{"entity": "journal", "iuid": "3a74b4f537704c08a71f6896186d3b93", "timestamp": "2026-06-13T21:43:35.545Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Commun%20Biol.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Commun%20Biol"}}, "title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "publications_count": 66, "publications": [{"entity": "publication", "iuid": "f8a7ffd49cad48eb8cb108d82f8b32ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8a7ffd49cad48eb8cb108d82f8b32ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8a7ffd49cad48eb8cb108d82f8b32ab"}}, "title": "Exploring microbial diversity using cell-size fractionated enrichment incubations from subsurface aquifers at \u00c4sp\u00f6, Sweden.", "authors": [{"family": "Westmeijer", "given": "George", "initials": "G", "orcid": "0000-0002-5529-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2146c3e286d4f858efb5787cb3c74a2.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S", "orcid": "0009-0007-1915-0139", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f779055bf334226a996f214182b41fc.json"}}, {"family": "Hevele", "given": "Patrik", "initials": "P"}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2026-02-14", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642"}, "abstract": "The continental subsurface hosts energy-constrained groundwaters with a high diversity of ecologically elusive microorganisms adapted to the prevailing low-energy conditions. This study explored potential interactions among microbes using anaerobic enrichment incubations with three types of groundwater of contrasting hydrochemistry from the \u00c4sp\u00f6 Hard Rock Laboratory, Sweden. Removing cells larger than 0.45 \u00b5m from the inoculum resulted in incubations enriched in populations characterized by very small genomes, including Patescibacteria, Nanobdellota, and Omnitrophota. These incubations had a higher diversity than non-fractionated incubations. However, cell numbers and community structure of the fractionated incubations did not change over an incubation period up to four months, despite high microbial diversity and experimental amendments with either simple (acetate) or more complex (cell lysate) carbon sources. In addition, network analysis on the groundwaters revealed multiple co-occurrences between populations affiliated with the Patescibacteria and the Desulfobacterota. Overall, these findings support that a considerable part of microbial diversity has a small cell size in these low energy groundwaters and strong co-occurrences among populations as an important survival strategy.", "doi": "10.1038/s42003-026-09706-8", "pmid": "41691100", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-026-09706-8"}], "notes": [], "created": "2026-02-26T13:35:39.634Z", "modified": "2026-02-26T13:35:39.923Z"}, {"entity": "publication", "iuid": "b4356e6f236f4a27b987ac01aea346a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4356e6f236f4a27b987ac01aea346a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4356e6f236f4a27b987ac01aea346a2"}}, "title": "Allergen-specific human IgE isolated through an allergen-agnostic pipeline\u2014understanding immune response and allergen recognition", "authors": [{"family": "Th\u00f6rnqvist", "given": "Linnea", "initials": "L"}, {"family": "Franciskovic", "given": "Eric", "initials": "E"}, {"family": "Godzwon", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-9745-1160", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa85685e9e149d8a341effcb1b924d0.json"}}, {"family": "Kristensen", "given": "Bjarne", "initials": "B"}, {"family": "Sultan", "given": "Kristin", "initials": "K", "orcid": "0009-0002-5619-517X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7288f4347b8440479e0f908b705f9df5.json"}}, {"family": "Nordstr\u00f6m", "given": "Franziska", "initials": "F", "orcid": "0000-0003-3730-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa587c1b382f4cd1b9486ba50eb8bb0e.json"}}, {"family": "Palmason", "given": "Robert", "initials": "R"}, {"family": "Todorovic", "given": "Nikolina", "initials": "N"}, {"family": "Keller", "given": "Walter", "initials": "W", "orcid": "0000-0002-2261-958X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dfdfb31e5a24ceb93609f4166c06f5c.json"}}, {"family": "Lindstedt", "given": "Malin", "initials": "M", "orcid": "0000-0001-9136-1087", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc58fdfd7f0a40e2bf2fa21c2d2bea36.json"}}, {"family": "Greiff", "given": "Lennart", "initials": "L", "orcid": "0000-0002-7004-1989", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a6c63fee50b446da172ddbb30f69fb2.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2026-01-28", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "9", "issue": "1", "issn-l": "2399-3642"}, "abstract": "Allergy, characterised by antibody responses of the IgE isotype, is a major health concern. The set of monoclonal human IgE used for studying the molecular mechanisms of allergies is limited. Single-cell sequencing offers opportunities to establish novel antibodies for researching, diagnosis, and treatment of allergies. We describe and exploit a pipeline for generating recombinant IgE directly from the immune repertoires of allergic subjects. It uses single-cell sequencing of IgM- B cells of bone marrow and peripheral blood in an allergen-agnostic manner, combined with high-throughput transcriptome sequencing to identify clonotypes populating the IgE repertoire. Immunochemical and immunoprecipitation analyses are used to deconvolute the specificity of identified antibodies. High-affinity antibodies were raised against four grass pollen allergens, antibodies that illustrated aspects of the development of allergen-specific humoral immunity. The pipeline provides a streamlined approach for the development and characterisation of native allergen-specific antibodies as they occur in allergy and during allergy desensitisation.", "doi": "10.1038/s42003-026-09600-3", "pmid": "41606257", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12953631"}, {"db": "pii", "key": "10.1038/s42003-026-09600-3"}], "notes": [], "created": "2026-02-09T12:51:20.129Z", "modified": "2026-03-24T09:14:00.807Z"}, {"entity": "publication", "iuid": "bdaeb5bc238e46fcbec53a574a0e9f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdaeb5bc238e46fcbec53a574a0e9f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdaeb5bc238e46fcbec53a574a0e9f89"}}, "title": "A morphology-based machine learning model for scoring epithelial-mesenchymal plasticity using organelle dynamics.", "authors": [{"family": "Slager", "given": "Justin", "initials": "J", "orcid": "0009-0005-0481-8154", "researcher": {"href": "https://publications.scilifelab.se/researcher/b628fcc675354b86989c79e30cedc71a.json"}}, {"family": "Gatto", "given": "Francesca", "initials": "F"}, {"family": "Frey", "given": "Benjamin", "initials": "B", "orcid": "0009-0004-7649-8340", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e352dfc1f814b2abf8d38cde784557c.json"}}, {"family": "Shi", "given": "Wenyang", "initials": "W"}, {"family": "Porebski", "given": "Bartlomiej", "initials": "B"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Parniewska", "given": "Malgorzata Maria", "initials": "MM"}, {"family": "Fuxe", "given": "Jonas", "initials": "J", "orcid": "0000-0003-4576-9377", "researcher": {"href": "https://publications.scilifelab.se/researcher/df87648f16bc45b9999eb5c0da269a4e.json"}}], "type": "journal article", "published": "2025-12-10", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642"}, "abstract": "Re-activation of epithelial-mesenchymal transition (EMT), a key developmental process, contributes to cancer progression and therapy resistance. Modulating EMT could be attractive as a therapeutic strategy, but there is a lack of methods that can quantify EMT states, including hybrid phenotypes. Here, we developed a morphology-based machine learning approach to score EMT based on changes in organelle dynamics. Using the Cell Painting assay and high-throughput microscopy, we trained a histogram gradient boosting classifier to identify stage-specific organelle remodeling during a time course of TGF-\u03b21-induced EMT in mammary epithelial cells. The model achieved robust performance across datasets, capturing EMT kinetics, hybrid states, and reversal by mesenchymal-epithelial transition (MET). Importantly, the method accurately scored EMT in human breast cancer cells and lung cancer cells undergoing hypoxia-induced EMT, demonstrating cross-species, cross-inducer, and cross-cancer applicability. The results establish organelle morphology profiling as a scalable framework for quantifying epithelial-mesenchymal plasticity. The method offers a platform for drug discovery and identifying strategies to overcome EMT-associated resistance.", "doi": "10.1038/s42003-025-09326-8", "pmid": "41372576", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-025-09326-8"}], "notes": [], "created": "2025-12-11T16:08:39.796Z", "modified": "2025-12-11T16:08:40.050Z"}, {"entity": "publication", "iuid": "61f674feb9bb47cc945261f439654003", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61f674feb9bb47cc945261f439654003.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61f674feb9bb47cc945261f439654003"}}, "title": "Single cell long read whole genome sequencing reveals somatic transposon activity in human brain.", "authors": [{"family": "Izydorczyk", "given": "Michal B", "initials": "MB"}, {"family": "Kalef-Ezra", "given": "Ester", "initials": "E", "orcid": "0000-0002-1297-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/7872b77059a7463a9d70214941f2da4e.json"}}, {"family": "Horner", "given": "Dominic W", "initials": "DW", "orcid": "0009-0002-1988-3838", "researcher": {"href": "https://publications.scilifelab.se/researcher/44931007770f44ce8e7f4d71ee2e0f53.json"}}, {"family": "Zheng", "given": "Xinchang", "initials": "X"}, {"family": "Holmes", "given": "Nadine", "initials": "N"}, {"family": "Toffoli", "given": "Marco", "initials": "M", "orcid": "0000-0002-3255-9648", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a1af99369b43d39dd36408491f25c2.json"}}, {"family": "Sahin", "given": "Zeliha", "initials": "Z"}, {"family": "Han", "given": "Yi", "initials": "Y", "orcid": "0000-0001-7605-8979", "researcher": {"href": "https://publications.scilifelab.se/researcher/2773c1d2c94f468fa78eed048bd13d3a.json"}}, {"family": "Mehta", "given": "Heer H", "initials": "HH"}, {"family": "Scholz", "given": "Sonja W", "initials": "SW", "orcid": "0000-0002-6623-0429", "researcher": {"href": "https://publications.scilifelab.se/researcher/7600f820a52a4e99b9b01480e8848669.json"}}, {"family": "Dalgard", "given": "Clifton L", "initials": "CL", "orcid": "0000-0003-2025-8239", "researcher": {"href": "https://publications.scilifelab.se/researcher/5476c12921064b89bd069f7942c40b71.json"}}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ", "orcid": "0000-0001-6040-2691", "researcher": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b.json"}}, {"family": "Proukakis", "given": "Christos", "initials": "C", "orcid": "0000-0001-6423-6539", "researcher": {"href": "https://publications.scilifelab.se/researcher/c159214a80944c8fa64910a0023d8c42.json"}}], "type": "journal article", "published": "2025-11-20", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "1627", "issn-l": "2399-3642"}, "abstract": "The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover previously uncharacterized genomic dynamics in 18 cells from three human brains utilizing single cell long-read whole genome sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements, but requires validation in larger studies.", "doi": "10.1038/s42003-025-08805-2", "pmid": "41266782", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-025-08805-2"}], "notes": [], "created": "2025-11-21T06:20:40.789Z", "modified": "2025-11-21T06:20:42.030Z"}, {"entity": "publication", "iuid": "73fee7c76bfd49a6944ca090feb04ef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73fee7c76bfd49a6944ca090feb04ef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73fee7c76bfd49a6944ca090feb04ef1"}}, "title": "Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP.", "authors": [{"family": "Azinas", "given": "Stavros", "initials": "S", "orcid": "0000-0002-3744-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ec0cb5b5df4b4f89780ce3a08efc89.json"}}, {"family": "Wallden", "given": "Karin", "initials": "K"}, {"family": "Katikaridis", "given": "Panagiotis", "initials": "P"}, {"family": "Jenne", "given": "Timo", "initials": "T", "orcid": "0009-0001-2033-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a27284b457b4d84b7104cfc0a3d989c.json"}}, {"family": "Schahl", "given": "Adrien", "initials": "A", "orcid": "0000-0001-5839-7715", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c1503f32d64435a8df615d167a5c6f.json"}}, {"family": "Mogk", "given": "Axel", "initials": "A", "orcid": "0000-0003-3674-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/56a1d7fc519743029c9ae615086d8093.