndrome (POTS). Patients with PACS, both in the absence or presence of POTS, exhibit a wide range of persisting symptoms long after the acute infection. Some of these symptoms may stem from alterations in cardiovascular homeostasis, but the exact mechanisms are poorly understood. The aim of this study was to provide a broad molecular characterization of patients with PACS with (PACS + POTS) and without (PACS-POTS) POTS compared to healthy subjects, including a broad proteomic characterization with a focus on plasma cardiometabolic proteins, quantification of cytokines/chemokines and determination of plasma sphingolipid levels. Twenty-one healthy subjects without a prior COVID-19 infection (mean age 43 years, 95% females), 20 non-hospitalized patients with PACS + POTS (mean age 39 years, 95% females) and 22 non-hospitalized patients with PACS-POTS (mean age 44 years, 100% females) were studied. PACS patients were non-hospitalized and recruited \u224818 months after the acute infection. Cardiometabolic proteomic analyses revealed a dysregulation of \u2248200 out of 700 analyzed proteins in both PACS groups vs. healthy subjects with the majority (> 90%) being upregulated. There was a large overlap (> 90%) with no major differences between the PACS groups. Gene ontology enrichment analysis revealed alterations in hemostasis/coagulation, metabolism, immune responses, and angiogenesis in PACS vs. healthy controls. Furthermore, 11 out of 33 cytokines/chemokines were significantly upregulated both in PACS + POTS and PACS-POTS vs. healthy controls and none of the cytokines were downregulated. There were no differences in between the PACS groups in the cytokine levels. Lastly, 16 and 19 out of 88 sphingolipids were significantly dysregulated in PACS + POTS and PACS-POTS, respectively, compared to controls with no differences between the groups. Collectively, these observations suggest a clear and distinct dysregulation in the proteome, cytokines/chemokines, and sphingolipid levels in PACS patients compared to healthy subjects without any clear signature associated with POTS. This enhances our understanding and might pave the way for future experimental and clinical investigations to elucidate and/or target resolution of inflammation and micro-clots and restore the hemostasis and immunity in PACS.", "doi": "10.1038/s41598-023-47539-1", "pmid": "37981644", "labels": {"Affinity Proteomics Uppsala": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10658082"}, {"db": "pii", "key": "10.1038/s41598-023-47539-1"}], "notes": [], "created": "2023-11-29T18:45:17.584Z", "modified": "2023-12-04T06:42:15.974Z"}, {"entity": "publication", "iuid": "cfad3d491ac3446ca70f18e88f73c834", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cfad3d491ac3446ca70f18e88f73c834.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cfad3d491ac3446ca70f18e88f73c834"}}, "title": "Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.", "authors": [{"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}, {"family": "Fegraeus", "given": "Kim", "initials": "K"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Waern", "given": "Ida", "initials": "I"}, {"family": "Wernersson", "given": "Sara", "initials": "S"}, {"family": "Akula", "given": "Srinivas", "initials": "S"}, {"family": "Hellman", "given": "Lars", "initials": "L"}, {"family": "Raine", "given": "Amanda", "initials": "A"}], "type": "journal article", "published": "2023-09-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "16261"}, "abstract": "Equine asthma (EA) is a heterogenous, complex disease, with a significant negative impact on horse welfare and performance. EA and human asthma share fundamental similarities, making EA a useful model for studying the disease. One relevant sample type for investigating chronic lung inflammation is bronchoalveolar lavage fluid (BALF), which provides a snapshot of the immune cells present in the alveolar space. To investigate the immune cell landscape of the respiratory tract in horses with mild-to-moderate equine asthma (mEA) and healthy controls, single-cell RNA sequencing was conducted on equine BALF cells. We characterized the major immune cell populations present in equine BALF, as well as subtypes thereof. Interestingly, the most significantly upregulated gene discovered in cases of mEA was FKBP5, a chaperone protein involved in regulating the activity of the glucocorticoid receptor.", "doi": "10.1038/s41598-023-43368-4", "pmid": "37758813", "labels": {"NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Single cell": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10533524"}, {"db": "pii", "key": "10.1038/s41598-023-43368-4"}], "notes": [], "created": "2023-11-27T21:49:44.494Z", "modified": "2024-02-27T08:16:23.788Z"}, {"entity": "publication", "iuid": "0fae2086fc6a4d428dd50502e0cf5ff4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fae2086fc6a4d428dd50502e0cf5ff4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fae2086fc6a4d428dd50502e0cf5ff4"}}, "title": "Genetic atlas of hygro-and thermosensory cells in the vinegar fly Drosophila melanogaster.", "authors": [{"family": "Corthals", "given": "Kristina", "initials": "K"}, {"family": "Andersson", "given": "Vilma", "initials": "V"}, {"family": "Churcher", "given": "Allison", "initials": "A"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Enjin", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2023-09-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "15202", "issn-l": "2045-2322"}, "abstract": "The ability of animals to perceive and respond to sensory information is essential for their survival in diverse environments. While much progress has been made in understanding various sensory modalities, the sense of hygrosensation, which involves the detection and response to humidity, remains poorly understood. In this study, we focused on the hygrosensory, and closely related thermosensory, systems in the vinegar fly Drosophila melanogaster to unravel the molecular profile of the cells of these senses. Using a transcriptomic analysis of over 37,000 nuclei, we identified twelve distinct clusters of cells corresponding to temperature-sensing arista neurons, humidity-sensing sacculus neurons, and support cells relating to these neurons. By examining the expression of known and novel marker genes, we validated the identity of these clusters and characterized their gene expression profiles. We found that each cell type could be characterized by a unique expression profile of ion channels, GPCR signaling molecules, synaptic vesicle cycle proteins, and cell adhesion molecules. Our findings provide valuable insights into the molecular basis of hygro- and thermosensation. Understanding the mechanisms underlying hygro- and thermosensation may shed light on the broader understanding of sensory systems and their adaptation to different environmental conditions in animals.", "doi": "10.1038/s41598-023-42506-2", "pmid": "37709909", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10502013"}, {"db": "pii", "key": "10.1038/s41598-023-42506-2"}], "notes": [], "created": "2023-10-25T14:15:21.679Z", "modified": "2024-01-16T13:48:32.259Z"}, {"entity": "publication", "iuid": "68e5e56f6e754304be4e58797b91095a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68e5e56f6e754304be4e58797b91095a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68e5e56f6e754304be4e58797b91095a"}}, "title": "The yeast guanine nucleotide exchange factor Sec7 is a bottleneck in spatial protein quality control and detoxifies neurological disease proteins.", "authors": [{"family": "Babazadeh", "given": "Roja", "initials": "R"}, {"family": "Schneider", "given": "Kara L", "initials": "KL"}, {"family": "Fischbach", "given": "Arthur", "initials": "A"}, {"family": "Hao", "given": "Xinxin", "initials": "X"}, {"family": "Liu", "given": "Beidong", "initials": "B"}, {"family": "Nystrom", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2023-08-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "14068", "issn-l": "2045-2322"}, "abstract": "ER-to-Golgi trafficking partakes in the sorting of misfolded cytoplasmic proteins to reduce their cytological toxicity. We show here that yeast Sec7, a protein involved in proliferation of the Golgi, is part of this pathway and participates in an Hsp70-dependent formation of insoluble protein deposits (IPOD). Sec7 associates with the disaggregase Hsp104 during a mild heat shock and increases the rate of Hsp104 diffusion in an Hsp70-dependent manner when overproduced. Sec7 overproduction increased formation of IPODs from smaller aggregates and mitigated the toxicity of Huntingtin exon-1 upon heat stress while Sec7 depletion increased sensitivity to a\u1e9e42 of the Alzheimer's disease and \u03b1-synuclein of the Parkinson's disease, suggesting a role of Sec7 in mitigating proteotoxicity.", "doi": "10.1038/s41598-023-41188-0", "pmid": "37640758", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10462735"}, {"db": "pii", "key": "10.1038/s41598-023-41188-0"}], "notes": [], "created": "2023-12-01T10:42:12.669Z", "modified": "2023-12-01T10:42:12.673Z"}, {"entity": "publication", "iuid": "d1055b0a45b84819829c3d72a62960ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1055b0a45b84819829c3d72a62960ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1055b0a45b84819829c3d72a62960ed"}}, "title": "Insights into cellular behavior and micromolecular communication in urothelial micrografts.", "authors": [{"family": "Juul", "given": "Nikolai", "initials": "N"}, {"family": "Willacy", "given": "Oliver", "initials": "O"}, {"family": "Mamand", "given": "Doste R", "initials": "DR"}, {"family": "Andaloussi", "given": "Samir El", "initials": "SE"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Chamorro", "given": "Clara I", "initials": "CI"}, {"family": "Fossum", "given": "Magdalena", "initials": "M"}], "type": "journal article", "published": "2023-08-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "13589", "issn-l": "2045-2322"}, "abstract": "Autologous micrografting is a technique currently applied within skin wound healing, however, the potential use for surgical correction of other organs with epithelial lining, including the urinary bladder, remains largely unexplored. Currently, little is known about the micrograft expansion potential and the micromolecular events that occur in micrografted urothelial cells. In this study, we aimed to evaluate the proliferative potential of different porcine urothelial micrograft sizes in vitro, and, furthermore, to explore how urothelial micrografts communicate and which microcellular events are triggered. We demonstrated that increased tissue fragmentation subsequently potentiated the yield of proliferative cells and the cellular expansion potential, which confirms, that the micrografting principles of skin epithelium also apply to uroepithelium. Furthermore, we targeted the expression of the extracellular signal-regulated kinase (ERK) pathway and demonstrated that ERK activation occurred predominately at the micrograft borders and that ERK inhibition led to decreased urothelial migration and proliferation. Finally, we successfully isolated extracellular vesicles from the micrograft culture medium and evaluated their contents and relevance within various enriched biological processes. Our findings substantiate the potential of applying urothelial micrografting in future tissue-engineering models for reconstructive urological surgery, and, furthermore, highlights certain mechanisms as potential targets for future wound healing treatments.", "doi": "10.1038/s41598-023-40049-0", "pmid": "37604899", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10442416"}, {"db": "pii", "key": "10.1038/s41598-023-40049-0"}], "notes": [], "created": "2023-11-29T13:15:36.374Z", "modified": "2023-11-30T13:00:31.275Z"}, {"entity": "publication", "iuid": "726fcfebe5af46edb7ce5edffa4eb88b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/726fcfebe5af46edb7ce5edffa4eb88b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/726fcfebe5af46edb7ce5edffa4eb88b"}}, "title": "A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing.", "authors": [{"family": "Johansson", "given": "Josefin", "initials": "J"}, {"family": "Lid\u00e9us", "given": "Sarah", "initials": "S"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Gudmundsson", "given": "Sanna", "initials": "S"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2023-08-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "12856", "issn-l": "2045-2322"}, "abstract": "X-chromosome inactivation (XCI) analyses often assist in diagnostics of X-linked traits, however accurate assessment remains challenging with current methods. We developed a novel strategy using amplification-free Cas9 enrichment and Oxford nanopore technologies sequencing called XCI-ONT, to investigate and rigorously quantify XCI in human androgen receptor gene (AR) and human X-linked retinitis pigmentosa 2 gene (RP2). XCI-ONT measures methylation over 116 CpGs in AR and 58 CpGs in RP2, and separate parental X-chromosomes without PCR bias. We show the usefulness of the XCI-ONT strategy over the PCR-based golden standard XCI technique that only investigates one or two CpGs per gene. The results highlight the limitations of using the golden standard technique when the XCI pattern is partially skewed and the advantages of XCI-ONT to rigorously quantify XCI. This study provides a universal XCI-method on DNA, which is highly valuable in clinical and research framework of X-linked traits.", "doi": "10.1038/s41598-023-34413-3", "pmid": "37553382", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10409790"}, {"db": "pii", "key": "10.1038/s41598-023-34413-3"}], "notes": [], "created": "2023-08-15T07:13:58.347Z", "modified": "2023-08-15T07:13:58.351Z"}, {"entity": "publication", "iuid": "30a1386e02c149b68921f0515981458f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30a1386e02c149b68921f0515981458f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30a1386e02c149b68921f0515981458f"}}, "title": "Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper.", "authors": [{"family": "Fridolfsson", "given": "Emil", "initials": "E", "orcid": "0000-0003-4871-7441", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f9f3d44ed8b46729bf6c3d9984bfbe6.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C", "orcid": "0000-0002-0683-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb255e90d0584d3e8128c5288a715c97.json"}}, {"family": "Lindehoff", "given": "Elin", "initials": "E", "orcid": "0000-0002-1149-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca95ca733ed448d3894e83739d758419.json"}}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K", "orcid": "0000-0002-6570-5525", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bcd7d3b7b47405185ba0d0062111a13.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Legrand", "given": "Catherine", "initials": "C", "orcid": "0000-0001-7155-3604", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2287e0a4ced4bb49ca18a67867a8815.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}], "type": "journal article", "published": "2023-07-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "11865", "issn-l": "2045-2322"}, "abstract": "The planktonic realm from bacteria to zooplankton provides the baseline for pelagic aquatic food webs. However, multiple trophic levels are seldomly included in time series studies, hampering a holistic understanding of the influence of seasonal dynamics and species interactions on food web structure and biogeochemical cycles. Here, we investigated plankton community composition, focusing on bacterio-, phyto- and large mesozooplankton, and how biotic and abiotic factors correlate at the Linnaeus Microbial Observatory (LMO) station in the Baltic Sea from 2011 to 2018. Plankton communities structures showed pronounced dynamic shifts with recurring patterns. Summarizing the parts of the planktonic microbial food web studied here to total carbon, a picture emerges with phytoplankton consistently contributing > 39% while bacterio- and large mesozooplankton contributed ~ 30% and ~ 7%, respectively, during summer. Cyanophyceae, Actinobacteria, Bacteroidetes, and Proteobacteria were important groups among the prokaryotes. Importantly, Dinophyceae, and not Bacillariophyceae, dominated the autotrophic spring bloom whereas Litostomatea (ciliates) and Appendicularia contributed significantly to the consumer entities together with the more traditionally observed mesozooplankton, Copepoda and Cladocera. Our findings of seasonality in both plankton composition and carbon stocks emphasize the importance of time series analyses of food web structure for characterizing the regulation of biogeochemical cycles and appropriately constraining ecosystem models.", "doi": "10.1038/s41598-023-38816-0", "pmid": "37481661", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10363133"}, {"db": "pii", "key": "10.1038/s41598-023-38816-0"}], "notes": [], "created": "2023-10-04T13:23:17.104Z", "modified": "2023-10-19T12:25:13.624Z"}, {"entity": "publication", "iuid": "9ac67eefe49643bc80efb1022d8ed2ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ac67eefe49643bc80efb1022d8ed2ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ac67eefe49643bc80efb1022d8ed2ce"}}, "title": "Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics.", "authors": [{"family": "Arora", "given": "Abishek", "initials": "A"}, {"family": "Becker", "given": "Martin", "initials": "M"}, {"family": "Marques", "given": "C\u00e1tia", "initials": "C"}, {"family": "Oksanen", "given": "Marika", "initials": "M"}, {"family": "Li", "given": "Danyang", "initials": "D"}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F"}, {"family": "Watts", "given": "Michelle Evelyn", "initials": "ME"}, {"family": "Arora", "given": "Manish", "initials": "M"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Daub", "given": "Carsten Oliver", "initials": "CO"}, {"family": "Lanekoff", "given": "Ingela", "initials": "I"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}], "type": "journal article", "published": "2023-06-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "10519", "issn-l": "2045-2322"}, "abstract": "Research continues to identify genetic variation, environmental exposures, and their mixtures underlying different diseases and conditions. There is a need for screening methods to understand the molecular outcomes of such factors. Here, we investigate a highly efficient and multiplexable, fractional factorial experimental design (FFED) to study six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine hydrochloride and zinc deficiency) and four human induced pluripotent stem cell line derived differentiating human neural progenitors. We showcase the FFED coupled with RNA-sequencing to identify the effects of low-grade exposures to these environmental factors and analyse the results in the context of autism spectrum disorder (ASD). We performed this after 5-day exposures on differentiating human neural progenitors accompanied by a layered analytical approach and detected several convergent and divergent, gene and pathway level responses. We revealed significant upregulation of pathways related to synaptic function and lipid metabolism following lead and fluoxetine exposure, respectively. Moreover, fluoxetine exposure elevated several fatty acids when validated using mass spectrometry-based metabolomics. Our study demonstrates that the FFED can be used for multiplexed transcriptomic analyses to detect relevant pathway-level changes in human neural development caused by low-grade environmental risk factors. Future studies will require multiple cell lines with different genetic backgrounds for characterising the effects of environmental exposures in ASD.", "doi": "10.1038/s41598-023-37488-0", "pmid": "37386098", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10310850"}, {"db": "pii", "key": "10.1038/s41598-023-37488-0"}], "notes": [], "created": "2023-10-11T08:41:00.302Z", "modified": "2024-01-16T13:48:33.099Z"}, {"entity": "publication", "iuid": "7e63444e5ef6436c8ea4f56a7fce1f29", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e63444e5ef6436c8ea4f56a7fce1f29.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e63444e5ef6436c8ea4f56a7fce1f29"}}, "title": "Investigation of enzalutamide, docetaxel, and cabazitaxel resistance in the castration resistant prostate cancer cell line C4 using genome-wide CRISPR/Cas9 screening.", "authors": [{"family": "Haldrup", "given": "Jakob", "initials": "J"}, {"family": "Weiss", "given": "Simone", "initials": "S"}, {"family": "Schmidt", "given": "Linn\u00e9a", "initials": "L"}, {"family": "S\u00f8rensen", "given": "Karina Dalsgaard", "initials": "KD"}], "type": "journal article", "published": "2023-06-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "9043", "issn-l": "2045-2322"}, "abstract": "Enzalutamide, docetaxel, and cabazitaxel treatment resistance is a major problem in metastatic castration resistant prostate cancer (mCRPC), but the underlying genetic determinants are poorly understood. To identify genes that modulate treatment response to these drugs, we performed three genome-wide CRISPR/Cas9 knockout screens in the mCRPC cell line C4. The screens identified seven candidates for enzalutamide (BCL2L13, CEP135, E2F4, IP6K2, KDM6A, SMS, and XPO4), four candidates for docetaxel (DRG1, LMO7, NCOA2, and ZNF268), and nine candidates for cabazitaxel (ARHGAP11B, DRG1, FKBP5, FRYL, PRKAB1, RP2, SMPD2, TCEA2, and ZNF585B). We generated single-gene C4 knockout clones/populations for all genes and could validate effect on treatment response for five genes (IP6K2, XPO4, DRG1, PRKAB1, and RP2). Altered enzalutamide response upon IP6K2 and XPO4 knockout was associated with deregulation of AR, mTORC1, and E2F signaling, and deregulated p53 signaling (IP6K2 only) in C4 mCRPC cells. Our study highlights the necessity of performing individual validation of candidate hits from genome-wide CRISPR screens. Further studies are needed to assess the generalizability and translational potential of these findings.", "doi": "10.1038/s41598-023-35950-7", "pmid": "37270558", "labels": {"CRISPR Functional Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10239467"}, {"db": "pii", "key": "10.1038/s41598-023-35950-7"}], "notes": [], "created": "2024-03-17T09:43:47.118Z", "modified": "2024-03-17T09:43:47.134Z"}, {"entity": "publication", "iuid": "4b81bd98a0fc4029a01c04e7e39e1464", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b81bd98a0fc4029a01c04e7e39e1464.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b81bd98a0fc4029a01c04e7e39e1464"}}, "title": "DNA methylation variations and epigenetic aging in telomere biology disorders.", "authors": [{"family": "Carlund", "given": "Olivia", "initials": "O"}, {"family": "Norberg", "given": "Anna", "initials": "A"}, {"family": "Osterman", "given": "Pia", "initials": "P"}, {"family": "Landfors", "given": "Mattias", "initials": "M"}, {"family": "Degerman", "given": "Sofie", "initials": "S"}, {"family": "Hultdin", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2023-05-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "7955", "issn-l": "2045-2322"}, "abstract": "Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length and disease severity. Epigenetic alterations are also markers of aging and we aimed to evaluate whether DNA methylation (DNAm) could be part of the pathogenesis of TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed and the cases were grouped based on relative telomere length (RTL): short (S), with RTL close to normal controls, and extremely short (ES). TBD cases had increased epigenetic age and DNAm alterations were most prominent in the ES-RTL group. Thus, the differentially methylated (DM) CpG sites could be markers of short telomeres but could also be one of the mechanisms contributing to disease phenotype since DNAm alterations were observed in symptomatic, but not asymptomatic, cases with S-RTL. Furthermore, two or more DM-CpGs were identified in four genes previously linked to TBD or telomere length (PRDM8, SMC4, VARS, and WNT6) and in three genes that were novel in telomere biology (MAS1L, NAV2, and TM4FS1). The DM-CpGs in these genes could be markers of aging in hematological cells, but they could also be of relevance for the progression of TBD.", "doi": "10.1038/s41598-023-34922-1", "pmid": "37193737", "labels": {"Clinical Genomics Ume\u00e5": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10188573"}, {"db": "pii", "key": "10.1038/s41598-023-34922-1"}], "notes": [], "created": "2023-11-29T09:45:06.307Z", "modified": "2023-11-29T09:45:06.311Z"}, {"entity": "publication", "iuid": "2cb756bff6294a6da881e10f16e2c5f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cb756bff6294a6da881e10f16e2c5f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cb756bff6294a6da881e10f16e2c5f8"}}, "title": "Metagenomic sequencing of human cardiac tissue reveals Microbial RNA which correlates with Toll-like receptor-associated inflammation in patients with heart disease.", "authors": [{"family": "Sandstedt", "given": "Joakim", "initials": "J"}, {"family": "Vukusic", "given": "Kristina", "initials": "K"}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G"}, {"family": "Jeppsson", "given": "Anders", "initials": "A"}, {"family": "Mattsson Hult\u00e9n", "given": "Lillemor", "initials": "L"}, {"family": "Rotter Sopasakis", "given": "Victoria", "initials": "V"}], "type": "journal article", "published": "2023-05-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "7884", "issn-l": "2045-2322"}, "abstract": "Cardiovascular disease (CVD) is strongly associated with chronic low-grade inflammation, involving activated Toll-like receptors and their downstream cellular machinery. Moreover, CVD and other related inflammatory conditions are associated with infiltration of bacteria and viruses originating from distant body sites. Thus, in this study we aimed to map the presence of microbes in the myocardium of patients with heart disease that we previously found to display upregulated Toll-like receptor signaling. We performed metagenomics analysis of atrial cardiac tissue from patients undergoing coronary artery bypass grafting (CABG) or aortic valve replacement (AVR) and compared with atrial cardiac tissue from organ donors. A total of 119 species of bacteria and seven species of virus were detected in the cardiac tissue. RNA expression of five bacterial species were increased in the patient group of which L. kefiranofaciens correlated positively with cardiac Toll-like receptor-associated inflammation. Interaction network analysis revealed four main gene set clusters involving cell growth and proliferation, Notch signaling, G protein signaling and cell communication in association with L. kefiranofaciens RNA expression. Taken together, intracardial expression of L. kefiranofaciens RNA correlates with pro-inflammatory markers in the diseased cardiac atrium and may have an effect on specific signaling processes important for cell growth, proliferation and cell communication.", "doi": "10.1038/s41598-023-35157-w", "pmid": "37188775", "labels": {"Clinical Genomics Gothenburg": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10185540"}, {"db": "pii", "key": "10.1038/s41598-023-35157-w"}], "notes": [], "created": "2023-11-30T22:37:51.743Z", "modified": "2023-11-30T22:37:51.747Z"}, {"entity": "publication", "iuid": "ccda4bb7a77c463da879114f20efb678", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ccda4bb7a77c463da879114f20efb678.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ccda4bb7a77c463da879114f20efb678"}}, "title": "A topical rectal douche product containing Q-Griffithsin does not disrupt the epithelial border or alter CD4+ cell distribution in the human rectal mucosa.", "authors": [{"family": "Franz\u00e9n Boger", "given": "Mathias", "initials": "M"}, {"family": "Benhach", "given": "Nora", "initials": "N"}, {"family": "Hasselrot", "given": "Tyra", "initials": "T"}, {"family": "Brand", "given": "Rhonda M", "initials": "RM"}, {"family": "Rohan", "given": "Lisa C", "initials": "LC"}, {"family": "Wang", "given": "Lin", "initials": "L"}, {"family": "McGowan", "given": "Ian", "initials": "I"}, {"family": "Edick", "given": "Stacey", "initials": "S"}, {"family": "Ho", "given": "Ken", "initials": "K"}, {"family": "Meyn", "given": "Leslie", "initials": "L"}, {"family": "Matoba", "given": "Nobuyuki", "initials": "N"}, {"family": "Palmer", "given": "Kenneth E", "initials": "KE"}, {"family": "Broliden", "given": "Kristina", "initials": "K"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}], "type": "journal article", "published": "2023-05-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "7547", "issn-l": "2045-2322"}, "abstract": "To reduce HIV transmission, locally applied pre-exposure prophylaxis (PrEP) products for anorectal use will be important complements to oral and injectable PrEP products already available. It is critical to preserve an intact rectal epithelium and avoid an influx of mucosal HIV target cells with such product use. In this phase 1 clinical trial, we evaluated application of a topical rectal douche product containing Q-Griffithsin (Q-GRFT). Colorectal tissue samples were obtained via sigmoidoscopy at baseline, 1 and 24 h after single-dose exposure in 15 healthy volunteers. In situ staining for epithelial junction markers and CD4+ cells were assessed as an exploratory endpoint. A high-throughput, digitalized in situ imaging analysis workflow was developed to visualize and quantify these HIV susceptibility markers. We observed no significant differences in epithelial distribution of E-cadherin, desmocollin-2, occludin, claudin-1, or zonula occludens-1 when comparing the three timepoints or Q-GRFT versus placebo. There were also no differences in %CD4+ cells within the epithelium or lamina propria in any of these comparisons. In conclusion, the rectal epithelium and CD4+ cell distribution remained unchanged following topical application of Q-GRFT. In situ visualization of HIV susceptibility markers at mucosal sites could be useful to complement standard product safety assessments.", "doi": "10.1038/s41598-023-34107-w", "pmid": "37161022", "labels": {"BioImage Informatics": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10169179"}, {"db": "pii", "key": "10.1038/s41598-023-34107-w"}], "notes": [], "created": "2023-10-24T14:51:04.919Z", "modified": "2023-10-24T14:51:04.923Z"}, {"entity": "publication", "iuid": "03f6f1b4cfe24ceea3859aa58e725308", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03f6f1b4cfe24ceea3859aa58e725308.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03f6f1b4cfe24ceea3859aa58e725308"}}, "title": "Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines.", "authors": [{"family": "Rosenbaum", "given": "Adam", "initials": "A"}, {"family": "Dahlin", "given": "Anna M", "initials": "AM"}, {"family": "Andersson", "given": "Ulrika", "initials": "U"}, {"family": "Bj\u00f6rkblom", "given": "Benny", "initials": "B"}, {"family": "Wu", "given": "Wendy Yi-Ying", "initials": "WY"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Melin", "given": "Beatrice", "initials": "B"}], "type": "journal article", "published": "2023-04-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "6777"}, "abstract": "Genome-wide association studies (GWAS) have contributed to our understanding of glioma susceptibility. To date, 25 risk loci for development of any of the glioma subtypes are known. However, GWAS studies reveal little about the molecular processes that lead to increased risk, especially for non-coding single nucleotide polymorphisms (SNP). A particular SNP in intron 2 of LRIG1, rs11706832, has been shown to increase the susceptibility for IDH1 mutated low-grade gliomas (LGG). Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is important in cancer development as it negatively regulates the epidermal growth factor receptor (EGFR); however, the mechanism responsible for this particular risk SNP and its potential effect on LRIG1 are not known. Using CRISPR-CAS9, we edited rs11706832 in HEK293T cells. Four HEK293T clones with the risk allele were compared to four clones with the non-risk allele for LRIG1 and SLC25A26 gene expression using RT-qPCR, for global gene expression using RNA-seq, and for metabolites using gas chromatography-mass spectrometry (GC-MS). The experiment did not reveal any significant effect of the SNP on the expression levels or splicing patterns of LRIG1 or SLC25A26. The global gene expression analysis revealed that the risk allele C was associated with upregulation of several mitochondrial genes. Gene enrichment analysis of 74 differentially expressed genes in the genome revealed a significant enrichment of type I interferon response genes, where many genes were downregulated for the risk allele C. Gene expression data of IDH1 mutated LGGs from the cancer genome atlas (TCGA) revealed a similar under expression of type I interferon genes associated with the risk allele. This study found the expression levels and splicing patterns of LRIG1 and SLC25A26 were not affected by the SNP in HEK293T cells. However, the risk allele was associated with a downregulation of genes involved in the innate immune response both in the HEK293T cells and in the LGG data from TCGA.", "doi": "10.1038/s41598-023-33923-4", "pmid": "37185361", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10130147"}, {"db": "pii", "key": "10.1038/s41598-023-33923-4"}], "notes": [], "created": "2023-08-30T07:04:23.132Z", "modified": "2025-10-17T13:03:14.040Z"}, {"entity": "publication", "iuid": "fad337f3c68442bbbc19a21c36f7dfd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fad337f3c68442bbbc19a21c36f7dfd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fad337f3c68442bbbc19a21c36f7dfd1"}}, "title": "Transcriptomics unravels molecular changes associated with cilia and COVID-19 in chronic rhinosinusitis with nasal polyps.", "authors": [{"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "\u00d6stensson", "given": "Malin", "initials": "M"}, {"family": "Fowler", "given": "Philippa C", "initials": "PC"}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lassesson", "given": "Stina", "initials": "S"}, {"family": "Jacobsson", "given": "Frida", "initials": "F"}, {"family": "Oscarsson", "given": "Martin", "initials": "M"}, {"family": "Bohman", "given": "Anton", "initials": "A"}, {"family": "Harandi", "given": "Ali M", "initials": "AM"}, {"family": "Bende", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2023-04-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "6592"}, "abstract": "Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common upper respiratory tract complication where the pathogenesis is largely unknown. Herein, we investigated the transcriptome profile in nasal mucosa biopsies of CRSwNP patients and healthy individuals. We further integrated the transcriptomics data with genes located in chromosomal regions containing genome-wide significant gene variants for COVID-19. Among the most significantly upregulated genes in polyp mucosa were CCL18, CLEC4G, CCL13 and SLC9A3. Pathways involving \"Ciliated epithelial cells\" were the most differentially expressed molecular pathways when polyp mucosa and non-polyp mucosa from the same patient was compared. Natural killer T-cell (NKT) and viral pathways were the most statistically significant pathways in the mucosa of CRSwNP patients compared with those of healthy control individuals. Upregulated genes in polyp mucosa, located within the genome-wide associated regions of COVID-19, included LZTFL1, CCR9, SLC6A20, IFNAR1, IFNAR2 and IL10RB. Interestingly, the second most over-expressed gene in our study, CLEC4G, has been shown to bind directly to SARS-CoV-2 spike's N-terminal domain and mediate its entry and infection. Our results on altered expression of genes related to cilia and viruses point to the de-regulation of viral defenses in CRSwNP patients, and may give clues to future intervention strategies.", "doi": "10.1038/s41598-023-32944-3", "pmid": "37085563", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10121071"}, {"db": "pii", "key": "10.1038/s41598-023-32944-3"}], "notes": [], "created": "2023-06-16T15:16:27.534Z", "modified": "2023-11-30T22:39:42.478Z"}, {"entity": "publication", "iuid": "347f4e6919984e159aa13938756ba62c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/347f4e6919984e159aa13938756ba62c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/347f4e6919984e159aa13938756ba62c"}}, "title": "Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.", "authors": [{"family": "Koskela von Sydow", "given": "Anita", "initials": "A"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Asghar", "given": "Naveed", "initials": "N"}, {"family": "Johansson", "given": "Magnus", "initials": "M"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}], "type": "journal article", "published": "2023-04-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "6461", "issn-l": "2045-2322"}, "abstract": "The severe acute respiratory syndrome coronavirus 2 (SARS\u2011CoV\u20112) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14-30 were run using three different protocols: the Twist Bioscience SARS\u2011CoV\u20112 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS\u2011CoV\u20112 sequencing and guidance in selecting suitable methods for various purposes.", "doi": "10.1038/s41598-023-33168-1", "pmid": "37081087", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC10116481"}, {"db": "pii", "key": "10.1038/s41598-023-33168-1"}], "notes": [], "created": "2023-09-25T13:34:58.667Z", "modified": "2023-09-25T13:34:58.672Z"}, {"entity": "publication", "iuid": "5ac9844505f448bab02167d3d467c4a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ac9844505f448bab02167d3d467c4a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ac9844505f448bab02167d3d467c4a4"}}, "title": "Genomic architecture of migration timing in a long-distance migratory songbird.", "authors": [{"family": "de Greef", "given": "Evelien", "initials": "E"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Thorstensen", "given": "Matt J", "initials": "MJ"}, {"family": "Delmore", "given": "Kira E", "initials": "KE"}, {"family": "Fraser", "given": "Kevin C", "initials": "KC"}], "type": "journal article", "published": "2023-02-10", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "2437"}, "abstract": "The impact of climate change on spring phenology poses risks to migratory birds, as migration timing is controlled predominantly by endogenous mechanisms. Despite recent advances in our understanding of the underlying genetic basis of migration timing, the ways that migration timing phenotypes in wild individuals may map to specific genomic regions requires further investigation. We examined the genetic architecture of migration timing in a long-distance migratory songbird (purple martin, Progne subis subis) by integrating genomic data with an extensive dataset of direct migratory tracks. A moderate to large amount of variance in spring migration arrival timing was explained by genomics (proportion of phenotypic variation explained by genomics = 0.74; polygenic score R2 = 0.24). On chromosome 1, a region that was differentiated between migration timing phenotypes contained genes that could facilitate nocturnal flights and act as epigenetic modifiers. Overall, these results advance our understanding of the genomic underpinnings of migration timing.", "doi": "10.1038/s41598-023-29470-7", "pmid": "36765096", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9918537"}, {"db": "pii", "key": "10.1038/s41598-023-29470-7"}], "notes": [], "created": "2023-03-06T13:47:41.654Z", "modified": "2024-11-25T10:20:21.866Z"}, {"entity": "publication", "iuid": "cb8bdac206dc430f8174e8cbcd6281cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb8bdac206dc430f8174e8cbcd6281cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb8bdac206dc430f8174e8cbcd6281cf"}}, "title": "PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia.", "authors": [{"family": "Arendt", "given": "Maja Louise", "initials": "ML"}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S"}, {"family": "Melin", "given": "Malin", "initials": "M"}, {"family": "Elvers", "given": "Ingegerd", "initials": "I"}, {"family": "Rivera", "given": "Patricio", "initials": "P"}, {"family": "Larsen", "given": "Majbritt", "initials": "M"}, {"family": "Saellstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Lingaas", "given": "Frode", "initials": "F"}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2023-01-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "632", "issn-l": "2045-2322"}, "abstract": "Biological features of neoplastic disease affecting mammary gland tissue are shared between canines and humans. Research performed in either species has translational value and early phase clinical trials performed in canines with spontaneous disease could be informative for human trials. The purpose of this study was to investigate the somatic genetic aberrations occurring in canine mammary neoplasia by exome capture and next generation sequencing. Based on 55 tumor-normal pairs we identified the PIK3CA gene as the most commonly mutated gene in canine mammary tumors, with 25% of samples carrying mutations in this gene. A recurrent missense mutation was identified, p.H1047R, which is homologous to the human PIK3CA hotspot mutation found in different types of breast neoplasia. Mutations homologous to other known human mutation hotspots such as the PIK3CA p.E545K and the KRAS p.G12V/D were also identified. We identified copy number aberrations affecting important tumor suppressor and oncogenic pathways including deletions affecting the PTEN tumor suppressor gene. We suggest that activation of the KRAS or PIK3CA oncogenes or loss of the PTEN suppressor gene may be important for mammary tumor development in dogs. This data endorses the conservation of cancer across species and the validity of studying cancer in non-human species.", "doi": "10.1038/s41598-023-27664-7", "pmid": "36635367", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9837039"}, {"db": "pii", "key": "10.1038/s41598-023-27664-7"}], "notes": [], "created": "2023-11-29T11:40:33.492Z", "modified": "2024-01-16T13:48:34.144Z"}, {"entity": "publication", "iuid": "6c44ffcfbec34a02ac3f694981742e15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c44ffcfbec34a02ac3f694981742e15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c44ffcfbec34a02ac3f694981742e15"}}, "title": "An investigation of metabolome in blood in patients with chronic peripheral, posttraumatic/postsurgical neuropathic pain.", "authors": [{"family": "Ghafouri", "given": "Bijar", "initials": "B"}, {"family": "Thordeman", "given": "Katarina", "initials": "K"}, {"family": "Hadjikani", "given": "Romina", "initials": "R"}, {"family": "Bay Nord", "given": "Anders", "initials": "A"}, {"family": "Gerdle", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "B\u00e4ckryd", "given": "Emmanuel", "initials": "E"}], "type": "journal article", "published": "2022-12-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "21714", "issn-l": "2045-2322"}, "abstract": "Neuropathic pain (NP) is a chronic pain condition resulting from a lesion or disease in the somatosensory nervous system. The aim of this study was to investigate the metabolome in plasma from patients with chronic peripheral, posttraumatic/postsurgical NP compared to healthy controls. Further, we aimed to investigate the correlation between pain intensity and the metabolome in plasma. The metabolic profile in plasma samples from 16 patients with chronic NP and 12 healthy controls was analyzed using a nuclear magnetic resonance spectroscopy method. Information about pain intensity, pain duration, body mass index (BMI), age, sex, and blood pressure were obtained through a questionnaire and clinical examination. Multivariate data analysis was used to identify metabolites significant for group separation and their correlation with pain intensity and duration, BMI, and age. We found 50 out of 326 features in plasma significantly contributing to group discrimination between NP and controls. Several of the metabolites that significantly differed were involved in inflammatory processes, while others were important for central nervous system functioning and neural signaling. There was no correlation between pain intensity and levels of metabolite in NP. These findings indicate that there seems to be peripheral/systemic differences in the metabolic profile between patients with chronic NP and healthy individuals.", "doi": "10.1038/s41598-022-26405-6", "pmid": "36522472", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9755304"}, {"db": "pii", "key": "10.1038/s41598-022-26405-6"}], "notes": [], "created": "2023-05-31T16:41:22.692Z", "modified": "2025-10-17T13:03:54.380Z"}, {"entity": "publication", "iuid": "80c8d0c6ac8144f2a9233396fcae3486", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c8d0c6ac8144f2a9233396fcae3486.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c8d0c6ac8144f2a9233396fcae3486"}}, "title": "Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo.", "authors": [{"family": "Tonge", "given": "Joseph J", "initials": "JJ"}, {"family": "Notley", "given": "Scott V", "initials": "SV"}, {"family": "Dunning", "given": "Mark J", "initials": "MJ"}, {"family": "L\u00f3pez-Guajardo", "given": "Ana", "initials": "A"}, {"family": "Medcalf", "given": "Jessica D", "initials": "JD"}, {"family": "Heldin", "given": "Paraskevi", "initials": "P"}, {"family": "Panoutsos", "given": "George", "initials": "G"}, {"family": "Gad", "given": "Annica K B", "initials": "AKB"}], "type": "journal article", "published": "2022-11-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "19835", "issn-l": "2045-2322"}, "abstract": "Infantile fibrosarcoma is a rare childhood tumour that originates in the fibrous connective tissue of the long bones for which there is an urgent need to identify novel therapeutic targets. This study aims to clarify the role of the extracellular matrix component hyaluronan in the invasion of child fibroblasts and Infantile fibrosarcoma into the surrounding environment. Using nanoscale super-resolution STED (Stimulated emission depletion) microscopy followed by computational image analysis, we observed, for the first time, that invasive child fibroblasts showed increased nanoscale clustering of hyaluronan at the cell periphery, as compared to control cells. Hyaluronan was not observed within focal adhesions. Bioinformatic analyses further revealed that the increased nanoscale hyaluronan clustering was accompanied by increased gene expression of Hyaluronan synthase 2, reduced expression of Hyaluronidase 2 and CD44, and no change of Hyaluronan synthase 1 and Hyaluronidases 1, 3, 4 or 5. We further observed that the expression of the Hyaluronan synthase 1, 2 and 3, and the Hyaluronidase 3 and 5 genes was linked to reduced life expectancy of fibrosarcoma patients. The invasive front of infantile fibrosarcoma tumours further showed increased levels of hyaluronan, as compared to the tumour centre. Taken together, our findings are consistent with the possibility that while Hyaluronan synthase 2 increases the levels, the Hyaluronidases 3 and 5 reduce the weight of hyaluronan, resulting in the nanoscale clustering of hyaluronan at the leading edge of cells, cell invasion and the spread of Infantile fibrosarcoma.", "doi": "10.1038/s41598-022-21952-4", "pmid": "36400790", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9674583"}, {"db": "pii", "key": "10.1038/s41598-022-21952-4"}], "notes": [], "created": "2023-02-19T17:55:17.361Z", "modified": "2023-02-19T17:55:17.364Z"}, {"entity": "publication", "iuid": "32e6b068d3204ca9b4f22398e9a55324", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32e6b068d3204ca9b4f22398e9a55324.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32e6b068d3204ca9b4f22398e9a55324"}}, "title": "Self-reported symptom severity, general health, and impairment in post-acute phases of COVID-19: retrospective cohort study of Swedish public employees.", "authors": [{"family": "Larsson", "given": "Simon B", "initials": "SB"}, {"family": "von Feilitzen", "given": "Gustaf Stuk\u00e1t", "initials": "GS"}, {"family": "Andersson", "given": "Maria E", "initials": "ME"}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Lindh", "given": "Magnus", "initials": "M"}, {"family": "Nord\u00e9n", "given": "Rickard", "initials": "R"}, {"family": "Nilsson", "given": "Staffan", "initials": "S"}, {"family": "Sigstr\u00f6m", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2022-11-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "19818"}, "abstract": "This study aimed to examine current symptom severity and general health in a sample of primarily non-hospitalized persons with polymerase chain reaction (PCR) confirmed COVID-19 in comparison to PCR negative controls. During the first quarter of 2021, we conducted an online survey among public employees in West Sweden, with a valid COVID-19 test result. The survey assessed past-month severity of 28 symptoms and signs, self-rated health, the WHO Disability Assessment Schedule (WHODAS) 2.0 and illness severity at the time of test. We linked participants' responses to their SARS-CoV-2 PCR tests results. We compared COVID-19 positive and negative participants using univariable and multivariable regression analyses. Out of 56,221 invited, 14,222 (25.3%) responded, with a response rate of 50% among SARS-CoV-2 positive individuals. Analysis included 10,194 participants (86.4% women, mean age 45 years) who tested positive 4-12 weeks (N = 1425; subacute) and > 12 weeks (N = 1584; postcovid) prior to the survey, and 7185 PCR negative participants who did not believe that they had had COVID-19. Symptoms were highly prevalent in all groups, with worst symptoms in subacute phase participants, followed by postcovid phase and PCR negative participants. The most specific symptom for COVID-19 was loss of smell or taste. Both WHODAS 2.0 score and self-rated health were worst in subacute participants, and modestly worse in postcovid participants than in negative controls. Female gender, older age and acute illness severity had larger effects on self-rated health and WHODAS 2.0 score in PCR positive participants than in PCR negative. Studies with longer follow-up are needed to determine the long-term improvement after COVID-19.", "doi": "10.1038/s41598-022-24307-1", "pmid": "36396860", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9672032"}, {"db": "pii", "key": "10.1038/s41598-022-24307-1"}], "notes": [], "created": "2022-12-02T12:21:21.108Z", "modified": "2023-05-15T16:26:21.641Z"}, {"entity": "publication", "iuid": "1722fbb67c6f43dd94b26537ac9d0fa3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1722fbb67c6f43dd94b26537ac9d0fa3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1722fbb67c6f43dd94b26537ac9d0fa3"}}, "title": "Pax3 loss of function delays tumour progression in kRAS-induced zebrafish rhabdomyosarcoma models.", "authors": [{"family": "Kahsay", "given": "A", "initials": "A"}, {"family": "Rodriguez-Marquez", "given": "E", "initials": "E"}, {"family": "L\u00f3pez-P\u00e9rez", "given": "A", "initials": "A"}, {"family": "H\u00f6rnblad", "given": "A", "initials": "A"}, {"family": "von Hofsten", "given": "J", "initials": "J"}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "17149"}, "abstract": "Rhabdomyosarcoma is a soft tissue cancer that arises in skeletal muscle due to mutations in myogenic progenitors that lead to ineffective differentiation and malignant transformation. The transcription factors Pax3 and Pax7 and their downstream target genes are tightly linked with the fusion positive alveolar subtype, whereas the RAS pathway is usually involved in the embryonal, fusion negative variant. Here, we analyse the role of Pax3 in a fusion negative context, by linking alterations in gene expression in pax3a/pax3b double mutant zebrafish with tumour progression in kRAS-induced rhabdomyosarcoma tumours. Several genes in the RAS/MAPK signalling pathway were significantly down-regulated in pax3a/pax3b double mutant zebrafish. Progression of rhabdomyosarcoma tumours was also delayed in the pax3a/pax3b double mutant zebrafish indicating that Pax3 transcription factors have an unappreciated role in mediating malignancy in fusion negative rhabdomyosarcoma.", "doi": "10.1038/s41598-022-21525-5", "pmid": "36229514", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9561152"}, {"db": "pii", "key": "10.1038/s41598-022-21525-5"}], "notes": [], "created": "2022-11-09T15:48:52.515Z", "modified": "2024-01-16T13:48:34.762Z"}, {"entity": "publication", "iuid": "02ca612014284b319f023360ee4fefe4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02ca612014284b319f023360ee4fefe4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02ca612014284b319f023360ee4fefe4"}}, "title": "Absence of oxygen effect on microbial structure and methane production during drying and rewetting events.", "authors": [{"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Li", "given": "Xiaoxiao", "initials": "X"}, {"family": "Yekta", "given": "Sepehr Shakeri", "initials": "SS"}, {"family": "Bj\u00f6rn", "given": "Annika", "initials": "A"}, {"family": "Mu", "given": "Bo-Zhong", "initials": "BZ"}, {"family": "Masuda", "given": "Laura Shizue Moriga", "initials": "LSM"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Enrich-Prast", "given": "Alex", "initials": "A"}], "type": "journal article", "published": "2022-10-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "16570", "issn-l": "2045-2322"}, "abstract": "Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.", "doi": "10.1038/s41598-022-20448-5", "pmid": "36195651", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9532411"}, {"db": "pii", "key": "10.1038/s41598-022-20448-5"}], "notes": [], "created": "2022-11-29T09:55:59.009Z", "modified": "2022-11-29T09:55:59.014Z"}, {"entity": "publication", "iuid": "89946fe4f9274f27854930948e438173", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89946fe4f9274f27854930948e438173.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89946fe4f9274f27854930948e438173"}}, "title": "Insight into the pulmonary molecular toxicity of heated tobacco products using human bronchial and alveolar mucosa models at air-liquid interface.", "authors": [{"family": "Rahman", "given": "Mizanur", "initials": "M"}, {"family": "Irmler", "given": "Martin", "initials": "M"}, {"family": "Introna", "given": "Micol", "initials": "M"}, {"family": "Beckers", "given": "Johannes", "initials": "J"}, {"family": "Palmberg", "given": "Lena", "initials": "L"}, {"family": "Johanson", "given": "Gunnar", "initials": "G"}, {"family": "Upadhyay", "given": "Swapna", "initials": "S"}, {"family": "Ganguly", "given": "Koustav", "initials": "K"}], "type": "journal article", "published": "2022-09-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "16396", "issn-l": "2045-2322"}, "abstract": "Heated tobacco products (HTP) are novel nicotine delivery products with limited toxicological data. HTP uses heating instead of combustion to generate aerosol (HTP-smoke). Physiologically relevant human bronchial and alveolar lung mucosa models developed at air-liquid interface were exposed to HTP-smoke to assess broad toxicological response (n = 6-7; ISO puffing regimen; compared to sham; non-parametric statistical analysis; significance: p < 0.05). Elevated levels of total cellular reactive oxygen species, stress responsive nuclear factor kappa-B, and DNA damage markers [8-hydroxy-2'-deoxyguanosine, phosphorylated histone H2AX, cleaved poly-(ADP-Ribose) polymerase] were detected in HTP-smoke exposed bronchial and/or alveolar models. RNA sequencing detected differential regulation of 724 genes in the bronchial- and 121 genes in the alveolar model following HTP-smoke exposure (cut off: p \u2264 0.01; fold change: \u2265 2). Common enriched pathways included estrogen biosynthesis, ferroptosis, superoxide radical degradation, xenobiotics, and \u03b1-tocopherol degradation. Secreted levels of interleukin (IL)1\ua7b5 and IL8 increased in the bronchial model whereas in the alveolar model, interferon-\u03b3 and IL4 increased and IL13 decreased following HTP-smoke exposure. Increased lipid peroxidation was detected in HTP-smoke exposed bronchial and alveolar models which was inhibited by ferrostatin-1. The findings form a basis to perform independent risk assessment studies on different flavours of HTP using different puffing topography and corresponding chemical characterization.", "doi": "10.1038/s41598-022-20657-y", "pmid": "36180488", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9525689"}, {"db": "pii", "key": "10.1038/s41598-022-20657-y"}], "notes": [], "created": "2022-12-02T10:49:13.530Z", "modified": "2022-12-02T10:49:13.533Z"}, {"entity": "publication", "iuid": "84870ae38812488595d58a590c3f912d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84870ae38812488595d58a590c3f912d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84870ae38812488595d58a590c3f912d"}}, "title": "Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea.", "authors": [{"family": "Zufia", "given": "Javier Alegria", "initials": "JA"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Farnelid", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2022-08-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "14330"}, "abstract": "Picocyanobacteria (< 2 \u00b5m in diameter) are significant contributors to total phytoplankton biomass. Due to the high diversity within this group, their seasonal dynamics and relationship with environmental parameters, especially in brackish waters, are largely unknown. In this study, the abundance and community composition of phycoerythrin rich picocyanobacteria (PE-SYN) and phycocyanin rich picocyanobacteria (PC-SYN) were monitored at a coastal (K-station) and at an offshore station (LMO; ~ 10 km from land) in the Baltic Sea over three years (2018-2020). Cell abundances of picocyanobacteria correlated positively to temperature and negatively to nitrate (NO3) concentration. While PE-SYN abundance correlated to the presence of nitrogen fixers, PC-SYN abundance was linked to stratification/shallow waters. The picocyanobacterial targeted amplicon sequencing revealed an unprecedented diversity of 2169 picocyanobacterial amplicons sequence variants (ASVs). A unique assemblage of distinct picocyanobacterial clades across seasons was identified. Clade A/B dominated the picocyanobacterial community, except during summer when low NO3, high phosphate (PO4) concentrations and warm temperatures promoted S5.2 dominance. This study, providing multiyear data, links picocyanobacterial populations to environmental parameters. The difference in the response of the two functional groups and clades underscore the need for further high-resolution studies to understand their role in the ecosystem.", "doi": "10.1038/s41598-022-18454-8", "pmid": "35995823", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9395346"}, {"db": "pii", "key": "10.1038/s41598-022-18454-8"}], "notes": [], "created": "2022-11-29T09:33:46.926Z", "modified": "2024-01-16T13:48:35.127Z"}, {"entity": "publication", "iuid": "42e87eafb84a4fb9ac71c5fb9c2d652b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42e87eafb84a4fb9ac71c5fb9c2d652b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42e87eafb84a4fb9ac71c5fb9c2d652b"}}, "title": "Amplification of CDK4 and MDM2: a detailed study of a high-risk neuroblastoma subgroup.", "authors": [{"family": "Martinez-Monleon", "given": "Angela", "initials": "A"}, {"family": "Kryh \u00d6berg", "given": "Hanna", "initials": "H"}, {"family": "Gaarder", "given": "Jennie", "initials": "J"}, {"family": "Berbegall", "given": "Ana P", "initials": "AP"}, {"family": "Javanmardi", "given": "Niloufar", "initials": "N"}, {"family": "Djos", "given": "Anna", "initials": "A"}, {"family": "Ussowicz", "given": "Marek", "initials": "M"}, {"family": "Taschner-Mandl", "given": "Sabine", "initials": "S"}, {"family": "Ambros", "given": "Inge M", "initials": "IM"}, {"family": "\u00d8ra", "given": "Ingrid", "initials": "I"}, {"family": "Sandstedt", "given": "Bengt", "initials": "B"}, {"family": "Beiske", "given": "Klaus", "initials": "K"}, {"family": "Ladenstein", "given": "Ruth", "initials": "R"}, {"family": "Noguera", "given": "Rosa", "initials": "R"}, {"family": "Ambros", "given": "Peter F", "initials": "PF"}, {"family": "Gordon Murkes", "given": "Lena", "initials": "L"}, {"family": "Ljungman", "given": "Gustaf", "initials": "G"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2022-07-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "12420", "issn-l": "2045-2322"}, "abstract": "In neuroblastoma, MYCN amplification and 11q-deletion are important, although incomplete, markers of high-risk disease. It is therefore relevant to characterize additional alterations that can function as prognostic and/or predictive markers. Using SNP-microarrays, a group of neuroblastoma patients showing amplification of one or multiple 12q loci was identified. Two loci containing CDK4 and MDM2 were commonly co-amplified, although amplification of either locus in the absence of the other was observed. Pharmacological inhibition of CDK4/6 with ribociclib or abemaciclib decreased proliferation in a broad set of neuroblastoma cell lines, including CDK4/MDM2-amplified, whereas MDM2 inhibition by Nutlin-3a was only effective in p53wild-type cells. Combined CDK4/MDM2 targeting had an additive effect in p53wild-type cell lines, while no or negative additive effect was observed in p53mutated cells. Most 12q-amplified primary tumors were of abdominal origin, including those of intrarenal origin initially suspected of being Wilms' tumor. An atypical metastatic pattern was also observed with low degree of bone marrow involvement, favoring other sites such as the lungs. Here we present detailed biological data of an aggressive neuroblastoma subgroup hallmarked by 12q amplification and atypical clinical presentation for which our in vitro studies indicate that CDK4 and/or MDM2 inhibition also could be beneficial.", "doi": "10.1038/s41598-022-16455-1", "pmid": "35859155", "labels": {"Clinical Genomics Gothenburg": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9300649"}, {"db": "pii", "key": "10.1038/s41598-022-16455-1"}], "notes": [], "created": "2022-12-02T12:21:55.087Z", "modified": "2022-12-02T12:21:55.101Z"}, {"entity": "publication", "iuid": "64ad69b112e8486882a7f3720623a583", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583"}}, "title": "Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.", "authors": [{"family": "Selvin", "given": "Tove", "initials": "T"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Andersson", "given": "Claes R", "initials": "CR"}], "type": "journal article", "published": "2022-07-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "11960"}, "abstract": "Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.", "doi": "10.1038/s41598-022-16077-7", "pmid": "35831404", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Single cell": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9279337"}, {"db": "pii", "key": "10.1038/s41598-022-16077-7"}], "notes": [], "created": "2022-08-22T07:53:44.772Z", "modified": "2024-01-16T13:48:35.689Z"}, {"entity": "publication", "iuid": "b476824c8ec54e5687ef3cd3b02390fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b476824c8ec54e5687ef3cd3b02390fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b476824c8ec54e5687ef3cd3b02390fb"}}, "title": "Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.", "authors": [{"family": "Hardt", "given": "Uta", "initials": "U"}, {"family": "Carlberg", "given": "Konstantin", "initials": "K"}, {"family": "Af Klint", "given": "Erik", "initials": "E"}, {"family": "Sahlstr\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "van Vollenhoven", "given": "Annika", "initials": "A"}, {"family": "Hernandez Machado", "given": "Susana", "initials": "S"}, {"family": "Israelsson", "given": "Lena", "initials": "L"}, {"family": "Amara", "given": "Khaled", "initials": "K"}, {"family": "Chemin", "given": "Karine", "initials": "K"}, {"family": "Korotkova", "given": "Marina", "initials": "M"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Teichmann", "given": "Sarah A", "initials": "SA"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}], "type": "journal article", "published": "2022-07-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "11876"}, "abstract": "B cells play a significant role in established Rheumatoid Arthritis (RA). However, it is unclear to what extent differentiated B cells are present in joint tissue already at the onset of disease. Here, we studied synovial biopsies (n = 8) captured from untreated patients at time of diagnosis. 3414 index-sorted B cells underwent RNA sequencing and paired tissue pieces were subjected to spatial transcriptomics (n = 4). We performed extensive bioinformatics analyses to dissect the local B cell composition. Select plasma cell immunoglobulin sequences were expressed as monoclonal antibodies and tested by ELISA. Memory and plasma cells were found irrespective of autoantibody status of the patients. Double negative memory B cells were prominent, but did not display a distinct transcriptional profile. The tissue architecture implicate both local B cell maturation via T cell help and plasma cell survival niches with a strong CXCL12-CXCR4 axis. The immunoglobulin sequence analyses revealed clonality between the memory B and plasma cell pools further supporting local maturation. One of the plasma cell-derived antibodies displayed citrulline autoreactivity, demonstrating local autoreactive plasma cell differentiation in joint biopsies captured from untreated early RA. Hence, plasma cell niches are not a consequence of chronic inflammation, but are already present at the time of diagnosis.", "doi": "10.1038/s41598-022-15293-5", "pmid": "35831338", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9279471"}, {"db": "pii", "key": "10.1038/s41598-022-15293-5"}], "notes": [], "created": "2022-08-19T08:38:18.413Z", "modified": "2024-01-16T13:48:35.776Z"}, {"entity": "publication", "iuid": "8b30b2a0bc7d4450858a511d977b85f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b30b2a0bc7d4450858a511d977b85f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b30b2a0bc7d4450858a511d977b85f6"}}, "title": "Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy.", "authors": [{"family": "Novotny", "given": "Andreas", "initials": "A"}, {"family": "Jan", "given": "Kinlan Mehdi Goulwen", "initials": "KMG"}, {"family": "Dierking", "given": "Jan", "initials": "J"}, {"family": "Winder", "given": "Monika", "initials": "M"}], "type": "journal article", "published": "2022-06-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "10952"}, "abstract": "Marine communities undergo rapid changes related to human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between the dominant planktivorous mesopredatory clupeid fish species herring (Clupea harengus) and sprat (Sprattus sprattus) and the rapidly increasing stickleback (Gasterosteus aculeatus) population is assumed to be high. Here, we investigate diet overlap between these three planktivorous fishes in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback, and highlight that rotifers play an important role in this pattern, as a resource that is not being used by the clupeids nor by other zooplankton in spring. We further show that all the diet assessment methods used in this study are consistent, but also that DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback may be supported by the open feeding niche offered by the rotifers.", "doi": "10.1038/s41598-022-15116-7", "pmid": "35768563", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9242992"}, {"db": "pii", "key": "10.1038/s41598-022-15116-7"}, {"db": "Dryad", "key": "10.5061/dryad.vq83bk3vk"}], "notes": [], "created": "2022-08-19T08:38:41.032Z", "modified": "2024-01-16T13:48:36.049Z"}, {"entity": "publication", "iuid": "cc45a385a1484a509a44e7c6f527b9f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc45a385a1484a509a44e7c6f527b9f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc45a385a1484a509a44e7c6f527b9f6"}}, "title": "Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches.", "authors": [{"family": "Lagos", "given": "Amaya Campillay", "initials": "AC"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "Dyrkell", "given": "Fredrik", "initials": "F"}, {"family": "Stegger", "given": "Marc", "initials": "M"}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2022-06-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "10541", "issn-l": "2045-2322"}, "abstract": "Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003-2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0-5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.", "doi": "10.1038/s41598-022-14640-w", "pmid": "35732699", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-022-14640-w"}, {"db": "pmc", "key": "PMC9214674"}], "notes": [], "created": "2022-11-08T07:52:20.067Z", "modified": "2022-11-08T07:55:59.793Z"}, {"entity": "publication", "iuid": "304b49e6219a4beb9a932d515c6e1453", "links": {"self": {"href": "https://publications.scilifelab.se/publication/304b49e6219a4beb9a932d515c6e1453.json"}, "display": {"href": "https://publications.scilifelab.se/publication/304b49e6219a4beb9a932d515c6e1453"}}, "title": "Development of gut microbiota during the first 2 years of life.", "authors": [{"family": "Wernroth", "given": "Mona-Lisa", "initials": "ML"}, {"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Hedman", "given": "Anna M", "initials": "AM"}, {"family": "Hetty", "given": "Susanne", "initials": "S"}, {"family": "Vicenzi", "given": "Silvia", "initials": "S"}, {"family": "Kennedy", "given": "Beatrice", "initials": "B"}, {"family": "Fall", "given": "Katja", "initials": "K"}, {"family": "Svennblad", "given": "Bodil", "initials": "B"}, {"family": "Andolf", "given": "Ellika", "initials": "E"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Theorell-Hagl\u00f6w", "given": "Jenny", "initials": "J"}, {"family": "Nguyen", "given": "Diem", "initials": "D"}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Fall", "given": "Tove", "initials": "T"}], "type": "journal article", "published": "2022-05-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "9080"}, "abstract": "Although development of microbiota in childhood has been linked to chronic immune-related conditions, early childhood determinants of microbiota development have not been fully elucidated. We used 16S rRNA sequencing to analyse faecal and saliva samples from 83 children at four time-points during their first 2 years of life and from their mothers. Our findings confirm that gut microbiota in infants have low diversity and highlight that some properties are shared with the oral microbiota, although inter-individual differences are present. A considerable convergence in gut microbiota composition was noted across the first 2 years of life, towards a more diverse adult-like microbiota. Mode of delivery accounted for some of the inter-individual variation in early childhood, but with a pronounced attenuation over time. Our study extends previous research with further characterization of the major shift in gut microbiota composition during the first 2 years of life.", "doi": "10.1038/s41598-022-13009-3", "pmid": "35641542", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-022-13009-3"}, {"db": "pmc", "key": "PMC9156670"}], "notes": [], "created": "2022-06-03T06:21:52.597Z", "modified": "2024-01-16T13:48:36.379Z"}, {"entity": "publication", "iuid": "6f200a54fb3244019d1dfb36ff5941c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f200a54fb3244019d1dfb36ff5941c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f200a54fb3244019d1dfb36ff5941c2"}}, "title": "Sorafenib and nitazoxanide disrupt mitochondrial function and inhibit regrowth capacity in three-dimensional models of hepatocellular and colorectal carcinoma.", "authors": [{"family": "Ek", "given": "Frida", "initials": "F"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Selvin", "given": "Tove", "initials": "T"}, {"family": "Rudfeldt", "given": "Jakob", "initials": "J"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Senkowski", "given": "Wojciech", "initials": "W"}, {"family": "Brechot", "given": "Christian", "initials": "C"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}], "type": "journal article", "published": "2022-05-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "8943", "issn-l": "2045-2322"}, "abstract": "Quiescent cancer cells in malignant tumors can withstand cell-cycle active treatment and cause cancer spread and recurrence. Three-dimensional (3D) cancer cell models have led to the identification of oxidative phosphorylation (OXPHOS) as a context-dependent vulnerability. The limited treatment options for advanced hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC) metastatic to the liver include the multikinase inhibitors sorafenib and regorafenib. Off-target effects of sorafenib and regorafenib are related to OXPHOS inhibition; however the importance of this feature to the effect on tumor cells has not been investigated in 3D models. We began by assessing global transcriptional responses in monolayer cell cultures, then moved on to multicellular tumor spheroids (MCTS) and tumoroids generated from a CRC patient. Cells were treated with chemotherapeutics, kinase inhibitors, and the OXPHOS inhibitors. Cells grown in 3D cultures were sensitive to the OXPHOS inhibitor nitazoxanide, sorafenib, and regorafenib and resistant to other multikinase inhibitors and chemotherapeutic drugs. Furthermore, nitazoxanide and sorafenib reduced viability, regrowth potential and inhibited mitochondrial membrane potential in an additive manner at clinically relevant concentrations. This study demonstrates that the OXPHOS inhibition caused by sorafenib and regorafenib parallels 3D activity and can be further investigated for new combination strategies.", "doi": "10.1038/s41598-022-12519-4", "pmid": "35624293", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9142582"}, {"db": "pii", "key": "10.1038/s41598-022-12519-4"}], "notes": [], "created": "2025-02-14T13:30:30.505Z", "modified": "2025-02-14T13:30:30.511Z"}, {"entity": "publication", "iuid": "72167cbead244ce59f20da44c13dd8a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72167cbead244ce59f20da44c13dd8a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72167cbead244ce59f20da44c13dd8a6"}}, "title": "Generalisation effects of predictive uncertainty estimation in deep learning for digital pathology.", "authors": [{"family": "Pocevi\u010di\u016bt\u0117", "given": "Milda", "initials": "M"}, {"family": "Eilertsen", "given": "Gabriel", "initials": "G"}, {"family": "Jarkman", "given": "Sofia", "initials": "S"}, {"family": "Lundstr\u00f6m", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2022-05-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "8329", "issn-l": "2045-2322"}, "abstract": "Deep learning (DL) has shown great potential in digital pathology applications. The robustness of a diagnostic DL-based solution is essential for safe clinical deployment. In this work we evaluate if adding uncertainty estimates for DL predictions in digital pathology could result in increased value for the clinical applications, by boosting the general predictive performance or by detecting mispredictions. We compare the effectiveness of model-integrated methods (MC dropout and Deep ensembles) with a model-agnostic approach (Test time augmentation, TTA). Moreover, four uncertainty metrics are compared. Our experiments focus on two domain shift scenarios: a shift to a different medical center and to an underrepresented subtype of cancer. Our results show that uncertainty estimates increase reliability by reducing a model's sensitivity to classification threshold selection as well as by detecting between 70 and 90% of the mispredictions done by the model. Overall, the deep ensembles method achieved the best performance closely followed by TTA.", "doi": "10.1038/s41598-022-11826-0", "pmid": "35585087", "labels": {"AIDA Data Hub": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9117245"}, {"db": "pii", "key": "10.1038/s41598-022-11826-0"}], "notes": [], "created": "2022-12-01T15:39:12.640Z", "modified": "2022-12-01T15:39:12.643Z"}, {"entity": "publication", "iuid": "6cf08a35c1634853b97c4caa33e04b32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cf08a35c1634853b97c4caa33e04b32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cf08a35c1634853b97c4caa33e04b32"}}, "title": "Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.", "authors": [{"family": "Lee", "given": "Hower", "initials": "H"}, {"family": "Marco Salas", "given": "Sergio", "initials": "S"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2022-05-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "7976", "issn-l": "2045-2322"}, "abstract": "Highly multiplexed spatial mapping of transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing chemistry. We benchmark a High Sensitivity Library Preparation Kit from CARTANA that circumvents the reverse transcription needed for cDNA-based in situ sequencing (ISS) via direct RNA detection. We found a fivefold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell clustering. With this increased efficiency, we also found to maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap to other fluorescent in situ hybridization-based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS.", "doi": "10.1038/s41598-022-11534-9", "pmid": "35562352", "labels": {"In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC9106737"}, {"db": "pii", "key": "10.1038/s41598-022-11534-9"}], "notes": [], "created": "2022-11-29T12:36:19.792Z", "modified": "2025-10-17T13:02:17.632Z"}, {"entity": "publication", "iuid": "0e1585b638064c99b51f7e0e203b34c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e1585b638064c99b51f7e0e203b34c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e1585b638064c99b51f7e0e203b34c1"}}, "title": "The impact of digital media on children's intelligence while controlling for genetic differences in cognition and socioeconomic background.", "authors": [{"family": "Sauce", "given": "Bruno", "initials": "B"}, {"family": "Liebherr", "given": "Magnus", "initials": "M"}, {"family": "Judd", "given": "Nicholas", "initials": "N"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}], "type": "journal article", "published": "2022-05-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "7720", "issn-l": "2045-2322"}, "abstract": "Digital media defines modern childhood, but its cognitive effects are unclear and hotly debated. We believe that studies with genetic data could clarify causal claims and correct for the typically unaccounted role of genetic predispositions. Here, we estimated the impact of different types of screen time (watching, socializing, or gaming) on children's intelligence while controlling for the confounding effects of genetic differences in cognition and socioeconomic status. We analyzed 9855 children from the USA who were part of the ABCD dataset with measures of intelligence at baseline (ages 9-10) and after two years. At baseline, time watching (r = - 0.12) and socializing (r = - 0.10) were negatively correlated with intelligence, while gaming did not correlate. After two years, gaming positively impacted intelligence (standardized \u03b2 = + 0.17), but socializing had no effect. This is consistent with cognitive benefits documented in experimental studies on video gaming. Unexpectedly, watching videos also benefited intelligence (standardized \u03b2 = + 0.12), contrary to prior research on the effect of watching TV. Although, in a posthoc analysis, this was not significant if parental education (instead of SES) was controlled for. Broadly, our results are in line with research on the malleability of cognitive abilities from environmental factors, such as cognitive training and the Flynn effect.", "doi": "10.1038/s41598-022-11341-2", "pmid": "35545630", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9095723"}, {"db": "pii", "key": "10.1038/s41598-022-11341-2"}], "notes": [], "created": "2022-11-25T08:08:47.964Z", "modified": "2022-11-25T08:08:47.967Z"}, {"entity": "publication", "iuid": "f1569994a6fe4b18b34353ab4833f934", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1569994a6fe4b18b34353ab4833f934.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1569994a6fe4b18b34353ab4833f934"}}, "title": "A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy.", "authors": [{"family": "Sun", "given": "Haipeng", "initials": "H"}, {"family": "Yamada", "given": "Pamella", "initials": "P"}, {"family": "Paetow", "given": "Alexandra", "initials": "A"}, {"family": "Chan", "given": "Michael", "initials": "M"}, {"family": "Arslan", "given": "Alan", "initials": "A"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Dominguez-Bello", "given": "Maria Gloria", "initials": "MG"}, {"family": "Young", "given": "Bruce K", "initials": "BK"}], "type": "journal article", "published": "2022-05-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "7509"}, "abstract": "Dietary whole grain consumption has been postulated to have metabolic benefits. The purpose of this study was to compare a pregnancy diet containing 75% of total carbohydrates as refined grains with a diet of 75% of total carbohydrates as whole grains for pregnancy outcomes and effects on the microbiome. Gestational weight gain, glucose tolerance and newborn outcomes were measured on 248 enrolled compliant women from whom a subset of 103 women consented to give 108 vaginal and 109 anal swabs. The data presented here are limited to the patients from whom the vaginal and anal swabs were obtained in order to study the microbiome. A microbiome-16SrRNA survey-was characterized in these samples. Samples and measurements were obtained at the first obstetrical visit, before beginning a prescribed diet (T1-baseline) and after 17-32 weeks on the prescribed diet (T3). Food frequency questionnaires and total plasma alkylresorcinols were used as a measure of whole grain consumption. There were no dietary differences in maternal weight gain, birth weight, or glucose tolerance test. Mothers consuming the whole grains diet showed a trend of gestational decrease in vaginal bacterial alpha diversity, with increasing Lactobacillus-dominance. No significant difference was observed for the anal microbiome. The results suggest that diet modulations of the vaginal microbiome during gestation may have important implications for maternal and neonatal health and in the intergenerational transfer of maternal microbiome. Trial registration: ClinicalTrials.gov Identifier: NCT03232762.", "doi": "10.1038/s41598-022-11571-4", "pmid": "35525865", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9079079"}, {"db": "pii", "key": "10.1038/s41598-022-11571-4"}, {"db": "ClinicalTrials.gov", "key": "NCT03232762"}], "notes": [], "created": "2022-12-05T08:24:06.732Z", "modified": "2023-05-24T05:50:16.155Z"}, {"entity": "publication", "iuid": "cf56fb5adbf444f7b60078ad7e8dcdb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf56fb5adbf444f7b60078ad7e8dcdb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf56fb5adbf444f7b60078ad7e8dcdb3"}}, "title": "Age and sex effects across the blood proteome after ionizing radiation exposure can bias biomarker screening and risk assessment.", "authors": [{"family": "Langen", "given": "Britta", "initials": "B"}, {"family": "Vorontsov", "given": "Egor", "initials": "E"}, {"family": "Spetz", "given": "Johan", "initials": "J"}, {"family": "Swanpalmer", "given": "John", "initials": "J"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2022-04-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "7000"}, "abstract": "Molecular biomarkers of ionizing radiation (IR) exposure are a promising new tool in various disciplines: they can give necessary information for adaptive treatment planning in cancer radiotherapy, enable risk projection for radiation-induced survivorship diseases, or facilitate triage and intervention in radiation hazard events. However, radiation biomarker discovery has not yet resolved the most basic features of personalized medicine: age and sex. To overcome this critical bias in biomarker identification, we quantitated age and sex effects and assessed their relevance in the radiation response across the blood proteome. We used high-throughput mass spectrometry on blood plasma collected 24 h after 0.5 Gy total body irradiation (15 MV nominal photon energy) from male and female C57BL/6 N mice at juvenile (7-weeks-old) or adult (18-weeks-old) age. We also assessed sex and strain effects using juvenile male and female BALB/c nude mice. We showed that age and sex created significant effects in the proteomic response regarding both extent and functional quality of IR-induced responses. Furthermore, we found that age and sex effects appeared non-linear and were often end-point specific. Overall, age contributed more to differences in the proteomic response than sex, most notably in immune responses, oxidative stress, and apoptotic cell death. Interestingly, sex effects were pronounced for DNA damage and repair pathways and associated cellular outcome (pro-survival vs. pro-apoptotic). Only one protein (AHSP) was identified as a potential general biomarker candidate across age and sex, while GMNN, REG3B, and SNCA indicated some response similarity across age. This low yield advocated that unisex or uniage biomarker screening approaches are not feasible. In conclusion, age- and sex-specific screening approaches should be implemented as standard protocol to ensure robustness and diagnostic power of biomarker candidates. Bias-free molecular biomarkers are a necessary progression towards personalized medicine and integral for advanced adaptive cancer radiotherapy and risk assessment.", "doi": "10.1038/s41598-022-10271-3", "pmid": "35487913", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9055069"}, {"db": "pii", "key": "10.1038/s41598-022-10271-3"}], "notes": [], "created": "2023-03-07T14:35:10.669Z", "modified": "2024-01-16T13:46:29.250Z"}, {"entity": "publication", "iuid": "ce377a5db8b74d6ab6f235cdeeecd39a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce377a5db8b74d6ab6f235cdeeecd39a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce377a5db8b74d6ab6f235cdeeecd39a"}}, "title": "Wastewater effluent affects behaviour and metabolomic endpoints in damselfly larvae.", "authors": [{"family": "Sp\u00e4th", "given": "Jana", "initials": "J"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "McCallum", "given": "Erin", "initials": "E"}, {"family": "Cerveny", "given": "Daniel", "initials": "D"}, {"family": "Nording", "given": "Malin L", "initials": "ML"}, {"family": "Brodin", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2022-04-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "6830", "issn-l": "2045-2322"}, "abstract": "Wastewater treatment plant effluents have been identified as a major contributor to increasing anthropogenic pollution in aquatic environments worldwide. Yet, little is known about the potentially adverse effects of wastewater treatment plant effluent on aquatic invertebrates. In this study, we assessed effects of wastewater effluent on the behaviour and metabolic profiles of damselfly larvae (Coenagrion hastulatum), a common aquatic invertebrate species. Four key behavioural traits: activity, boldness, escape response, and foraging (traits all linked tightly to individual fitness) were studied in larvae before and after one week of exposure to a range of effluent dilutions (0, 50, 75, 100%). Effluent exposure reduced activity and foraging, but generated faster escape response. Metabolomic analyses via targeted and non-targeted mass spectrometry methods revealed that exposure caused significant changes to 14 individual compounds (4 amino acids, 3 carnitines, 3 lysolipids, 1 peptide, 2 sugar acids, 1 sugar). Taken together, these compound changes indicate an increase in protein metabolism and oxidative stress. Our findings illustrate that wastewater effluent can affect both behavioural and physiological traits of aquatic invertebrates, and as such might pose an even greater threat to aquatic ecosystems than previously assumed. More long-term studies are now needed evaluate if these changes are linked to adverse effects on fitness. The combination of behavioural and metabolomic assessments provide a promising tool for detecting effects of wastewater effluent, on multiple biological levels of organisation, in aquatic ecosystems.", "doi": "10.1038/s41598-022-10805-9", "pmid": "35474093", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9042914"}, {"db": "pii", "key": "10.1038/s41598-022-10805-9"}], "notes": [], "created": "2022-12-05T08:15:14.624Z", "modified": "2025-10-17T13:03:15.130Z"}, {"entity": "publication", "iuid": "bc870a45f0344e1e8e4a7fe8930a4fcc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc870a45f0344e1e8e4a7fe8930a4fcc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc870a45f0344e1e8e4a7fe8930a4fcc"}}, "title": "scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation.", "authors": [{"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Annett", "given": "Alva", "initials": "A"}, {"family": "Wiman", "given": "Ann-Christin", "initials": "AC"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}], "type": "journal article", "published": "2022-04-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "5772", "issn-l": "2045-2322"}, "abstract": "DNA methylation is a central epigenetic mark that has diverse roles in gene regulation, development, and maintenance of genome integrity. 5 methyl cytosine (5mC) can be interrogated at base resolution in single cells by using bisulfite sequencing (scWGBS). Several different scWGBS strategies have been described in recent years to study DNA methylation in single cells. However, there remain limitations with respect to cost-efficiency and yield. Herein, we present a new development in the field of scWGBS library preparation; single cell Splinted Ligation Adapter Tagging (scSPLAT). scSPLAT employs a pooling strategy to facilitate sample preparation at a higher scale and throughput than previously possible. We demonstrate the accuracy and robustness of the method by generating data from 225 single K562 cells and from 309 single liver nuclei and compare scSPLAT against other scWGBS methods.", "doi": "10.1038/s41598-022-09798-2", "pmid": "35388090", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Single cell": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Microbial Single Cell Genomics": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8986790"}, {"db": "pii", "key": "10.1038/s41598-022-09798-2"}], "notes": [], "created": "2022-05-09T11:05:24.613Z", "modified": "2024-01-16T13:48:37.083Z"}, {"entity": "publication", "iuid": "d5b3ee7e27ba471da937ed5d5474ecf0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5b3ee7e27ba471da937ed5d5474ecf0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5b3ee7e27ba471da937ed5d5474ecf0"}}, "title": "An inverse association between plasma benzoxazinoid metabolites and PSA after rye intake in men with prostate cancer revealed with a new method.", "authors": [{"family": "Nordin", "given": "Elise", "initials": "E"}, {"family": "Steffensen", "given": "Stine K", "initials": "SK"}, {"family": "Laursen", "given": "Bente B", "initials": "BB"}, {"family": "Andersson", "given": "Sven-Olof", "initials": "S"}, {"family": "Johansson", "given": "Jan-Erik", "initials": "J"}, {"family": "\u00c5man", "given": "Per", "initials": "P"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Borre", "given": "Michael", "initials": "M"}, {"family": "St\u00e6rk", "given": "Dan", "initials": "D"}, {"family": "Hanhineva", "given": "Kati", "initials": "K"}, {"family": "Fomsgaard", "given": "Inge S", "initials": "IS"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2022-03-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "5260"}, "abstract": "Prostate cancer (PC) is a common cancer among men, and preventive strategies are warranted. Benzoxazinoids (BXs) in rye have shown potential against PC in vitro but human studies are lacking. The aim was to establish a quantitative method for analysis of BXs and investigate their plasma levels after a whole grain/bran rye vs refined wheat intervention, as well as exploring their association with PSA, in men with PC. A quantitative method for analysis of 22 BXs, including novel metabolites identified by mass spectrometry and NMR, was established, and applied to plasma samples from a randomized crossover study where patients with indolent PC (n = 17) consumed 485 g whole grain rye/rye bran or fiber supplemented refined wheat daily for 6 wk. Most BXs were significantly higher in plasma after rye (0.3-19.4 nmol/L in plasma) vs. refined wheat (0.05-2.9 nmol/L) intake. HBOA-glc, 2-HHPAA, HBOA-glcA, 2-HPAA-glcA were inversely correlated to PSA in plasma (p < 0.04). To conclude, BXs in plasma, including metabolites not previously analyzed, were quantified. BX metabolites were significantly higher after rye vs refined wheat consumption. Four BX-related metabolites were inversely associated with PSA, which merits further investigation.", "doi": "10.1038/s41598-022-08856-z", "pmid": "35347164", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8960836"}, {"db": "pii", "key": "10.1038/s41598-022-08856-z"}], "notes": [], "created": "2022-12-05T08:24:14.476Z", "modified": "2023-04-13T09:03:21.458Z"}, {"entity": "publication", "iuid": "56ad17fa213342238981a37ec38ba045", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56ad17fa213342238981a37ec38ba045.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56ad17fa213342238981a37ec38ba045"}}, "title": "Elevated mid-pregnancy plasma levels of angiotensin-converting enzyme 2 in women prior to the development of preeclampsia.", "authors": [{"family": "Junus", "given": "Katja", "initials": "K"}, {"family": "Bj\u00f6rk Ragnarsd\u00f3ttir", "given": "Inger", "initials": "I"}, {"family": "Nordl\u00f6f Callbo", "given": "Paliz", "initials": "P"}, {"family": "Bergman", "given": "Lina", "initials": "L"}, {"family": "Lager", "given": "Susanne", "initials": "S"}, {"family": "Wikstr\u00f6m", "given": "Anna-Karin", "initials": "AK"}], "type": "journal article", "published": "2022-03-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "4109", "issn-l": "2045-2322"}, "abstract": "Preeclampsia and cardiovascular disease (CVD) share multiple features and risk factors. Circulating angiotensin-converting enzyme 2 (ACE2) is increased in CVD and mediates SARS-CoV-2 entry into host cells, causing COVID-19 infection. The role of ACE2 in preeclampsia pathophysiology is unknown. We hypothesized that circulating ACE2 is increased in mid-pregnancy in women later developing preeclampsia. We included 296 women later developing preeclampsia (cases) and 333 women with a continuous healthy pregnancy (controls). Circulating ACE2 was measured with an immunoassay based on proximity extension assay technology, with levels being expressed as relative quantification on a log2 scale. Median (interquartile range) ACE2 levels were higher in cases than in controls; 3.84 (3.50-4.24) vs. 3.72 (3.45-4.04), p = 0.002. Adjusted logistic regression models showed a 60% increased risk for later development of preeclampsia with one unit elevation of ACE2 (adjusted odds ratio (aOR) 1.60, 95% confidence intervals (CI) 1.17-2.18). Preterm preeclampsia (diagnosis before 37 gestational weeks, n = 97) seemed to have a stronger ACE2 association than term preeclampsia, n = 199 (aORs, 95% Cis 2.14, 1.15-3.96 and 1.52, 1.04-2.23, respectively). Circulating ACE2 is increased at mid-pregnancy in women later developing preeclampsia, particularly preterm preeclampsia. Thus, our finding indicates a partly shared pathophysiological pathway between preeclampsia and CVD.", "doi": "10.1038/s41598-022-08081-8", "pmid": "35260736", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8902901"}, {"db": "pii", "key": "10.1038/s41598-022-08081-8"}], "notes": [], "created": "2022-12-02T08:52:16.795Z", "modified": "2022-12-02T08:52:16.799Z"}, {"entity": "publication", "iuid": "246d84f9602246ebba032a85afb84833", "links": {"self": {"href": "https://publications.scilifelab.se/publication/246d84f9602246ebba032a85afb84833.json"}, "display": {"href": "https://publications.scilifelab.se/publication/246d84f9602246ebba032a85afb84833"}}, "title": "Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics.", "authors": [{"family": "Olausson", "given": "Josefin", "initials": "J"}, {"family": "Brunet", "given": "Sofia", "initials": "S"}, {"family": "Vracar", "given": "Diana", "initials": "D"}, {"family": "Tian", "given": "Yarong", "initials": "Y"}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Meghadri", "given": "Sri Harsha", "initials": "SH"}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Lind Karlberg", "given": "Maria", "initials": "M"}, {"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Tang", "given": "Ka-Wei", "initials": "K"}], "type": "journal article", "published": "2022-03-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "3378"}, "abstract": "Infection in the central nervous system is a severe condition associated with high morbidity and mortality. Despite ample testing, the majority of encephalitis and meningitis cases remain undiagnosed. Metagenomic sequencing of cerebrospinal fluid has emerged as an unbiased approach to identify rare microbes and novel pathogens. However, several major hurdles remain, including establishment of individual limits of detection, removal of false positives and implementation of universal controls. Twenty-one cerebrospinal fluid samples, in which a known pathogen had been positively identified by available clinical techniques, were subjected to metagenomic DNA sequencing. Fourteen samples contained minute levels of Epstein-Barr virus. The detection threshold for each sample was calculated by using the total leukocyte content in the sample and environmental contaminants found in the bioinformatic classifiers. Virus sequences were detected in all ten samples, in which more than one read was expected according to the calculations. Conversely, no viral reads were detected in seven out of eight samples, in which less than one read was expected according to the calculations. False positive pathogens of computational or environmental origin were readily identified, by using a commonly available cell control. For bacteria, additional filters including a comparison between classifiers removed the remaining false positives and alleviated pathogen identification. Here we show a generalizable method for identification of pathogen species using DNA metagenomic sequencing. The choice of bioinformatic method mainly affected the efficiency of pathogen identification, but not the sensitivity of detection. Identification of pathogens requires multiple filtering steps including read distribution, sequence diversity and complementary verification of pathogen reads.", "doi": "10.1038/s41598-022-07260-x", "pmid": "35233021", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8888594"}, {"db": "pii", "key": "10.1038/s41598-022-07260-x"}], "notes": [], "created": "2022-12-02T12:22:05.047Z", "modified": "2024-01-16T13:48:37.301Z"}, {"entity": "publication", "iuid": "09ecf1316a10492d86992a3bf48be8a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09ecf1316a10492d86992a3bf48be8a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09ecf1316a10492d86992a3bf48be8a2"}}, "title": "Salivary biomarkers in children with juvenile idiopathic arthritis and healthy age-matched controls: a prospective observational study.", "authors": [{"family": "Collin", "given": "Malin", "initials": "M"}, {"family": "Ernberg", "given": "Malin", "initials": "M"}, {"family": "Christidis", "given": "Nikolaos", "initials": "N"}, {"family": "Hedenberg-Magnusson", "given": "Britt", "initials": "B"}], "type": "journal article", "published": "2022-02-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "3240", "issn-l": "2045-2322"}, "abstract": "Monitoring the immune system's regulation and signaling using saliva could be of interest for clinicians and researchers. Saliva, a biofluid with close exchange with serum, is influenced by circadian variance and oral factors such as masticatory function. This study investigated the detectability and concentration of cytokines and chemokines in saliva in children with juvenile idiopathic arthritis (JIA) as well as saliva flow and the influence of orofacial pain on saliva flow. Of the 60 participants (7-14 years old) enrolled, 30 had a diagnosis of JIA and active disease, and 30 were sex- and age-matched healthy controls. Demographic data and three validated questions regarding presence of orofacial pain and dysfunction were recorded. Stimulated whole saliva was collected and analyzed using a customized R&D bead-based immunoassay with 21 targeted biomarkers. Fourteen of these were detectable and showed similar levels in both children with JIA and controls: TNF-alpha, TNFRSF1B, MMP-2, MMP-3, IL-1alpha, IL-1beta, IL-6R alpha, IL-8, S100A8, CCL2, CCL3, IL-10, CCL11, and CXCL9. In addition, there was no difference in salivary flow rate between groups, but there was an association between orofacial pain and reduced saliva flow rate for both groups.Trial registration: ClinicalTrials.gov Protocol id: 2010/2089-31/2.", "doi": "10.1038/s41598-022-07233-0", "pmid": "35217774", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8881454"}, {"db": "pii", "key": "10.1038/s41598-022-07233-0"}], "notes": [], "created": "2022-12-05T16:36:49.798Z", "modified": "2022-12-05T16:36:49.800Z"}, {"entity": "publication", "iuid": "e81eb31d821a40828379bb55f47f3f19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e81eb31d821a40828379bb55f47f3f19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e81eb31d821a40828379bb55f47f3f19"}}, "title": "Age-related long-term response in rat thyroid tissue and plasma after internal low dose exposure to 131I.", "authors": [{"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Rudqvist", "given": "Nils-Petter", "initials": "NP"}, {"family": "Spetz", "given": "Johan", "initials": "J"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Langen", "given": "Britta", "initials": "B"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2022-02-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "2107", "issn-l": "2045-2322"}, "abstract": "131I is used clinically for therapy, and may be released during nuclear accidents. After the Chernobyl accident papillary thyroid carcinoma incidence increased in children, but not adults. The aims of this study were to compare 131I irradiation-dependent differences in RNA and protein expression in the thyroid and plasma of young and adult rats, and identify potential age-dependent biomarkers for 131I exposure. Twelve young (5 weeks) and twelve adult Sprague Dawley rats (17 weeks) were i.v. injected with 50 kBq 131I (absorbed dose to thyroid = 0.1 Gy), and sixteen unexposed age-matched rats were used as controls. The rats were killed 3-9 months after administration. Microarray analysis was performed using RNA from thyroid samples, while LC-MS/MS analysis was performed on proteins extracted from thyroid tissue and plasma. Canonical pathways, biological functions and upstream regulators were analysed for the identified transcripts and proteins. Distinct age-dependent differences in gene and protein expression were observed. Novel biomarkers for thyroid 131I exposure were identified: (PTH), age-dependent dose response (CA1, FTL1, PVALB (youngsters) and HSPB6 (adults)), thyroid function (Vegfb (adults)). Further validation using clinical samples are needed to explore the role of the identified biomarkers.", "doi": "10.1038/s41598-022-06071-4", "pmid": "35136135", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8825795"}, {"db": "pii", "key": "10.1038/s41598-022-06071-4"}], "notes": [], "created": "2023-03-07T14:34:17.761Z", "modified": "2024-01-16T13:46:29.621Z"}, {"entity": "publication", "iuid": "4a6ebd48c6af40f79918a31bb57a0488", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a6ebd48c6af40f79918a31bb57a0488.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a6ebd48c6af40f79918a31bb57a0488"}}, "title": "The role of caspase-1, caspase-4 and NLRP3 in regulating the host cell response evoked by uropathogenic Escherichia coli.", "authors": [{"family": "Lindblad", "given": "Anna", "initials": "A"}, {"family": "Johansson", "given": "Charlotte", "initials": "C"}, {"family": "Persson", "given": "Katarina", "initials": "K"}, {"family": "Demirel", "given": "Isak", "initials": "I"}], "type": "journal article", "published": "2022-02-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "2005", "issn-l": "2045-2322"}, "abstract": "The inflammasome-associated proteins caspase-1, caspase-4 and NLRP3 have been emphasised to be essential in the host cell response during urinary tract infection (UTI) by regulating IL-1\u03b2 release. Our aim was to investigate how the inflammasome-associated proteins regulate the cell response of bladder epithelial cells during infection with uropathogenic Escherichia coli (UPEC). Human bladder epithelial cells (5637) and CRISPR/Cas9 generated caspase-1, caspase-4 and NLRP3 knockdown cells were stimulated with the UPEC strain CFT073. Using Olink proteomics and real time RT-PCR, we showed that caspase-1, caspase-4 and NLRP3 are vital for the expression of many inflammatory genes and proteins from bladder epithelial cells. When investigating the effect of inflammasome-associated proteins on neutrophils, we found that conditioned medium from UPEC-infected caspase-4 knockdown cells significantly increased phagocytosis of CFT073 and significantly decreased ROS production from neutrophils. In contrast, conditioned medium from UPEC-infected NLRP3 knockdown cells significantly decreased the phagocytosis of CFT073 and significantly increased the ROS production from neutrophils. In conclusion, we showed that the inflammasome-associated proteins contribute to the host cell response during UPEC infection.", "doi": "10.1038/s41598-022-06052-7", "pmid": "35132157", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8821701"}, {"db": "pii", "key": "10.1038/s41598-022-06052-7"}], "notes": [], "created": "2023-11-29T19:13:01.325Z", "modified": "2023-11-29T19:13:01.338Z"}, {"entity": "publication", "iuid": "f771c137a5d34760841b0766852196d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f771c137a5d34760841b0766852196d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f771c137a5d34760841b0766852196d3"}}, "title": "The involvement of cyclotides in mutual interactions of violets and the two-spotted spider mite.", "authors": [{"family": "Slazak", "given": "Blazej", "initials": "B"}, {"family": "J\u0119drzejska", "given": "Aleksandra", "initials": "A"}, {"family": "Badyra", "given": "Bogna", "initials": "B"}, {"family": "Sybilska", "given": "Anna", "initials": "A"}, {"family": "Lewandowski", "given": "Mariusz", "initials": "M"}, {"family": "Kozak", "given": "Marcin", "initials": "M"}, {"family": "Kapusta", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U"}, {"family": "Kie\u0142kiewicz", "given": "Ma\u0142gorzata", "initials": "M"}], "type": "comparative study", "published": "2022-02-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "1914", "issn-l": "2045-2322"}, "abstract": "Plants employ different chemicals to protect themselves from herbivory. These defenses may be constitutive or triggered by stress. The chemicals can be toxic, act as repellents, phagosuppressants and/or phago-deterrents. The two-spotted spider mite (Tetranychus urticae) is a generalist arthropod herbivorous pest and its feeding causes extensive damage both to crops and wild plants. Cyclotides are cyclic peptides involved in host-plant defenses. A single Viola sp. can produce more than a hundred cyclotides with different biological activities and roles. The organ and tissue specific cyclotide patterns change over the seasons and/or with environment, but the role of biotic/abiotic stress in shaping them remains unclear. Here, we demonstrate the involvement of cyclotides in mutual interactions between violets and mites. We used immunohistochemistry and mass spectrometry imaging to show the ingested cyclotides in T. urticae and assess the Viola odorata response to mite feeding. Moreover, to assess how mites are affected by feeding on violets, acceptance and reproductive performance was compared between Viola uliginosa, V. odorata and Phaseolus vulgaris. We demonstrate that cyclotides had been taken in by mites feeding on the violets. The ingested peptides were found in contact with epithelial cells of the mite digestive system, in the fecal matter, feces, ovary and eggs. Mites preferred common bean plants (P. vulgaris) to any of the violet species; the latter affected their reproductive performance. The production of particular cyclotides in V. odorata (denoted by molecular weights: 2979, 3001, 3017, 3068, 3084, 3123) was activated by mite feeding and their levels were significantly elevated compared to the control after 5 and 21 days of infestation. Specific cyclotides may affect mites by being indigestible or through direct interaction with cells in the mite digestive tract and reproductive organs. A group of particular peptides in V. odorata appears to be involved in defense response against herbivores.", "doi": "10.1038/s41598-022-05461-y", "pmid": "35115562", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-022-05461-y"}, {"db": "pmc", "key": "PMC8814195"}], "notes": [], "created": "2022-11-16T14:02:33.931Z", "modified": "2022-11-16T14:02:33.934Z"}, {"entity": "publication", "iuid": "39f5460c30fa4f17ab3d458eec388e09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39f5460c30fa4f17ab3d458eec388e09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39f5460c30fa4f17ab3d458eec388e09"}}, "title": "Overexpression of the SARS-CoV-2 receptor angiotensin converting enzyme 2 in cardiomyocytes of failing hearts.", "authors": [{"family": "Vukusic", "given": "Kristina", "initials": "K"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Muslimovic", "given": "Aida", "initials": "A"}, {"family": "Jonsson", "given": "Marianne", "initials": "M"}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G"}, {"family": "Lindahl", "given": "Anders", "initials": "A"}, {"family": "Sandstedt", "given": "Joakim", "initials": "J"}, {"family": "Hammarsten", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2022-01-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "965", "issn-l": "2045-2322"}, "abstract": "Hospitalized patients who die from Covid-19 often have pre-existing heart disease. The SARS-CoV-2 virus is dependent on the ACE2 receptor to be able to infect cells. It is possible that the strong link between cardiovascular comorbidities and a poor outcome following a SARS-CoV-2 infection is sometimes due to viral myocarditis. The aim was to examine the expression of ACE2 in normal hearts and hearts from patients with terminal heart failure. The ACE2 expression was measured by global quantitative proteomics and RT-qPCR in left ventricular (LV) tissue from explanted hearts. Immunohistochemistry was used to examine ACE2 expression in cardiomyocytes, fibroblasts and endothelial cells. In total, tissue from 14 organ donors and 11 patients with terminal heart failure were included. ACE2 expression was 2.6 times higher in 4 hearts from patients with terminal heart failure compared with 6 healthy donor hearts. The results were confirmed by immunohistochemistry where more than half of cardiomyocytes or fibroblasts showed expression of ACE2 in hearts from patients with terminal heart failure. In healthy donor hearts ACE2 was not expressed or found in few fibroblasts. A small subpopulation of endothelial cells expressed ACE2 in both groups. Upregulated ACE2 expression in cardiomyocytes may increase the risk of SARS-CoV-2 myocarditis in patients with heart failure.", "doi": "10.1038/s41598-022-04956-y", "pmid": "35046458", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8770525"}, {"db": "pii", "key": "10.1038/s41598-022-04956-y"}], "notes": [], "created": "2023-03-07T14:31:46.125Z", "modified": "2024-01-16T13:46:29.694Z"}, {"entity": "publication", "iuid": "5fc6905e6f4249c1a04c4e11cce0d197", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5fc6905e6f4249c1a04c4e11cce0d197.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5fc6905e6f4249c1a04c4e11cce0d197"}}, "title": "Global CO2 fertilization of Sphagnum peat mosses via suppression of photorespiration during the twentieth century.", "authors": [{"family": "Serk", "given": "Henrik", "initials": "H"}, {"family": "Nilsson", "given": "Mats B", "initials": "MB"}, {"family": "Bohlin", "given": "Elisabet", "initials": "E"}, {"family": "Ehlers", "given": "Ina", "initials": "I"}, {"family": "Wieloch", "given": "Thomas", "initials": "T"}, {"family": "Olid", "given": "Carolina", "initials": "C"}, {"family": "Grover", "given": "Samantha", "initials": "S"}, {"family": "Kalbitz", "given": "Karsten", "initials": "K"}, {"family": "Limpens", "given": "Juul", "initials": "J"}, {"family": "Moore", "given": "Tim", "initials": "T"}, {"family": "M\u00fcnchberger", "given": "Wiebke", "initials": "W"}, {"family": "Talbot", "given": "Julie", "initials": "J"}, {"family": "Wang", "given": "Xianwei", "initials": "X"}, {"family": "Knorr", "given": "Klaus-Holger", "initials": "KH"}, {"family": "Pancotto", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}], "type": "journal article", "published": "2021-12-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24517", "issn-l": "2045-2322"}, "abstract": "Natural peatlands contribute significantly to global carbon sequestration and storage of biomass, most of which derives from Sphagnum peat mosses. Atmospheric CO2 levels have increased dramatically during the twentieth century, from 280 to > 400 ppm, which has affected plant carbon dynamics. Net carbon assimilation is strongly reduced by photorespiration, a process that depends on the CO2 to O2 ratio. Here we investigate the response of the photorespiration to photosynthesis ratio in Sphagnum mosses to recent CO2 increases by comparing deuterium isotopomers of historical and contemporary Sphagnum tissues collected from 36 peat cores from five continents. Rising CO2 levels generally suppressed photorespiration relative to photosynthesis but the magnitude of suppression depended on the current water table depth. By estimating the changes in water table depth, temperature, and precipitation during the twentieth century, we excluded potential effects of these climate parameters on the observed isotopomer responses. Further, we showed that the photorespiration to photosynthesis ratio varied between Sphagnum subgenera, indicating differences in their photosynthetic capacity. The global suppression of photorespiration in Sphagnum suggests an increased net primary production potential in response to the ongoing rise in atmospheric CO2, in particular for mire structures with intermediate water table depths.", "doi": "10.1038/s41598-021-02953-1", "pmid": "34972838", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-02953-1"}, {"db": "pmc", "key": "PMC8720097"}], "notes": [], "created": "2022-01-11T11:32:41.486Z", "modified": "2025-10-17T13:03:55.236Z"}, {"entity": "publication", "iuid": "651f205cc503452bad97d24143804bae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/651f205cc503452bad97d24143804bae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/651f205cc503452bad97d24143804bae"}}, "title": "Biased TCR gene usage in citrullinated Tenascin C specific T-cells in rheumatoid arthritis.", "authors": [{"family": "Sharma", "given": "Ravi K", "initials": "RK"}, {"family": "Boddul", "given": "Sanjay V", "initials": "SV"}, {"family": "Yoosuf", "given": "Niyaz", "initials": "N"}, {"family": "Turcinov", "given": "Sara", "initials": "S"}, {"family": "Dubnovitsky", "given": "Anatoly", "initials": "A"}, {"family": "Kozhukh", "given": "Genadiy", "initials": "G"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F"}, {"family": "Kwok", "given": "William W", "initials": "WW"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}], "type": "journal article", "published": "2021-12-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24512", "issn-l": "2045-2322"}, "abstract": "We aimed to search for common features in the autoreactive T cell receptor (TCR) repertoire in patients with rheumatoid arthritis (RA), focusing on the newly identified candidate antigen citrullinated Tenascin C (cit-TNC). Mononuclear cells from peripheral blood or synovial fluid of eight RA-patients positive for the RA-associated HLA-DRB1*04:01 allele were in-vitro cultured with recently identified citrullinated peptides from Tenascin C. Antigen-specific T cells were isolated using peptide-HLA tetramer staining and subsequently single-cell sequenced for paired alpha/beta TCR analyses by bioinformatic tools. TCRs were re-expressed for further studies of antigen-specificity and T cell responses. Autoreactive T cell lines could be grown out from both peripheral blood and synovial fluid. We demonstrate the feasibility of retrieving true autoreactive TCR sequences by validating antigen-specificity in T cell lines with re-expressed TCRs. One of the Tenascin C peptides, cit-TNC22, gave the most robust T cell responses including biased TCR gene usage patterns. The shared TCR-beta chain signature among the cit-TNC22-specific TCRs was evident in blood and synovial fluid of different patients. The identification of common elements in the autoreactive TCR repertoire gives promise to the possibility of both immune monitoring of the autoimmune components in RA and of future antigen- or TCR-targeted specific intervention in subsets of patients.", "doi": "10.1038/s41598-021-04291-8", "pmid": "34972837", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-04291-8"}, {"db": "pmc", "key": "PMC8720095"}], "notes": [], "created": "2022-03-29T13:47:59.715Z", "modified": "2022-03-29T13:47:59.743Z"}, {"entity": "publication", "iuid": "96c83998b0094d1fb65b42c04148fdd6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96c83998b0094d1fb65b42c04148fdd6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96c83998b0094d1fb65b42c04148fdd6"}}, "title": "Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera).", "authors": [{"family": "Ghanavi", "given": "Hamid Reza", "initials": "HR", "orcid": "0000-0003-1029-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfd99c0fbe0945aa99ff793866bab3fc.json"}}, {"family": "Twort", "given": "Victoria G", "initials": "VG", "orcid": "0000-0002-5581-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e16117b957446a1bd9eee7200b22f09.json"}}, {"family": "Duplouy", "given": "Anne", "initials": "A", "orcid": "0000-0002-7147-5199", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dccb9fe8c2b4308941b69b2ae87535f.json"}}], "type": "journal article", "published": "2021-12-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24499", "issn-l": "2045-2322"}, "abstract": "Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.", "doi": "10.1038/s41598-021-03327-3", "pmid": "34969947", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-03327-3"}, {"db": "pmc", "key": "PMC8718532"}], "notes": [], "created": "2022-11-09T15:49:25.018Z", "modified": "2024-01-16T13:48:37.959Z"}, {"entity": "publication", "iuid": "6dce5b8f2ec844a4b64c2a4d04bbbe5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dce5b8f2ec844a4b64c2a4d04bbbe5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dce5b8f2ec844a4b64c2a4d04bbbe5e"}}, "title": "CD105+CD90+CD13+ identifies a clonogenic subset of adventitial lung fibroblasts.", "authors": [{"family": "Kadefors", "given": "M\u00e5ns", "initials": "M"}, {"family": "Rolandsson Enes", "given": "Sara", "initials": "S"}, {"family": "\u00c5hrman", "given": "Emma", "initials": "E"}, {"family": "Michalikov\u00e1", "given": "Barbora", "initials": "B"}, {"family": "L\u00f6fdahl", "given": "Anna", "initials": "A"}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G"}, {"family": "Scheding", "given": "Stefan", "initials": "S"}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G"}], "type": "journal article", "published": "2021-12-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24417", "issn-l": "2045-2322"}, "abstract": "Mesenchymal cells are important components of specified niches in the lung, and can mediate a wide range of processes including tissue regeneration and repair. Dysregulation of these processes can lead to improper remodeling of tissue as observed in several lung diseases. The mesenchymal cells responsible remain poorly described, partially due to the heterogenic nature of the mesenchymal compartment and the absence of appropriate markers. Here, we describe that CD105+CD90+ mesenchymal cells can be divided into two populations based on their expression of CD13/aminopeptidase N (CD105+CD90+CD13- and CD105+CD90+CD13+). By prospective isolation using FACS, we show that both these populations give rise to clonogenic fibroblast-like cells, but with an increased clonogenic and proliferative capacity of CD105+CD90+CD13+ cells. Transcriptomic and spatial analysis pinpoints an adventitial fibroblast subset as the origin of CD105+CD90+CD13+ clonogenic mesenchymal cells in human lung.", "doi": "10.1038/s41598-021-03963-9", "pmid": "34952905", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-03963-9"}], "notes": [], "created": "2021-12-27T14:03:52.413Z", "modified": "2021-12-27T14:03:52.419Z"}, {"entity": "publication", "iuid": "9b5f41c85c154d97a689abf4c3ad468b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b5f41c85c154d97a689abf4c3ad468b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b5f41c85c154d97a689abf4c3ad468b"}}, "title": "Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice.", "authors": [{"family": "L\u00f3pez-P\u00e9rez", "given": "Ana", "initials": "A"}, {"family": "Norlin", "given": "Stefan", "initials": "S"}, {"family": "Steneberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Remeseiro", "given": "Silvia", "initials": "S"}, {"family": "Edlund", "given": "Helena", "initials": "H"}, {"family": "H\u00f6rnblad", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2021-12-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24410", "issn-l": "2045-2322"}, "abstract": "AMP-activated protein kinase (AMPK) has an important role in cellular energy homeostasis and has emerged as a promising target for treatment of Type 2 Diabetes (T2D) due to its beneficial effects on insulin sensitivity and glucose homeostasis. O304 is a pan-AMPK activator that has been shown to improve glucose homeostasis in both mouse models of diabetes and in human T2D subjects. Here, we describe the genome-wide transcriptional profile and chromatin landscape of pancreatic islets following O304 treatment of mice fed high-fat diet (HFD). O304 largely prevented genome-wide gene expression changes associated with HFD feeding in CBA mice and these changes were associated with remodelling of active and repressive chromatin marks. In particular, the increased expression of the \u03b2-cell stress marker Aldh1a3 in islets from HFD-mice is completely abrogated following O304 treatment, which is accompanied by loss of active chromatin marks in the promoter as well as distant non-coding regions upstream of the Aldh1a3 gene. Moreover, O304 treatment restored dysfunctional glucose homeostasis as well as expression of key markers associated with \u03b2-cell function in mice with already established obesity. Our findings provide preclinical evidence that O304 is a promising therapeutic compound not only for T2D remission but also for restoration of \u03b2-cell function following remission of T2D diabetes.", "doi": "10.1038/s41598-021-03567-3", "pmid": "34949756", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-03567-3"}, {"db": "pmc", "key": "PMC8702551"}], "notes": [], "created": "2022-03-29T13:48:23.081Z", "modified": "2022-03-29T13:48:23.093Z"}, {"entity": "publication", "iuid": "2580178a81f6434f9c0146ac18759ecc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2580178a81f6434f9c0146ac18759ecc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2580178a81f6434f9c0146ac18759ecc"}}, "title": "Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities.", "authors": [{"family": "Albert", "given": "S\u00e9r\u00e9na", "initials": "S"}, {"family": "Hedberg", "given": "Per", "initials": "P"}, {"family": "Motwani", "given": "Nisha H", "initials": "NH"}, {"family": "Sj\u00f6ling", "given": "Sara", "initials": "S"}, {"family": "Winder", "given": "Monika", "initials": "M"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2021-12-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24033", "issn-l": "2045-2322"}, "abstract": "In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.", "doi": "10.1038/s41598-021-03303-x", "pmid": "34911983", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-03303-x"}, {"db": "pmc", "key": "PMC8674317"}], "notes": [], "created": "2022-03-29T13:48:06.335Z", "modified": "2024-01-16T13:48:37.970Z"}, {"entity": "publication", "iuid": "c9474748c2934ce1a9ff72a666d0ce39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9474748c2934ce1a9ff72a666d0ce39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9474748c2934ce1a9ff72a666d0ce39"}}, "title": "Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2021-12-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "23384", "issn-l": "2045-2322"}, "abstract": "Coastal aquatic systems suffer from nutrient enrichment, which results in accelerated eutrophication effects due to increased microbial metabolic rates. Climate change related prolonged warming will likely accelerate existing eutrophication effects, including low oxygen concentrations. However, how the interplay between these environmental changes will alter coastal ecosystems is poorly understood. In this study, we compared 16S rRNA gene amplicon based bacterial communities in coastal sediments of a Baltic Sea basin in November 2013 and 2017 at three sites along a water depth gradient with varying bottom water oxygen histories. The shallow site showed changes of only 1.1% in relative abundance of bacterial populations in 2017 compared to 2013, while the deep oxygen-deficient site showed up to 11% changes in relative abundance including an increase of sulfate-reducing bacteria along with a 36% increase in organic matter content. The data suggested that bacterial communities in shallow sediments were more resilient to seasonal oxygen decline, while bacterial communities in sediments subjected to long-term hypoxia seemed to be sensitive to oxygen changes and were likely to be under hypoxic/anoxic conditions in the future. Our data demonstrate that future climate changes will likely fuel eutrophication related spread of low oxygen zones.", "doi": "10.1038/s41598-021-02725-x", "pmid": "34862412", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-02725-x"}, {"db": "pmc", "key": "PMC8642432"}], "notes": [], "created": "2022-03-29T13:47:33.570Z", "modified": "2024-01-16T13:48:37.994Z"}, {"entity": "publication", "iuid": "e3ad82ca8ea244d3b232a5c192785632", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3ad82ca8ea244d3b232a5c192785632.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3ad82ca8ea244d3b232a5c192785632"}}, "title": "Global similarity, and some key differences, in the metagenomes of Swedish varroa-surviving and varroa-susceptible honeybees.", "authors": [{"family": "Thaduri", "given": "Srinivas", "initials": "S"}, {"family": "Marupakula", "given": "Srisailam", "initials": "S"}, {"family": "Terenius", "given": "Olle", "initials": "O"}, {"family": "Onorati", "given": "Piero", "initials": "P"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Locke", "given": "Barbara", "initials": "B"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR"}], "type": "journal article", "published": "2021-12-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "23214", "issn-l": "2045-2322"}, "abstract": "There is increasing evidence that honeybees (Apis mellifera L.) can adapt naturally to survive Varroa destructor, the primary cause of colony mortality world-wide. Most of the adaptive traits of naturally varroa-surviving honeybees concern varroa reproduction. Here we investigate whether factors in the honeybee metagenome also contribute to this survival. The quantitative and qualitative composition of the bacterial and viral metagenome fluctuated greatly during the active season, but with little overall difference between varroa-surviving and varroa-susceptible colonies. The main exceptions were Bartonella apis and sacbrood virus, particularly during early spring and autumn. Bombella apis was also strongly associated with early and late season, though equally for all colonies. All three affect colony protein management and metabolism. Lake Sinai virus was more abundant in varroa-surviving colonies during the summer. Lake Sinai virus and deformed wing virus also showed a tendency towards seasonal genetic change, but without any distinction between varroa-surviving and varroa-susceptible colonies. Whether the changes in these taxa contribute to survival or reflect demographic differences between the colonies (or both) remains unclear.", "doi": "10.1038/s41598-021-02652-x", "pmid": "34853367", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-02652-x"}, {"db": "pmc", "key": "PMC8636477"}], "notes": [], "created": "2021-12-03T15:02:45.758Z", "modified": "2024-01-16T13:48:38.031Z"}, {"entity": "publication", "iuid": "46533631c4d646e590c2e04ec5cbdf0f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46533631c4d646e590c2e04ec5cbdf0f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46533631c4d646e590c2e04ec5cbdf0f"}}, "title": "In vitro evaluation of chemical decontamination of titanium discs.", "authors": [{"family": "Ichioka", "given": "Yuki", "initials": "Y"}, {"family": "Derks", "given": "Jan", "initials": "J"}, {"family": "Dahl\u00e9n", "given": "Gunnar", "initials": "G"}, {"family": "Berglundh", "given": "Tord", "initials": "T"}, {"family": "Larsson", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2021-11-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "22753", "issn-l": "2045-2322"}, "abstract": "Peri-implant diseases are caused by bacterial biofilm colonizing implant surfaces. Prevention and management of peri-implant mucositis and peri-implantitis rely on effective biofilm removal. This study aimed to evaluate biofilm removal and cytocompatibility following chemo-mechanical surface decontamination of biofilm-coated titanium discs. Biofilm-coated (Streptococcus gordonii) discs, with either non-modified (smooth) or modified (rough) surfaces, were instrumented using a sterile gauze soaked in one out of four solutions: saline (NaCl), alkaline electrized water (AEW), citric acid (CA) or N-acetyl-L-cysteine (NAC). Non-contaminated, untreated titanium discs served as controls (C). Residual deposits (bacteria and gauze fibers) and cytocompatibility for osteoblast-like cells were evaluated using SEM and immunofluorescence. Cytotoxicity was assessed using WST-8 assay and immunofluorescence. All protocols were equally effective in removing bacteria from smooth surfaces, while AEW and CA were found to be superior at rough surfaces. AEW and NAC were superior in promoting cytocompatibility over NaCl. NAC and CA had a strong cytotoxic effect on osteoblast-like and fibroblast cells. In conclusion, AEW may be beneficial in the decontamination of implant surfaces, effectively removing bacterial biofilm and restoring cytocompatibility.", "doi": "10.1038/s41598-021-02220-3", "pmid": "34815486", "labels": {"Integrated Microscopy Technologies Gothenburg": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8611041"}, {"db": "pii", "key": "10.1038/s41598-021-02220-3"}], "notes": [], "created": "2023-02-16T08:17:30.177Z", "modified": "2023-02-16T08:17:30.180Z"}, {"entity": "publication", "iuid": "58a8042a127b4e0b849ec2354eada4a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58a8042a127b4e0b849ec2354eada4a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58a8042a127b4e0b849ec2354eada4a0"}}, "title": "HPA axis dysregulation is associated with differential methylation of CpG-sites in related genes.", "authors": [{"family": "Chatzittofis", "given": "Andreas", "initials": "A"}, {"family": "Bostr\u00f6m", "given": "Adrian Desai E", "initials": "ADE"}, {"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "\u00d6berg", "given": "Katarina G\u00f6rts", "initials": "KG"}, {"family": "Arver", "given": "Stefan", "initials": "S"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2021-10-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "20134"}, "abstract": "DNA methylation shifts in Hypothalamic-pituitary-adrenal (HPA) axis related genes is reported in psychiatric disorders including hypersexual disorder. This study, comprising 20 dexamethasone suppression test (DST) non-suppressors and 73 controls, examined the association between the HPA axis dysregulation, shifts in DNA methylation of HPA axis related genes and importantly, gene expression. Individuals with cortisol level \u2265 138 nmol/l, after the low dose (0.5 mg) dexamethasone suppression test (DST) were classified as non-suppressors. Genome-wide methylation pattern, measured in whole blood using the EPIC BeadChip, investigated CpG sites located within 2000 bp of the transcriptional start site of key HPA axis genes, i.e.: CRH, CRHBP, CRHR-1, CRHR-2, FKBP5 and NR3C1. Regression models including DNA methylation M-values and the binary outcome (DST non-suppression status) were performed. Gene transcripts with an abundance of differentially methylated CpG sites were identified with binomial tests. Pearson correlations and robust linear regressions were performed between CpG methylation and gene expression in two independent cohorts. Six of 76 CpG sites were significantly hypermethylated in DST non-suppressors (nominal P < 0.05), associated with genes CRH, CRHR1, CRHR2, FKBP5 and NR3C1. NR3C1 transcript AJ877169 showed statistically significant abundance of probes differentially methylated by DST non-suppression status and correlated with DST cortisol levels. Further, methylation levels of cg07733851 and cg27122725 were positively correlated with gene expression levels of the NR3C1 gene. Methylation levels of cg08636224 (FKBP5) correlated with baseline cortisol and gene expression. Our findings revealed that DNA methylation shifts are involved in the altered mechanism of the HPA axis suggesting that new epigenetic targets should be considered behind psychiatric disorders.", "doi": "10.1038/s41598-021-99714-x", "pmid": "34635736", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-99714-x"}, {"db": "pmc", "key": "PMC8505644"}], "notes": [], "created": "2021-10-19T14:10:12.164Z", "modified": "2024-01-16T13:48:38.261Z"}, {"entity": "publication", "iuid": "e2c7e0df97dc45de9a909aafc53e6ff6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2c7e0df97dc45de9a909aafc53e6ff6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2c7e0df97dc45de9a909aafc53e6ff6"}}, "title": "ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression.", "authors": [{"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Younis", "given": "Shady", "initials": "S"}], "type": "journal article", "published": "2021-09-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "19484", "issn-l": "2045-2322"}, "abstract": "The expression of Igf2 in mammals shows a complex regulation involving multiple promoters and epigenetic mechanisms. We previously identified a novel regulatory mechanism based on the interaction between the transcriptional factor ZBED6 and Igf2 intron. Disruption of the ZBED6-Igf2 interaction leads to a dramatic up-regulation of IGF2 expression postnatally. In the current study we characterize an additional layer of regulation involving miR483 encoded by another Igf2 intron. We found a highly significant up-regulation of miR483 expression when the ZBED6-Igf2 axis is disrupted in transgenic mice. Furthermore, CRISPR/Cas9 mediated knock-out of miR483 in C2C12 myoblast cells, both wild-type and cells with disrupted ZBED6-Igf2 axis (Igf2dGGCT), resulted in down-regulation of Igf2 expression and a reduced proliferation rate. This was further validated using miR483 mimics and inhibitors. RNA-seq analysis revealed a significant enrichment of genes involved in the PI3K-Akt signaling pathway among genes down-regulated in miR483-/- cells, including Igf2 down-regulation. The opposite pattern was observed in Igf2dGGCT cells, where Igf2 is up-regulated. Our data suggest a positive feedback between miR483 and Igf2 promoter activity, strongly affecting how ZBED6 controls Igf2 expression in various cell types.", "doi": "10.1038/s41598-021-98777-0", "pmid": "34593874", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-98777-0"}, {"db": "pmc", "key": "PMC8484269"}], "notes": [], "created": "2022-01-16T20:56:35.213Z", "modified": "2022-01-16T20:56:35.229Z"}, {"entity": "publication", "iuid": "5bd96c5ba07a441284381c33d5ac429b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bd96c5ba07a441284381c33d5ac429b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bd96c5ba07a441284381c33d5ac429b"}}, "title": "The localization of amyloid precursor protein to ependymal cilia in vertebrates and its role in ciliogenesis and brain development in zebrafish.", "authors": [{"family": "Chebli", "given": "Jasmine", "initials": "J", "orcid": "0000-0003-0791-3198", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b0dd51631ce4c3c89a98b9d6c7d3d35.json"}}, {"family": "Rahmati", "given": "Maryam", "initials": "M"}, {"family": "Lashley", "given": "Tammaryn", "initials": "T", "orcid": "0000-0001-7389-0348", "researcher": {"href": "https://publications.scilifelab.se/researcher/533fe74a716840b2a55fddf0452f2a23.json"}}, {"family": "Edeman", "given": "Brigitta", "initials": "B"}, {"family": "Oldfors", "given": "Anders", "initials": "A", "orcid": "0000-0002-5758-7397", "researcher": {"href": "https://publications.scilifelab.se/researcher/e82034663f6647cd9827871bfca633ef.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Abramsson", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-4715-9225", "researcher": {"href": "https://publications.scilifelab.se/researcher/7abde12dab2e4d338bc6e55933f07531.json"}}], "type": "journal article", "published": "2021-09-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "19115", "issn-l": "2045-2322"}, "abstract": "Amyloid precursor protein (APP) is expressed in many tissues in human, mice and in zebrafish. In zebrafish, there are two orthologues, Appa and Appb. Interestingly, some cellular processes associated with APP overlap with cilia-mediated functions. Whereas the localization of APP to primary cilia of in vitro-cultured cells has been reported, we addressed the presence of APP in motile and in non-motile sensory cilia and its potential implication for ciliogenesis using zebrafish, mouse, and human samples. We report that Appa and Appb are expressed by ciliated cells and become localized at the membrane of cilia in the olfactory epithelium, otic vesicle and in the brain ventricles of zebrafish embryos. App in ependymal cilia persisted in adult zebrafish and was also detected in mouse and human brain. Finally, we found morphologically abnormal ependymal cilia and smaller brain ventricles in appa-/-appb-/- mutant zebrafish. Our findings demonstrate an evolutionary conserved localisation of APP to cilia and suggest a role of App in ciliogenesis and cilia-related functions.", "doi": "10.1038/s41598-021-98487-7", "pmid": "34580355", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8476544"}, {"db": "pii", "key": "10.1038/s41598-021-98487-7"}], "notes": [], "created": "2023-02-16T08:14:17.553Z", "modified": "2023-02-16T08:14:17.703Z"}, {"entity": "publication", "iuid": "474380e733ea4bffaeeccbb1bfa94ade", "links": {"self": {"href": "https://publications.scilifelab.se/publication/474380e733ea4bffaeeccbb1bfa94ade.json"}, "display": {"href": "https://publications.scilifelab.se/publication/474380e733ea4bffaeeccbb1bfa94ade"}}, "title": "Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.", "authors": [{"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Ure", "given": "Agustin Enrique", "initials": "AE"}, {"family": "Sundstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Hultin", "given": "Emilie", "initials": "E"}], "type": "journal article", "published": "2021-09-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "18852", "issn-l": "2045-2322"}, "abstract": "Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.", "doi": "10.1038/s41598-021-98452-4", "pmid": "34552145", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-98452-4"}, {"db": "pmc", "key": "PMC8458301"}], "notes": [], "created": "2021-10-01T09:09:05.660Z", "modified": "2021-12-06T13:48:44.578Z"}, {"entity": "publication", "iuid": "d4e5acaf0f90469f8e83c8653dbeff7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4e5acaf0f90469f8e83c8653dbeff7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4e5acaf0f90469f8e83c8653dbeff7e"}}, "title": "Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid.", "authors": [{"family": "Peters", "given": "Kristian", "initials": "K"}, {"family": "Herman", "given": "Stephanie", "initials": "S"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Burman", "given": "Joachim", "initials": "J"}, {"family": "Neumann", "given": "Steffen", "initials": "S"}, {"family": "Kultima", "given": "Kim", "initials": "K"}], "type": "journal article", "published": "2021-09-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "18822", "issn-l": "2045-2322"}, "abstract": "Chronic diseases affecting the central nervous system (CNS) like Alzheimer's or Parkinson's disease typically develop with advanced chronological age. Yet, aging at the metabolic level has been explored only sporadically in humans using biofluids in close proximity to the CNS such as the cerebrospinal fluid (CSF). We have used an untargeted liquid chromatography high-resolution mass spectrometry (LC-HRMS) based metabolomics approach to measure the levels of metabolites in the CSF of non-neurological control subjects in the age of 20 up to 74. Using a random forest-based feature selection strategy, we extracted 69 features that were strongly related to age (page < 0.001, rage = 0.762, R2Boruta age = 0.764). Combining an in-house library of known substances with in silico chemical classification and functional semantic annotation we successfully assigned putative annotations to 59 out of the 69 CSF metabolites. We found alterations in metabolites related to the Cytochrome P450 system, perturbations in the tryptophan and kynurenine pathways, metabolites associated with cellular energy (NAD+, ADP), mitochondrial and ribosomal metabolisms, neurological dysfunction, and an increase of adverse microbial metabolites. Taken together our results point at a key role for metabolites found in CSF related to the Cytochrome P450 system as most often associated with metabolic aging.", "doi": "10.1038/s41598-021-97491-1", "pmid": "34552125", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-97491-1"}, {"db": "pmc", "key": "PMC8458502"}], "notes": [], "created": "2021-10-15T09:28:38.958Z", "modified": "2024-01-16T13:48:38.456Z"}, {"entity": "publication", "iuid": "49d7f88a4b4a46af8d50dbdab7de9479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49d7f88a4b4a46af8d50dbdab7de9479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49d7f88a4b4a46af8d50dbdab7de9479"}}, "title": "Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.", "authors": [{"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Salas", "given": "Beatriz", "initials": "B"}, {"family": "Ganji", "given": "Suresh", "initials": "S"}, {"family": "Jorquera-Rom\u00e1n", "given": "Cristian", "initials": "C"}, {"family": "Valenzuela", "given": "Maria Luisa", "initials": "ML"}, {"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Unelius", "given": "C Rikard", "initials": "CR"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Vera", "given": "Mario", "initials": "M"}], "type": "journal article", "published": "2021-08-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "16275", "issn-l": "2045-2322"}, "abstract": "Bioleaching of metal sulfide ores involves acidophilic microbes that catalyze the chemical dissolution of the metal sulfide bond that is enhanced by attached and planktonic cell mediated oxidation of iron(II)-ions and inorganic sulfur compounds. Leptospirillum spp. often predominate in sulfide mineral-containing environments, including bioheaps for copper recovery from chalcopyrite, as they are effective primary mineral colonizers and oxidize iron(II)-ions efficiently. In this study, we demonstrated a functional diffusible signal factor interspecies quorum sensing signaling mechanism in Leptospirillum ferriphilum and Leptospirillum ferrooxidans that produces (Z)-11-methyl-2-dodecenoic acid when grown with pyrite as energy source. In addition, pure diffusible signal factor and extracts from supernatants of pyrite grown Leptospirillum spp. inhibited biological iron oxidation in various species, and that pyrite grown Leptospirillum cells were less affected than iron grown cells to self inhibition. Finally, transcriptional analyses for the inhibition of iron-grown L. ferriphilum cells due to diffusible signal factor was compared with the response to exposure of cells to N- acyl-homoserine-lactone type quorum sensing signal compounds. The data suggested that Leptospirillum spp. diffusible signal factor production is a strategy for niche protection and defense against other microbes and it is proposed that this may be exploited to inhibit unwanted acidophile species.", "doi": "10.1038/s41598-021-95324-9", "pmid": "34381075", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-95324-9"}, {"db": "pmc", "key": "PMC8357829"}], "notes": [], "created": "2021-10-01T09:03:16.277Z", "modified": "2024-01-16T13:48:38.805Z"}, {"entity": "publication", "iuid": "4fc47fbead1f4a22811bb59baaed3383", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fc47fbead1f4a22811bb59baaed3383.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fc47fbead1f4a22811bb59baaed3383"}}, "title": "Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.", "authors": [{"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Nystedt", "given": "Sara", "initials": "S"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Fogelstrand", "given": "Linda", "initials": "L"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}], "type": "journal article", "published": "2021-08-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "15988"}, "abstract": "The mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.", "doi": "10.1038/s41598-021-95109-0", "pmid": "34362951", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-95109-0"}, {"db": "pmc", "key": "PMC8346595"}], "notes": [], "created": "2021-08-09T12:21:51.023Z", "modified": "2024-01-16T13:48:38.827Z"}, {"entity": "publication", "iuid": "a9f5e65b684848218600bf30df2a82fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9f5e65b684848218600bf30df2a82fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9f5e65b684848218600bf30df2a82fc"}}, "title": "High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction.", "authors": [{"family": "Gra\u00e7a", "given": "Andr\u00e9 T", "initials": "AT"}, {"family": "Hall", "given": "Michael", "initials": "M", "orcid": "0000-0003-0864-9798", "researcher": {"href": "https://publications.scilifelab.se/researcher/7489a92a241f4d0d9f8ef6eb4fcb3858.json"}}, {"family": "Persson", "given": "Karina", "initials": "K", "orcid": "0000-0003-0807-0348", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b999cf004141468eefb2504b7c5b99.json"}}, {"family": "Schr\u00f6der", "given": "Wolfgang P", "initials": "WP"}], "type": "journal article", "published": "2021-07-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "15534"}, "abstract": "In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 \u00c5, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn4CaO5-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.", "doi": "10.1038/s41598-021-94914-x", "pmid": "34330992", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-94914-x"}, {"db": "pmc", "key": "PMC8324835"}], "notes": [], "created": "2021-08-31T09:10:56.616Z", "modified": "2023-12-04T10:17:35.530Z"}, {"entity": "publication", "iuid": "0e967e9b60494dd292eadc8c4e0724ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e967e9b60494dd292eadc8c4e0724ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e967e9b60494dd292eadc8c4e0724ce"}}, "title": "Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99.", "authors": [{"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Hammond", "given": "Maria", "initials": "M"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Ed\u00e9n", "given": "Malin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}], "type": "journal article", "published": "2021-07-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "15160"}, "abstract": "Mosaic loss of chromosome Y (LOY) in immune cells is a male-specific mutation associated with increased risk for morbidity and mortality. The CD99 gene, positioned in the pseudoautosomal regions of chromosomes X and Y, encodes a cell surface protein essential for several key properties of leukocytes and immune system functions. Here we used CITE-seq for simultaneous quantification of CD99 derived mRNA and cell surface CD99 protein abundance in relation to LOY in single cells. The abundance of CD99 molecules was lower on the surfaces of LOY cells compared with cells without this aneuploidy in all six types of leukocytes studied, while the abundance of CD proteins encoded by genes located on autosomal chromosomes were independent from LOY. These results connect LOY in single cells with immune related cellular properties at the protein level, providing mechanistic insight regarding disease vulnerability in men affected with mosaic chromosome Y loss in blood leukocytes.", "doi": "10.1038/s41598-021-94588-5", "pmid": "34312421", "labels": {"Affinity Proteomics Uppsala": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-94588-5"}, {"db": "pmc", "key": "PMC8313698"}], "notes": [], "created": "2021-08-27T13:32:48.686Z", "modified": "2024-01-16T13:48:39.087Z"}, {"entity": "publication", "iuid": "567f1e445eab4cdc987f086685d0350b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/567f1e445eab4cdc987f086685d0350b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/567f1e445eab4cdc987f086685d0350b"}}, "title": "A search for modifying genetic factors in CHEK2:c.1100delC breast cancer patients.", "authors": [{"family": "Wendt", "given": "Camilla", "initials": "C"}, {"family": "Muranen", "given": "Taru A", "initials": "TA"}, {"family": "Mielik\u00e4inen", "given": "Lotta", "initials": "L"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Blomqvist", "given": "Carl", "initials": "C"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H"}, {"family": "Tham", "given": "Emma", "initials": "E"}, {"family": "Arver", "given": "Brita", "initials": "B"}, {"family": "Melin", "given": "Beatrice", "initials": "B"}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E"}, {"family": "Stenmark Askmalm", "given": "Marie", "initials": "M"}, {"family": "Paulsson-Karlsson", "given": "Ylva", "initials": "Y"}, {"family": "Einbeigi", "given": "Zakaria", "initials": "Z"}, {"family": "von Wachenfeldt V\u00e4ppling", "given": "Anna", "initials": "A"}, {"family": "Kalso", "given": "Eija", "initials": "E"}, {"family": "Tasmuth", "given": "Tiina", "initials": "T"}, {"family": "Kallioniemi", "given": "Anne", "initials": "A"}, {"family": "Aittom\u00e4ki", "given": "Kristiina", "initials": "K"}, {"family": "Nevanlinna", "given": "Heli", "initials": "H"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2021-07-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "14763", "issn-l": "2045-2322"}, "abstract": "The risk of breast cancer associated with CHEK2:c.1100delC is 2-threefold but higher in carriers with a family history of breast cancer than without, suggesting that other genetic loci in combination with CHEK2:c.1100delC confer an increased risk in a polygenic model. Part of the excess familial risk has been associated with common low-penetrance variants. This study aimed to identify genetic loci that modify CHEK2:c.1100delC-associated breast cancer risk by searching for candidate risk alleles that are overrepresented in CHEK2:c.1100delC carriers with breast cancer compared with controls. We performed whole-exome sequencing in 28 breast cancer cases with germline CHEK2:c.1100delC, 28 familial breast cancer cases and 70 controls. Candidate alleles were selected for validation in larger cohorts. One recessive synonymous variant, rs16897117, was suggested, but no overrepresentation of homozygous CHEK2:c.1100delC carriers was found in the following validation. Furthermore, 11 non-synonymous candidate alleles were suggested for further testing, but no significant difference in allele frequency could be detected in the validation in CHEK2:c.1100delC cases compared with familial breast cancer, sporadic breast cancer and controls. With this method, we found no support for a CHEK2:c.1100delC-specific genetic modifier. Further studies of CHEK2:c.1100delC genetic modifiers are warranted to improve risk assessment in clinical practice.", "doi": "10.1038/s41598-021-93926-x", "pmid": "34285278", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-93926-x"}, {"db": "pmc", "key": "PMC8292481"}], "notes": [], "created": "2021-09-13T06:42:16.025Z", "modified": "2024-01-16T13:48:39.103Z"}, {"entity": "publication", "iuid": "a9d9770e79f5443f8c7c4171a2bbfebd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9d9770e79f5443f8c7c4171a2bbfebd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9d9770e79f5443f8c7c4171a2bbfebd"}}, "title": "Computing the orientational-average of diffusion-weighted MRI signals: a comparison of different techniques.", "authors": [{"family": "Afzali", "given": "Maryam", "initials": "M"}, {"family": "Knutsson", "given": "Hans", "initials": "H"}, {"family": "\u00d6zarslan", "given": "Evren", "initials": "E"}, {"family": "Jones", "given": "Derek K", "initials": "DK"}], "type": "journal article", "published": "2021-07-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "14345", "issn-l": "2045-2322"}, "abstract": "Numerous applications in diffusion MRI involve computing the orientationally-averaged diffusion-weighted signal. Most approaches implicitly assume, for a given b-value, that the gradient sampling vectors are uniformly distributed on a sphere (or 'shell'), computing the orientationally-averaged signal through simple arithmetic averaging. One challenge with this approach is that not all acquisition schemes have gradient sampling vectors distributed over perfect spheres. To ameliorate this challenge, alternative averaging methods include: weighted signal averaging; spherical harmonic representation of the signal in each shell; and using Mean Apparent Propagator MRI (MAP-MRI) to derive a three-dimensional signal representation and estimate its 'isotropic part'. Here, these different methods are simulated and compared under different signal-to-noise (SNR) realizations. With sufficiently dense sampling points (61 orientations per shell), and isotropically-distributed sampling vectors, all averaging methods give comparable results, (MAP-MRI-based estimates give slightly higher accuracy, albeit with slightly elevated bias as b-value increases). As the SNR and number of data points per shell are reduced, MAP-MRI-based approaches give significantly higher accuracy compared with the other methods. We also apply these approaches to in vivo data where the results are broadly consistent with our simulations. A statistical analysis of the simulated data shows that the orientationally-averaged signals at each b-value are largely Gaussian distributed.", "doi": "10.1038/s41598-021-93558-1", "pmid": "34253770", "labels": {"AIDA Data Hub": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8275746"}, {"db": "pii", "key": "10.1038/s41598-021-93558-1"}], "notes": [], "created": "2023-05-25T16:02:42.370Z", "modified": "2023-05-25T16:02:42.383Z"}, {"entity": "publication", "iuid": "d16d934635db4fd4bc7a958e5c3f71a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d16d934635db4fd4bc7a958e5c3f71a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d16d934635db4fd4bc7a958e5c3f71a7"}}, "title": "Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP.", "authors": [{"family": "Singh", "given": "Abhijeet", "initials": "A"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2021-06-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "13298", "issn-l": "2045-2322"}, "abstract": "Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.", "doi": "10.1038/s41598-021-92658-2", "pmid": "34168213", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-92658-2"}, {"db": "pmc", "key": "PMC8225771"}], "notes": [], "created": "2021-12-07T21:36:38.543Z", "modified": "2024-01-16T13:48:39.463Z"}, {"entity": "publication", "iuid": "25601442c8aa4f76ad06728698be20f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25601442c8aa4f76ad06728698be20f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25601442c8aa4f76ad06728698be20f8"}}, "title": "A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism.", "authors": [{"family": "Melo", "given": "Geraldo Acl\u00e9cio", "initials": "GA"}, {"family": "Abreu", "given": "Ilka Nacif", "initials": "IN"}, {"family": "de Oliveira", "given": "Ma\u00edra Baista", "initials": "MB"}, {"family": "Budzinski", "given": "Ilara Gabriela Frasson", "initials": "IGF"}, {"family": "Silva", "given": "Lucin\u00e9lia Vieira", "initials": "LV"}, {"family": "Pimenta", "given": "Marcio Ant\u00f4nio Silva", "initials": "MAS"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2021-06-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "12933", "issn-l": "2045-2322"}, "abstract": "Drought is the main factor that limits the distribution and productivity of plant species. In the Brazilian Cerrado, the vegetation is adapted to a seasonal climate with long- and short-term periods of drought. To analyze the metabolic strategies under such conditions, a metabolomic approach was used to characterize Gomphrena agrestis Mart. (Amaranthaceae) a native species that grows under natural conditions, in a rock-field area. Roots and leaves material from native specimens were sampled along different seasons of the year and LC-MS and GC-MS analyzed for multiple chemical constituents. The datasets derived from the different measurements were combined and evaluated using multivariate analysis. Principal component analysis was used to obtain an overview of the samples and identify outliers. Later, the data was analyzed with orthogonal projection to latent structures discriminant analysis to obtain valid models that could explain the metabolite variations in the different seasons. Two hundred and eighty metabolites were annotated, generating a unique database to characterize metabolic strategies used to cope with the effects of drought. The accumulation of fructans in the thickened roots is consistent with the storage of carbons during the rainy season to support the energy demand during a long period of drought. The accumulation of Abscisic acid, sugars and sugar alcohols, phenolics, and pigment in the leaves suggests physiological adaptations. To cope with long-term drought, the data suggests that tissue water status and storage of reserves are important to support plant survival and regrowth. However, during short-term drought, osmoregulation and oxidative protection seems to be essential, probably to support the maintenance of active photosynthesis.", "doi": "10.1038/s41598-021-92449-9", "pmid": "34155311", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-92449-9"}, {"db": "pmc", "key": "PMC8217525"}], "notes": [], "created": "2021-12-09T20:06:51.156Z", "modified": "2025-10-17T13:03:16.012Z"}, {"entity": "publication", "iuid": "c96b3d4caecd4710a6a99a969cdd45ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c96b3d4caecd4710a6a99a969cdd45ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c96b3d4caecd4710a6a99a969cdd45ec"}}, "title": "Associations of maternal and infant metabolomes with immune maturation and allergy development at 12 months in the Swedish NICE-cohort.", "authors": [{"family": "Hartvigsson", "given": "Olle", "initials": "O"}, {"family": "Barman", "given": "Malin", "initials": "M", "orcid": "0000-0002-5317-2768", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f9dea43f1b46bb9e63f76ce946f1d7.json"}}, {"family": "Rabe", "given": "Hardis", "initials": "H"}, {"family": "Sandin", "given": "Anna", "initials": "A"}, {"family": "Wold", "given": "Agnes E", "initials": "AE"}, {"family": "Brunius", "given": "Carl", "initials": "C", "orcid": "0000-0003-3957-870X", "researcher": {"href": "https://publications.scilifelab.se/researcher/560a5d14ee83421680058b00df2ac9e2.json"}}, {"family": "Sandberg", "given": "Ann-Sofie", "initials": "AS", "orcid": "0000-0002-9681-3342", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd34d8e107be4a87b60c8dc525277463.json"}}], "type": "journal article", "published": "2021-06-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "12706"}, "abstract": "Allergic diseases are the most common chronic diseases in childrenin the Western world, but little is know about what factors influence immune maturation and allergy development. We therefore aimed to associate infant and maternal metabolomes to T- and B-cell subpopulations and allergy diagnosis. We performed liquid chromatography-mass spectrometry based untargeted metabolomics on blood plasma from mothers (third trimester, n = 605; delivery, n = 558) and from the umbilical cord (n = 366). The measured metabolomes were associated to T- and B-cell subpopulations up to 4 months after delivery and to doctor\u00b4s diagnosed eczema, food allergy and asthma at one year of age using random forest analysis. Maternal and cord plasma at delivery could predict the number of CD24+CD38low memory B-cells (p = 0.033, n = 26 and p = 0.009, n = 22), but future allergy status could not be distinguished from any of the three measured metabolomes. Replication of previous literature findings showed hypoxanthine to be upregulated in the umbilical cord of children with subsequent asthma. This exploratory study suggests foetal immune programming occuring during pregnancy as the metabolomic profiles of mothers and infants at delivery related to infants' B-cell maturation.", "doi": "10.1038/s41598-021-92239-3", "pmid": "34135462", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8209090"}, {"db": "pii", "key": "10.1038/s41598-021-92239-3"}], "notes": [], "created": "2022-06-30T09:11:52.567Z", "modified": "2023-06-19T12:53:39.577Z"}, {"entity": "publication", "iuid": "ea01bc3eb8a84d70b9e9a6b6e555ae33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea01bc3eb8a84d70b9e9a6b6e555ae33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea01bc3eb8a84d70b9e9a6b6e555ae33"}}, "title": "Cyclotide host-defense tailored for species and environments in violets from the Canary Islands.", "authors": [{"family": "Slazak", "given": "Blazej", "initials": "B"}, {"family": "Kaltenb\u00f6ck", "given": "Klara", "initials": "K"}, {"family": "Steffen", "given": "Karin", "initials": "K"}, {"family": "Rogala", "given": "Martyna", "initials": "M"}, {"family": "Rodr\u00edguez-Rodr\u00edguez", "given": "Priscila", "initials": "P"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2021-06-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "12452"}, "abstract": "Cyclotides are cyclic peptides produced by plants. Due to their insecticidal properties, they are thought to be involved in host defense. Violets produce complex mixtures of cyclotides, that are characteristic for each species and variable in different environments. Herein, we utilized mass spectrometry (LC-MS, MALDI-MS), transcriptomics and biological assays to investigate the diversity, differences in cyclotide expression based on species and different environment, and antimicrobial activity of cyclotides found in violets from the Canary Islands. A wide range of different habitats can be found on these islands, from subtropical forests to dry volcano peaks at high altitudes. The islands are inhabited by the endemic Viola palmensis, V. cheiranthifolia, V. anagae and the common V. odorata. The number of cyclotides produced by a given species varied in plants from different environments. The highest diversity was noted in V. anagae which resides in subtropical forest and the lowest in V. cheiranthifolia from the Teide volcano. Transcriptome sequencing and LC-MS were used to identify 23 cyclotide sequences from V. anagae. Cyclotide extracts exhibited antifungal activities with the lowest minimal inhibitory concentrations noted for V. anagae (15.62 \u03bcg/ml against Fusarium culmorum). The analysis of the relative abundance of 30 selected cyclotides revealed patterns characteristic to both species and populations, which can be the result of genetic variability or environmental conditions in different habitats. The current study exemplifies how plants tailor their host defense peptides for various habitats, and the usefulness of cyclotides as markers for chemosystematics.", "doi": "10.1038/s41598-021-91555-y", "pmid": "34127703", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-91555-y"}, {"db": "pmc", "key": "PMC8203695"}], "notes": [], "created": "2021-12-03T11:47:59.306Z", "modified": "2021-12-09T13:45:30.801Z"}, {"entity": "publication", "iuid": "dc88b48592bb4a6287ba95ca416bb0a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc88b48592bb4a6287ba95ca416bb0a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc88b48592bb4a6287ba95ca416bb0a3"}}, "title": "Inflammation-related plasma protein levels and association with adiposity measurements in young adults.", "authors": [{"family": "Klevebro", "given": "Susanna", "initials": "S"}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S"}, {"family": "Ekstr\u00f6m", "given": "Sandra", "initials": "S"}, {"family": "Merid", "given": "Simon K", "initials": "SK"}, {"family": "Gruzieva", "given": "Olena", "initials": "O"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kull", "given": "Inger", "initials": "I"}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2021-05-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "11391", "issn-l": "2045-2322"}, "abstract": "Obesity-related inflammation is associated with cardiovascular, metabolic, and pulmonary diseases. The aim of this study was to demonstrate associations between adiposity measurements and levels of inflammation-related plasma proteins in a population of young adults. Subjects from a population-based birth cohort with a mean age of 22.5 years were included in the study population (n = 2074). Protein levels were analyzed using the Olink Proseek Multiplex Inflammation panel. Percentage body fat (%BF) and visceral fat rating (VFR) measurements were collected using Tanita MC 780 body composition monitor. Linear regression of standardized values was used to investigate associations. Potential effect modifications by sex and BMI category were assessed. Of 71 investigated proteins, 54 were significantly associated with all adiposity measurements [%BF, body mass index (BMI), VFR and waist circumference]. Among proteins associated with %BF, seven showed a larger or unique association in overweight/obese subjects and three showed a significant effect modification by sex. Fourteen proteins more strongly associated with VFR in females compared to males. Adipose-associated systemic inflammation was observed in this young adult population. Sex and adiposity localization influenced some of the associations. Our results highlight specific proteins as suitable biomarkers related to adiposity.", "doi": "10.1038/s41598-021-90843-x", "pmid": "34059769", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-90843-x"}, {"db": "pmc", "key": "PMC8166979"}], "notes": [], "created": "2021-12-10T09:26:42.868Z", "modified": "2021-12-10T09:26:42.883Z"}, {"entity": "publication", "iuid": "9437e98e801f4411bb65ad98062e8b08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9437e98e801f4411bb65ad98062e8b08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9437e98e801f4411bb65ad98062e8b08"}}, "title": "Adsorption of bio-organic eco-corona molecules reduces the toxic response to metallic nanoparticles in Daphnia magna.", "authors": [{"family": "Ekvall", "given": "Mikael T", "initials": "MT"}, {"family": "Hedberg", "given": "Jonas", "initials": "J"}, {"family": "Odnevall Wallinder", "given": "Inger", "initials": "I"}, {"family": "Malmendal", "given": "Anders", "initials": "A"}, {"family": "Hansson", "given": "Lars-Anders", "initials": "LA"}, {"family": "Cedervall", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2021-05-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "10784", "issn-l": "2045-2322"}, "abstract": "As the use of engineered nanomaterials increases, so does the risk of them spreading to natural ecosystems. Hitherto, knowledge regarding the toxic properties of nanoparticles (NP's) and their potential interactions with natural bio-organic molecules adsorbed to them, and thereby forming surface coronas, is limited. However, we show here that the toxic effect of NPs of tungsten carbide cobalt (WC-Co) and cobalt (Co) on the crustacean Daphnia magna is postponed in the presence of natural biological degradation products (eco-corona biomolecules). For Daphnia exposed to WC-Co NPs the survival time increased with 20-25% and for Co NPs with 30-47% after mixing the particles with a solution of eco-corona biomolecules before exposure. This suggests that an eco-corona, composed of biomolecules always present in natural ecosystems, reduces the toxic potency of both studied NPs. Further, the eco-coronas did not affect the particle uptake, suggesting that the reduction in toxicity was related to the particle-organism interaction after eco-corona formation. In a broader context, this implies that although the increasing use and production of NPs may constitute a novel, global environmental threat, the acute toxicity and long-term effects of some NPs will, at least under certain conditions, be reduced as they enter natural ecosystems.", "doi": "10.1038/s41598-021-90053-5", "pmid": "34031463", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-90053-5"}, {"db": "pmc", "key": "PMC8144400"}], "notes": [], "created": "2021-07-02T14:05:43.322Z", "modified": "2025-10-17T13:03:55.843Z"}, {"entity": "publication", "iuid": "11b8839fb4694d75bc19aab767987019", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11b8839fb4694d75bc19aab767987019.