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}], "type": "journal article", "published": "2025-10-14", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "1467", "issn-l": "2399-3642"}, "abstract": "Bacterial AAA+ proteases are composed of a AAA+ partner (e.g., ClpC) and an associated peptidase (e.g., ClpP). They represent ATP-fuelled and self-compartmentalized proteolytic machines that are crucial for stress resistance and virulence. ClpC requires cooperation with adaptor proteins such as MecA for activation and complex formation with ClpP. Here, we present the cryo-EM structure of the MecA/ClpC/ClpP complex from the major pathogen Staphylococcus aureus. MecA forms a dynamic crown on top of the ClpC/ClpP complex with its substrate-binding domain positioned near the ClpC pore site, likely facilitating substrate transfer. ClpC/ClpP complex formation involves ClpC P-loops and ClpP N-terminal \u03b2-hairpins, which insert into the central ClpC threading channel and contact sites next to the ClpC ATPase center. ClpC and ClpP interactions are asymmetric and dictated by the activity states of ClpC ATPase subunits. ClpP binding increases ClpC ATPase and threading activities in a \u03b2-hairpin dependent manner, illuminating an allosteric pathway in the cooperation of ATPase and peptidase components in bacterial AAA+ proteases.", "doi": "10.1038/s42003-025-08908-w", "pmid": "41087538", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12521514"}, {"db": "pii", "key": "10.1038/s42003-025-08908-w"}], "notes": [], "created": "2025-10-25T10:21:15.566Z", "modified": "2025-10-25T10:21:15.656Z"}, {"entity": "publication", "iuid": "e3c4916f5c6c4103a058b9d484952882", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3c4916f5c6c4103a058b9d484952882.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3c4916f5c6c4103a058b9d484952882"}}, "title": "Structural and biochemical basis for activity of Aspergillus nidulans \u03b1-1,3-glucanases from glycoside hydrolase family 71", "authors": [{"family": "Mazurkewich", "given": "Scott", "initials": "S", "orcid": "0000-0002-9238-0615", "researcher": {"href": "https://publications.scilifelab.se/researcher/39a1e4f9d3a74121937087f8875a975a.json"}}, {"family": "Wid\u00e9n", "given": "Tove", "initials": "T", "orcid": "0009-0001-6830-9608", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cc9e7875b5a43f7b41f9b95a65d9634.json"}}, {"family": "Karlsson", "given": "Hampus", "initials": "H"}, {"family": "Even\u00e4s", "given": "Lars", "initials": "L", "orcid": "0000-0002-6580-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d5546ed87b0480aae72d8574db96911.json"}}, {"family": "Ramamohan", "given": "Poornima", "initials": "P"}, {"family": "Wohlert", "given": "Jakob", "initials": "J"}, {"family": "Br\u00e4nd\u00e9n", "given": "Gisela", "initials": "G", "orcid": "0000-0001-5615-7187", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0bd1188c26448398026757fef34469f.json"}}, {"family": "Larsbrink", "given": "Johan", "initials": "J", "orcid": "0000-0001-8386-2914", "researcher": {"href": "https://publications.scilifelab.se/researcher/99badc395dbc46d1a43ae5c3d39fd8aa.json"}}], "type": "journal-article", "published": "2025-08-28", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "issn-l": "2399-3642"}, "abstract": null, "doi": "10.1038/s42003-025-08696-3", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:05:25.939Z", "modified": "2025-11-27T08:05:26.165Z"}, {"entity": "publication", "iuid": "7f700b3e5e634b2295705bc2ae62f3eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb"}}, "title": "Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons.", "authors": [{"family": "Krauter", "given": "Doris", "initials": "D", "orcid": "0000-0002-1779-093X", "researcher": {"href": "https://publications.scilifelab.se/researcher/631f89b570c44663b8c6a29f0759aca2.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J", "orcid": "0000-0003-1540-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/96dfeacf7fe04bf099fbddf0c45ef693.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "908", "issn-l": "2399-3642"}, "abstract": "Heterogeneity among somatosensory neurons is necessary for internal and external sensation. Precise patterns of gene transcription orchestrated through enhancer activation maintain heterogeneity. Thus, high-resolution cell type classification, chromatin accessibility and its relation to enhancer activation can explain the governing principles for sensory neuron heterogeneity. Here, we present an integrated atlas from published high-quality scRNA-seq datasets and resequencing the dorsal root ganglion, including over 44,000 neurons. MERSCOPE spatial transcriptomics confirms cell types in situ, including previously unrecognized neuronal types, and a spatial zonation of both neurons and non-neuronal cells. We present a cell type specific open chromatin atlas revealing enhancer driven regulons and gene-regulatory networks organized into co-regulated gene-programs that together define sensory neuron diversity. Cell type complexity is shown to be generated by layered co-regulated transcriptional modules representing shared functions across different scales of the neuronal type hierarchy with cell type specific contribution as the exception.", "doi": "10.1038/s42003-025-08315-1", "pmid": "40500276", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12159162"}, {"db": "pii", "key": "10.1038/s42003-025-08315-1"}], "notes": [], "created": "2025-07-18T10:23:45.299Z", "modified": "2025-11-14T11:07:16.782Z"}, {"entity": "publication", "iuid": "87a87989503945b7842ab3f695a22318", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87a87989503945b7842ab3f695a22318.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87a87989503945b7842ab3f695a22318"}}, "title": "Pooled optical screening in bacteria using chromosomally expressed barcodes.", "authors": [{"family": "Soares", "given": "Ruben R G", "initials": "RRG", "orcid": "0000-0001-5958-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/88ea8e0d81284c35a271f05187289390.json"}}, {"family": "Garc\u00eda-Soriano", "given": "Daniela A", "initials": "DA", "orcid": "0000-0003-2849-8528", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aeeed6de99647a1878352e0da2220af.json"}}, {"family": "Larsson", "given": "Jimmy", "initials": "J"}, {"family": "Fange", "given": "David", "initials": "D", "orcid": "0009-0006-3981-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/195ab3e1f94e4ad39b4aa32da6b3e217.json"}}, {"family": "Schirman", "given": "Dvir", "initials": "D", "orcid": "0000-0001-5175-0176", "researcher": {"href": "https://publications.scilifelab.se/researcher/02550d8122ed486fb67691b456926aed.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd8bec6567444558acbcbd1b3d28f7a.json"}}, {"family": "Kn\u00f6ppel", "given": "Anna", "initials": "A"}, {"family": "Sen", "given": "Beer Chakra", "initials": "BC"}, {"family": "Svahn", "given": "Fabian", "initials": "F", "orcid": "0000-0002-5914-520X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f015b5855854d40b853c17a31d3d632.json"}}, {"family": "Zikrin", "given": "Spartak", "initials": "S", "orcid": "0000-0002-7802-8869", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a82f27ea7bf43deaded33d359270820.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}], "type": "journal article", "published": "2025-06-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "851", "issn-l": "2399-3642"}, "abstract": "Optical pooled screening is an important tool to study dynamic phenotypes for libraries of genetically engineered cells. However, the desired engineering often requires that the barcodes used for in situ genotyping are expressed from the chromosome. This has not previously been achieved in bacteria. Here we describe a method for in situ genotyping of libraries with genomic barcodes in Escherichia coli. The method is applied to measure the intracellular maturation time of 84 red fluorescent proteins.", "doi": "10.1038/s42003-025-08268-5", "pmid": "40461651", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12134211"}, {"db": "pii", "key": "10.1038/s42003-025-08268-5"}], "notes": [], "created": "2025-11-28T10:47:35.410Z", "modified": "2025-11-28T10:47:35.689Z"}, {"entity": "publication", "iuid": "fd8026fc626a4b06a20c3d7bb29a29e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd8026fc626a4b06a20c3d7bb29a29e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd8026fc626a4b06a20c3d7bb29a29e6"}}, "title": "Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Jansson", "given": "Ingela", "initials": "I", "orcid": "0000-0002-2255-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/44e799cd5f7f4343955b0a261ff6df96.