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11b8839fb4694d75bc19aab767987019"}}, "title": "X-chromosome variants are associated with aldosterone producing adenomas.", "authors": [{"family": "Dutta", "given": "Ravi Kumar", "initials": "RK"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Arnesen", "given": "Thomas", "initials": "T"}, {"family": "Heie", "given": "Anette", "initials": "A"}, {"family": "Walz", "given": "Martin", "initials": "M"}, {"family": "Alesina", "given": "Piero", "initials": "P"}, {"family": "Gimm", "given": "Oliver", "initials": "O"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2021-05-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "10562"}, "abstract": "Aldosterone-producing adenomas (APAs) are a major cause of primary aldosteronism (PA) and are characterized by constitutively producing aldosterone, which leads to hypertension. Several mutations have been identified in ion channels or ion channel-associated genes that result in APAs. To date, no studies have used a genome-wide association study (GWAS) approach to search for predisposing loci for APAs. Thus, we investigated Scandinavian APA cases (n = 35) and Swedish controls (n = 60) in a GWAS and discovered a susceptibility locus on chromosome Xq13.3 (rs2224095, OR = 7.9, 95% CI = 2.8-22.4, P = 1 \u00d7 10-7) in a 4-Mb region that was significantly associated with APA. Direct genotyping of sentinel SNP rs2224095 in a replication cohort of APAs (n = 83) and a control group (n = 740) revealed persistently strong significance (OR = 6.1, 95% CI = 3.5-10.6, p < 0.0005). We sequenced an adjacent gene, MAGEE1, of the sentinel SNP and identified a rare variant in one APA, p.Gly327Glu, which is complementary to other mutations in our primary cohort. Expression quantitative trait loci (eQTL) were investigated on the X-chromosome, and 24 trans-eQTL were identified. Some of the genes identified by trans-eQTL point towards a novel mechanistic explanation for the association of the SNPs with APAs. In conclusion, our study provides further insights into the genetic basis of APAs.", "doi": "10.1038/s41598-021-89986-8", "pmid": "34006971", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Clinical Genomics Link\u00f6ping": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-89986-8"}, {"db": "pmc", "key": "PMC8131628"}], "notes": [], "created": "2021-09-16T12:45:50.059Z", "modified": "2024-01-16T13:48:39.732Z"}, {"entity": "publication", "iuid": "a27ec54fcc1c4fcfa2ee0463e3b004a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a27ec54fcc1c4fcfa2ee0463e3b004a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a27ec54fcc1c4fcfa2ee0463e3b004a0"}}, "title": "Alternative redox forms of ASNA-1 separate insulin signaling from tail-anchored protein targeting and cisplatin resistance in C. elegans.", "authors": [{"family": "Raj", "given": "Dorota", "initials": "D"}, {"family": "Billing", "given": "Ola", "initials": "O"}, {"family": "Podraza-Farhanieh", "given": "Agnieszka", "initials": "A"}, {"family": "Kraish", "given": "Bashar", "initials": "B"}, {"family": "Hemmingsson", "given": "Oskar", "initials": "O"}, {"family": "Kao", "given": "Gautam", "initials": "G"}, {"family": "Naredi", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2021-04-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "8678", "issn-l": "2045-2322"}, "abstract": "Cisplatin is a frontline cancer therapeutic, but intrinsic or acquired resistance is common. We previously showed that cisplatin sensitivity can be achieved by inactivation of ASNA-1/TRC40 in mammalian cancer cells and in Caenorhabditis elegans. ASNA-1 has two more conserved functions: in promoting tail-anchored protein (TAP) targeting to the endoplasmic reticulum membrane and in promoting insulin secretion. However, the relation between its different functions has remained unknown. Here, we show that ASNA-1 exists in two redox states that promote TAP-targeting and insulin secretion separately. The reduced state is the one required for cisplatin resistance: an ASNA-1 point mutant, in which the protein preferentially was found in the oxidized state, was sensitive to cisplatin and defective for TAP targeting but had no insulin secretion defect. The same was true for mutants in wrb-1, which we identify as the C. elegans homolog of WRB, the ASNA1/TRC40 receptor. Finally, we uncover a previously unknown action of cisplatin induced reactive oxygen species: cisplatin induced ROS drives ASNA-1 into the oxidized form, and selectively prevents an ASNA-1-dependent TAP substrate from reaching the endoplasmic reticulum. Our work suggests that ASNA-1 acts as a redox-sensitive target for cisplatin cytotoxicity and that cisplatin resistance is likely mediated by ASNA-1-dependent TAP substrates. Treatments that promote an oxidizing tumor environment should be explored as possible means to combat cisplatin resistance.", "doi": "10.1038/s41598-021-88085-y", "pmid": "33883621", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8060345"}, {"db": "pii", "key": "10.1038/s41598-021-88085-y"}], "notes": [], "created": "2023-02-16T08:21:59.374Z", "modified": "2023-02-16T08:21:59.388Z"}, {"entity": "publication", "iuid": "ee230c2ac0734f4b80a980d5eee44e51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee230c2ac0734f4b80a980d5eee44e51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee230c2ac0734f4b80a980d5eee44e51"}}, "title": "Methodological considerations for identifying multiple plasma proteins associated with all-cause mortality in a population-based prospective cohort.", "authors": [{"family": "Drake", "given": "Isabel", "initials": "I"}, {"family": "Hindy", "given": "George", "initials": "G"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Nilsson", "given": "Jan", "initials": "J"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}], "type": "journal article", "published": "2021-03-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "6734", "issn-l": "2045-2322"}, "abstract": "Novel methods to characterize the plasma proteome has made it possible to examine a wide range of proteins in large longitudinal cohort studies, but the complexity of the human proteome makes it difficult to identify robust protein-disease associations. Nevertheless, identification of individuals at high risk of early mortality is a central issue in clinical decision making and novel biomarkers may be useful to improve risk stratification. With adjustment for established risk factors, we examined the associations between 138 plasma proteins measured using two proximity extension assays and long-term risk of all-cause mortality in 3,918 participants of the population-based Malm\u00f6 Diet and Cancer Study. To examine the reproducibility of protein-mortality associations we used a two-step random-split approach to simulate a discovery and replication cohort and conducted analyses using four different methods: Cox regression, stepwise Cox regression, Lasso-Cox regression, and random survival forest (RSF). In the total study population, we identified eight proteins that associated with all-cause mortality after adjustment for established risk factors and with Bonferroni correction for multiple testing. In the two-step analyses, the number of proteins selected for model inclusion in both random samples ranged from 6 to 21 depending on the method used. However, only three proteins were consistently included in both samples across all four methods (growth/differentiation factor-15 (GDF-15), N-terminal pro-B-type natriuretic peptide, and epididymal secretory protein E4). Using the total study population, the C-statistic for a model including established risk factors was 0.7222 and increased to 0.7284 with inclusion of the most predictive protein (GDF-15; P < 0.0001). All multiple protein models showed additional improvement in the C-statistic compared to the single protein model (all P < 0.0001). We identified several plasma proteins associated with increased risk of all-cause mortality independently of established risk factors. Further investigation into the putatively causal role of these proteins for longevity is needed. In addition, the examined methods for identifying multiple proteins showed tendencies for overfitting by including several putatively false positive findings. Thus, the reproducibility of findings using such approaches may be limited.", "doi": "10.1038/s41598-021-85991-z", "pmid": "33762603", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-85991-z"}, {"db": "pmc", "key": "PMC7990913"}], "notes": [], "created": "2021-12-10T15:27:31.206Z", "modified": "2021-12-10T15:27:31.221Z"}, {"entity": "publication", "iuid": "39b779b2142a463492160dd0c2f149da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39b779b2142a463492160dd0c2f149da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39b779b2142a463492160dd0c2f149da"}}, "title": "Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex.", "authors": [{"family": "Stenmark", "given": "Bianca", "initials": "B"}, {"family": "Eriksson", "given": "Lorraine", "initials": "L"}, {"family": "Thulin Hedberg", "given": "Sara", "initials": "S"}, {"family": "Anton", "given": "Brian P", "initials": "BP"}, {"family": "Fomenkov", "given": "Alexey", "initials": "A"}, {"family": "Roberts", "given": "Richard J", "initials": "RJ"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2021-03-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "6239"}, "abstract": "A rising incidence of meningococcal serogroup W disease has been evident in many countries worldwide. Serogroup W isolates belonging to the sequence type (ST)-11 clonal complex have been associated with atypical symptoms and increased case fatality rates. The continued expansion of this clonal complex in the later part of the 2010s has been largely due to a shift from the so-called original UK strain to the 2013 strain. Here we used single-molecule real-time (SMRT) sequencing to determine the methylomes of the two major serogroup W strains belonging to ST-11 clonal complex. Five methylated motifs were identified in this study, and three of the motifs, namely 5'-GATC-3', 5'-GAAGG-3', 5'-GCGCGC-3', were found in all 13 isolates investigated. The results showed no strain-specific motifs or difference in active restriction modification systems between the two strains. Two phase variable methylases were identified and the enrichment or depletion of the methylation motifs generated by these methylases varied between the two strains. Results from this work give further insight into the low diversity of methylomes in highly related strains and encourage further research to decipher the role of regions with under- or overrepresented methylation motifs.", "doi": "10.1038/s41598-021-85266-7", "pmid": "33737546", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-85266-7"}, {"db": "pmc", "key": "PMC7973814"}], "notes": [], "created": "2021-12-08T10:03:13.416Z", "modified": "2021-12-08T12:29:33.622Z"}, {"entity": "publication", "iuid": "b3c72707ac064b0c8c7434c3d0f93d4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3c72707ac064b0c8c7434c3d0f93d4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3c72707ac064b0c8c7434c3d0f93d4c"}}, "title": "Proteomic blood profiling in mild, severe and critical COVID-19 patients.", "authors": [{"family": "Patel", "given": "Hamel", "initials": "H", "orcid": "0000-0001-7951-6728", "researcher": {"href": "https://publications.scilifelab.se/researcher/159bd008db1c4b78b68bdc4996944f4d.json"}}, {"family": "Ashton", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-3579-8804", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a9f8df1bf6f4c4d998e04cc806de93d.json"}}, {"family": "Dobson", "given": "Richard J B", "initials": "RJB", "orcid": "0000-0003-4224-9245", "researcher": {"href": "https://publications.scilifelab.se/researcher/098ba38a51a64ba89362ed2a2e51455f.json"}}, {"family": "Andersson", "given": "Lars-Magnus", "initials": "LM"}, {"family": "Yilmaz", "given": "Aylin", "initials": "A"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Gisslen", "given": "Magnus", "initials": "M"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}], "type": "comparative study", "published": "2021-03-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "6357", "issn-l": "2045-2322"}, "abstract": "The recent SARS-CoV-2 pandemic manifests itself as a mild respiratory tract infection in most individuals, leading to COVID-19 disease. However, in some infected individuals, this can progress to severe pneumonia and acute respiratory distress syndrome (ARDS), leading to multi-organ failure and death. This study explores the proteomic differences between mild, severe, and critical COVID-19 positive patients to further understand the disease progression, identify proteins associated with disease severity, and identify potential therapeutic targets. Blood protein profiling was performed on 59 COVID-19 mild (n = 26), severe (n = 9) or critical (n = 24) cases and 28 controls using the OLINK inflammation, autoimmune, cardiovascular and neurology panels. Differential expression analysis was performed within and between disease groups to generate nine different analyses. From the 368 proteins measured per individual, more than 75% were observed to be significantly perturbed in COVID-19 cases. Six proteins (IL6, CKAP4, Gal-9, IL-1ra, LILRB4 and PD-L1) were identified to be associated with disease severity. The results have been made readily available through an interactive web-based application for instant data exploration and visualization, and can be accessed at https://phidatalab-shiny.rosalind.kcl.ac.uk/COVID19/ . Our results demonstrate that dynamic changes in blood proteins associated with disease severity can potentially be used as early biomarkers to monitor disease severity in COVID-19 and serve as potential therapeutic targets.", "doi": "10.1038/s41598-021-85877-0", "pmid": "33737684", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-85877-0"}, {"db": "pmc", "key": "PMC7973581"}], "notes": [], "created": "2021-12-10T09:30:03.774Z", "modified": "2021-12-10T09:30:03.901Z"}, {"entity": "publication", "iuid": "ca4dafbbd83345d6a632399e59edbea3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca4dafbbd83345d6a632399e59edbea3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca4dafbbd83345d6a632399e59edbea3"}}, "title": "Prevalence of germline pathogenic variants in 22 cancer susceptibility genes in Swedish pediatric cancer patients.", "authors": [{"family": "von Stedingk", "given": "Kristoffer", "initials": "K"}, {"family": "Stjernfelt", "given": "Karl-Johan", "initials": "KJ"}, {"family": "Kvist", "given": "Anders", "initials": "A"}, {"family": "Wahlstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Kristoffersson", "given": "Ulf", "initials": "U"}, {"family": "Stenmark-Askmalm", "given": "Marie", "initials": "M"}, {"family": "Wiebe", "given": "Thomas", "initials": "T"}, {"family": "Hjorth", "given": "Lars", "initials": "L"}, {"family": "Koster", "given": "Jan", "initials": "J"}, {"family": "Olsson", "given": "H\u00e5kan", "initials": "H"}, {"family": "\u00d8ra", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2021-03-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "5307", "issn-l": "2045-2322"}, "abstract": "Up to 10% of pediatric cancer patients harbor pathogenic germline variants in one or more cancer susceptibility genes. A recent study from the US reported pathogenic variants in 22 out of 60 analyzed autosomal dominant cancer susceptibility genes, implicating 8.5% of pediatric cancer patients. Here we aimed to assess the prevalence of germline pathogenic variants in these 22 genes in a population-based Swedish cohort and to compare the results to those described in other populations. We found pathogenic variants in 10 of the 22 genes covering 3.8% of these patients. The prevalence of TP53 mutations was significantly lower than described in previous studies, which can largely be attributed to differences in tumor diagnosis distributions across the three cohorts. Matched family history for relatives allowed assessment of familial cancer incidence, however, no significant difference in cancer incidence was found in families of children carrying pathogenic variants compared to those who did not.", "doi": "10.1038/s41598-021-84502-4", "pmid": "33674644", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-84502-4"}, {"db": "pmc", "key": "PMC7935871"}], "notes": [], "created": "2021-11-23T13:36:54.901Z", "modified": "2021-11-23T13:36:54.913Z"}, {"entity": "publication", "iuid": "0559012b6a794712a2e715cd54bf57e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0559012b6a794712a2e715cd54bf57e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0559012b6a794712a2e715cd54bf57e3"}}, "title": "A two-tiered targeted proteomics approach to identify pre-diagnostic biomarkers of colorectal cancer risk.", "authors": [{"family": "Harlid", "given": "Sophia", "initials": "S"}, {"family": "Harbs", "given": "Justin", "initials": "J"}, {"family": "Myte", "given": "Robin", "initials": "R"}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Gunter", "given": "Marc J", "initials": "MJ"}, {"family": "Palmqvist", "given": "Richard", "initials": "R"}, {"family": "Liu", "given": "Xijia", "initials": "X"}, {"family": "Van Guelpen", "given": "Bethany", "initials": "B"}], "type": "journal article", "published": "2021-03-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "5151", "issn-l": "2045-2322"}, "abstract": "Colorectal cancer prognosis is dependent on stage, and measures to improve early detection are urgently needed. Using prospectively collected plasma samples from the population-based Northern Sweden Health and Disease Study, we evaluated protein biomarkers in relation to colorectal cancer risk. Applying a two-tiered approach, we analyzed 160 proteins in matched sequential samples from 58 incident colorectal cancer case-control pairs. Twenty-one proteins selected from both this discovery phase and the literature were then analyzed in a validation set of 450 case-control pairs. Odds ratios were estimated by conditional logistic regression. LASSO regression and ROC analysis were used for multi-marker analyses. In the main validation analysis, no proteins retained statistical significance. However, exploratory subgroup analyses showed associations between FGF-21 and colon cancer risk (multivariable OR per 1 SD: 1.23 95% CI 1.03-1.47) as well as between PPY and rectal cancer risk (multivariable OR per 1 SD: 1.47 95% CI 1.12-1.92). Adding protein markers to basic risk predictive models increased performance modestly. Our results highlight the challenge of developing biomarkers that are effective in the asymptomatic, prediagnostic window of opportunity for early detection of colorectal cancer. Distinguishing between cancer subtypes may improve prediction accuracy. However, single biomarkers or small panels may not be sufficient for effective precision screening.", "doi": "10.1038/s41598-021-83968-6", "pmid": "33664295", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-83968-6"}, {"db": "pmc", "key": "PMC7933352"}], "notes": [], "created": "2021-12-10T09:23:12.082Z", "modified": "2021-12-10T09:23:12.096Z"}, {"entity": "publication", "iuid": "5e5f1508d37040dcb78aba8b44f02efd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e5f1508d37040dcb78aba8b44f02efd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e5f1508d37040dcb78aba8b44f02efd"}}, "title": "Antibodies to SARS-CoV-2 and risk of past or future sick leave.", "authors": [{"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Elfstr\u00f6m", "given": "K Miriam", "initials": "KM"}, {"family": "Blomqvist", "given": "Jonas", "initials": "J"}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Nordqvist-Kleppe", "given": "Sara", "initials": "S"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Jernbom Falk", "given": "August", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Hultin", "given": "Emilie", "initials": "E"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Mattsson", "given": "Johan", "initials": "J"}, {"family": "M\u00fchr", "given": "Laila Sara Arroyo", "initials": "LSA"}, {"family": "Conneryd Lundgren", "given": "Kalle", "initials": "K"}], "type": "journal article", "published": "2021-03-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "5160", "issn-l": "2045-2322"}, "abstract": "The extent that antibodies to SARS-CoV-2 may protect against future virus-associated disease is unknown. We invited all employees (n = 15,300) at work at the Karolinska University Hospital, Stockholm, Sweden to participate in a study examining SARS-Cov-2 antibodies in relation to registered sick leave. For consenting 12,928 healthy hospital employees antibodies to SARS-CoV-2 could be determined and compared to participant sick leave records. Subjects with viral serum antibodies were not at excess risk for future sick leave (adjusted odds ratio (OR) controlling for age and sex: 0.85 [95% confidence interval (CI) (0.85 (0.43-1.68)]. By contrast, subjects with antibodies had an excess risk for sick leave in the weeks prior to testing [adjusted OR in multivariate analysis: 3.34 (2.98-3.74)]. Thus, presence of viral antibodies marks past disease and protection against excess risk of future disease. Knowledge of whether exposed subjects have had disease in the past or are at risk for future disease is essential for planning of control measures.Trial registration: First registered on 02/06/20, ClinicalTrials.gov NCT04411576.", "doi": "10.1038/s41598-021-84356-w", "pmid": "33664279", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-84356-w"}, {"db": "pmc", "key": "PMC7933367"}, {"db": "ClinicalTrials.gov", "key": "NCT04411576"}], "notes": [], "created": "2021-03-06T13:49:00.332Z", "modified": "2021-11-10T12:26:31.510Z"}, {"entity": "publication", "iuid": "5c5a5f2b09394d1bb33632eb074d5aaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c5a5f2b09394d1bb33632eb074d5aaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c5a5f2b09394d1bb33632eb074d5aaa"}}, "title": "Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.", "authors": [{"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2021-02-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "4076", "issn-l": "2045-2322"}, "abstract": "Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.", "doi": "10.1038/s41598-021-83541-1", "pmid": "33603054", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-83541-1"}, {"db": "pmc", "key": "PMC7893067"}], "notes": [], "created": "2021-02-23T09:14:46.854Z", "modified": "2024-01-16T13:48:40.658Z"}, {"entity": "publication", "iuid": "07220ba9675142568fe544ad74d55546", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07220ba9675142568fe544ad74d55546.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07220ba9675142568fe544ad74d55546"}}, "title": "The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals.", "authors": [{"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Johnston", "given": "Keira J A", "initials": "KJA"}, {"family": "Bailey", "given": "Mark E S", "initials": "MES"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Cullen", "given": "Breda", "initials": "B"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "deFaire", "given": "Ulf", "initials": "U"}, {"family": "Ferguson", "given": "Amy", "initials": "A"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Graham", "given": "Nicholas", "initials": "N"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Lyall", "given": "Donald M", "initials": "DM"}, {"family": "Lyall", "given": "Laura M", "initials": "LM"}, {"family": "Pell", "given": "Jill P", "initials": "JP"}, {"family": "Pirro", "given": "Matteo", "initials": "M"}, {"family": "Savonen", "given": "Kai", "initials": "K"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Tomainen", "given": "Tomi-Pekka", "initials": "T"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Ward", "given": "Joey", "initials": "J"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Smith", "given": "Daniel J", "initials": "DJ"}], "type": "journal article", "published": "2021-01-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "632"}, "abstract": "Understanding why individuals with severe mental illness (Schizophrenia, Bipolar Disorder and Major Depressive Disorder) have increased risk of cardiometabolic disease (including obesity, type 2 diabetes and cardiovascular disease), and identifying those at highest risk of cardiometabolic disease are important priority areas for researchers. For individuals with European ancestry we explored whether genetic variation could identify sub-groups with different metabolic profiles. Loci associated with schizophrenia, bipolar disorder and major depressive disorder from previous genome-wide association studies and loci that were also implicated in cardiometabolic processes and diseases were selected. In the IMPROVE study (a high cardiovascular risk sample) and UK Biobank (general population sample) multidimensional scaling was applied to genetic variants implicated in both psychiatric and cardiometabolic disorders. Visual inspection of the resulting plots used to identify distinct clusters. Differences between these clusters were assessed using chi-squared and Kruskall-Wallis tests. In IMPROVE, genetic loci associated with both schizophrenia and cardiometabolic disease (but not bipolar disorder or major depressive disorder) identified three groups of individuals with distinct metabolic profiles. This grouping was replicated within UK Biobank, with somewhat less distinction between metabolic profiles. This work focused on individuals of European ancestry and is unlikely to apply to more genetically diverse populations. Overall, this study provides proof of concept that common biology underlying mental and physical illness may help to stratify subsets of individuals with different cardiometabolic profiles.", "doi": "10.1038/s41598-020-79964-x", "pmid": "33436761", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-79964-x"}, {"db": "pmc", "key": "PMC7804422"}], "notes": [], "created": "2021-01-14T11:58:56.919Z", "modified": "2021-12-07T13:38:31.951Z"}, {"entity": "publication", "iuid": "68b97a92c535461cb6c041f6d14df2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68b97a92c535461cb6c041f6d14df2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68b97a92c535461cb6c041f6d14df2d1"}}, "title": "Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer.", "authors": [{"family": "Rendo", "given": "Veronica", "initials": "V"}, {"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "Rameika", "given": "Natallia", "initials": "N"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Palin", "given": "Kimmo", "initials": "K"}, {"family": "Aaltonen", "given": "Lauri", "initials": "L"}, {"family": "Stoimenov", "given": "Ivaylo", "initials": "I"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2020-12-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "22436"}, "abstract": "Therapies targeting somatic bystander genetic events represent a new avenue for cancer treatment. We recently identified a subset of colorectal cancer (CRC) patients who are heterozygous for a wild-type and a low activity allele (NAT2*6) but lack the wild-type allele in their tumors due to loss of heterozygosity (LOH) at 8p22. These tumors were sensitive to treatment with a cytotoxic substrate of NAT2 (6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine, APA), and pointed to NAT2 loss being a therapeutically exploitable vulnerability of CRC tumors. To better estimate the total number of treatable CRC patients, we here determined whether tumor cells retaining also other NAT2 low activity variants after LOH respond to APA treatment. The prevalent low activity alleles NAT2*5 and NAT2*14, but not NAT2*7, were found to be low metabolizers with high sensitivity to APA. By analysis of two different CRC patient cohorts, we detected heterozygosity for NAT2 alleles targetable by APA, along with allelic imbalances pointing to LOH, in ~ 24% of tumors. Finally, to haplotype the NAT2 locus in tumor and patient-matched normal samples in a clinical setting, we develop and demonstrate a long-read sequencing based assay. In total, > 79.000 CRC patients per year fulfil genetic criteria for high sensitivity to a NAT2 LOH therapy and their eligibility can be assessed by clinical sequencing.", "doi": "10.1038/s41598-020-80288-z", "pmid": "33384440", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-80288-z"}, {"db": "pmc", "key": "PMC7775439"}], "notes": [], "created": "2021-01-08T12:11:29.314Z", "modified": "2024-01-16T13:48:41.098Z"}, {"entity": "publication", "iuid": "ccdbb2999539431788b8756ce0867a5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ccdbb2999539431788b8756ce0867a5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ccdbb2999539431788b8756ce0867a5e"}}, "title": "Whole-genome sequencing of recurrent neuroblastoma reveals somatic mutations that affect key players in cancer progression and telomere maintenance.", "authors": [{"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "Martinez-Monleon", "given": "Angela", "initials": "A"}, {"family": "Johansson", "given": "Mathias", "initials": "M"}, {"family": "Sj\u00f6berg", "given": "Rose-Marie", "initials": "RM"}, {"family": "Bj\u00f6rklund", "given": "Caroline", "initials": "C"}, {"family": "Ljungman", "given": "Gustaf", "initials": "G"}, {"family": "Ek", "given": "Torben", "initials": "T"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2020-12-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "22432", "issn-l": "2045-2322"}, "abstract": "Neuroblastoma is the most common and deadly childhood tumor. Relapsed or refractory neuroblastoma has a very poor prognosis despite recent treatment advances. To investigate genomic alterations associated with relapse and therapy resistance, whole-genome sequencing was performed on diagnostic and relapsed lesions together with constitutional DNA from seven children. Sequencing of relapsed tumors indicates somatic alterations in diverse genes, including those involved in RAS-MAPK signaling, promoting cell cycle progression or function in telomere maintenance and immortalization. Among recurrent alterations, CCND1-gain, TERT-rearrangements, and point mutations in POLR2A, CDK5RAP, and MUC16 were shown in \u2265 2 individuals. Our cohort contained examples of converging genomic alterations in primary-relapse tumor pairs, indicating dependencies related to specific genetic lesions. We also detected rare genetic germline variants in DNA repair genes (e.g., BARD1, BRCA2, CHEK2, and WRN) that might cooperate with somatically acquired variants in these patients with highly aggressive recurrent neuroblastoma. Our data indicate the importance of monitoring recurrent neuroblastoma through sequential genomic characterization and that new therapeutic approaches combining the targeting of MAPK signaling, cell cycle progression, and telomere activity are required for this challenging patient group.", "doi": "10.1038/s41598-020-78370-7", "pmid": "33384420", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-78370-7"}, {"db": "pmc", "key": "PMC7775426"}], "notes": [], "created": "2022-03-29T13:38:03.020Z", "modified": "2022-03-29T13:38:03.033Z"}, {"entity": "publication", "iuid": "95f1d478c59c4366bc3dbf6010d97d4d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95f1d478c59c4366bc3dbf6010d97d4d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95f1d478c59c4366bc3dbf6010d97d4d"}}, "title": "A biomimetic engineered bone platform for advanced testing of prosthetic implants.", "authors": [{"family": "Sladkova-Faure", "given": "Martina", "initials": "M"}, {"family": "Pujari-Palmer", "given": "Michael", "initials": "M"}, {"family": "\u00d6hman-M\u00e4gi", "given": "Caroline", "initials": "C"}, {"family": "L\u00f3pez", "given": "Alejandro", "initials": "A"}, {"family": "Wang", "given": "Hanbin", "initials": "H"}, {"family": "Engqvist", "given": "H\u00e5kan", "initials": "H"}, {"family": "de Peppo", "given": "Giuseppe Maria", "initials": "GM"}], "type": "journal article", "published": "2020-12-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "22154", "issn-l": "2045-2322"}, "abstract": "Existing methods for testing prosthetic implants suffer from critical limitations, creating an urgent need for new strategies that facilitate research and development of implants with enhanced osseointegration potential. Herein, we describe a novel, biomimetic, human bone platform for advanced testing of implants in vitro, and demonstrate the scientific validity and predictive value of this approach using an assortment of complementary evaluation methods. We anchored titanium (Ti) and stainless steel (SS) implants into biomimetic scaffolds, seeded with human induced mesenchymal stem cells, to recapitulate the osseointegration process in vitro. We show distinct patterns of gene expression, matrix deposition, and mineralization in response to the two materials, with Ti implants ultimately resulting in stronger integration strength, as seen in other preclinical and clinical studies. Interestingly, RNAseq analysis reveals that the TGF-beta and the FGF2 pathways are overexpressed in response to Ti implants, while the Wnt, BMP, and IGF pathways are overexpressed in response to SS implants. High-resolution imaging shows significantly increased tissue mineralization and calcium deposition at the tissue-implant interface in response to Ti implants, contributing to a twofold increase in pullout strength compared to SS implants. Our technology creates unprecedented research opportunities towards the design of implants and biomaterials that can be personalized, and exhibit enhanced osseointegration potential, with reduced need for animal testing.", "doi": "10.1038/s41598-020-78416-w", "pmid": "33335113", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7747643"}, {"db": "pii", "key": "10.1038/s41598-020-78416-w"}], "notes": [], "created": "2022-11-25T08:01:42.131Z", "modified": "2022-11-25T08:01:42.135Z"}, {"entity": "publication", "iuid": "aac256774d0444cdbb512faa4cd1b346", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aac256774d0444cdbb512faa4cd1b346.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aac256774d0444cdbb512faa4cd1b346"}}, "title": "Genome-wide identification of Argonautes in Solanaceae with emphasis on potato.", "authors": [{"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Hod\u00e9n", "given": "Kristian Persson", "initials": "KP"}, {"family": "Singh", "given": "Ravi Kumar", "initials": "RK"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2020-11-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "20577", "issn-l": "2045-2322"}, "abstract": "Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.", "doi": "10.1038/s41598-020-77593-y", "pmid": "33239724", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-77593-y"}, {"db": "pmc", "key": "PMC7689493"}], "notes": [], "created": "2020-12-07T16:36:39.190Z", "modified": "2021-11-10T12:45:03.177Z"}, {"entity": "publication", "iuid": "4fb5d06e3be24800b8c60fd0a947e6b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fb5d06e3be24800b8c60fd0a947e6b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fb5d06e3be24800b8c60fd0a947e6b9"}}, "title": "High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood.", "authors": [{"family": "Petkov", "given": "Stefan", "initials": "S"}, {"family": "Bekele", "given": "Yonas", "initials": "Y"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Hejdeman", "given": "Bo", "initials": "B"}, {"family": "Zazzi", "given": "Maurizio", "initials": "M"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Chiodi", "given": "Francesca", "initials": "F"}], "type": "journal article", "published": "2020-11-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "20425", "issn-l": "2045-2322"}, "abstract": "Using mass cytometry, we investigated the expression of 28 markers on CD8+ and CD4+ T cells from HIV-1 infected patients with a variable size of HIV-1 reservoir defined as high (HR) and low (LR) reservoir; we aimed at identifying phenotypic associations of T cells with size of HIV-1 reservoir. We showed that the frequency of CD45+ CD8+ and CD4+ T cells was directly proportional to the size of HIV-1 reservoir; HR patients had a significantly larger frequency of blood CD45high T cells and higher CD45 expression on both CD8+ and CD4+ T cells. CD45 is a receptor-type protein tyrosine phosphatase essential in TCR signaling. Functional and phenotypical analysis of CD45high cells revealed that they express activation and proliferation markers (CD38 + HLA-DR + and Ki-67) and produce cytokines upon in vitro activation. CD45high T cells also expressed high levels of immune check-point PD-1. Our results link CD45 expression on T cells to HIV-1 reservoir; PD-1 expression on CD45high T cells may contribute to their exhaustion.", "doi": "10.1038/s41598-020-77433-z", "pmid": "33235273", "labels": {"Cellular Immunomonitoring": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-77433-z"}, {"db": "pmc", "key": "PMC7686502"}], "notes": [], "created": "2020-11-30T08:25:42.449Z", "modified": "2024-01-16T13:48:41.309Z"}, {"entity": "publication", "iuid": "f5382fa2acda4d9c8e8301fb63479538", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5382fa2acda4d9c8e8301fb63479538.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5382fa2acda4d9c8e8301fb63479538"}}, "title": "\u03b1-Synuclein promotes IAPP fibril formation in vitro and \u03b2-cell amyloid formation in vivo in mice.", "authors": [{"family": "Mucibabic", "given": "Marija", "initials": "M"}, {"family": "Steneberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Lidh", "given": "Emmelie", "initials": "E"}, {"family": "Straseviciene", "given": "Jurate", "initials": "J"}, {"family": "Ziolkowska", "given": "Agnieszka", "initials": "A", "orcid": "0000-0002-4262-7106", "researcher": {"href": "https://publications.scilifelab.se/researcher/1355ff26d9cf4626bad7b3b93bf0a90d.json"}}, {"family": "Dahl", "given": "Ulf", "initials": "U"}, {"family": "Lindahl", "given": "Emma", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Edlund", "given": "Helena", "initials": "H"}], "type": "journal article", "published": "2020-11-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "20438", "issn-l": "2045-2322"}, "abstract": "Type 2 diabetes (T2D), alike Parkinson's disease (PD), belongs to the group of protein misfolding diseases (PMDs), which share aggregation of misfolded proteins as a hallmark. Although the major aggregating peptide in \u03b2-cells of T2D patients is Islet Amyloid Polypeptide (IAPP), alpha-synuclein (\u03b1Syn), the aggregating peptide in substantia nigra neurons of PD patients, is expressed also in \u03b2-cells. Here we show that \u03b1Syn, encoded by Snca, is a component of amyloid extracted from pancreas of transgenic mice overexpressing human IAPP (denoted hIAPPtg mice) and from islets of T2D individuals. Notably, \u03b1Syn dose-dependently promoted IAPP fibril formation in vitro and tail-vein injection of \u03b1Syn in hIAPPtg mice enhanced \u03b2-cell amyloid formation in vivo whereas \u03b2-cell amyloid formation was reduced in hIAPPtg mice on a Snca -/- background. Taken together, our findings provide evidence that \u03b1Syn and IAPP co-aggregate both in vitro and in vivo, suggesting a role for \u03b1Syn in \u03b2-cell amyloid formation.", "doi": "10.1038/s41598-020-77409-z", "pmid": "33235246", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-77409-z"}, {"db": "pmc", "key": "PMC7686322"}], "notes": [], "created": "2020-12-10T11:07:23.272Z", "modified": "2023-12-04T10:15:38.252Z"}, {"entity": "publication", "iuid": "29d8a642e60f4a8ca18b324c9ff46682", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29d8a642e60f4a8ca18b324c9ff46682.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29d8a642e60f4a8ca18b324c9ff46682"}}, "title": "Inactivation of mediator complex protein 22 in podocytes results in intracellular vacuole formation, podocyte loss and premature death.", "authors": [{"family": "Rodriguez", "given": "Patricia Q", "initials": "PQ"}, {"family": "Unnersj\u00f6-Jess", "given": "David", "initials": "D"}, {"family": "Zambrano", "given": "Sonia S", "initials": "SS"}, {"family": "Guo", "given": "Jing", "initials": "J"}, {"family": "M\u00f6ller-Hackbarth", "given": "Katja", "initials": "K"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Jahnukainen", "given": "Timo", "initials": "T"}, {"family": "Ebarasi", "given": "Lwaki", "initials": "L"}, {"family": "Patrakka", "given": "Jaakko", "initials": "J"}], "type": "journal article", "published": "2020-11-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "20037", "issn-l": "2045-2322"}, "abstract": "Podocytes are critical for the maintenance of kidney ultrafiltration barrier and play a key role in the progression of glomerular diseases. Although mediator complex proteins have been shown to be important for many physiological and pathological processes, their role in kidney tissue has not been studied. In this study, we identified a mediator complex protein 22 (Med22) as a renal podocyte cell-enriched molecule. Podocyte-specific Med22 knockout mouse showed that Med22 was not needed for normal podocyte maturation. However, it was critical for the maintenance of podocyte health as the mice developed progressive glomerular disease and died due to renal failure. Detailed morphological analyses showed that Med22-deficiency in podocytes resulted in intracellular vacuole formation followed by podocyte loss. Moreover, Med22-deficiency in younger mice promoted the progression of glomerular disease, suggesting Med22-mediated processes may have a role in the development of glomerulopathies. This study shows for the first time that mediator complex has a critical role in kidney physiology.", "doi": "10.1038/s41598-020-76870-0", "pmid": "33208756", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-76870-0"}, {"db": "pmc", "key": "PMC7676236"}], "notes": [], "created": "2020-11-18T16:01:37.186Z", "modified": "2021-11-10T12:45:08.719Z"}, {"entity": "publication", "iuid": "ecde5defaf5b4cf9bfcd95fb462ff3b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecde5defaf5b4cf9bfcd95fb462ff3b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecde5defaf5b4cf9bfcd95fb462ff3b8"}}, "title": "Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship.", "authors": [{"family": "Marzouka", "given": "Nour-Al-Dain", "initials": "NA"}, {"family": "Lindgren", "given": "David", "initials": "D"}, {"family": "Eriksson", "given": "Pontus", "initials": "P"}, {"family": "Sj\u00f6dahl", "given": "Gottfrid", "initials": "G"}, {"family": "Bernardo", "given": "Carina", "initials": "C"}, {"family": "Liedberg", "given": "Fredrik", "initials": "F"}, {"family": "Axelson", "given": "H\u00e5kan", "initials": "H"}, {"family": "H\u00f6glund", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2020-11-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "19539", "issn-l": "2045-2322"}, "abstract": "We used the fact that patients with non-muscle invasive bladder tumors show local recurrences and multiple tumors to study re-initiation of tumor growth from the same urothelium. By extensive genomic analyses we show that tumors from the same patient are clonal. We show that gross genomic chromosomal aberrations may be detected in one tumor, only to be undetected in a recurrent tumor. By analyses of incompatible changes i.e., genomic alterations that cannot be reversed, we show that almost all tumors from a single patient may show such changes, thus the tumors cannot have originated from each other. As recurring tumors share both genomic alterations and driver gene mutations, these must have been present in the urothelium in periods with no tumor growth. We present a model that includes a growing and evolving field of urothelial cells that occasionally, and locally, produce bursts of cellular growth leading to overt tumors.", "doi": "10.1038/s41598-020-75854-4", "pmid": "33177554", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-75854-4"}, {"db": "pmc", "key": "PMC7658206"}], "notes": [], "created": "2021-11-25T09:35:36.155Z", "modified": "2021-11-25T09:35:36.161Z"}, {"entity": "publication", "iuid": "a8fd622b15c7467f997c96de28f1a14e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8fd622b15c7467f997c96de28f1a14e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8fd622b15c7467f997c96de28f1a14e"}}, "title": "Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.", "authors": [{"family": "Mathioudaki", "given": "Argyri", "initials": "A"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Melin", "given": "Malin", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "Arendt", "given": "Maja Louise", "initials": "ML"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Saksena", "given": "Pushpa", "initials": "P"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2020-11-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "19304", "issn-l": "2045-2322"}, "abstract": "Breast cancer (BC) is a genetically heterogeneous disease with high prevalence in Northern Europe. However, there has been no detailed investigation into the Scandinavian somatic landscape. Here, in a homogeneous Swedish cohort, we describe the somatic events underlying BC, leveraging a targeted next-generation sequencing approach. We designed a 20.5 Mb array targeting coding and regulatory regions of genes with a known role in BC (n = 765). The selected genes were either from human BC studies (n = 294) or from within canine mammary tumor associated regions (n = 471). A set of predominantly estrogen receptor positive tumors (ER + 85%) and their normal tissue counterparts (n = 61) were sequenced to ~ 140 \u00d7 and 85 \u00d7 mean target coverage, respectively. MuTect2 and VarScan2 were employed to detect single nucleotide variants (SNVs) and copy number aberrations (CNAs), while MutSigCV (SNVs) and GISTIC (CNAs) algorithms estimated the significance of recurrent somatic events. The significantly mutated genes (q \u2264 0.01) were PIK3CA (28% of patients), TP53 (21%) and CDH1 (11%). However, histone modifying genes contained the largest number of variants (KMT2C and ARID1A, together 28%). Mutations in KMT2C were mutually exclusive with PI3KCA mutations (p \u2264 0. 001) and half of these affect the formation of a functional PHD domain. The tumor suppressor CDK10 was deleted in 80% of the cohort while the oncogene MDM4 was amplified. Mutational signature analyses pointed towards APOBEC deaminase activity (COSMIC signature 2) and DNA mismatch repair (COSMIC signature 6). We noticed two significantly distinct patterns related to patient age; TP53 being more mutated in the younger group (29% vs 9% of patients) and CDH23 mutations were absent from the older group. The increased somatic mutation prevalence in the histone modifying genes KMT2C and ARID1A distinguishes the Swedish cohort from previous studies. KMT2C regulates enhancer activation and assists tumor proliferation in a hormone-rich environment, possibly pointing to a role in ER + BC, especially in older cases. Finally, age of onset appears to affect the mutational landscape suggesting that a larger age-diverse population incorporating more molecular subtypes should be studied to elucidate the underlying mechanisms.", "doi": "10.1038/s41598-020-74580-1", "pmid": "33168853", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-74580-1"}, {"db": "pmc", "key": "PMC7653953"}], "notes": [], "created": "2020-12-08T23:29:22.318Z", "modified": "2024-01-16T13:48:41.384Z"}, {"entity": "publication", "iuid": "50a7dfe154a54741bad9e00e32d6c6c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50a7dfe154a54741bad9e00e32d6c6c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50a7dfe154a54741bad9e00e32d6c6c5"}}, "title": "Evolution from adherent to suspension: systems biology of HEK293 cell line development.", "authors": [{"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Saghaleyni", "given": "Rasool", "initials": "R"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Giudici", "given": "Marco", "initials": "M"}, {"family": "Chotteau", "given": "Veronique", "initials": "V"}, {"family": "Field", "given": "Ray", "initials": "R"}, {"family": "Varley", "given": "Paul G", "initials": "PG"}, {"family": "Hatton", "given": "Diane", "initials": "D"}, {"family": "Grassi", "given": "Luigi", "initials": "L"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "comparative study", "published": "2020-11-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "18996"}, "abstract": "The need for new safe and efficacious therapies has led to an increased focus on biologics produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for human-like production attributes and is currently used for manufacturing of several therapeutic proteins and viral vectors. Despite the increased popularity of this strain we still have limited knowledge on the genetic composition of its derivatives. Here we present a genomic, transcriptomic and metabolic gene analysis of six of the most widely used HEK293 cell lines. Changes in gene copy and expression between industrial progeny cell lines and the original HEK293 were associated with cellular component organization, cell motility and cell adhesion. Changes in gene expression between adherent and suspension derivatives highlighted switching in cholesterol biosynthesis and expression of five key genes (RARG, ID1, ZIC1, LOX and DHRS3), a pattern validated in 63 human adherent or suspension cell lines of other origin.", "doi": "10.1038/s41598-020-76137-8", "pmid": "33149219", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-76137-8"}, {"db": "pmc", "key": "PMC7642379"}], "notes": [], "created": "2020-12-07T16:34:45.132Z", "modified": "2022-02-14T12:16:01.662Z"}, {"entity": "publication", "iuid": "61faf99df7d143678abba24c31bdb534", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61faf99df7d143678abba24c31bdb534.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61faf99df7d143678abba24c31bdb534"}}, "title": "Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.", "authors": [{"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Gyllenstrand", "given": "Niclas", "initials": "N"}, {"family": "Widemo", "given": "Fredrik", "initials": "F"}, {"family": "Liljeb\u00e4ck", "given": "Niklas", "initials": "N"}, {"family": "Svensson", "given": "Mikael", "initials": "M"}, {"family": "Sj\u00f6gren-Gulve", "given": "Per", "initials": "P"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2020-10-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "18347", "issn-l": "2045-2322"}, "abstract": "Interspecific introgression is considered a potential threat to endangered taxa. One example where this has had a major impact on conservation policy is the lesser white-fronted goose (LWfG). After a dramatic decline in Sweden, captive breeding birds were released between 1981-1999 with the aim to reinforce the population. However, the detection of greater white-fronted goose (GWfG) mitochondrial DNA in the LWfG breeding stock led to the release program being dismantled, even though the presence of GWfG introgression in the actual wild Swedish LWfG population was never documented. To examine this, we sequenced the complete genomes of 21 LWfG birds from the Swedish, Russian and Norwegian populations, and compared these with genomes from other goose species, including the GWfG. We found no evidence of interspecific introgression into the wild Swedish LWfG population in either nuclear genomic or mitochondrial data. Moreover, Swedish LWfG birds are genetically distinct from the Russian and Norwegian populations and display comparatively low genomic diversity and high levels of inbreeding. Our findings highlight the utility of genomic approaches in providing scientific evidence that can help improve conservation management as well as policies for breeding and reinforcement programmes.", "doi": "10.1038/s41598-020-75315-y", "pmid": "33110153", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-75315-y"}, {"db": "pmc", "key": "PMC7591532"}], "notes": [], "created": "2020-12-07T16:34:43.881Z", "modified": "2024-01-16T13:48:41.531Z"}, {"entity": "publication", "iuid": "81637524a179454eacfeca141c6eac13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81637524a179454eacfeca141c6eac13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81637524a179454eacfeca141c6eac13"}}, "title": "Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients.", "authors": [{"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Bruhn", "given": "S\u00f6ren", "initials": "S"}, {"family": "Andersson", "given": "Anna", "initials": "A"}, {"family": "Wikberg", "given": "Gustav", "initials": "G"}, {"family": "Lundeberg", "given": "Lena", "initials": "L"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Greco", "given": "Dario", "initials": "D"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2020-10-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "18020", "issn-l": "2045-2322"}, "abstract": "T cells expressing the cutaneous lymphocyte antigen (CLA) mediate pathogenic inflammation in atopic dermatitis (AD). The molecular alterations contributing to their dysregulation remain unclear. With the aim to elucidate putative altered pathways in AD we profiled DNA methylation levels and miRNA expression in sorted T cell populations (CD4+, CD4+CD45RA+ na\u00efve, CD4+CLA+, and CD8+) from adult AD patients and healthy controls (HC). Skin homing CD4+CLA+ T cells from AD patients showed significant differences in DNA methylation in 40 genes compared to HC (p < 0.05). Reduced DNA methylation levels in the upstream region of the interleukin-13 gene (IL13) in CD4+CLA+ T cells from AD patients correlated with increased IL13 mRNA expression in these cells. Sixteen miRNAs showed differential expression in CD4+CLA+ T cells from AD patients targeting genes in 202 biological processes (p < 0.05). An integrated network analysis of miRNAs and CpG sites identified two communities of strongly interconnected regulatory elements with strong antagonistic behaviours that recapitulated the differences between AD patients and HC. Functional analysis of the genes linked to these communities revealed their association with key cytokine signaling pathways, MAP kinase signaling and protein ubiquitination. Our findings support that epigenetic mechanisms play a role in the pathogenesis of AD by affecting inflammatory signaling molecules in skin homing CD4+CLA+ T cells and uncover putative molecules participating in AD pathways.", "doi": "10.1038/s41598-020-74798-z", "pmid": "33093567", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-74798-z"}, {"db": "pmc", "key": "PMC7582180"}], "notes": [], "created": "2020-10-26T09:04:32.192Z", "modified": "2024-01-16T13:48:41.543Z"}, {"entity": "publication", "iuid": "73ca2e71397248f8a37be2560bd5c0e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73ca2e71397248f8a37be2560bd5c0e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73ca2e71397248f8a37be2560bd5c0e7"}}, "title": "High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.", "authors": [{"family": "Hases", "given": "L", "initials": "L"}, {"family": "Archer", "given": "A", "initials": "A"}, {"family": "Indukuri", "given": "R", "initials": "R"}, {"family": "Birgersson", "given": "M", "initials": "M"}, {"family": "Savva", "given": "C", "initials": "C"}, {"family": "Korach-Andr\u00e9", "given": "M", "initials": "M"}, {"family": "Williams", "given": "C", "initials": "C"}], "type": "journal article", "published": "2020-09-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "16160", "issn-l": "2045-2322"}, "abstract": "There is a strong association between obesity and colorectal cancer (CRC), especially in men, whereas estrogen protects against both the metabolic syndrome and CRC. Colon is the first organ to respond to high-fat diet (HFD), and estrogen receptor beta (ER\u03b2) can attenuate CRC development. How estrogen impacts the colon under HFD and related sex differences has, however, not been investigated. To dissect this, mice were fed control diet or HFD for 13 weeks and administered receptor-selective estrogenic ligands for the last three weeks. We recorded impact on metabolism, colon crypt proliferation, macrophage infiltration, and the colon transcriptome. We found clear sex differences in the colon transcriptome and in the impact by HFD and estrogens, including on clock genes. ER\u03b1-selective activation reduced body weight and generated systemic effects, whereas ER\u03b2-selective activation had local effects in the colon, attenuating HFD-induced macrophage infiltration and epithelial cell proliferation. We here demonstrate how HFD and estrogens modulate the colon microenvironment in a sex- and ER-specific manner.", "doi": "10.1038/s41598-020-73166-1", "pmid": "32999402", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-73166-1"}, {"db": "pmc", "key": "PMC7527340"}], "notes": [], "created": "2020-12-07T16:32:31.546Z", "modified": "2024-01-16T13:48:41.674Z"}, {"entity": "publication", "iuid": "c61c5e3bfa1f45f0b6deccba8623d717", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c61c5e3bfa1f45f0b6deccba8623d717.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c61c5e3bfa1f45f0b6deccba8623d717"}}, "title": "Parvimonas micra as a putative non-invasive faecal biomarker for colorectal cancer.", "authors": [{"family": "L\u00f6wenmark", "given": "Thyra", "initials": "T"}, {"family": "L\u00f6fgren-Burstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Zingmark", "given": "Carl", "initials": "C"}, {"family": "Ekl\u00f6f", "given": "Vincy", "initials": "V"}, {"family": "Dahlberg", "given": "Michael", "initials": "M"}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN"}, {"family": "Larsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-9054-5191", "researcher": {"href": "https://publications.scilifelab.se/researcher/573c6350305a49cba2ac0798dea21ae0.json"}}, {"family": "Ljuslinder", "given": "Ingrid", "initials": "I"}, {"family": "Edin", "given": "Sofia", "initials": "S"}, {"family": "Palmqvist", "given": "Richard", "initials": "R", "orcid": "0000-0002-9933-2843", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ae823e5364458b8f957a65a82c741f.json"}}], "type": "journal article", "published": "2020-09-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "15250"}, "abstract": "The use of faecal microbial markers as non-invasive biomarkers for colorectal cancer (CRC) has been suggested, but not fully elucidated. Here, we have evaluated the importance of Parvimonas micra as a potential non-invasive faecal biomarker in CRC and its relation to other microbial biomarkers. The levels of P. micra, F. nucleatum and clbA + bacteria were quantified using qPCR in faecal samples from a population-based cohort of patients undergoing colonoscopy due to symptoms from the large bowel. The study included 38 CRC patients, 128 patients with dysplasia and 63 controls. The results were validated in a second consecutive CRC cohort including faecal samples from 238 CRC patients and 94 controls. We found significantly higher levels of P. micra in faecal samples from CRC patients compared to controls. A test for P. micra could detect CRC with a specificity of 87.3% and a sensitivity of 60.5%. In addition, we found that combining P. micra with other microbial markers, could further enhance test sensitivity. Our findings support the potential use of P. micra as a non-invasive biomarker for CRC. Together with other microbial faecal markers, P. micra may identify patients with \"high risk\" microbial patterns, indicating increased risk and incidence of cancer.", "doi": "10.1038/s41598-020-72132-1", "pmid": "32943695", "labels": {"Clinical Genomics Ume\u00e5": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-72132-1"}, {"db": "pmc", "key": "PMC7499209"}], "notes": [], "created": "2021-06-18T12:03:49.145Z", "modified": "2021-12-08T14:18:07.401Z"}, {"entity": "publication", "iuid": "0a4b469382934005bf79f0c29264def6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a4b469382934005bf79f0c29264def6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a4b469382934005bf79f0c29264def6"}}, "title": "Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.", "authors": [{"family": "Vaga", "given": "Stefania", "initials": "S"}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Ji", "given": "Boyang", "initials": "B"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ"}, {"family": "Agr\u00e9us", "given": "Lars", "initials": "L"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Kovatcheva-Datchary", "given": "Petia", "initials": "P"}, {"family": "Park", "given": "Junseok", "initials": "J"}, {"family": "Lee", "given": "Doheon", "initials": "D"}, {"family": "Proctor", "given": "Gordon", "initials": "G"}, {"family": "Ehrlich", "given": "Stanislav Dusko", "initials": "SD"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}], "type": "clinical trial", "published": "2020-09-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "14977", "issn-l": "2045-2322"}, "abstract": "Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.", "doi": "10.1038/s41598-020-71939-2", "pmid": "32917913", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-71939-2"}, {"db": "pmc", "key": "PMC7486370"}], "notes": [], "created": "2020-12-07T16:28:54.238Z", "modified": "2024-01-16T13:48:41.733Z"}, {"entity": "publication", "iuid": "be2d410b6d474dcdb78678c145767abe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be2d410b6d474dcdb78678c145767abe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be2d410b6d474dcdb78678c145767abe"}}, "title": "Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.", "authors": [{"family": "Liang", "given": "Shuo", "initials": "S"}, {"family": "Ezerskyte", "given": "Monika", "initials": "M"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Dreij", "given": "Kristian", "initials": "K"}], "type": "journal article", "published": "2020-08-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "13513", "issn-l": "2045-2322"}, "abstract": "The transcriptional error rate can be significantly increased by the presence of DNA lesions that instruct mis-insertion during transcription; a process referred to as transcriptional mutagenesis (TM) that can result in altered protein function. Herein, we determined the effect of O6-methylguanine (O6-meG) on transcription and subsequent transactivation activity of p53 in human lung H1299 cells. Levels of TM and effects on transactivation were determined genome wide by RNA-seq. Results showed that 47% of all p53 transcripts contained an uridine misincorporation opposite the lesion at 6 h post transfection, which was decreased to 18% at 24 h. TM at these levels reduced DNA binding activity of p53 to 21% and 80% compared to wild type p53, respectively. Gene expression data were analysed to identify differentially expressed genes due to TM of p53. We show a temporal repression of transactivation of > 100 high confidence p53 target genes including regulators of the cell cycle, DNA damage response and apoptosis. In addition, TM repressed the transcriptional downregulation by p53 of several negative regulators of proliferation and differentiation. Our work demonstrates that TM, even when restricting its effect to an individual transcription factor, has the potential to alter gene expression programs and diversify cellular phenotypes.", "doi": "10.1038/s41598-020-70412-4", "pmid": "32782319", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-70412-4"}, {"db": "pmc", "key": "PMC7419513"}], "notes": [], "created": "2021-01-08T16:29:43.891Z", "modified": "2021-11-10T12:48:22.899Z"}, {"entity": "publication", "iuid": "334ff8346e7c4ab08d762177f2e68739", "links": {"self": {"href": "https://publications.scilifelab.se/publication/334ff8346e7c4ab08d762177f2e68739.json"}, "display": {"href": "https://publications.scilifelab.se/publication/334ff8346e7c4ab08d762177f2e68739"}}, "title": "Mebendazole is unique among tubulin-active drugs in activating the MEK-ERK pathway.", "authors": [{"family": "Andersson", "given": "Claes R", "initials": "CR"}, {"family": "Selvin", "given": "Tove", "initials": "T"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Rubin", "given": "Jenny", "initials": "J"}, {"family": "Berglund", "given": "Malin", "initials": "M"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Lenhammar", "given": "Lena", "initials": "L"}, {"family": "Parrow", "given": "Vendela", "initials": "V"}, {"family": "Loskog", "given": "Angelica", "initials": "A"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2020-08-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "13124", "issn-l": "2045-2322"}, "abstract": "We recently showed that the anti-helminthic compound mebendazole (MBZ) has immunomodulating activity in monocyte/macrophage models and induces ERK signalling. In the present study we investigated whether MBZ induced ERK activation is shared by other tubulin binding agents (TBAs) and if it is observable also in other human cell types. Curated gene signatures for a panel of TBAs in the LINCS Connectivity Map (CMap) database showed a unique strong negative correlation of MBZ with MEK/ERK inhibitors indicating ERK activation also in non-haematological cell lines. L1000 gene expression signatures for MBZ treated THP-1 monocytes also connected negatively to MEK inhibitors. MEK/ERK phosphoprotein activity testing of a number of TBAs showed that only MBZ increased the activity in both THP-1 monocytes and PMA differentiated macrophages. Distal effects on ERK phosphorylation of the substrate P90RSK and release of IL1B followed the same pattern. The effect of MBZ on MEK/ERK phosphorylation was inhibited by RAF/MEK/ERK inhibitors in THP-1 models, CD3/IL2 stimulated PBMCs and a MAPK reporter HEK-293 cell line. MBZ was also shown to increase ERK activity in CD4+ T-cells from lupus patients with known defective ERK signalling. Given these mechanistic features MBZ is suggested suitable for treatment of diseases characterized by defective ERK signalling, notably difficult to treat autoimmune diseases.", "doi": "10.1038/s41598-020-68986-0", "pmid": "32753665", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-68986-0"}, {"db": "pmc", "key": "PMC7403428"}], "notes": [], "created": "2020-12-10T12:22:36.140Z", "modified": "2025-10-17T13:05:07.972Z"}, {"entity": "publication", "iuid": "800346346d7a4a988909546711807aeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/800346346d7a4a988909546711807aeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/800346346d7a4a988909546711807aeb"}}, "title": "Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce.", "authors": [{"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Lund\u00e9n", "given": "Karl", "initials": "K"}, {"family": "Dalman", "given": "Kerstin", "initials": "K"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}, {"family": "Nemesio-Gorriz", "given": "Miguel", "initials": "M"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}], "type": "journal article", "published": "2020-07-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "12711", "issn-l": "2045-2322"}, "abstract": "The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.", "doi": "10.1038/s41598-020-69386-0", "pmid": "32728135", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-69386-0"}, {"db": "pmc", "key": "PMC7391732"}], "notes": [], "created": "2020-12-08T23:27:29.107Z", "modified": "2024-01-16T13:48:42.109Z"}, {"entity": "publication", "iuid": "80d309ad52724e478307f7267291dec2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80d309ad52724e478307f7267291dec2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80d309ad52724e478307f7267291dec2"}}, "title": "First evidence of microbial wood degradation in the coastal waters of the Antarctic.", "authors": [{"family": "Bj\u00f6rdal", "given": "Charlotte G", "initials": "CG"}, {"family": "Dayton", "given": "Paul K", "initials": "PK"}], "type": "journal article", "published": "2020-07-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "12774", "issn-l": "2045-2322"}, "abstract": "Wood submerged in saline and oxygenated marine waters worldwide is efficiently degraded by crustaceans and molluscs. Nevertheless, in the cold coastal waters of the Antarctic, these degraders seem to be absent and no evidence of other wood-degrading organisms has been reported so far. Here we examine long-term exposed anthropogenic wood material (Douglas Fir) collected at the seafloor close to McMurdo station, Antarctica. We used light and scanning electron microscopy and demonstrate that two types of specialized lignocellulolytic microbes-soft rot fungi and tunnelling bacteria-are active and degrade wood in this extreme environment. Fungal decay dominates and hyphae penetrate the outer 2-4 mm of the wood surface. Decay rates observed are about two orders of magnitude lower than normal. The fungi and bacteria, as well as their respective cavities and tunnels, are slightly smaller than normal, which might represent an adaptation to the extreme cold environment. Our results establish that there is ongoing wood degradation also in the Antarctic, albeit at a vastly reduced rate compared to warmer environments. Historical shipwrecks resting on the seafloor are most likely still in good condition, although surface details such as wood carvings, tool marks, and paint slowly disintegrate due to microbial decay.", "doi": "10.1038/s41598-020-68613-y", "pmid": "32728072", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7391713"}, {"db": "pii", "key": "10.1038/s41598-020-68613-y"}], "notes": [], "created": "2023-02-16T08:04:18.196Z", "modified": "2023-02-16T08:04:18.198Z"}, {"entity": "publication", "iuid": "8e7a9d42330c43e1965e9b1e2bc5fb5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e7a9d42330c43e1965e9b1e2bc5fb5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e7a9d42330c43e1965e9b1e2bc5fb5a"}}, "title": "Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.", "authors": [{"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "Plotnikov", "given": "Valery", "initials": "V"}, {"family": "Androsov", "given": "Semyon", "initials": "S"}, {"family": "Grigoriev", "given": "Semyon", "initials": "S"}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Nagel", "given": "Doris", "initials": "D"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Barnes", "given": "Ian", "initials": "I"}, {"family": "Barnett", "given": "Ross", "initials": "R"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "D\u00f6ppes", "given": "Doris", "initials": "D"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2020-07-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "12621", "issn-l": "2045-2322"}, "abstract": "The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52- 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.", "doi": "10.1038/s41598-020-69474-1", "pmid": "32724178", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-69474-1"}, {"db": "pmc", "key": "PMC7387438"}], "notes": [], "created": "2020-12-07T16:29:55.459Z", "modified": "2021-11-10T12:48:58.284Z"}, {"entity": "publication", "iuid": "87e07ded7de44a53ae4395ae27dfc8d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4"}}, "title": "Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach", "authors": [{"family": "von der Heyde", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-9889-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/803c0e0639174a50b59ae597802e824f.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Vicenzi", "given": "Silvia", "initials": "S"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Klingstr\u00f6m", "given": "Tiffany", "initials": "T"}, {"family": "Jumaa", "given": "Sitaf", "initials": "S"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "de Geus", "given": "Eco", "initials": "E", "orcid": "0000-0001-6022-2666", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abb01a905f347df8214d469d6c5ac45.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Brooke", "given": "Hannah L", "initials": "HL"}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}], "type": "journal-article", "published": "2020-07-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "11831"}, "abstract": "A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30 s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25 \u00b5M ivabradine-an open channel blocker of HCNs-for 24 h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).", "doi": "10.1038/s41598-020-68567-1", "pmid": "32678143", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "BioImage Informatics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Genome Engineering Zebrafish": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7367351"}, {"db": "pii", "key": "10.1038/s41598-020-68567-1"}], "notes": [], "created": "2020-08-19T09:27:04.550Z", "modified": "2024-01-16T13:48:42.137Z"}, {"entity": "publication", "iuid": "9415049166944ab6990231e492323800", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9415049166944ab6990231e492323800.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9415049166944ab6990231e492323800"}}, "title": "Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances.", "authors": [{"family": "Renes", "given": "Sophia Elise", "initials": "SE"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Fetzer", "given": "Ingo", "initials": "I"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}], "type": "journal article", "published": "2020-07-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "11333"}, "abstract": "Climate change is expected to increase the incidences of extremes in environmental conditions. To investigate how repeated disturbances affect microbial ecosystem resistance, natural lake bacterioplankton communities were subjected to repeated temperature disturbances of two intensities (25 \u00b0C and 35 \u00b0C), and subsequently to an acidification event. We measured functional parameters (bacterial production, abundance, extracellular enzyme activities) and community composition parameters (richness, evenness, niche width) and found that, compared to undisturbed control communities, the 35 \u00b0C treatment was strongly affected in all parameters, while the 25 \u00b0C treatment did not significantly differ from the control. Interestingly, exposure to multiple temperature disturbances caused gradually increasing stability in the 35 \u00b0C treatment in some parameters, while others parameters showed the opposite, indicating that the choice of parameters can strongly affect the outcome of a study. The acidification event did not lead to stronger changes in community structure, but functional resistance of bacterial production towards acidification in the 35 \u00b0C treatments increased. This indicates that functional resistance in response to a novel disturbance can be increased by previous exposure to another disturbance, suggesting similarity in stress tolerance mechanisms for both disturbances. These results highlight the need for understanding function- and disturbance-specific responses, since general responses are likely to be unpredictable.", "doi": "10.1038/s41598-020-68104-0", "pmid": "32647292", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-68104-0"}, {"db": "pmc", "key": "PMC7347917"}], "notes": [], "created": "2020-12-08T23:18:02.286Z", "modified": "2024-01-16T13:48:42.181Z"}, {"entity": "publication", "iuid": "d44fd9d44752484f996cf097d055c88b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d44fd9d44752484f996cf097d055c88b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d44fd9d44752484f996cf097d055c88b"}}, "title": "CAM-Delam: an in vivo approach to visualize and quantify the delamination and invasion capacity of human cancer cells.", "authors": [{"family": "Palaniappan", "given": "Tamilarasan K", "initials": "TK"}, {"family": "\u0160lekien\u0117", "given": "Lina", "initials": "L"}, {"family": "Jonasson", "given": "Anna-Karin", "initials": "AK"}, {"family": "Gilthorpe", "given": "Jonathan", "initials": "J"}, {"family": "Gunhaga", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2020-06-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "10472", "issn-l": "2045-2322"}, "abstract": "The development of metastases is the major cause of cancer related death. To develop a standardized method that define the ability of human cancer cells to degrade the basement membrane, e.g. the delamination capacity, is of importance to assess metastatic aggressiveness. We now present the in vivo CAM-Delam assay to visualize and quantify the ability of human cancer cells to delaminate and invade. The method includes seeding cancer cells on the chick chorioallantoic membrane (CAM), followed by the evaluation of cancer-induced delamination and potential invasion within hours to a few days. By testing a range of human cancer cell lines in the CAM-Delam assay, our results show that the delamination capacity can be divided into four categories and used to quantify metastatic aggressiveness. Our results emphasize the usefulness of this assay for quantifying delamination capacity as a measurement of metastatic aggressiveness, and in unraveling the molecular mechanisms that regulate delamination, invasion, formation of micro-metastases and modulations of the tumor microenvironment. This method will be useful in both the preclinical and clinical characterization of tumor biopsies, and in the validation of compounds that may improve survival in metastatic cancer.", "doi": "10.1038/s41598-020-67492-7", "pmid": "32591581", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-67492-7"}, {"db": "pmc", "key": "PMC7320147"}], "notes": [], "created": "2021-12-06T13:45:24.619Z", "modified": "2021-12-06T13:45:24.635Z"}, {"entity": "publication", "iuid": "ad6c085540e747d5ac95fbe1622c8b7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad6c085540e747d5ac95fbe1622c8b7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad6c085540e747d5ac95fbe1622c8b7d"}}, "title": "RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity.", "authors": [{"family": "Nilsson", "given": "Linn\u00e9a M", "initials": "LM"}, {"family": "Castresana-Aguirre", "given": "Miguel", "initials": "M", "orcid": "0000-0002-4665-6537", "researcher": {"href": "https://publications.scilifelab.se/researcher/df8394cb200743c4b13ee549bfe8492b.json"}}, {"family": "Scott", "given": "Lena", "initials": "L"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}], "type": "journal article", "published": "2020-06-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "10390", "issn-l": "2045-2322"}, "abstract": "Cell cultures are often used to study physiological processes in health and disease. It is well-known that cells change their gene expression in vitro compared to in vivo, but it is rarely experimentally addressed. High glucose is a known trigger of apoptosis in proximal tubular cells (PTC). Here we used RNA-seq to detect differentially expressed genes in cultures of primary rat PTC, 3 days old, compared to cells retrieved directly from rat outer renal cortex and between PTC exposed to 15 mM glucose and control for 8 h. The expression of 6,174 genes was significantly up- or downregulated in the cultures of PTC compared to the cells in the outer renal cortex. Most altered were mitochondrial and metabolism related genes. Gene expression of proapoptotic proteins were upregulated and gene expression of antiapoptotic proteins were downregulated in PTC. Expression of transporter related genes were generally downregulated. After 8 h, high glucose had not altered the gene expression in PTC. The current study provides evidence that cells alter their gene expression in vitro compared to in vivo and suggests that short-term high glucose exposure can trigger apoptosis in PTC without changing the gene expression levels of apoptotic proteins.", "doi": "10.1038/s41598-020-67361-3", "pmid": "32587318", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-67361-3"}, {"db": "pmc", "key": "PMC7316724"}], "notes": [], "created": "2020-12-07T16:27:02.399Z", "modified": "2021-11-10T12:50:06.705Z"}, {"entity": "publication", "iuid": "ee18a396f79f4e90a668a1318fc73ed8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee18a396f79f4e90a668a1318fc73ed8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee18a396f79f4e90a668a1318fc73ed8"}}, "title": "Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish.", "authors": [{"family": "Banote", "given": "Rakesh Kumar", "initials": "RK"}, {"family": "Chebli", "given": "Jasmine", "initials": "J"}, {"family": "\u015eat\u0131r", "given": "Tu\u011f\u00e7e Munise", "initials": "TM"}, {"family": "Varshney", "given": "Gaurav K", "initials": "GK", "orcid": "0000-0002-0429-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5b107029a9844de8b103873831b54f2.json"}}, {"family": "Camacho", "given": "Rafael", "initials": "R", "orcid": "0000-0003-2325-6407", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a7a8cfe28634821984b078ce3246343.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}, {"family": "Abramsson", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-4715-9225", "researcher": {"href": "https://publications.scilifelab.se/researcher/7abde12dab2e4d338bc6e55933f07531.