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Packer", "given": "Craig", "initials": "C", "orcid": "0000-0002-3939-8162", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cacbf9051428186cf6fe23d4f8a02.json"}}, {"family": "Norman", "given": "Anita", "initials": "A"}, {"family": "Kissui", "given": "Bernard M", "initials": "BM"}, {"family": "E Mjingo", "given": "Ernest", "initials": "E"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1246-5046", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccdce43407204828b73bce24fc4e6453.json"}}], "type": "journal article", "published": "2025-04-21", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "640", "issn-l": "2399-3642"}, "abstract": "Small, isolated populations are at greater risk of genome erosion than larger populations. Successful conservation efforts may lead to demographic recovery and mitigate the negative genetic effects of bottlenecks. However, constrained gene flow can hamper genomic recovery. Here, we use population genomic analyses and forward simulations to assess the genomic impacts of near extinction in the isolated Ngorongoro Crater lion (Panthera leo) sub-population. We show that 200 years of quasi-isolation and the recent epizootic in 1962 resulted in a two-fold increase in inbreeding and an excess in the frequency of highly deleterious mutations relative to other populations of the Greater Serengeti. There was little evidence for purging of genetic load. Furthermore, forward simulations indicate that higher gene flow from outside of the Crater is needed to prevent future genomic erosion in the population, with a minimum of one to five effective male migrants per decade required to reduce the risk of long-term inbreeding depression and reduction in genetic diversity. Our results suggest that in spite of a rapid post-epizootic demographic recovery since the 1970s, continued isolation of the population driven by habitat fragmentation and potentially male territoriality, exacerbate the effects of genome erosion.", "doi": "10.1038/s42003-025-07986-0", "pmid": "40258987", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12012037"}, {"db": "pii", "key": "10.1038/s42003-025-07986-0"}], "notes": [], "created": "2025-05-26T07:51:41.058Z", "modified": "2025-11-14T11:07:11.711Z"}, {"entity": "publication", "iuid": "fe11d7e323b2447091d2e5073a72931f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe11d7e323b2447091d2e5073a72931f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe11d7e323b2447091d2e5073a72931f"}}, "title": "Breast cancer patient-derived scaffolds enhance the understanding of PD-L1 regulation and T cell cytotoxicity.", "authors": [{"family": "Garre", "given": "Elena", "initials": "E", "orcid": "0000-0002-3827-4977", "researcher": {"href": "https://publications.scilifelab.se/researcher/90df2c41baee4b0c98035fbc5f77a438.json"}}, {"family": "Rhost", "given": "Sara", "initials": "S"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Szeponik", "given": "Louis", "initials": "L", "orcid": "0000-0002-8627-6969", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca113a84f7d14ae89fc0165885e21972.json"}}, {"family": "Araujo", "given": "Thais Fenz", "initials": "TF"}, {"family": "Quiding-J\u00e4rbrink", "given": "Marianne", "initials": "M"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}, {"family": "Landberg", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9004-9403", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa3b79caacba4566897f136a1200476f.json"}}], "type": "journal article", "published": "2025-04-16", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "621", "issn-l": "2399-3642"}, "abstract": "Recent advances as well as obstacles for immune-based cancer treatment strategies, highlight the notable impact of patient cancer microenvironments on the immune cells and immune targets. Here, we use patient-derived scaffolds (PDS) generated from 110 primary breast cancers to monitor the impact of the cancer microenvironment on immune regulators. Pronounced variation in PD-L1 expression is observed in cancer cells adapted to different patient scaffolds. This variation is further linked to clinical observations and correlated with specific proteins detected in the cell-free PDSs using mass spectrometry. When adding T cells to the PDS-based cancer cultures, the killing efficiency of activated T cells vary between the cultures, whereas non-activated T cells modulate the cancer cell PD-L1 expression to treatment-predictive values, matching killing capacities of activated T cells. Surviving cancer cells show enrichment in cancer stem cell and epithelial-to-mesenchymal transition (EMT) features, suggesting that T cells may not efficiently target cells with metastatic potential. We conclude that clinically relevant insights in how to optimally target and guide immune-based cancer therapies can be obtained by including patient-derived scaffolds and cues from the cancer microenvironment in cancer patient handling and drug development.", "doi": "10.1038/s42003-025-08054-3", "pmid": "40240529", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12003762"}, {"db": "pii", "key": "10.1038/s42003-025-08054-3"}], "notes": [], "created": "2025-10-23T16:17:59.440Z", "modified": "2025-10-23T16:17:59.771Z"}, {"entity": "publication", "iuid": "92139d604e30428c85b0f16ddccb99c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92139d604e30428c85b0f16ddccb99c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92139d604e30428c85b0f16ddccb99c8"}}, "title": "Spatial profiling of the mouse colonic immune landscape associated with colitis and sex.", "authors": [{"family": "Holm", "given": "Matilda", "initials": "M"}, {"family": "Stepanauskait\u0117", "given": "Lina", "initials": "L", "orcid": "0000-0003-4173-6009", "researcher": {"href": "https://publications.scilifelab.se/researcher/429f33fed9a44ff4b70ff88d5af917d9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Birgersson", "given": "Madeleine", "initials": "M", "orcid": "0000-0002-5876-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/68ea3a27e23a4f978e9c4e74ebdfbf11.json"}}, {"family": "Socciarelli", "given": "Fabio", "initials": "F"}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2024-11-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "7", "issue": "1", "pages": "1595"}, "abstract": "Inflammatory intestinal conditions are a major disease burden. Numerous factors shape the distribution of immune cells in the colon, but a spatial characterization of the homeostatic and inflamed colonic immune microenvironment is lacking. Here, we use the COMET platform for multiplex immunofluorescence to profile the infiltration of nine immune cell populations in mice of both sexes (N = 16) with full spatial context, including in regions of squamous metaplasia. Unsupervised clustering, neighborhood analysis, and manual quantification along the proximal-distal axis characterized the colonic immune landscape, quantified cell-cell interactions, and revealed sex differences. The distal colon was the most affected region during colitis, which was pronounced in males, who exhibited a sex-dependent increase of B cells and reduction of M2-like macrophages. Regions of squamous metaplasia exhibited strong infiltration of numerous immune cell populations, especially in males. Females exhibited more helper T cells and neutrophils at homeostasis and increased M2-like macrophage infiltration in the mid-colon upon colitis. Sex differences were corroborated by plasma cytokine profiles. Our results provide a foundation for future studies of inflammatory intestinal conditions.", "doi": "10.1038/s42003-024-07276-1", "pmid": "39613949", "labels": {"Affinity Proteomics Stockholm": "Service", "Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11606951"}, {"db": "pii", "key": "10.1038/s42003-024-07276-1"}], "notes": [], "created": "2024-12-04T20:14:13.972Z", "modified": "2025-02-17T09:58:33.843Z"}, {"entity": "publication", "iuid": "f4ecf70c0f124d118f067a49621b872e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4ecf70c0f124d118f067a49621b872e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4ecf70c0f124d118f067a49621b872e"}}, "title": "Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle.", "authors": [{"family": "Karempudi", "given": "Praneeth", "initials": "P", "orcid": "0000-0002-5925-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/660b0381d6d248e7a3fc1737d88539b0.json"}}, {"family": "Gras", "given": "Konrad", "initials": "K"}, {"family": "Amselem", "given": "Elias", "initials": "E", "orcid": "0000-0003-2846-9225", "researcher": {"href": "https://publications.scilifelab.se/researcher/b36dcc99173f461e84941241665eaedf.json"}}, {"family": "Zikrin", "given": "Spartak", "initials": "S"}, {"family": "Schirman", "given": "Dvir", "initials": "D", "orcid": "0000-0001-5175-0176", "researcher": {"href": "https://publications.scilifelab.se/researcher/02550d8122ed486fb67691b456926aed.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}], "type": "journal article", "published": "2024-11-05", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "1443", "issn-l": "2399-3642"}, "abstract": "The intracellular position of genes may impact their expression, but it has not been possible to accurately measure the 3D position of chromosomal loci. In 2D, loci can be tracked using arrays of DNA-binding sites for transcription factors (TFs) fused with fluorescent proteins. However, the same 2D data can result from different 3D trajectories. Here, we have developed a deep learning method for super-resolved astigmatism-based 3D localization of chromosomal loci in live E. coli cells which enables a precision better than 61 nm at a signal-to-background ratio of ~4 on a heterogeneous cell background. Determining the spatial localization of chromosomal loci, we find that some loci are at the periphery of the nucleoid for large parts of the cell cycle. Analyses of individual trajectories reveal that these loci are subdiffusive both longitudinally (x) and radially (r), but that individual loci explore the full radial width on a minute time scale.", "doi": "10.1038/s42003-024-07155-9", "pmid": "39501081", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11538341"}, {"db": "pii", "key": "10.1038/s42003-024-07155-9"}], "notes": [], "created": "2024-11-25T10:21:54.835Z", "modified": "2025-02-28T14:16:15.992Z"}, {"entity": "publication", "iuid": "cae717df84f14906a43842087e3af2e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cae717df84f14906a43842087e3af2e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cae717df84f14906a43842087e3af2e8"}}, "title": "Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden.", "authors": [{"family": "Westmeijer", "given": "George", "initials": "G", "orcid": "0000-0002-5529-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2146c3e286d4f858efb5787cb3c74a2.json"}}, {"family": "van Dam", "given": "Femke", "initials": "F", "orcid": "0000-0002-5526-5044", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6869844c377483abb30634c303da5fb.json"}}, {"family": "Kiet\u00e4v\u00e4inen", "given": "Riikka", "initials": "R", "orcid": "0000-0002-4867-777X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8bf051894324f9c8ed0cbafe2e8edec.json"}}, {"family": "Gonz\u00e1lez-Rosales", "given": "Carolina", "initials": "C"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Drake", "given": "Henrik", "initials": "H", "orcid": "0000-0001-7230-6509", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25c4627832844518873bb13021a2ef0.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2024-10-15", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "1332", "issn-l": "2399-3642"}, "abstract": "The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.", "doi": "10.1038/s42003-024-07027-2", "pmid": "39406897", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11480212"}, {"db": "pii", "key": "10.1038/s42003-024-07027-2"}], "notes": [], "created": "2024-11-25T10:21:49.669Z", "modified": "2025-02-28T14:16:10.456Z"}, {"entity": "publication", "iuid": "27029ecb1350438b992c88328a5fc815", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27029ecb1350438b992c88328a5fc815.