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-06-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "10127", "issn-l": "2045-2322"}, "abstract": "Understanding the biological function of amyloid beta (A\u03b2) precursor protein (APP) beyond its role in Alzheimer's disease is emerging. Yet, its function during embryonic development is poorly understood. The zebrafish APP orthologue, Appb, is strongly expressed during early development but thus far has only been studied via morpholino-mediated knockdown. Zebrafish enables analysis of cellular processes in an ontogenic context, which is limited in many other vertebrates. We characterized zebrafish carrying a homozygous mutation that introduces a premature stop in exon 2 of the appb gene. We report that appb mutants are significantly smaller until 2 dpf and display perturbed enveloping layer (EVL) integrity and cell protrusions at the blastula stage. Moreover, appb mutants surviving beyond 48 hpf exhibited no behavioral defects at 6 dpf and developed into healthy and fertile adults. The expression of the app family member, appa, was also found to be altered in appb mutants. Taken together, we show that appb is involved in the initial development of zebrafish by supporting the integrity of the EVL, likely by mediating cell adhesion properties. The loss of Appb might then be compensated for by other app family members to maintain normal development.", "doi": "10.1038/s41598-020-66584-8", "pmid": "32576936", "labels": {"Genome Engineering Zebrafish": "Collaborative", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7311384"}, {"db": "pii", "key": "10.1038/s41598-020-66584-8"}], "notes": [], "created": "2020-06-24T09:03:55.674Z", "modified": "2023-02-16T08:03:52.996Z"}, {"entity": "publication", "iuid": "c0f9c1e3aaba4bf78198e30390d7a5cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0f9c1e3aaba4bf78198e30390d7a5cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0f9c1e3aaba4bf78198e30390d7a5cb"}}, "title": "Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes.", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K"}, {"family": "Visvanathar", "given": "Robin", "initials": "R"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Skrtic", "given": "Stanko", "initials": "S"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Kullberg", "given": "Joel", "initials": "J"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H"}], "type": "journal article", "published": "2020-05-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "8343", "issn-l": "2045-2322"}, "abstract": "Alteration of various metabolites has been linked to type 2 diabetes (T2D) and insulin resistance. However, identifying significant associations between metabolites and tissue-specific phenotypes requires a multi-omics approach. In a cohort of 42 subjects with different levels of glucose tolerance (normal, prediabetes and T2D) matched for age and body mass index, we calculated associations between parameters of whole-body positron emission tomography (PET)/magnetic resonance imaging (MRI) during hyperinsulinemic euglycemic clamp and non-targeted metabolomics profiling for subcutaneous adipose tissue (SAT) and plasma. Plasma metabolomics profiling revealed that hepatic fat content was positively associated with tyrosine, and negatively associated with lysoPC(P-16:0). Visceral adipose tissue (VAT) and SAT insulin sensitivity (Ki), were positively associated with several lysophospholipids, while the opposite applied to branched-chain amino acids. The adipose tissue metabolomics revealed a positive association between non-esterified fatty acids and, VAT and liver Ki. Bile acids and carnitines in adipose tissue were inversely associated with VAT Ki. Furthermore, we detected several metabolites that were significantly higher in T2D than normal/prediabetes. In this study we present novel associations between several metabolites from SAT and plasma with the fat fraction, volume and insulin sensitivity of various tissues throughout the body, demonstrating the benefit of an integrative multi-omics approach.", "doi": "10.1038/s41598-020-64524-0", "pmid": "32433479", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-64524-0"}, {"db": "pmc", "key": "PMC7239946"}], "notes": [], "created": "2020-12-11T11:56:10.100Z", "modified": "2025-10-17T13:03:16.813Z"}, {"entity": "publication", "iuid": "00954388bf944b23a0de53ff10845a71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00954388bf944b23a0de53ff10845a71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00954388bf944b23a0de53ff10845a71"}}, "title": "Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.", "authors": [{"family": "Grankvist", "given": "Rikard", "initials": "R"}, {"family": "Chireh", "given": "Arvin", "initials": "A"}, {"family": "Sandell", "given": "Mikael", "initials": "M"}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK"}, {"family": "Jaff", "given": "Nasren", "initials": "N"}, {"family": "Berggren", "given": "Ingrid", "initials": "I"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Arnberg", "given": "Fabian", "initials": "F"}, {"family": "Lundberg", "given": "Johan", "initials": "J"}, {"family": "Ugander", "given": "Martin", "initials": "M"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Jonsson", "given": "Stefan", "initials": "S"}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda6a90f9d9046ada163d9843d169393.json"}}, {"family": "Holmin", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2020-05-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "8029", "issn-l": "2045-2322"}, "abstract": "Endomyocardial biopsy is a valuable tool in cardiac diagnostics but is limited by low diagnostic yield and significant complication risks. Meanwhile, recent developments in transcriptomic and proteomic technologies promise a wealth of biological data from minimal tissue samples. To take advantage of the minimal tissue amount needed for molecular analyses, we have developed a sub-millimeter endovascular biopsy device, considerably smaller than current clinical equipment, and devised a low-input RNA-sequencing protocol for analyzing small tissue samples. In in vivo evaluation in swine, 81% of biopsy attempts (n = 157) were successful. High quality RNA-sequencing data was generated from 91% of the sequenced cardiac micro-biopsy samples (n = 32). Gene expression signatures of samples taken with the novel device were comparable with a conventional device. No major complications were detected either during procedures or during 7 days' follow-up, despite acquiring a relatively large number of biopsies (median 30) in each animal. In conclusion, the novel device coupled with RNA-sequencing provides a feasible method to obtain molecular data from the myocardium. The method is less traumatic and has a higher flexibility compared to conventional methods, enabling safer and more targeted sampling from different parts of the myocardium.", "doi": "10.1038/s41598-020-64900-w", "pmid": "32415191", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-64900-w"}, {"db": "pmc", "key": "PMC7229024"}], "notes": [], "created": "2020-07-08T13:04:40.159Z", "modified": "2024-01-16T13:48:42.501Z"}, {"entity": "publication", "iuid": "5740889604b145baac1f446821f3da8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5740889604b145baac1f446821f3da8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5740889604b145baac1f446821f3da8d"}}, "title": "Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes.", "authors": [{"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Larsson", "given": "Peter", "initials": "P"}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2020-05-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "7946", "issn-l": "2045-2322"}, "abstract": "Ovarian cancer comprises multiple subtypes (clear-cell (CCC), endometrioid (EC), high-grade serous (HGSC), low-grade serous (LGSC), and mucinous carcinomas (MC)) with differing molecular and clinical behavior. However, robust histotype-specific biomarkers for clinical use have yet to be identified. Here, we utilized a multi-omics approach to identify novel histotype-specific genetic markers associated with ovarian carcinoma histotypes (CCC, EC, HGSC, and MC) using DNA methylation, DNA copy number alteration and RNA sequencing data for 96 primary invasive early-stage (stage I and II) ovarian carcinomas. More specifically, the DNA methylation analysis revealed hypermethylation for CCC in comparison with the other histotypes. Moreover, copy number imbalances and novel chromothripsis-like rearrangements (n = 64) were identified in ovarian carcinoma, with the highest number of chromothripsis-like patterns in HGSC. For the 1000 most variable transcripts, underexpression was most prominent for all histotypes in comparison with normal ovarian samples. Overall, the integrative approach identified 46 putative oncogenes (overexpressed, hypomethylated and DNA gain) and three putative tumor suppressor genes (underexpressed, hypermethylated and DNA loss) when comparing the different histotypes. In conclusion, the current study provides novel insights into molecular features associated with early-stage ovarian carcinoma that may improve patient stratification and subclassification of the histotypes.", "doi": "10.1038/s41598-020-64794-8", "pmid": "32409713", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-64794-8"}, {"db": "pmc", "key": "PMC7224294"}], "notes": [], "created": "2020-05-27T13:29:27.972Z", "modified": "2024-01-16T13:48:42.508Z"}, {"entity": "publication", "iuid": "a67f74b1dcdf445da4ec370ee216c8d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a67f74b1dcdf445da4ec370ee216c8d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a67f74b1dcdf445da4ec370ee216c8d6"}}, "title": "Genetic and environmental influences on human height from infancy through adulthood at different levels of parental education.", "authors": [{"family": "Jelenkovic", "given": "Aline", "initials": "A"}, {"family": "Sund", "given": "Reijo", "initials": "R", "orcid": "0000-0002-6268-8117", "researcher": {"href": "https://publications.scilifelab.se/researcher/27f81bab545a4b158866a08fe5263e08.json"}}, {"family": "Yokoyama", "given": "Yoshie", "initials": "Y"}, {"family": "Latvala", "given": "Antti", "initials": "A", "orcid": "0000-0001-5695-117X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e675261bb7354ca782cc267262fbdaba.json"}}, {"family": "Sugawara", "given": "Masumi", "initials": "M"}, {"family": "Tanaka", "given": "Mami", "initials": "M"}, {"family": "Matsumoto", "given": "Satoko", "initials": "S"}, {"family": "Freitas", "given": "Duarte L", "initials": "DL"}, {"family": "Maia", "given": "Jos\u00e9 Antonio", "initials": "JA"}, {"family": "Knafo-Noam", "given": "Ariel", "initials": "A"}, {"family": "Mankuta", "given": "David", "initials": "D"}, {"family": "Abramson", "given": "Lior", "initials": "L"}, {"family": "Ji", "given": "Fuling", "initials": "F"}, {"family": "Ning", "given": "Feng", "initials": "F"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Saudino", "given": "Kimberly J", "initials": "KJ"}, {"family": "Cutler", "given": "Tessa L", "initials": "TL"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Hwang", "given": "Amie E", "initials": "AE"}, {"family": "Mack", "given": "Thomas M", "initials": "TM"}, {"family": "Nelson", "given": "Tracy L", "initials": "TL"}, {"family": "Whitfield", "given": "Keith E", "initials": "KE"}, {"family": "Sung", "given": "Joohon", "initials": "J"}, {"family": "Kim", "given": "Jina", "initials": "J", "orcid": "0000-0003-1684-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/869e611833bc4f6aab2f47f540f89581.json"}}, {"family": "Lee", "given": "Jooyeon", "initials": "J", "orcid": "0000-0001-5220-0950", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5e4b2f4f3b34e41a3901c90f6dc0ec2.json"}}, {"family": "Lee", "given": "Sooji", "initials": "S"}, {"family": "Llewellyn", "given": "Clare H", "initials": "CH", "orcid": "0000-0002-0066-2827", "researcher": {"href": "https://publications.scilifelab.se/researcher/97213af3e4704e13b608af74637dbb2e.json"}}, {"family": "Fisher", "given": "Abigail", "initials": "A"}, {"family": "Medda", "given": "Emanuela", "initials": "E"}, {"family": "Nistic\u00f2", "given": "Lorenza", "initials": "L", "orcid": "0000-0003-1805-6240", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6a2e9c1a6a34419b4661afce3e01d3e.json"}}, {"family": "Toccaceli", "given": "Virgilia", "initials": "V"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM", "orcid": "0000-0003-0977-7249", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9df70acb87f443eb6da650b151a679c.json"}}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF", "orcid": "0000-0002-8532-5087", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5b6c24c302d42828806076ded81afe1.json"}}, {"family": "Burt", "given": "S Alexandra", "initials": "SA"}, {"family": "Klump", "given": "Kelly L", "initials": "KL"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Butler", "given": "David A", "initials": "DA"}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Brandt", "given": "Ingunn", "initials": "I"}, {"family": "Nilsen", "given": "Thomas S", "initials": "TS"}, {"family": "Harden", "given": "K Paige", "initials": "KP"}, {"family": "Tucker-Drob", "given": "Elliot M", "initials": "EM"}, {"family": "Franz", "given": "Carol E", "initials": "CE", "orcid": "0000-0002-8987-1755", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f24c335b7f544328bca9e9e73b8560e.json"}}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Lyons", "given": "Michael J", "initials": "MJ"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P", "orcid": "0000-0003-3037-5287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db67c51837b4cdfa18cacbc3fca1173.json"}}, {"family": "Bartels", "given": "Meike", "initials": "M", "orcid": "0000-0002-9667-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a91c095e993411b99e81e21f40d8597.json"}}, {"family": "Beijsterveldt", "given": "Catharina E M van", "initials": "CEMV", "orcid": "0000-0002-6617-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c3073fc4d1e4454bfc4bc7aad11b357.json"}}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F", "orcid": "0000-0001-8357-4699", "researcher": {"href": "https://publications.scilifelab.se/researcher/85556629452a4054bf7228b5f7049811.json"}}, {"family": "Jeong", "given": "Hoe-Uk", "initials": "HU"}, {"family": "Hur", "given": "Yoon-Mi", "initials": "YM"}, {"family": "Turkheimer", "given": "Eric", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA", "orcid": "0000-0003-4821-430X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3495a648342a491d9105817cc30d5d56.json"}}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Silventoinen", "given": "Karri", "initials": "K"}], "type": "journal article", "published": "2020-05-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "7974", "issn-l": "2045-2322"}, "abstract": "Genetic factors explain a major proportion of human height variation, but differences in mean stature have also been found between socio-economic categories suggesting a possible effect of environment. By utilizing a classical twin design which allows decomposing the variation of height into genetic and environmental components, we tested the hypothesis that environmental variation in height is greater in offspring of lower educated parents. Twin data from 29 cohorts including 65,978 complete twin pairs with information on height at ages 1 to 69 years and on parental education were pooled allowing the analyses at different ages and in three geographic-cultural regions (Europe, North America and Australia, and East Asia). Parental education mostly showed a positive association with offspring height, with significant associations in mid-childhood and from adolescence onwards. In variance decomposition modeling, the genetic and environmental variance components of height did not show a consistent relation to parental education. A random-effects meta-regression analysis of the aggregate-level data showed a trend towards greater shared environmental variation of height in low parental education families. In conclusion, in our very large dataset from twin cohorts around the globe, these results provide only weak evidence for the study hypothesis.", "doi": "10.1038/s41598-020-64883-8", "pmid": "32409744", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-64883-8"}, {"db": "pmc", "key": "PMC7224277"}], "notes": [], "created": "2020-05-27T13:29:27.487Z", "modified": "2021-11-10T12:51:04.364Z"}, {"entity": "publication", "iuid": "f5c4593d66bd47b7b8c4b6ec46b98e11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5c4593d66bd47b7b8c4b6ec46b98e11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5c4593d66bd47b7b8c4b6ec46b98e11"}}, "title": "The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission.", "authors": [{"family": "Ya\u00f1ez", "given": "Orlando", "initials": "O", "orcid": "0000-0001-8493-2726", "researcher": {"href": "https://publications.scilifelab.se/researcher/e202e4f4253b4e6f91d6f3bfcf8247cb.json"}}, {"family": "Ch\u00e1vez-Galarza", "given": "Julio", "initials": "J"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C", "orcid": "0000-0003-0502-3693", "researcher": {"href": "https://publications.scilifelab.se/researcher/982873aade554b38b26b877298db5115.json"}}, {"family": "Pinto", "given": "M Alice", "initials": "MA", "orcid": "0000-0001-9663-8399", "researcher": {"href": "https://publications.scilifelab.se/researcher/62c4785cb6714a09be0ec688ed4fce92.json"}}, {"family": "Neumann", "given": "Peter", "initials": "P"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR", "orcid": "0000-0002-0335-0386", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0bd25adff9b48e694c30279d0db901b.json"}}], "type": "journal article", "published": "2020-04-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "5956", "issn-l": "2045-2322"}, "abstract": "The main biological threat to the western honeybee (Apis mellifera) is the parasitic mite Varroa destructor, largely because it vectors lethal epidemics of honeybee viruses that, in the absence of this mite, are relatively innocuous. The severe pathology is a direct consequence of excessive virus titres caused by this novel transmission route. However, little is known about how the virus adapts genetically during transmission and whether this influences the pathology. Here, we show that upon injection into honeybee pupae, the deformed wing virus type-A (DWV-A) quasispecies undergoes a rapid, extensive expansion of its sequence space, followed by strong negative selection towards a uniform, common shape by the time the pupae have completed their development, with no difference between symptomatic and asymptomatic adults in either DWV titre or genetic composition. This suggests that the physiological and molecular environment during pupal development has a strong, conservative influence on shaping the DWV-A quasispecies in emerging adults. There was furthermore no evidence of any progressive adaptation of the DWV-A quasispecies to serial intra-abdominal injection, simulating mite transmission, despite the generation of ample variation immediately following each transmission, suggesting that the virus either had already adapted to transmission by injection, or was unaffected by it.", "doi": "10.1038/s41598-020-62673-w", "pmid": "32249797", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-62673-w"}, {"db": "pmc", "key": "PMC7136270"}], "notes": [], "created": "2020-09-15T07:19:57.145Z", "modified": "2024-01-16T13:48:42.634Z"}, {"entity": "publication", "iuid": "411b0e8ddd4f4cf98234230c57fb780c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/411b0e8ddd4f4cf98234230c57fb780c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/411b0e8ddd4f4cf98234230c57fb780c"}}, "title": "Plant resistance does not compromise parasitoid-based biocontrol of a strawberry pest.", "authors": [{"family": "Weber", "given": "Daniela", "initials": "D"}, {"family": "Egan", "given": "Paul A", "initials": "PA"}, {"family": "Muola", "given": "Anne", "initials": "A"}, {"family": "Ericson", "given": "Lars E", "initials": "LE"}, {"family": "Stenberg", "given": "Johan A", "initials": "JA"}], "type": "journal article", "published": "2020-04-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "5899", "issn-l": "2045-2322"}, "abstract": "Plant nutritional quality can influence interactions between herbivores and their parasitoids. While most previous work has focused on a limited set of secondary plant metabolites, the tri-trophic effects of overall phenotypic resistance have been understudied. Furthermore, the joint effects of secondary and primary metabolites on parasitoids are almost unexplored. In this study, we compared the performance and survival of the parasitoid species Asecodes parviclava Thompson on wild woodland strawberry (Fragaria vesca L.) genotypes showing variation in resistance against the parasitoid's host, the strawberry leaf beetle (Galerucella tenella L.). Additionally, we related the metabolic profiles of these plant genotypes to the tritrophic outcomes in order to identify primary and secondary metabolites involved in regulating plant potential to facilitate parasitism. We found that parasitoid performance was strongly affected by plant genotype, but those differences in plant resistance to the herbivore were not reflected in parasitoid survival. These findings could be explained in particular by a significant link between parasitoid survival and foliar carbohydrate levels, which appeared to be the most important compounds for parasitism success. The fact that plant quality strongly affects parasitism should be further explored and utilized in plant breeding programs for a synergistic application in sustainable pest management.", "doi": "10.1038/s41598-020-62698-1", "pmid": "32246069", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-62698-1"}, {"db": "pmc", "key": "PMC7125231"}], "notes": [], "created": "2020-12-11T12:05:25.341Z", "modified": "2025-10-17T13:03:16.868Z"}, {"entity": "publication", "iuid": "b8409eb1124c41258c01b678e729e7e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8409eb1124c41258c01b678e729e7e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8409eb1124c41258c01b678e729e7e6"}}, "title": "The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce.", "authors": [{"family": "Hu", "given": "Yang", "initials": "Y"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "Durling", "given": "Mikael Brandstr\u00f6m", "initials": "MB", "orcid": "0000-0001-6485-197X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be72d0dcc48489495509b23c7ad3d38.json"}}, {"family": "Olson", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0001-8998-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a79139c2b94d9f97cf038e1cab8c03.json"}}], "type": "journal article", "published": "2020-04-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "5884", "issn-l": "2045-2322"}, "abstract": "Heterobasidion irregulare and H. occidentale are two closely related conifer root rot pathogens in the H. annosum sensu lato (s.l.) species complex. The two species H. irregulare and H. occidentale have different host preference with pine and non-pine tree species favored, respectively. The comparison of transcriptomes of H. irregulare and H. occidentale growing in Norway spruce bark, a susceptible host non-native to North America, showed large differences in gene expression. Heterobasidion irregulare induced more genes involved in detoxification of host compounds and in production of secondary metabolites, while the transcriptome induced in H. occidentale was more oriented towards carbohydrate degradation. Along with their separated evolutionary history, the difference might be driven by their host preferences as indicated by the differentially expressed genes enriched in particular Gene Ontology terms.", "doi": "10.1038/s41598-020-62521-x", "pmid": "32246017", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-62521-x"}, {"db": "pmc", "key": "PMC7125170"}], "notes": [], "created": "2020-07-03T05:24:05.280Z", "modified": "2024-01-16T13:48:42.649Z"}, {"entity": "publication", "iuid": "f96a5077385748b2a9baf3c7ce7dc352", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f96a5077385748b2a9baf3c7ce7dc352.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f96a5077385748b2a9baf3c7ce7dc352"}}, "title": "Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus.", "authors": [{"family": "Wildeman", "given": "Peter", "initials": "P"}, {"family": "Tevell", "given": "Staffan", "initials": "S"}, {"family": "Eriksson", "given": "Carl", "initials": "C"}, {"family": "Lagos", "given": "Amaya Campillay", "initials": "AC"}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}], "type": "journal article", "published": "2020-04-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "5938"}, "abstract": "Staphylococcus aureus is a commensal colonizing the skin and mucous membranes. It can also act as a pathogen, and is the most common microorganism isolated from prosthetic joint infections (PJIs). The aim of this study was to explore the genomic relatedness between commensal and PJI S. aureus strains as well as microbial traits and host-related risk factors for treatment failure. Whole-genome sequencing (WGS) was performed on S. aureus isolates obtained from PJIs (n = 100) and control isolates from nares (n = 101). Corresponding clinical data for the PJI patients were extracted from medical records. No PJI-specific clusters were found in the WGS phylogeny, and the distribution of the various clonal complexes and prevalence of virulence genes among isolates from PJIs and nares was almost equal. Isolates from patients with treatment success and failure were genetically very similar, while the presence of an antibiotic-resistant phenotype and the use of non-biofilm-active antimicrobial treatment were both associated with failure.In conclusion, commensal and PJI isolates of S. aureus in arthroplasty patients were genetically indistinguishable, suggesting that commensal S. aureus clones are capable of causing PJIs. Furthermore, no association between genetic traits and outcome could be demonstrated, stressing the importance of patient-related factors in the treatment of S. aureus PJIs.", "doi": "10.1038/s41598-020-62751-z", "pmid": "32246045", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-62751-z"}, {"db": "pmc", "key": "PMC7125104"}], "notes": [], "created": "2020-11-27T13:56:08.647Z", "modified": "2021-12-08T12:31:56.319Z"}, {"entity": "publication", "iuid": "64b8dd1c84934112a999fca1e18e8ac2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64b8dd1c84934112a999fca1e18e8ac2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64b8dd1c84934112a999fca1e18e8ac2"}}, "title": "Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress.", "authors": [{"family": "Crawford", "given": "Tim", "initials": "T"}, {"family": "Karamat", "given": "Fazeelat", "initials": "F"}, {"family": "Lehotai", "given": "N\u00f3ra", "initials": "N"}, {"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Blomberg", "given": "Jeanette", "initials": "J"}, {"family": "Strand", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2020-03-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "5073", "issn-l": "2045-2322"}, "abstract": "Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.", "doi": "10.1038/s41598-020-61758-w", "pmid": "32193425", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-61758-w"}, {"db": "pmc", "key": "PMC7081235"}], "notes": [], "created": "2021-07-02T06:44:54.540Z", "modified": "2021-11-10T12:52:58.039Z"}, {"entity": "publication", "iuid": "6cb7046ed9eb44dfbf9eb8ac97264bef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cb7046ed9eb44dfbf9eb8ac97264bef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cb7046ed9eb44dfbf9eb8ac97264bef"}}, "title": "Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease.", "authors": [{"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Harrison", "given": "Odile B", "initials": "OB"}, {"family": "Eriksson", "given": "Lorraine", "initials": "L"}, {"family": "Anton", "given": "Brian P", "initials": "BP"}, {"family": "Fomenkov", "given": "Alexey", "initials": "A"}, {"family": "Roberts", "given": "Richard J", "initials": "RJ"}, {"family": "Tooming-Klunderud", "given": "Ave", "initials": "A"}, {"family": "Bratcher", "given": "Holly B", "initials": "HB"}, {"family": "Bray", "given": "James E", "initials": "JE"}, {"family": "Thulin-Hedberg", "given": "Sara", "initials": "S"}, {"family": "Maiden", "given": "Martin C J", "initials": "MCJ"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2020-02-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "3644"}, "abstract": "Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis emerged in Europe during the 2000s. Draft genomes of serogroup Y isolates in Sweden revealed that although the population structure of these isolates was similar to other serogroup Y isolates internationally, a distinct strain (YI) and more specifically a sublineage (1) of this strain was responsible for the increase of serogroup Y IMD in Sweden. We performed single molecule real-time (SMRT) sequencing on eight serogroup Y isolates from different sublineages to unravel the genetic and epigenetic factors delineating them, in order to understand the serogroup Y emergence. Extensive comparisons between the serogroup Y sublineages of all coding sequences, complex genomic regions, intergenic regions, and methylation motifs revealed small point mutations in genes mainly encoding hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron acquisition, and endotoxin production. The methylation motif CACNNNNNTAC was only found in isolates of sublineage 2. Only seven genes were putatively differentially expressed, and another two genes encoding hypothetical proteins were only present in sublineage 2. These data suggest that the serogroup Y IMD increase in Sweden was most probably due to small changes in genes important for colonization and transmission.", "doi": "10.1038/s41598-020-59509-y", "pmid": "32108139", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-59509-y"}, {"db": "pmc", "key": "PMC7046676"}], "notes": [], "created": "2020-11-27T13:55:39.557Z", "modified": "2021-12-08T12:32:12.168Z"}, {"entity": "publication", "iuid": "c1de8d695c1944ae8db24b9a04b4ab8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1de8d695c1944ae8db24b9a04b4ab8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1de8d695c1944ae8db24b9a04b4ab8a"}}, "title": "Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing.", "authors": [{"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2020-02-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "2512", "issn-l": "2045-2322"}, "abstract": "Structural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). Traditional methods such as karyotyping and FISH struggle to accurately identify and phase such large-scale chromosomal aberrations in ALL genomes. We therefore evaluated linked-read WGS for detecting chromosomal rearrangements in primary samples of from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations and structural variants in the ALL genomes. We found that biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified previously unknown structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. We conclude that linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping and FISH.", "doi": "10.1038/s41598-020-59214-w", "pmid": "32054878", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-59214-w"}, {"db": "pmc", "key": "PMC7018692"}], "notes": [], "created": "2020-11-05T12:22:11.615Z", "modified": "2024-01-16T13:48:42.944Z"}, {"entity": "publication", "iuid": "e5f1bff2a04840b1a4bde038251fa843", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5f1bff2a04840b1a4bde038251fa843.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5f1bff2a04840b1a4bde038251fa843"}}, "title": "Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions.", "authors": [{"family": "Vass", "given": "M\u00e1t\u00e9", "initials": "M", "orcid": "0000-0003-0718-7659", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fed30af96e540269edcb565cb34bc39.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/9290d334ce5a4488b8afd2af511e02ad.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S", "orcid": "0000-0002-5245-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/efa9e8f2174a4c7cb903b0f9b895a183.json"}}], "type": "journal article", "published": "2020-02-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "2455", "issn-l": "2045-2322"}, "abstract": "Temporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null model approaches (elements of metacommunity structure, Raup-Crick beta-diversity and quantitative process estimates) to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in the case of bacteria and microeukaryotes, respectively. We distinguished these processes from dispersal-related processes using additional tests. Regardless of the applied null model, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.", "doi": "10.1038/s41598-020-59182-1", "pmid": "32051469", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-59182-1"}, {"db": "pmc", "key": "PMC7016149"}], "notes": [], "created": "2020-12-08T23:47:42.006Z", "modified": "2024-01-16T13:48:42.952Z"}, {"entity": "publication", "iuid": "bb7a04bc18cd4f11adcb9f73addb3cc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb7a04bc18cd4f11adcb9f73addb3cc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb7a04bc18cd4f11adcb9f73addb3cc5"}}, "title": "Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia.", "authors": [{"family": "Gr\u00f6nroos", "given": "Toni", "initials": "T"}, {"family": "M\u00e4kinen", "given": "Artturi", "initials": "A"}, {"family": "Laukkanen", "given": "Saara", "initials": "S"}, {"family": "Mehtonen", "given": "Juha", "initials": "J", "orcid": "0000-0003-0554-4667", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7a49312223a458dbb35c809f20372af.json"}}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Oksa", "given": "Laura", "initials": "L"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Pohjolainen", "given": "Virva", "initials": "V"}, {"family": "Paavonen", "given": "Timo", "initials": "T"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M"}, {"family": "Lohi", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2020-02-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "2043", "issn-l": "2045-2322"}, "abstract": "Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differentiation, self-renewal, and proliferative features. We sought to identify the transcription factors exhibiting altered and subtype-specific expression patterns in B-ALL and report here that SOX11, a developmental and neuronal transcription factor, is aberrantly expressed in the ETV6-RUNX1 and TCF3-PBX1 subtypes of acute B-cell leukemias. We show that a high expression of SOX11 leads to alterations of gene expression that are typically associated with cell adhesion, migration, and differentiation. A high expression is associated with DNA hypomethylation at the SOX11 locus and a favorable outcome. The results indicate that SOX11 expression marks a group of patients with good outcomes and thereby prompts further study of its use as a biomarker.", "doi": "10.1038/s41598-020-58970-z", "pmid": "32029838", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-58970-z"}, {"db": "pmc", "key": "PMC7005266"}], "notes": [], "created": "2020-02-20T11:30:30.655Z", "modified": "2021-11-10T12:54:08.673Z"}, {"entity": "publication", "iuid": "796149f9eb4f4e3980d73a2969461850", "links": {"self": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850.json"}, "display": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850"}}, "title": "Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.", "authors": [{"family": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ellis", "given": "Barbara", "initials": "B"}, {"family": "Kutschera", "given": "Verena Esther", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2020-01-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "1303"}, "abstract": "The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.", "doi": "10.1038/s41598-020-58025-3", "pmid": "31992756", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Microbial Single Cell Genomics": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-58025-3"}, {"db": "pmc", "key": "PMC6987183"}], "notes": [], "created": "2020-02-03T10:35:42.153Z", "modified": "2024-01-16T13:48:43.036Z"}, {"entity": "publication", "iuid": "ab3cc4d0906f402b8e0f5a5fecb6f0a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab3cc4d0906f402b8e0f5a5fecb6f0a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab3cc4d0906f402b8e0f5a5fecb6f0a0"}}, "title": "CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.", "authors": [{"family": "Fogelholm", "given": "J", "initials": "J"}, {"family": "Henriksen", "given": "R", "initials": "R"}, {"family": "H\u00f6glund", "given": "A", "initials": "A"}, {"family": "Huq", "given": "N", "initials": "N"}, {"family": "Johnsson", "given": "M", "initials": "M"}, {"family": "Lenz", "given": "R", "initials": "R"}, {"family": "Jensen", "given": "P", "initials": "P"}, {"family": "Wright", "given": "D", "initials": "D"}], "type": "journal article", "published": "2020-01-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "1161", "issn-l": "2045-2322"}, "abstract": "Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic \u00d7 wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. By treating colour as a quantitative rather than qualitative trait, we have identified both QTL and genes of small effect. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.", "doi": "10.1038/s41598-020-57710-7", "pmid": "31980681", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-57710-7"}, {"db": "pmc", "key": "PMC6981141"}], "notes": [], "created": "2020-02-04T11:55:41.471Z", "modified": "2024-01-16T13:48:43.050Z"}, {"entity": "publication", "iuid": "8e7d434d65094896b5c0c4f4328ae62e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e7d434d65094896b5c0c4f4328ae62e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e7d434d65094896b5c0c4f4328ae62e"}}, "title": "Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes.", "authors": [{"family": "Etemadikhah", "given": "Mitra", "initials": "M", "orcid": "0000-0001-5795-9085", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e68ca63254a4b5697188bb87087852f.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Wetterberg", "given": "Lennart", "initials": "L"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2020-01-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "630", "issn-l": "2045-2322"}, "abstract": "Schizophrenia is a complex neurodevelopmental disorder with high rate of morbidity and mortality. While the heritability rate is high, the precise etiology is still unknown. Although schizophrenia is a central nervous system disorder, studies using peripheral tissues have also been established to search for patient specific biomarkers and to increase understanding of schizophrenia etiology. Among all peripheral tissues, fibroblasts stand out as they are easy to obtain and culture. Furthermore, they keep genetic stability for long period and exhibit molecular similarities to cells from nervous system. Using a unique set of fibroblast samples from a genetically isolated population in northern Sweden, we performed whole transcriptome sequencing to compare differentially expressed genes in seven controls and nine patients. We found differential fibroblast expression between cases and controls for 48 genes, including eight genes previously implicated in schizophrenia or schizophrenia related pathways; HGF, PRRT2, EGR1, EGR3, C11orf87, TLR3, PLEKHH2 and PIK3CD. Weighted gene correlation network analysis identified three differentially co-expressed networks of genes significantly-associated with schizophrenia. All three modules were significantly suppressed in patients compared to control, with one module highly enriched in genes involved in synaptic plasticity, behavior and synaptic transmission. In conclusion, our results support the use of fibroblasts for identification of differentially expressed genes in schizophrenia and highlight dysregulation of synaptic networks as an important mechanism in schizophrenia.", "doi": "10.1038/s41598-020-57467-z", "pmid": "31959813", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-57467-z"}, {"db": "pmc", "key": "PMC6971273"}], "notes": [], "created": "2020-07-03T05:23:47.172Z", "modified": "2024-01-16T13:48:43.065Z"}, {"entity": "publication", "iuid": "c952428d377045e9ad74857689029e7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c952428d377045e9ad74857689029e7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c952428d377045e9ad74857689029e7e"}}, "title": "Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling.", "authors": [{"family": "Ahi", "given": "Ehsan Pashay", "initials": "EP"}, {"family": "Brunel", "given": "Mathilde", "initials": "M"}, {"family": "Tsakoumis", "given": "Emmanouil", "initials": "E"}, {"family": "Schmitz", "given": "Monika", "initials": "M"}], "type": "journal article", "published": "2019-12-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "20166", "issn-l": "2045-2322"}, "abstract": "The hormone leptin is a key regulator of body weight, food intake and metabolism. In mammals, leptin acts as an anorexigen and inhibits food intake centrally by affecting the appetite centres in the hypothalamus. In teleost fish, the regulatory connections between leptin and other appetite-regulating genes are largely unknown. In the present study, we used a zebrafish mutant with a loss of function leptin receptor to investigate brain expression patterns of 12 orexigenic and 24 anorexigenic genes under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-hours refeeding). Expression patterns were compared to wild-type zebrafish, in order to identify leptin-dependent differentially expressed genes under different feeding conditions. We provide evidence that the transcription of certain orexigenic and anorexigenic genes is influenced by leptin signalling in the zebrafish brain. We found that the expression of orexigenic genes was not affected by impaired leptin signalling under normal feeding conditions; however, several orexigenic genes showed increased transcription during fasting and refeeding, including agrp, apln, galr1a and cnr1. This suggests an inhibitory effect of leptin signal on the transcription of these orexigenic genes during short-term fasting and refeeding in functional zebrafish. Most pronounced effects were observed in the group of anorexigenic genes, where the impairment of leptin signalling resulted in reduced gene expression in several genes, including cart family, crhb, gnrh2, mc4r, pomc and spx, in the control group. This suggests a stimulatory effect of leptin signal on the transcription of these anorexigenic genes under normal feeding condition. In addition, we found multiple gain and loss in expression correlations between the appetite-regulating genes, in zebrafish with impaired leptin signal, suggesting the presence of gene regulatory networks downstream of leptin signal in zebrafish brain. The results provide the first evidence for the effects of leptin signal on the transcription of various appetite-regulating genes in zebrafish brain, under different feeding conditions. Altogether, these transcriptional changes suggest an anorexigenic role for leptin signal, which is likely to be mediated through distinct set of appetite-regulating genes under different feeding conditions.", "doi": "10.1038/s41598-019-56779-z", "pmid": "31882937", "labels": {"Genome Engineering Zebrafish": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-56779-z"}, {"db": "pmc", "key": "PMC6934527"}], "notes": [], "created": "2020-01-01T23:15:49.611Z", "modified": "2020-01-01T23:15:49.621Z"}, {"entity": "publication", "iuid": "fa14c3d7e65e4526a320df7f80d7ef60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa14c3d7e65e4526a320df7f80d7ef60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa14c3d7e65e4526a320df7f80d7ef60"}}, "title": "A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.", "authors": [{"family": "Rivera", "given": "Natalia V", "initials": "NV"}, {"family": "Patasova", "given": "Karina", "initials": "K"}, {"family": "Kullberg", "given": "Susanna", "initials": "S"}, {"family": "Diaz-Gallo", "given": "Lina Marcela", "initials": "LM"}, {"family": "Iseda", "given": "Tomoko", "initials": "T"}, {"family": "Bengtsson", "given": "Camilla", "initials": "C"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Eklund", "given": "Anders", "initials": "A"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal article", "published": "2019-12-09", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "18633", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The influence and effect of cigarette smoking in sarcoidosis is unclear. Here, we evaluated gene-environment interaction between multiple genetic variants including HLA genes and smoking in sarcoidosis defined by two clinical phenotypes, L\u00f6fgren's syndrome (LS) and patients without L\u00f6fgren's syndrome (non-LS). To quantify smoking effects in sarcoidosis, we performed a gene-environment interaction study in a Swedish population-based case-control study consisting of 3,713 individuals. Cases and controls were classified according to their cigarette smoking status and genotypes by Immunochip platform. Gene-smoking interactions were quantified by an additive interaction model using a logistic regression adjusted by sex, age and first two principal components. The estimated attributable proportion (AP) was used to quantify the interaction effect. Assessment of smoking effects with inclusion of genetic information revealed 53 (in LS) and 34 (in non-LS) SNP-smoking additive interactions at false discovery rate (FDR) below 5%. The lead signals interacting with smoking were rs12132140 (AP = 0.56, 95% CI = 0.22-0.90), p = 1.28e-03) in FCRL1 for LS and rs61780312 (AP = 0.62, 95% CI = 0.28-0.90), p = 3e-04) in IL23R for non-LS. We further identified 16 genomic loci (in LS) and 13 (in non-LS) that interact with cigarette smoking. These findings suggest that sarcoidosis risk is modulated by smoking due to genetic susceptibility. Therefore, patients having certain gene variants, are at a higher risk for the disease. Consideration of individual's genetic predisposition is crucial to quantify effects of smoking in sarcoidosis.", "doi": "10.1038/s41598-019-54612-1", "pmid": "31819081", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-54612-1"}], "notes": [], "created": "2019-12-16T13:39:42.295Z", "modified": "2024-01-16T13:48:43.304Z"}, {"entity": "publication", "iuid": "906ecb6620684f13bfc9d7701554df7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/906ecb6620684f13bfc9d7701554df7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/906ecb6620684f13bfc9d7701554df7a"}}, "title": "Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa.", "authors": [{"family": "G\u00fcnayd\u0131n", "given": "G\u00f6k\u00e7e", "initials": "G"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G"}, {"family": "Garber", "given": "David A", "initials": "DA", "orcid": "0000-0003-3608-7104", "researcher": {"href": "https://publications.scilifelab.se/researcher/d63f276e79684aef8661654bc329f226.json"}}, {"family": "Asghar", "given": "Muhammad", "initials": "M"}, {"family": "No\u0205l-Romas", "given": "Laura", "initials": "L"}, {"family": "Burgener", "given": "Adam", "initials": "A"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Wang", "given": "Lin", "initials": "L"}, {"family": "Rohan", "given": "Lisa C", "initials": "LC"}, {"family": "Guenthner", "given": "Patricia", "initials": "P"}, {"family": "Mitchell", "given": "James", "initials": "J"}, {"family": "Matoba", "given": "Nobuyuki", "initials": "N"}, {"family": "McNicholl", "given": "Janet M", "initials": "JM"}, {"family": "Palmer", "given": "Kenneth E", "initials": "KE"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Broliden", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2019-12-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "9", "issue": "1", "pages": "18120"}, "abstract": "Natural-product derived lectins can function as potent viral inhibitors with minimal toxicity as shown in vitro and in small animal models. We here assessed the effect of rectal application of an anti-HIV lectin-based microbicide Q-Griffithsin (Q-GRFT) in rectal tissue samples from rhesus macaques. E-cadherin+ cells, CD4+ cells and total mucosal cells were assessed using in situ staining combined with a novel customized digital image analysis platform. Variations in cell numbers between baseline, placebo and Q-GRFT treated samples were analyzed using random intercept linear mixed effect models. The frequencies of rectal E-cadherin+ cells remained stable despite multiple tissue samplings and Q-GRFT gel (0.1%, 0.3% and 1%, respectively) treatment. Whereas single dose application of Q-GRFT did not affect the frequencies of rectal CD4+ cells, multi-dose Q-GRFT caused a small, but significant increase of the frequencies of intra-epithelial CD4+ cells (placebo: median 4%; 1% Q-GRFT: median 7%) and of the CD4+ lamina propria cells (placebo: median 30%; 0.1-1% Q-GRFT: median 36-39%). The resting time between sampling points were further associated with minor changes in the total and CD4+ rectal mucosal cell levels. The results add to general knowledge of in vivo evaluation of anti-HIV microbicide application concerning cellular effects in rectal mucosa.", "doi": "10.1038/s41598-019-54493-4", "pmid": "31792342", "labels": {"BioImage Informatics": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-54493-4"}, {"db": "pmc", "key": "PMC6889265"}], "notes": [], "created": "2020-01-08T07:07:49.842Z", "modified": "2022-03-29T11:57:29.767Z"}, {"entity": "publication", "iuid": "9797ffcb4104436abf36713e3e05d177", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9797ffcb4104436abf36713e3e05d177.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9797ffcb4104436abf36713e3e05d177"}}, "title": "High throughput barcoding method for genome-scale phasing.", "authors": [{"family": "Redin", "given": "David", "initials": "D"}, {"family": "Frick", "given": "Tobias", "initials": "T"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2019-12-02", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "18116", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.", "doi": "10.1038/s41598-019-54446-x", "pmid": "31792271", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-54446-x"}, {"db": "pmc", "key": "PMC6889410"}], "notes": [], "created": "2020-01-08T16:49:20.740Z", "modified": "2021-07-07T15:18:57.764Z"}, {"entity": "publication", "iuid": "1352e2277ea64042b7223339b4060434", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1352e2277ea64042b7223339b4060434.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1352e2277ea64042b7223339b4060434"}}, "title": "Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden", "authors": [{"family": "Alaridah", "given": "Nader", "initials": "N"}, {"family": "Hallb\u00e4ck", "given": "Erika T\u00e5ng", "initials": "ET"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Winqvist", "given": "Niclas", "initials": "N"}, {"family": "Stureg\u00e5rd", "given": "Erik", "initials": "E"}, {"family": "Flor\u00e9n-Johansson", "given": "Kerstin", "initials": "K"}, {"family": "J\u00f6nsson", "given": "Bodil", "initials": "B"}, {"family": "Tenland", "given": "Erik", "initials": "E"}, {"family": "Welinder-Olsson", "given": "Christina", "initials": "C"}, {"family": "Medstrand", "given": "Patrik", "initials": "P"}, {"family": "Kaijser", "given": "Bertil", "initials": "B"}, {"family": "Godaly", "given": "Gabriela", "initials": "G"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.", "doi": "10.1038/s41598-019-39971-z", "pmid": "30894568", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-23T15:06:38.395Z", "modified": "2020-01-21T13:56:17.604Z"}, {"entity": "publication", "iuid": "25fbf226ef374458b7cfc14adfa5922e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25fbf226ef374458b7cfc14adfa5922e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25fbf226ef374458b7cfc14adfa5922e"}}, "title": "Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial", "authors": [{"family": "He", "given": "Xuan", "initials": "X"}, {"family": "Parenti", "given": "Mariana", "initials": "M"}, {"family": "Grip", "given": "Tove", "initials": "T"}, {"family": "Domell\u00f6f", "given": "Magnus", "initials": "M"}, {"family": "L\u00f6nnerdal", "given": "Bo", "initials": "B"}, {"family": "Hernell", "given": "Olle", "initials": "O"}, {"family": "Timby", "given": "Niklas", "initials": "N"}, {"family": "Slupsky", "given": "Carolyn M", "initials": "CM"}], "type": "journal-article", "published": "2019-12-00", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "339", "issn-l": "2045-2322"}, "abstract": "Formula-fed (FF) infants exhibit a different metabolic profile than breast-fed (BF) infants. Two potential mechanisms are the higher protein level in formula compared with breast milk and the removal of the milk fat and associated milk fat globule membranes (MFGM) during production of infant formula. To determine whether MFGM may impact metabolism, formula-fed infants were randomly assigned to receive either an MFGM isolate-supplemented experimental formula (EF) or a standard formula (SF) from 2 until 6 months and compared with a BF reference group. Infants consuming EF had higher levels of fatty acid oxidation products compared to infants consuming SF. Although the protein level in the study formula was approximately 12 g/L (lower than most commercial formulas), a metabolic difference between FF and BF remained such that FF infants had higher levels of amino acid catabolism by-products and a low efficiency of amino acid clearance (preference for protein metabolism). BF infants had higher levels of fatty acid oxidation products (preference for fat metabolism). These unique, energy substrate-driven metabolic outcomes did not persist after diet was shifted to weaning foods and appeared to be disrupted by complementary feeding. Our results suggest that MFGM may have a role in directing infant metabolism.", "doi": "10.1038/s41598-018-36292-5", "pmid": "30674917", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-36292-5"}, {"db": "pmc", "key": "PMC6344597"}], "notes": [], "created": "2020-01-21T10:13:10.739Z", "modified": "2025-10-17T13:03:17.086Z"}, {"entity": "publication", "iuid": "7c287c7d0ca54e8ca5d8e7996a0e8550", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c287c7d0ca54e8ca5d8e7996a0e8550.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c287c7d0ca54e8ca5d8e7996a0e8550"}}, "title": "Coro2b, a podocyte protein downregulated in human diabetic nephropathy, is involved in the development of protamine sulphate-induced foot process effacement", "authors": [{"family": "Schwarz", "given": "Angelina", "initials": "A"}, {"family": "M\u00f6ller-Hackbarth", "given": "Katja", "initials": "K"}, {"family": "Ebarasi", "given": "Lwaki", "initials": "L"}, {"family": "Unnersj\u00f6 Jess", "given": "David", "initials": "D"}, {"family": "Zambrano", "given": "Sonia", "initials": "S"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Wernerson", "given": "Annika", "initials": "A"}, {"family": "Lal", "given": "Mark", "initials": "M"}, {"family": "Patrakka", "given": "Jaakko", "initials": "J"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "8888", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Podocytes have an important role in the pathogenesis of diabetic nephropathy (DN). Podocyte foot process effacement, mediated largely by the actin-based cytoskeleton of foot processes, is commonly detected in DN and is believed to be a key pathogenic event in the development of proteinuria. In this study, we identified coronin 2b (Coro2b), a member of known actin-regulating proteins, the coronins, as a highly podocyte-enriched molecule located at the cytoplasmic side of the apical plasma membrane. Studies in human renal biopsies show that glomerular Coro2b expression is significantly down-regulated in patients with DN. Studies in knockout mice indicate that Coro2b is not required for the development or maintenance of the glomerular filtration barrier. Moreover, inactivation of Coro2b specifically in podocytes does not affect the outcome of nephropathy in a streptozotocin-induced diabetes model. However, Coro2b seems to modulate the reorganization of foot processes under pathological conditions as Coro2b knockout podocytes are partially protected from protamine sulfate perfusion-induced foot process effacement. Taken together, our study suggests a role for Coro2b in the pathogenesis of glomerulopathies. Further studies regarding the involvement of Coro2b in podocyte health and diseases are warranted.", "doi": "10.1038/s41598-019-45303-y", "pmid": "31221975", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-45303-y"}, {"db": "pmc", "key": "PMC6586875"}], "notes": [], "created": "2019-06-26T12:59:25.526Z", "modified": "2021-07-05T13:48:51.555Z"}, {"entity": "publication", "iuid": "7d00b2f694174425a4e820b73f5c248b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d00b2f694174425a4e820b73f5c248b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d00b2f694174425a4e820b73f5c248b"}}, "title": "Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Ramesh", "given": "Malavika", "initials": "M"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "19259", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Nontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern \"omics\" approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, Mmuc T, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.", "doi": "10.1038/s41598-019-55464-5", "pmid": "31848383", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-55464-5"}, {"db": "pmc", "key": "PMC6917791"}], "notes": [], "created": "2020-01-08T12:38:20.448Z", "modified": "2021-06-16T14:51:44.614Z"}, {"entity": "publication", "iuid": "aadffd1889e544f1b9aa22c5a6ca91ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aadffd1889e544f1b9aa22c5a6ca91ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aadffd1889e544f1b9aa22c5a6ca91ac"}}, "title": "Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ", "orcid": "0000-0001-5498-3899", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6367673ade411a885a20ecefdac3c1.json"}}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Skrtic", "given": "Stanko", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "9653", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Type 2 diabetes (T2D) mellitus is a complex metabolic disease commonly caused by insulin resistance in several tissues. We performed a matched two-dimensional metabolic screening in tissue samples from 43 multi-organ donors. The intra-individual analysis was assessed across five key metabolic tissues (serum, visceral adipose tissue, liver, pancreatic islets and skeletal muscle), and the inter-individual across three different groups reflecting T2D progression. We identified 92 metabolites differing significantly between non-diabetes and T2D subjects. In diabetes cases, carnitines were significantly higher in liver, while lysophosphatidylcholines were significantly lower in muscle and serum. We tracked the primary tissue of origin for multiple metabolites whose alterations were reflected in serum. An investigation of three major stages spanning from controls, to pre-diabetes and to overt T2D indicated that a subset of lysophosphatidylcholines was significantly lower in the muscle of pre-diabetes subjects. Moreover, glycodeoxycholic acid was significantly higher in liver of pre-diabetes subjects while additional increase in T2D was insignificant. We confirmed many previously reported findings and substantially expanded on them with altered markers for early and overt T2D. Overall, the analysis of this unique dataset can increase the understanding of the metabolic interplay between organs in the development of T2D.", "doi": "10.1038/s41598-019-45906-5", "pmid": "31273253", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-45906-5"}, {"db": "pmc", "key": "PMC6609645"}], "notes": [], "created": "2020-01-07T15:53:12.510Z", "modified": "2025-10-17T13:03:17.098Z"}, {"entity": "publication", "iuid": "ab1a9e92b16c4435ad348245129368c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab1a9e92b16c4435ad348245129368c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab1a9e92b16c4435ad348245129368c5"}}, "title": "ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes", "authors": [{"family": "Bysani", "given": "Madhusudhan", "initials": "M"}, {"family": "Agren", "given": "Rasmus", "initials": "R"}, {"family": "Daveg\u00e5rdh", "given": "Cajsa", "initials": "C"}, {"family": "Volkov", "given": "Petr", "initials": "P"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and rs878521 near TCF7L2, KCNQ1, HNF1B, ADCY5 and GCK, respectively) and with additional 67 SNPs in LD with known T2D SNPs (e.g. SNPs annotated to GIPR, KCNJ11, GLIS3, IGF2BP2, FTO and PPARG). There was enrichment of open chromatin regions near highly expressed genes in human islets. Moreover, 1,078 open chromatin peaks, annotated to 898 genes, differed in prevalence between diabetic and non-diabetic islet donors. Some of these peaks are annotated to candidate genes for T2D and islet dysfunction (e.g. HHEX, HMGA2, GLIS3, MTNR1B and PARK2) and some overlap with SNPs associated with T2D (e.g. rs3821943 near WFS1 and rs508419 near ANK1). Enhancer regions and motifs specific to key TFs including BACH2, FOXO1, FOXA2, NEUROD1, MAFA and PDX1 were enriched in differential islet ATAC-seq peaks of T2D versus non-diabetic donors. Our study provides new understanding into how T2D alters the chromatin landscape, and thereby accessibility for TFs and gene expression, in human pancreatic islets.", "doi": "10.1038/s41598-019-44076-8", "pmid": "31123324", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Systems Biology": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "GEO", "description": "ATAC-seq data", "key": "GSE129383"}], "notes": [], "created": "2019-06-18T10:42:51.751Z", "modified": "2020-01-21T13:56:17.683Z"}, {"entity": "publication", "iuid": "b1c8e445bafa421699e0ca5d311d02b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1c8e445bafa421699e0ca5d311d02b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1c8e445bafa421699e0ca5d311d02b9"}}, "title": "Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers", "authors": [{"family": "H\u00f6glund", "given": "Julia", "initials": "J"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Genome-wide association studies (GWAS) have identified associations between thousands of common genetic variants and human traits. However, common variants usually explain a limited fraction of the heritability of a trait. A powerful resource for identifying trait-associated variants is whole genome sequencing (WGS) data in cohorts comprised of families or individuals from a limited geographical area. To evaluate the power of WGS compared to imputations, we performed GWAS on WGS data for 72 inflammatory biomarkers, in a kinship-structured cohort. When using WGS data, we identified 18 novel associations that were not detected when analyzing the same biomarkers with genotyped or imputed SNPs. Five of the novel top variants were low frequency variants with a minor allele frequency (MAF) of <5%. Our results suggest that, even when applying a GWAS approach, we gain power and precision using WGS data, presumably due to more accurate determination of genotypes. The lack of a comparable dataset for replication of our results is a limitation in our study. However, this further highlights that there is a need for more genetic epidemiological studies based on WGS data.", "doi": "10.1038/s41598-019-53111-7", "pmid": "31727947", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-29T12:36:47.798Z", "modified": "2024-01-16T13:48:43.415Z"}, {"entity": "publication", "iuid": "c5320b00cf0741ca95e0c5e91858b2aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5320b00cf0741ca95e0c5e91858b2aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5320b00cf0741ca95e0c5e91858b2aa"}}, "title": "The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway", "authors": [{"family": "Gul", "given": "Nadia", "initials": "N"}, {"family": "Karlsson", "given": "Joakim", "initials": "J", "orcid": "0000-0001-6332-4043", "researcher": {"href": "https://publications.scilifelab.se/researcher/6190c1a8a7d54cd6807f120e8748cfcd.json"}}, {"family": "T\u00e4ngemo", "given": "Carolina", "initials": "C"}, {"family": "Linsefors", "given": "Sanna", "initials": "S"}, {"family": "Tuyizere", "given": "Samuel", "initials": "S"}, {"family": "Perkins", "given": "Rosie", "initials": "R"}, {"family": "Ala", "given": "Chandu", "initials": "C"}, {"family": "Zou", "given": "Zhiyuan", "initials": "Z"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Berg\u00f6", "given": "Martin O", "initials": "MO"}, {"family": "Lindahl", "given": "Per", "initials": "P"}], "type": "journal-article", "published": "2019-12-00", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "14667", "issn-l": "2045-2322"}, "abstract": "The mut-T homolog-1 (MTH1) inhibitor TH588 has shown promise in preclinical cancer studies but its targeting specificity has been questioned. Alternative mechanisms for the anti-cancer effects of TH588 have been suggested but the question remains unresolved. Here, we performed an unbiased CRISPR screen on human lung cancer cells to identify potential mechanisms behind the cytotoxic effect of TH588. The screen identified pathways and complexes involved in mitotic spindle regulation. Using immunofluorescence and live cell imaging, we showed that TH588 rapidly reduced microtubule plus-end mobility, disrupted mitotic spindles, and prolonged mitosis in a concentration-dependent but MTH1-independent manner. These effects activated a USP28-p53 pathway - the mitotic surveillance pathway - that blocked cell cycle reentry after prolonged mitosis; USP28 acted upstream of p53 to arrest TH588-treated cells in the G1-phase of the cell cycle. We conclude that TH588 is a microtubule-modulating agent that activates the mitotic surveillance pathway and thus prevents cancer cells from re-entering the cell cycle.", "doi": "10.1038/s41598-019-51205-w", "pmid": "31604991", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-51205-w"}, {"db": "pmc", "key": "PMC6789014"}], "notes": [], "created": "2020-01-23T16:02:13.461Z", "modified": "2021-06-16T14:42:57.467Z"}, {"entity": "publication", "iuid": "5b59dfa32e5f440fa3619f3f00d31b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b59dfa32e5f440fa3619f3f00d31b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b59dfa32e5f440fa3619f3f00d31b21"}}, "title": "Carnivores, competition and genetic connectivity in the Anthropocene.", "authors": [{"family": "Creel", "given": "Scott", "initials": "S"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Becker", "given": "Matthew", "initials": "M"}, {"family": "Simukonda", "given": "Chuma", "initials": "C"}, {"family": "Norman", "given": "Anita", "initials": "A"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Chifunte", "given": "Clive", "initials": "C"}], "type": "journal article", "published": "2019-11-08", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "16339", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Current extinction rates are comparable to five prior mass extinctions in the earth's history, and are strongly affected by human activities that have modified more than half of the earth's terrestrial surface. Increasing human activity restricts animal movements and isolates formerly connected populations, a particular concern for the conservation of large carnivores, but no prior research has used high throughput sequencing in a standardized manner to examine genetic connectivity for multiple species of large carnivores and multiple ecosystems. Here, we used RAD SNP genotypes to test for differences in connectivity between multiple ecosystems for African wild dogs (Lycaon pictus) and lions (Panthera leo), and to test correlations between genetic distance, geographic distance and landscape resistance due to human activity. We found weaker connectivity, a stronger correlation between genetic distance and geographic distance, and a stronger correlation between genetic distance and landscape resistance for lions than for wild dogs, and propose a new hypothesis that adaptations to interspecific competition may help to explain differences in vulnerability to isolation by humans.", "doi": "10.1038/s41598-019-52904-0", "pmid": "31705017", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-52904-0"}, {"db": "pmc", "key": "PMC6841969"}], "notes": [], "created": "2019-12-02T17:21:18.825Z", "modified": "2020-01-21T13:56:15.790Z"}, {"entity": "publication", "iuid": "1522544bc8764e269d7fff491aa8d1a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1522544bc8764e269d7fff491aa8d1a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1522544bc8764e269d7fff491aa8d1a7"}}, "title": "Amyloid fibrils prepared using an acetylated and methyl amidated peptide model of the \u03b1-Synuclein NAC 71-82 amino acid stretch contain an additional cross-\u03b2 structure also found in prion proteins.", "authors": [{"family": "N\u00e4sstr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "Andersson", "given": "Per Ola", "initials": "PO"}, {"family": "Lejon", "given": "Christian", "initials": "C"}, {"family": "Karlsson", "given": "Bj\u00f6rn C G", "initials": "BCG", "orcid": "0000-0002-7392-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/522f052f4b8a42208d3c4e4561212ff4.json"}}], "type": "journal article", "published": "2019-11-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "15949", "issn-l": "2045-2322"}, "abstract": "The 71-82 fragment of the non-amyloid-\u03b2 component (NAC) region of the Parkinson's disease (PD) and dementia with Lewy bodies (DLB) related protein \u03b1-Synuclein, has been reported to be important during protein misfolding. Although reports have demonstrated the importance of this fragment for the aggregation properties of the full-length protein, its exact role in pre-fibrillar oligomerisation, fibrillar growth and morphology has not yet been fully elucidated. Here, we provide evidence that fibrils prepared from an acetylated and methyl amidated peptide of the NAC 71-82 amino acid stretch of \u03b1-Synuclein are amyloid and contain, in addition to the cross-\u03b2 structure detected in the full-length protein fibrils, a cross-\u03b2 structure previously observed in prion proteins. These results shed light on the aggregation propensity of the NAC 71-82 amino acid stretch of the full-length protein but also the roles of the N- and C-terminal domains of \u03b1-Synuclein in balancing this aggregation propensity. The results also suggest that early aggregated forms of the capped NAC 71-82 peptide generated structures were stabilised by an anti-parallel and twisted \u03b2-sheet motif. Due to its expected toxicity, this \u03b2-sheet motif may be a promising molecular target for the development of therapeutic strategies for PD and DLB.", "doi": "10.1038/s41598-019-52206-5", "pmid": "31685848", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-52206-5"}, {"db": "pmc", "key": "PMC6828723"}], "notes": [], "created": "2020-01-10T13:28:35.168Z", "modified": "2021-06-16T16:13:35.943Z"}, {"entity": "publication", "iuid": "ff423e974db94cfabfc2296c9c38de11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff423e974db94cfabfc2296c9c38de11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff423e974db94cfabfc2296c9c38de11"}}, "title": "The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.", "authors": [{"family": "Stjelja", "given": "Suzana", "initials": "S"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2019-10-31", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "15753", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Plasmodiophora brassicae is a soil-borne pathogen that attacks roots of cruciferous plants causing clubroot disease. The pathogen belongs to the Plasmodiophorida order in Phytomyxea. Here we used long-read SMRT technology to clarify the P. brassicae e3 genomic constituents along with comparative and phylogenetic analyses. Twenty contigs representing the nuclear genome and one mitochondrial (mt) contig were generated, together comprising 25.1 Mbp. Thirteen of the 20 nuclear contigs represented chromosomes from telomere to telomere characterized by [TTTTAGGG] sequences. Seven active gene candidates encoding synaptonemal complex-associated and meiotic-related protein homologs were identified, a finding that argues for possible genetic recombination events. The circular mt genome is large (114,663 bp), gene dense and intron rich. It shares high synteny with the mt genome of Spongospora subterranea, except in a unique 12 kb region delimited by shifts in GC content and containing tandem minisatellite- and microsatellite repeats with partially palindromic sequences. De novo annotation identified 32 protein-coding genes, 28 structural RNA genes and 19 ORFs. ORFs predicted in the repeat-rich region showed similarities to diverse organisms suggesting possible evolutionary connections. The data generated here form a refined platform for the next step involving functional analysis, all to clarify the complex biology of P. brassicae.", "doi": "10.1038/s41598-019-52274-7", "pmid": "31673019", "labels": {"National Genomics Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-52274-7"}, {"db": "pmc", "key": "PMC6823432"}], "notes": [], "created": "2019-11-24T12:29:14.530Z", "modified": "2020-01-21T13:56:17.807Z"}, {"entity": "publication", "iuid": "247bdff2ab064225a339777c8411075a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/247bdff2ab064225a339777c8411075a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/247bdff2ab064225a339777c8411075a"}}, "title": "Inhibition of translation termination by small molecules targeting ribosomal release factors.", "authors": [{"family": "Ge", "given": "Xueliang", "initials": "X", "orcid": "0000-0001-7954-3195", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d0da6ede33c4780ba09400c10b80565.json"}}, {"family": "Oliveira", "given": "Ana", "initials": "A"}, {"family": "Hjort", "given": "Karin", "initials": "K", "orcid": "0000-0003-3326-8495", "researcher": {"href": "https://publications.scilifelab.se/researcher/209ad64e44824ec2ab12aa8ea9e8ba49.json"}}, {"family": "Bergfors", "given": "Terese", "initials": "T", "orcid": "0000-0002-6463-9116", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda8871f860d483ebb92b7244b211ef0.json"}}, {"family": "Guti\u00e9rrez-de-Ter\u00e1n", "given": "Hugo", "initials": "H", "orcid": "0000-0003-0459-3491", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c1a83f44474224b4788bfcbfcd1a43.json"}}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}, {"family": "Sanyal", "given": "Suparna", "initials": "S", "orcid": "0000-0002-7124-792X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5ffabce284f28885f6594da1460d6.json"}}, {"family": "\u00c5qvist", "given": "Johan", "initials": "J", "orcid": "0000-0003-2091-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/9777a1c6e1bd4181bc46dce4be3c2146.json"}}], "type": "journal article", "published": "2019-10-28", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "15424", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The bacterial ribosome is an important drug target for antibiotics that can inhibit different stages of protein synthesis. Among the various classes of compounds that impair translation there are, however, no known small-molecule inhibitors that specifically target ribosomal release factors (RFs). The class I RFs are essential for correct termination of translation and they differ considerably between bacteria and eukaryotes, making them potential targets for inhibiting bacterial protein synthesis. We carried out virtual screening of a large compound library against 3D structures of free and ribosome-bound RFs in order to search for small molecules that could potentially inhibit termination by binding to the RFs. Here, we report identification of two such compounds which are found both to bind free RFs in solution and to inhibit peptide release on the ribosome, without affecting peptide bond formation.", "doi": "10.1038/s41598-019-51977-1", "pmid": "31659219", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-51977-1"}, {"db": "pmc", "key": "PMC6817905"}], "notes": [], "created": "2019-11-21T11:53:28.797Z", "modified": "2025-10-17T13:05:08.153Z"}, {"entity": "publication", "iuid": "55008ccf77894ae4b746abf036fdc7c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55008ccf77894ae4b746abf036fdc7c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55008ccf77894ae4b746abf036fdc7c9"}}, "title": "Comparative analysis of obesity-related cardiometabolic and renal biomarkers in human plasma and serum.", "authors": [{"family": "Rajan", "given": "Meenu Rohini", "initials": "MR"}, {"family": "Sotak", "given": "Matus", "initials": "M", "orcid": "0000-0002-9984-9340", "researcher": {"href": "https://publications.scilifelab.se/researcher/106689ff31cd45c98137b00ed207b43a.json"}}, {"family": "Barren\u00e4s", "given": "Fredrik", "initials": "F"}, {"family": "Shen", "given": "Tong", "initials": "T"}, {"family": "Borkowski", "given": "Kamil", "initials": "K"}, {"family": "Ashton", "given": "Nicholas J", "initials": "NJ"}, {"family": "Bi\u00f6rserud", "given": "Christina", "initials": "C"}, {"family": "Lindahl", "given": "Tomas L", "initials": "TL"}, {"family": "Ramstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Sch\u00f6ll", "given": "Michael", "initials": "M"}, {"family": "Lindahl", "given": "Per", "initials": "P"}, {"family": "Fiehn", "given": "Oliver", "initials": "O", "orcid": "0000-0002-6261-8928", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb9b7a750974012be39518c1962180c.json"}}, {"family": "Newman", "given": "John W", "initials": "JW", "orcid": "0000-0001-9632-6571", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ab4314a5f924eab9fe741a45ad852f2.json"}}, {"family": "Perkins", "given": "Rosie", "initials": "R", "orcid": "0000-0003-2447-3286", "researcher": {"href": "https://publications.scilifelab.se/researcher/5879cbc5b79945c8886359e2c0acd9fd.json"}}, {"family": "Wallenius", "given": "Ville", "initials": "V"}, {"family": "Lange", "given": "Stephan", "initials": "S", "orcid": "0000-0001-9361-6602", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4764ee6cc7c4d16ab49b2b38ec866e8.json"}}, {"family": "B\u00f6rgeson", "given": "Emma", "initials": "E", "orcid": "0000-0002-2290-9472", "researcher": {"href": "https://publications.scilifelab.se/researcher/5777a7087f3047ac9f2ea74e061ad374.json"}}], "type": "clinical trial", "published": "2019-10-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "9", "issue": "1", "pages": "15385"}, "abstract": "The search for biomarkers associated with obesity-related diseases is ongoing, but it is not clear whether plasma and serum can be used interchangeably in this process. Here we used high-throughput screening to analyze 358 proteins and 76 lipids, selected because of their relevance to obesity-associated diseases, in plasma and serum from age- and sex-matched lean and obese humans. Most of the proteins/lipids had similar concentrations in plasma and serum, but a subset showed significant differences. Notably, a key marker of cardiovascular disease PAI-1 showed a difference in concentration between the obese and lean groups only in plasma. Furthermore, some biomarkers showed poor correlations between plasma and serum, including PCSK9, an important regulator of cholesterol homeostasis. Collectively, our results show that the choice of biofluid may impact study outcome when screening for obesity-related biomarkers and we identify several markers where this will be the case.", "doi": "10.1038/s41598-019-51673-0", "pmid": "31659186", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-51673-0"}, {"db": "pmc", "key": "PMC6817872"}], "notes": [], "created": "2020-01-23T16:04:35.823Z", "modified": "2023-04-14T13:55:54.787Z"}, {"entity": "publication", "iuid": "805f4972c06d4192afc3c9f150458320", "links": {"self": {"href": "https://publications.scilifelab.se/publication/805f4972c06d4192afc3c9f150458320.json"}, "display": {"href": "https://publications.scilifelab.se/publication/805f4972c06d4192afc3c9f150458320"}}, "title": "Publisher Correction: Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial.", "authors": [{"family": "He", "given": "Xuan", "initials": "X"}, {"family": "Parenti", "given": "Mariana", "initials": "M"}, {"family": "Grip", "given": "Tove", "initials": "T"}, {"family": "Domell\u00f6f", "given": "Magnus", "initials": "M"}, {"family": "L\u00f6nnerdal", "given": "Bo", "initials": "B"}, {"family": "Hernell", "given": "Olle", "initials": "O"}, {"family": "Timby", "given": "Niklas", "initials": "N"}, {"family": "Slupsky", "given": "Carolyn M", "initials": "CM"}], "type": "published erratum", "published": "2019-08-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "12382", "issn-l": "2045-2322"}, "abstract": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.", "doi": "10.1038/s41598-019-48858-y", "pmid": "31434987", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-48858-y"}, {"db": "pmc", "key": "PMC6704142"}], "notes": [], "created": "2020-01-07T15:43:31.704Z", "modified": "2025-10-17T13:03:17.414Z"}, {"entity": "publication", "iuid": "ddacb29df4184d21903954634a557d81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddacb29df4184d21903954634a557d81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddacb29df4184d21903954634a557d81"}}, "title": "Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.", "authors": [{"family": "Fernandes", "given": "Sunjay Jude", "initials": "SJ"}, {"family": "Morikawa", "given": "Hiromasa", "initials": "H"}, {"family": "Ewing", "given": "Ewoud", "initials": "E"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Joshi", "given": "Rubin Narayan", "initials": "RN"}, {"family": "Lagani", "given": "Vincenzo", "initials": "V"}, {"family": "Karathanasis", "given": "Nestoras", "initials": "N"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Planell", "given": "Nuria", "initials": "N"}, {"family": "Schmidt", "given": "Angelika", "initials": "A"}, {"family": "Tsamardinos", "given": "Ioannis", "initials": "I"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}], "type": "journal article", "published": "2019-08-19", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "11996", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Multiple Sclerosis (MS) is an autoimmune disease of the central nervous system with prominent neurodegenerative components. The triggering and progression of MS is associated with transcriptional and epigenetic alterations in several tissues, including peripheral blood. The combined influence of transcriptional and epigenetic changes associated with MS has not been assessed in the same individuals. Here we generated paired transcriptomic (RNA-seq) and DNA methylation (Illumina 450 K array) profiles of CD4+ and CD8+ T cells (CD4, CD8), using clinically accessible blood from healthy donors and MS patients in the initial relapsing-remitting and subsequent secondary-progressive stage. By integrating the output of a differential expression test with a permutation-based non-parametric combination methodology, we identified 149 differentially expressed (DE) genes in both CD4 and CD8 cells collected from MS patients. Moreover, by leveraging the methylation-dependent regulation of gene expression, we identified the gene SH3YL1, which displayed significant correlated expression and methylation changes in MS patients. Importantly, silencing of SH3YL1 in primary human CD4 cells demonstrated its influence on T cell activation. Collectively, our strategy based on paired sampling of several cell-types provides a novel approach to increase sensitivity for identifying shared mechanisms altered in CD4 and CD8 cells of relevance in MS in small sized clinical materials.", "doi": "10.1038/s41598-019-48493-7", "pmid": "31427643", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-48493-7"}, {"db": "pmc", "key": "PMC6700160"}], "notes": [], "created": "2020-01-08T16:47:42.719Z", "modified": "2020-01-21T13:56:16.382Z"}, {"entity": "publication", "iuid": "46cd7cf01fbc4ddf87f7503100fbaaab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46cd7cf01fbc4ddf87f7503100fbaaab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46cd7cf01fbc4ddf87f7503100fbaaab"}}, "title": "TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish.", "authors": [{"family": "Gudmundsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-2332-074X", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb097c987504b2ca309e5f4e1cea5d2.json"}}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Filipek-G\u00f3rniok", "given": "Beata", "initials": "B", "orcid": "0000-0002-6757-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f0b7b3e0b045f082d2aff1dd23ec0e.json"}}, {"family": "Molin", "given": "Anna-Maja", "initials": "A"}, {"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Johansson", "given": "Josefin", "initials": "J", "orcid": "0000-0002-5152-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e568827124304b769a3f336d76b6954e.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Gylje", "given": "Hans", "initials": "H"}, {"family": "Kalscheuer", "given": "Vera M", "initials": "VM", "orcid": "0000-0001-6898-3259", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb8107a11ed144bc8f4c236042f9bc8c.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "M"}], "type": "journal article", "published": "2019-07-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "9", "issue": "1", "pages": "10730"}, "abstract": "The TATA-box binding protein associated factor 1 (TAF1) protein is a key unit of the transcription factor II D complex that serves a vital function during transcription initiation. Variants of TAF1 have been associated with neurodevelopmental disorders, but TAF1's molecular functions remain elusive. In this study, we present a five-generation family affected with X-linked intellectual disability that co-segregated with a TAF1 c.3568C>T, p.(Arg1190Cys) variant. All affected males presented with intellectual disability and dysmorphic features, while heterozygous females were asymptomatic and had completely skewed X-chromosome inactivation. We investigated the role of TAF1 and its association to neurodevelopment by creating the first complete knockout model of the TAF1 orthologue in zebrafish. A crucial function of human TAF1 during embryogenesis can be inferred from the model, demonstrating that intact taf1 is essential for embryonic development. Transcriptome analysis of taf1 zebrafish knockout revealed enrichment for genes associated with neurodevelopmental processes. In conclusion, we propose that functional TAF1 is essential for embryonic development and specifically neurodevelopmental processes.", "doi": "10.1038/s41598-019-46632-8", "pmid": "31341187", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Genome Engineering Zebrafish": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "BioImage Informatics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-46632-8"}, {"db": "pmc", "key": "PMC6656882"}], "notes": [], "created": "2019-11-29T13:27:12.056Z", "modified": "2024-01-16T13:48:44.102Z"}, {"entity": "publication", "iuid": "2b01b061b37c46979ad61d662bafb774", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b01b061b37c46979ad61d662bafb774.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b01b061b37c46979ad61d662bafb774"}}, "title": "Genome and plasmid diversity of Extended-Spectrum \u03b2-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.", "authors": [{"family": "Ny", "given": "Sofia", "initials": "S"}, {"family": "Sandegren", "given": "Linus", "initials": "L"}, {"family": "Salemi", "given": "Marco", "initials": "M"}, {"family": "Giske", "given": "Christian G", "initials": "CG"}], "type": "journal article", "published": "2019-07-16", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "10291", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Clonal lineages of ESBL (Extended-Spectrum \u03b2-Lactamase)-producing E. coli belonging to sequence type 131 (ST131) have disseminated globally during the last 30 years, leading to an increased prevalence of resistance to fluoroquinolones and extended-spectrum cephalosporins in clinical isolates of E. coli. We aimed to study if Swedish ESBL-producing ST131 isolates originated from single or multiple introductions to the population by assessing the amount of genetic variation, on chromosomal and plasmid level, between Swedish and international E. coli ST131. Bayesian inference of Swedish E. coli ST131 isolates (n = 29), sequenced using PacBio RSII, together with an international ST131 dataset showed that the Swedish isolates were part of the international ST131 A, C1 and C2 clades. Highly conserved plasmids were identified in three clusters although they were separated by several years, which indicates a strong co-evolution between some ST131 lineages and specific plasmids. In conclusion, the tight clonal relationship observed within the ST131 clades, together with highly conserved plasmids, challenges investigation of strain transmission events. A combination of few SNPs on a genome-wide scale and an epidemiological temporospatial link, are needed to track the spread of the ST131 subclones.", "doi": "10.1038/s41598-019-46580-3", "pmid": "31312006", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-46580-3"}, {"db": "pmc", "key": "PMC6635401"}], "notes": [], "created": "2019-11-25T13:12:11.098Z", "modified": "2024-01-16T13:48:44.118Z"}, {"entity": "publication", "iuid": "846062a626a84b52bb27e5240d995f59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/846062a626a84b52bb27e5240d995f59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/846062a626a84b52bb27e5240d995f59"}}, "title": "Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder.", "authors": [{"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}, {"family": "Li", "given": "Danyang", "initials": "D"}, {"family": "Rabkina", "given": "Ielyzaveta", "initials": "I"}, {"family": "Stamouli", "given": "Sofia", "initials": "S"}, {"family": "Becker", "given": "Martin", "initials": "M"}, {"family": "Nicolaou", "given": "Veronika", "initials": "V"}, {"family": "Berggren", "given": "Steve", "initials": "S"}, {"family": "Coco", "given": "Christina", "initials": "C"}, {"family": "Falkmer", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Jonsson", "given": "Ulf", "initials": "U"}, {"family": "Choque-Olsson", "given": "Nora", "initials": "N"}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S"}], "type": "comparative study", "published": "2019-07-08", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "9810", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Challenges in social communication and interaction are core features of autism spectrum disorder (ASD) for which social skills group training (SSGT) is a commonly used intervention. SSGT has shown modest and heterogeneous effects. One of the major genetic risk factors in ASD is rare copy number variation (CNV). However, limited information exists whether CNV profiles could be used to aid intervention decisions. Here, we analyzed the rare genic CNV carrier status for 207 children, of which 105 received SSGT and 102 standard care as part of a randomized clinical trial for SSGT. We found that being a carrier of rare genic CNV did not have an impact on the SSGT outcome measured by the parent-report Social Responsiveness Scale (SRS). However, when stratifying by pathogenicity and size of the CNVs, we identified that carriers of clinically significant and large genic CNVs (>500 kb) showed inferior SRS outcomes at post-intervention (P = 0.047 and P = 0.036, respectively) and follow-up (P = 0.008 and P = 0.072, respectively) when adjusting for standard care effects. Our study provides preliminary evidence that carriers of clinically significant and large genic CNVs might not benefit as much from SSGT as non-carriers. Our results indicate that genetic information might help guide the modifications of interventions in ASD.", "doi": "10.1038/s41598-019-46396-1", "pmid": "31285490", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-46396-1"}, {"db": "pmc", "key": "PMC6614458"}], "notes": [], "created": "2020-01-07T15:58:18.966Z", "modified": "2024-01-16T13:48:44.124Z"}, {"entity": "publication", "iuid": "8a875a9c10bd4ceb8b4e950698f18082", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a875a9c10bd4ceb8b4e950698f18082.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a875a9c10bd4ceb8b4e950698f18082"}}, "title": "Proteomic profiling of extracellular vesicles reveals additional diagnostic biomarkers for myocardial infarction compared to plasma alone.", "authors": [{"family": "Gidl\u00f6f", "given": "Olof", "initials": "O", "orcid": "0000-0002-7402-3139", "researcher": {"href": "https://publications.scilifelab.se/researcher/83f5453e507041b995e0d69a74540c24.json"}}, {"family": "Evander", "given": "Mikael", "initials": "M"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Marko-Varga", "given": "Gy\u00f6rgy", "initials": "G"}, {"family": "Laurell", "given": "Thomas", "initials": "T"}, {"family": "Erlinge", "given": "David", "initials": "D"}], "type": "journal article", "published": "2019-06-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "9", "issue": "1", "pages": "8991"}, "abstract": "Extracellular vesicles (EVs) are submicron, membrane-enclosed particles that are released from cells in various pathophysiological states. The molecular cargo of these vesicles is considered to reflect the composition of the cell of origin, and the EV proteome is therefore a potential source of biomarkers for various diseases. Our aim was to determine whether EVs isolated from plasma provide additional diagnostic value or improved pathophysiological understanding compared to plasma alone in the context of myocardial infarction (MI). A panel of proximity extension assays (n = 92) was employed to analyze EV lysates and plasma from patients with MI (n = 60) and healthy controls (n = 22). After adjustment for multiple comparisons, a total of 11 dysregulated proteins were identified in EVs of MI patients compared to the controls (q < 0.01). Three of these proteins: chymotrypsin C (CTRC), proto-oncogene tyrosine-protein kinase SRC (SRC) and C-C motif chemokine ligand 17 (CCL17) were unaltered in the corresponding plasma samples. As biomarkers for MI, rudimentary to no evidence exists for these proteins. In a separate group of patients with varying degrees of coronary artery disease, the decrease in EV-associated (but not plasma-related) SRC levels was confirmed by ELISA. Confirmation of the presence of SRC on EVs of different sizes and cellular origins was performed with ELISA, flow cytometry and nanoparticle tracking analysis. In conclusion, the data revealed that despite a similarity in the EV and plasma proteomes, analysis of isolated EVs does indeed provide additional diagnostic information that cannot be obtained from plasma alone.", "doi": "10.1038/s41598-019-45473-9", "pmid": "31222168", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-45473-9"}, {"db": "pmc", "key": "PMC6586849"}], "notes": [], "created": "2020-01-23T16:04:51.937Z", "modified": "2023-04-14T13:55:57.174Z"}, {"entity": "publication", "iuid": "d81332752ac544d4a3f4e26a9be1bf56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d81332752ac544d4a3f4e26a9be1bf56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d81332752ac544d4a3f4e26a9be1bf56"}}, "title": "Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.", "authors": [{"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Ioannou", "given": "Marina", "initials": "M"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Branca", "given": "Rui M", "initials": "RM"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2019-06-06", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "8324", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "There is a strong need for procedures that enable context and application dependent validation of antibodies. Here, we applied a magnetic bead assisted workflow and immunoprecipitation mass spectrometry (IP-MS/MS) to assess antibody selectivity for the detection of proteins in human plasma. A resource was built on 414 IP experiments using 157 antibodies (targeting 120 unique proteins) in assays with heat-treated or untreated EDTA plasma. For each protein we determined their antibody related degrees of enrichment using z-scores and their frequencies of identification across all IP assays. Out of 1,313 unique endogenous proteins, 426 proteins (33%) were detected in >20% of IPs, and these background components were mainly comprised of proteins from the complement system. For 45% (70/157) of the tested antibodies, the expected target proteins were enriched (z-score \u2265 3). Among these 70 antibodies, 59 (84%) co-enriched other proteins beside the intended target and mainly due to sequence homology or protein abundance. We also detected protein interactions in plasma, and for IGFBP2 confirmed these using several antibodies and sandwich immunoassays. The protein enrichment data with plasma provide a very useful and yet lacking resource for the assessment of antibody selectivity. Our insights will contribute to a more informed use of affinity reagents for plasma proteomics assays.", "doi": "10.1038/s41598-019-43552-5", "pmid": "31171813", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-43552-5"}, {"db": "pmc", "key": "PMC6554399"}], "notes": [], "created": "2019-11-06T15:11:37.992Z", "modified": "2024-01-16T13:48:44.259Z"}, {"entity": "publication", "iuid": "e1f13bf4143743d6b98f0a69314d34ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1f13bf4143743d6b98f0a69314d34ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1f13bf4143743d6b98f0a69314d34ff"}}, "title": "Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes.", "authors": [{"family": "Henriksen", "given": "T I", "initials": "TI", "orcid": "0000-0003-1568-8920", "researcher": {"href": "https://publications.scilifelab.se/researcher/98143c432afe462b9106099c2420ed3a.json"}}, {"family": "Wigge", "given": "L V", "initials": "LV"}, {"family": "Nielsen", "given": "J", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Pedersen", "given": "B K", "initials": "BK", "orcid": "0000-0001-6508-6288", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f5c99493d524344bdb25fb9c163c90e.json"}}, {"family": "Sandri", "given": "M", "initials": "M"}, {"family": "Scheele", "given": "C", "initials": "C", "orcid": "0000-0002-6055-9709", "researcher": {"href": "https://publications.scilifelab.se/researcher/b407ecc01c1549578cc0f560a706d7a2.json"}}], "type": "journal article", "published": "2019-06-03", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "8169", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Autophagy is active during cellular remodeling including muscle differentiation. Muscle differentiation is dysregulated in type 2 diabetes and we therefore hypothesize that muscle precursor cells from people with type 2 diabetes (T2DM) have a dysregulation of their autophagy leading to impaired myogenesis. Muscle precursor cells were isolated from people with T2DM or healthy controls and differentiated in vitro. Autophagy marker levels were assessed by immunoblotting. Differentially expressed autophagy-related genes between healthy and T2DM groups were identified based on a previously published RNA-sequencing data-set, which we verified by RT-qPCR. siRNA was used to assess the function of differentially expressed autophagy genes. Basal autophagy increases during human muscle differentiation, while T2DM muscle cells have reduced levels of autophagy marker ATG7 and show a blunted response to starvation. Moreover, we demonstrate that the 3 non-canonical autophagy genes DRAM1, VAMP8 and TP53INP1 as differentially expressed between healthy and T2DM groups during myoblast differentiation, and that T53INP1 knock-down alters expression of both pro-and anti-apoptotic genes. In vitro differentiated T2DM muscle cells show differential expression of autophagy-related genes. These genes do not regulate myogenic transcription factors but may rather be involved in p53-associated myoblast apoptosis during early myogenesis.", "doi": "10.1038/s41598-019-44535-2", "pmid": "31160616", "labels": {"Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-44535-2"}, {"db": "pmc", "key": "PMC6546785"}], "notes": [], "created": "2020-01-07T14:23:20.811Z", "modified": "2021-06-16T14:40:44.871Z"}, {"entity": "publication", "iuid": "5c89b2604ecd4e0eb9cbc8a13f7b3b5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c89b2604ecd4e0eb9cbc8a13f7b3b5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c89b2604ecd4e0eb9cbc8a13f7b3b5a"}}, "title": "Genetic variation in CADM2 as a link between psychological traits and obesity.", "authors": [{"family": "Morris", "given": "Julia", "initials": "J"}, {"family": "Bailey", "given": "Mark E S", "initials": "MES", "orcid": "0000-0002-9788-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/3919edd84f254870a5644770152360b6.json"}}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Cullen", "given": "Breda", "initials": "B", "orcid": "0000-0002-7259-9505", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff824f9a62154c718c075ad56b01177b.json"}}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Ferguson", "given": "Amy", "initials": "A"}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Graham", "given": "Nicholas", "initials": "N"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Johnston", "given": "Keira J A", "initials": "KJA", "orcid": "0000-0002-1370-3149", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff151def49174d388b1b3e8619c2b329.json"}}, {"family": "Lyall", "given": "Donald M", "initials": "DM", "orcid": "0000-0003-3850-1487", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1b08351693e4fb5b387edd6d9a9d347.json"}}, {"family": "Lyall", "given": "Laura M", "initials": "LM"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Ward", "given": "Joey", "initials": "J"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Smith", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0002-2267-1951", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bba9787f512483d8eaf6cffc8743271.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}], "type": "journal article", "published": "2019-05-14", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "7339", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "CADM2 has been associated with a range of behavioural and metabolic traits, including physical activity, risk-taking, educational attainment, alcohol and cannabis use and obesity. Here, we set out to determine whether CADM2 contributes to mechanisms shared between mental and physical health disorders. We assessed genetic variants in the CADM2 locus for association with phenotypes in the UK Biobank, IMPROVE, PROCARDIS and SCARFSHEEP studies, before performing meta-analyses. A wide range of metabolic phenotypes were meta-analysed. Psychological phenotypes analysed in UK Biobank only were major depressive disorder, generalised anxiety disorder, bipolar disorder, neuroticism, mood instability and risk-taking behaviour. In UK Biobank, four, 88 and 172 genetic variants were significantly (p < 1 \u00d7 10 -5) associated with neuroticism, mood instability and risk-taking respectively. In meta-analyses of 4 cohorts, we identified 362, 63 and 11 genetic variants significantly (p < 1 \u00d7 10-5) associated with BMI, SBP and CRP respectively. Genetic effects on BMI, CRP and risk-taking were all positively correlated, and were consistently inversely correlated with genetic effects on SBP, mood instability and neuroticism. Conditional analyses suggested an overlap in the signals for physical and psychological traits. Many significant variants had genotype-specific effects on CADM2 expression levels in adult brain and adipose tissues. CADM2 variants influence a wide range of both psychological and metabolic traits, suggesting common biological mechanisms across phenotypes via regulation of CADM2 expression levels in adipose tissue. Functional studies of CADM2 are required to fully understand mechanisms connecting mental and physical health conditions.", "doi": "10.1038/s41598-019-43861-9", "pmid": "31089183", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-43861-9"}, {"db": "pmc", "key": "PMC6517397"}], "notes": [], "created": "2019-05-24T13:45:02.246Z", "modified": "2021-06-16T14:52:17.199Z"}, {"entity": "publication", "iuid": "7c9ca836b2d640fe827a0c70884fbbe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c9ca836b2d640fe827a0c70884fbbe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c9ca836b2d640fe827a0c70884fbbe0"}}, "title": "RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas.", "authors": [{"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "\u00c5kerstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Maharjan", "given": "Rajani", "initials": "R", "orcid": "0000-0001-8171-5451", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e62885ee4d4f1987cb2b03f483f005.json"}}, {"family": "Cupisti", "given": "Kenko", "initials": "K"}, {"family": "Willenberg", "given": "Holger S", "initials": "HS"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}], "type": "journal article", "published": "2019-04-18", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "6269", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Aldosterone producing adenomas (APAs) occur in the adrenal glands of around 30% of patients with primary aldosteronism, the most common form of secondary hypertension. Somatic mutations in KCNJ5, ATP1A1, ATP2B3, CACNA1D and CTNNB1 have been described in ~60% of these tumours. We subjected 15 aldosterone producing adenomas (13 with known mutations and two without) to RNA Sequencing and Whole Genome Sequencing (n = 2). All known mutations were detected in the RNA-Seq reads, and mutations in ATP2B3 (G123R) and CACNA1D (S410L) were discovered in the tumours without known mutations. Adenomas with CTNNB1 mutations showed a large number of differentially expressed genes (1360 compared to 106 and 75 for KCNJ5 and ATP1A1/ATP2B3 respectively) and clustered together in a hierarchical clustering analysis. RT-PCR in an extended cohort of 49 APAs confirmed higher expression of AFF3 and ISM1 in APAs with CTNNB1 mutations. Investigation of the expression of genes involved in proliferation and apoptosis revealed subtle differences between tumours with and without CTNNB1 mutations. Together our results consolidate the notion that CTNNB1 mutations characterize a distinct subgroup of APAs.", "doi": "10.1038/s41598-019-41525-2", "pmid": "31000732", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-41525-2"}, {"db": "pmc", "key": "PMC6472367"}], "notes": [], "created": "2019-04-23T10:02:48.530Z", "modified": "2024-01-16T13:48:44.470Z"}, {"entity": "publication", "iuid": "bfeb495043cf4c5699df7e2a30f09caf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bfeb495043cf4c5699df7e2a30f09caf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bfeb495043cf4c5699df7e2a30f09caf"}}, "title": "Improved predictions of time-dependent drug-drug interactions by determination of cytosolic drug concentrations.", "authors": [{"family": "Filppula", "given": "Anne M", "initials": "AM", "orcid": "0000-0002-7932-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/26b4707474ac4045a1ae206b3c6b003d.json"}}, {"family": "Parvizi", "given": "Rezvan", "initials": "R", "orcid": "0000-0001-8650-1225", "researcher": {"href": "https://publications.scilifelab.se/researcher/24d90167ae484978a79562922cafbae5.json"}}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/d79942eca68f4b2d8c2e72cf258f1213.json"}}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Artursson", "given": "Per", "initials": "P", "orcid": "0000-0002-3708-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/31575936c2714e1eb2f35c12df9a65a8.json"}}], "type": "journal article", "published": "2019-04-10", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "5850", "issn-l": "2045-2322"}, "abstract": "The clinical impact of drug-drug interactions based on time-dependent inhibition of cytochrome P450 (CYP) 3A4 has often been overpredicted, likely due to use of improper inhibitor concentration estimates at the enzyme. Here, we investigated if use of cytosolic unbound inhibitor concentrations could improve predictions of time-dependent drug-drug interactions. First, we assessed the inhibitory effects of ten time-dependent CYP3A inhibitors on midazolam 1'-hydroxylation in human liver microsomes. Then, using a novel method, we determined the cytosolic bioavailability of the inhibitors in human hepatocytes, and used the obtained values to calculate their concentrations at the active site of the enzyme, i.e. the cytosolic unbound concentrations. Finally, we combined the data in mechanistic static predictions, by considering different combinations of inhibitor concentrations in intestine and liver, including hepatic concentrations corrected for cytosolic bioavailability. The results were then compared to clinical data. Compared to no correction, correction for cytosolic bioavailability resulted in higher accuracy and precision, generally in line with those obtained by more demanding modelling. The best predictions were obtained when the inhibition of hepatic CYP3A was based on unbound maximal inhibitor concentrations corrected for cytosolic bioavailability. Our findings suggest that cytosolic unbound inhibitor concentrations improves predictions of time-dependent drug-drug interactions for CYP3A.", "doi": "10.1038/s41598-019-42051-x", "pmid": "30971754", "labels": {"Drug Discovery and Development": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-42051-x"}, {"db": "pmc", "key": "PMC6458156"}], "notes": [], "created": "2019-11-13T15:59:58.628Z", "modified": "2025-10-17T13:05:08.237Z"}, {"entity": "publication", "iuid": "030d62b79240496f923ef0e5483fc499", "links": {"self": {"href": "https://publications.scilifelab.se/publication/030d62b79240496f923ef0e5483fc499.json"}, "display": {"href": "https://publications.scilifelab.se/publication/030d62b79240496f923ef0e5483fc499"}}, "title": "Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden.", "authors": [{"family": "Bai", "given": "Xiangning", "initials": "X"}, {"family": "Zhang", "given": "Ji", "initials": "J"}, {"family": "Ambikan", "given": "Anoop", "initials": "A"}, {"family": "Jernberg", "given": "Cecilia", "initials": "C"}, {"family": "Ehricht", "given": "Ralf", "initials": "R"}, {"family": "Scheutz", "given": "Flemming", "initials": "F"}, {"family": "Xiong", "given": "Yanwen", "initials": "Y"}, {"family": "Matussek", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2019-04-04", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "5619", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Hybrid E. coli pathotypes are representing emerging public health threats with enhanced virulence from different pathotypes. Hybrids of Shiga toxin-producing and enterotoxigenic E. coli (STEC/ETEC) have been reported to be associated with diarrheal disease and hemolytic uremic syndrome (HUS) in humans. Here, we identified and characterized four clinical STEC/ETEC hybrids from diarrheal patients with or without fever or abdominal pain and healthy contact in Sweden. Rare stx2 subtypes were present in STEC/ETEC hybrids. Stx2 production was detectable in stx2a and stx2e containing strains. Different copies of ETEC virulence marker, sta gene, were found in two hybrids. Three sta subtypes, namely, sta1, sta4 and sta5 were designated, with sta4 being predominant. The hybrids represented diverse and rare serotypes (O15:H16, O187:H28, O100:H30, and O136:H12). Genome-wide phylogeny revealed that these hybrids exhibited close relatedness with certain ETEC, STEC/ETEC hybrid and commensal E. coli strains, implying the potential acquisition of Stx-phages or/and ETEC virulence genes in the emergence of STEC/ETEC hybrids. Given the emergence and public health significance of hybrid pathotypes, a broader range of virulence markers should be considered in the E. coli pathotypes diagnostics, and targeted follow up of cases is suggested to better understand the hybrid infection.", "doi": "10.1038/s41598-019-42122-z", "pmid": "30948755", "labels": {"Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-42122-z"}, {"db": "pmc", "key": "PMC6449507"}], "notes": [], "created": "2019-11-24T19:53:36.619Z", "modified": "2024-01-16T13:48:44.540Z"}, {"entity": "publication", "iuid": "4e7ec3b7746c4191a20d401179d6f471", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e7ec3b7746c4191a20d401179d6f471.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e7ec3b7746c4191a20d401179d6f471"}}, "title": "Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data.", "authors": [{"family": "Betancourt", "given": "Lazaro Hiram", "initials": "LH"}, {"family": "Paw\u0142owski", "given": "Krzysztof", "initials": "K"}, {"family": "Eriksson", "given": "Jonatan", "initials": "J"}, {"family": "Szasz", "given": "A Marcell", "initials": "AM"}, {"family": "Mitra", "given": "Shamik", "initials": "S"}, {"family": "Pla", "given": "Indira", "initials": "I"}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Ekedahl", "given": "Henrik", "initials": "H"}, {"family": "Broberg", "given": "Per", "initials": "P"}, {"family": "Appelqvist", "given": "Roger", "initials": "R"}, {"family": "Yakovleva", "given": "Maria", "initials": "M"}, {"family": "Sugihara", "given": "Yutaka", "initials": "Y"}, {"family": "Miharada", "given": "Kenichi", "initials": "K"}, {"family": "Ingvar", "given": "Christian", "initials": "C"}, {"family": "Lundgren", "given": "Lotta", "initials": "L"}, {"family": "Baldetorp", "given": "Bo", "initials": "B"}, {"family": "Olsson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Wieslander", "given": "Elisabet", "initials": "E"}, {"family": "Horvatovich", "given": "Peter", "initials": "P"}, {"family": "Malm", "given": "Johan", "initials": "J"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Marko-Varga", "given": "Gy\u00f6rgy", "initials": "G"}], "type": "journal article", "published": "2019-03-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "5154", "issn-l": "2045-2322"}, "abstract": "Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research.", "doi": "10.1038/s41598-019-41625-z", "pmid": "30914758", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-41625-z"}, {"db": "pmc", "key": "PMC6435712"}], "notes": [], "created": "2020-01-27T10:09:30.533Z", "modified": "2021-05-24T15:39:50.201Z"}, {"entity": "publication", "iuid": "a014663cca0947d8baf49994504a6cd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a014663cca0947d8baf49994504a6cd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a014663cca0947d8baf49994504a6cd9"}}, "title": "Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly.", "authors": [{"family": "Suarez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5988-4048", "researcher": {"href": "https://publications.scilifelab.se/researcher/86cadb16f7cf45eca8030af1a8ae860e.json"}}, {"family": "Piculell", "given": "Maria", "initials": "M"}, {"family": "Modin", "given": "Oskar", "initials": "O", "orcid": "0000-0002-9232-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1cfa2dd97cc472c9307498a65b5a8c6.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Persson", "given": "Frank", "initials": "F"}, {"family": "Hermansson", "given": "Malte", "initials": "M"}], "type": "journal article", "published": "2019-03-25", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "5110", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Microbial biofilms are ubiquitous in aquatic environments where they provide important ecosystem functions. A key property believed to influence the community structure and function of biofilms is thickness. However, since biofilm thickness is inextricably linked to external factors such as water flow, temperature, development age and nutrient conditions, its importance is difficult to quantify. Here, we designed an experimental system in a wastewater treatment plant whereby nitrifying biofilms with different thicknesses (50 or 400 \u00b5m) were grown in a single reactor, and thus subjected to identical external conditions. The 50 and 400 \u00b5m biofilm communities were significantly different. This beta-diversity between biofilms of different thickness was primarily caused by deterministic factors. Turnover (species replacement) contributed more than nestedness (species loss) to the beta-diversity, i.e. the 50 \u00b5m communities were not simply a subset of the 400 \u00b5m communities. Moreover, the two communities differed in the composition of nitrogen-transforming bacteria and in nitrogen transformation rates. The study illustrates that biofilm thickness alone is a key driver for community composition and ecosystem function, which has implications for biotechnological applications and for our general understanding of biofilm ecology.", "doi": "10.1038/s41598-019-41542-1", "pmid": "30911066", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-41542-1"}, {"db": "pmc", "key": "PMC6434030"}], "notes": [], "created": "2020-01-23T16:13:32.374Z", "modified": "2021-06-16T14:44:51.298Z"}, {"entity": "publication", "iuid": "9d4a6d1f011642a5b37d753122fb5053", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d4a6d1f011642a5b37d753122fb5053.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d4a6d1f011642a5b37d753122fb5053"}}, "title": "Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains.", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Shirreff", "given": "Lisa", "initials": "L"}, {"family": "DuCote", "given": "Tanner", "initials": "T"}, {"family": "Jacobsson", "given": "Karl-Gustav", "initials": "K"}, {"family": "Ennis", "given": "Don G", "initials": "DG"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2019-03-14", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "4603", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Members of the Mycobacterium chelonae-abscessus complex (MCAC) are close to the mycobacterial ancestor and includes both human, animal and fish pathogens. We present the genomes of 14 members of this complex: the complete genomes of Mycobacterium salmoniphilum and Mycobacterium chelonae type strains, seven M. salmoniphilum isolates, and five M. salmoniphilum-like strains including strains isolated during an outbreak in an animal facility at Uppsala University. Average nucleotide identity (ANI) analysis and core gene phylogeny revealed that the M. salmoniphilum-like strains are variants of the human pathogen Mycobacterium franklinii and phylogenetically close to Mycobacterium abscessus. Our data further suggested that M. salmoniphilum separates into three branches named group I, II and III with the M. salmoniphilum type strain belonging to group II. Among predicted virulence factors, the presence of phospholipase C (plcC), which is a major virulence factor that makes M. abscessus highly cytotoxic to mouse macrophages, and that M. franklinii originally was isolated from infected humans make it plausible that the outbreak in the animal facility was caused by a M. salmoniphilum-like strain. Interestingly, M. salmoniphilum-like was isolated from tap water suggesting that it can be present in the environment. Moreover, we predicted the presence of mutational hotspots in the M. salmoniphilum isolates and 26% of these hotspots overlap with genes categorized as having roles in virulence, disease and defense. We also provide data about key genes involved in transcription and translation such as sigma factor, ribosomal protein and tRNA genes.", "doi": "10.1038/s41598-019-40922-x", "pmid": "30872669", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-40922-x"}, {"db": "pmc", "key": "PMC6418233"}], "notes": [], "created": "2019-04-10T09:37:39.069Z", "modified": "2024-01-16T13:48:44.610Z"}, {"entity": "publication", "iuid": "4a08d72c0bfa47c99f5af0a3c53b9c52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a08d72c0bfa47c99f5af0a3c53b9c52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a08d72c0bfa47c99f5af0a3c53b9c52"}}, "title": "Surveillance of cell wall diffusion barrier integrity modulates water and solute transport in plants.", "authors": [{"family": "Wang", "given": "Peng", "initials": "P"}, {"family": "Calvo-Polanco", "given": "Monica", "initials": "M"}, {"family": "Reyt", "given": "Guilhem", "initials": "G"}, {"family": "Barberon", "given": "Marie", "initials": "M"}, {"family": "Champeyroux", "given": "Chloe", "initials": "C"}, {"family": "Santoni", "given": "V\u00e9ronique", "initials": "V"}, {"family": "Maurel", "given": "Christophe", "initials": "C"}, {"family": "Franke", "given": "Rochus B", "initials": "RB"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Novak", "given": "Ondrej", "initials": "O"}, {"family": "Geldner", "given": "Niko", "initials": "N"}, {"family": "Boursiac", "given": "Yann", "initials": "Y"}, {"family": "Salt", "given": "David E", "initials": "DE"}], "type": "journal article", "published": "2019-03-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "4227", "issn-l": "2045-2322"}, "abstract": "The endodermis is a key cell layer in plant roots that contributes to the controlled uptake of water and mineral nutrients into plants. In order to provide such functionality the endodermal cell wall has specific chemical modifications consisting of lignin bands (Casparian strips) that encircle each cell, and deposition of a waxy-like substance (suberin) between the wall and the plasma membrane. These two extracellular deposits provide control of diffusion enabling the endodermis to direct the movement of water and solutes into and out of the vascular system in roots. Loss of integrity of the Casparian strip-based apoplastic barrier is sensed by the leakage of a small peptide from the stele into the cortex. Here, we report that such sensing of barrier integrity leads to the rebalancing of water and mineral nutrient uptake, compensating for breakage of Casparian strips. This rebalancing involves both a reduction in root hydraulic conductivity driven by deactivation of aquaporins, and downstream limitation of ion leakage through deposition of suberin. These responses in the root are also coupled to a reduction in water demand in the shoot mediated by ABA-dependent stomatal closure.", "doi": "10.1038/s41598-019-40588-5", "pmid": "30862916", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-40588-5"}, {"db": "pmc", "key": "PMC6414709"}], "notes": [], "created": "2020-01-21T10:14:13.131Z", "modified": "2025-10-17T13:03:17.745Z"}, {"entity": "publication", "iuid": "87b64d623963438b88febe3b5e721bf5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87b64d623963438b88febe3b5e721bf5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87b64d623963438b88febe3b5e721bf5"}}, "title": "A microfluidic platform towards automated multiplexed in situ sequencing.", "authors": [{"family": "Ma\u00efno", "given": "N", "initials": "N"}, {"family": "Hauling", "given": "T", "initials": "T"}, {"family": "Cappi", "given": "G", "initials": "G"}, {"family": "Madaboosi", "given": "N", "initials": "N"}, {"family": "Dupouy", "given": "D G", "initials": "DG"}, {"family": "Nilsson", "given": "M", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2019-03-05", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "3542", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Advancements in multiplexed in situ RNA profiling techniques have given unprecedented insight into spatial organization of tissues by enabling single-molecule quantification and sub-micron localization of dozens to thousands of RNA species simultaneously in cells and entire tissue sections. However, the lack of automation of the associated complex experimental procedures represents a potential hurdle towards their routine use in laboratories. Here, we demonstrate an approach towards automated generation and sequencing of barcoded mRNA amplicons in situ, directly in fixed cells. This is achieved through adaptation of a microfluidic tool compatible with standard microscope slides and cover glasses. The adapted tool combines a programmable reagent delivery system with temperature controller and flow cell to perform established in situ sequencing protocols, comprising hybridization and ligation of gene-specific padlock probes, rolling circle amplification of the probes yielding barcoded amplicons and identification of amplicons through barcode sequencing. By adapting assay parameters (e.g. enzyme concentration and temperature), we achieve a near-identical performance in identifying mouse beta-actin transcripts, in comparison with the conventional manual protocol. The technically adapted assay features i) higher detection efficiency, ii) shorter protocol time, iii) lower consumption of oligonucleotide reagents but slightly more enzyme. Such an automated microfluidic tissue processor for in situ sequencing studies would greatly enhance its research potentials especially for cancer diagnostics, thus paving way to rapid and effective therapies.", "doi": "10.1038/s41598-019-40026-6", "pmid": "30837556", "labels": {"In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-40026-6"}, {"db": "pmc", "key": "PMC6401021"}], "notes": [], "created": "2020-01-10T04:54:58.840Z", "modified": "2025-10-17T13:02:18.509Z"}, {"entity": "publication", "iuid": "f7cf107063f3409a88a49fd4035438eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f7cf107063f3409a88a49fd4035438eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f7cf107063f3409a88a49fd4035438eb"}}, "title": "Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.", "authors": [{"family": "Das", "given": "Sarbashis", "initials": "S", "orcid": "0000-0001-8799-691X", "researcher": {"href": "https://publications.scilifelab.se/researcher/978ddc1e4d8f46499f60b1d343934063.json"}}, {"family": "Frisk", "given": "Christoffer", "initials": "C"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Walentinsson", "given": "Anna", "initials": "A"}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Hage", "given": "Camilla", "initials": "C"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Maret", "given": "Eva", "initials": "E"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}], "type": "journal article", "published": "2019-02-28", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "3179", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Heart failure affects 2-3% of adult Western population. Prevalence of heart failure with preserved left ventricular (LV) ejection fraction (HFpEF) increases. Studies suggest HFpEF patients to have altered myocardial structure and functional changes such as incomplete relaxation and increased cardiac stiffness. We hypothesised that patients undergoing elective coronary bypass surgery (CABG) with HFpEF characteristics would show distinctive gene expression compared to patients with normal LV physiology. Myocardial biopsies for mRNA expression analysis were obtained from sixteen patients with LV ejection fraction \u226545%. Five out of 16 patients (31%) had echocardiographic characteristics and increased NTproBNP levels indicative of HFpEF and this group was used as HFpEF proxy, while 11 patients had Normal LV physiology. Utilising principal component analysis, the gene expression data clustered into two groups, corresponding to HFpEF proxy and Normal physiology, and 743 differentially expressed genes were identified. The associated top biological functions were cardiac muscle contraction, oxidative phosphorylation, cellular remodelling and matrix organisation. Our results also indicate that upstream regulatory events, including inhibition of transcription factors STAT4, SRF and TP53, and activation of transcription repressors HEY2 and KDM5A, could provide explanatory mechanisms to observed gene expression differences and ultimately cardiac dysfunction in the HFpEF proxy group.", "doi": "10.1038/s41598-019-39445-2", "pmid": "30816197", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-39445-2"}, {"db": "pmc", "key": "PMC6395693"}], "notes": [], "created": "2019-12-02T16:50:33.258Z", "modified": "2024-01-16T13:48:44.655Z"}, {"entity": "publication", "iuid": "8f8b8be2ec454cc494da08f27985613a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f8b8be2ec454cc494da08f27985613a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f8b8be2ec454cc494da08f27985613a"}}, "title": "Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.", "authors": [{"family": "Franco", "given": "Marcela", "initials": "M"}, {"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Peuget", "given": "Sylvain", "initials": "S"}, {"family": "B\u00f6ttger", "given": "Franziska", "initials": "F"}, {"family": "Selivanova", "given": "Galina", "initials": "G"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}], "type": "journal article", "published": "2019-02-20", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "2379", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Despite the widening range of high-throughput platforms and exponential growth of generated data volume, the validation of biomarkers discovered from large-scale data remains a challenging field. In order to tackle cancer heterogeneity and comply with the data dimensionality, a number of network and pathway approaches were invented but rarely systematically applied to this task. We propose a new method, called NEAmarker, for finding sensitive and robust biomarkers at the pathway level. scores from network enrichment analysis transform the original space of altered genes into a lower-dimensional space of pathways. These dimensions are then correlated with phenotype variables. The method was first tested using in vitro data from three anti-cancer drug screens and then on clinical data of The Cancer Genome Atlas. It proved superior to the single-gene and alternative enrichment analyses in terms of (1) universal applicability to different data types with a possibility of cross-platform integration, (2) consistency of the discovered correlates between independent drug screens, and (3) ability to explain differential survival of treated patients. Our new screen of anti-cancer compounds validated the performance of multivariate models of drug sensitivity. The previously proposed methods of enrichment analysis could achieve comparable levels of performance in certain tests. However, only our method could discover predictors of both in vitro response and patient survival given administration of the same drug.", "doi": "10.1038/s41598-019-39019-2", "pmid": "30787419", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-39019-2"}, {"db": "pmc", "key": "PMC6382934"}], "notes": [], "created": "2020-01-07T13:26:35.148Z", "modified": "2024-01-16T13:48:44.681Z"}, {"entity": "publication", "iuid": "6cc66373dc394583886020d0a1ba7c07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cc66373dc394583886020d0a1ba7c07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cc66373dc394583886020d0a1ba7c07"}}, "title": "Genomic regions of speciation and adaptation among three species of grouse.", "authors": [{"family": "Kozma", "given": "Radoslav", "initials": "R"}, {"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}], "type": "journal article", "published": "2019-01-28", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "812", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region.", "doi": "10.1038/s41598-018-36880-5", "pmid": "30692562", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-36880-5"}, {"db": "pmc", "key": "PMC6349846"}], "notes": [], "created": "2020-01-08T12:37:53.909Z", "modified": "2021-06-16T14:50:59.101Z"}, {"entity": "publication", "iuid": "d1a4105876624a43a0384572921bc580", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1a4105876624a43a0384572921bc580.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1a4105876624a43a0384572921bc580"}}, "title": "Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide.", "authors": [{"family": "Wu", "given": "Min", "initials": "M"}, {"family": "Farkas", "given": "Daniel", "initials": "D"}, {"family": "Eriksson", "given": "Leif A", "initials": "LA", "orcid": "0000-0001-5654-3109", "researcher": {"href": "https://publications.scilifelab.se/researcher/53b168b3ab17495783f874c427edd0c3.json"}}, {"family": "Strid", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0003-3315-8835", "researcher": {"href": "https://publications.scilifelab.se/researcher/da80ca55a0d54cd082fe18a56d025830.json"}}], "type": "journal article", "published": "2019-01-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "818", "issn-l": "2045-2322"}, "abstract": "UVR8 (UV RESISTANCE LOCUS 8) is a UV-B photoreceptor responsible for initiating UV-B signalling in plants. UVR8 is a homodimer in its signalling inactive form. Upon absorption of UV radiation, the protein monomerizes into its photoactivated state. In the monomeric form, UVR8 binds the E3 ubiquitin ligase COP1 (CONSTITUTIVELY PHOTOMORPHOGENIC 1), triggering subsequent UV-B-dependent photomorphogenic development in plants. Recent in vivo experiments have shown that the UVR8 C-terminal region (aa 397-423; UVR8C27) alone is sufficient to regulate the activity of COP1. In this work, CD spectroscopy and NMR experiments showed that the UVR8C27 domain was non-structured but gained secondary structure at higher temperatures leading to increased order. Bias-exchange metadynamics simulations were also performed to evaluate the free energy landscape of UVR8C27. An inverted free energy landscape was revealed, with a disordered structure in the global energy minimum. Flanking the global energy minimum, more structured states were found at higher energies. Furthermore, stabilization of the low energy disordered state was attributed to a proline residue, P411, as evident from P411A mutant data. P411 is also a key residue in UVR8 binding to COP1. UVR8C27 is therefore structurally competent to function as a molecular switch for interaction of UVR8 with different binding partners since at higher free energies different structural conformations are being induced in this peptide. P411 has a key role for this function.", "doi": "10.1038/s41598-018-37005-8", "pmid": "30692548", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-37005-8"}, {"db": "pmc", "key": "PMC6349876"}], "notes": [], "created": "2020-01-07T11:39:43.195Z", "modified": "2025-10-17T13:03:58.226Z"}, {"entity": "publication", "iuid": "2c7b5a8890f74a13b826cafed1ac185b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c7b5a8890f74a13b826cafed1ac185b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c7b5a8890f74a13b826cafed1ac185b"}}, "title": "Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents.", "authors": [{"family": "Esberg", "given": "A", "initials": "A"}, {"family": "Haworth", "given": "S", "initials": "S"}, {"family": "Brunius", "given": "C", "initials": "C"}, {"family": "Lif Holgerson", "given": "P", "initials": "P"}, {"family": "Johansson", "given": "I", "initials": "I"}], "type": "journal article", "published": "2019-01-24", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "452", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Carbonic anhydrase VI (CA6) catalyses the reversible hydration of carbon dioxide in saliva with possible pH regulation, taste perception, and tooth formation effects. This study assessed effects of variation in the CA6 gene on oral microbiota and specifically the acidophilic and caries-associated Streptococcus mutans in 17-year old Swedish adolescents (n\u2009=\u2009154). Associations with caries status and secreted CA6 protein were also evaluated. Single Nucleotide Polymorphisms (27 SNPs in 5 haploblocks) and saliva and tooth biofilm microbiota from Illumina MiSeq 16S rDNA (V3-V4) sequencing and culturing were analysed. Haploblock 4 (rs10864376, rs3737665, rs12138897) CCC associated with low prevalence of S. mutans (OR (95% CI): 0.5 (0.3, 0.8)), and caries (OR 0.6 (0.3, 0.9)), whereas haploblock 4 TTG associated with high prevalence of S. mutans (OR: 2.7 (1.2, 5.9)) and caries (OR: 2.3 (1.2, 4.4)). The TTG-haploblock 4 (represented by rs12138897(G)) was characterized by S. mutans, Scardovia wiggsiae, Treponema sp. HOT268, Tannerella sp. HOT286, Veillonella gp.1 compared with the CCC-haploblock 4 (represented by rs12138897(C)). Secreted CA6 in saliva was weakly linked to CA6 gene variation. In conclusion, the results indicate that CA6 gene polymorphisms influence S. mutans colonization, tooth biofilm microbiota composition and risk of dental caries in Swedish adolescents.", "doi": "10.1038/s41598-018-36832-z", "pmid": "30679524", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-36832-z"}, {"db": "pmc", "key": "PMC6345836"}], "notes": [], "created": "2019-09-17T16:24:29.013Z", "modified": "2024-01-16T13:48:44.805Z"}, {"entity": "publication", "iuid": "c18905fcb7164ee28fa05a65c5c65439", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18905fcb7164ee28fa05a65c5c65439.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18905fcb7164ee28fa05a65c5c65439"}}, "title": "Mercury methylating microbial communities of boreal forest soils.", "authors": [{"family": "Xu", "given": "Jingying", "initials": "J"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Ekl\u00f6f", "given": "Karin", "initials": "K"}, {"family": "Ahmed", "given": "Omneya O", "initials": "OO"}, {"family": "Schaefer", "given": "Jeffra K", "initials": "JK"}, {"family": "Bishop", "given": "Kevin", "initials": "K", "orcid": "0000-0002-8057-1051", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cf39f8ead0744f591dcdbcb6caee99a.json"}}, {"family": "Skyllberg", "given": "Ulf", "initials": "U"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG", "orcid": "0000-0002-8341-3462", "researcher": {"href": "https://publications.scilifelab.se/researcher/749bb106ca6b452d82603ef8cf3cbdee.json"}}], "type": "journal article", "published": "2019-01-24", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "518", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is also linked to the composition of non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.", "doi": "10.1038/s41598-018-37383-z", "pmid": "30679728", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-37383-z"}, {"db": "pmc", "key": "PMC6345997"}], "notes": [], "created": "2019-04-23T10:00:57.684Z", "modified": "2024-01-16T13:48:44.797Z"}, {"entity": "publication", "iuid": "67fc6e8185bc429ea4745399b202d2cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67fc6e8185bc429ea4745399b202d2cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67fc6e8185bc429ea4745399b202d2cd"}}, "title": "The bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli.", "authors": [{"family": "Joffre", "given": "Enrique", "initials": "E"}, {"family": "Nicklasson", "given": "Matilda", "initials": "M"}, {"family": "\u00c1lvarez-Carretero", "given": "Sandra", "initials": "S"}, {"family": "Xiao", "given": "Xue", "initials": "X"}, {"family": "Sun", "given": "Lei", "initials": "L"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Zhu", "given": "Baoli", "initials": "B"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2019-01-14", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "108", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Pathogenic bacteria use specific host factors to modulate virulence and stress responses during infection. We found previously that the host factor bile and the bile component glyco-conjugated cholate (NaGCH, sodium glycocholate) upregulate the colonization factor CS5 in enterotoxigenic Escherichia coli (ETEC). To further understand the global regulatory effects of bile and NaGCH, we performed Illumina RNA-Seq and found that crude bile and NaGCH altered the expression of 61 genes in CS5 + CS6 ETEC isolates. The most striking finding was high induction of the CS5 operon (csfA-F), its putative transcription factor csvR, and the putative ETEC virulence factor cexE. iTRAQ-coupled LC-MS/MS proteomic analyses verified induction of the plasmid-borne virulence proteins CS5 and CexE and also showed that NaGCH affected the expression of bacterial membrane proteins. Furthermore, NaGCH induced bacteria to aggregate, increased their adherence to epithelial cells, and reduced their motility. Our results indicate that CS5 + CS6 ETEC use NaGCH present in the small intestine as a signal to initiate colonization of the epithelium.", "doi": "10.1038/s41598-018-36414-z", "pmid": "30643184", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-36414-z"}, {"db": "pmc", "key": "PMC6331568"}], "notes": [], "created": "2020-01-30T15:59:12.765Z", "modified": "2024-01-16T13:46:32.003Z"}, {"entity": "publication", "iuid": "36de95cf2a8b44d88955b26e73c84105", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36de95cf2a8b44d88955b26e73c84105.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36de95cf2a8b44d88955b26e73c84105"}}, "title": "Mycobacterium tuberculosis virulence inhibitors discovered by Mycobacterium marinum high-throughput screening.", "authors": [{"family": "T\u00fckenmez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-2259-6883", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e2a6e729c344f2a9ea0c76ff9366fe.json"}}, {"family": "Edstr\u00f6m", "given": "Isabel", "initials": "I"}, {"family": "Ummanni", "given": "Ramesh", "initials": "R"}, {"family": "Fick", "given": "Stina Berglund", "initials": "SB", "orcid": "0000-0003-4968-8830", "researcher": {"href": "https://publications.scilifelab.se/researcher/29ba8a613d394ef4bd333eb052219035.json"}}, {"family": "Sundin", "given": "Charlotta", "initials": "C"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Larsson", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2019-01-10", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "26", "issn-l": "2045-2322"}, "abstract": "High-throughput screening facilities do not generally support biosafety level 3 organisms such as Mycobacterium tuberculosis. To discover not only antibacterials, but also virulence inhibitors with either bacterial or host cell targets, an assay monitoring lung fibroblast survival upon infection was developed and optimized for 384-plate format and robotic liquid handling. By using Mycobacterium marinum as surrogate organism, 28,000 compounds were screened at biosafety level 2 classification, resulting in 49 primary hits. Exclusion of substances with unfavourable properties and known antimicrobials resulted in 11 validated hits of which 7 had virulence inhibiting properties and one had bactericidal effect also in wild type Mycobacterium tuberculosis. This strategy to discover virulence inhibitors using a model organism in high-throughput screening can be a valuable tool for other researchers working on drug discovery against tuberculosis and other biosafety level 3 infectious agents.", "doi": "10.1038/s41598-018-37176-4", "pmid": "30631100", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-37176-4"}, {"db": "pmc", "key": "PMC6328581"}], "notes": [], "created": "2019-02-20T12:10:09.394Z", "modified": "2025-10-17T13:04:28.639Z"}, {"entity": "publication", "iuid": "0dc67e907cf74f1d9332d303ebc4e9f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dc67e907cf74f1d9332d303ebc4e9f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dc67e907cf74f1d9332d303ebc4e9f6"}}, "title": "Comprehensive analysis of CTNNB1 in adrenocortical carcinomas: Identification of novel mutations and correlation to survival", "authors": [{"family": "Maharjan", "given": "Rajani", "initials": "R"}, {"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "\u00c5kerstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "8610", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-018-26799-2", "pmid": "29872083", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:11:02.761Z", "modified": "2020-01-21T13:56:13.600Z"}, {"entity": "publication", "iuid": "3b0e5545334447cb9c85f6d6924c0dfc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b0e5545334447cb9c85f6d6924c0dfc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b0e5545334447cb9c85f6d6924c0dfc"}}, "title": "Intramolecular 13C analysis of tree rings provides multiple plant ecophysiology signals covering decades", "authors": [{"family": "Wieloch", "given": "Thomas", "initials": "T"}, {"family": "Ehlers", "given": "Ina", "initials": "I"}, {"family": "Yu", "given": "Jun", "initials": "J"}, {"family": "Frank", "given": "David", "initials": "D"}, {"family": "Grabner", "given": "Michael", "initials": "M"}, {"family": "Gessler", "given": "Arthur", "initials": "A"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-018-23422-2", "pmid": "29567963", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T14:46:24.643Z", "modified": "2025-10-17T13:03:58.404Z"}, {"entity": "publication", "iuid": "41cfd0759db84dcea10e76c92a8204b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41cfd0759db84dcea10e76c92a8204b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41cfd0759db84dcea10e76c92a8204b1"}}, "title": "Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing", "authors": [{"family": "Onu\u021b-Br\u00e4nnstr\u00f6m", "given": "Ioana", "initials": "I"}, {"family": "Benjamin", "given": "Mitchell", "initials": "M"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Hei\u00f0marsson", "given": "Starri", "initials": "S"}, {"family": "Andersson", "given": "Martin G I", "initials": "MGI"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-018-22470-y", "pmid": "29535321", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "ENA", "description": "https://www.ebi.ac.uk/ena/data/view/ERR2307093", "key": "ERR2307093"}, {"db": "ENA", "description": "https://www.ebi.ac.uk/ena/data/view/ERR2307094", "key": "ERR2307094"}, {"db": "ENA", "description": "https://www.ebi.ac.uk/ena/data/view/ERR2307095", "key": "ERR2307095"}, {"db": "ENA", "description": "https://www.ebi.ac.uk/ena/data/view/ERR2307096", "key": "ERR2307096"}, {"db": "ENA", "description": "https://www.ebi.ac.uk/ena/data/view/ERR2307097", "key": "ERR2307097"}, {"db": "ENA", "description": "https://www.ebi.ac.uk/ena/data/view/ERR2307098", "key": "ERR2307098"}, {"db": "GENBANK", "description": "This just first sequence, there are multiple sequences from MG372066 - MG372097", "key": "MG372066"}], "notes": [], "created": "2018-06-25T14:04:58.454Z", "modified": "2024-01-16T13:48:45.006Z"}, {"entity": "publication", "iuid": "968ff582e6ce4c67a000773d416bd58e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/968ff582e6ce4c67a000773d416bd58e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/968ff582e6ce4c67a000773d416bd58e"}}, "title": "Anti-Rift Valley fever virus activity in vitro, pre-clinical pharmacokinetics and oral bioavailability of benzavir-2, a broad-acting antiviral compound", "authors": [{"family": "Islam", "given": "Md Koushikul", "initials": "MK"}, {"family": "Strand", "given": "M\u00e5rten", "initials": "M"}, {"family": "Saleeb", "given": "Michael", "initials": "M"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Wadell", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ahlm", "given": "Clas", "initials": "C"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Evander", "given": "Magnus", "initials": "M"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-018-20362-9", "pmid": "29386590", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-15T12:38:47.090Z", "modified": "2025-10-17T13:05:08.325Z"}, {"entity": "publication", "iuid": "ae28c25c11f74bc182125086f0dec5ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae28c25c11f74bc182125086f0dec5ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae28c25c11f74bc182125086f0dec5ca"}}, "title": "RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Di Bucchianico", "given": "Sebastiano", "initials": "S"}, {"family": "Lindvall", "given": "Jessica", "initials": "J", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Despite a considerable focus on the adverse effects of silver nanoparticles (AgNPs) in recent years, studies on the potential long-term effects of AgNPs are scarce. The aim of this study was to explore the effects of AgNPs following repeated low-dose, long-term exposure of human bronchial epithelial cells. To this end, the human BEAS-2B cell line was exposed to 1\u2009\u00b5g/mL AgNPs (10\u2009nm) for 6 weeks followed by RNA-sequencing (RNA-Seq) as well as genome-wide DNA methylation analysis. The transcriptomics analysis showed that a substantial number of genes (1717) were differentially expressed following AgNP exposure whereas only marginal effects on DNA methylation were observed. Downstream analysis of the transcriptomics data identified several affected pathways including the 'fibrosis' and 'epithelial-mesenchymal transition' (EMT) pathway. Subsequently, functional validation studies were performed using AgNPs of two different sizes (10\u2009nm and 75\u2009nm). Both NPs increased collagen deposition, indicative of fibrosis, and induced EMT, as evidenced by an increased invasion index, anchorage independent cell growth, as well as cadherin switching. In conclusion, using a combination of RNA-Seq and functional assays, our study revealed that repeated low-dose, long-term exposure of human BEAS-2B cells to AgNPs is pro-fibrotic, induces EMT and cell transformation.", "doi": "10.1038/s41598-018-25085-5", "pmid": "29703973", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "ArrayExpress", "description": "RNA-Seq of BEAS-2B cells treated with low doses of Ag nanoparticles for 6 weeks", "key": "E-MTAB-6321"}, {"db": "ArrayExpress", "description": "DNA methylation profiling of BEAS-2B cells exposed to low doses of Ag nanoparticles for 6 weeks", "key": "E-MTAB-6331"}], "notes": [], "created": "2018-05-03T10:11:16.742Z", "modified": "2021-07-05T12:48:15.926Z"}, {"entity": "publication", "iuid": "c2bae09d27474f77ac877a7d02ed8dd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2bae09d27474f77ac877a7d02ed8dd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2bae09d27474f77ac877a7d02ed8dd0"}}, "title": "Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants", "authors": [{"family": "Delgado-Vega", "given": "Ang\u00e9lica M", "initials": "AM"}, {"family": "Mart\u00ednez-Bueno", "given": "Manuel", "initials": "M"}, {"family": "Oparina", "given": "Nina Y", "initials": "NY"}, {"family": "L\u00f3pez Herr\u00e1ez", "given": "David", "initials": "D"}, {"family": "Kristjansdottir", "given": "Helga", "initials": "H"}, {"family": "Steinsson", "given": "Kristj\u00e1n", "initials": "K"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-018-26274-y", "pmid": "29884787", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2018-06-25T14:14:20.258Z", "modified": "2020-01-21T13:56:12.185Z"}, {"entity": "publication", "iuid": "c513594b717d41568e7a836fb7437a2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c513594b717d41568e7a836fb7437a2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c513594b717d41568e7a836fb7437a2f"}}, "title": "Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin", "authors": [{"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Vallhov", "given": "Helen", "initials": "H"}, {"family": "Holm", "given": "Tina", "initials": "T"}, {"family": "Gehrmann", "given": "Ulf", "initials": "U"}, {"family": "Andersson", "given": "Anna", "initials": "A"}, {"family": "Johansson", "given": "Catharina", "initials": "C"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Scheynius", "given": "Annika", "initials": "A"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Malassezia sympodialis is a dominant commensal fungi in the human skin mycobiome but is also associated with common skin disorders including atopic eczema (AE). M. sympodialis releases extracellular vesicles, designated MalaEx, which are carriers of small RNAs and allergens, and they can induce inflammatory cytokine responses. Here we explored how MalaEx are involved in host-microbe interactions by comparing protein content of MalaEx with that of the parental yeast cells, and by investigating interactions of MalaEx with cells in the skin. Cryo-electron tomography revealed a heterogeneous population of MalaEx. iTRAQ based quantitative proteomics identified in total 2439 proteins in all replicates of which 110 were enriched in MalaEx compared to the yeast cells. Among the MalaEx enriched proteins were two of the M. sympodialis allergens, Mala s 1 and s 7. Functional experiments indicated an active binding and internalization of MalaEx into human keratinocytes and monocytes, and MalaEx were found in close proximity of the nuclei using super-resolution fluorescence 3D-SIM imaging. Our results provides new insights into host-microbe interactions, supporting that MalaEx may have a role in the sensitization and maintenance of inflammation in AE by containing enriched amounts of allergens and with their ability to interact with skin cells.", "doi": "10.1038/s41598-018-27451-9", "pmid": "29907748", "labels": {"Cryo-EM": "Service", "Global Proteomics and Proteogenomics": "Collaborative", "Integrated Microscopy Technologies Stockholm": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "jPOSTrepo", "description": "https://repository.jpostdb.org/entry/JPST000288", "key": "JPST000288"}], "notes": [], "created": "2018-06-20T09:34:38.559Z", "modified": "2024-01-16T13:48:45.085Z"}, {"entity": "publication", "iuid": "edd1a78ec7af4c3ba7088af9c6dc62a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edd1a78ec7af4c3ba7088af9c6dc62a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edd1a78ec7af4c3ba7088af9c6dc62a6"}}, "title": "A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901", "authors": [{"family": "Konasani", "given": "Venkat Rao", "initials": "VR"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Albers", "given": "Eva", "initials": "E", "orcid": "0000-0002-1921-3415", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc02c2b6700049e18c94250597f3081c.json"}}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Ulvan, which is one of the major structural polysaccharides of the cell walls of green macroalgae, is degraded by ulvan lyases via the \u03b2-elimination mechanism with the release of oligosaccharides that have unsaturated 4-deoxy-L-threo-hex-4-enopyranosiduronic acid (\u2206) at the non-reducing end. These ulvan lyases belong to the PL24 or PL25 or PL28 family in the CAZy database. In this study, we identify and biochemically characterise a periplasmic novel broad-spectrum ulvan lyase from Formosa agariphila KMM 3901. The lyase was overexpressed in Escherichia coli, and the purified recombinant enzyme depolymerised ulvan in an endolytic manner with a K m of 0.77 mg/ml, and displayed optimum activity at 40 \u00b0C and pH 8. This lyase also degraded heparan sulphate and chondroitin sulphate. Detailed analyses of the end-products of the enzymatic degradation of ulvan using 1H- and 13C-NMR and LC-MS revealed an unsaturated disaccharide (\u2206Rha3S) and a tetrasaccharide (\u2206Rha3S-Xyl-Rha) as the principal end-products. In contrast to the previously described ulvan lyases, this novel lyase is mostly composed of \u03b1-helices that form an (\u03b1/\u03b1)6 incomplete toroid domain and displays a remarkably broad-spectrum activity. This novel lyase is the first member of a new family of ulvan lyases.", "doi": "10.1038/s41598-018-32922-0", "pmid": "30279430", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T13:03:32.316Z", "modified": "2025-10-17T13:03:58.433Z"}, {"entity": "publication", "iuid": "ee94eab47af144b0a91add67c1458f35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee94eab47af144b0a91add67c1458f35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee94eab47af144b0a91add67c1458f35"}}, "title": "Expression profiling and in situ screening of circular RNAs in human tissues.", "authors": [{"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Wu", "given": "Chenglin", "initials": "C"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Manivannan", "given": "Manimozhi", "initials": "M"}, {"family": "Bramlett", "given": "Kelli", "initials": "K"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2018-11-16", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "16953", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Circular RNAs (circRNAs) were recently discovered as a class of widely expressed noncoding RNA and have been implicated in regulation of gene expression. However, the function of the majority of circRNAs remains unknown. Studies of circRNAs have been hampered by a lack of essential approaches for detection, quantification and visualization. We therefore developed a target-enrichment sequencing method suitable for screening of circRNAs and their linear counterparts in large number of samples. We also applied padlock probes and in situ sequencing to visualize and determine circRNA localization in human brain tissue at subcellular levels. We measured circRNA abundance across different human samples and tissues. Our results highlight the potential of this RNA class to act as a specific diagnostic marker in blood and serum, by detection of circRNAs from genes exclusively expressed in the brain. The powerful and scalable tools we present will enable studies of circRNA function and facilitate screening of circRNA as diagnostic biomarkers.", "doi": "10.1038/s41598-018-35001-6", "pmid": "30446675", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-35001-6"}, {"db": "pmc", "key": "PMC6240052"}], "notes": [], "created": "2018-11-19T13:50:06.813Z", "modified": "2025-10-17T13:02:18.588Z"}, {"entity": "publication", "iuid": "1c854d000cef41898abc281c3f96c4e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c854d000cef41898abc281c3f96c4e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c854d000cef41898abc281c3f96c4e3"}}, "title": "Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.", "authors": [{"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Yamada", "given": "Keith", "initials": "K"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2018-11-14", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "16824", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. We generated the first-ever transcriptome assembly for this species, and found 3,233 differentially expressed genes across feeding regimes. However, only a handful of biological functions were enriched with regard to differentially expressed genes, the most notable being \"alkaloid metabolic process\". Within this category, we found eight differentially expressed cytochrome P450 (CYP) unigenes, all of which had a higher expression in the U. lactuca diet treatment. A phylogenetic analysis showed that the differentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxification. This is a first step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.", "doi": "10.1038/s41598-018-34937-z", "pmid": "30429500", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-34937-z"}, {"db": "pmc", "key": "PMC6235865"}], "notes": [], "created": "2019-01-04T14:04:11.901Z", "modified": "2020-01-21T13:56:13.568Z"}, {"entity": "publication", "iuid": "814bc0f2347147d09206e9eaeb1977f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/814bc0f2347147d09206e9eaeb1977f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/814bc0f2347147d09206e9eaeb1977f8"}}, "title": "Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins.", "authors": [{"family": "S\u00f6derholm", "given": "Niklas", "initials": "N"}, {"family": "Javadi", "given": "Ala", "initials": "A"}, {"family": "Flores", "given": "Isabel Sierra", "initials": "IS"}, {"family": "Fl\u00e4rdh", "given": "Klas", "initials": "K", "orcid": "0000-0002-7131-9743", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfd785cebfc64364b2c4206a568c8681.json"}}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}], "type": "journal article", "published": "2018-11-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "16524", "issn-l": "2045-2322"}, "abstract": "Coiled-coil domains of intermediate filaments (IF) and prokaryotic IF-like proteins enable oligomerisation and filamentation, and no additional function is ascribed to these coiled-coil domains. However, an IF-like protein from Streptomyces reticuli was reported to display cellulose affinity. We demonstrate that cellulose affinity is an intrinsic property of the IF-like proteins FilP and Scy and the coiled-coil protein DivIVA from the genus Streptomyces. Furthermore, IF-like proteins and DivIVA from other prokaryotic species and metazoan IF display cellulose affinity despite having little sequence homology. Cellulose affinity-based purification is utilised to isolate native FilP protein from the whole cell lysate of S. coelicolor. Moreover, cellulose affinity allowed for the isolation of IF and IF-like protein from the whole cell lysate of C. crescentus and a mouse macrophage cell line. The binding to cellulose is mediated by certain combinations of coiled-coil domains, as demornstrated for FilP and lamin. Fusions of target proteins to cellulose-binding coiled-coil domains allowed for cellulose-based protein purification. The data presented show that cellulose affinity is a novel function of certain coiled-coil domains of IF and IF-like proteins from evolutionary diverse species.", "doi": "10.1038/s41598-018-34886-7", "pmid": "30410115", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-34886-7"}, {"db": "pmc", "key": "PMC6224456"}], "notes": [], "created": "2019-01-10T21:17:58.974Z", "modified": "2021-07-05T17:20:56.117Z"}, {"entity": "publication", "iuid": "6c018d7fe577404c9ce7c148a8d5ecd4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c018d7fe577404c9ce7c148a8d5ecd4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c018d7fe577404c9ce7c148a8d5ecd4"}}, "title": "Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.", "authors": [{"family": "J\u00e4rver", "given": "Peter", "initials": "P", "orcid": "0000-0001-9643-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/7645ffd2a3f7458b805892f41fd1e124.json"}}, {"family": "Dondalska", "given": "Aleksandra", "initials": "A"}, {"family": "Poux", "given": "Candice", "initials": "C"}, {"family": "Sandberg", "given": "AnnSofi", "initials": "A"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Sk\u00f6ld", "given": "Annette E", "initials": "AE"}, {"family": "Dereuddre-Bosquet", "given": "Nathalie", "initials": "N"}, {"family": "Martinon", "given": "Fr\u00e9deric", "initials": "F"}, {"family": "P\u00e5lsson", "given": "Sandra", "initials": "S"}, {"family": "Zaghloul", "given": "Eman", "initials": "E"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Sander", "given": "Birgitta", "initials": "B"}, {"family": "Lennox", "given": "Kim A", "initials": "KA"}, {"family": "Behlke", "given": "Mark A", "initials": "MA"}, {"family": "El-Andaloussi", "given": "Samir", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "LeGrand", "given": "Roger", "initials": "R"}, {"family": "Spetz", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-3964-9512", "researcher": {"href": "https://publications.scilifelab.se/researcher/70270e32d48d486799cc9dd61e36a4f1.json"}}], "type": "journal article", "published": "2018-10-26", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "15841", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Recognition of nucleic acids by endosomal Toll-like receptors (TLR) is essential to combat pathogens, but requires strict control to limit inflammatory responses. The mechanisms governing this tight regulation are unclear. We found that single-stranded oligonucleotides (ssON) inhibit endocytic pathways used by cargo destined for TLR3/4/7 signaling endosomes. Both ssDNA and ssRNA conferred the endocytic inhibition, it was concentration dependent, and required a certain ssON length. The ssON-mediated inhibition modulated signaling downstream of TLRs that localized within the affected endosomal pathway. We further show that injection of ssON dampens dsRNA-mediated inflammatory responses in the skin of non-human primates. These studies reveal a regulatory role for extracellular ssON in the endocytic uptake of TLR ligands and provide a mechanistic explanation of their immunomodulation. The identified ssON-mediated interference of endocytosis (SOMIE) is a regulatory process that temporarily dampens TLR3/4/7 signaling, thereby averting excessive immune responses.", "doi": "10.1038/s41598-018-33960-4", "pmid": "30367171", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-33960-4"}, {"db": "pmc", "key": "PMC6203749"}], "notes": [], "created": "2019-01-04T14:04:14.911Z", "modified": "2021-07-08T11:26:36.978Z"}, {"entity": "publication", "iuid": "c2fc73d105ea45eea83cf40d8c8cede0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2fc73d105ea45eea83cf40d8c8cede0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2fc73d105ea45eea83cf40d8c8cede0"}}, "title": "Amplification of the Melanocortin-1 Receptor in Nephrotic Syndrome Identifies a Target for Podocyte Cytoskeleton Stabilization.", "authors": [{"family": "Bergwall", "given": "Lovisa", "initials": "L"}, {"family": "Wallentin", "given": "Hanna", "initials": "H"}, {"family": "Elvin", "given": "Johannes", "initials": "J"}, {"family": "Liu", "given": "Peidi", "initials": "P"}, {"family": "Boi", "given": "Roberto", "initials": "R"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Hayes", "given": "Kyle", "initials": "K"}, {"family": "Wright", "given": "Dale", "initials": "D"}, {"family": "Haraldsson", "given": "B\u00f6rje", "initials": "B"}, {"family": "Nystr\u00f6m", "given": "Jenny", "initials": "J"}, {"family": "Buvall", "given": "Lisa", "initials": "L"}], "type": "journal article", "published": "2018-10-24", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "15731", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The melanocortin-1 receptor (MC1R) in podocytes has been suggested as the mediator of the ACTH renoprotective effect in patients with nephrotic syndrome with the mechanism of action beeing stabilization of the podocyte actin cytoskeleton. To understand how melanocortin receptors are regulated in nephrotic syndrome and how they are involved in restoration of filtration barrier function, melanocortin receptor expression was evaluated in patients and a rat model of nephrotic syndrome in combination with cell culture analysis. Phosphoproteomics was applied and identified MC1R pathways confirmed using biochemical analysis. We found that glomerular MC1R expression was increased in nephrotic syndrome, both in humans and in a rat model. A MC1R agonist protected podocytes from protamine sulfate induced stress fiber loss with the top ranked phoshoproteomic MC1R activated pathway beeing actin cytoskeleton signaling. Actin stabilization through the MC1R consisted of ERK1/2 dependent phosphorylation and inactivation of EGFR signaling with stabilization of synaptopodin and stressfibers in podocytes. These results further explain how patients with nephrotic syndrome show responsiveness to MC1R receptor activation by decreasing EGFR signaling and as a consequence restore filtration barrier function by stabilizing the podocyte actin cytoskeleton.", "doi": "10.1038/s41598-018-34004-7", "pmid": "30356069", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-34004-7"}, {"db": "pmc", "key": "PMC6200758"}], "notes": [], "created": "2020-01-27T22:43:04.055Z", "modified": "2024-01-16T13:46:32.170Z"}, {"entity": "publication", "iuid": "56eeca5c99ad4f519428e5c2b73e2b3c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56eeca5c99ad4f519428e5c2b73e2b3c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56eeca5c99ad4f519428e5c2b73e2b3c"}}, "title": "A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein.", "authors": [{"family": "Dusart", "given": "Philip", "initials": "P", "orcid": "0000-0003-2747-3214", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dffee863552446eb498f96e04a0fe4d.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Perisic", "given": "Ljubica", "initials": "L"}, {"family": "Civelek", "given": "Mete", "initials": "M", "orcid": "0000-0002-8141-0284", "researcher": {"href": "https://publications.scilifelab.se/researcher/647c7636e87f43ec960627d299d4cc2b.json"}}, {"family": "Struck", "given": "Eike", "initials": "E"}, {"family": "Hedin", "given": "Ulf", "initials": "U", "orcid": "0000-0001-9212-3945", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a6ec281f5d4f1a8f317dedf0404cdd.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb3fe1a732b41d79a4a165a64c322d1.json"}}, {"family": "Renn\u00e9", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4594-5975", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc8b1c2969a74aa8bdc4a8ca8bee335a.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Butler", "given": "Lynn M", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}], "type": "journal article", "published": "2018-10-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "8", "issue": "1", "pages": "14668"}, "abstract": "The intermediate filament protein nestin is expressed during embryonic development, but considered largely restricted to areas of regeneration in the adult. Here, we perform a body-wide transcriptome and protein-profiling analysis to reveal that nestin is constitutively, and highly-selectively, expressed in adult human endothelial cells (EC), independent of proliferative status. Correspondingly, we demonstrate that it is not a marker for tumour EC in multiple malignancy types. Imaging of EC from different vascular beds reveals nestin subcellular distribution is shear-modulated. siRNA inhibition of nestin increases EC proliferation, and nestin expression is reduced in atherosclerotic plaque neovessels. eQTL analysis reveals an association between SNPs linked to cardiovascular disease and reduced aortic EC nestin mRNA expression. Our study challenges the dogma that nestin is a marker of proliferation, and provides insight into its regulation and function in EC. Furthermore, our systems-based approach can be applied to investigate body-wide expression profiles of any candidate protein.", "doi": "10.1038/s41598-018-32859-4", "pmid": "30279450", "labels": {"Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6168570"}, {"db": "pii", "key": "10.1038/s41598-018-32859-4"}], "notes": [], "created": "2018-10-31T21:32:11.479Z", "modified": "2023-06-19T13:09:54.659Z"}, {"entity": "publication", "iuid": "e95c350ec27c42b5b2a77001f603a269", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e95c350ec27c42b5b2a77001f603a269.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e95c350ec27c42b5b2a77001f603a269"}}, "title": "Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome.", "authors": [{"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Gran\u00e9r", "given": "Marit", "initials": "M"}, {"family": "Bjornson", "given": "Elias", "initials": "E"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Nyman", "given": "Kristofer", "initials": "K"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Pentik\u00e4inen", "given": "Markku O", "initials": "MO"}, {"family": "Lundbom", "given": "Jesper", "initials": "J"}, {"family": "Hakkarainen", "given": "Antti", "initials": "A", "orcid": "0000-0002-7367-2532", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e71ce9ceb9840ffbda146e9c84171bd.json"}}, {"family": "Sir\u00e9n", "given": "Reijo", "initials": "R", "orcid": "0000-0002-5191-6145", "researcher": {"href": "https://publications.scilifelab.se/researcher/2240f3a7acb04e9f8b37b91db0f0716c.json"}}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Lundbom", "given": "Nina", "initials": "N"}, {"family": "Lauerma", "given": "Kirsi", "initials": "K"}, {"family": "Taskinen", "given": "Marja-Riitta", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}], "type": "journal article", "published": "2018-09-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "8", "issue": "1", "pages": "14200"}, "abstract": "Non-alcoholic fatty liver disease (NAFLD) is recognized as a liver manifestation of metabolic syndrome, accompanied with excessive fat accumulation in the liver and other vital organs. Ectopic fat accumulation was previously associated with negative effects at the systemic and local level in the human body. Thus, we aimed to identify and assess the predictive capability of novel potential metabolic biomarkers for ectopic fat depots in non-diabetic men with NAFLD, using the inflammation-associated proteome, lipidome and metabolome. Myocardial and hepatic triglycerides were measured with magnetic spectroscopy while function of left ventricle, pericardial and epicardial fat, subcutaneous and visceral adipose tissue were measured with magnetic resonance imaging. Measured ectopic fat depots were profiled and predicted using a Random Forest algorithm, and by estimating the Area Under the Receiver Operating Characteristic curves. We have identified distinct metabolic signatures of fat depots in the liver (TAG50:1, glutamate, diSM18:0 and CE20:3), pericardium (N-palmitoyl-sphinganine, HGF, diSM18:0, glutamate, and TNFSF14), epicardium (sphingomyelin, CE20:3, PC38:3 and TNFSF14), and myocardium (CE20:3, LAPTGF-\u03b21, glutamate and glucose). Our analyses highlighted non-invasive biomarkers that accurately predict ectopic fat depots, and reflect their distinct metabolic signatures in subjects with NAFLD.", "doi": "10.1038/s41598-018-31865-w", "pmid": "30242179", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-31865-w"}, {"db": "pmc", "key": "PMC6155005"}], "notes": [], "created": "2020-01-23T16:03:44.595Z", "modified": "2023-04-14T13:56:02.616Z"}, {"entity": "publication", "iuid": "1c357307784744458239c44f393eb441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c357307784744458239c44f393eb441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c357307784744458239c44f393eb441"}}, "title": "Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.", "authors": [{"family": "Tan", "given": "David J X", "initials": "DJX"}, {"family": "Chattopadhyay", "given": "Balaji", "initials": "B"}, {"family": "Garg", "given": "Kritika M", "initials": "KM"}, {"family": "Cros", "given": "Emilie", "initials": "E"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE"}], "type": "journal article", "published": "2018-08-24", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "12804", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Although edge-tolerant species are known to benefit from habitat fragmentation, less is known about the population genetic impacts fragmentation may exert on edge-tolerant species. We examined the landscape genomic structure of an edge-tolerant forest-dependent bird species, the Striped Tit-Babbler Mixornis gularis, in the heavily urbanized island of Singapore to determine if two centuries of fragmentation have led to signs of isolation and loss of population-genetic diversity in different parts of the island. We obtained a high-quality complete reference genome with 78x coverage. Using almost 4000 SNPs from double-digest RAD-Sequencing across 46 individuals, we found that the population has likely experienced a recent contraction in effective population size and presently exhibits low population genetic diversity. Using empirical and simulation-based landscape genomic analyses, we also found that the subtle population genetic structure observed in the Striped Tit-Babbler population in Singapore is likely driven by isolation by distance resulting from limited dispersal. Our results demonstrate that population genetic impoverishment and subdivision can accumulate at relatively rapid rates in edge-tolerant bird species such as the Striped Tit-Babbler as a result of fragmentation, and that subtle spatial genetic structure can be detected over fine spatial and temporal scales using relatively few multilocus genomic SNPs.", "doi": "10.1038/s41598-018-31074-5", "pmid": "30143731", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-31074-5"}, {"db": "pmc", "key": "PMC6109123"}, {"db": "BioProject", "description": "Complete genome and RAD-seq study of Mixornis gularis", "key": "PRJNA392017"}], "notes": [], "created": "2018-10-31T19:47:38.570Z", "modified": "2024-01-16T13:48:45.713Z"}, {"entity": "publication", "iuid": "eda563d110614789bbab92cb01dd72d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eda563d110614789bbab92cb01dd72d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eda563d110614789bbab92cb01dd72d2"}}, "title": "Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing", "authors": [{"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Pettersson", "given": "Fredrik", "initials": "F"}, {"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Mallick", "given": "Amrita", "initials": "A"}, {"family": "Cheramie", "given": "Martin", "initials": "M"}, {"family": "Shirreff", "given": "Lisa", "initials": "L"}, {"family": "Tanner DuCote", "given": "Tanner", "initials": "T"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Ennis", "given": "Don G", "initials": "DG"}, {"family": "Kirsebom", "given": "Leif", "initials": "L", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "posted-content", "published": "2018-08-13", "journal": {"title": "Sci. Rep.", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "8", "issue": "1", "pages": null}, "abstract": "Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the \"M\"- and the \"Aronson\"-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.", "doi": "10.1038/s41598-018-30152-y", "pmid": "30104693", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:51:10.898Z", "modified": "2024-01-16T13:48:45.750Z"}, {"entity": "publication", "iuid": "68c53403732e496f9fd2f1e5affc34d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3"}}, "title": "Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.", "authors": [{"family": "Hu", "given": "Yue O O", "initials": "YOO", "orcid": "0000-0002-2025-2198", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8675dd0fbc44f892614c848dbade8f.json"}}, {"family": "Ndegwa", "given": "Nelson", "initials": "N", "orcid": "0000-0002-5853-879X", "researcher": {"href": "https://publications.scilifelab.se/researcher/69494d497aca4285a950e335c2978135.json"}}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Johansson", "given": "Sebastian", "initials": "S"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fagerberg", "given": "Jens", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "11907", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.", "doi": "10.1038/s41598-018-29920-7", "pmid": "30093614", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-29920-7"}, {"db": "pmc", "key": "PMC6085348"}], "notes": [], "created": "2018-10-31T19:44:54.553Z", "modified": "2024-01-16T13:48:45.757Z"}, {"entity": "publication", "iuid": "04ade1bc910d44469483303138adb9a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04ade1bc910d44469483303138adb9a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04ade1bc910d44469483303138adb9a5"}}, "title": "Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.", "authors": [{"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Lallias", "given": "Delphine", "initials": "D"}, {"family": "Bik", "given": "Holly M", "initials": "HM"}, {"family": "Creer", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2018-08-06", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "11737", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2\u2009cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18\u2009S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2\u2009g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.", "doi": "10.1038/s41598-018-30179-1", "pmid": "30082688", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-30179-1"}, {"db": "pmc", "key": "PMC6078945"}, {"db": "figshare", "description": "https://figshare.com/articles/Sample_size_effects_on_the_assessment_of_eukaryotic_diversity_and_community_structure_in_aquatic_sediments_using_high-throughput_sequencing/4993667", "key": "doi:10.6084/m9.figshare.4993667"}], "notes": [], "created": "2018-10-31T19:48:05.881Z", "modified": "2024-01-16T13:48:45.803Z"}, {"entity": "publication", "iuid": "f1eee09fba5c43128c0165bafd38680f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1eee09fba5c43128c0165bafd38680f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1eee09fba5c43128c0165bafd38680f"}}, "title": "ClpB mutants of Francisella tularensis subspecies holarctica and tularensis are defective for type VI secretion and intracellular replication.", "authors": [{"family": "Alam", "given": "Athar", "initials": "A"}, {"family": "Golovliov", "given": "Igor", "initials": "I"}, {"family": "Javed", "given": "Eram", "initials": "E"}, {"family": "Sj\u00f6stedt", "given": "Anders", "initials": "A", "orcid": "0000-0002-0768-8405", "researcher": {"href": "https://publications.scilifelab.se/researcher/52b15132704f48609be086c9d256cb14.json"}}], "type": "journal article", "published": "2018-07-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "8", "issue": "1", "pages": "11324"}, "abstract": "Francisella tularensis, a highly infectious, intracellular bacterium possesses an atypical type VI secretion system (T6SS), which is essential for the virulence of the bacterium. Recent data suggest that the HSP100 family member, ClpB, is involved in T6SS disassembly in the subspecies Francisella novicida. Here, we investigated the role of ClpB for the function of the T6SS and for phenotypic characteristics of the human pathogenic subspecies holarctica and tularensis. The \u2206clpB mutants of the human live vaccine strain, LVS, belonging to subspecies holarctica, and the highly virulent SCHU S4 strain, belonging to subspecies tularensis, both showed extreme susceptibility to heat shock and low pH, severely impaired type VI secretion (T6S), and significant, but impaired intracellular replication compared to the wild-type strains. Moreover, they showed essentially intact phagosomal escape. Infection of mice demonstrated that both \u0394clpB mutants were highly attenuated, but the SCHU S4 mutant showed more effective replication than the LVS strain. Collectively, our data demonstrate that ClpB performs multiple functions in the F. tularensis subspecies holarctica and tularensis and its function is important for T6S, intracellular replication, and virulence.", "doi": "10.1038/s41598-018-29745-4", "pmid": "30054549", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-29745-4"}, {"db": "pmc", "key": "PMC6063899"}], "notes": [], "created": "2020-01-08T08:52:47.719Z", "modified": "2022-11-21T15:21:27.486Z"}, {"entity": "publication", "iuid": "dda4d85de2cd439395be3e3bcc05281d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dda4d85de2cd439395be3e3bcc05281d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dda4d85de2cd439395be3e3bcc05281d"}}, "title": "Glyco-engineered cell line and computational docking studies reveals enterotoxigenic Escherichia coli CFA/I fimbriae bind to Lewis a glycans.", "authors": [{"family": "Mottram", "given": "Lynda", "initials": "L"}, {"family": "Liu", "given": "Jining", "initials": "J"}, {"family": "Chavan", "given": "Sonali", "initials": "S"}, {"family": "Tobias", "given": "Joshua", "initials": "J"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}, {"family": "Holgersson", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2018-07-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "11250", "issn-l": "2045-2322"}, "abstract": "We have previously reported clinical data to suggest that colonization factor I (CFA/I) fimbriae of enterotoxigenic Escherichia coli (ETEC) can bind to Lewis a (Le a), a glycan epitope ubiquitous in the small intestinal mucosa of young children (<2 years of age), and individuals with a genetic mutation of FUT2. To further elucidate the physiological binding properties of this interaction, we engineered Chinese Hamster Ovary (CHO-K1) cells to express Lea or Leb determinants on both N- and O-glycans. We used our glyco-engineered CHO-K1 cell lines to demonstrate that CfaB, the major subunit of ETEC CFA/I fimbriae, as well as four related ETEC fimbriae, bind more to our CHO-K1 cell-line expressing Lea, compared to cells carrying Leb or the CHO-K1 wild-type glycan phenotype. Furthermore, using in-silico docking analysis, we predict up to three amino acids (Glu25, Asn27, Thr29) found in the immunoglobulin (Ig)-like groove region of CfaB of CFA/I and related fimbriae, could be important for the preferential and higher affinity binding of CFA/I fimbriae to the potentially structurally flexible Lea glycan. These findings may lead to a better molecular understanding of ETEC pathogenesis, aiding in the development of vaccines and/or anti-infection therapeutics.", "doi": "10.1038/s41598-018-29258-0", "pmid": "30050155", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-29258-0"}, {"db": "pmc", "key": "PMC6062558"}], "notes": [], "created": "2020-01-23T16:27:24.079Z", "modified": "2021-06-21T13:55:45.320Z"}, {"entity": "publication", "iuid": "c5ac8923292c4f80b7f141382febd809", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5ac8923292c4f80b7f141382febd809.