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27029ecb1350438b992c88328a5fc815"}}, "title": "Ichthyosporea: a window into the origin of animals.", "authors": [{"family": "Shabardina", "given": "Victoria", "initials": "V", "orcid": "0000-0002-8898-8660", "researcher": {"href": "https://publications.scilifelab.se/researcher/665020e8c7934a4c9b954a31aac7864f.json"}}, {"family": "Dharamshi", "given": "Jennah E", "initials": "JE", "orcid": "0000-0003-4563-3939", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c4fab7c00a48b29be068ac41016947.json"}}, {"family": "Ara", "given": "Patricia S", "initials": "PS", "orcid": "0000-0002-3508-9688", "researcher": {"href": "https://publications.scilifelab.se/researcher/6281795407b54a7aa3707c9b62c2dc71.json"}}, {"family": "Ant\u00f3", "given": "Meritxell", "initials": "M", "orcid": "0009-0004-0172-3830", "researcher": {"href": "https://publications.scilifelab.se/researcher/c93a152a06384efbbb603a788c34cb00.json"}}, {"family": "Basc\u00f3n", "given": "Fernando J", "initials": "FJ", "orcid": "0009-0009-4473-4405", "researcher": {"href": "https://publications.scilifelab.se/researcher/70add2232ee3490da1caba0731003559.json"}}, {"family": "Suga", "given": "Hiroshi", "initials": "H", "orcid": "0000-0003-1795-2174", "researcher": {"href": "https://publications.scilifelab.se/researcher/82fc860aa1844fc4909b9994c0f5f61d.json"}}, {"family": "Marshall", "given": "Wyth", "initials": "W"}, {"family": "Scazzocchio", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8800-2534", "researcher": {"href": "https://publications.scilifelab.se/researcher/766d9c8ab6c244b7b47a402550b58e1e.json"}}, {"family": "Casacuberta", "given": "Elena", "initials": "E", "orcid": "0000-0002-8203-8357", "researcher": {"href": "https://publications.scilifelab.se/researcher/440b6cb0797f44b886fb666292ece797.json"}}, {"family": "Ruiz-Trillo", "given": "I\u00f1aki", "initials": "I", "orcid": "0000-0001-6547-5304", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e6ce1eb58f945379c6dbb7a8a014462.json"}}], "type": "journal article", "published": "2024-07-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "915", "issn-l": "2399-3642"}, "abstract": "Ichthyosporea is an underexplored group of unicellular eukaryotes closely related to animals. Thanks to their phylogenetic position, genomic content, and development through a multinucleate coenocyte reminiscent of some animal embryos, the members of Ichthyosporea are being increasingly recognized as pivotal to the study of animal origins. We delve into the existing knowledge of Ichthyosporea, identify existing gaps and discuss their life cycles, genomic insights, development, and potential to be model organisms. We also discuss the underestimated diversity of ichthyosporeans, based on new environmental data analyses. This review will be an essential resource for researchers venturing into the study of ichthyosporeans.", "doi": "10.1038/s42003-024-06608-5", "pmid": "39075159", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11286789"}, {"db": "pii", "key": "10.1038/s42003-024-06608-5"}], "notes": [], "created": "2024-11-25T10:21:44.345Z", "modified": "2025-02-28T14:16:05.248Z"}, {"entity": "publication", "iuid": "1495b67f923e43a5b3548539c1ca1303", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1495b67f923e43a5b3548539c1ca1303.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1495b67f923e43a5b3548539c1ca1303"}}, "title": "Normoglycemia and physiological cortisone level maintain glucose homeostasis in a pancreas-liver microphysiological system.", "authors": [{"family": "Rigal", "given": "Sophie", "initials": "S"}, {"family": "Casas", "given": "Bel\u00e9n", "initials": "B"}, {"family": "Kanebratt", "given": "Kajsa P", "initials": "KP"}, {"family": "Wennberg Huldt", "given": "Charlotte", "initials": "C"}, {"family": "Magnusson", "given": "Lisa U", "initials": "LU"}, {"family": "M\u00fcllers", "given": "Erik", "initials": "E", "orcid": "0000-0002-2176-3248", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a060ead5074f1aa3c0e782665814a8.json"}}, {"family": "Karlsson", "given": "Fredrik", "initials": "F"}, {"family": "Clausen", "given": "Maryam", "initials": "M"}, {"family": "Hansson", "given": "Sara F", "initials": "SF"}, {"family": "Leonard", "given": "Louise", "initials": "L"}, {"family": "Cairns", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9982-1401", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c0d942bccc46ef9afe4a3578aa4841.json"}}, {"family": "Jansson L\u00f6fmark", "given": "Rasmus", "initials": "R"}, {"family": "\u00c4mm\u00e4l\u00e4", "given": "Carina", "initials": "C"}, {"family": "Marx", "given": "Uwe", "initials": "U"}, {"family": "Gennemark", "given": "Peter", "initials": "P", "orcid": "0000-0002-7865-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/75d3c260cab344f49e8a79cbb2ea6a6f.json"}}, {"family": "Cedersund", "given": "Gunnar", "initials": "G"}, {"family": "Andersson", "given": "Tommy B", "initials": "TB"}, {"family": "Vil\u00e9n", "given": "Liisa K", "initials": "LK", "orcid": "0000-0001-9184-4847", "researcher": {"href": "https://publications.scilifelab.se/researcher/03d10eddd2a84a22afa0beb276af4f59.json"}}], "type": "journal article", "published": "2024-07-18", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "877", "issn-l": "2399-3642"}, "abstract": "Current research on metabolic disorders and diabetes relies on animal models because multi-organ diseases cannot be well studied with standard in vitro assays. Here, we have connected cell models of key metabolic organs, the pancreas and liver, on a microfluidic chip to enable diabetes research in a human-based in vitro system. Aided by mechanistic mathematical modeling, we demonstrate that hyperglycemia and high cortisone concentration induce glucose dysregulation in the pancreas-liver microphysiological system (MPS), mimicking a diabetic phenotype seen in patients with glucocorticoid-induced diabetes. In this diseased condition, the pancreas-liver MPS displays beta-cell dysfunction, steatosis, elevated ketone-body secretion, increased glycogen storage, and upregulated gluconeogenic gene expression. Conversely, a physiological culture condition maintains glucose tolerance and beta-cell function. This method was reproducible in two laboratories and was effective in multiple pancreatic islet donors. The model also provides a platform to identify new therapeutic proteins, as demonstrated with a combined transcriptome and proteome analysis.", "doi": "10.1038/s42003-024-06514-w", "pmid": "39025915", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11258270"}, {"db": "pii", "key": "10.1038/s42003-024-06514-w"}], "notes": [], "created": "2024-11-27T15:36:58.123Z", "modified": "2024-11-27T15:36:58.294Z"}, {"entity": "publication", "iuid": "f6952d433d3d4a739c73bcfe7118c1ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6952d433d3d4a739c73bcfe7118c1ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6952d433d3d4a739c73bcfe7118c1ae"}}, "title": "Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.", "authors": [{"family": "Wallerstein", "given": "Johan", "initials": "J"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Levkovets", "given": "Maria", "initials": "M", "orcid": "0000-0002-1805-9057", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf8cc61d91474483ab51728701d2f75a.json"}}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Malmodin", "given": "Daniel", "initials": "D"}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Sun", "given": "Renhua", "initials": "R", "orcid": "0000-0002-8203-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/f639c1a9dca647c0b583ce74ab398f02.json"}}, {"family": "Sandalova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-7694-6420", "researcher": {"href": "https://publications.scilifelab.se/researcher/8adca17a49fc47b696cb2b2795f83e6f.json"}}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1821-4715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6463abd05b415696c52be577ca2be6.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39682601d1a24f5ba1d103bf74c9acbd.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}], "type": "journal article", "published": "2024-07-16", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "868", "issn-l": "2399-3642"}, "abstract": "Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) is an attractive target for the development of modulatory compounds in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1 has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained unexplored. We present here dynamic analyses of the apo MALT1 form along with the E549A mutation. This investigation used NMR 15N relaxation and NOE measurements between side-chain methyl groups. Our findings confirm that MALT1 exists as a monomer in solution, and demonstrate that the domains display semi-independent movements in relation to each other. Our dynamic study, covering multiple time scales, along with the assessment of conformational populations by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, put the side chain of residue W580 in an inward position, shedding light at potential mechanisms underlying the allosteric regulation of this enzyme.", "doi": "10.1038/s42003-024-06558-y", "pmid": "39014105", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development", "Swedish NMR Centre": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11252132"}, {"db": "pii", "key": "10.1038/s42003-024-06558-y"}], "notes": [], "created": "2024-08-06T09:19:26.577Z", "modified": "2025-10-17T13:03:52.905Z"}, {"entity": "publication", "iuid": "0bef12e55ae9444aa253b1051601f4fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0bef12e55ae9444aa253b1051601f4fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0bef12e55ae9444aa253b1051601f4fd"}}, "title": "Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping.", "authors": [{"family": "Thal\u00e9n", "given": "Niklas Berndt", "initials": "NB"}, {"family": "Karlander", "given": "Maximilian", "initials": "M", "orcid": "0000-0001-7679-2145", "researcher": {"href": "https://publications.scilifelab.se/researcher/55bfbed7d0d4471195db56a20a8fb07c.json"}}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Hofstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Turunen", "given": "S Pauliina", "initials": "SP", "orcid": "0000-0001-8060-9876", "researcher": {"href": "https://publications.scilifelab.se/researcher/10fc348cd3ee458da92a0947807c5d7c.json"}}, {"family": "Godzwon", "given": "Magdalena", "initials": "M"}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL", "orcid": "0000-0003-1096-9061", "researcher": {"href": "https://publications.scilifelab.se/researcher/e12aeda9f68c49418761bff791c2f834.json"}}, {"family": "Malm", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-1763-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c4c6c276dd64fe2abe27da888cd0925.json"}}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "805", "issn-l": "2399-3642"}, "abstract": "Precise epitope determination of therapeutic antibodies is of great value as it allows for further comprehension of mechanism of action, therapeutic responsiveness prediction, avoidance of unwanted cross reactivity, and vaccine design. The golden standard for discontinuous epitope determination is the laborious X-ray crystallography method. Here, we present a combinatorial method for rapid mapping of discontinuous epitopes by mammalian antigen display, eliminating the need for protein expression and purification. The method is facilitated by automated workflows and tailored software for antigen analysis and oligonucleotide design. These oligos are used in automated mutagenesis to generate an antigen receptor library displayed on mammalian cells for direct binding analysis by flow cytometry. Through automated analysis of 33930 primers an optimized single condition cloning reaction was defined allowing for mutation of all surface-exposed residues of the receptor binding domain of SARS-CoV-2. All variants were functionally expressed, and two reference binders validated the method. Furthermore, epitopes of three novel therapeutic antibodies were successfully