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5ac8923292c4f80b7f141382febd809"}}, "title": "Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome.", "authors": [{"family": "Sork", "given": "Helena", "initials": "H", "orcid": "0000-0002-5390-4420", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5d08dad4f2d4ee0a3e3a8f060383da5.json"}}, {"family": "Corso", "given": "Giulia", "initials": "G"}, {"family": "Krjutskov", "given": "Kaarel", "initials": "K"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Nordin", "given": "Joel Z", "initials": "JZ"}, {"family": "Wiklander", "given": "Oscar P B", "initials": "OPB"}, {"family": "Lee", "given": "Yi Xin Fiona", "initials": "YXF", "orcid": "0000-0002-9092-1932", "researcher": {"href": "https://publications.scilifelab.se/researcher/619d8471b5704b45bc8a35ee560b47f7.json"}}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Wood", "given": "Matthew J A", "initials": "MJA"}, {"family": "M\u00e4ger", "given": "Imre", "initials": "I"}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}], "type": "journal article", "published": "2018-07-17", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "10813", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Extracellular vesicles (EVs) mediate cell-to-cell communication by delivering or displaying macromolecules to their recipient cells. While certain broad-spectrum EV effects reflect their protein cargo composition, others have been attributed to individual EV-loaded molecules such as specific miRNAs. In this work, we have investigated the contents of vesicular cargo using small RNA sequencing of cells and EVs from HEK293T, RD4, C2C12, Neuro2a and C17.2. The majority of RNA content in EVs (49-96%) corresponded to rRNA-, coding- and tRNA fragments, corroborating with our proteomic analysis of HEK293T and C2C12 EVs which showed an enrichment of ribosome and translation-related proteins. On the other hand, the overall proportion of vesicular small RNA was relatively low and variable (2-39%) and mostly comprised of miRNAs and sequences mapping to piRNA loci. Importantly, this is one of the few studies, which systematically links vesicular RNA and protein cargo of vesicles. Our data is particularly useful for future work in unravelling the biological mechanisms underlying vesicular RNA and protein sorting and serves as an important guide in developing EVs as carriers for RNA therapeutics.", "doi": "10.1038/s41598-018-28485-9", "pmid": "30018314", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Global Proteomics and Proteogenomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-28485-9"}, {"db": "pmc", "key": "PMC6050237"}], "notes": [], "created": "2018-08-07T08:38:11.195Z", "modified": "2024-01-16T13:48:45.984Z"}, {"entity": "publication", "iuid": "736d53a3e91243fe9fea1220d17bc7a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/736d53a3e91243fe9fea1220d17bc7a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/736d53a3e91243fe9fea1220d17bc7a1"}}, "title": "Enteric Species F Human Adenoviruses use Laminin-Binding Integrins as Co-Receptors for Infection of Ht-29 Cells.", "authors": [{"family": "Rajan", "given": "Anandi", "initials": "A"}, {"family": "Persson", "given": "B David", "initials": "BD"}, {"family": "Fr\u00e4ngsmyr", "given": "Lars", "initials": "L"}, {"family": "Olofsson", "given": "Annelie", "initials": "A"}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Heino", "given": "Jyrki", "initials": "J"}, {"family": "Takada", "given": "Yoshikazu", "initials": "Y"}, {"family": "Mould", "given": "A Paul", "initials": "AP"}, {"family": "Schnapp", "given": "Lynn M", "initials": "LM"}, {"family": "Gall", "given": "Jason", "initials": "J"}, {"family": "Arnberg", "given": "Niklas", "initials": "N", "orcid": "0000-0002-7069-6678", "researcher": {"href": "https://publications.scilifelab.se/researcher/8764d7981e174798ab8411d36e7d0f1b.json"}}], "type": "journal article", "published": "2018-07-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "10019", "issn-l": "2045-2322"}, "abstract": "The enteric species F human adenovirus types 40 and 41 (HAdV-40 and -41) are the third most common cause of infantile gastroenteritis in the world. Knowledge about HAdV-40 and -41 cellular infection is assumed to be fundamentally different from that of other HAdVs since HAdV-40 and -41 penton bases lack the \u03b1V-integrin-interacting RGD motif. This motif is used by other HAdVs mainly for internalization and endosomal escape. We hypothesised that the penton bases of HAdV-40 and -41 interact with integrins independently of the RGD motif. HAdV-41 transduction of a library of rodent cells expressing specific human integrin subunits pointed to the use of laminin-binding \u03b12-, \u03b13- and \u03b16-containing integrins as well as other integrins as candidate co-receptors. Specific laminins prevented internalisation and infection, and recombinant, soluble HAdV-41 penton base proteins prevented infection of human intestinal HT-29 cells. Surface plasmon resonance analysis demonstrated that HAdV-40 and -41 penton base proteins bind to \u03b16-containing integrins with an affinity similar to that of previously characterised penton base:integrin interactions. With these results, we propose that laminin-binding integrins are co-receptors for HAdV-40 and -41.", "doi": "10.1038/s41598-018-28255-7", "pmid": "29968781", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-28255-7"}, {"db": "pmc", "key": "PMC6030200"}], "notes": [], "created": "2019-01-10T21:29:28.960Z", "modified": "2021-07-05T17:20:56.109Z"}, {"entity": "publication", "iuid": "2e77c536a8b44468a4ac3e357ddf6b32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e77c536a8b44468a4ac3e357ddf6b32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e77c536a8b44468a4ac3e357ddf6b32"}}, "title": "Confined photo-release of nitric oxide with simultaneous two-photon fluorescence tracking in a cellular system.", "authors": [{"family": "Thomsen", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6719-0919", "researcher": {"href": "https://publications.scilifelab.se/researcher/e54054e4c2d2407883628c54ee3ecd91.json"}}, {"family": "Marino", "given": "Nino", "initials": "N"}, {"family": "Conoci", "given": "Sabrina", "initials": "S"}, {"family": "Sortino", "given": "Salvatore", "initials": "S", "orcid": "0000-0002-2086-1276", "researcher": {"href": "https://publications.scilifelab.se/researcher/78f156fd27a04054a2f8b4c5acca4c13.json"}}, {"family": "Ericson", "given": "Marica B", "initials": "MB", "orcid": "0000-0002-5987-5915", "researcher": {"href": "https://publications.scilifelab.se/researcher/af1f53e7cd234c36bdde7121e7204ed5.json"}}], "type": "journal article", "published": "2018-06-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "9753", "issn-l": "2045-2322"}, "abstract": "Nitric oxide (NO) is a key signaling molecule in biological systems. New tools are required to therapeutically modulate NO levels with confined precision. This study explores the photoactivatable properties of an NO releasing compound (CPA), based on cupferron O-alkylated with an anthracene derivative. Upon light stimulation, CPA uncages two species: cupferron, which liberates NO, and an anthrylmethyl carbocation, which evolves into a fluorescent reporter. Proof-of-principle is demonstrated using one- and two-photon excitation (1PE and 2PE) in a cellular system (A431 cells). It was found that 1PE induces cell toxicity, while 2PE does not. Since 1PE using UV light is more likely to generate cellular photodamage, the cell toxicity observed using 1PE is most likely a combinatory effect of NO release and other UV-induced damage, which should be subject to further investigation. On the other hand, absence of phototoxicity using 2PE suggests that NO alone is not cytotoxic. This leads to the conclusion that the concept of 2PE photorelease of NO from CPA enable opportunities for biological studies of NO signaling with confined precision of NO release with minimal cytotoxicity.", "doi": "10.1038/s41598-018-27939-4", "pmid": "29950654", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-27939-4"}, {"db": "pmc", "key": "PMC6021447"}], "notes": [], "created": "2020-01-23T16:31:54.073Z", "modified": "2021-06-21T13:59:16.663Z"}, {"entity": "publication", "iuid": "0e1b3f3ba66e44708551ca9d3cbaf781", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e1b3f3ba66e44708551ca9d3cbaf781.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e1b3f3ba66e44708551ca9d3cbaf781"}}, "title": "Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.", "authors": [{"family": "Lundmark", "given": "Anna", "initials": "A", "orcid": "0000-0002-3655-3710", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c320c868d5d4eb09bed08fa3836f7e8.json"}}, {"family": "Gerasimcik", "given": "Natalija", "initials": "N"}, {"family": "B\u00e5ge", "given": "Tove", "initials": "T"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2018-06-19", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "9370", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Periodontitis is a highly prevalent chronic inflammatory disease of the periodontium, leading ultimately to tooth loss. In order to characterize the gene expression of periodontitis-affected gingival tissue, we have here simultaneously quantified and localized gene expression in periodontal tissue using spatial transcriptomics, combining RNA sequencing with histological analysis. Our analyses revealed distinct clusters of gene expression, which were identified to correspond to epithelium, inflamed areas of connective tissue, and non-inflamed areas of connective tissue. Moreover, 92 genes were identified as significantly up-regulated in inflamed areas of the gingival connective tissue compared to non-inflamed tissue. Among these, immunoglobulin lambda-like polypeptide 5 (IGLL5), signal sequence receptor subunit 4 (SSR4), marginal zone B and B1 cell specific protein (MZB1), and X-box binding protein 1 (XBP1) were the four most highly up-regulated genes. These genes were also verified as significantly higher expressed in gingival tissue of patients with periodontitis compared to healthy controls, using reverse transcription quantitative polymerase chain reaction. Moreover, the protein expressions of up-regulated genes were verified in gingival biopsies by immunohistochemistry. In summary, in this study, we report distinct gene expression signatures within periodontitis-affected gingival tissue, as well as specific genes that are up-regulated in inflamed areas compared to non-inflamed areas of gingival tissue. The results obtained from this study may add novel information on the genes and cell types contributing to pathogenesis of the chronic inflammatory disease periodontitis.", "doi": "10.1038/s41598-018-27627-3", "pmid": "29921943", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-27627-3"}, {"db": "pmc", "key": "PMC6008462"}], "notes": [], "created": "2018-10-31T19:44:55.950Z", "modified": "2024-01-16T13:48:46.104Z"}, {"entity": "publication", "iuid": "768c0a397b7f434a8c5c02c6d5cfaeb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/768c0a397b7f434a8c5c02c6d5cfaeb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/768c0a397b7f434a8c5c02c6d5cfaeb4"}}, "title": "Investigating Holocene human population history in North Asia using ancient mitogenomes.", "authors": [{"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "S\u00fcmer", "given": "Arev Pelin", "initials": "AP"}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E"}, {"family": "Shergin", "given": "Dmitrij", "initials": "D"}, {"family": "Ivanov", "given": "Grigorij Leonidovich", "initials": "GL"}, {"family": "Kichigin", "given": "Dmitrii", "initials": "D"}, {"family": "Pestereva", "given": "Kjunnej", "initials": "K"}, {"family": "Volkov", "given": "Denis", "initials": "D"}, {"family": "Mandryka", "given": "Pavel", "initials": "P"}, {"family": "Kharinskii", "given": "Artur", "initials": "A"}, {"family": "Tishkin", "given": "Alexey", "initials": "A"}, {"family": "Ineshin", "given": "Evgenij", "initials": "E"}, {"family": "Kovychev", "given": "Evgeniy", "initials": "E"}, {"family": "Stepanov", "given": "Aleksandr", "initials": "A"}, {"family": "Alekseev", "given": "Aanatolij", "initials": "A"}, {"family": "Fedoseeva", "given": "Svetlana Aleksandrovna", "initials": "SA"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-06-12", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "8969", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.", "doi": "10.1038/s41598-018-27325-0", "pmid": "29895902", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-27325-0"}, {"db": "pmc", "key": "PMC5997703"}], "notes": [], "created": "2018-10-31T19:48:02.044Z", "modified": "2024-01-16T13:48:46.130Z"}, {"entity": "publication", "iuid": "363baf22ded848369cab003f044d527c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/363baf22ded848369cab003f044d527c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/363baf22ded848369cab003f044d527c"}}, "title": "Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden.", "authors": [{"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Dalin", "given": "Frida", "initials": "F"}, {"family": "Skov", "given": "Jakob", "initials": "J"}, {"family": "Hultin-Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Mathioudaki", "given": "Argyri", "initials": "A"}, {"family": "Nordin", "given": "Jessika", "initials": "J"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Rantap\u00e4\u00e4 Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P", "orcid": "0000-0001-9867-8706", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fc163b9a08421180f7f235af3897f4.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Hulting", "given": "Anna-Lena", "initials": "AL"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Dahlqvist", "given": "Per", "initials": "P"}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}], "type": "journal article", "published": "2018-05-30", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "8395", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Autoimmune Addison's disease (AAD) is the predominating cause of primary adrenal failure. Despite its high heritability, the rarity of disease has long made candidate-gene studies the only feasible methodology for genetic studies. Here we conducted a comprehensive reinvestigation of suggested AAD risk loci and more than 1800 candidate genes with associated regulatory elements in 479 patients with AAD and 2394 controls. Our analysis enabled us to replicate many risk variants, but several other previously suggested risk variants failed confirmation. By exploring the full set of 1800 candidate genes, we further identified common variation in the autoimmune regulator (AIRE) as a novel risk locus associated to sporadic AAD in our study. Our findings not only confirm that multiple loci are associated with disease risk, but also show to what extent the multiple risk loci jointly associate to AAD. In total, risk loci discovered to date only explain about 7% of variance in liability to AAD in our study population.", "doi": "10.1038/s41598-018-26842-2", "pmid": "29849176", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-26842-2"}, {"db": "pmc", "key": "PMC5976627"}], "notes": [], "created": "2018-06-15T07:31:30.585Z", "modified": "2024-01-16T13:48:46.273Z"}, {"entity": "publication", "iuid": "9fbcd3915ba44ca9ae17976d8120258a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fbcd3915ba44ca9ae17976d8120258a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fbcd3915ba44ca9ae17976d8120258a"}}, "title": "Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants.", "authors": [{"family": "Zhou", "given": "Ang", "initials": "A"}, {"family": "Taylor", "given": "Amy E", "initials": "AE"}, {"family": "Karhunen", "given": "Ville", "initials": "V"}, {"family": "Zhan", "given": "Yiqiang", "initials": "Y"}, {"family": "Rovio", "given": "Suvi P", "initials": "SP"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Sj\u00f6gren", "given": "Per", "initials": "P"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Lyall", "given": "Donald M", "initials": "DM"}, {"family": "Auvinen", "given": "Juha", "initials": "J"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Per\u00e4l\u00e4", "given": "Mia Maria", "initials": "MM"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Veijola", "given": "Juha", "initials": "J"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Munaf\u00f2", "given": "Marcus R", "initials": "MR"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Llewellyn", "given": "David J", "initials": "DJ"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}], "type": "journal article", "published": "2018-05-14", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "7526", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Coffee's long-term effect on cognitive function remains unclear with studies suggesting both benefits and adverse effects. We used Mendelian randomization to investigate the causal relationship between habitual coffee consumption and cognitive function in mid- to later life. This included up to 415,530 participants and 300,760 coffee drinkers from 10 meta-analysed European ancestry cohorts. In each cohort, composite cognitive scores that capture global cognition and memory were computed using available tests. A genetic score derived using CYP1A1/2 (rs2472297) and AHR (rs6968865) was chosen as a proxy for habitual coffee consumption. Null associations were observed when examining the associations of the genetic score with global and memory cognition (\u03b2\u2009=\u2009-0.0007, 95% C.I. -0.009 to 0.008, P\u2009=\u20090.87; \u03b2\u2009=\u2009-0.001, 95% C.I. -0.005 to 0.002, P\u2009=\u20090.51, respectively), with high consistency between studies (P", "doi": "10.1038/s41598-018-25919-2", "pmid": "29760501", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-25919-2"}, {"db": "pmc", "key": "PMC5951917"}], "notes": [], "created": "2018-05-25T13:25:46.689Z", "modified": "2024-01-16T13:48:46.323Z"}, {"entity": "publication", "iuid": "98783fcd568e4f5085d98d1465719950", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98783fcd568e4f5085d98d1465719950.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98783fcd568e4f5085d98d1465719950"}}, "title": "Humanizing Miniature Hearts through 4-Flow Cannulation Perfusion Decellularization and Recellularization.", "authors": [{"family": "Nguyen", "given": "Duong T", "initials": "DT", "orcid": "0000-0002-4700-9067", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e63e8c6a9e47c2b6d3e61e61cf0cc2.json"}}, {"family": "O'Hara", "given": "Matthew", "initials": "M"}, {"family": "Graneli", "given": "Cecilia", "initials": "C"}, {"family": "Hicks", "given": "Ryan", "initials": "R"}, {"family": "Miliotis", "given": "Tasso", "initials": "T"}, {"family": "Nystr\u00f6m", "given": "Ann-Christin", "initials": "AC"}, {"family": "Hansson", "given": "Sara", "initials": "S"}, {"family": "Davidsson", "given": "Pia", "initials": "P"}, {"family": "Gan", "given": "Li-Ming", "initials": "LM"}, {"family": "Magnone", "given": "Maria Chiara", "initials": "MC"}, {"family": "Althage", "given": "Magnus", "initials": "M"}, {"family": "Heydarkhan-Hagvall", "given": "Sepideh", "initials": "S"}], "type": "journal article", "published": "2018-05-10", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "7458", "issn-l": "2045-2322"}, "abstract": "Despite improvements in pre-clinical drug testing models, predictability of clinical outcomes continues to be inadequate and costly due to poor evidence of drug metabolism. Humanized miniature organs integrating decellularized rodent organs with tissue specific cells are translational models that can provide further physiological understanding and evidence. Here, we evaluated 4-Flow cannulated rat hearts as the fundamental humanized organ model for cardiovascular drug validation. Results show clearance of cellular components in all chambers in 4-Flow hearts with efficient perfusion into both coronary arteries and cardiac veins. Furthermore, material characterization depicts preserved organization and content of important matrix proteins such as collagens, laminin, and elastin. With access to the complete vascular network, different human cell types were delivered to show spatial distribution and integration into the matrix under perfusion for up to three weeks. The feature of 4-Flow cannulation is the preservation of whole heart conformity enabling ventricular pacing via the pulmonary vein as demonstrated by noninvasive monitoring with fluid pressure and ultrasound imaging. Consequently, 4-Flow hearts surmounting organ mimicry challenges with intact complexity in vasculature and mechanical compliance of the whole organ providing an ideal platform for improving pre-clinical drug validation in addition to understanding cardiovascular diseases.", "doi": "10.1038/s41598-018-25883-x", "pmid": "29748585", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-25883-x"}, {"db": "pmc", "key": "PMC5945628"}], "notes": [], "created": "2020-01-23T16:51:37.952Z", "modified": "2021-06-21T13:56:58.378Z"}, {"entity": "publication", "iuid": "1147aae594d748ba8261d71fb2525932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1147aae594d748ba8261d71fb2525932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1147aae594d748ba8261d71fb2525932"}}, "title": "Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.", "authors": [{"family": "Vdovikova", "given": "Svitlana", "initials": "S"}, {"family": "Gilfillan", "given": "Siv", "initials": "S"}, {"family": "Wang", "given": "Shixiong", "initials": "S"}, {"family": "Dongre", "given": "Mitesh", "initials": "M"}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN"}, {"family": "Hurtado", "given": "Antoni", "initials": "A"}], "type": "journal article", "published": "2018-05-09", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "7434", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Interactions between bacteria and colon cancer cells influence the transcription of the host cell. Yet is it undetermined whether the bacteria itself or the communication between the host and bacteria is responsible for the genomic changes in the eukaryotic cell. Now, we have investigated the genomic and epigenetic consequences of co-culturing colorectal carcinoma cells with membrane vesicles from pathogenic bacteria Vibrio cholerae and non-pathogenic commensal bacteria Escherichia coli. Our study reveals that membrane vesicles from pathogenic and commensal bacteria have a global impact on the gene expression of colon-carcinoma cells. The changes in gene expression correlate positively with both epigenetic changes and chromatin accessibility of promoters at transcription start sites of genes induced by both types of membrane vesicles. Moreover, we have demonstrated that membrane vesicles obtained only from V. cholerae induced the expression of genes associated with epithelial cell differentiation. Altogether, our study suggests that the observed genomic changes in host cells might be due to specific components of membrane vesicles and do not require communication by direct contact with the bacteria.", "doi": "10.1038/s41598-018-25308-9", "pmid": "29743643", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-25308-9"}, {"db": "pmc", "key": "PMC5943334"}], "notes": [], "created": "2019-01-15T08:25:32.974Z", "modified": "2020-01-21T13:53:22.499Z"}, {"entity": "publication", "iuid": "2fbe656ef4894b12b0e51cf2485d8978", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fbe656ef4894b12b0e51cf2485d8978.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fbe656ef4894b12b0e51cf2485d8978"}}, "title": "Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Sandoval-Castellanos", "given": "Edson", "initials": "E", "orcid": "0000-0002-0840-8225", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a78dc09c8441438303e4cf539d8832.json"}}, {"family": "Caillaud", "given": "Damien", "initials": "D"}, {"family": "Ngobobo", "given": "Urbain", "initials": "U"}, {"family": "Binyinyi", "given": "Escobar", "initials": "E"}, {"family": "Nishuli", "given": "Radar", "initials": "R"}, {"family": "Stoinski", "given": "Tara", "initials": "T"}, {"family": "Gilissen", "given": "Emmanuel", "initials": "E"}, {"family": "Sonet", "given": "Gontran", "initials": "G"}, {"family": "Semal", "given": "Patrick", "initials": "P"}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2018-04-25", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "6551", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.", "doi": "10.1038/s41598-018-24497-7", "pmid": "29695730", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-24497-7"}, {"db": "pmc", "key": "PMC5917027"}], "notes": [], "created": "2018-09-14T12:10:20.876Z", "modified": "2024-01-16T13:48:46.451Z"}, {"entity": "publication", "iuid": "99256f2660b146e589a8e734ce7e0fe2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99256f2660b146e589a8e734ce7e0fe2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99256f2660b146e589a8e734ce7e0fe2"}}, "title": "Abundant fish protein inhibits \u03b1-synuclein amyloid formation.", "authors": [{"family": "Werner", "given": "Tony", "initials": "T"}, {"family": "Kumar", "given": "Ranjeet", "initials": "R"}, {"family": "Horvath", "given": "Istvan", "initials": "I"}, {"family": "Scheers", "given": "Nathalie", "initials": "N", "orcid": "0000-0001-8812-9025", "researcher": {"href": "https://publications.scilifelab.se/researcher/247e0ccd008f4795af5d666a181269b5.json"}}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2018-04-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "5465", "issn-l": "2045-2322"}, "abstract": "The most common allergen in fish, the highly-abundant protein \u03b2-parvalbumin, forms amyloid structures as a way to avoid gastrointestinal degradation and transit to the blood. In humans, the same amyloid structures are mostly associated with neurodegenerative disorders such as Alzheimer's and Parkinson's. We here assessed a putative connection between these amyloids using recombinant Atlantic cod \u03b2-parvalbumin and the key amyloidogenic protein in Parkinson's disease, \u03b1-synuclein. Using a set of in vitro biophysical methods, we discovered that \u03b2-parvalbumin readily inhibits amyloid formation of \u03b1-synuclein. The underlying mechanism was found to involve \u03b1-synuclein binding to the surface of \u03b2-parvalbumin amyloid fibers. In addition to being a new amyloid inhibition mechanism, the data suggest that health benefits of fish may be explained in part by cross-reaction of \u03b2-parvalbumin with human amyloidogenic proteins.", "doi": "10.1038/s41598-018-23850-0", "pmid": "29615738", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-23850-0"}, {"db": "pmc", "key": "PMC5882657"}], "notes": [], "created": "2020-01-23T16:33:32.278Z", "modified": "2021-06-21T13:56:47.848Z"}, {"entity": "publication", "iuid": "81119cdb3d66446b84f3b461ac2a1910", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81119cdb3d66446b84f3b461ac2a1910.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81119cdb3d66446b84f3b461ac2a1910"}}, "title": "Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes.", "authors": [{"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Grannas", "given": "Karin", "initials": "K"}, {"family": "Ebai", "given": "Tonge", "initials": "T"}, {"family": "Heldin", "given": "Johan", "initials": "J"}, {"family": "Koos", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Leino", "given": "Mattias", "initials": "M"}, {"family": "Raykova", "given": "Doroteya", "initials": "D"}, {"family": "Oelrich", "given": "Johan", "initials": "J"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2018-03-29", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "5400", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "We have redesigned probes for in situ proximity ligation assay (PLA), resulting in more efficient localized detection of target proteins. In situ PLA depends on recognition of target proteins by pairs of antibody-oligonucleotide conjugates (PLA probes), which jointly give rise to DNA circles that template localized rolling circle amplification reactions. The requirement for dual recognition of the target proteins improves selectivity by ignoring any cross-reactivity not shared by the antibodies, and it allows detection of protein-protein interactions and post-translational modifications. We herein describe an improved design of the PLA probes -UnFold probes\u00a0- where all elements required for formation of circular DNA strands are incorporated in the probes. Premature interactions between the UnFold probes are prevented by including an enzymatic \"unfolding\" step in the detection reactions. This allows DNA circles to form by pairs of reagents only after excess reagents have been removed. We demonstrate the performance of UnFold probes for detection of protein-protein interactions and post-translational modifications in fixed cells and tissues, revealing considerably more efficient signal generation. We also apply the UnFold probes to detect IL-6 in solution phase after capture on solid supports, demonstrating increased sensitivity over both normal sandwich enzyme-linked immunosorbent assays and conventional PLA assays.", "doi": "10.1038/s41598-018-23582-1", "pmid": "29599435", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-23582-1"}, {"db": "pmc", "key": "PMC5876389"}], "notes": [], "created": "2018-10-30T09:00:00.386Z", "modified": "2023-04-14T13:56:04.936Z"}, {"entity": "publication", "iuid": "0b5a699813124ee1ba64f2d1fafc0763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b5a699813124ee1ba64f2d1fafc0763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b5a699813124ee1ba64f2d1fafc0763"}}, "title": "Peptide ion channel toxins from the bootlace worm, the longest animal on Earth.", "authors": [{"family": "Jacobsson", "given": "Erik", "initials": "E"}, {"family": "Andersson", "given": "H\u00e5kan S", "initials": "HS"}, {"family": "Strand", "given": "Malin", "initials": "M"}, {"family": "Peigneur", "given": "Steve", "initials": "S"}, {"family": "Eriksson", "given": "Camilla", "initials": "C"}, {"family": "Lod\u00e9n", "given": "Henrik", "initials": "H"}, {"family": "Shariatgorji", "given": "Mohammadreza", "initials": "M"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}, {"family": "Lebbe", "given": "Eline K M", "initials": "EKM"}, {"family": "Rosengren", "given": "K Johan", "initials": "KJ"}, {"family": "Tytgat", "given": "Jan", "initials": "J"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U", "orcid": "0000-0002-5005-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae076a1dcc714afc90e56d93e95a10c4.json"}}], "type": "journal article", "published": "2018-03-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "4596", "issn-l": "2045-2322"}, "abstract": "Polypeptides from animal venoms have found important uses as drugs, pharmacological tools, and within biotechnological and agricultural applications. We here report a novel family of cystine knot peptides from nemertean worms, with potent activity on voltage-gated sodium channels. These toxins, named the \u03b1-nemertides, were discovered in the epidermal mucus of Lineus longissimus, the 'bootlace worm' known as the longest animal on earth. The most abundant peptide, the 31-residue long \u03b1-1, was isolated, synthesized, and its 3D NMR structure determined. Transcriptome analysis including 17 species revealed eight \u03b1-nemertides, mainly distributed in the genus Lineus. \u03b1-1 caused paralysis and death in green crabs (Carcinus maenas) at 1 \u00b5g/kg (~300 pmol/kg). It showed profound effect on invertebrate voltage-gated sodium channels (e.g. Blattella germanica Nav1) at low nanomolar concentrations. Strong selectivity for insect over human sodium channels indicates that \u03b1-nemertides can be promising candidates for development of bioinsecticidal agents.", "doi": "10.1038/s41598-018-22305-w", "pmid": "29567943", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-22305-w"}, {"db": "pmc", "key": "PMC5864730"}], "notes": [], "created": "2020-01-24T09:05:57.919Z", "modified": "2021-12-03T11:57:01.490Z"}, {"entity": "publication", "iuid": "393b99fadee3457f861d2abb322eb0a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/393b99fadee3457f861d2abb322eb0a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/393b99fadee3457f861d2abb322eb0a1"}}, "title": "ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.", "authors": [{"family": "Bremer", "given": "Hanna D", "initials": "HD"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Renneker", "given": "Stefanie", "initials": "S"}, {"family": "Lattwein", "given": "Erik", "initials": "E"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Lillieh\u00f6\u00f6k", "given": "Inger", "initials": "I"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Hansson-Hamlin", "given": "Helene", "initials": "H"}], "type": "journal article", "published": "2018-03-19", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "4852", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Dogs can spontaneously develop complex systemic autoimmune disorders, with similarities to human autoimmune disease. Autoantibodies directed at self-antigens are a key feature of these autoimmune diseases. Here we report the identification of interleukin enhancer-binding factors 2 and 3 (ILF2 and ILF3) as autoantigens in canine immune-mediated rheumatic disease. The ILF2 autoantibodies were discovered in a small, selected canine cohort through the use of human protein arrays; a method not previously described in dogs. Subsequently, ILF3 autoantibodies were also identified in the same cohort. The results were validated with an independent method in a larger cohort of dogs. ILF2 and ILF3 autoantibodies were found exclusively, and at a high frequency, in dogs that showed a speckled pattern of antinuclear antibodies on immunofluorescence. ILF2 and ILF3 autoantibodies were also found at low frequency in human patients with SLE and Sj\u00f6gren's syndrome. These autoantibodies have the potential to be used as diagnostic biomarkers for canine, and possibly also human, autoimmune disease.", "doi": "10.1038/s41598-018-23034-w", "pmid": "29556082", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-23034-w"}, {"db": "pmc", "key": "PMC5859008"}], "notes": [], "created": "2018-09-11T08:06:07.439Z", "modified": "2024-01-16T13:48:46.724Z"}, {"entity": "publication", "iuid": "fffb461dc95c4148b32555dcc16d46db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fffb461dc95c4148b32555dcc16d46db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fffb461dc95c4148b32555dcc16d46db"}}, "title": "Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface.", "authors": [{"family": "Quintana", "given": "Maria Del Pilar", "initials": "MDP"}, {"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Idris", "given": "Zulkarnain Md", "initials": "ZM"}, {"family": "Saiwaew", "given": "Somporn", "initials": "S"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2018-02-19", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "3262", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Naturally acquired antibodies to proteins expressed on the Plasmodium falciparum parasitized red blood cell (pRBC) surface steer the course of a malaria infection by reducing sequestration and stimulating phagocytosis of pRBC. Here we have studied a selection of proteins representing three different parasite gene families employing a well-characterized parasite with a severe malaria phenotype (FCR3S1.2). The presence of naturally acquired antibodies, impact on rosetting rate, surface reactivity and opsonization for phagocytosis in relation to different blood groups of the ABO system were assessed in a set of sera from children with mild or complicated malaria from an endemic area. We show that the naturally acquired immune responses, developed during malaria natural infection, have limited access to the pRBCs inside a blood group A rosette. The data also indicate that SURFIN", "doi": "10.1038/s41598-018-21026-4", "pmid": "29459776", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-21026-4"}, {"db": "pmc", "key": "PMC5818650"}], "notes": [], "created": "2018-09-11T08:08:52.221Z", "modified": "2024-01-16T13:48:46.915Z"}, {"entity": "publication", "iuid": "53eaaa7ffacc4f81b74119dcf025b234", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53eaaa7ffacc4f81b74119dcf025b234.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53eaaa7ffacc4f81b74119dcf025b234"}}, "title": "Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro - a potential pathway affecting proliferation.", "authors": [{"family": "L\u00f6fdahl", "given": "Anna", "initials": "A"}, {"family": "Rydell-T\u00f6rm\u00e4nen", "given": "Kristina", "initials": "K"}, {"family": "Larsson-Callerfelt", "given": "Anna-Karin", "initials": "A"}, {"family": "Wengl\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G"}], "type": "journal article", "published": "2018-01-31", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "1927", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Serotonin (5-hydroxytryptamine) has repeatedly been associated with the development of fibrotic disorders such as pulmonary fibrosis. By blocking the binding of 5-HT to 5-HT\r\n            2B receptors with receptor antagonists, several pro-fibrotic mechanisms can be inhibited. Bleomycin-induced pulmonary fibrosis is a model used to evaluate pathological mechanisms and pharmacological interventions. Previously we have shown attenuated fibrosis in systemic bleomycin-treated mice following treatment with two 5-HT2B receptor antagonists (EXT5 and EXT9). Our aim is to further identify cellular effects and signaling pathways associated with the anti-fibrotic effects of EXT5/9. Gene expressions in lung tissues from systemic bleomycin-treated mice were examined, revealing significant increased expression of Cdkn1\u03b1 (a gene coding for p21), particularly in distal regions of the lung. In vitro studies in human lung fibroblasts revealed increased levels of p21 (p\u2009=\u20090.0032) and pAkt (p\u2009=\u20090.12) following treatment with 5-HT (10\u2009\u00b5M). The induction of p21 and pAkt appears to be regulated by 5-HT2B receptors, with diminished protein levels following EXT9-treatment (p21 p\u2009=\u20090.0024, pAkt p\u2009=\u20090.15). Additionally, 5-HT induced fibroblast proliferation, an event significantly reduced by EXT5 (10\u2009\u00b5M) and EXT9 (10\u2009\u00b5M). In conclusion, our results suggest that 5-HT2B receptor antagonism attenuates pulmonary fibrosis in part by anti-proliferative effects, associated with inhibited pAkt/p21 signaling pathway.", "doi": "10.1038/s41598-018-20430-0", "pmid": "29386571", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-20430-0"}, {"db": "pmc", "key": "PMC5792547"}], "notes": [], "created": "2019-01-14T17:49:02.094Z", "modified": "2020-01-21T13:53:22.762Z"}, {"entity": "publication", "iuid": "db65681a7824495b8a0d65c93763a2b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db65681a7824495b8a0d65c93763a2b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db65681a7824495b8a0d65c93763a2b9"}}, "title": "A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome.", "authors": [{"family": "Kokosar", "given": "Milana", "initials": "M"}, {"family": "Benrick", "given": "Anna", "initials": "A"}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Nilsson", "given": "Emma", "initials": "E"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}, {"family": "Stener-Victorin", "given": "Elisabet", "initials": "E"}], "type": "journal article", "published": "2018-01-30", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "1878", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A single bout of electroacupuncture results in muscle contractions and increased whole body glucose uptake in women with polycystic ovary syndrome (PCOS). Women with PCOS have transcriptional and epigenetic alterations in the adipose tissue and we hypothesized that electroacupuncture induces epigenetic and transcriptional changes to restore metabolic alterations. Twenty-one women with PCOS received a single bout of electroacupuncture, which increased the whole body glucose uptake. In subcutaneous adipose tissue biopsies, we identified treatment-induced expression changes of 2369 genes (Q\u2009<\u20090.05) and DNA methylation changes of 7055 individual genes (Q\u2009=\u20090.11). The largest increase in expression was observed for FOSB (2405%), and the largest decrease for LOC100128899 (54%). The most enriched pathways included Acute phase response signaling and LXR/RXR activation. The DNA methylation changes ranged from 1-16%, and 407 methylation sites correlated with gene expression. Among genes known to be differentially expressed in PCOS, electroacupuncture reversed the expression of 80 genes, including PPAR\u03b3 and ADIPOR2. Changes in the expression of Nr4a2 and Junb are reversed by adrenergic blockers in rats demonstrating that changes in gene expression, in part, is due to activation of the sympathetic nervous system. In conclusion, low-frequency electroacupuncture with muscle contractions remodels epigenetic and transcriptional changes that elicit metabolic improvement.", "doi": "10.1038/s41598-017-17919-5", "pmid": "29382850", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-17919-5"}, {"db": "pmc", "key": "PMC5790004"}], "notes": [], "created": "2018-12-14T13:52:37.615Z", "modified": "2020-01-21T13:53:22.064Z"}, {"entity": "publication", "iuid": "ee8321c6e41b4864a316587ea205b8b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee8321c6e41b4864a316587ea205b8b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee8321c6e41b4864a316587ea205b8b4"}}, "title": "Innate immune alterations are elicited in microglial cells before plaque deposition in the Alzheimer's disease mouse model 5xFAD.", "authors": [{"family": "Boza-Serrano", "given": "Antonio", "initials": "A"}, {"family": "Yang", "given": "Yiyi", "initials": "Y"}, {"family": "Paulus", "given": "Agnes", "initials": "A"}, {"family": "Deierborg", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2018-01-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "1550", "issn-l": "2045-2322"}, "abstract": "Alzheimer's disease (AD) is the most common form of dementia characterized by the formation of amyloid plaques (A\u03b2). Over the last decade, the important role of the innate immune system for the disease development has been established. Chronic activation of microglial cells creates a proinflammatory environment, which is believed to be central for the development of the disease as well as its progression. We used the AD mouse model 5xFAD to investigate if inflammatory alterations are present in microglial cells before plaque deposition. We applied mass spectrometry and bioinformation analysis to elucidate early microglial alterations. Interestingly, we found the cytokines IL1\u03b2 and IL10 to be elevated in the 5xFAD brain after the formation of A\u03b2 plaque at 10 weeks only. Using mass spectrometry analysis of microglial cells with bioinformation analysis, we found JAK/STAT, p38 MAPK and Interleukin pathways affected in microglial cells before plaque deposition at 6 weeks. At 10 weeks, GO analysis showed affected pathways related to interferon-gamma regulation and MAPK pathways. Our study points toward early inflammatory changes in microglial cells even before the accumulation of A\u03b2.", "doi": "10.1038/s41598-018-19699-y", "pmid": "29367720", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-19699-y"}, {"db": "pmc", "key": "PMC5784016"}], "notes": [], "created": "2020-01-30T15:59:53.232Z", "modified": "2024-01-16T13:46:32.395Z"}, {"entity": "publication", "iuid": "fcd37a8280914a0bb0b0796744b1796a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcd37a8280914a0bb0b0796744b1796a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcd37a8280914a0bb0b0796744b1796a"}}, "title": "Identification of shared genetic variants between schizophrenia and lung cancer.", "authors": [{"family": "Zuber", "given": "Verena", "initials": "V"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Frei", "given": "Oleksandr", "initials": "O"}, {"family": "Witoelar", "given": "Aree", "initials": "A"}, {"family": "Thompson", "given": "Wesley K", "initials": "WK"}, {"family": "Schork", "given": "Andrew J", "initials": "AJ"}, {"family": "Bettella", "given": "Francesco", "initials": "F"}, {"family": "Wang", "given": "Yunpeng", "initials": "Y"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Smeland", "given": "Olav B", "initials": "OB"}, {"family": "Dieset", "given": "Ingrid", "initials": "I"}, {"family": "Fanous", "given": "Ayman H", "initials": "AH"}, {"family": "Desikan", "given": "Rahul S", "initials": "RS"}, {"family": "K\u00fcry", "given": "S\u00e9bastien", "initials": "S"}, {"family": "B\u00e9zieau", "given": "St\u00e9phane", "initials": "S"}, {"family": "Dale", "given": "Anders M", "initials": "AM"}, {"family": "Mills", "given": "Ian G", "initials": "IG"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}], "type": "journal article", "published": "2018-01-12", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "674", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Epidemiology studies suggest associations between schizophrenia and cancer. However, the underlying genetic mechanisms are not well understood, and difficult to identify from epidemiological data. We investigated if there is a shared genetic architecture between schizophrenia and cancer, with the aim to identify specific overlapping genetic loci. First, we performed genome-wide enrichment analysis and second, we analyzed specific loci jointly associated with schizophrenia and cancer by the conjunction false discovery rate. We analyzed the largest genome-wide association studies of schizophrenia and lung, breast, prostate, ovary, and colon-rectum cancer including more than 220,000 subjects, and included genetic association with smoking behavior. Polygenic enrichment of associations with lung cancer was observed in schizophrenia, and weak enrichment for the remaining cancer sites. After excluding the major histocompatibility complex region, we identified three independent loci jointly associated with schizophrenia and lung cancer. The strongest association included nicotinic acetylcholine receptors and is an established pleiotropic locus shared between lung cancer and smoking. The two other loci were independent of genetic association with smoking. Functional analysis identified downstream pleiotropic effects on epigenetics and gene-expression in lung and brain tissue. These findings suggest that genetic factors may explain partly the observed epidemiological association of lung cancer and schizophrenia.", "doi": "10.1038/s41598-017-16481-4", "pmid": "29330379", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-16481-4"}, {"db": "pmc", "key": "PMC5766533"}], "notes": [], "created": "2018-05-25T13:31:03.834Z", "modified": "2020-01-21T13:56:10.912Z"}, {"entity": "publication", "iuid": "a60b6a97c659488e90cccb7c10b92482", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a60b6a97c659488e90cccb7c10b92482.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a60b6a97c659488e90cccb7c10b92482"}}, "title": "Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.", "authors": [{"family": "Nassa", "given": "Giovanni", "initials": "G", "orcid": "0000-0001-7453-1240", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c29044382c44e18a098f3825567f4fb.json"}}, {"family": "Giurato", "given": "Giorgio", "initials": "G"}, {"family": "Cimmino", "given": "Giovanni", "initials": "G"}, {"family": "Rizzo", "given": "Francesca", "initials": "F"}, {"family": "Ravo", "given": "Maria", "initials": "M"}, {"family": "Salvati", "given": "Annamaria", "initials": "A"}, {"family": "Nyman", "given": "Tuula A", "initials": "TA", "orcid": "0000-0001-8787-5886", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a2a62d54ba4be2a5a747fbbfc5bcc3.json"}}, {"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Golino", "given": "Paolo", "initials": "P"}, {"family": "Weisz", "given": "Alessandro", "initials": "A"}, {"family": "Tarallo", "given": "Roberta", "initials": "R", "orcid": "0000-0001-9668-3632", "researcher": {"href": "https://publications.scilifelab.se/researcher/27138966f8b84f5d810aafa53a7e9304.json"}}], "type": "journal article", "published": "2018-01-11", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "498", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Platelet activation triggers thrombus formation in physiological and pathological conditions, such as acute coronary syndromes. Current therapies still fail to prevent thrombotic events in numerous patients, indicating that the mechanisms modulating platelet response during activation need to be clarified. The evidence that platelets are capable of de novo protein synthesis in response to stimuli raised the issue of how megakaryocyte-derived mRNAs are regulated in these anucleate cell fragments. Proteogenomics was applied here to investigate this phenomeon in platelets activated in vitro with Collagen or Thrombin Receptor Activating Peptide. Combining proteomics and transcriptomics allowed in depth platelet proteome characterization, revealing a significant effect of either stimulus on proteome composition. In silico analysis revealed the presence of resident immature RNAs in resting platelets, characterized by retained introns, while unbiased proteogenomics correlated intron removal by RNA splicing with changes on proteome composition upon activation. This allowed identification of a set of transcripts undergoing maturation by intron removal during activation and resulting in accumulation of the corresponding peptides at exon-exon junctions. These results indicate that RNA splicing events occur in platelets during activation and that maturation of specific pre-mRNAs is part of the activation cascade, contributing to a dynamic fine-tuning of the transcriptome.", "doi": "10.1038/s41598-017-18985-5", "pmid": "29323256", "labels": {"Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-18985-5"}, {"db": "pmc", "key": "PMC5765118"}], "notes": [], "created": "2019-01-07T12:26:09.138Z", "modified": "2021-07-08T11:36:15.124Z"}, {"entity": "publication", "iuid": "6f0551fe582b4a17af988f9e315308e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f0551fe582b4a17af988f9e315308e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f0551fe582b4a17af988f9e315308e6"}}, "title": "Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues.", "authors": [{"family": "Adamczyk", "given": "Barbara", "initials": "B"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Polom", "given": "Karol", "initials": "K"}, {"family": "Mu\u00f1oz", "given": "Pedro", "initials": "P"}, {"family": "Rojas-Macias", "given": "Miguel A", "initials": "MA"}, {"family": "Zeeberg", "given": "David", "initials": "D"}, {"family": "Bor\u00e9n", "given": "Mats", "initials": "M"}, {"family": "Roviello", "given": "Franco", "initials": "F"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2018-01-10", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "242", "issn-l": "2045-2322"}, "abstract": "Sample collection, handling and storage are the most critical steps for ensuring the highest preservation of specimens. Pre-analytical variability can influence the results as protein signatures alter rapidly after tissue excision or during long-term storage. Hence, we evaluated current state-of-the-art biobank preservation methods from a glycomics perspective and analyzed O-glycan alterations occurring in the gastric cancer tissues. Paired tumor and adjacent normal tissue samples were obtained from six patients undergoing gastric cancer surgery. Collected samples (n = 24) were either snap-frozen or heat stabilized and then homogenized. Glycans were released from extracted glycoproteins and analyzed by LC-MS/MS. In total, the relative abundance of 83 O-glycans and 17 derived structural features were used for comparison. There was no statistically significant difference found in variables between snap frozen and heat-stabilized samples, which indicated the two preservation methods were comparable. The data also showed significant changes between normal and cancerous tissue. In addition to a shift from high sialylation in the cancer area towards blood group ABO in the normal area, we also detected that the LacdiNAc epitope (N,N'-diacetyllactosamine) was significantly decreased in cancer samples. The O-glycan alterations that are presented here may provide predictive power for the detection and prognosis of gastric cancer.", "doi": "10.1038/s41598-017-18299-6", "pmid": "29321476", "labels": {"Glycoproteomics and MS Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-18299-6"}, {"db": "pmc", "key": "PMC5762837"}], "notes": [], "created": "2020-01-30T16:24:13.378Z", "modified": "2024-01-16T13:46:32.417Z"}, {"entity": "publication", "iuid": "cddd0536b8af495a92e67d2c2bdedb91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cddd0536b8af495a92e67d2c2bdedb91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cddd0536b8af495a92e67d2c2bdedb91"}}, "title": "Discovering viral genomes in human metagenomic data by predicting unknown protein families.", "authors": [{"family": "Barrientos-Somarribas", "given": "Mauricio", "initials": "M"}, {"family": "Messina", "given": "David N", "initials": "DN"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Lysholm", "given": "Fredrik", "initials": "F"}, {"family": "Bjerkner", "given": "Annelie", "initials": "A"}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}], "type": "journal article", "published": "2018-01-08", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "28", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM.", "doi": "10.1038/s41598-017-18341-7", "pmid": "29311716", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-18341-7"}, {"db": "pmc", "key": "PMC5758519"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB17838", "key": "PRJEB17838"}], "notes": [], "created": "2018-10-31T19:44:53.198Z", "modified": "2024-01-16T13:48:47.101Z"}, {"entity": "publication", "iuid": "25667b18e9cd4a24be39919d778fcecb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25667b18e9cd4a24be39919d778fcecb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25667b18e9cd4a24be39919d778fcecb"}}, "title": "Highly sensitive and specific protein detection via combined capillary isoelectric focusing and proximity ligation", "authors": [{"family": "Padhan", "given": "Narendra", "initials": "N"}, {"family": "Yan", "given": "Junhong", "initials": "J"}, {"family": "Boge", "given": "Annegret", "initials": "A"}, {"family": "Scrivener", "given": "Elaine", "initials": "E"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Gullberg", "given": "Mats", "initials": "M"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-01516-7", "pmid": "28473697", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T14:47:02.649Z", "modified": "2023-04-14T13:56:08.329Z"}, {"entity": "publication", "iuid": "793737c7164b487eb6f97d8b1b3b984a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/793737c7164b487eb6f97d8b1b3b984a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/793737c7164b487eb6f97d8b1b3b984a"}}, "title": "Automated Training of Deep Convolutional Neural Networks for Cell Segmentation", "authors": [{"family": "Sadanandan", "given": "Sajith Kecheril", "initials": "SK"}, {"family": "Ranefall", "given": "Petter", "initials": "P"}, {"family": "Le Guyader", "given": "Sylvie", "initials": "S"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-07599-6", "pmid": "28798336", "labels": {"BioImage Informatics": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "cb.uu.se", "description": "Images and code", "key": "http://www.cb.uu.se/~carolina/timelapse_data/"}, {"db": "data.broadinstitute.org", "description": "Images", "key": "https://data.broadinstitute.org/bbbc/BBBC022/"}], "notes": [], "created": "2017-11-01T08:05:25.830Z", "modified": "2021-07-05T14:18:24.353Z"}, {"entity": "publication", "iuid": "8be977a6fe724420894f3df784d9aff1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8be977a6fe724420894f3df784d9aff1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8be977a6fe724420894f3df784d9aff1"}}, "title": "Novel risk genes for systemic lupus erythematosus predicted by random forest classification", "authors": [{"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Sylwan", "given": "Lina", "initials": "L"}, {"family": "B\u00e4cklin", "given": "Christofer", "initials": "C"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Eloranta", "given": "Maija Leena", "initials": "ML"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Bengtsson", "given": "Christine", "initials": "C"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Dahlqvist", "given": "Solbritt Rantap\u00e4\u00e4", "initials": "SR"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Syv\u00e4nen", "given": "Ann Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-06516-1", "pmid": "28740209", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:02.637Z", "modified": "2024-01-16T13:48:47.265Z"}, {"entity": "publication", "iuid": "a2b9445a65e8490793fea171bd20486e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b9445a65e8490793fea171bd20486e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b9445a65e8490793fea171bd20486e"}}, "title": "Increasing the permeability of Escherichia coli using MAC13243", "authors": [{"family": "Muheim", "given": "Claudio", "initials": "C"}, {"family": "G\u00f6tzke", "given": "Hansj\u00f6rg", "initials": "H"}, {"family": "Eriksson", "given": "Anna U", "initials": "AU"}, {"family": "Lindberg", "given": "Stina", "initials": "S"}, {"family": "Lauritsen", "given": "Ida", "initials": "I"}, {"family": "N\u00f8rholm", "given": "Morten H H", "initials": "MHH"}, {"family": "Daley", "given": "Daniel O", "initials": "DO"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-17772-6", "pmid": "29247166", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-02-12T12:53:39.343Z", "modified": "2025-10-17T13:04:29.085Z"}, {"entity": "publication", "iuid": "b0c456eb98294268808bdeeb2a0263c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c456eb98294268808bdeeb2a0263c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c456eb98294268808bdeeb2a0263c0"}}, "title": "Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells", "authors": [{"family": "Piltti", "given": "Juha", "initials": "J"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Fern\u00e1ndez-Echevarr\u00eda", "given": "Cecilia", "initials": "C"}, {"family": "Marcellino", "given": "Daniel", "initials": "D"}, {"family": "Lammi", "given": "Mikko J", "initials": "MJ"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-03958-5", "pmid": "28623370", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:54:58.518Z", "modified": "2020-01-21T13:53:21.859Z"}, {"entity": "publication", "iuid": "04e76f0947204c27a9f2e4e51b7d1713", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e76f0947204c27a9f2e4e51b7d1713.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e76f0947204c27a9f2e4e51b7d1713"}}, "title": "STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.", "authors": [{"family": "Hochgerner", "given": "Hannah", "initials": "H", "orcid": "0000-0002-7739-666X", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b8fc33efd44cfb2bb60a3f250a518.json"}}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Hodge", "given": "Rebecca", "initials": "R"}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Heskol", "given": "Abeer", "initials": "A"}, {"family": "Hubschle", "given": "Hermann", "initials": "H"}, {"family": "Lin", "given": "Philip", "initials": "P"}, {"family": "Picelli", "given": "Simone", "initials": "S"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Ratz", "given": "Michael", "initials": "M"}, {"family": "Dunne", "given": "Jude", "initials": "J"}, {"family": "Husain", "given": "Syed", "initials": "S"}, {"family": "Lein", "given": "Ed", "initials": "E", "orcid": "0000-0001-9012-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd450c764a4431aa798630053343cd6.json"}}, {"family": "Srinivasan", "given": "Maithreyan", "initials": "M"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}], "type": "journal article", "published": "2017-11-27", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "16327", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform while retaining a high degree of flexibility, potentially also for other high-throughput applications.", "doi": "10.1038/s41598-017-16546-4", "pmid": "29180631", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5703850"}, {"db": "pii", "key": "10.1038/s41598-017-16546-4"}], "notes": [], "created": "2018-01-10T09:45:09.064Z", "modified": "2024-01-21T18:00:22.804Z"}, {"entity": "publication", "iuid": "10063878eda648f79dc68fd0c818180e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10063878eda648f79dc68fd0c818180e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10063878eda648f79dc68fd0c818180e"}}, "title": "Dog ownership and the risk of cardiovascular disease and death - a nationwide cohort study.", "authors": [{"family": "Mubanga", "given": "Mwenya", "initials": "M"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Nowak", "given": "Christoph", "initials": "C"}, {"family": "Egenvall", "given": "Agneta", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}], "type": "journal article", "published": "2017-11-17", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15821", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Dogs may be beneficial in reducing cardiovascular risk in their owners by providing social support and motivation for physical activity. We aimed to investigate the association of dog ownership with incident cardiovascular disease (CVD) and death in a register-based prospective nation-wide cohort (n = 3,432,153) with up to 12 years of follow-up. Self-reported health and lifestyle habits were available for 34,202 participants in the Swedish Twin Register. Time-to-event analyses with time-updated covariates were used to calculate hazard ratios (HR) with 95% confidence intervals (CI). In single- and multiple-person households, dog ownership (13.1%) was associated with lower risk of death, HR 0.67 (95% CI, 0.65-0.69) and 0.89 (0.87-0.91), respectively; and CVD death, HR 0.64 (0.59-0.70), and 0.85 (0.81-0.90), respectively. In single-person households, dog ownership was inversely associated with cardiovascular outcomes (HR composite CVD 0.92, 95% CI, 0.89-0.94). Ownership of hunting breed dogs was associated with lowest risk of CVD. Further analysis in the Twin Register could not replicate the reduced risk of CVD or death but also gave no indication of confounding by disability, comorbidities or lifestyle factors. In conclusion, dog ownership appears to be associated with lower risk of CVD in single-person households and lower mortality in the general population.", "doi": "10.1038/s41598-017-16118-6", "pmid": "29150678", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-16118-6"}, {"db": "pmc", "key": "PMC5693989"}], "notes": [], "created": "2017-11-22T08:32:46.202Z", "modified": "2021-06-21T15:00:47.391Z"}, {"entity": "publication", "iuid": "86b4dfef19e14e50a0aa6009e61cb8e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86b4dfef19e14e50a0aa6009e61cb8e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86b4dfef19e14e50a0aa6009e61cb8e7"}}, "title": "Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.", "authors": [{"family": "Hammarsj\u00f6", "given": "A", "initials": "A"}, {"family": "Wang", "given": "Z", "initials": "Z"}, {"family": "Vaz", "given": "R", "initials": "R"}, {"family": "Taylan", "given": "F", "initials": "F"}, {"family": "Sedghi", "given": "M", "initials": "M"}, {"family": "Girisha", "given": "K M", "initials": "KM"}, {"family": "Chitayat", "given": "D", "initials": "D"}, {"family": "Neethukrishna", "given": "K", "initials": "K"}, {"family": "Shannon", "given": "P", "initials": "P"}, {"family": "Godoy", "given": "R", "initials": "R"}, {"family": "Gowrishankar", "given": "K", "initials": "K"}, {"family": "Lindstrand", "given": "A", "initials": "A"}, {"family": "Nasiri", "given": "J", "initials": "J"}, {"family": "Baktashian", "given": "M", "initials": "M"}, {"family": "Newton", "given": "P T", "initials": "PT"}, {"family": "Guo", "given": "L", "initials": "L"}, {"family": "Hofmeister", "given": "W", "initials": "W"}, {"family": "Pettersson", "given": "M", "initials": "M"}, {"family": "Chagin", "given": "A S", "initials": "AS"}, {"family": "Nishimura", "given": "G", "initials": "G"}, {"family": "Yan", "given": "L", "initials": "L"}, {"family": "Matsumoto", "given": "N", "initials": "N"}, {"family": "Nordgren", "given": "A", "initials": "A"}, {"family": "Miyake", "given": "N", "initials": "N"}, {"family": "Grigelioniene", "given": "G", "initials": "G"}, {"family": "Ikegawa", "given": "S", "initials": "S"}], "type": "journal article", "published": "2017-11-14", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15585", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The skeletal ciliopathies are a heterogeneous group of disorders with a significant clinical and genetic variability and the main clinical features are thoracic hypoplasia and short tubular bones. To date, 25 genes have been identified in association with skeletal ciliopathies. Mutations in the KIAA0753 gene have recently been associated with Joubert syndrome\u00a0(JBTS) and orofaciodigital (OFD) syndrome. We report biallelic pathogenic variants in KIAA0753 in four patients with short-rib type skeletal dysplasia. The manifestations in our patients are variable and ranging from fetal lethal to viable and moderate skeletal dysplasia with narrow thorax and abnormal metaphyses. We demonstrate that KIAA0753 is expressed in normal fetal human growth plate and show that the affected fetus, with a compound heterozygous frameshift and a nonsense mutation in KIAA0753, has an abnormal proliferative zone and a broad hypertrophic zone. The importance of KIAA0753 for normal skeletal development is further confirmed by our findings that zebrafish embryos homozygous for a nonsense mutation in kiaa0753 display altered cartilage patterning.", "doi": "10.1038/s41598-017-15442-1", "pmid": "29138412", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-15442-1"}, {"db": "pmc", "key": "PMC5686170"}], "notes": [], "created": "2018-01-10T09:44:15.685Z", "modified": "2020-01-21T13:56:11.126Z"}, {"entity": "publication", "iuid": "322d19d8a8f24583bfce02ae7f8a2aa2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/322d19d8a8f24583bfce02ae7f8a2aa2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/322d19d8a8f24583bfce02ae7f8a2aa2"}}, "title": "Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema.", "authors": [{"family": "Ega\u00f1a", "given": "Isabel", "initials": "I"}, {"family": "Kaito", "given": "Hiroshi", "initials": "H"}, {"family": "Nitzsche", "given": "Anja", "initials": "A"}, {"family": "Becker", "given": "Lore", "initials": "L"}, {"family": "Ballester-Lopez", "given": "Carolina", "initials": "C"}, {"family": "Niaudet", "given": "Colin", "initials": "C"}, {"family": "Petkova", "given": "Milena", "initials": "M"}, {"family": "Liu", "given": "Wei", "initials": "W"}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M"}, {"family": "Vernaleken", "given": "Alexandra", "initials": "A"}, {"family": "Klopstock", "given": "Thomas", "initials": "T"}, {"family": "Fuchs", "given": "Helmut", "initials": "H"}, {"family": "Gailus-Durner", "given": "Valerie", "initials": "V"}, {"family": "Hrabe de Angelis", "given": "Martin", "initials": "M"}, {"family": "Rask-Andersen", "given": "Helge", "initials": "H"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Yildirim", "given": "Ali \u00d6", "initials": "A\u00d6"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "German Mouse Clinic Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-11-13", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15453", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Paladin (Pald1, mKIAA1274 or x99384) was identified in screens for vascular-specific genes and is a putative phosphatase. Paladin has also been proposed to be involved in various biological processes such as insulin signaling, innate immunity and neural crest migration. To determine the role of paladin we have now characterized the Pald1 knock-out mouse in a broad array of behavioral, physiological and biochemical tests. Here, we show that female, but not male, Pald1 heterozygous and homozygous knock-out mice display an emphysema-like histology with increased alveolar air spaces and impaired lung function with an obstructive phenotype. In contrast to many other tissues where Pald1 is restricted to the vascular compartment, Pald1 is expressed in both the epithelial and mesenchymal compartments of the postnatal lung. However, in Pald1 knock-out females, there is a specific increase in apoptosis and proliferation of endothelial cells, but not in non-endothelial cells. This results in a transient reduction of endothelial cells in the maturing lung. Our data suggests that Pald1 is required during lung vascular development and for normal function of the developing and adult lung in a sex-specific manner. To our knowledge, this is the first report of a sex-specific effect on endothelial cell apoptosis.", "doi": "10.1038/s41598-017-14894-9", "pmid": "29133847", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-14894-9"}, {"db": "pmc", "key": "PMC5684320"}], "notes": [], "created": "2017-12-05T16:14:22.822Z", "modified": "2021-07-08T11:36:15.159Z"}, {"entity": "publication", "iuid": "15afba9fe77f49b9a4b972893156fd87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15afba9fe77f49b9a4b972893156fd87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15afba9fe77f49b9a4b972893156fd87"}}, "title": "Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51.", "authors": [{"family": "Kumar", "given": "Rajnish", "initials": "R"}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Pavlov", "given": "Pavel F", "initials": "PF"}], "type": "journal article", "published": "2017-10-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "14288", "issn-l": "2045-2322"}, "abstract": "FK506 binding protein of 51\u2009kDa (FKBP51) is a heat shock protein 90 (Hsp90) co-chaperone involved in the regulation of steroid hormone receptors activity. It is known for its role in various regulatory pathways implicated in mood and stress-related disorders, cancer, obesity, Alzheimer's disease and corticosteroid resistant asthma. It consists of two FKBP12 like active peptidyl prolyl isomerase (PPIase) domains (an active FK1 and inactive FK2 domain) and one tetratricopeptide repeat (TPR) domain that mediates interaction with Hsp90 via its C-terminal MEEVD peptide. Here, we report a combined x-ray crystallography and molecular dynamics study to reveal the binding mechanism of Hsp90 MEEVD peptide to the TPR domain of FKBP51. The results demonstrated that the Hsp90 C-terminal peptide binds to the TPR domain of FKBP51 with the help of di-carboxylate clamp involving Lys272, Glu273, Lys352, Asn322, and Lys329 which are conserved throughout several di-carboxylate clamp TPR proteins. Interestingly, the results from molecular dynamics study are also in agreement to the complex structure where all the contacts between these two partners were consistent throughout the simulation period. In a nutshell, our findings provide new opportunity to engage this important protein-protein interaction target by small molecules designed by structure based drug design strategy.", "doi": "10.1038/s41598-017-14731-z", "pmid": "29079741", "labels": {"Protein Science Facility (PSF)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-14731-z"}], "notes": [], "created": "2017-10-30T11:35:55.545Z", "modified": "2017-10-30T11:35:55.556Z"}, {"entity": "publication", "iuid": "20350e23da2b43b187e363633928219f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20350e23da2b43b187e363633928219f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20350e23da2b43b187e363633928219f"}}, "title": "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo.", "authors": [{"family": "Saravanan", "given": "Rathi", "initials": "R"}, {"family": "Adav", "given": "Sunil S", "initials": "SS"}, {"family": "Choong", "given": "Yeu Khai", "initials": "YK"}, {"family": "van der Plas", "given": "Mariena J A", "initials": "MJA"}, {"family": "Petrlova", "given": "Jitka", "initials": "J"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Sze", "given": "Siu Kwan", "initials": "SK"}, {"family": "Schmidtchen", "given": "Artur", "initials": "A"}], "type": "journal article", "published": "2017-10-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "13136", "issn-l": "2045-2322"}, "abstract": "The disease burden of failing skin repair and non-healing ulcers is extensive. There is an unmet need for new diagnostic approaches to better predict healing activity and wound infection. Uncontrolled and excessive protease activity, of endogenous or bacterial origin, has been described as a major contributor to wound healing impairments. Proteolytic peptide patterns could therefore correlate and \"report\" healing activity and infection. This work describes a proof of principle delineating a strategy by which peptides from a selected protein, human thrombin, are detected and attributed to proteolytic actions. With a particular focus on thrombin-derived C-terminal peptides (TCP), we show that distinct peptide patterns are generated in vitro by the human S1 peptidases human neutrophil elastase and cathepsin G, and the bacterial M4 peptidases Pseudomonas aeruginosa elastase and Staphylococcus aureus aureolysin, respectively. Corresponding peptide sequences were identified in wound fluids from acute and non-healing ulcers, and notably, one peptide, FYT21 (FYTHVFRLKKWIQKVIDQFGE), was only present in wound fluid from non-healing ulcers colonized by P. aeruginosa and S. aureus. Our result is a proof of principle pointing at the possibility of defining peptide biomarkers reporting distinct proteolytic activities, of potential implication for improved diagnosis of wound healing and infection.", "doi": "10.1038/s41598-017-13197-3", "pmid": "29030565", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-13197-3"}, {"db": "pmc", "key": "PMC5640616"}], "notes": [], "created": "2020-01-27T10:03:54.414Z", "modified": "2021-05-24T15:39:50.141Z"}, {"entity": "publication", "iuid": "dccc5b57e965405481a268f2e6289c07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dccc5b57e965405481a268f2e6289c07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dccc5b57e965405481a268f2e6289c07"}}, "title": "Lubricin binds cartilage proteins, cartilage oligomeric matrix protein, fibronectin and collagen II at the cartilage surface.", "authors": [{"family": "Flowers", "given": "Sarah A", "initials": "SA"}, {"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "\u00d6rnros", "given": "Jessica", "initials": "J"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Rolfson", "given": "Ola", "initials": "O"}, {"family": "Bj\u00f6rkman", "given": "Lena I", "initials": "LI"}, {"family": "Eisler", "given": "Thomas", "initials": "T"}, {"family": "Kalamajski", "given": "Sebastian", "initials": "S"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2017-10-13", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "13149", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Lubricin, a heavily O-glycosylated protein, is essential for boundary lubrication of articular cartilage. Strong surface adherence of lubricin is required given the extreme force it must withstand. Disulfide bound complexes of lubricin and cartilage oligomeric matrix protein (COMP) have recently been identified in arthritic synovial fluid suggesting they may be lost from the cartilage surface in osteoarthritis and inflammatory arthritis. This investigation was undertaken to localise COMP-lubricin complexes within cartilage and investigate if other cartilage proteins are involved in anchoring lubricin to the joint. Immunohistochemical analysis of human cartilage biopsies showed lubricin and COMP co-localise to the cartilage surface. COMP knockout mice, however, presented with a lubricin layer on the articular cartilage leading to the further investigation of additional lubricin binding mechanisms. Proximity ligation assays (PLA) on human cartilage biopsies was used to localise additional lubricin binding partners and demonstrated that lubricin bound COMP, but also fibronectin and collagen II on the cartilage surface. Fibronectin and collagen II binding to lubricin was confirmed and characterised by solid phase binding assays with recombinant lubricin fragments. Overall, COMP, fibronectin and collagen II bind lubricin, exposed on the articular cartilage surface suggesting they may be involved in maintaining essential boundary lubrication.", "doi": "10.1038/s41598-017-13558-y", "pmid": "29030641", "labels": {"PLA and Single Cell Proteomics": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative", "Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-13558-y"}, {"db": "pmc", "key": "PMC5640667"}], "notes": [], "created": "2017-11-02T14:29:24.618Z", "modified": "2024-01-16T13:46:32.458Z"}, {"entity": "publication", "iuid": "0531312ee42d448cb3d9ac4c140ea664", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0531312ee42d448cb3d9ac4c140ea664.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0531312ee42d448cb3d9ac4c140ea664"}}, "title": "Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.", "authors": [{"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Felldin", "given": "Ulrika", "initials": "U"}, {"family": "L\u00f6fling", "given": "Marie", "initials": "M"}, {"family": "Fernandez Navarro", "given": "Jos\u00e9", "initials": "J"}, {"family": "Maaskola", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-9039-6023", "researcher": {"href": "https://publications.scilifelab.se/researcher/632b5a1e903240d5a0bf0ccbe13a1890.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2017-10-11", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "12941", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.", "doi": "10.1038/s41598-017-13462-5", "pmid": "29021611", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-13462-5"}, {"db": "pmc", "key": "PMC5636908"}], "notes": [], "created": "2017-11-03T16:20:56.701Z", "modified": "2024-01-16T13:48:47.424Z"}, {"entity": "publication", "iuid": "52d76d09eecb42a7a4304b6c9869ef23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52d76d09eecb42a7a4304b6c9869ef23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52d76d09eecb42a7a4304b6c9869ef23"}}, "title": "Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).", "authors": [{"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Tobias", "given": "Joshua", "initials": "J"}, {"family": "Wiklund", "given": "Gudrun", "initials": "G"}, {"family": "Nordqvist", "given": "Stefan", "initials": "S"}, {"family": "Aslett", "given": "Martin", "initials": "M"}, {"family": "Dougan", "given": "Gordon", "initials": "G"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}], "type": "journal article", "published": "2017-10-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "12514", "issn-l": "2045-2322"}, "abstract": "The ability to colonize the small intestine is essential for enterotoxigenic Escherichia coli (ETEC) to cause diarrhea. Although 22 antigenically different colonization factors (CFs) have been identified and characterized in ETEC at least 30% of clinical ETEC isolates lack known CFs. Ninety-four whole genome sequenced \"CF negative\" isolates were searched for novel CFs using a reverse genetics approach followed by phenotypic analyses. We identified a novel CF, CS30, encoded by a set of seven genes, csmA-G, related to the human CF operon CS18 and the porcine CF operon 987P (F6). CS30 was shown to be thermo-regulated, expressed at 37 \u00b0C, but not at 20 \u00b0C, by SDS-page and mass spectrometry analyses as well as electron microscopy imaging. Bacteria expressing CS30 were also shown to bind to differentiated human intestinal Caco-2 cells. The genes encoding CS30 were located on a plasmid (E873p3) together with the genes encoding LT and STp. PCR screening of ETEC isolates revealed that 8.6% (n = 13) of \"CF negative\" (n = 152) and 19.4% (n = 13) of \"CF negative\" LT + STp (n = 67) expressing isolates analyzed harbored CS30. Hence, we conclude that CS30 is common among \"CF negative\" LT + STp isolates and is associated with ETEC that cause diarrhea.", "doi": "10.1038/s41598-017-12743-3", "pmid": "28970563", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-12743-3"}, {"db": "pmc", "key": "PMC5624918"}], "notes": [], "created": "2020-01-30T16:00:46.181Z", "modified": "2024-01-16T13:46:32.470Z"}, {"entity": "publication", "iuid": "1e2ade93efce4c0f8d791467a61493cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb"}}, "title": "Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.", "authors": [{"family": "Verma", "given": "Deepti", "initials": "D"}, {"family": "Parasa", "given": "Venkata Ramanarao", "initials": "VR"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J"}, {"family": "Martis", "given": "Mihaela", "initials": "M"}, {"family": "Mehta", "given": "Ratnesh B", "initials": "RB"}, {"family": "Netea", "given": "Mihai", "initials": "M"}, {"family": "Lerm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2017-09-26", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "12305", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The reason for the largely variable protective effect against TB of the vaccine Bacille Calmette-Guerin (BCG) is not understood. In this study, we investigated whether epigenetic mechanisms are involved in the response of immune cells to the BCG vaccine. We isolated peripheral blood mononuclear cells (PBMCs) from BCG-vaccinated subjects and performed global DNA methylation analysis in combination with functional assays representative of innate immunity against Mycobacterium tuberculosis infection. Enhanced containment of replication was observed in monocyte-derived macrophages from a sub-group of BCG-vaccinated individuals (identified as 'responders'). A stable and robust differential DNA methylation pattern in response to BCG could be observed in PBMCs isolated from the responders but not from the non-responders. Gene ontology analysis revealed that promoters with altered DNA methylation pattern were strongly enriched among genes belonging to immune pathways in responders, however no enrichments could be observed in the non-responders. Our findings suggest that BCG-induced epigenetic reprogramming of immune cell function can enhance anti-mycobacterial immunity in macrophages. Understanding why BCG induces this response in responders but not in non-responders could provide clues to improvement of TB vaccine efficacy.", "doi": "10.1038/s41598-017-12110-2", "pmid": "28951586", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-12110-2"}, {"db": "pmc", "key": "PMC5615063"}], "notes": [], "created": "2017-10-25T15:27:48.394Z", "modified": "2024-01-16T13:48:47.507Z"}, {"entity": "publication", "iuid": "05b4dacde1b34c7db34d7a6b147d1346", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05b4dacde1b34c7db34d7a6b147d1346.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05b4dacde1b34c7db34d7a6b147d1346"}}, "title": "Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.", "authors": [{"family": "Yu", "given": "Nancy Y", "initials": "NY"}, {"family": "Bieder", "given": "Andrea", "initials": "A"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Mileti", "given": "Enrichetta", "initials": "E"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Fredholm", "given": "Bertil B", "initials": "BB"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Tapia-P\u00e1ez", "given": "Isabel", "initials": "I"}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2017-09-13", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "11458", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Caffeine is a widely consumed psychoactive substance, but little is known about the effects of caffeine stimulation on global gene expression changes in neurons. Here, we conducted gene expression profiling of human neuroepithelial stem cell-derived neurons, stimulated with normal consumption levels of caffeine (3\u2009\u03bcM and 10\u2009\u03bcM), over a period of 9\u2009h. We found dosage-dependent activation of immediate early genes after 1\u2009h. Neuronal projection development processes were up-regulated and negative regulation of axon extension processes were down-regulated at 3\u2009h. In addition, genes involved in extracellular matrix organization, response for wound healing, and regulation of immune system processes were down-regulated by caffeine at 3\u2009h. This study identified novel genes within the neuronal projection guidance pathways that respond to acute caffeine stimulation and suggests potential mechanisms for the effects of caffeine on neuronal cells.", "doi": "10.1038/s41598-017-11574-6", "pmid": "28904364", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-11574-6"}, {"db": "pmc", "key": "PMC5597620"}, {"db": "BioProject", "description": "raw RNA-seq", "key": "PRJEB20092"}], "notes": [], "created": "2017-11-03T16:18:37.631Z", "modified": "2024-01-16T13:48:47.529Z"}, {"entity": "publication", "iuid": "dd70e362cb6943229c091af5a0fe1185", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd70e362cb6943229c091af5a0fe1185.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd70e362cb6943229c091af5a0fe1185"}}, "title": "Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.", "authors": [{"family": "Amlinger", "given": "Lina", "initials": "L"}, {"family": "Hoekzema", "given": "Mirthe", "initials": "M"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "Lundgren", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1122-3352", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e56842987ca489ba79c0606d9ce6849.json"}}], "type": "journal article", "published": "2017-09-04", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10392", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.", "doi": "10.1038/s41598-017-10876-z", "pmid": "28871175", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10876-z"}, {"db": "pmc", "key": "PMC5583386"}], "notes": [], "created": "2017-10-17T09:52:30.751Z", "modified": "2024-01-16T13:48:47.536Z"}, {"entity": "publication", "iuid": "7168010a658143b6885ba6d7ded87f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7168010a658143b6885ba6d7ded87f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7168010a658143b6885ba6d7ded87f69"}}, "title": "Neuroblastoma patient-derived xenograft cells cultured in stem-cell promoting medium retain tumorigenic and metastatic capacities but differentiate in serum.", "authors": [{"family": "Persson", "given": "Camilla U", "initials": "CU"}, {"family": "von Stedingk", "given": "Kristoffer", "initials": "K"}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Merselius", "given": "My", "initials": "M"}, {"family": "Braekeveldt", "given": "No\u00e9mie", "initials": "N"}, {"family": "Gisselsson", "given": "David", "initials": "D"}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M"}, {"family": "P\u00e5hlman", "given": "Sven", "initials": "S"}, {"family": "Wigerup", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2017-08-31", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10274", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cultured cancer cells serve as important models for preclinical testing of anti-cancer compounds. However, the optimal conditions for retaining original tumor features during in vitro culturing of cancer cells have not been investigated in detail. Here we show that serum-free conditions are critical for maintaining an immature phenotype of neuroblastoma cells isolated from orthotopic patient-derived xenografts (PDXs). PDX cells could be grown either as spheres or adherent on laminin in serum-free conditions with retained patient-specific genomic aberrations as well as tumorigenic and metastatic capabilities. However, addition of serum led to morphological changes, neuronal differentiation and reduced cell proliferation. The epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) were central for PDX cell proliferation and MYCN expression, and also hindered the serum-induced differentiation. Although serum induced a robust expression of neurotrophin receptors, stimulation with their cognate ligands did not induce further sympathetic differentiation, which likely reflects a block in PDX cell differentiation capacity coupled to their tumor genotype. Finally, PDX cells cultured as spheres or adherent on laminin responded similarly to various cytotoxic drugs, suggesting that both conditions are suitable in vitro screening models for neuroblastoma-targeting compounds.", "doi": "10.1038/s41598-017-09662-8", "pmid": "28860499", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09662-8"}, {"db": "pmc", "key": "PMC5579187"}], "notes": [], "created": "2017-10-17T09:34:44.876Z", "modified": "2020-01-21T13:56:06.568Z"}, {"entity": "publication", "iuid": "fd24c7f3c9d14b86bcabb5a7734c46a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd24c7f3c9d14b86bcabb5a7734c46a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd24c7f3c9d14b86bcabb5a7734c46a5"}}, "title": "A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors.", "authors": [{"family": "Br\u00e6nne", "given": "Ingrid", "initials": "I"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Reiz", "given": "Benedikt", "initials": "B"}, {"family": "Kleinecke", "given": "Mariana", "initials": "M"}, {"family": "von Ameln", "given": "Simon", "initials": "S"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}], "type": "journal article", "published": "2017-08-31", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10252", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cyclooxygenase-2 inhibitors (coxibs) are characterized by multiple molecular off-target effects and increased coronary artery disease (CAD) risk. Here, we systematically explored common variants of genes representing molecular targets of coxibs for association with CAD. Given a broad spectrum of pleiotropic effects of coxibs, our intention was to narrow potential mechanisms affecting CAD risk as we hypothesized that the affected genes may also display genomic signals of coronary disease risk. A Drug Gene Interaction Database search identified 47 gene products to be affected by coxibs. We traced association signals in 200-kb regions surrounding these genes in 84,813 CAD cases and 202,543 controls. Based on a threshold of 1\u2009\u00d7\u200910(-5) (Bonferroni correction for 3131 haplotype blocks), four gene loci yielded significant associations. The lead SNPs were rs7270354 (MMP9), rs4888383 (BCAR1), rs6905288 (VEGFA1), and rs556321 (CACNA1E). By additional genotyping, rs7270354 at MMP9 and rs4888383 at BCAR1 also reached the established GWAS threshold for genome-wide significance. The findings demonstrate overlap of genes affected by coxibs and those mediating CAD risk and points to further mechanisms, which are potentially responsible for coxib-associated CAD risk. The novel approach furthermore suggests that genetic studies may be useful to explore the clinical relevance of off-target drug effects.", "doi": "10.1038/s41598-017-10928-4", "pmid": "28860667", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10928-4"}, {"db": "pmc", "key": "PMC5579257"}], "notes": [], "created": "2017-10-25T15:27:50.730Z", "modified": "2024-01-16T13:48:47.586Z"}, {"entity": "publication", "iuid": "5521219aa1794ec98838a8591df79469", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469"}}, "title": "Cerium oxide nanoparticles inhibit differentiation of neural stem cells.", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Edoff", "given": "Karin", "initials": "K"}, {"family": "Caputo", "given": "Fanny", "initials": "F"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}, {"family": "Ghibelli", "given": "Lina", "initials": "L"}, {"family": "Traversa", "given": "Enrico", "initials": "E"}, {"family": "Ceccatelli", "given": "Sandra", "initials": "S"}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "9284", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cerium oxide nanoparticles (nanoceria) display antioxidant properties and have shown cytoprotective effects both in vitro and in vivo. Here, we explored the effects of nanoceria on neural progenitor cells using the C17.2 murine cell line as a model. First, we assessed the effects of nanoceria versus samarium (Sm) doped nanoceria on cell viability in the presence of the prooxidant, DMNQ. Both particles were taken up by cells and nanoceria, but not Sm-doped nanoceria, elicited a temporary cytoprotective effect upon exposure to DMNQ. Next, we employed RNA sequencing to explore the transcriptional responses induced by nanoceria or Sm-doped nanoceria during neuronal differentiation. Detailed computational analyses showed that nanoceria altered pathways and networks relevant for neuronal development, leading us to hypothesize that nanoceria inhibits neuronal differentiation, and that nanoceria and Sm-doped nanoceria both interfere with cytoskeletal organization. We confirmed that nanoceria reduced neuron specific \u03b23-tubulin expression, a marker of neuronal differentiation, and GFAP, a neuroglial marker. Furthermore, using super-resolution microscopy approaches, we could show that both particles interfered with cytoskeletal organization and altered the structure of neural growth cones. Taken together, these results reveal that nanoceria may impact on neuronal differentiation, suggesting that nanoceria could pose a developmental neurotoxicity hazard.", "doi": "10.1038/s41598-017-09430-8", "pmid": "28839176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Integrated Microscopy Technologies Stockholm": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09430-8"}, {"db": "pmc", "key": "PMC5570910"}, {"db": "ArrayExpress", "description": "raw RNA-seq", "key": "E-MTAB-4398"}], "notes": [], "created": "2017-10-05T09:22:50.002Z", "modified": "2021-07-05T13:48:51.542Z"}, {"entity": "publication", "iuid": "964b8cd9b8d4479290d16cee188d3b8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/964b8cd9b8d4479290d16cee188d3b8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/964b8cd9b8d4479290d16cee188d3b8c"}}, "title": "Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry.", "authors": [{"family": "Rolandsson Enes", "given": "Sara", "initials": "S"}, {"family": "\u00c5hrman", "given": "Emma", "initials": "E"}, {"family": "Palani", "given": "Anitha", "initials": "A"}, {"family": "Hallgren", "given": "Oskar", "initials": "O"}, {"family": "Bjermer", "given": "Leif", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Scheding", "given": "Stefan", "initials": "S"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G"}], "type": "comparative study", "published": "2017-08-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "9316", "issn-l": "2045-2322"}, "abstract": "Mesenchymal stromal cells (MSC) are ideal candidates for cell therapies, due to their immune-regulatory and regenerative properties. We have previously reported that lung-derived MSC are tissue-resident cells with lung-specific properties compared to bone marrow-derived MSC. Assessing relevant molecular differences between lung-MSC and bone marrow-MSC is important, given that such differences may impact their behavior and potential therapeutic use. Here, we present an in-depth mass spectrometry (MS) based strategy to investigate the proteomes of lung-MSC and bone marrow-MSC. The MS-strategy relies on label free quantitative data-independent acquisition (DIA) analysis and targeted data analysis using a MSC specific spectral library. We identified several significantly differentially expressed proteins between lung-MSC and bone marrow-MSC within the cell layer (352 proteins) and in the conditioned medium (49 proteins). Bioinformatics analysis revealed differences in regulation of cell proliferation, which was functionally confirmed by decreasing proliferation rate through Cytochrome P450 stimulation. Our study reveals important differences within proteome and matrisome profiles between lung- and bone marrow-derived MSC that may influence their behavior and affect the clinical outcome when used for cell-therapy.", "doi": "10.1038/s41598-017-09127-y", "pmid": "28839187", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09127-y"}, {"db": "pmc", "key": "PMC5570998"}], "notes": [], "created": "2020-01-27T10:14:39.128Z", "modified": "2021-05-24T15:39:50.294Z"}, {"entity": "publication", "iuid": "c000b2d71662419d80ada5c60423b8dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c000b2d71662419d80ada5c60423b8dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c000b2d71662419d80ada5c60423b8dd"}}, "title": "Identification of NCAN as a candidate gene for developmental dyslexia.", "authors": [{"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Peyrard-Janvid", "given": "Myriam", "initials": "M"}, {"family": "Darki", "given": "Fahimeh", "initials": "F"}, {"family": "Tuulari", "given": "Jetro J", "initials": "JJ"}, {"family": "Merisaari", "given": "Harri", "initials": "H", "orcid": "0000-0002-8515-5399", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca8ef9e0084e48db88fd47fd51dd23a4.json"}}, {"family": "Karlsson", "given": "Linnea", "initials": "L"}, {"family": "Scheinin", "given": "Noora M", "initials": "NM"}, {"family": "Saunavaara", "given": "Jani", "initials": "J"}, {"family": "Parkkola", "given": "Riitta", "initials": "R"}, {"family": "Kantoj\u00e4rvi", "given": "Katri", "initials": "K"}, {"family": "\u00c4mm\u00e4l\u00e4", "given": "Antti-Jussi", "initials": "AJ"}, {"family": "Yiu-Lin Yu", "given": "Nancy", "initials": "N", "orcid": "0000-0001-8321-8141", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff7b0ebe0de64edca6546aff2292c376.json"}}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Nopola-Hemmi", "given": "Jaana", "initials": "J"}, {"family": "Karlsson", "given": "Hasse", "initials": "H"}, {"family": "Paunio", "given": "Tiina", "initials": "T"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}, {"family": "Leinonen", "given": "Eira", "initials": "E"}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "9294", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A whole-genome linkage analysis in a Finnish pedigree of eight cases with developmental dyslexia (DD) revealed several regions shared by the affected individuals. Analysis of coding variants from two affected individuals identified rs146011974G > A (Ala1039Thr), a rare variant within the NCAN gene co-segregating with DD in the pedigree. This variant prompted us to consider this gene as a putative candidate for DD. The RNA expression pattern of the NCAN gene in human tissues was highly correlated (R > 0.8) with that of the previously suggested DD susceptibility genes KIAA0319, CTNND2, CNTNAP2 and GRIN2B. We investigated the association of common variation in NCAN to brain structures in two data sets: young adults (Brainchild study, Sweden) and infants (FinnBrain study, Finland). In young adults, we found associations between a common genetic variant in NCAN, rs1064395, and white matter volume in the left and right temporoparietal as well as the left inferior frontal brain regions. In infants, this same variant was found to be associated with cingulate and prefrontal grey matter volumes. Our results suggest NCAN as a new candidate gene for DD and indicate that NCAN variants affect brain structure.", "doi": "10.1038/s41598-017-10175-7", "pmid": "28839234", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10175-7"}, {"db": "pmc", "key": "PMC5570950"}], "notes": [], "created": "2017-10-17T09:24:33.409Z", "modified": "2024-01-16T13:48:47.593Z"}, {"entity": "publication", "iuid": "b41ba5e6c6044499b5c69eb35fec418c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b41ba5e6c6044499b5c69eb35fec418c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b41ba5e6c6044499b5c69eb35fec418c"}}, "title": "Identification of bacterial biofilm and the Staphylococcus aureus derived protease, staphopain, on the skin surface of patients with atopic dermatitis.", "authors": [{"family": "Sonesson", "given": "Andreas", "initials": "A"}, {"family": "Przybyszewska", "given": "Kornelia", "initials": "K"}, {"family": "Eriksson", "given": "Sigrid", "initials": "S"}, {"family": "M\u00f6rgelin", "given": "Matthias", "initials": "M"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Davies", "given": "Julia", "initials": "J"}, {"family": "Potempa", "given": "Jan", "initials": "J"}, {"family": "Schmidtchen", "given": "Artur", "initials": "A"}], "type": "journal article", "published": "2017-08-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "8689", "issn-l": "2045-2322"}, "abstract": "Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by an impaired epidermal barrier, dysregulation of innate and adaptive immunity, and a high susceptibility to bacterial colonization and infection. In the present study, bacterial biofilm was visualized by electron microscopy at the surface of AD skin. Correspondingly, Staphylococcus aureus (S. aureus) isolates from lesional skin of patients with AD, produced a substantial amount of biofilm in vitro. S. aureus biofilms showed less susceptibility to killing by the antimicrobial peptide LL-37 when compared with results obtained using planktonic cells. Confocal microscopy analysis showed that LL-37 binds to the S. aureus biofilms. Immuno-gold staining of S. aureus biofilm of AD skin detected the S. aureus derived protease staphopain adjacent to the bacteria. In vitro, staphopain B degraded LL-37 into shorter peptide fragments. Further, LL-37 significantly inhibited S. aureus biofilm formation, but no such effects were observed for the degradation products. The data presented here provide novel information on staphopains present in S. aureus biofilms in vivo, and illustrate the complex interplay between biofilm and LL-37 in skin of AD patients, possibly leading to a disturbed host defense, which facilitates bacterial persistence.", "doi": "10.1038/s41598-017-08046-2", "pmid": "28821865", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-08046-2"}, {"db": "pmc", "key": "PMC5562790"}], "notes": [], "created": "2020-01-27T10:04:35.026Z", "modified": "2021-05-24T15:39:50.372Z"}, {"entity": "publication", "iuid": "214fed5eee6944f5813ceee80a079e90", "links": {"self": {"href": "https://publications.scilifelab.se/publication/214fed5eee6944f5813ceee80a079e90.json"}, "display": {"href": "https://publications.scilifelab.se/publication/214fed5eee6944f5813ceee80a079e90"}}, "title": "Mass Spectrometry Imaging proves differential absorption profiles of well-characterised permeability markers along the crypt-villus axis.", "authors": [{"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Peric", "given": "Alexandra", "initials": "A"}, {"family": "Strimfors", "given": "Marie", "initials": "M"}, {"family": "Goodwin", "given": "Richard J A", "initials": "RJA"}, {"family": "Hayes", "given": "Martin A", "initials": "MA"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "Hilgendorf", "given": "Constanze", "initials": "C"}], "type": "journal article", "published": "2017-07-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "6352", "issn-l": "2045-2322"}, "abstract": "Knowledge about the region-specific absorption profiles from the gastrointestinal tract of orally administered drugs is a critical factor guiding dosage form selection in drug development. We have used a novel approach to study three well-characterized permeability and absorption marker drugs in the intestine. Propranolol and metoprolol (highly permeable compounds) and atenolol (low-moderate permeability compound) were orally co-administered to rats. The site of drug absorption was revealed by high spatial resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and complemented by quantitative measurement of drug concentration in tissue homogenates. MALDI-MSI identified endogenous molecular markers that illustrated the villi structures and confirmed the different absorption sites assigned to histological landmarks for the three drugs. Propranolol and metoprolol showed a rapid absorption and shorter transit distance in contrast to atenolol, which was absorbed more slowly from more distal sites. This study provides novel insights into site specific absorption for each of the compounds along the crypt-villus axis, as well as confirming a proximal-distal absorption gradient along the intestine. The combined analytical approach allowed the quantification and spatial resolution of drug distribution in the intestine and provided experimental evidence for the suggested absorption behaviour of low and highly permeable compounds.", "doi": "10.1038/s41598-017-06583-4", "pmid": "28743866", "labels": {"Spatial Mass Spectrometry": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-06583-4"}, {"db": "pmc", "key": "PMC5526999"}], "notes": [], "created": "2020-01-24T08:59:38.975Z", "modified": "2021-05-17T08:47:18.642Z"}, {"entity": "publication", "iuid": "3da58343c0134a8797edd61438e049be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3da58343c0134a8797edd61438e049be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3da58343c0134a8797edd61438e049be"}}, "title": "Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.", "authors": [{"family": "Neogi", "given": "Ujjwal", "initials": "U"}, {"family": "Siddik", "given": "Abu Bakar", "initials": "AB"}, {"family": "Kalaghatgi", "given": "Prabhav", "initials": "P"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Bratt", "given": "G\u00f6ran", "initials": "G"}, {"family": "Marrone", "given": "Gaetano", "initials": "G"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "6371", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A temporal increase in non-B subtypes has earlier been described in Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex and unique recombinant forms (URFs) if the epidemics converge. In the present study, we performed subtyping using four automated tools and phylogenetic analysis by RAxML of pol gene sequences (n\u2009=\u20095246) and HIV-1 near full-length genome (HIV-NFLG) sequences (n\u2009=\u2009104). A CD4+ T-cell decline trajectory algorithm was used to estimate time of HIV infection. Transmission clusters were identified using the family-joining method. The analysis of HIV-NFLG and pol gene described 10.6% (11/104) and 2.6% (137/5246) of the strains as URFs, respectively. An increasing trend of URFs was observed in recent years by both approaches (p\u2009=\u20090\u00b70082; p\u2009<\u20090\u00b70001). Transmission cluster analysis using the pol gene of all URFs identified 14 clusters with two to eight sequences. Larger transmission clusters of URFs (BF1 and 01B) were observed among MSM who mostly were sero-diagnosed in recent time. Understanding the increased appearance and transmission of URFs in recent years could have importance for public health interventions and the use of HIV-NFLG would provide better statistical support for such assessments.", "doi": "10.1038/s41598-017-06860-2", "pmid": "28744024", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-06860-2"}, {"db": "pmc", "key": "PMC5527090"}], "notes": [], "created": "2018-01-10T09:44:11.655Z", "modified": "2020-01-21T13:56:10.864Z"}, {"entity": "publication", "iuid": "d02a556562e44a34b6ef847d62486f9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d02a556562e44a34b6ef847d62486f9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d02a556562e44a34b6ef847d62486f9a"}}, "title": "Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered.", "authors": [{"family": "Koukalov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Amaro", "given": "Mariana", "initials": "M", "orcid": "0000-0002-4868-227X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b32679d78144a5b89cee7fecc2f0271.json"}}, {"family": "Aydogan", "given": "Gokcan", "initials": "G"}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-7380-8797", "researcher": {"href": "https://publications.scilifelab.se/researcher/85bd86ebc85d4653bc880bc9be25bc80.json"}}, {"family": "Williamson", "given": "Philip T F", "initials": "PTF", "orcid": "0000-0002-0231-8640", "researcher": {"href": "https://publications.scilifelab.se/researcher/034a75ccf4884c4ba4b2f9962734d693.json"}}, {"family": "Mikhalyov", "given": "Ilya", "initials": "I"}, {"family": "Hof", "given": "Martin", "initials": "M", "orcid": "0000-0003-2884-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ee7e14809ee4a579220428faa1cb058.json"}}, {"family": "\u0160achl", "given": "Radek", "initials": "R"}], "type": "journal article", "published": "2017-07-14", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "5460", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "It is a fundamental question in cell biology and biophysics whether sphingomyelin (SM)- and cholesterol (Chol)- driven nanodomains exist in living cells and in model membranes. Biophysical studies on model membranes revealed SM and Chol driven micrometer-sized liquid-ordered domains. Although the existence of such microdomains has not been proven for the plasma membrane, such lipid mixtures have been often used as a model system for 'rafts'. On the other hand, recent super resolution and single molecule results indicate that the plasma membrane might organize into nanocompartments. However, due to the limited resolution of those techniques their unambiguous characterization is still missing. In this work, a novel combination of F\u00f6rster resonance energy transfer and Monte Carlo simulations (MC-FRET) identifies directly 10 nm large nanodomains in liquid-disordered model membranes composed of lipid mixtures containing SM and Chol. Combining MC-FRET with solid-state wide-line and high resolution magic angle spinning NMR as well as with fluorescence correlation spectroscopy we demonstrate that these nanodomains containing hundreds of lipid molecules are fluid and disordered. In terms of their size, fluidity, order and lifetime these nanodomains may represent a relevant model system for cellular membranes and are closely related to nanocompartments suggested to exist in cellular membranes.", "doi": "10.1038/s41598-017-05539-y", "pmid": "28710349", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-05539-y"}, {"db": "pmc", "key": "PMC5511215"}], "notes": [], "created": "2017-11-02T17:26:50.120Z", "modified": "2025-10-17T13:03:59.712Z"}, {"entity": "publication", "iuid": "44e0dcce999c41adb598ab8a38a2cc4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44e0dcce999c41adb598ab8a38a2cc4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44e0dcce999c41adb598ab8a38a2cc4c"}}, "title": "Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.", "authors": [{"family": "Panizza", "given": "Elena", "initials": "E"}, {"family": "Branca", "given": "Rui M M", "initials": "RMM"}, {"family": "Oliviusson", "given": "Peter", "initials": "P"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2017-07-03", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "4513", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Protein phosphorylation is involved in the regulation of most eukaryotic cells functions and mass spectrometry-based analysis has made major contributions to our understanding of this regulation. However, low abundance of phosphorylated species presents a major challenge in achieving comprehensive phosphoproteome coverage and robust quantification. In this study, we developed a workflow employing titanium dioxide phospho-enrichment coupled with isobaric labeling by Tandem Mass Tags (TMT) and high-resolution isoelectric focusing (HiRIEF) fractionation to perform in-depth quantitative phosphoproteomics starting with a low sample quantity. To benchmark the workflow, we analyzed HeLa cells upon pervanadate treatment or cell cycle arrest in mitosis. Analyzing 300 \u00b5g of peptides per sample, we identified 22,712 phosphorylation sites, of which 19,075 were localized with high confidence and 1,203 are phosphorylated tyrosine residues, representing 6.3% of all detected phospho-sites. HiRIEF fractions with the most acidic isoelectric points are enriched in multiply phosphorylated peptides, which represent 18% of all the phospho-peptides detected in the pH range 2.5-3.7. Cross-referencing with the PhosphoSitePlus database reveals 1,264 phosphorylation sites that have not been previously reported and kinase association analysis suggests that a subset of these may be functional during the mitotic phase.", "doi": "10.1038/s41598-017-04798-z", "pmid": "28674419", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-04798-z"}, {"db": "pmc", "key": "PMC5495806"}], "notes": [], "created": "2017-12-05T16:14:26.493Z", "modified": "2021-07-08T11:36:15.117Z"}, {"entity": "publication", "iuid": "8debe2b674394b34846e436ba217e239", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8debe2b674394b34846e436ba217e239.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8debe2b674394b34846e436ba217e239"}}, "title": "SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.", "authors": [{"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Henning", "given": "Petra", "initials": "P"}, {"family": "Klar", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4185-7409", "researcher": {"href": "https://publications.scilifelab.se/researcher/3310cb2ab70f43d78cc7cd7e36ac8f83.json"}}, {"family": "McDermott", "given": "Emma", "initials": "E"}, {"family": "Stecksen-Blicks", "given": "Christina", "initials": "C"}, {"family": "Sandstr\u00f6m", "given": "Per-Erik", "initials": "PE"}, {"family": "Kellgren", "given": "Therese G", "initials": "TG"}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "L\u00f6nnerholm", "given": "Torsten", "initials": "T"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Helfrich", "given": "Miep H", "initials": "MH"}, {"family": "Coxon", "given": "Fraser P", "initials": "FP"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Wikstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Lerner", "given": "Ulf H", "initials": "UH"}], "type": "journal article", "published": "2017-06-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "3012", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Autosomal recessive osteopetrosis (ARO) is a heterogeneous disorder, characterized by defective osteoclastic resorption of bone that results in increased bone density. We have studied nine individuals with an intermediate form of ARO, from the county of V\u00e4sterbotten in Northern Sweden. All afflicted individuals had an onset in early infancy with optic atrophy, and in four patients anemia was present at diagnosis. Tonsillar herniation, foramen magnum stenosis, and severe osteomyelitis of the jaw were common clinical features. Whole exome sequencing, verified by Sanger sequencing, identified a splice site mutation c.212 + 1 G > T in the SNX10 gene encoding sorting nexin 10. Sequence analysis of the SNX10 transcript in patients revealed activation of a cryptic splice site in intron 4 resulting in a frame shift and a premature stop (p.S66Nfs * 15). Haplotype analysis showed that all cases originated from a single mutational event, and the age of the mutation was estimated to be approximately 950 years. Functional analysis of osteoclast progenitors isolated from peripheral blood of patients revealed that stimulation with receptor activator of nuclear factor kappa-B ligand (RANKL) resulted in a robust formation of large, multinucleated osteoclasts which generated sealing zones; however these osteoclasts exhibited defective ruffled borders and were unable to resorb bone in vitro.", "doi": "10.1038/s41598-017-02533-2", "pmid": "28592808", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-02533-2"}, {"db": "pmc", "key": "PMC5462793"}], "notes": [], "created": "2017-10-30T13:36:01.438Z", "modified": "2024-01-16T13:48:47.879Z"}, {"entity": "publication", "iuid": "986e55f889574733b2df4e85fba55ee5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/986e55f889574733b2df4e85fba55ee5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/986e55f889574733b2df4e85fba55ee5"}}, "title": "Mass spectrometry imaging identifies palmitoylcarnitine as an immunological mediator during Salmonella Typhimurium infection.", "authors": [{"family": "Hulme", "given": "Heather E", "initials": "HE"}, {"family": "Meikle", "given": "Lynsey M", "initials": "LM"}, {"family": "Wessel", "given": "Hannah", "initials": "H"}, {"family": "Strittmatter", "given": "Nicole", "initials": "N"}, {"family": "Swales", "given": "John", "initials": "J"}, {"family": "Thomson", "given": "Carolyn", "initials": "C"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Nibbs", "given": "Robert J B", "initials": "RJB"}, {"family": "Milling", "given": "Simon", "initials": "S"}, {"family": "Andren", "given": "Per E", "initials": "PE"}, {"family": "Mackay", "given": "C Logan", "initials": "CL"}, {"family": "Dexter", "given": "Alex", "initials": "A"}, {"family": "Bunch", "given": "Josephine", "initials": "J"}, {"family": "Goodwin", "given": "Richard J A", "initials": "RJA"}, {"family": "Burchmore", "given": "Richard", "initials": "R"}, {"family": "Wall", "given": "Daniel M", "initials": "DM"}], "type": "journal article", "published": "2017-06-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "2786", "issn-l": "2045-2322"}, "abstract": "Salmonella Typhimurium causes a self-limiting gastroenteritis that may lead to systemic disease. Bacteria invade the small intestine, crossing the intestinal epithelium from where they are transported to the mesenteric lymph nodes (MLNs) within migrating immune cells. MLNs are an important site at which the innate and adaptive immune responses converge but their architecture and function is severely disrupted during S. Typhimurium infection. To further understand host-pathogen interactions at this site, we used mass spectrometry imaging (MSI) to analyse MLN tissue from a murine model of S. Typhimurium infection. A molecule, identified as palmitoylcarnitine (PalC), was of particular interest due to its high abundance at loci of S. Typhimurium infection and MLN disruption. High levels of PalC localised to sites within the MLNs where B and T cells were absent and where the perimeter of CD169 + sub capsular sinus macrophages was disrupted. MLN cells cultured ex vivo and treated with PalC had reduced CD4+CD25+ T cells and an increased number of B220+CD19+ B cells. The reduction in CD4+CD25+ T cells was likely due to apoptosis driven by increased caspase-3/7 activity. These data indicate that PalC significantly alters the host response in the MLNs, acting as a decisive factor in infection outcome.", "doi": "10.1038/s41598-017-03100-5", "pmid": "28584281", "labels": {"Spatial Mass Spectrometry": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-03100-5"}, {"db": "pmc", "key": "PMC5459799"}], "notes": [], "created": "2020-01-24T08:59:38.206Z", "modified": "2021-05-17T08:47:18.753Z"}, {"entity": "publication", "iuid": "5b3c0a685bee4780824ad53cccfcd08c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b3c0a685bee4780824ad53cccfcd08c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b3c0a685bee4780824ad53cccfcd08c"}}, "title": "SnoN Stabilizes the SMAD3/SMAD4 Protein Complex", "authors": [{"family": "Walld\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Nyman", "given": "Tomas", "initials": "T"}, {"family": "H\u00e4llberg", "given": "B Martin", "initials": "BM"}], "type": "journal-article", "published": "2017-04-11", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "46370", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/srep46370", "pmid": "28397834", "labels": {"Protein Science Facility (PSF)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:18.362Z", "modified": "2017-11-09T13:17:11.248Z"}, {"entity": "publication", "iuid": "cc9a907e212c47deb1bf893bc47087c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc9a907e212c47deb1bf893bc47087c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc9a907e212c47deb1bf893bc47087c6"}}, "title": "Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia.", "authors": [{"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Olsson-Str\u00f6mberg", "given": "Ulla", "initials": "U"}, {"family": "Siart", "given": "Benjamin", "initials": "B"}, {"family": "Jansson", "given": "Mattias", "initials": "M"}, {"family": "Dahlin", "given": "Joakim S", "initials": "JS", "orcid": "0000-0003-3007-9875", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d022071f86a451aba84b18fb0774461.json"}}, {"family": "Th\u00f6rn", "given": "Ingrid", "initials": "I"}, {"family": "Christiansson", "given": "Lisa", "initials": "L"}, {"family": "Hermansson", "given": "Monica", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Ahlstrand", "given": "Erik", "initials": "E"}, {"family": "W\u00e5linder", "given": "G\u00f6ran", "initials": "G"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications.scilifelab.se/researcher/87392e51288f4ef9a38fe3989d10d180.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2017-04-04", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "623", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Chronic myeloid leukemia (CML) is characterized in the majority of cases by a t(9;22)(q34;q11) translocation, also called the Philadelphia chromosome, giving rise to the BCR-ABL1 fusion protein. Current treatment with tyrosine kinase inhibitors is directed against the constitutively active ABL1 domain of the fusion protein, and minimal residual disease (MRD) after therapy is monitored by real-time quantitative PCR (RQ-PCR) of the fusion transcript. Here, we describe a novel approach to detect and enumerate cells positive for the BCR-ABL1 fusion protein by combining the in situ proximity ligation assay with flow cytometry as readout (PLA-flow). By targeting of the BCR and ABL1 parts of the fusion protein with one antibody each, and creating strong fluorescent signals through rolling circle amplification, PLA-flow allowed sensitive detection of cells positive for the BCR-ABL1 fusion at frequencies as low as one in 10,000. Importantly, the flow cytometric results correlated strongly to those of RQ-PCR, both in diagnostic testing and for MRD measurements over time. In summary, we believe this flow cytometry-based method can serve as an attractive approach for routine measurement of cells harboring BCR-ABL1 fusions, also allowing simultaneously assessment of other cell surface markers as well as sensitive longitudinal follow-up.", "doi": "10.1038/s41598-017-00755-y", "pmid": "28377570", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-00755-y"}, {"db": "pmc", "key": "PMC5429594"}], "notes": [], "created": "2017-11-02T14:39:48.739Z", "modified": "2023-04-14T13:56:15.652Z"}, {"entity": "publication", "iuid": "66e2871d10da49c9a15ec3ccaf63231e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66e2871d10da49c9a15ec3ccaf63231e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66e2871d10da49c9a15ec3ccaf63231e"}}, "title": "Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology", "authors": [{"family": "Vi\u013cuma", "given": "Agnese", "initials": "A"}, {"family": "Mikko", "given": "Sofia", "initials": "S"}, {"family": "Hahn", "given": "Daniela", "initials": "D"}, {"family": "Skow", "given": "Loren", "initials": "L"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF"}], "type": "journal-article", "published": "2017-03-31", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "45518", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region. The final assembly resulted in a 1,165,328\u2009bp continuous gap free sequence with 35 manually curated genomic loci of which 23 were considered to be functional and 12 to be pseudogenes. In comparison to the MHC class II region in other mammals, the corresponding region in horse shows extraordinary copy number variation and different relative location and directionality of the Eqca-DRB, -DQA, -DQB and -DOB loci. This is the first long-read sequence assembly of the horse MHC class II region with rigorous manual gene annotation, and it will serve as an important resource for association studies of immune-mediated equine diseases and for evolutionary analysis of genetic diversity in this region.", "doi": "10.1038/srep45518", "pmid": "28361880", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:40:57.204Z", "modified": "2024-01-16T13:48:48.234Z"}, {"entity": "publication", "iuid": "0990de43373146d69c60334dffbe0590", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0990de43373146d69c60334dffbe0590.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0990de43373146d69c60334dffbe0590"}}, "title": "The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.", "authors": [{"family": "Chang", "given": "Dan", "initials": "D"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Enk", "given": "Jacob", "initials": "J"}, {"family": "Lippold", "given": "Sebastian", "initials": "S"}, {"family": "Kircher", "given": "Martin", "initials": "M"}, {"family": "Lister", "given": "Adrian", "initials": "A"}, {"family": "MacPhee", "given": "Ross D E", "initials": "RD"}, {"family": "Widga", "given": "Christopher", "initials": "C"}, {"family": "Czechowski", "given": "Paul", "initials": "P"}, {"family": "Sommer", "given": "Robert", "initials": "R"}, {"family": "Hodges", "given": "Emily", "initials": "E"}, {"family": "St\u00fcmpel", "given": "Nikolaus", "initials": "N"}, {"family": "Barnes", "given": "Ian", "initials": "I"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Derevianko", "given": "Anatoly", "initials": "A"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Hillebrand-Voiculescu", "given": "Alexandra", "initials": "A"}, {"family": "Constantin", "given": "Silviu", "initials": "S"}, {"family": "Kuznetsova", "given": "Tatyana", "initials": "T"}, {"family": "Mol", "given": "Dick", "initials": "D"}, {"family": "Rathgeber", "given": "Thomas", "initials": "T"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Tikhonov", "given": "Alexey N", "initials": "AN"}, {"family": "Willerslev", "given": "Eske", "initials": "E"}, {"family": "Hannon", "given": "Greg", "initials": "G"}, {"family": "Lalueza-Fox", "given": "Carles", "initials": "C"}, {"family": "Joger", "given": "Ulrich", "initials": "U"}, {"family": "Poinar", "given": "Hendrik", "initials": "H"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}], "type": "journal article", "published": "2017-03-22", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "44585", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.", "doi": "10.1038/srep44585", "pmid": "28327635", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep44585"}, {"db": "pmc", "key": "PMC5361112"}], "notes": [], "created": "2017-11-03T16:21:50.396Z", "modified": "2021-07-07T20:31:10.689Z"}, {"entity": "publication", "iuid": "d2131eeeed404689b6cf4dba0f546d6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2131eeeed404689b6cf4dba0f546d6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2131eeeed404689b6cf4dba0f546d6e"}}, "title": "Discovery of circulating proteins associated to knee radiographic osteoarthritis.", "authors": [{"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Fern\u00e1ndez-Tajes", "given": "Juan", "initials": "J"}, {"family": "Oreiro", "given": "Natividad", "initials": "N"}, {"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Blanco", "given": "Francisco J", "initials": "FJ"}], "type": "journal article", "published": "2017-03-09", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "137", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Currently there are no sufficiently sensitive biomarkers able to reflect changes in joint remodelling during osteoarthritis (OA). In this work, we took an affinity proteomic approach to profile serum samples for proteins that could serve as indicators for the diagnosis of radiographic knee OA. Antibody suspension bead arrays were applied to analyze serum samples from patients with OA (n\u2009=\u2009273), control subjects (n\u2009=\u200976) and patients with rheumatoid arthritis (RA, n\u2009=\u2009244). For verification, a focused bead array was built and applied to an independent set of serum samples from patients with OA (n\u2009=\u2009188), control individuals (n\u2009=\u200983) and RA (n\u2009=\u2009168) patients. A linear regression analysis adjusting for sex, age and body mass index (BMI) revealed that three proteins were significantly elevated (P\u2009<\u20090.05) in serum from OA patients compared to controls: C3, ITIH1 and S100A6. A panel consisting of these three proteins had an area under the curve of 0.82 for the classification of OA and control samples. Moreover, C3 and ITIH1 levels were also found to be significantly elevated (P\u2009<\u20090.05) in OA patients compared to RA patients. Upon validation in additional study sets, the alterations of these three candidate serum biomarker proteins could support the diagnosis of radiographic knee OA.", "doi": "10.1038/s41598-017-00195-8", "pmid": "28273936", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-00195-8"}, {"db": "pmc", "key": "PMC5427840"}], "notes": [], "created": "2017-10-30T10:15:33.970Z", "modified": "2021-07-08T12:07:34.275Z"}, {"entity": "publication", "iuid": "233b062d1f5d47e5ac0971cd9ea0a47f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f"}}, "title": "Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG"}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Sinika", "given": "Vitaly", "initials": "V"}, {"family": "Piontek", "given": "Janusz", "initials": "J"}, {"family": "Ivanova", "given": "Svetlana", "initials": "S"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2017-03-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43950", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.", "doi": "10.1038/srep43950", "pmid": "28266657", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep43950"}, {"db": "pmc", "key": "PMC5339713"}], "notes": [], "created": "2017-11-03T16:18:39.704Z", "modified": "2021-07-07T10:48:05.331Z"}, {"entity": "publication", "iuid": "71cb03a7aa104761b89ada3693fad56c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71cb03a7aa104761b89ada3693fad56c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71cb03a7aa104761b89ada3693fad56c"}}, "title": "Postnatal development of the small intestinal mucosa drives age-dependent, regio-selective susceptibility to Escherichia coli K1 infection.", "authors": [{"family": "Birchenough", "given": "George M H", "initials": "GM"}, {"family": "Dalgakiran", "given": "Fatma", "initials": "F"}, {"family": "Witcomb", "given": "Luci A", "initials": "LA"}, {"family": "Johansson", "given": "Malin E V", "initials": "ME", "orcid": "0000-0002-4237-6677", "researcher": {"href": "https://publications.scilifelab.se/researcher/520dab35c19049c8b3f1083a92e60d56.json"}}, {"family": "McCarthy", "given": "Alex J", "initials": "AJ"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC", "orcid": "0000-0002-1900-1869", "researcher": {"href": "https://publications.scilifelab.se/researcher/44b3815603154322a6dac16f2fc1c1e9.json"}}, {"family": "Taylor", "given": "Peter W", "initials": "PW"}], "type": "journal article", "published": "2017-03-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "83", "issn-l": "2045-2322"}, "abstract": "The strong age dependency of neonatal systemic infection with Escherichia coli K1 can be replicated in the neonatal rat. Gastrointestinal (GI) colonization of two-day-old (P2) rats leads to invasion of the blood within 48 h of initiation of colonization; pups become progressively less susceptible to infection over the P2-P9 period. We show that, in animals colonized at P2 but not at P9, E. coli K1 bacteria gain access to the enterocyte surface in the mid-region of the small intestine and translocate through the epithelial cell monolayer by an intracellular pathway to the submucosa. In this region of the GI tract, the protective mucus barrier is poorly developed but matures to full thickness over P2-P9, coincident with the development of resistance to invasion. At P9, E. coli K1 bacteria are physically separated from villi by the mucus layer and their numbers controlled by mucus-embedded antimicrobial peptides, preventing invasion of host tissues.", "doi": "10.1038/s41598-017-00123-w", "pmid": "28250440", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-00123-w"}, {"db": "pmc", "key": "PMC5427930"}], "notes": [], "created": "2020-01-23T16:34:09.203Z", "modified": "2021-06-21T14:59:19.303Z"}, {"entity": "publication", "iuid": "4463761683c544979c68bd54d04d4690", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4463761683c544979c68bd54d04d4690.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4463761683c544979c68bd54d04d4690"}}, "title": "Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing.", "authors": [{"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Sirel", "given": "Madle", "initials": "M"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Del Pilar Quintana", "given": "Maria", "initials": "M"}, {"family": "Chun Leung Chan", "given": "Sherwin", "initials": "S"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Tellgren-Roth", "given": "Asa", "initials": "A"}, {"family": "Nilsson", "given": "IngMarie", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43190", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.", "doi": "10.1038/srep43190", "pmid": "28233866", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "srep43190"}, {"db": "pmc", "key": "PMC5324397"}], "notes": [], "created": "2017-11-02T11:40:03.653Z", "modified": "2021-07-07T15:50:03.085Z"}, {"entity": "publication", "iuid": "bd94aea05d1b4f7da7b5165ed48d553a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd94aea05d1b4f7da7b5165ed48d553a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd94aea05d1b4f7da7b5165ed48d553a"}}, "title": "Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.", "authors": [{"family": "Sandmann", "given": "Sarah", "initials": "S"}, {"family": "de Graaf", "given": "Aniek O", "initials": "AO"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "van der Reijden", "given": "Bert A", "initials": "BA"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Jansen", "given": "Joop H", "initials": "JH"}, {"family": "Dugas", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43169", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322\u2009bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.", "doi": "10.1038/srep43169", "pmid": "28233799", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "srep43169"}, {"db": "pmc", "key": "PMC5324109"}], "notes": [], "created": "2018-01-10T09:44:12.939Z", "modified": "2020-01-21T13:56:10.961Z"}, {"entity": "publication", "iuid": "8a981796d792400d95224a22b3d2a76a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a981796d792400d95224a22b3d2a76a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a981796d792400d95224a22b3d2a76a"}}, "title": "Intracellular drug bioavailability: a new predictor of system dependent drug disposition.", "authors": [{"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Treyer", "given": "Andrea", "initials": "A"}, {"family": "Wegler", "given": "Christine", "initials": "C"}, {"family": "Karlgren", "given": "Maria", "initials": "M"}, {"family": "Matsson", "given": "P\u00e4r", "initials": "P"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2017-02-22", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43047", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Intracellular drug exposure is influenced by cell- and tissue-dependent expression of drug-transporting proteins and metabolizing enzymes. Here, we introduce the concept of intracellular bioavailability (Fic) as the fraction of extracellular drug available to bind intracellular targets, and we assess how Fic is affected by cellular drug disposition processes. We first investigated the impact of two essential drug transporters separately, one influx transporter (OATP1B1; SLCO1B1) and one efflux transporter (P-gp; ABCB1), in cells overexpressing these proteins. We showed that OATP1B1 increased Fic of its substrates, while P-gp decreased Fic. We then investigated the impact of the concerted action of multiple transporters and metabolizing enzymes in freshly-isolated human hepatocytes in culture configurations with different levels of expression and activity of these proteins. We observed that Fic was up to 35-fold lower in the configuration with high expression of drug-eliminating transporters and enzymes. We conclude that Fic provides a measurement of the net impact of all cellular drug disposition processes on intracellular bioavailable drug levels. Importantly, no prior knowledge of the involved drug distribution pathways is required, allowing for high-throughput determination of drug access to intracellular targets in highly defined cell systems (e.g., single-transporter transfectants) or in complex ones (including primary human cells).", "doi": "10.1038/srep43047", "pmid": "28225057", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "srep43047"}, {"db": "pmc", "key": "PMC5320532"}], "notes": [], "created": "2017-10-24T12:55:23.366Z", "modified": "2025-10-17T13:05:09.017Z"}, {"entity": "publication", "iuid": "24344bb489604ac38a35c61b68e2a68c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24344bb489604ac38a35c61b68e2a68c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24344bb489604ac38a35c61b68e2a68c"}}, "title": "SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics.", "authors": [{"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}, {"family": "Aarsland", "given": "Dag", "initials": "D"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2017-02-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "41929", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The human blood proteome is frequently assessed by protein abundance profiling using a combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS). In traditional sequence database search, many good-quality MS/MS data remain unassigned. Here we uncover the hidden part of the blood proteome via novel SpotLight approach. This method combines de novo MS/MS sequencing of enriched antibodies and co-extracted proteins with subsequent label-free quantification of new and known peptides in both enriched and unfractionated samples. In a pilot study on differentiating early stages of Alzheimer's disease (AD) from Dementia with Lewy Bodies (DLB), on peptide level the hidden proteome contributed almost as much information to patient stratification as the apparent proteome. Intriguingly, many of the new peptide sequences are attributable to antibody variable regions, and are potentially indicative of disease etiology. When the hidden and apparent proteomes are combined, the accuracy of differentiating AD (n = 97) and DLB (n = 47) increased from \u224885% to \u224895%. The low added burden of SpotLight proteome analysis makes it attractive for use in clinical settings.", "doi": "10.1038/srep41929", "pmid": "28167817", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "srep41929"}, {"db": "pmc", "key": "PMC5294601"}], "notes": [], "created": "2020-01-23T13:29:59.536Z", "modified": "2021-07-08T08:58:46.741Z"}, {"entity": "publication", "iuid": "0237c96aa2a14dc0ae3a6b465cecfd6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0237c96aa2a14dc0ae3a6b465cecfd6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0237c96aa2a14dc0ae3a6b465cecfd6f"}}, "title": "Profile of upregulated inflammatory proteins in sera of Myasthenia Gravis patients.", "authors": [{"family": "Molin", "given": "Carl Johan", "initials": "CJ"}, {"family": "Westerberg", "given": "Elisabet", "initials": "E"}, {"family": "Punga", "given": "Anna Rostedt", "initials": "AR"}], "type": "journal article", "published": "2017-01-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "7", "issue": "1", "pages": "39716"}, "abstract": "This study describes specific patterns of elevated inflammatory proteins in clinical subtypes of myasthenia gravis (MG) patients. MG is a chronic, autoimmune neuromuscular disease with antibodies most commonly targeting the acetylcholine receptors (AChRab), which causes fluctuating skeletal muscle fatigue. MG pathophysiology includes a strong component of inflammation, and a large proportion of patients with early onset MG additionally present thymus hyperplasia. Due to the fluctuating nature and heterogeneity of the disease, there is a great need for objective biomarkers as well as novel potential inflammatory targets. We examined the sera of 45 MG patients (40 AChRab seropositive and 5 AChRab seronegative), investigating 92 proteins associated with inflammation. Eleven of the analysed proteins were significantly elevated compared to healthy controls, out of which the three most significant were: matrix metalloproteinase 10 (MMP-10; p = 0.0004), transforming growth factor alpha (TGF-\u03b1; p = 0.0017) and extracellular newly identified receptor for advanced glycation end-products binding protein (EN-RAGE) (also known as protein S100-A12; p = 0.0054). Further, levels of MMP-10, C-X-C motif ligand 1 (CXCL1) and brain derived neurotrophic factor (BDNF) differed between early and late onset MG. These novel targets provide valuable additional insight into the systemic inflammatory response in MG.", "doi": "10.1038/srep39716", "pmid": "28045063", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "srep39716"}, {"db": "pmc", "key": "PMC5206650"}], "notes": [], "created": "2020-01-23T15:13:42.026Z", "modified": "2023-04-14T13:56:17.836Z"}, {"entity": "publication", "iuid": "e1b23dc0f9144052aae3948a4926f244", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1b23dc0f9144052aae3948a4926f244.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1b23dc0f9144052aae3948a4926f244"}}, "title": "Iron chelators target both proliferating and quiescent cancer cells.", "authors": [{"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Zhang", "given": "Xiaonan", "initials": "X"}, {"family": "Bremberg", "given": "Ulf", "initials": "U"}, {"family": "Senkowski", "given": "Wojciech", "initials": "W"}, {"family": "Olofsson", "given": "Maria H\u00e4gg", "initials": "MH"}, {"family": "Brandt", "given": "Peter", "initials": "P"}, {"family": "Persson", "given": "Ingmar", "initials": "I"}, {"family": "D'Arcy", "given": "Padraig", "initials": "P"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Schughart", "given": "Leoni Kunz", "initials": "LK"}, {"family": "Linder", "given": "Stig", "initials": "S"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2016-12-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "6", "issue": null, "pages": "38343", "issn-l": "2045-2322"}, "abstract": "Poorly vascularized areas of solid tumors contain quiescent cell populations that are resistant to cell cycle-active cancer drugs. The compound VLX600 was recently identified to target quiescent tumor cells and to inhibit mitochondrial respiration. We here performed gene expression analysis in order to characterize the cellular response to VLX600. The compound-specific signature of VLX600 revealed a striking similarity to signatures generated by compounds known to chelate iron. Validation experiments including addition of ferrous and ferric iron in excess, EXAFS measurements, and structure activity relationship analyses showed that VLX600 chelates iron and supported the hypothesis that the biological effects of this compound is due to iron chelation. Compounds that chelate iron possess anti-cancer activity, an effect largely attributed to inhibition of ribonucleotide reductase in proliferating cells. Here we show that iron chelators decrease mitochondrial energy production, an effect poorly tolerated by metabolically stressed tumor cells. These pleiotropic features make iron chelators an attractive option for the treatment of solid tumors containing heterogeneous populations of proliferating and quiescent cells.", "doi": "10.1038/srep38343", "pmid": "27924826", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "srep38343"}, {"db": "pmc", "key": "PMC5141479"}], "notes": [], "created": "2020-12-10T12:16:53.923Z", "modified": "2025-10-17T13:05:09.098Z"}, {"entity": "publication", "iuid": "74c6c3bf65fc4da4a1fbf3f2503c9473", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74c6c3bf65fc4da4a1fbf3f2503c9473.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74c6c3bf65fc4da4a1fbf3f2503c9473"}}, "title": "A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing.", "authors": [{"family": "Davidsson", "given": "Marcus", "initials": "M"}, {"family": "Diaz-Fernandez", "given": "Paula", "initials": "P"}, {"family": "Schwich", "given": "Oliver D", "initials": "OD"}, {"family": "Torroba", "given": "Marcos", "initials": "M"}, {"family": "Wang", "given": "Gang", "initials": "G"}, {"family": "Bj\u00f6rklund", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2016-11-22", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "37563", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode.", "doi": "10.1038/srep37563", "pmid": "27874090", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "srep37563"}, {"db": "pmc", "key": "PMC5118689"}], "notes": [], "created": "2017-05-03T13:02:08.333Z", "modified": "2020-01-21T13:56:03.026Z"}, {"entity": "publication", "iuid": "9851dccf90c74df7b967de69cb54985c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9851dccf90c74df7b967de69cb54985c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9851dccf90c74df7b967de69cb54985c"}}, "title": "An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.", "authors": [{"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Fern\u00e1ndez Navarro", "given": "Jos\u00e9", "initials": "J"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2016-11-16", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "37137", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Sequencing the nucleic acid content of individual cells or specific biological samples is becoming increasingly common. This drives the need for robust, scalable and automated library preparation protocols. Furthermore, an increased understanding of tissue heterogeneity has lead to the development of several unique sequencing protocols that aim to retain or infer spatial context. In this study, a protocol for retaining spatial information of transcripts has been adapted to run on a robotic workstation. The method spatial transcriptomics is evaluated in terms of robustness and variability through the preparation of reference RNA, as well as through preparation and sequencing of six replicate sections of a gingival tissue biopsy from a patient with periodontitis. The results are reduced technical variability between replicates and a higher throughput, processing four times more samples with less than a third of the hands on time, compared to the standard protocol.", "doi": "10.1038/srep37137", "pmid": "27849009", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep37137"}, {"db": "pmc", "key": "PMC5111054"}], "notes": [], "created": "2017-05-03T13:00:03.893Z", "modified": "2024-01-16T13:48:48.988Z"}, {"entity": "publication", "iuid": "5b58b6fa88f54e13933f6fa401f3c653", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b58b6fa88f54e13933f6fa401f3c653.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b58b6fa88f54e13933f6fa401f3c653"}}, "title": "Image analysis-derived metrics of histomorphological complexity predicts prognosis and treatment response in stage II-III colon cancer.", "authors": [{"family": "Mezheyeuski", "given": "Artur", "initials": "A"}, {"family": "Hrynchyk", "given": "Ina", "initials": "I"}, {"family": "Karlberg", "given": "Mia", "initials": "M"}, {"family": "Portyanko", "given": "Anna", "initials": "A"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Ragnhammar", "given": "Peter", "initials": "P"}, {"family": "Edler", "given": "David", "initials": "D"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "\u00d6stman", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2016-11-02", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "36149", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The complexity of tumor histomorphology reflects underlying tumor biology impacting on natural course and response to treatment. This study presents a method of computer-aided analysis of tissue sections, relying on multifractal (MF) analyses, of cytokeratin-stained tumor sections which quantitatively evaluates of the morphological complexity of the tumor-stroma interface. This approach was applied to colon cancer collection, from an adjuvant treatment randomized study. Metrics obtained with the method acted as independent markers for natural course of the disease, and for benefit of adjuvant treatment. Comparative analyses demonstrated that MF metrics out-performed standard histomorphological features such as tumor grade, budding and configuration of invasive front. Notably, the MF analyses-derived \"\u03b1max\" -metric constitutes the first response-predictive biomarker in stage II-III colon cancer showing significant interactions with treatment in analyses using a randomized trial-derived study population. Based on these results the method appears as an attractive and easy-to-implement tool for biomarker identification.", "doi": "10.1038/srep36149", "pmid": "27805003", "labels": {"Tissue Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "srep36149"}, {"db": "pmc", "key": "PMC5095346"}], "notes": "Laboratories for Chemical Biology at Karolinska Institutet (LCBKI)", "created": "2017-05-03T12:58:52.505Z", "modified": "2017-10-09T08:56:11.236Z"}, {"entity": "publication", "iuid": "020698099138404ebd24dce553bc56f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/020698099138404ebd24dce553bc56f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/020698099138404ebd24dce553bc56f3"}}, "title": "Rawcopy: Improved copy number analysis with Affymetrix arrays.", "authors": [{"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Viklund", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2016-10-31", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "36158", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Microarray data is subject to noise and systematic variation that negatively affects the resolution of copy number analysis. We describe Rawcopy, an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). Noise characteristics of a large number of reference samples are used to estimate log ratio and B-allele frequency for total and allele-specific copy number analysis. Rawcopy achieves better signal-to-noise ratio and higher proportion of validated alterations than commonly used free and proprietary alternatives. In addition, Rawcopy visualizes each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states. Software and instructions are available at http://rawcopy.org.", "doi": "10.1038/srep36158", "pmid": "27796336", "labels": {"Array and Analysis Facility": "Technology development"}, "xrefs": [{"db": "pii", "key": "srep36158"}, {"db": "pmc", "key": "PMC5086940"}], "notes": [], "created": "2017-05-03T13:02:27.306Z", "modified": "2017-06-12T11:40:00.216Z"}, {"entity": "publication", "iuid": "4f90bb3bf07a4fe28c6fd66458e7aa15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f90bb3bf07a4fe28c6fd66458e7aa15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f90bb3bf07a4fe28c6fd66458e7aa15"}}, "title": "Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves.", "authors": [{"family": "Maleki", "given": "Shohreh", "initials": "S"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Paloschi", "given": "Valentina", "initials": "V"}, {"family": "Magn\u00e9", "given": "Joelle", "initials": "J"}, {"family": "Branca", "given": "Rui Miguel Mamede", "initials": "RM"}, {"family": "Du", "given": "Lei", "initials": "L"}, {"family": "Hultenby", "given": "Kjell", "initials": "K"}, {"family": "Petrini", "given": "Johan", "initials": "J"}, {"family": "Fuxe", "given": "Jonas", "initials": "J"}, {"family": "MIBAVA Leducq Consortium", "given": "", "initials": ""}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM"}], "type": "journal article", "published": "2016-10-25", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "35712", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Individuals with a bicuspid aortic valve (BAV) are at significantly higher risk of developing aortic complications than individuals with tricuspid aortic valves (TAV) and defective signaling during the embryonic development and/or life time exposure to abnormal hemodynamic have been proposed as underlying factors. However, an explanation for the molecular mechanisms of aortopathy in BAV has not yet been provided. We combined proteomics, RNA analyses, immunohistochemistry, and electron microscopy to identify molecular differences in samples of non-dilated ascending aortas from BAV (N = 62) and TAV (N = 54) patients. Proteomic analysis was also performed for dilated aortas (N = 6 BAV and N = 5 TAV) to gain further insight into the aortopathy of BAV. Our results collectively showed the molecular signature of an endothelial/epithelial-mesenchymal (EndMT/EMT) transition-like process, associated with instability of intimal cell junctions and activation of RHOA pathway in the intima and media layers of ascending aorta in BAV patients. We propose that an improper regulation of EndMT/EMT during the spatiotemporally related embryogenesis of semilunar valves and ascending aorta in BAV individuals may result in aortic immaturity and instability prior to dilation. Exasperation of EndMT/EMT state in post embryonic life and/or exposure to non-physiological hemodynamic could lead to the aneurysm of ascending aorta in BAV individuals.", "doi": "10.1038/srep35712", "pmid": "27779199", "labels": {"Clinical Proteomics Mass spectrometry": "Collaborative", "Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "srep35712"}, {"db": "pmc", "key": "PMC5078843"}], "notes": [], "created": "2017-05-03T13:02:33.158Z", "modified": "2021-07-08T11:36:15.208Z"}, {"entity": "publication", "iuid": "58b908552486434789e2c732abbbaeea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58b908552486434789e2c732abbbaeea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58b908552486434789e2c732abbbaeea"}}, "title": "Auxotrophy-based High Throughput Screening assay for the identification of Bacillus subtilis stringent response inhibitors.", "authors": [{"family": "Andresen", "given": "Liis", "initials": "L"}, {"family": "Varik", "given": "Vallo", "initials": "V"}, {"family": "Tozawa", "given": "Yuzuru", "initials": "Y"}, {"family": "Jimmy", "given": "Steffi", "initials": "S"}, {"family": "Lindberg", "given": "Stina", "initials": "S"}, {"family": "Tenson", "given": "Tanel", "initials": "T"}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V"}], "type": "journal article", "published": "2016-10-24", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "35824", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The stringent response is a central adaptation mechanism that allows bacteria to adjust their growth and metabolism according to environmental conditions. The functionality of the stringent response is crucial for bacterial virulence, survival during host invasion as well as antibiotic resistance and tolerance. Therefore, specific inhibitors of the stringent response hold great promise as molecular tools for disarming and pacifying bacterial pathogens. By taking advantage of the valine amino acid auxotrophy of the Bacillus subtilis stringent response-deficient strain, we have set up a High Throughput Screening assay for the identification of stringent response inhibitors. By screening 17,500 compounds, we have identified a novel class of antibacterials based on the 4-(6-(phenoxy)alkyl)-3,5-dimethyl-1H-pyrazole core. Detailed characterization of the hit compounds as well as two previously identified promising stringent response inhibitors - a ppGpp-mimic nucleotide Relacin and cationic peptide 1018 - showed that neither of the compounds is sufficiently specific, thus motivating future application of our screening assay to larger and more diverse molecular libraries.", "doi": "10.1038/srep35824", "pmid": "27775002", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "srep35824"}, {"db": "pmc", "key": "PMC5075769"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-03T12:59:28.222Z", "modified": "2025-10-17T13:04:29.430Z"}, {"entity": "publication", "iuid": "f1cce8e886ef43968171b6032e2d342c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1cce8e886ef43968171b6032e2d342c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1cce8e886ef43968171b6032e2d342c"}}, "title": "Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites.", "authors": [{"family": "Grijseels", "given": "Sietske", "initials": "S"}, {"family": "Nielsen", "given": "Jens Christian", "initials": "JC", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Randelovic", "given": "Milica", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Nielsen", "given": "Kristian Fog", "initials": "KF"}, {"family": "Workman", "given": "Mhairi", "initials": "M"}, {"family": "Frisvad", "given": "Jens Christian", "initials": "JC"}], "type": "journal article", "published": "2016-10-14", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "35112", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311(T)\u2009=\u2009IBT 12289(T)). The genome was sequenced and assembled into 33.7\u2009Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species.", "doi": "10.1038/srep35112", "pmid": "27739446", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep35112"}, {"db": "pmc", "key": "PMC5064400"}], "notes": [], "created": "2017-05-03T13:00:03.295Z", "modified": "2024-01-16T13:48:49.145Z"}, {"entity": "publication", "iuid": "b0e5a7e53d3d44e6911e6160e8d60ca5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0e5a7e53d3d44e6911e6160e8d60ca5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0e5a7e53d3d44e6911e6160e8d60ca5"}}, "title": "No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis.", "authors": [{"family": "Loley", "given": "Christina", "initials": "C"}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Bjonnes", "given": "Andrew", "initials": "A"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Hernesniemi", "given": "Jussi", "initials": "J"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Lau", "given": "King Wai", "initials": "KW"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Nikpay", "given": "Majid", "initials": "M"}, {"family": "Qu", "given": "Liming", "initials": "L"}, {"family": "Salfati", "given": "Elias", "initials": "E"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Tukiainen", "given": "Taru", "initials": "T"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Won", "given": "Hong-Hee", "initials": "HH"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Anand", "given": "Sonia S", "initials": "SS"}, {"family": "Beutner", "given": "Frank", "initials": "F"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Do", "given": "Ron", "initials": "R"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Eskola", "given": "Markku", "initials": "M"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Gauguier", "given": "Dominique", "initials": "D"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Granger", "given": "Christopher B", "initials": "CB"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kyriakou", "given": "Theodosios", "initials": "T"}, {"family": "Laaksonen", "given": "Reijo", "initials": "R"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Pedersen", "given": "Nancy", "initials": "N"}, {"family": "Rallidis", "given": "Loukianos", "initials": "L"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Shah", "given": "Svati H", "initials": "SH"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AF"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "Zalloua", "given": "Pierre A", "initials": "PA"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Collins", "given": "Rory", "initials": "R"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Iribarren", "given": "Carlos", "initials": "C"}, {"family": "Karhunen", "given": "Pekka J", "initials": "PJ"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Sanghera", "given": "Dharambir K", "initials": "DK"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "K\u00f6nig", "given": "Inke R", "initials": "IR"}], "type": "journal article", "published": "2016-10-12", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "35278", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "In recent years, genome-wide association studies have identified 58 independent risk loci for coronary artery disease (CAD) on the autosome. However, due to the sex-specific data structure of the X chromosome, it has been excluded from most of these analyses. While females have 2 copies of chromosome X, males have only one. Also, one of the female X chromosomes may be inactivated. Therefore, special test statistics and quality control procedures are required. Thus, little is known about the role of X-chromosomal variants in CAD. To fill this gap, we conducted a comprehensive X-chromosome-wide meta-analysis including more than 43,000 CAD cases and 58,000 controls from 35 international study cohorts. For quality control, sex-specific filters were used to adequately take the special structure of X-chromosomal data into account. For single study analyses, several logistic regression models were calculated allowing for inactivation of one female X-chromosome, adjusting for sex and investigating interactions between sex and genetic variants. Then, meta-analyses including all 35 studies were conducted using random effects models. None of the investigated models revealed genome-wide significant associations for any variant. Although we analyzed the largest-to-date sample, currently available methods were not able to detect any associations of X-chromosomal variants with CAD.", "doi": "10.1038/srep35278", "pmid": "27731410", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep35278"}, {"db": "pmc", "key": "PMC5059659"}], "notes": [], "created": "2017-05-03T13:00:03.596Z", "modified": "2024-01-16T13:48:49.170Z"}, {"entity": "publication", "iuid": "b0dd5269a2024cd0a185edebda98873e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0dd5269a2024cd0a185edebda98873e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0dd5269a2024cd0a185edebda98873e"}}, "title": "Analysis of the brain mural cell transcriptome.", "authors": [{"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M"}, {"family": "Raschperger", "given": "Elisabeth", "initials": "E"}, {"family": "Andaloussi M\u00e4e", "given": "Maarja", "initials": "M"}, {"family": "Jung", "given": "Bongnam", "initials": "B"}, {"family": "Lebouvier", "given": "Thibaud", "initials": "T"}, {"family": "Ando", "given": "Koji", "initials": "K"}, {"family": "Hofmann", "given": "Jennifer", "initials": "J"}, {"family": "Keller", "given": "Annika", "initials": "A"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2016-10-11", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "35108", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Pericytes, the mural cells of blood microvessels, regulate microvascular development and function and have been implicated in many brain diseases. However, due to a paucity of defining markers, pericyte identification and functional characterization remain ambiguous and data interpretation problematic. In mice carrying two transgenic reporters, Pdgfrb-eGFP and NG2-DsRed, we found that double-positive cells were vascular mural cells, while the single reporters marked additional, but non-overlapping, neuroglial cells. Double-positive cells were isolated by fluorescence-activated cell sorting (FACS) and analyzed by RNA sequencing. To reveal defining patterns of mural cell transcripts, we compared the RNA sequencing data with data from four previously published studies. The meta-analysis provided a conservative catalogue of 260 brain mural cell-enriched gene transcripts. We validated pericyte-specific expression of two novel markers, vitronectin (Vtn) and interferon-induced transmembrane protein 1 (Ifitm1), using fluorescent in situ hybridization and immunohistochemistry. We further analyzed signaling pathways and interaction networks of the pericyte-enriched genes in silico. This work provides novel insight into the molecular composition of brain mural cells. The reported gene catalogue facilitates identification of brain pericytes by providing numerous new candidate marker genes and is a rich source for new hypotheses for future studies of brain mural cell physiology and pathophysiology.", "doi": "10.1038/srep35108", "pmid": "27725773", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "srep35108"}, {"db": "pmc", "key": "PMC5057134"}], "notes": [], "created": "2017-05-03T13:01:41.218Z", "modified": "2020-01-21T13:56:04.656Z"}, {"entity": "publication", "iuid": "2413d5f4ab0b41d7b39874104dc31007", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2413d5f4ab0b41d7b39874104dc31007.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2413d5f4ab0b41d7b39874104dc31007"}}, "title": "ProQ3: Improved model quality assessments using Rosetta energy terms.", "authors": [{"family": "Uziela", "given": "Karolis", "initials": "K"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2016-10-04", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "33509", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/.", "doi": "10.1038/srep33509", "pmid": "27698390", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "srep33509"}, {"db": "pmc", "key": "PMC5048106"}], "notes": [], "created": "2017-05-03T13:00:42.093Z", "modified": "2020-01-21T13:53:21.242Z"}, {"entity": "publication", "iuid": "506385b639e8409aa2a518f8f8b50598", "links": {"self": {"href": "https://publications.scilifelab.se/publication/506385b639e8409aa2a518f8f8b50598.json"}, "display": {"href": "https://publications.scilifelab.se/publication/506385b639e8409aa2a518f8f8b50598"}}, "title": "The domesticated brain: genetics of brain mass and brain structure in an avian species.", "authors": [{"family": "Henriksen", "given": "R", "initials": "R"}, {"family": "Johnsson", "given": "M", "initials": "M"}, {"family": "Andersson", "given": "L", "initials": "L"}, {"family": "Jensen", "given": "P", "initials": "P"}, {"family": "Wright", "given": "D", "initials": "D"}], "type": "journal article", "published": "2016-09-30", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": "34031", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "As brain size usually increases with body size it has been assumed that the two are tightly constrained and evolutionary studies have therefore often been based on relative brain size (i.e. brain size proportional to body size) rather than absolute brain size. The process of domestication offers an excellent opportunity to disentangle the linkage between body and brain mass due to the extreme selection for increased body mass that has occurred. By breeding an intercross between domestic chicken and their wild progenitor, we address this relationship by simultaneously mapping the genes that control inter-population variation in brain mass and body mass. Loci controlling variation in brain mass and body mass have separate genetic architectures and are therefore not directly constrained. Genetic mapping of brain regions indicates that domestication has led to a larger body mass and to a lesser extent a larger absolute brain mass in chickens, mainly due to enlargement of the cerebellum. Domestication has traditionally been linked to brain mass regression, based on measurements of relative brain mass, which confounds the large body mass augmentation due to domestication. Our results refute this concept in the chicken.", "doi": "10.1038/srep34031", "pmid": "27687864", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5043184"}, {"db": "pii", "key": "srep34031"}], "notes": [], "created": "2017-12-05T12:58:24.406Z", "modified": "2021-06-21T15:52:21.209Z"}, {"entity": "publication", "iuid": "b823bf88c8f34496bc8d7bc3366313c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b823bf88c8f34496bc8d7bc3366313c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b823bf88c8f34496bc8d7bc3366313c2"}}, "title": "Genomic Regions Associated With Interspecies Communication in Dogs Contain Genes Related to Human Social Disorders.", "authors": [{"family": "Persson", "given": "Mia E", "initials": "ME"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Roth", "given": "Lina S V", "initials": "LS"}, {"family": "Batakis", "given": "Petros", "initials": "P"}, {"family": "Jensen", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2016-09-29", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "33439", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Unlike their wolf ancestors, dogs have unique social skills for communicating and cooperating with humans. Previously, significant heritabilities for human-directed social behaviors have been found in laboratory beagles. Here, a Genome-Wide Association Study identified two genomic regions associated with dog's human-directed social behaviors. We recorded the propensity of laboratory beagles, bred, kept and handled under standardized conditions, to initiate physical interactions with a human during an unsolvable problem-task, and 190 individuals were genotyped with an HD Canine SNP-chip. One genetic marker on chromosome 26 within the SEZ6L gene was significantly associated with time spent close to, and in physical contact with, the human. Two suggestive markers on chromosome 26, located within the ARVCF gene, were also associated with human contact seeking. Strikingly, four additional genes present in the same linkage blocks affect social abilities in humans, e.g., SEZ6L has been associated with autism and COMT affects aggression in adolescents with ADHD. This is, to our knowledge, the first genome-wide study presenting candidate genomic regions for dog sociability and inter-species communication. These results advance our understanding of dog domestication and raise the use of the dog as a novel model system for human social disorders.", "doi": "10.1038/srep33439", "pmid": "27685260", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5041581"}, {"db": "pii", "key": "srep33439"}], "notes": [], "created": "2017-05-03T13:01:40.925Z", "modified": "2020-01-21T13:56:04.829Z"}, {"entity": "publication", "iuid": "e68d3001182f4c29a9dad85ffabfe505", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e68d3001182f4c29a9dad85ffabfe505.