determined followed by evaluation of binding also towards SARS-CoV-2 Omicron BA.2. We find the method to be highly relevant for rapid construction of antigen libraries and determination of antibody epitopes, especially for the development of therapeutic interventions against novel pathogens.", "doi": "10.1038/s42003-024-06508-8", "pmid": "38961245", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11222437"}, {"db": "pii", "key": "10.1038/s42003-024-06508-8"}], "notes": [], "created": "2024-11-08T09:49:19.777Z", "modified": "2025-10-17T13:05:07.354Z"}, {"entity": "publication", "iuid": "4ef5551cdf454ceab1ac54f8d3a45c8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ef5551cdf454ceab1ac54f8d3a45c8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ef5551cdf454ceab1ac54f8d3a45c8a"}}, "title": "Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy \u2013 identification and correction", "authors": [{"family": "Adler", "given": "Jeremy", "initials": "J", "orcid": "0000-0003-1741-7876", "researcher": {"href": "https://publications.scilifelab.se/researcher/2be5c7aa3c2d4fd3b90db02d64b288fc.json"}}, {"family": "Bernhem", "given": "Kristoffer", "initials": "K", "orcid": "0000-0003-3669-9848", "researcher": {"href": "https://publications.scilifelab.se/researcher/d39d22a3572a4d718a389600e74097b7.json"}}, {"family": "Parmryd", "given": "Ingela", "initials": "I", "orcid": "0000-0003-4834-3611", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6807c0e1424720aa8a1c6518bced2d.json"}}], "type": "journal-article", "published": "2024-06-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "issn-l": "2399-3642"}, "abstract": null, "doi": "10.1038/s42003-024-06472-3", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2024-07-09T08:03:43.374Z", "modified": "2024-07-09T08:03:43.940Z"}, {"entity": "publication", "iuid": "8c7130dfb41048cfab1512c157df9c8f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c7130dfb41048cfab1512c157df9c8f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c7130dfb41048cfab1512c157df9c8f"}}, "title": "MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.", "authors": [{"family": "Sydow", "given": "Saskia", "initials": "S", "orcid": "0009-0003-0358-8268", "researcher": {"href": "https://publications.scilifelab.se/researcher/549dec30972c44d89378c04fc5f57aa1.json"}}, {"family": "Piccinelli", "given": "Paul", "initials": "P"}, {"family": "Mitra", "given": "Shamik", "initials": "S", "orcid": "0000-0001-6995-0600", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3b10a7bd10941d58ee17b74795931fd.json"}}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P"}, {"family": "Hesla", "given": "Asle", "initials": "A", "orcid": "0000-0001-6205-0773", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c3368bd0fa243eea704f1163a815caa.json"}}, {"family": "B R De Mattos", "given": "Camila", "initials": "C", "orcid": "0000-0002-5698-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/b21c8d7c09424208984c0f16c66e1a82.json"}}, {"family": "K\u00f6ster", "given": "Jan", "initials": "J"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Wardenaar", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0001-9891-1897", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb1c5b299299417b807addb300a87ba4.json"}}, {"family": "Foijer", "given": "Floris", "initials": "F", "orcid": "0000-0003-0989-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ef3e70e2b5249029ff65894fd11b851.json"}}, {"family": "Spierings", "given": "Diana", "initials": "D", "orcid": "0000-0001-8403-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/62825465dc084c7ebd10b71e274d5eb2.json"}}, {"family": "Mertens", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-6278-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/909230c16f7840a49798794167232e76.json"}}], "type": "journal article", "published": "2024-05-20", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "606", "issn-l": "2399-3642"}, "abstract": "Well-differentiated liposarcoma (WDLS) displays amplification of genes on chromosome 12 (Chr12) in supernumerary ring or giant marker chromosomes. These structures have been suggested to develop through chromothripsis, followed by circularization and breakage-fusion-bridge (BFB) cycles. To test this hypothesis, we compared WDLSs with Chr12 amplification in rod-shaped chromosomes with WDLSs with rings. Both types of amplicons share the same spectrum of structural variants (SVs), show higher SV frequencies in Chr12 than in co-amplified segments, have SVs that fuse the telomeric ends of co-amplified chromosomes, and lack interspersed deletions. Combined with the finding of cells with transient rod-shaped structures in tumors with ring chromosomes, this suggests a stepwise process starting with the gain of Chr12 material that, after remodeling which does not fit with classical chromothripsis, forms a dicentric structure with other chromosomes. Depending on if and when telomeres from other chromosomes are captured, circularized or linear gain of 12q sequences will predominate.", "doi": "10.1038/s42003-024-06307-1", "pmid": "38769442", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11106292"}, {"db": "pii", "key": "10.1038/s42003-024-06307-1"}], "notes": [], "created": "2024-08-02T12:15:20.754Z", "modified": "2024-11-14T09:20:12.214Z"}, {"entity": "publication", "iuid": "60a28d8ccf1c42869def63646361a306", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60a28d8ccf1c42869def63646361a306.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60a28d8ccf1c42869def63646361a306"}}, "title": "Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies.", "authors": [{"family": "Zhao", "given": "Xiaodan", "initials": "X"}, {"family": "Vogirala", "given": "Vinod Kumar", "initials": "VK"}, {"family": "Liu", "given": "Meihan", "initials": "M"}, {"family": "Zhou", "given": "Yu", "initials": "Y"}, {"family": "Rhodes", "given": "Daniela", "initials": "D", "orcid": "0000-0002-2363-2591", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe153c046b604af492259157dd93e543.json"}}, {"family": "Sandin", "given": "Sara", "initials": "S", "orcid": "0000-0001-6071-2761", "researcher": {"href": "https://publications.scilifelab.se/researcher/a52c9c37f07b465781e64958a0edb780.json"}}, {"family": "Yan", "given": "Jie", "initials": "J", "orcid": "0000-0002-8555-7291", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49e888eb6744ea3b607822def3c86ad.json"}}], "type": "journal article", "published": "2024-02-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "148", "issn-l": "2399-3642"}, "abstract": "TRF2 is a component of shelterin, a telomere-specific protein complex that protects the ends of mammalian chromosomes from DNA damage signaling and improper repair. TRF2 functions as a homodimer and its interaction with telomeric DNA has been studied, but its full-length DNA-binding properties are unknown. This study examines TRF2's interaction with single-DNA strands and focuses on the conformation of the TRF2-DNA complex and TRF2's preference for DNA chirality. The results show that TRF2-DNA can switch between extended and compact conformations, indicating multiple DNA-binding modes, and TRF2's binding does not have a strong preference for DNA supercoiling chirality when DNA is under low tension. Instead, TRF2 induces DNA bending under tension. Furthermore, both the N-terminal domain of TRF2 and the Myb domain enhance its affinity for the telomere sequence, highlighting the crucial role of multivalent DNA binding in enhancing its affinity and specificity for telomere sequence. These discoveries offer unique insights into TRF2's interaction with telomeric DNA.", "doi": "10.1038/s42003-024-05838-x", "pmid": "38310140", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10838314"}, {"db": "pii", "key": "10.1038/s42003-024-05838-x"}], "notes": [], "created": "2024-11-27T15:05:11.404Z", "modified": "2024-11-27T15:05:11.577Z"}, {"entity": "publication", "iuid": "05ed7f33d6124a1a9894b922310b7fe9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05ed7f33d6124a1a9894b922310b7fe9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05ed7f33d6124a1a9894b922310b7fe9"}}, "title": "Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro.", "authors": [{"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Lomzov", "given": "Alexander", "initials": "A", "orcid": "0000-0003-3889-9464", "researcher": {"href": "https://publications.scilifelab.se/researcher/4883dd36bfcf43f0a93f1f4c3137e2c8.json"}}, {"family": "Sun", "given": "Renhua", "initials": "R", "orcid": "0000-0002-8203-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/f639c1a9dca647c0b583ce74ab398f02.json"}}, {"family": "Sandalova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-7694-6420", "researcher": {"href": "https://publications.scilifelab.se/researcher/8adca17a49fc47b696cb2b2795f83e6f.json"}}, {"family": "Orekhov", "given": "Vladislav Yu", "initials": "VY"}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39682601d1a24f5ba1d103bf74c9acbd.json"}}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}}], "type": "journal article", "published": "2023-11-24", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "1193", "issn-l": "2399-3642"}, "abstract": "The dengue protease NS2B/NS3pro has been reported to adopt either an 'open' or a 'closed' conformation. We have developed a conformational filter that combines NMR with MD simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the 'closed' conformational ensemble while the 'open' conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a 'partially' open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential step for reliable drug discovery.", "doi": "10.1038/s42003-023-05584-6", "pmid": "38001280", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10673835"}, {"db": "pii", "key": "10.1038/s42003-023-05584-6"}], "notes": [], "created": "2023-12-04T09:35:34.802Z", "modified": "2025-10-17T13:03:53.330Z"}, {"entity": "publication", "iuid": "28a8e085d9004e98b312750d425227bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28a8e085d9004e98b312750d425227bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28a8e085d9004e98b312750d425227bb"}}, "title": "Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Kurland", "given": "Sara", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ericsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ekblom", "given": "Robert", "initials": "R", "orcid": "0000-0003-2222-1966", "researcher": {"href": "https://publications.scilifelab.se/researcher/e326451a036042b89707ea3d68af0c5c.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2023-10-17", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "1035", "issn-l": "2399-3642"}, "abstract": "Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.", "doi": "10.1038/s42003-023-05385-x", "pmid": "37848497", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10582009"}, {"db": "pii", "key": "10.1038/s42003-023-05385-x"}], "notes": [], "created": "2023-11-25T05:31:13.184Z", "modified": "2024-01-16T13:48:31.935Z"}, {"entity": "publication", "iuid": "c48c857b0f664fc8802da70c86d0d433", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c48c857b0f664fc8802da70c86d0d433.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c48c857b0f664fc8802da70c86d0d433"}}, "title": "O304 ameliorates hyperglycemia in mice by dually promoting muscle glucose effectiveness and preserving \u03b2-cell function.", "authors": [{"family": "Norlin", "given": "Stefan", "initials": "S"}, {"family": "Axelsson", "given": "Jan", "initials": "J"}, {"family": "Ericsson", "given": "Madelene", "initials": "M"}, {"family": "Edlund", "given": "Helena", "initials": "H", "orcid": "0000-0002-3553-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/fde25f37d7d441a6874a0f707d6cc4a1.json"}}], "type": "journal article", "published": "2023-08-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "877", "issn-l": "2399-3642"}, "abstract": "Although insulin mediated glucose uptake in skeletal muscle is a major mechanism ensuring glucose disposal in humans, glucose effectiveness, i.e., the ability of glucose itself to stimulate its own uptake independent of insulin, accounts for roughly half of the glucose disposed during an oral glucose tolerance test. Both insulin dependent and insulin independent skeletal muscle glucose uptake are however reduced in individuals with diabetes. We here show that AMPK activator O304 stimulates insulin independent glucose uptake and utilization in skeletal muscle and heart in vivo, while preventing glycogen accumulation. Combined glucose uptake and utilization requires an increased metabolic demand and we show that O304 acts as a mitochondrial uncoupler, i.e., generates a metabolic demand. O304 averts gene expression changes associated with metabolic inflexibility in skeletal muscle and heart of diabetic mice and reverts diabetic cardiomyopathy. In Type 2 diabetes, insulin resistance elicits compensatory insulin hypersecretion, provoking \u03b2-cell stress and eventually compensatory failure. In db/db mice O304 preserves \u03b2-cell function by preventing decline in insulin secretion, \u03b2-cell mass, and pancreatic insulin content. Thus, as a dual AMPK activator and mitochondrial uncoupler O304 mitigates two central defects of T2D; impaired glucose uptake/utilization and \u03b2-cell failure, which today lack effective treatment.", "doi": "10.1038/s42003-023-05255-6", "pmid": "37626210", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10457357"}, {"db": "pii", "key": "10.1038/s42003-023-05255-6"}], "notes": [], "created": "2023-11-27T21:50:12.335Z", "modified": "2024-01-16T13:48:32.382Z"}, {"entity": "publication", "iuid": "9343655379b04dd9a0b4d89466148dab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9343655379b04dd9a0b4d89466148dab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9343655379b04dd9a0b4d89466148dab"}}, "title": "Bacterial bioindicators enable biological status classification along the continental Danube river.", "authors": [{"family": "Fontaine", "given": "Laurent", "initials": "L"}, {"family": "Pin", "given": "Lorenzo", "initials": "L"}, {"family": "Savio", "given": "Domenico", "initials": "D"}, {"family": "Friberg", "given": "Nikolai", "initials": "N"}, {"family": "Kirschner", "given": "Alexander K T", "initials": "AKT"}, {"family": "Farnleitner", "given": "Andreas H", "initials": "AH"}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "862", "issn-l": "2399-3642"}, "abstract": "Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium, and Rhodoluna, and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2-3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems.", "doi": "10.1038/s42003-023-05237-8", "pmid": "37596339", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-023-05237-8"}, {"db": "pmc", "key": "PMC10439154"}], "notes": [], "created": "2023-08-21T05:58:55.824Z", "modified": "2023-08-21T05:58:55.835Z"}, {"entity": "publication", "iuid": "3bc1aebcc63f41edbfce850538cda6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4"}}, "title": "Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.", "authors": [{"family": "Mattila", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Ala-Hulkko", "given": "Terhi", "initials": "T", "orcid": "0000-0002-0884-2152", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f4036f2bc54136a489b22aaba390d7.json"}}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Constantinescu", "given": "Mihai", "initials": "M"}, {"family": "Rotea", "given": "Mihai", "initials": "M"}, {"family": "Palinca\u0219", "given": "Nona", "initials": "N", "orcid": "0000-0001-5308-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4275405ad5045da8909e05ac7fb9dd9.json"}}, {"family": "Wilk", "given": "Stanis\u0142aw", "initials": "S"}, {"family": "Czerniak", "given": "Lech", "initials": "L", "orcid": "0000-0002-0352-5385", "researcher": {"href": "https://publications.scilifelab.se/researcher/73f2691cdc7f424784c4a7d1dbb2957e.json"}}, {"family": "Kruk", "given": "Janusz", "initials": "J"}, {"family": "\u0141apo", "given": "Jerzy", "initials": "J"}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "Soficaru", "given": "Andrei", "initials": "A"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Netea", "given": "Mihai G", "initials": "MG", "orcid": "0000-0003-2421-6052", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b25efbd9ee43e7a873baaaec4cf34c.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Persson", "given": "Per", "initials": "P", "orcid": "0009-0007-4490-2494", "researcher": {"href": "https://publications.scilifelab.se/researcher/178194b694e04e8d9520328ddda9bd11.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2023-08-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "793", "issn-l": "2399-3642"}, "abstract": "The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.", "doi": "10.1038/s42003-023-05131-3", "pmid": "37558731", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10412644"}, {"db": "pii", "key": "10.1038/s42003-023-05131-3"}], "notes": [], "created": "2023-08-14T06:19:02.423Z", "modified": "2024-01-16T13:48:32.510Z"}, {"entity": "publication", "iuid": "8ccb2185171e4920aba5fe4a63acd358", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ccb2185171e4920aba5fe4a63acd358.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ccb2185171e4920aba5fe4a63acd358"}}, "title": "Alternating L4 loop architecture of the bacterial polysaccharide co-polymerase WzzE.", "authors": [{"family": "Wiseman", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-2994-5839", "researcher": {"href": "https://publications.scilifelab.se/researcher/2098646fa9de4dbc8f7cca8aeabad319.json"}}, {"family": "Widmalm", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-8303-4481", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eb393e8ba544f67b39fd6571b4e6efc.json"}}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications.scilifelab.se/researcher/d968fcccace74b689185bb9fa2d33bf8.json"}}], "type": "journal article", "published": "2023-08-02", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "802", "issn-l": "2399-3642"}, "abstract": "Lipopolysaccharides such as the enterobacterial common antigen are important components of the enterobacterial cell envelope that act as a protective barrier against the environment and are often polymerized by the inner membrane bound Wzy-dependent pathway. By employing cryo-electron microscopy we show that WzzE, the co-polymerase component of this pathway that is responsible for the length modulation of the enterobacterial common antigen, is octameric with alternating up-down conformations of its L4 loops. The alternating up-down nature of these essential loops, located at the top of the periplasmic bell, are modulated by clashing helical faces between adjacent protomers that flank the L4 loops around the octameric periplasmic bell. This alternating arrangement and a highly negatively charged binding face create a dynamic environment in which the polysaccharide chain is extended, and suggest a ratchet-type mechanism for polysaccharide elongation.", "doi": "10.1038/s42003-023-05157-7", "pmid": "37532793", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10397196"}, {"db": "pii", "key": "10.1038/s42003-023-05157-7"}], "notes": [], "created": "2023-08-15T12:44:22.734Z", "modified": "2023-11-24T18:13:09.485Z"}, {"entity": "publication", "iuid": "818deda624df4b0f953c5d290a05ed4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/818deda624df4b0f953c5d290a05ed4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/818deda624df4b0f953c5d290a05ed4a"}}, "title": "Bone mineral density loci specific to the skull portray potential pleiotropic effects on craniosynostosis.", "authors": [{"family": "Medina-Gomez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-7999-5538", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1f97914d1c34f1f8190738c2d2e27b0.json"}}, {"family": "Mullin", "given": "Benjamin H", "initials": "BH", "orcid": "0000-0003-0743-770X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc36788ecbd64ce6a0d9ff3311c15e59.json"}}, {"family": "Chesi", "given": "Alessandra", "initials": "A"}, {"family": "Prijatelj", "given": "Vid", "initials": "V", "orcid": "0000-0002-9463-3962", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac480b4f7b964169a845cceaac252420.json"}}, {"family": "Kemp", "given": "John P", "initials": "JP", "orcid": "0000-0002-9105-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/405cc434238b46b1984a2f1d9999e37a.json"}}, {"family": "Shochat-Carvalho", "given": "Chen", "initials": "C"}, {"family": "Trajanoska", "given": "Katerina", "initials": "K"}, {"family": "Wang", "given": "Carol", "initials": "C"}, {"family": "Joro", "given": "Raimo", "initials": "R"}, {"family": "Evans", "given": "Tavia E", "initials": "TE", "orcid": "0000-0003-2390-286X", "researcher": {"href": "https://publications.scilifelab.se/researcher/253058dc9f2d4cd8b041d9fbea739f58.json"}}, {"family": "Schraut", "given": "Katharina E", "initials": "KE"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS", "orcid": "0000-0002-7464-3354", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fde142189574b44a72155785763a327.json"}}, {"family": "Zillikens", "given": "M Carola", "initials": "MC", "orcid": "0000-0001-9186-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c71c257a4de4ac7b59381237a0fa500.json"}}, {"family": "Zhu", "given": "Kun", "initials": "K", "orcid": "0000-0002-8723-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d598b0ca9b454b9c08d5596d58063c.json"}}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Evans", "given": "Daniel S", "initials": "DS"}, {"family": "Nethander", "given": "Maria", "initials": "M", "orcid": "0000-0003-3688-906X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d61951f51c4d40bef24672866382cb.json"}}, {"family": "Knol", "given": "Maria J", "initials": "MJ", "orcid": "0000-0002-3597-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/0edb736bd840429bbb57ecd1b2924561.json"}}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G", "orcid": "0000-0003-4623-9087", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc2210fecc9043c6b901506d35ca33e0.json"}}, {"family": "Prokic", "given": "Ivana", "initials": "I", "orcid": "0000-0002-0370-1473", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba397832a2a043c58abc1242c1f5599c.json"}}, {"family": "Zemel", "given": "Babette", "initials": "B", "orcid": "0000-0002-6164-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e365d159aec4d4691dfeef1cd3a014b.json"}}, {"family": "Broer", "given": "Linda", "initials": "L", "orcid": "0000-0003-0011-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c13301e242214773852a42c19b272289.json"}}, {"family": "McGuigan", "given": "Fiona E", "initials": "FE"}, {"family": "van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "Reppe", "given": "Sjur", "initials": "S", "orcid": "0000-0002-4330-5379", "researcher": {"href": "https://publications.scilifelab.se/researcher/559c6027c01a4c69914cd8c9438a32d7.json"}}, {"family": "Pawlak", "given": "Mikolaj