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e68d3001182f4c29a9dad85ffabfe505"}}, "title": "Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout.", "authors": [{"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Ebai", "given": "Tonge", "initials": "T"}, {"family": "Dubois", "given": "Louise", "initials": "L"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Ronquist", "given": "K G\u00f6ran", "initials": "KG"}, {"family": "Nolander", "given": "Olivia", "initials": "O"}, {"family": "Lundin", "given": "Emma", "initials": "E"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2016-09-29", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": "34358", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Flow cytometry is a powerful method for quantitative and qualitative analysis of individual cells. However, flow cytometric analysis of extracellular vesicles (EVs), and the proteins present on their surfaces has been hampered by the small size of the EVs - in particular for the smallest EVs, which can be as little as 40 nm in diameter, the limited number of antigens present, and their low refractive index. We addressed these limitations for detection and characterization of EV by flow cytometry through the use of multiplex and multicolor in situ proximity ligation assays (in situ PLA), allowing each detected EV to be easily recorded over background noise using a conventional flow cytometer. By targeting sets of proteins on the surface that are specific for distinct classes of EVs, the method allows for selective recognition of populations of EVs in samples containing more than one type of EVs. The method presented herein opens up for analyses of EVs using flow cytometry for their characterization and quantification.", "doi": "10.1038/srep34358", "pmid": "27681459", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC5041182"}, {"db": "pii", "key": "srep34358"}], "notes": [], "created": "2017-05-03T12:59:12.434Z", "modified": "2023-04-14T13:56:19.170Z"}, {"entity": "publication", "iuid": "885ef4eea0274699a8ff4fe57d743b59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/885ef4eea0274699a8ff4fe57d743b59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/885ef4eea0274699a8ff4fe57d743b59"}}, "title": "Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples.", "authors": [{"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Skoog", "given": "Tiina", "initials": "T"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Kaartokallio", "given": "Tea", "initials": "T"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}, {"family": "Grauers", "given": "Anna", "initials": "A"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}, {"family": "Hyt\u00f6nen", "given": "Marjo", "initials": "M"}, {"family": "Lohi", "given": "Hannes", "initials": "H"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Jiao", "given": "Hong", "initials": "H"}], "type": "journal article", "published": "2016-09-16", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "33256", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "High-throughput sequencing using pooled DNA samples can facilitate genome-wide studies on rare and low-frequency variants in a large population. Some major questions concerning the pooling sequencing strategy are whether rare and low-frequency variants can be detected reliably, and whether estimated minor allele frequencies (MAFs) can represent the actual values obtained from individually genotyped samples. In this study, we evaluated MAF estimates using three variant detection tools with two sets of pooled whole exome sequencing (WES) and one set of pooled whole genome sequencing (WGS) data. Both GATK and Freebayes displayed high sensitivity, specificity and accuracy when detecting rare or low-frequency variants. For the WGS study, 56% of the low-frequency variants in Illumina array have identical MAFs and 26% have one allele difference between sequencing and individual genotyping data. The MAF estimates from WGS correlated well (r\u2009=\u20090.94) with those from Illumina arrays. The MAFs from the pooled WES data also showed high concordance (r\u2009=\u20090.88) with those from the individual genotyping data. In conclusion, the MAFs estimated from pooled DNA sequencing data reflect the MAFs in individually genotyped samples well. The pooling strategy can thus be a rapid and cost-effective approach for the initial screening in large-scale association studies.", "doi": "10.1038/srep33256", "pmid": "27633116", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep33256"}, {"db": "pmc", "key": "PMC5025741"}], "notes": [], "created": "2017-05-03T13:00:02.994Z", "modified": "2024-01-16T13:48:49.513Z"}, {"entity": "publication", "iuid": "c882c5012bfb4a08b63da6a75c675f35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c882c5012bfb4a08b63da6a75c675f35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c882c5012bfb4a08b63da6a75c675f35"}}, "title": "Genome-wide association analysis reveals variants on chromosome 19 that contribute to childhood risk of chronic otitis media with effusion.", "authors": [{"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Hafr\u00e9n", "given": "Lena", "initials": "L"}, {"family": "Leinonen", "given": "Eira", "initials": "E"}, {"family": "Bhutta", "given": "Mahmood F", "initials": "MF"}, {"family": "Kentala", "given": "Erna", "initials": "E"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Mattila", "given": "Petri S", "initials": "PS"}], "type": "journal article", "published": "2016-09-16", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "33240", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "To identify genetic risk factors of childhood otitis media (OM), a genome-wide association study was performed on Finnish subjects, 829 affected children, and 2118 randomly selected controls. The most significant and validated finding was an association with an 80\u2009kb region on chromosome 19. It includes the variants rs16974263 (P\u2009=\u20091.77\u2009\u00d7\u200910(-7), OR\u2009=\u20091.59), rs268662 (P\u2009=\u20091.564\u2009\u00d7\u200910(-6), OR\u2009=\u20091.54), and rs4150992 (P\u2009=\u20093.37\u2009\u00d7\u200910(-6), OR\u2009=\u20091.52), and harbors the genes PLD3, SERTAD1, SERTAD3, HIPK4, PRX, and BLVRB, all in strong linkage disequilibrium. In a sub-phenotype analysis of the 512 patients with chronic otitis media with effusion, one marker reached genome-wide significance (rs16974263, P\u2009=\u20092.92\u2009\u00d7\u200910(-8)). The association to this locus was confirmed but with an association signal in the opposite direction, in a UK family cohort of 4860 subjects (rs16974263, P\u2009=\u20093.21\u2009\u00d7\u200910(-4), OR\u2009=\u20090.72; rs4150992, P\u2009=\u20091.62\u2009\u00d7\u200910(-4), OR\u2009=\u20090.71). Thus we hypothesize that this region is important for COME risk in both the Finnish and UK populations, although the precise risk variants or haplotype background remain unclear. Our study suggests that the identified region on chromosome 19 includes a novel and previously uncharacterized risk locus for OM.", "doi": "10.1038/srep33240", "pmid": "27632927", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep33240"}, {"db": "pmc", "key": "PMC5025747"}], "notes": [], "created": "2017-05-03T13:00:02.698Z", "modified": "2024-01-16T13:48:49.521Z"}, {"entity": "publication", "iuid": "83ce542c90944860b9f0d963d39f3beb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83ce542c90944860b9f0d963d39f3beb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83ce542c90944860b9f0d963d39f3beb"}}, "title": "The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes.", "authors": [{"family": "Okamoto", "given": "Kenta", "initials": "K"}, {"family": "Miyazaki", "given": "Naoyuki", "initials": "N"}, {"family": "Larsson", "given": "Daniel S D", "initials": "DS"}, {"family": "Kobayashi", "given": "Daisuke", "initials": "D"}, {"family": "Svenda", "given": "Martin", "initials": "M"}, {"family": "M\u00fchlig", "given": "Kerstin", "initials": "K"}, {"family": "Maia", "given": "Filipe R N C", "initials": "FR"}, {"family": "Gunn", "given": "Laura H", "initials": "LH"}, {"family": "Isawa", "given": "Haruhiko", "initials": "H"}, {"family": "Kobayashi", "given": "Mutsuo", "initials": "M"}, {"family": "Sawabe", "given": "Kyoko", "initials": "K"}, {"family": "Murata", "given": "Kazuyoshi", "initials": "K"}, {"family": "Hajdu", "given": "Janos", "initials": "J"}], "type": "journal article", "published": "2016-09-12", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "33170", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9\u2009\u00c5 resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3\u2009\u00c5 resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short \"plug\" structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.", "doi": "10.1038/srep33170", "pmid": "27616740", "labels": {"Mass Spectrometry-based Proteomics, Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "srep33170"}, {"db": "pmc", "key": "PMC5018817"}], "notes": [], "created": "2017-05-08T07:59:51.694Z", "modified": "2017-06-12T11:40:05.844Z"}, {"entity": "publication", "iuid": "a45902c4bb764244af071b5a7736a6e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a45902c4bb764244af071b5a7736a6e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a45902c4bb764244af071b5a7736a6e3"}}, "title": "Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.", "authors": [{"family": "Ferreira", "given": "Pedro G", "initials": "PG"}, {"family": "Oti", "given": "Martin", "initials": "M"}, {"family": "Barann", "given": "Matthias", "initials": "M"}, {"family": "Wieland", "given": "Thomas", "initials": "T"}, {"family": "Ezquina", "given": "Suzana", "initials": "S"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Rivas", "given": "Manuel A", "initials": "MA"}, {"family": "Esteve-Codina", "given": "Anna", "initials": "A"}, {"family": "GEUVADIS Consortium", "given": null, "initials": null}, {"family": "Rosenstiel", "given": "Philip", "initials": "P"}, {"family": "Strom", "given": "Tim M", "initials": "TM"}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T"}, {"family": "Guig\u00f3", "given": "Roderic", "initials": "R"}, {"family": "Sammeth", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2016-09-12", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "32406", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.", "doi": "10.1038/srep32406", "pmid": "27617755", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep32406"}, {"db": "pmc", "key": "PMC5019111"}], "notes": [], "created": "2017-05-03T13:00:02.404Z", "modified": "2024-01-16T13:48:49.537Z"}, {"entity": "publication", "iuid": "e7aa8bb8c70b4b3ba992a62c9da38faa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7aa8bb8c70b4b3ba992a62c9da38faa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7aa8bb8c70b4b3ba992a62c9da38faa"}}, "title": "The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.", "authors": [{"family": "Schulte", "given": "Tim", "initials": "T"}, {"family": "Mikaelsson", "given": "Cecilia", "initials": "C"}, {"family": "Beaussart", "given": "Audrey", "initials": "A"}, {"family": "Kikhney", "given": "Alexey", "initials": "A"}, {"family": "Deshmukh", "given": "Maya", "initials": "M"}, {"family": "Wolniak", "given": "Sebastian", "initials": "S"}, {"family": "Pathak", "given": "Anuj", "initials": "A"}, {"family": "Ebel", "given": "Christine", "initials": "C"}, {"family": "L\u00f6fling", "given": "Jonas", "initials": "J"}, {"family": "Fogolari", "given": "Federico", "initials": "F"}, {"family": "Henriques-Normark", "given": "Birgitta", "initials": "B"}, {"family": "Dufr\u00eane", "given": "Yves F", "initials": "YF"}, {"family": "Svergun", "given": "Dmitri", "initials": "D"}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P\u00c5"}, {"family": "Achour", "given": "Adnane", "initials": "A"}], "type": "journal article", "published": "2016-09-01", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "32371", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The major human pathogen Streptococcus pneumoniae is a leading cause of disease and death worldwide. Pneumococcal biofilm formation within the nasopharynx leads to long-term colonization and persistence within the host. We have previously demonstrated that the capsular surface-associated pneumococcal serine rich repeat protein (PsrP), key factor for biofilm formation, binds to keratin-10 (KRT10) through its microbial surface component recognizing adhesive matrix molecule (MSCRAMM)-related globular binding region domain (BR187-385). Here, we show that BR187-385 also binds to DNA, as demonstrated by electrophoretic mobility shift assays and size exclusion chromatography. Further, heterologous expression of BR187-378 or the longer BR120-378 construct on the surface of a Gram-positive model host bacterium resulted in the formation of cellular aggregates that was significantly enhanced in the presence of DNA. Crystal structure analyses revealed the formation of BR187-385 homo-dimers via an intermolecular \u03b2-sheet, resulting in a positively charged concave surface, shaped to accommodate the acidic helical DNA structure. Furthermore, small angle X-ray scattering and circular dichroism studies indicate that the aggregate-enhancing N-terminal region of BR120-166 adopts an extended, non-globular structure. Altogether, our results suggest that PsrP adheres to extracellular DNA in the biofilm matrix and thus promotes pneumococcal biofilm formation.", "doi": "10.1038/srep32371", "pmid": "27582320", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "srep32371"}, {"db": "pmc", "key": "PMC5007671"}], "notes": [], "created": "2017-05-03T13:02:42.402Z", "modified": "2017-09-06T11:42:09.440Z"}, {"entity": "publication", "iuid": "17050c6756994b8aac25bf604512b098", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17050c6756994b8aac25bf604512b098.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17050c6756994b8aac25bf604512b098"}}, "title": "Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes", "authors": [{"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Dabir\u00e9", "given": "Roch K", "initials": "RK"}, {"family": "Hopkins", "given": "Richard", "initials": "R"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2016-09-00", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/srep22806", "pmid": "26960555", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:05.270Z", "modified": "2020-01-21T13:53:21.704Z"}, {"entity": "publication", "iuid": "79da525d578e49858d9311a9c79edce3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79da525d578e49858d9311a9c79edce3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79da525d578e49858d9311a9c79edce3"}}, "title": "Factors regulating capillary remodeling in a reversible model of inflammatory corneal angiogenesis.", "authors": [{"family": "Mukwaya", "given": "Anthony", "initials": "A"}, {"family": "Peebo", "given": "Beatrice", "initials": "B"}, {"family": "Xeroudaki", "given": "Maria", "initials": "M"}, {"family": "Ali", "given": "Zaheer", "initials": "Z"}, {"family": "Lennikov", "given": "Anton", "initials": "A"}, {"family": "Jensen", "given": "Lasse", "initials": "L"}, {"family": "Lagali", "given": "Neil", "initials": "N"}], "type": "journal article", "published": "2016-08-26", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": "32137", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Newly formed microcapillary networks arising in adult organisms by angiogenic and inflammatory stimuli contribute to pathologies such as corneal and retinal blindness, tumor growth, and metastasis. Therapeutic inhibition of pathologic angiogenesis has focused on targeting the VEGF pathway, while comparatively little attention has been given to remodeling of the new microcapillaries into a stabilized, functional, and persistent vascular network. Here, we used a novel reversible model of inflammatory angiogenesis in the rat cornea to investigate endogenous factors rapidly invoked to remodel, normalize and regress microcapillaries as part of the natural response to regain corneal avascularity. Rapid reversal of an inflammatory angiogenic stimulus suppressed granulocytic activity, enhanced recruitment of remodelling macrophages, induced capillary intussusception, and enriched pathways and processes involving immune cells, chemokines, morphogenesis, axonal guidance, and cell motility, adhesion, and cytoskeletal functions. Whole transcriptome gene expression analysis revealed suppression of numerous inflammatory and angiogenic factors and enhancement of endogenous inhibitors. Many of the identified genes function independently of VEGF and represent potentially new targets for molecular control of the critical process of microvascular remodeling and regression in the cornea.", "doi": "10.1038/srep32137", "pmid": "27561355", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "srep32137"}, {"db": "pmc", "key": "PMC4999823"}], "notes": [], "created": "2017-11-01T12:35:55.899Z", "modified": "2021-06-21T15:55:05.487Z"}, {"entity": "publication", "iuid": "8798ba5c101743bdb402113da96aa17d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8798ba5c101743bdb402113da96aa17d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8798ba5c101743bdb402113da96aa17d"}}, "title": "Identification of Multiple QTLs Linked to Neuropathology in the Engrailed-1 Heterozygous Mouse Model of Parkinson's Disease.", "authors": [{"family": "Kurowska", "given": "Zuzanna", "initials": "Z"}, {"family": "Jewett", "given": "Michael", "initials": "M"}, {"family": "Bratt\u00e5s", "given": "Per Ludvik", "initials": "PL"}, {"family": "Jimenez-Ferrer", "given": "Itzia", "initials": "I"}, {"family": "Ken\u00e9z", "given": "Xuyian", "initials": "X"}, {"family": "Bj\u00f6rklund", "given": "Tomas", "initials": "T"}, {"family": "Nordstr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Brundin", "given": "Patrik", "initials": "P"}, {"family": "Swanberg", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2016-08-23", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "31701", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Motor symptoms in Parkinson's disease are attributed to degeneration of midbrain dopaminergic neurons (DNs). Heterozygosity for Engrailed-1 (En1), one of the key factors for programming and maintenance of DNs, results in a parkinsonian phenotype featuring progressive degeneration of DNs in substantia nigra pars compacta (SNpc), decreased striatal dopamine levels and swellings of nigro-striatal axons in the SwissOF1-En1+/- mouse strain. In contrast, C57Bl/6-En1+/- mice do not display this neurodegenerative phenotype, suggesting that susceptibility to En1 heterozygosity is genetically regulated. Our goal was to identify quantitative trait loci (QTLs) that regulate the susceptibility to PD-like neurodegenerative changes in response to loss of one En1 allele. We intercrossed SwissOF1-En1+/- and C57Bl/6 mice to obtain F2 mice with mixed genomes and analyzed number of DNs in SNpc and striatal axonal swellings in 120 F2-En1+/- 17 week-old male mice. Linkage analyses revealed 8 QTLs linked to number of DNs (p\u2009=\u20092.4e-09, variance explained\u2009=\u200974%), 7 QTLs linked to load of axonal swellings (p\u2009=\u20091.7e-12, variance explained\u2009=\u200980%) and 8 QTLs linked to size of axonal swellings (p\u2009=\u20097.0e-11, variance explained\u2009=\u200974%). These loci should be of prime interest for studies of susceptibility to Parkinson's disease-like damage in rodent disease models and considered in clinical association studies in PD.", "doi": "10.1038/srep31701", "pmid": "27550741", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "srep31701"}, {"db": "pmc", "key": "PMC4994027"}], "notes": [], "created": "2017-05-03T13:01:40.038Z", "modified": "2020-01-21T13:56:03.458Z"}, {"entity": "publication", "iuid": "455643c8ae0642f1a0eb0f5ff2361068", "links": {"self": {"href": "https://publications.scilifelab.se/publication/455643c8ae0642f1a0eb0f5ff2361068.json"}, "display": {"href": "https://publications.scilifelab.se/publication/455643c8ae0642f1a0eb0f5ff2361068"}}, "title": "A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.", "authors": [{"family": "Bijlmakers", "given": "Marie-Jos\u00e9", "initials": "MJ"}, {"family": "Teixeira", "given": "Jo\u00e3o M C", "initials": "JM"}, {"family": "Boer", "given": "Roeland", "initials": "R"}, {"family": "Mayzel", "given": "Maxim", "initials": "M"}, {"family": "Puig-S\u00e0rries", "given": "Pilar", "initials": "P"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1821-4715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6463abd05b415696c52be577ca2be6.json"}}, {"family": "Coll", "given": "Miquel", "initials": "M"}, {"family": "Pons", "given": "Miquel", "initials": "M"}, {"family": "Crosas", "given": "Bernat", "initials": "B"}], "type": "journal article", "published": "2016-07-14", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "29232", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The activity of RING ubiquitin ligases (E3s) depends on an interaction between the RING domain and ubiquitin conjugating enzymes (E2), but posttranslational events or additional structural elements, yet largely undefined, are frequently required to enhance or regulate activity. Here, we show for the ubiquitin ligase RNF125 that, in addition to the RING domain, a C2HC Zn finger (ZnF) is crucial for activity, and a short linker sequence (Li2(120-128)) enhances activity. The contribution of these regions was first shown with truncated proteins, and the essential role of the ZnF was confirmed with mutations at the Zn chelating Cys residues. Using NMR, we established that the C2HC ZnF/Li2(120-128) region is crucial for binding of the RING domain to the E2 UbcH5a. The partial X-ray structure of RNF125 revealed the presence of extensive intramolecular interactions between the RING and C2HC ZnF. A mutation at one of the contact residues in the C2HC ZnF, a highly conserved M112, resulted in the loss of ubiquitin ligase activity. Thus, we identified the structural basis for an essential role of the C2HC ZnF and conclude that this domain stabilizes the RING domain, and is therefore required for binding of RNF125 to an E2.", "doi": "10.1038/srep29232", "pmid": "27411375", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "srep29232"}, {"db": "pmc", "key": "PMC4944129"}], "notes": [], "created": "2017-05-08T08:00:17.477Z", "modified": "2025-10-17T13:04:00.457Z"}, {"entity": "publication", "iuid": "9dbdcd74f6ad456e982606a5bcc4e5df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9dbdcd74f6ad456e982606a5bcc4e5df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9dbdcd74f6ad456e982606a5bcc4e5df"}}, "title": "Rosette-Disrupting Effect of an Anti-Plasmodial Compound for the Potential Treatment of Plasmodium falciparum Malaria Complications.", "authors": [{"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Quintana", "given": "Maria Del Pilar", "initials": "Mdel P"}, {"family": "Chan", "given": "Sherwin Chun Leung", "initials": "SC"}, {"family": "Masters", "given": "Ellen", "initials": "E"}, {"family": "Moles", "given": "Ernest", "initials": "E"}, {"family": "Liu", "given": "Jianping", "initials": "J"}, {"family": "Eriksson", "given": "Anders B", "initials": "AB"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2016-07-11", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "29317", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The spread of artemisinin-resistant parasites could lead to higher incidence of patients with malaria complications. However, there are no current treatments that directly dislodge sequestered parasites from the microvasculature. We show that four common antiplasmodial drugs do not disperse rosettes (erythrocyte clusters formed by malaria parasites) and therefore develop a cell-based high-throughput assay to identify potential rosette-disrupting compounds. A pilot screen of 2693 compounds identified Malaria Box compound MMV006764 as a potential candidate. Although it reduced rosetting by a modest 20%, MMV006764 was validated to be similarly effective against both blood group O and A rosettes of three laboratory parasite lines. Coupled with its antiplasmodial activity and drug-likeness, MMV006764 represents the first small-molecule compound that disrupts rosetting and could potentially be used in a resource-limited setting to treat patients deteriorating rapidly from malaria complications. Such dual-action drugs that simultaneously restore microcirculation and reduce parasite load could significantly reduce malaria morbidity and mortality.", "doi": "10.1038/srep29317", "pmid": "27403804", "labels": {"Karolinska High Throughput Center (KHTC)": "Service"}, "xrefs": [{"db": "pii", "key": "srep29317"}, {"db": "pmc", "key": "PMC4941523"}], "notes": [], "created": "2017-05-08T07:56:47.273Z", "modified": "2017-06-12T11:37:46.608Z"}, {"entity": "publication", "iuid": "a54fcff0811145f6946e924649231bf8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a54fcff0811145f6946e924649231bf8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a54fcff0811145f6946e924649231bf8"}}, "title": "Exome sequencing in pooled DNA samples to identify maternal pre-eclampsia risk variants.", "authors": [{"family": "Kaartokallio", "given": "Tea", "initials": "T"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Heinonen", "given": "Seppo", "initials": "S"}, {"family": "Kajantie", "given": "Eero", "initials": "E"}, {"family": "Kivinen", "given": "Katja", "initials": "K"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2016-07-07", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "29085", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Pre-eclampsia is a common pregnancy disorder that is a major cause for maternal and perinatal mortality and morbidity. Variants predisposing to pre-eclampsia might be under negative evolutionary selection that is likely to keep their population frequencies low. We exome sequenced samples from a hundred Finnish pre-eclamptic women in pools of ten to screen for low-frequency, large-effect risk variants for pre-eclampsia. After filtering and additional genotyping steps, we selected 28 low-frequency missense, nonsense and splice site variants that were enriched in the pre-eclampsia pools compared to reference data, and genotyped the variants in 1353 pre-eclamptic and 699 non-pre-eclamptic women to test the association of them with pre-eclampsia and quantitative traits relevant for the disease. Genotypes from the SISu project (n\u2009=\u20096118 exome sequenced Finnish samples) were included in the binary trait association analysis as a population reference to increase statistical power. In these analyses, none of the variants tested reached genome-wide significance. In conclusion, the genetic risk for pre-eclampsia is likely complex even in a population isolate like Finland, and larger sample sizes will be necessary to detect risk variants.", "doi": "10.1038/srep29085", "pmid": "27384325", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep29085"}, {"db": "pmc", "key": "PMC4935848"}], "notes": [], "created": "2017-05-03T13:00:02.106Z", "modified": "2024-01-16T13:48:49.832Z"}, {"entity": "publication", "iuid": "9aa7b2f7a8ff48b396ec3f9ea85a16a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9aa7b2f7a8ff48b396ec3f9ea85a16a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9aa7b2f7a8ff48b396ec3f9ea85a16a3"}}, "title": "Genetic and environmental influences on height from infancy to early adulthood: An individual-based pooled analysis of 45 twin cohorts.", "authors": [{"family": "Jelenkovic", "given": "Aline", "initials": "A"}, {"family": "Sund", "given": "Reijo", "initials": "R"}, {"family": "Hur", "given": "Yoon-Mi", "initials": "YM"}, {"family": "Yokoyama", "given": "Yoshie", "initials": "Y"}, {"family": "Hjelmborg", "given": "Jacob V B", "initials": "JV"}, {"family": "M\u00f6ller", "given": "S\u00f6ren", "initials": "S"}, {"family": "Honda", "given": "Chika", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Ooki", "given": "Syuichi", "initials": "S"}, {"family": "Aaltonen", "given": "Sari", "initials": "S"}, {"family": "Stazi", "given": "Maria A", "initials": "MA"}, {"family": "Fagnani", "given": "Corrado", "initials": "C"}, {"family": "D'Ippolito", "given": "Cristina", "initials": "C"}, {"family": "Freitas", "given": "Duarte L", "initials": "DL"}, {"family": "Maia", "given": "Jos\u00e9 Antonio", "initials": "JA"}, {"family": "Ji", "given": "Fuling", "initials": "F"}, {"family": "Ning", "given": "Feng", "initials": "F"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Busjahn", "given": "Andreas", "initials": "A"}, {"family": "Kandler", "given": "Christian", "initials": "C"}, {"family": "Saudino", "given": "Kimberly J", "initials": "KJ"}, {"family": "Jang", "given": "Kerry L", "initials": "KL"}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Hwang", "given": "Amie E", "initials": "AE"}, {"family": "Mack", "given": "Thomas M", "initials": "TM"}, {"family": "Gao", "given": "Wenjing", "initials": "W"}, {"family": "Yu", "given": "Canqing", "initials": "C"}, {"family": "Li", "given": "Liming", "initials": "L"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM"}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Heikkil\u00e4", "given": "Kauko", "initials": "K"}, {"family": "Wardle", "given": "Jane", "initials": "J"}, {"family": "Llewellyn", "given": "Clare H", "initials": "CH"}, {"family": "Fisher", "given": "Abigail", "initials": "A"}, {"family": "McAdams", "given": "Tom A", "initials": "TA"}, {"family": "Eley", "given": "Thalia C", "initials": "TC"}, {"family": "Gregory", "given": "Alice M", "initials": "AM"}, {"family": "He", "given": "Mingguang", "initials": "M"}, {"family": "Ding", "given": "Xiaohu", "initials": "X"}, {"family": "Bjerregaard-Andersen", "given": "Morten", "initials": "M"}, {"family": "Beck-Nielsen", "given": "Henning", "initials": "H"}, {"family": "Sodemann", "given": "Morten", "initials": "M"}, {"family": "Tarnoki", "given": "Adam D", "initials": "AD"}, {"family": "Tarnoki", "given": "David L", "initials": "DL"}, {"family": "Knafo-Noam", "given": "Ariel", "initials": "A"}, {"family": "Mankuta", "given": "David", "initials": "D"}, {"family": "Abramson", "given": "Lior", "initials": "L"}, {"family": "Burt", "given": "S Alexandra", "initials": "SA"}, {"family": "Klump", "given": "Kelly L", "initials": "KL"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Eaves", "given": "Lindon J", "initials": "LJ"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Butler", "given": "David A", "initials": "DA"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "van Beijsterveldt", "given": "Toos C E M", "initials": "TC"}, {"family": "Craig", "given": "Jeffrey M", "initials": "JM"}, {"family": "Saffery", "given": "Richard", "initials": "R"}, {"family": "Dubois", "given": "Lise", "initials": "L"}, {"family": "Boivin", "given": "Michel", "initials": "M"}, {"family": "Brendgen", "given": "Mara", "initials": "M"}, {"family": "Dionne", "given": "Ginette", "initials": "G"}, {"family": "Vitaro", "given": "Frank", "initials": "F"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "Krasnow", "given": "Ruth", "initials": "R"}, {"family": "Tynelius", "given": "Per", "initials": "P"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Haworth", "given": "Claire M A", "initials": "CM"}, {"family": "Plomin", "given": "Robert", "initials": "R"}, {"family": "Bayasgalan", "given": "Gombojav", "initials": "G"}, {"family": "Narandalai", "given": "Danshiitsoodol", "initials": "D"}, {"family": "Harden", "given": "K Paige", "initials": "KP"}, {"family": "Tucker-Drob", "given": "Elliot M", "initials": "EM"}, {"family": "Spector", "given": "Timothy", "initials": "T"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Lachance", "given": "Genevieve", "initials": "G"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Duncan", "given": "Glen E", "initials": "GE"}, {"family": "Buchwald", "given": "Dedra", "initials": "D"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Skytthe", "given": "Axel", "initials": "A"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F"}, {"family": "Rasmussen", "given": "Finn", "initials": "F"}, {"family": "Goldberg", "given": "Jack H", "initials": "JH"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TI"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Silventoinen", "given": "Karri", "initials": "K"}], "type": "journal article", "published": "2016-06-23", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "28496", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Height variation is known to be determined by both genetic and environmental factors, but a systematic description of how their influences differ by sex, age and global regions is lacking. We conducted an individual-based pooled analysis of 45 twin cohorts from 20 countries, including 180,520 paired measurements at ages 1-19\u2009years. The proportion of height variation explained by shared environmental factors was greatest in early childhood, but these effects remained present until early adulthood. Accordingly, the relative genetic contribution increased with age and was greatest in adolescence (up to 0.83 in boys and 0.76 in girls). Comparing geographic-cultural regions (Europe, North-America and Australia, and East-Asia), genetic variance was greatest in North-America and Australia and lowest in East-Asia, but the relative proportion of genetic variation was roughly similar across these regions. Our findings provide further insights into height variation during childhood and adolescence in populations representing different ethnicities and exposed to different environments.", "doi": "10.1038/srep28496", "pmid": "27333805", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep28496"}, {"db": "pmc", "key": "PMC4917845"}], "notes": [], "created": "2017-05-08T07:57:47.087Z", "modified": "2024-01-16T13:48:49.924Z"}, {"entity": "publication", "iuid": "1f569b02fad4412093fb86a85265123f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f569b02fad4412093fb86a85265123f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f569b02fad4412093fb86a85265123f"}}, "title": "Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30\u2009\u00b0C.", "authors": [{"family": "Caspeta", "given": "Luis", "initials": "L"}, {"family": "Chen", "given": "Yun", "initials": "Y"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2016-05-27", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "27003", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Exposure to long-term environmental changes across >100s of generations results in adapted phenotypes, but little is known about how metabolic and transcriptional responses are optimized in these processes. Here, we show that thermotolerant yeast strains selected by adaptive laboratory evolution to grow at increased temperature, activated a constitutive heat stress response when grown at the optimal ancestral temperature, and that this is associated with a reduced growth rate. This preventive response was perfected by additional transcriptional changes activated when the cultivation temperature is increased. Remarkably, the sum of global transcriptional changes activated in the thermotolerant strains when transferred from the optimal to the high temperature, corresponded, in magnitude and direction, to the global changes observed in the ancestral strain exposed to the same transition. This demonstrates robustness of the yeast transcriptional program when exposed to heat, and that the thermotolerant strains streamlined their path to rapidly and optimally reach post-stress transcriptional and metabolic levels. Thus, long-term adaptation to heat improved yeasts ability to rapidly adapt to increased temperatures, but this also causes a trade-off in the growth rate at the optimal ancestral temperature.", "doi": "10.1038/srep27003", "pmid": "27229477", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep27003"}, {"db": "pmc", "key": "PMC4882594"}], "notes": [], "created": "2017-05-03T13:00:01.805Z", "modified": "2024-01-16T13:48:50.050Z"}, {"entity": "publication", "iuid": "0fe9c3d9c9944920a4f1ff97ead1062f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fe9c3d9c9944920a4f1ff97ead1062f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fe9c3d9c9944920a4f1ff97ead1062f"}}, "title": "Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2016-05-04", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "25274", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.", "doi": "10.1038/srep25274", "pmid": "27143688", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "srep25274"}, {"db": "pmc", "key": "PMC4855147"}], "notes": [], "created": "2017-05-03T12:58:50.081Z", "modified": "2021-07-07T20:31:10.696Z"}, {"entity": "publication", "iuid": "21e3b46404d64b53b70917d735291b2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21e3b46404d64b53b70917d735291b2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21e3b46404d64b53b70917d735291b2c"}}, "title": "The chemosensory receptors of codling moth Cydia pomonella-expression in larvae and adults.", "authors": [{"family": "Walker", "given": "William B", "initials": "WB"}, {"family": "Gonzalez", "given": "Francisco", "initials": "F"}, {"family": "Garczynski", "given": "Stephen F", "initials": "SF"}, {"family": "Witzgall", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2016-03-23", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "23518", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Olfaction and gustation play critical roles in the life history of insects, mediating vital behaviors such as food, mate and host seeking. Chemosensory receptor proteins, including odorant receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) function to interface the insect with its chemical environment. Codling moth, Cydia pomonella, is a worldwide pest of apple, pear and walnut, and behavior-modifying semiochemicals are used for environmentally safe control. We produced an Illumina-based transcriptome from antennae of males and females as well as neonate head tissue, affording a qualitative and quantitative analysis of the codling moth chemosensory receptor repertoire. We identified 58 ORs, 20 GRs and 21 IRs, and provide a revised nomenclature that is consistent with homologous sequences in related species. Importantly, we have identified several OR transcripts displaying sex-biased expression in adults, as well as larval-enriched transcripts. Our analyses have expanded annotations of the chemosensory receptor gene families, and provide first-time transcript abundance estimates for codling moth. The results presented here provide a strong foundation for future work on codling moth behavioral physiology and ecology at the molecular level, and may lead to the development of more precise biorational control strategies.", "doi": "10.1038/srep23518", "pmid": "27006164", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep23518"}, {"db": "pmc", "key": "PMC4804390"}], "notes": [], "created": "2017-05-03T13:00:01.511Z", "modified": "2024-01-16T13:48:50.341Z"}, {"entity": "publication", "iuid": "13a79f3ecf9e4607999f5cbcab5393fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13a79f3ecf9e4607999f5cbcab5393fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13a79f3ecf9e4607999f5cbcab5393fb"}}, "title": "Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia.", "authors": [{"family": "Gyarmati", "given": "P", "initials": "P"}, {"family": "Kjellander", "given": "C", "initials": "C"}, {"family": "Aust", "given": "C", "initials": "C"}, {"family": "Song", "given": "Y", "initials": "Y"}, {"family": "\u00d6hrmalm", "given": "L", "initials": "L"}, {"family": "Giske", "given": "C G", "initials": "CG"}], "type": "journal article", "published": "2016-03-21", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "23532", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Leukemic patients are often immunocompromised due to underlying conditions, comorbidities and the effects of chemotherapy, and thus at risk for developing systemic infections. Bloodstream infection (BSI) is a severe complication in neutropenic patients, and is associated with increased mortality. BSI is routinely diagnosed with blood culture, which only detects culturable pathogens. We analyzed 27 blood samples from 9 patients with acute leukemia and suspected BSI at different time points of their antimicrobial treatment using shotgun metagenomics sequencing in order to detect unculturable and non-bacterial pathogens. Our findings confirm the presence of bacterial, fungal and viral pathogens alongside antimicrobial resistance genes. Decreased white blood cell (WBC) counts were associated with the presence of microbial DNA, and was inversely proportional to the number of sequencing reads. This study could indicate the use of high-throughput sequencing for personalized antimicrobial treatments in BSIs.", "doi": "10.1038/srep23532", "pmid": "26996149", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep23532"}, {"db": "pmc", "key": "PMC4800731"}], "notes": [], "created": "2017-05-03T12:58:56.671Z", "modified": "2020-01-21T13:56:00.833Z"}, {"entity": "publication", "iuid": "845967e99a9241bb9066d04642cd73bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/845967e99a9241bb9066d04642cd73bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/845967e99a9241bb9066d04642cd73bb"}}, "title": "Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans.", "authors": [{"family": "Zangenah", "given": "Salah", "initials": "S"}, {"family": "Abbasi", "given": "Nasir", "initials": "N"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bergman", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2016-03-07", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "22919", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "C. canimorsus and C. cynodegmi are dog and cat commensals which can be transmitted to humans via bites or scratches and can cause sepsis, meningitis, endocarditis, and eye- or wound infections. Recently an additional Capnocytophaga species was identified as part of the oral flora of healthy dogs and was given the name \"C. canis\". We previously identified a Capnocytophaga isolate that could not be typed with available diagnostic tests including MALDI-TOF, 16S rRNA sequencing or species-specific PCR. This strain and 21 other Capnocytophaga spp isolated in Sweden from clinical blood- or wound-cultures were subjected to whole genome sequencing using the Illumina platform. Phylogenetic analysis revealed that the previously non-typable isolate belongs to the putative new species \"C. canis\". Since this strain was isolated from a wound it also shows that members of \"C. canis\" have the potential to be pathogenic. In addition, our phylogenetic analysis uncovered an additional species of Capnocytophaga, which can be transmitted from dogs and cats to humans, suggesting a speciation within the Capnocytophaga family that has not been observed before. We propose the name of \"C. stomatis\" for this putative novel species.", "doi": "10.1038/srep22919", "pmid": "26947740", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep22919"}, {"db": "pmc", "key": "PMC4780008"}], "notes": [], "created": "2017-05-03T13:00:01.213Z", "modified": "2024-01-16T13:48:50.364Z"}, {"entity": "publication", "iuid": "cfe4260e16314a9ea8a28ff73a6111df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cfe4260e16314a9ea8a28ff73a6111df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cfe4260e16314a9ea8a28ff73a6111df"}}, "title": "Cells release subpopulations of exosomes with distinct molecular and biological properties.", "authors": [{"family": "Willms", "given": "Eduard", "initials": "E"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "M\u00e4ger", "given": "Imre", "initials": "I"}, {"family": "Lee", "given": "Yi", "initials": "Y"}, {"family": "Blomberg", "given": "K Emelie M", "initials": "KE"}, {"family": "Sadik", "given": "Mariam", "initials": "M"}, {"family": "Alaarg", "given": "Amr", "initials": "A"}, {"family": "Smith", "given": "C I Edvard", "initials": "CI"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}, {"family": "Wood", "given": "Matthew J A", "initials": "MJ"}, {"family": "Vader", "given": "Pieter", "initials": "P"}], "type": "journal article", "published": "2016-03-02", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "22519", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cells release nano-sized membrane vesicles that are involved in intercellular communication by transferring biological information between cells. It is generally accepted that cells release at least three types of extracellular vesicles (EVs): apoptotic bodies, microvesicles and exosomes. While a wide range of putative biological functions have been attributed to exosomes, they are assumed to represent a homogenous population of EVs. We hypothesized the existence of subpopulations of exosomes with defined molecular compositions and biological properties. Density gradient centrifugation of isolated exosomes revealed the presence of two distinct subpopulations, differing in biophysical properties and their proteomic and RNA repertoires. Interestingly, the subpopulations mediated differential effects on the gene expression programmes in recipient cells. In conclusion, we demonstrate that cells release distinct exosome subpopulations with unique compositions that elicit differential effects on recipient cells. Further dissection of exosome heterogeneity will advance our understanding of exosomal biology in health and disease and accelerate the development of exosome-based diagnostics and therapeutics.", "doi": "10.1038/srep22519", "pmid": "26931825", "labels": {"Clinical Proteomics Mass spectrometry": "Technology development"}, "xrefs": [{"db": "pii", "key": "srep22519"}, {"db": "pmc", "key": "PMC4773763"}], "notes": [], "created": "2017-05-03T13:02:32.859Z", "modified": "2021-07-08T11:36:15.276Z"}, {"entity": "publication", "iuid": "d48238f7395548c49a05f2682302195a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d48238f7395548c49a05f2682302195a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d48238f7395548c49a05f2682302195a"}}, "title": "GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.", "authors": [{"family": "Edsg\u00e4rd", "given": "Daniel", "initials": "D"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Reilly", "given": "Sarah-Jayne", "initials": "SJ"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Tornvall", "given": "Per", "initials": "P"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}], "type": "journal article", "published": "2016-02-18", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "21134", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Allele-specific expression (ASE) is the imbalance in transcription between maternal and paternal alleles at a locus and can be probed in single individuals using massively parallel DNA sequencing technology. Assessing ASE within a single sample provides a static picture of the ASE, but the magnitude of ASE for a given transcript may vary between different biological conditions in an individual. Such condition-dependent ASE could indicate a genetic variation with a functional role in the phenotypic difference. We investigated ASE through RNA-sequencing of primary white blood cells from eight human individuals before and after the controlled induction of an inflammatory response, and detected condition-dependent and static ASE at 211 and 13021 variants, respectively. We developed a method, GeneiASE, to detect genes exhibiting static or condition-dependent ASE in single individuals. GeneiASE performed consistently over a range of read depths and ASE effect sizes, and did not require phasing of variants to estimate haplotypes. We observed condition-dependent ASE related to the inflammatory response in 19 genes, and static ASE in 1389 genes. Allele-specific expression was confirmed by validation of variants through real-time quantitative RT-PCR, with RNA-seq and RT-PCR ASE effect-size correlations r = 0.67 and r = 0.94 for static and condition-dependent ASE, respectively.", "doi": "10.1038/srep21134", "pmid": "26887787", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep21134"}, {"db": "pmc", "key": "PMC4758070"}], "notes": [], "created": "2017-05-03T13:00:00.913Z", "modified": "2024-01-16T13:48:50.435Z"}, {"entity": "publication", "iuid": "c20f0bcf05514700a52f34b7a89cd0f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c20f0bcf05514700a52f34b7a89cd0f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c20f0bcf05514700a52f34b7a89cd0f4"}}, "title": "Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1", "authors": [{"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Sharon", "given": "Donald", "initials": "D"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Edqvist", "given": "Per Henrik", "initials": "PH"}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Nelson", "given": "Lawrence M", "initials": "LM"}, {"family": "Gustafsson", "given": "Jan", "initials": "J"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Anderson", "given": "Mark S", "initials": "MS"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2016-02-01", "journal": {"volume": "6", "issn": "2045-2322", "issue": "1", "pages": "20104", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Autoimmune polyendocrine syndrome type 1 (APS1) is a monogenic disorder that features multiple autoimmune disease manifestations. It is caused by mutations in the Autoimmune regulator (AIRE) gene, which promote thymic display of thousands of peripheral tissue antigens in a process critical for establishing central immune tolerance. We here used proteome arrays to perform a comprehensive study of autoimmune targets in APS1. Interrogation of established autoantigens revealed highly reliable detection of autoantibodies, and by exploring the full panel of more than 9000 proteins we further identified MAGEB2 and PDILT as novel major autoantigens in APS1. Our proteome-wide assessment revealed a marked enrichment for tissue-specific immune targets, mirroring AIRE's selectiveness for this category of genes. Our findings also suggest that only a very limited portion of the proteome becomes targeted by the immune system in APS1, which contrasts the broad defect of thymic presentation associated with AIRE-deficiency and raises novel questions what other factors are needed for break of tolerance.", "doi": "10.1038/srep20104", "pmid": "26830021", "labels": {"Tissue Profiling": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC4735587"}, {"db": "pii", "key": "srep20104"}], "notes": [], "created": "2017-05-03T12:59:19.123Z", "modified": "2023-06-19T09:06:28.995Z"}, {"entity": "publication", "iuid": "5acd66e438084ca2bee217d62bc57bfc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5acd66e438084ca2bee217d62bc57bfc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5acd66e438084ca2bee217d62bc57bfc"}}, "title": "Sequence and gene expression evolution of paralogous genes in willows.", "authors": [{"family": "Harikrishnan", "given": "Srilakshmy L", "initials": "SL"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Berlin", "given": "Sofia", "initials": "S"}], "type": "journal article", "published": "2015-12-22", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "18662", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Whole genome duplications (WGD) have had strong impacts on species diversification by triggering evolutionary novelties, however, relatively little is known about the balance between gene loss and forces involved in the retention of duplicated genes originating from a WGD. We analyzed putative Salicoid duplicates in willows, originating from the Salicoid WGD, which took place more than 45 Mya. Contigs were constructed by de novo assembly of RNA-seq data derived from leaves and roots from two genotypes. Among the 48,508 contigs, 3,778 pairs were, based on fourfold synonymous third-codon transversion rates and syntenic positions, predicted to be Salicoid duplicates. Both copies were in most cases expressed in both tissues and 74% were significantly differentially expressed. Mean Ka/Ks was 0.23, suggesting that the Salicoid duplicates are evolving by purifying selection. Gene Ontology enrichment analyses showed that functions related to DNA- and nucleic acid binding were over-represented among the non-differentially expressed Salicoid duplicates, while functions related to biosynthesis and metabolism were over-represented among the differentially expressed Salicoid duplicates. We propose that the differentially expressed Salicoid duplicates are regulatory neo- and/or subfunctionalized, while the non-differentially expressed are dose sensitive, hence, functionally conserved. Multiple evolutionary processes, thus drive the retention of Salicoid duplicates in willows.", "doi": "10.1038/srep18662", "pmid": "26689951", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "srep18662"}, {"db": "pmc", "key": "PMC4687058"}, {"db": "ENA", "description": "RNA-seq data for willow", "key": "PRJEB10883"}], "notes": [], "created": "2017-10-30T09:32:38.264Z", "modified": "2020-01-21T13:56:11.133Z"}, {"entity": "publication", "iuid": "831286c09f7e42ce987b6b5b948920dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/831286c09f7e42ce987b6b5b948920dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/831286c09f7e42ce987b6b5b948920dd"}}, "title": "Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases.", "authors": [{"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Davanian", "given": "Haleh", "initials": "H"}, {"family": "B\u00e5ge", "given": "Tove", "initials": "T"}, {"family": "Johannsen", "given": "Gunnar", "initials": "G"}, {"family": "Koro", "given": "Catalin", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2015-12-21", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "18475", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The multifactorial chronic inflammatory disease periodontitis, which is characterized by destruction of tooth-supporting tissues, has also been implicated as a risk factor for various systemic diseases. Although periodontitis has been studied extensively, neither disease-specific biomarkers nor therapeutic targets have been identified, nor its link with systemic diseases. Here, we analyzed the global transcriptome of periodontitis and compared its gene expression profile with those of other inflammatory conditions, including cardiovascular disease (CVD), rheumatoid arthritis (RA), and ulcerative colitis (UC). Gingival biopsies from 62 patients with periodontitis and 62 healthy subjects were subjected to RNA sequencing. The up-regulated genes in periodontitis were related to inflammation, wounding and defense response, and apoptosis, whereas down-regulated genes were related to extracellular matrix organization and structural support. The most highly up-regulated gene was mucin 4 (MUC4), and its protein product was confirmed to be over-expressed in periodontitis. When comparing the expression profile of periodontitis with other inflammatory diseases, several gene ontology categories, including inflammatory response, cell death, cell motion, and homeostatic processes, were identified as common to all diseases. Only one gene, pleckstrin (PLEK), was significantly overexpressed in periodontitis, CVD, RA, and UC, implicating this gene as an important networking link between these chronic inflammatory diseases.", "doi": "10.1038/srep18475", "pmid": "26686060", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep18475"}, {"db": "pmc", "key": "PMC4685297"}], "notes": [], "created": "2017-05-02T12:57:54.257Z", "modified": "2021-07-08T13:26:08.230Z"}, {"entity": "publication", "iuid": "48d8ba1ce62d40b4acfcbdf772e3d082", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48d8ba1ce62d40b4acfcbdf772e3d082.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48d8ba1ce62d40b4acfcbdf772e3d082"}}, "title": "Protein profiling reveals consequences of lifestyle choices on predicted biological aging.", "authors": [{"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Enroth", "given": "Sofia Bosdotter", "initials": "SB"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "clinical trial", "published": "2015-12-01", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "5", "issue": "1", "pages": "17282"}, "abstract": "Ageing is linked to a number of changes in how the body and its organs function. On a molecular level, ageing is associated with a reduction of telomere length, changes in metabolic and gene-transcription profiles and an altered DNA-methylation pattern. Lifestyle factors such as smoking or stress can impact some of these molecular processes and thereby affect the ageing of an individual. Here we demonstrate by analysis of 77 plasma proteins in 976 individuals, that the abundance of circulating proteins accurately predicts chronological age, as well as anthropometrical measurements such as weight, height and hip circumference. The plasma protein profile can also be used to identify lifestyle factors that accelerate and decelerate ageing. We found smoking, high BMI and consumption of sugar-sweetened beverages to increase the predicted chronological age by 2-6 years, while consumption of fatty fish, drinking moderate amounts of coffee and exercising reduced the predicted age by approximately the same amount. This method can be applied to dried blood spots and may thus be useful in forensic medicine to provide basic anthropometrical measures for an individual based on a biological evidence sample.", "doi": "10.1038/srep17282", "pmid": "26619799", "labels": {"Clinical Biomarkers": "", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "srep17282"}, {"db": "pmc", "key": "PMC4664859"}], "notes": [], "created": "2017-05-02T12:56:57.567Z", "modified": "2023-04-14T13:56:23.515Z"}, {"entity": "publication", "iuid": "9529d31ff6fd4e1ca213ed3b76d4c1fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9529d31ff6fd4e1ca213ed3b76d4c1fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9529d31ff6fd4e1ca213ed3b76d4c1fb"}}, "title": "Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.", "authors": [{"family": "Kvastad", "given": "L", "initials": "L"}, {"family": "Werne Solnestam", "given": "B", "initials": "B"}, {"family": "Johansson", "given": "E", "initials": "E"}, {"family": "Nygren", "given": "A O", "initials": "AO"}, {"family": "Laddach", "given": "N", "initials": "N"}, {"family": "Sahl\u00e9n", "given": "P", "initials": "P"}, {"family": "Vickovic", "given": "S", "initials": "S"}, {"family": "Bendigtsen", "given": "Schirmer C", "initials": "SC"}, {"family": "Aaserud", "given": "M", "initials": "M"}, {"family": "Floer", "given": "L", "initials": "L"}, {"family": "Borgen", "given": "E", "initials": "E"}, {"family": "Schwind", "given": "C", "initials": "C"}, {"family": "Himmelreich", "given": "R", "initials": "R"}, {"family": "Latta", "given": "D", "initials": "D"}, {"family": "Lundeberg", "given": "J", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2015-11-12", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "16519", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Single cell analysis techniques have great potential in the cancer genomics field. The detection and characterization of circulating tumour cells are important for identifying metastatic disease at an early stage and monitoring it. This protocol is based on transcript profiling using Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (RT-MLPA), which is a specific method for simultaneous detection of multiple mRNA transcripts. Because of the small amount of (circulating) tumour cells, a pre-amplification reaction is performed after reverse transcription to generate a sufficient number of target molecules for the MLPA reaction. We designed a highly sensitive method for detecting and quantifying a panel of seven genes whose expression patterns are associated with breast cancer, and optimized the method for single cell analysis. For detection we used a fluorescence-dependent semi-quantitative method involving hybridization of unique barcodes to an array. We evaluated the method using three human breast cancer cell lines and identified specific gene expression profiles for each line. Furthermore, we applied the method to single cells and confirmed the heterogeneity of a cell population. Successful gene detection from cancer cells in human blood from metastatic breast cancer patients supports the use of RT-MLPA as a diagnostic tool for cancer genomics.", "doi": "10.1038/srep16519", "pmid": "26558529", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep16519"}, {"db": "pmc", "key": "PMC4642268"}], "notes": [], "created": "2017-05-02T12:57:41.587Z", "modified": "2021-07-08T13:26:08.246Z"}, {"entity": "publication", "iuid": "4e8b4856e2284782a9664cdf229e8c7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e8b4856e2284782a9664cdf229e8c7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e8b4856e2284782a9664cdf229e8c7e"}}, "title": "Membrane vesicle-mediated release of bacterial RNA.", "authors": [{"family": "Sj\u00f6str\u00f6m", "given": "Annika E", "initials": "AE"}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Uhlin", "given": "Bernt Eric", "initials": "BE"}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN"}], "type": "journal article", "published": "2015-10-20", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "15329", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Many Gram-negative bacterial species release outer membrane vesicles (OMVs) that interact with the host by delivering virulence factors. Here, we report for the first time that RNA is among the wide variety of bacterial components that are associated with OMVs. To characterize the RNA profiles of bacterial OMVs, we performed RNA deep sequencing analysis using OMV samples isolated from a wild type Vibrio cholerae O1 El Tor strain. The results showed that RNAs originating from intergenic regions were the most abundant. Our findings reveal a hitherto unrecognised feature of OMVs mimicking eukaryotic exosomes and highlight a need to evaluate the potential role of RNA-containing bacterial membrane vesicles in bacteria-host interactions.", "doi": "10.1038/srep15329", "pmid": "26483327", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "srep15329"}, {"db": "pmc", "key": "PMC4612299"}], "notes": [], "created": "2017-05-02T12:58:35.118Z", "modified": "2021-07-05T17:20:56.077Z"}, {"entity": "publication", "iuid": "5dea6ccd488843b989319330fede3e1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5dea6ccd488843b989319330fede3e1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5dea6ccd488843b989319330fede3e1c"}}, "title": "The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.", "authors": [{"family": "Gustafsson Sheppard", "given": "Nina", "initials": "N"}, {"family": "Jarl", "given": "Lisa", "initials": "L"}, {"family": "Mahadessian", "given": "Diana", "initials": "D"}, {"family": "Strittmatter", "given": "Laura", "initials": "L"}, {"family": "Schmidt", "given": "Angelika", "initials": "A"}, {"family": "Madhusudan", "given": "Nikhil", "initials": "N"}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J"}, {"family": "Lundberg", "given": "Emma K", "initials": "EK", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Jain", "given": "Mohit", "initials": "M"}, {"family": "Nilsson", "given": "Roland", "initials": "R"}], "type": "journal article", "published": "2015-10-13", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "15029", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Folate metabolism is central to cell proliferation and a target of commonly used cancer chemotherapeutics. In particular, the mitochondrial folate-coupled metabolism is thought to be important for proliferating cancer cells. The enzyme MTHFD2 in this pathway is highly expressed in human tumors and broadly required for survival of cancer cells. Although the enzymatic activity of the MTHFD2 protein is well understood, little is known about its larger role in cancer cell biology. We here report that MTHFD2 is co-expressed with two distinct gene sets, representing amino acid metabolism and cell proliferation, respectively. Consistent with a role for MTHFD2 in cell proliferation, MTHFD2 expression was repressed in cells rendered quiescent by deprivation of growth signals (serum) and rapidly re-induced by serum stimulation. Overexpression of MTHFD2 alone was sufficient to promote cell proliferation independent of its dehydrogenase activity, even during growth restriction. In addition to its known mitochondrial localization, we found MTHFD2 to have a nuclear localization and co-localize with DNA replication sites. These findings suggest a previously unknown role for MTHFD2 in cancer cell proliferation, adding to its known function in mitochondrial folate metabolism.", "doi": "10.1038/srep15029", "pmid": "26461067", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "srep15029"}, {"db": "pmc", "key": "PMC4602236"}], "notes": [], "created": "2017-05-02T12:57:10.159Z", "modified": "2021-07-05T16:33:38.805Z"}, {"entity": "publication", "iuid": "861dfa4538c64bb987ff79cf41607da8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/861dfa4538c64bb987ff79cf41607da8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/861dfa4538c64bb987ff79cf41607da8"}}, "title": "Dormant phages of Helicobacter pylori reveal distinct populations in Europe.", "authors": [{"family": "Vale", "given": "F F", "initials": "FF"}, {"family": "Vadivelu", "given": "J", "initials": "J"}, {"family": "Oleastro", "given": "M", "initials": "M"}, {"family": "Breurec", "given": "S", "initials": "S"}, {"family": "Engstrand", "given": "L", "initials": "L"}, {"family": "Perets", "given": "T T", "initials": "TT"}, {"family": "M\u00e9graud", "given": "F", "initials": "F"}, {"family": "Lehours", "given": "P", "initials": "P"}], "type": "journal article", "published": "2015-09-21", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "14333", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.", "doi": "10.1038/srep14333", "pmid": "26387443", "labels": {"Clinical Genomics Stockholm": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "srep14333"}, {"db": "pmc", "key": "PMC4585682"}], "notes": [], "created": "2017-05-03T13:02:20.723Z", "modified": "2017-09-06T11:51:11.934Z"}, {"entity": "publication", "iuid": "abda054a1679462f8fb7b278c1b968b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abda054a1679462f8fb7b278c1b968b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abda054a1679462f8fb7b278c1b968b2"}}, "title": "Gene expression profiling of pre-eclamptic placentae by RNA sequencing.", "authors": [{"family": "Kaartokallio", "given": "Tea", "initials": "T"}, {"family": "Cervera", "given": "Alejandra", "initials": "A"}, {"family": "Kyll\u00f6nen", "given": "Anjuska", "initials": "A"}, {"family": "Laivuori", "given": "Krista", "initials": "K"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}, {"family": "FINNPEC Core Investigator Group", "given": null, "initials": null}], "type": "journal article", "published": "2015-09-21", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "14107", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Pre-eclampsia is a common and complex pregnancy disorder that often involves impaired placental development. In order to identify altered gene expression in pre-eclamptic placenta, we sequenced placental transcriptomes of nine pre-eclamptic and nine healthy pregnant women in pools of three. The differential gene expression was tested both by including all the pools in the analysis and by excluding some of the pools based on phenotypic characteristics. From these analyses, we identified altogether 53 differently expressed genes, a subset of which was validated by qPCR in 20 cases and 19 controls. Furthermore, we conducted pathway and functional analyses which revealed disturbed vascular function and immunological balance in pre-eclamptic placenta. Some of the genes identified in our study have been reported by numerous microarray studies (BHLHE40, FSTL3, HK2, HTRA4, LEP, PVRL4, SASH1, SIGLEC6), but many have been implicated in only few studies or have not previously been linked to pre-eclampsia (ARMS2, BTNL9, CCSAP, DIO2, FER1L4, HPSE, LOC100129345, LYN, MYO7B, NCMAP, NDRG1, NRIP1, PLIN2, SBSPON, SERPINB9, SH3BP5, TET3, TPBG, ZNF175). Several of the molecules produced by these genes may have a role in the pathogenesis of pre-eclampsia, and some could qualify as biomarkers for prediction or detection of this pregnancy complication.", "doi": "10.1038/srep14107", "pmid": "26388242", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep14107"}, {"db": "pmc", "key": "PMC4585671"}], "notes": [], "created": "2017-05-02T12:57:32.623Z", "modified": "2020-01-21T13:56:04.490Z"}, {"entity": "publication", "iuid": "8dac5e0b21e742039ce39d65201da20f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8dac5e0b21e742039ce39d65201da20f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8dac5e0b21e742039ce39d65201da20f"}}, "title": "Design, Synthesis and Inhibitory Activity of Photoswitchable RET Kinase Inhibitors", "authors": [{"family": "Ferreira", "given": "Rub\u00e9n", "initials": "R"}, {"family": "Nilsson", "given": "Jesper R", "initials": "JR"}, {"family": "Solano", "given": "Carlos", "initials": "C"}, {"family": "Andr\u00e9asson", "given": "Joakim", "initials": "J"}, {"family": "Gr\u00f8tli", "given": "Morten", "initials": "M"}], "type": "journal-article", "published": "2015-09-00", "journal": {"volume": "5", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/srep09769", "pmid": "25944708", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": "Laboratories for Chemical Biology at Karolinska Institutet (LCBKI)", "created": "2017-05-02T12:58:26.802Z", "modified": "2025-10-17T13:04:29.748Z"}, {"entity": "publication", "iuid": "8a731b002afd4687b02d25ba783fe634", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a731b002afd4687b02d25ba783fe634.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a731b002afd4687b02d25ba783fe634"}}, "title": "Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio.", "authors": [{"family": "Clausson", "given": "Carl-Magnus", "initials": "C"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Ishaq", "given": "Omer", "initials": "O"}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "K\u00fchnemund", "given": "Malte", "initials": "M"}, {"family": "Grannas", "given": "Karin", "initials": "K"}, {"family": "Koos", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "Ranefall", "given": "Petter", "initials": "P"}, {"family": "Krzywkowski", "given": "Tomasz", "initials": "T"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}], "type": "comparative study", "published": "2015-07-23", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "12317", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.", "doi": "10.1038/srep12317", "pmid": "26202090", "labels": {"BioImage Informatics": "Technology development", "Integrated Microscopy Technologies Stockholm": "Collaborative", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "srep12317"}, {"db": "pmc", "key": "PMC4511876"}], "notes": [], "created": "2017-05-02T12:56:40.263Z", "modified": "2021-07-07T13:54:46.097Z"}, {"entity": "publication", "iuid": "8ecb72b2ac3543c29928f333daae44fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ecb72b2ac3543c29928f333daae44fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ecb72b2ac3543c29928f333daae44fd"}}, "title": "Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes.", "authors": [{"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Sinclair", "given": "Lucas", "initials": "L"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2015-07-10", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "12102", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the bottom waters, rare and poorly characterized taxa, such as \u03b5-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. These oxygen-depleted layers exhibited high genetic potential for mineralization, but also for fixation of carbon and nitrogen, and genetic markers for both methane production and oxidation were present. Our study provides a first glimpse of the genetic versatility of freshwater anoxic zones, and demonstrates the potential for complete turnover of carbon compounds within the water column.", "doi": "10.1038/srep12102", "pmid": "26159227", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "srep12102"}, {"db": "pmc", "key": "PMC4498382"}], "notes": [], "created": "2017-05-02T12:58:18.526Z", "modified": "2020-01-21T13:56:03.688Z"}, {"entity": "publication", "iuid": "ba6c59a90be24996b1c5c9e83945e863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba6c59a90be24996b1c5c9e83945e863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba6c59a90be24996b1c5c9e83945e863"}}, "title": "Scaffolding of a bacterial genome using MinION nanopore sequencing.", "authors": [{"family": "Karlsson", "given": "E", "initials": "E"}, {"family": "L\u00e4rkeryd", "given": "A", "initials": "A"}, {"family": "Sj\u00f6din", "given": "A", "initials": "A"}, {"family": "Forsman", "given": "M", "initials": "M"}, {"family": "Stenberg", "given": "P", "initials": "P"}], "type": "journal article", "published": "2015-07-07", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "11996", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program. The latter has highly advantageous portability and sequences samples by measuring changes in ionic current when single-stranded DNA molecules are translocated through nanopores. We show that the MinION system produces long reads with high mapability that can be used for scaffolding bacterial genomes, despite currently producing substantially higher error rates than PacBio reads. With further development we anticipate that MinION will be useful not only for assembling genomes, but also for rapid detection of organisms, potentially in the field.", "doi": "10.1038/srep11996", "pmid": "26149338", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "srep11996"}, {"db": "pmc", "key": "PMC4493687"}], "notes": [], "created": "2017-05-02T12:56:53.738Z", "modified": "2020-01-21T13:56:04.883Z"}, {"entity": "publication", "iuid": "a0c40b72913b482b8f3fb8bb2a00f79b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0c40b72913b482b8f3fb8bb2a00f79b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0c40b72913b482b8f3fb8bb2a00f79b"}}, "title": "The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.", "authors": [{"family": "Schwelm", "given": "Arne", "initials": "A"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Knaust", "given": "Andrea", "initials": "A"}, {"family": "J\u00fclke", "given": "Sabine", "initials": "S"}, {"family": "Lilja", "given": "Tua", "initials": "T"}, {"family": "Bonilla-Rosso", "given": "German", "initials": "G"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Shevchenko", "given": "Andrej", "initials": "A"}, {"family": "Dhandapani", "given": "Vignesh", "initials": "V"}, {"family": "Choi", "given": "Su Ryun", "initials": "SR"}, {"family": "Kim", "given": "Hong Gi", "initials": "HG"}, {"family": "Park", "given": "Ju Young", "initials": "JY"}, {"family": "Lim", "given": "Yong Pyo", "initials": "YP"}, {"family": "Ludwig-M\u00fcller", "given": "Jutta", "initials": "J"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2015-06-18", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "11153", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.", "doi": "10.1038/srep11153", "pmid": "26084520", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "srep11153"}, {"db": "pmc", "key": "PMC4471660"}], "notes": [], "created": "2017-05-02T12:56:27.293Z", "modified": "2020-01-21T13:56:04.138Z"}, {"entity": "publication", "iuid": "5f885fa6b30a46f0a58a357472cdbfcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f885fa6b30a46f0a58a357472cdbfcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f885fa6b30a46f0a58a357472cdbfcf"}}, "title": "Elevated Serum GAD65 and GAD65-GADA Immune Complexes in Stiff Person Syndrome.", "authors": [{"family": "Gu Urban", "given": "Gucci Jijuan", "initials": "GJ"}, {"family": "Friedman", "given": "Mikaela", "initials": "M"}, {"family": "Ren", "given": "Ping", "initials": "P"}, {"family": "T\u00f6rn", "given": "Carina", "initials": "C"}, {"family": "Fex", "given": "Malin", "initials": "M"}, {"family": "Hampe", "given": "Christiane S", "initials": "CS"}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2015-06-16", "journal": {"volume": "5", "issn": "2045-2322", "issue": "1", "pages": "11196", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Glutamic acid decarboxylase 65 (GAD65) and autoantibodies specific for GAD65 (GADA) are associated with autoimmune diseases including Stiff Person Syndrome (SPS) and Type 1 diabetes (T1D). GADA is recognized as a biomarker of value for clinical diagnosis and prognostication in these diseases. Nonetheless, it remains medically interesting to develop sensitive and specific assays to detect GAD65 preceding GADA emergence, and to monitor GADA-GAD65 immune complexes in blood samples. In the present study, we developed a highly sensitive proximity ligation assay to measure serum GAD65. This novel assay allowed detection of as little as 0.65 pg/ml GAD65. We were also able to detect immune complexes involving GAD65 and GADA. Both free GAD65 and GAD65-GADA levels were significantly higher in serum samples from SPS patients compared to healthy controls. The proximity ligation assays applied for detection of GAD65 and its immune complexes may thus enable improved diagnosis and better understanding of SPS.", "doi": "10.1038/srep11196", "pmid": "26080009", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "srep11196"}, {"db": "pmc", "key": "PMC4468815"}], "notes": [], "created": "2017-11-02T14:50:56.443Z", "modified": "2023-04-14T13:56:25.643Z"}, {"entity": "publication", "iuid": "2c162d656e014b59ab15b97ca25bd449", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c162d656e014b59ab15b97ca25bd449.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c162d656e014b59ab15b97ca25bd449"}}, "title": "Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs.", "authors": [{"family": "Chernobrovkin", "given": "Alexey", "initials": "A"}, {"family": "Marin-Vicente", "given": "Consuelo", "initials": "C"}, {"family": "Visa", "given": "Neus", "initials": "N"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2015-06-08", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "11176", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Phenomenological screening of small molecule libraries for anticancer activity yields potentially interesting candidate molecules, with a bottleneck in the determination of drug targets and the mechanism of anticancer action. We have found that, for the protein target of a small-molecule drug, the abundance change in late apoptosis is exceptional compared to the expectations based on the abundances of co-regulated proteins. Based on this finding, a novel method to drug target deconvolution is proposed. In a proof of principle experiment, the method yielded known targets of several common anticancer agents among a few (often, just one) likely candidates identified in an unbiased way from cellular proteome comprising more than 4,000 proteins. A validation experiment with a different set of cells and drugs confirmed the findings. As an additional benefit, mapping most specifically regulated proteins on known protein networks highlighted the mechanism of drug action. The new method, if proven to be general, can significantly shorten drug target identification, and thus facilitate the emergence of novel anticancer treatments.", "doi": "10.1038/srep11176", "pmid": "26052917", "labels": {"Chemical Proteomics": "Technology development", "Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pii", "key": "srep11176"}, {"db": "pmc", "key": "PMC4459150"}], "notes": [], "created": "2017-05-02T12:56:29.879Z", "modified": "2021-07-08T08:58:46.753Z"}, {"entity": "publication", "iuid": "e6d1fc47050848cd805e2ceaa9e80441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6d1fc47050848cd805e2ceaa9e80441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6d1fc47050848cd805e2ceaa9e80441"}}, "title": "Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.", "authors": [{"family": "Nasrollahzadeh", "given": "Dariush", "initials": "D"}, {"family": "Malekzadeh", "given": "Reza", "initials": "R"}, {"family": "Ploner", "given": "Alexander", "initials": "A"}, {"family": "Shakeri", "given": "Ramin", "initials": "R"}, {"family": "Sotoudeh", "given": "Masoud", "initials": "M"}, {"family": "Fahimi", "given": "Saman", "initials": "S"}, {"family": "Nasseri-Moghaddam", "given": "Siavosh", "initials": "S"}, {"family": "Kamangar", "given": "Farin", "initials": "F"}, {"family": "Abnet", "given": "Christian C", "initials": "CC"}, {"family": "Winckler", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Islami", "given": "Farhad", "initials": "F"}, {"family": "Boffetta", "given": "Paolo", "initials": "P"}, {"family": "Brennan", "given": "Paul", "initials": "P"}, {"family": "Dawsey", "given": "Sanford M", "initials": "SM"}, {"family": "Ye", "given": "Weimin", "initials": "W"}], "type": "journal article", "published": "2015-03-06", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "8820", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Observational studies revealed a relationship between changes in gastric mucosa and risk of esophageal squamous cell carcinoma (ESCC) which suggested a possible role for gastric microbiota in ESCC carcinogenesis. In this study we aimed to compare pattern of gastric corpus microbiota in ESCC with normal esophagus. Cases were included subjects with early ESCC (stage I-II) and esophageal squamous dysplasia (ESD) as the cancer precursor. Control groups included age and sex-matched subjects with mid-esophagus esophagitis (diseased-control), and histologically normal esophagus (healthy-control). DNA was extracted from snap-frozen gastric corpus tissues and 16S rRNA was sequenced on GS-FLX Titanium. After noise removal, an average of 3004 reads per sample was obtained from 93 subjects. We applied principal coordinate analysis to ordinate distances from beta diversity data. Pattern of gastric microbiota using Unifrac (p = 0.004) and weighted Unifrac distances (p = 0.018) statistically varied between cases and healthy controls. Sequences were aligned to SILVA database and Clostridiales and Erysipelotrichales orders were more abundant among cases after controling for multiple testing (p = 0.011). No such difference was observed between mid-esophagitis and healthy controls. This study is the first to show that composition of gastric corpus mucosal microbiota differs in early ESCC and ESD from healthy esophagus.", "doi": "10.1038/srep08820", "pmid": "25743945", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep08820"}, {"db": "pmc", "key": "PMC4351546"}], "notes": [], "created": "2017-05-02T12:58:08.100Z", "modified": "2020-01-21T13:56:05.900Z"}, {"entity": "publication", "iuid": "c9bacc76e60b47b389bea37e1f3af589", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9bacc76e60b47b389bea37e1f3af589.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9bacc76e60b47b389bea37e1f3af589"}}, "title": "Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Meiring", "given": "Tracy L", "initials": "TL"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Lindau", "given": "Cecilia", "initials": "C"}, {"family": "Lindberg", "given": "Julia Hedlund", "initials": "JH"}, {"family": "Gustavsson", "given": "Inger", "initials": "I"}, {"family": "Mbulawa", "given": "Zizipho Z A", "initials": "ZZ"}, {"family": "Williamson", "given": "Anna-Lise", "initials": "AL"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2014-03-18", "journal": {"volume": "4", "issn": "2045-2322", "issue": null, "pages": "4398", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Infections by HIV increase the risk of acquiring secondary viral and bacterial infections and methods are needed to determine the spectrum of co-infections for proper treatment. We used rolling circle amplification (RCA) and Ion Proton sequencing to investigate the vaginal microbiome of 20 HIV positive women from South Africa. A total of 46 different human papillomavirus (HPV) types were found, many of which are not detected by existing genotyping assays. Moreover, the complete genomes of two novel HPV types were determined. Abundance of HPV infections was highly correlated with real-time PCR estimates, indicating that the RCA-Proton method can be used for quantification of individual pathogens. We also identified a large number of other viral, bacterial and parasitic co-infections and the spectrum of these co-infections varied widely between individuals. Our method provides rapid detection of a broad range of pathogens and the ability to reconstruct complete genomes of novel infectious agents.", "doi": "10.1038/srep04398", "pmid": "24637939", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "srep04398"}, {"db": "pmc", "key": "PMC3957130"}], "notes": [], "created": "2017-05-04T14:58:59.758Z", "modified": "2021-07-07T14:37:06.609Z"}, {"entity": "publication", "iuid": "bb9b79fb1a9f423892352a8eb8c5a56d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb9b79fb1a9f423892352a8eb8c5a56d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb9b79fb1a9f423892352a8eb8c5a56d"}}, "title": "Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.", "authors": [{"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Lexow", "given": "Preben", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2013-03-09", "journal": {"volume": "3", "issn": "2045-2322", "issue": null, "pages": "1186", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region.", "doi": "10.1038/srep01186", "pmid": "23470464", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep01186"}, {"db": "pmc", "key": "PMC3592332"}], "notes": [], "created": "2017-05-04T14:58:18.306Z", "modified": "2021-07-08T13:26:08.313Z"}, {"entity": "publication", "iuid": "c0f68dbcb6cc404990f25cd0cc929989", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0f68dbcb6cc404990f25cd0cc929989.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0f68dbcb6cc404990f25cd0cc929989"}}, "title": "A novel mutation in the Lipase H gene underlies autosomal recessive hypotrichosis and woolly hair.", "authors": [{"family": "Tariq", "given": "Muhammad", "initials": "M"}, {"family": "Azhar", "given": "Aysha", "initials": "A"}, {"family": "Baig", "given": "Shahid Mahmood", "initials": "SM"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Klar", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2012-10-12", "journal": {"volume": "2", "issn": "2045-2322", "issue": null, "pages": "730", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Mutations in the lipase member H (LIPH) gene cause autosomal recessive hypotrichosis with woolly hair. We report herein on five consanguineous families from Pakistan segregating hypotrichosis and woolly hair. Genetic investigation using polymorphic microsatellite markers revealed homozygosity for a region spanning the HYPT7 locus on chromosome 3 in affected individuals of all five families. Sequence analysis of the LIPH gene revealed a novel nonsense mutation (p.Arg260X) associated with hypotrichosis without woolly hair in one family. In the remaining four families we identified previously described mutations in a homozygous state in affected members. These findings extend the spectrum of known LIPH mutations in the Pakistani population.", "doi": "10.1038/srep00730", "pmid": "23066499", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3470015"}], "notes": [], "created": "2017-05-04T14:57:46.321Z", "modified": "2020-01-21T13:56:05.011Z"}, {"entity": "publication", "iuid": "951aea7e94e94e769ea8d79a783a125a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/951aea7e94e94e769ea8d79a783a125a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/951aea7e94e94e769ea8d79a783a125a"}}, "title": "Multiplex epitope mapping using bacterial surface display reveals both linear and conformational epitopes.", "authors": [{"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2012-10-04", "journal": {"volume": "2", "issn": "2045-2322", "issue": null, "pages": "706", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "As antibody-based diagnosis and therapy grow at an increased pace, there is a need for methods which rapidly and accurately determine antibody-antigen interactions. Here, we report a method for the multiplex determination of antibody epitopes using bacterial cell-surface display. A protein-fragment library with 10(7) cell clones, covering 60 clinically-relevant protein targets, was created and characterized with massively parallel sequencing. Using this multi-target fragment library we determined simultaneously epitopes of commercial monoclonal and polyclonal antibodies targeting PSMA, EGFR, and VEGF. Off-target binding was observed for one of the antibodies, which demonstrates the methods ability to reveal cross-reactivity. We exemplify the detection of structural epitopes by mapping the therapeutic antibody Avastin. Based on our findings we suggest this method to be suitable for mapping linear and structural epitopes of monoclonal and polyclonal antibodies in a multiplex fashion and could find applicability in serum profiling as well as other protein-protein interaction studies.", "doi": "10.1038/srep00706", "pmid": "23050090", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3463815"}], "notes": [], "created": "2017-05-04T14:57:46.018Z", "modified": "2021-07-08T13:44:33.449Z"}], "created": "2017-05-09T09:12:29.885Z", "modified": "2020-11-27T13:14:08.788Z"}