A", "initials": "MA", "orcid": "0000-0002-8607-0194", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d66d43db71040c08faf598a4a23e6db.json"}}, {"family": "Ralston", "given": "Stuart H", "initials": "SH", "orcid": "0000-0002-2804-7586", "researcher": {"href": "https://publications.scilifelab.se/researcher/7363cc37bb8e406e8d37a9dd8ed6a4df.json"}}, {"family": "van der Velde", "given": "Nathalie", "initials": "N"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Adams", "given": "Hieab H H", "initials": "HHH", "orcid": "0000-0003-3687-2508", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab5c4744d60d4290a3a8a6b80c107f42.json"}}, {"family": "Wilson", "given": "Scott G", "initials": "SG", "orcid": "0000-0002-0357-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b292912e02d464f9e0bffa13136c017.json"}}, {"family": "Ikram", "given": "M Arfan", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}, {"family": "Walsh", "given": "John P", "initials": "JP"}, {"family": "Lakka", "given": "Timo A", "initials": "TA", "orcid": "0000-0002-9199-2871", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf0d612e609d4b4caeab4dfd8fa503e6.json"}}, {"family": "Gautvik", "given": "Kaare M", "initials": "KM"}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}, {"family": "Orwoll", "given": "Eric S", "initials": "ES", "orcid": "0000-0002-8520-7355", "researcher": {"href": "https://publications.scilifelab.se/researcher/a48a5abda98c4650bc1007cd53f95823.json"}}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM", "orcid": "0000-0002-2374-9204", "researcher": {"href": "https://publications.scilifelab.se/researcher/354ccf94e95f40da96e61c89a0a60adb.json"}}, {"family": "B\u00f8nnelykke", "given": "Klaus", "initials": "K", "orcid": "0000-0003-2003-1018", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e0992f23e69443c8bf08589711cb9b9.json"}}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Styrk\u00e1rsd\u00f3ttir", "given": "Unnur", "initials": "U", "orcid": "0000-0001-8146-8278", "researcher": {"href": "https://publications.scilifelab.se/researcher/327b14e1055744e8976d926ddaa4d502.json"}}, {"family": "Akesson", "given": "Kristina E", "initials": "KE"}, {"family": "Spector", "given": "Timothy D", "initials": "TD", "orcid": "0000-0002-9795-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3b149961364ccbb448a8cc3cdd6687.json"}}, {"family": "Tobias", "given": "Jonathan H", "initials": "JH"}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}, {"family": "Felix", "given": "Janine F", "initials": "JF", "orcid": "0000-0002-9801-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4482378cb24a9f832729f7004a41bf.json"}}, {"family": "Bisgaard", "given": "Hans", "initials": "H"}, {"family": "Grant", "given": "Struan F A", "initials": "SFA"}, {"family": "Richards", "given": "J Brent", "initials": "JB", "orcid": "0000-0002-3746-9086", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2c20c901fd041c194dae79b29b94ec2.json"}}, {"family": "Evans", "given": "David M", "initials": "DM", "orcid": "0000-0003-0663-4621", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b9b78a6c5b94bf18b798318935f62fd.json"}}, {"family": "van der Eerden", "given": "Bram", "initials": "B", "orcid": "0000-0003-4403-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/42514d51463941c5aad5083d181f0fe2.json"}}, {"family": "van de Peppel", "given": "Jeroen", "initials": "J"}, {"family": "Ackert-Bicknell", "given": "Cheryl", "initials": "C", "orcid": "0000-0003-4253-4775", "researcher": {"href": "https://publications.scilifelab.se/researcher/c843d9e827da46be81741184b57a4e38.json"}}, {"family": "Karasik", "given": "David", "initials": "D", "orcid": "0000-0002-8826-0530", "researcher": {"href": "https://publications.scilifelab.se/researcher/309cc98072424c52a29438620f03bfa0.json"}}, {"family": "Kague", "given": "Erika", "initials": "E", "orcid": "0000-0002-0266-9424", "researcher": {"href": "https://publications.scilifelab.se/researcher/cde5eaa107d04bb494e2567e66d75f71.json"}}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F", "orcid": "0000-0001-9435-9441", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8894904d3cf4671a2e563169829322a.json"}}], "type": "meta-analysis", "published": "2023-07-04", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "6", "issue": "1", "pages": "691"}, "abstract": "Skull bone mineral density (SK-BMD) provides a suitable trait for the discovery of key genes in bone biology, particularly to intramembranous ossification, not captured at other skeletal sites. We perform a genome-wide association meta-analysis (n ~ 43,800) of SK-BMD, identifying 59 loci, collectively explaining 12.5% of the trait variance. Association signals cluster within gene-sets involved in skeletal development and osteoporosis. Among the four novel loci (ZIC1, PRKAR1A, AZIN1/ATP6V1C1, GLRX3), there are factors implicated in intramembranous ossification and as we show, inherent to craniosynostosis processes. Functional follow-up in zebrafish confirms the importance of ZIC1 on cranial suture patterning. Likewise, we observe abnormal cranial bone initiation that culminates in ectopic sutures and reduced BMD in mosaic atp6v1c1 knockouts. Mosaic prkar1a knockouts present asymmetric bone growth and, conversely, elevated BMD. In light of this evidence linking SK-BMD loci to craniofacial abnormalities, our study provides new insight into the pathophysiology, diagnosis and treatment of skeletal diseases.", "doi": "10.1038/s42003-023-04869-0", "pmid": "37402774", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10319806"}, {"db": "pii", "key": "10.1038/s42003-023-04869-0"}], "notes": [], "created": "2023-11-30T22:35:09.520Z", "modified": "2023-11-30T22:36:33.714Z"}, {"entity": "publication", "iuid": "07fe9e3eec8b4340aa05343a657ea24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d"}}, "title": "Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.", "authors": [{"family": "Rifkin", "given": "Riaan F", "initials": "RF", "orcid": "0000-0003-1791-3706", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b6691b2d64749e197ef0ddd36fd5af1.json"}}, {"family": "Vikram", "given": "Surendra", "initials": "S", "orcid": "0000-0002-4721-2890", "researcher": {"href": "https://publications.scilifelab.se/researcher/9171a14995cc47de9fb4d70bf4fe9aa9.json"}}, {"family": "Alcorta", "given": "Jaime", "initials": "J"}, {"family": "Ramond", "given": "Jean-Baptiste", "initials": "JB", "orcid": "0000-0003-4790-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f9b3ec176bd489daeeb78e1ef0a1acf.json"}}, {"family": "Cowan", "given": "Don A", "initials": "DA", "orcid": "0000-0001-8059-861X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc756e07160f4c888fbdc7612936db03.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "240", "issn-l": "2399-3642"}, "abstract": "The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.", "doi": "10.1038/s42003-023-04582-y", "pmid": "36869137", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9984395"}, {"db": "pii", "key": "10.1038/s42003-023-04582-y"}], "notes": [], "created": "2023-11-29T11:28:26.513Z", "modified": "2023-11-29T11:28:26.659Z"}, {"entity": "publication", "iuid": "17288dcf31b84d78a26fa2b94fac5081", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17288dcf31b84d78a26fa2b94fac5081.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17288dcf31b84d78a26fa2b94fac5081"}}, "title": "Proteogenomics decodes the evolution of human ipsilateral breast cancer.", "authors": [{"family": "De Marchi", "given": "Tommaso", "initials": "T", "orcid": "0000-0002-4845-1084", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc71f9c0b051472990fd717a9369ccd7.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT"}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications.scilifelab.se/researcher/131aeb4c85a3431e819aff743112f6e2.json"}}, {"family": "Reinsbach", "given": "Susanne Erika", "initials": "SE", "orcid": "0000-0003-0509-2488", "researcher": {"href": "https://publications.scilifelab.se/researcher/a19438fc9f1a4f6ea1e72f9532dffd80.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Tran", "given": "Lena", "initials": "L"}, {"family": "Pekar", "given": "Gyula", "initials": "G"}, {"family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0130-7296", "researcher": {"href": "https://publications.scilifelab.se/researcher/25bbcad19da944faa9aa6b32377ae212.json"}}, {"family": "Fredriksson", "given": "Irma", "initials": "I"}, {"family": "Malmstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Fern\u00f6", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0003-2220-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/af4c4c621256430b9086600228b5be1f.json"}}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L", "orcid": "0000-0001-9885-9312", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e99f34fb854beb8d810b05fe941057.json"}}, {"family": "Malmst\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3c999da10c41e4a3afda2718815083.json"}}, {"family": "Nim\u00e9us", "given": "Emma", "initials": "E", "orcid": "0000-0003-0262-9083", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cb00ec7dcb9461d915a635fc569668d.json"}}], "type": "journal article", "published": "2023-02-02", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "6", "issue": "1", "pages": "139"}, "abstract": "Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy.", "doi": "10.1038/s42003-023-04526-6", "pmid": "36732562", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9894938"}, {"db": "pii", "key": "10.1038/s42003-023-04526-6"}], "notes": [], "created": "2023-02-17T09:33:04.476Z", "modified": "2024-11-12T12:26:20.981Z"}, {"entity": "publication", "iuid": "923e09636e01418bba0d80b842c05813", "links": {"self": {"href": "https://publications.scilifelab.se/publication/923e09636e01418bba0d80b842c05813.json"}, "display": {"href": "https://publications.scilifelab.se/publication/923e09636e01418bba0d80b842c05813"}}, "title": "High-fat diet and estrogen modulate the gut microbiota in a sex-dependent manner in mice.", "authors": [{"family": "Hases", "given": "Linnea", "initials": "L", "orcid": "0000-0001-6741-7204", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb5e09b88e94ab59a6ca9f8c457c5f4.json"}}, {"family": "Stepanauskaite", "given": "Lina", "initials": "L", "orcid": "0000-0003-4173-6009", "researcher": {"href": "https://publications.scilifelab.se/researcher/429f33fed9a44ff4b70ff88d5af917d9.json"}}, {"family": "Birgersson", "given": "Madeleine", "initials": "M", "orcid": "0000-0002-5876-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/68ea3a27e23a4f978e9c4e74ebdfbf11.json"}}, {"family": "Brusselaers", "given": "Nele", "initials": "N"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2023-01-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "20", "issn-l": "2399-3642"}, "abstract": "A high-fat diet can lead to gut microbiota dysbiosis, chronic intestinal inflammation, and metabolic syndrome. Notably, resulting phenotypes, such as glucose and insulin levels, colonic crypt cell proliferation, and macrophage infiltration, exhibit sex differences, and females are less affected. This is, in part, attributed to sex hormones. To investigate if there are sex differences in the microbiota and if estrogenic ligands can attenuate high-fat diet-induced dysbiosis, we used whole-genome shotgun sequencing to characterize the impact of diet, sex, and estrogenic ligands on the microbial composition of the cecal content of mice. We here report clear host sex differences along with remarkably sex-dependent responses to high-fat diet. Females, specifically, exhibited increased abundance of Blautia hansenii, and its levels correlated negatively with insulin levels in both sexes. Estrogen treatment had a modest impact on the microbiota diversity but altered a few important species in males. This included Collinsella aerofaciens F, which we show correlated with colonic macrophage infiltration. In conclusion, male and female mice exhibit clear differences in their cecal microbial composition and in how diet and estrogens impact the composition. Further, specific microbial strains are significantly correlated with metabolic parameters.", "doi": "10.1038/s42003-022-04406-5", "pmid": "36624306", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9829864"}, {"db": "pii", "key": "10.1038/s42003-022-04406-5"}], "notes": [], "created": "2023-11-27T21:49:55.417Z", "modified": "2024-01-16T13:48:34.180Z"}, {"entity": "publication", "iuid": "b6538257193e4bda9387d19ec84faaa0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6538257193e4bda9387d19ec84faaa0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6538257193e4bda9387d19ec84faaa0"}}, "title": "Metabolic reprogramming and membrane glycan remodeling as potential drivers of zebrafish heart regeneration.", "authors": [{"family": "Spelat", "given": "Renza", "initials": "R", "orcid": "0000-0001-5794-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7974e486fb24bbf979eb920f9d49380.json"}}, {"family": "Ferro", "given": "Federico", "initials": "F", "orcid": "0000-0002-6023-8227", "researcher": {"href": "https://publications.scilifelab.se/researcher/27810903638948feb4391fa537a7eda3.json"}}, {"family": "Contessotto", "given": "Paolo", "initials": "P"}, {"family": "Aljaabary", "given": "Amal", "initials": "A", "orcid": "0000-0003-0361-166X", "researcher": {"href": "https://publications.scilifelab.se/researcher/af820e3a3c8f441c9ed519c8849f163d.json"}}, {"family": "Martin-Salda\u00f1a", "given": "Sergio", "initials": "S", "orcid": "0000-0002-9506-8483", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7a4a6088c0a4597b6c18c2a48c74b7a.json"}}, {"family": "Jin", "given": "Chunsheng", "initials": "C", "orcid": "0000-0002-0229-102X", "researcher": {"href": "https://publications.scilifelab.se/researcher/458804f3f7274b8a9efe7a90469d0e56.json"}}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG", "orcid": "0000-0002-3045-2628", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e0b7440ff1447c9611d938d185fbc7.json"}}, {"family": "Grealy", "given": "Maura", "initials": "M"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Magni", "given": "Fulvio", "initials": "F"}, {"family": "Chinello", "given": "Clizia", "initials": "C"}, {"family": "Kilcoyne", "given": "Michelle", "initials": "M", "orcid": "0000-0002-8870-1308", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1d1606f98e540fbb09f7251adf921a2.json"}}, {"family": "Pandit", "given": "Abhay", "initials": "A", "orcid": "0000-0002-6292-4933", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4611c209a394949bd971c8b12692fac.json"}}], "type": "journal article", "published": "2022-12-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "1365", "issn-l": "2399-3642"}, "abstract": "The ability of the zebrafish heart to regenerate following injury makes it a valuable model to deduce why this capability in mammals is limited to early neonatal stages. Although metabolic reprogramming and glycosylation remodeling have emerged as key aspects in many biological processes, how they may trigger a cardiac regenerative response in zebrafish is still a crucial question. Here, by using an up-to-date panel of transcriptomic, proteomic and glycomic approaches, we identify a metabolic switch from mitochondrial oxidative phosphorylation to glycolysis associated with membrane glycosylation remodeling during heart regeneration. Importantly, we establish the N- and O-linked glycan structural repertoire of the regenerating zebrafish heart, and link alterations in both sialylation and high mannose structures across the phases of regeneration. Our results show that metabolic reprogramming and glycan structural remodeling are potential drivers of tissue regeneration after cardiac injury, providing the biological rationale to develop novel therapeutics to elicit heart regeneration in mammals.", "doi": "10.1038/s42003-022-04328-2", "pmid": "36509839", "labels": {"In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9744865"}, {"db": "pii", "key": "10.1038/s42003-022-04328-2"}], "notes": [], "created": "2023-05-31T10:56:03.689Z", "modified": "2025-10-17T13:02:17.158Z"}, {"entity": "publication", "iuid": "de1b7b013894428fbdf16c8aaaec4514", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de1b7b013894428fbdf16c8aaaec4514.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de1b7b013894428fbdf16c8aaaec4514"}}, "title": "Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis.", "authors": [{"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Bergvall", "given": "Kerstin", "initials": "K"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Pederson", "given": "Eric", "initials": "E"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Harvey", "given": "Naomi D", "initials": "ND"}, {"family": "Blott", "given": "Sarah C", "initials": "SC"}, {"family": "Olby", "given": "Natasha", "initials": "N", "orcid": "0000-0003-1349-3484", "researcher": {"href": "https://publications.scilifelab.se/researcher/99d7ecf8e71a4b92b0da71f6a7c031eb.json"}}, {"family": "Olivry", "given": "Thierry", "initials": "T"}, {"family": "Brander", "given": "Gustaf", "initials": "G", "orcid": "0000-0002-9549-4909", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c4831e82d3643c4b81e2359b6418066.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Roosje", "given": "Petra", "initials": "P"}, {"family": "Leeb", "given": "Tosso", "initials": "T", "orcid": "0000-0003-0553-4880", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3aab15785e4875a06b659c9ded0ddd.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.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": "2022-12-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "1348", "issn-l": "2399-3642"}, "abstract": "Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated.", "doi": "10.1038/s42003-022-04279-8", "pmid": "36482174", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-04279-8"}], "notes": [], "created": "2022-12-09T14:39:22.770Z", "modified": "2022-12-09T14:39:22.914Z"}, {"entity": "publication", "iuid": "61fa13eeb4e7471fb3fc42d11ed00aeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61fa13eeb4e7471fb3fc42d11ed00aeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61fa13eeb4e7471fb3fc42d11ed00aeb"}}, "title": "Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle.", "authors": [{"family": "Lovri\u0107", "given": "Alen", "initials": "A"}, {"family": "Rassolie", "given": "Ali", "initials": "A"}, {"family": "Alam", "given": "Seher", "initials": "S"}, {"family": "Mandi\u0107", "given": "Mirko", "initials": "M"}, {"family": "Saini", "given": "Amarjit", "initials": "A"}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Fernandez-Gonzalo", "given": "Rodrigo", "initials": "R"}, {"family": "Gustafsson", "given": "Thomas", "initials": "T"}, {"family": "Rullman", "given": "Eric", "initials": "E", "orcid": "0000-0003-2854-7262", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf3c60e63af042eba26ce2732374fcdb.json"}}], "type": "journal article", "published": "2022-10-22", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "1121"}, "abstract": "Skeletal muscle adaptations to exercise have been associated with a range of health-related benefits, but cell type-specific adaptations within the muscle are incompletely understood. Here we use single-cell sequencing to determine the effects of exercise on cellular composition and cell type-specific processes in human skeletal muscle before and after intense exercise. Fifteen clusters originating from six different cell populations were identified. Most cell populations remained quantitatively stable after exercise, but a large transcriptional response was observed in mesenchymal, endothelial, and myogenic cells, suggesting that these cells are specifically involved in skeletal muscle remodeling. We found three subpopulations of myogenic cells characterized by different maturation stages based on the expression of markers such as PAX7, MYOD1, TNNI1, and TNNI2. Exercise accelerated the trajectory of myogenic progenitor cells towards maturation by increasing the transcriptional features of fast- and slow-twitch muscle fibers. The transcriptional regulation of these contractile elements upon differentiation was validated in vitro on primary myoblast cells. The cell type-specific adaptive mechanisms induced by exercise presented here contribute to the understanding of the skeletal muscle adaptations triggered by physical activity and may ultimately have implications for physiological and pathological processes affecting skeletal muscle, such as sarcopenia, cachexia, and glucose homeostasis.", "doi": "10.1038/s42003-022-04088-z", "pmid": "36273106", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9588010"}, {"db": "pii", "key": "10.1038/s42003-022-04088-z"}], "notes": [], "created": "2022-12-19T10:36:03.073Z", "modified": "2023-10-16T12:41:05.413Z"}, {"entity": "publication", "iuid": "301efd49a74e490ea103f7210d81aa56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/301efd49a74e490ea103f7210d81aa56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/301efd49a74e490ea103f7210d81aa56"}}, "title": "A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Zuccon", "given": "Dario", "initials": "D"}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Tison", "given": "Jean-Luc", "initials": "JL"}, {"family": "Emslie", "given": "Steven D", "initials": "SD"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Hume", "given": "Julian P", "initials": "JP"}, {"family": "Werdelin", "given": "Lars", "initials": "L"}, {"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}], "type": "journal article", "published": "2022-08-23", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "857"}, "abstract": "The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.", "doi": "10.1038/s42003-022-03811-0", "pmid": "35999361", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9399080"}, {"db": "pii", "key": "10.1038/s42003-022-03811-0"}, {"db": "Dryad", "key": "10.5061/dryad.qz612jmjm"}], "notes": [], "created": "2022-11-09T15:56:49.491Z", "modified": "2024-01-16T13:48:35.118Z"}, {"entity": "publication", "iuid": "20044ca7f045473daf17863e0344b451", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20044ca7f045473daf17863e0344b451.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20044ca7f045473daf17863e0344b451"}}, "title": "Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals.", "authors": [{"family": "Winkler", "given": "Thomas W", "initials": "TW", "orcid": "0000-0003-0292-5421", "researcher": {"href": "https://publications.scilifelab.se/researcher/613c02e5736a4357bcfff184bebb714e.json"}}, {"family": "Rasheed", "given": "Humaira", "initials": "H", "orcid": "0000-0002-3331-5864", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfbae7ea55074f9292e48aaf6d815a03.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Rowan", "given": "Bryce X", "initials": "BX"}, {"family": "Stanzick", "given": "Kira J", "initials": "KJ"}, {"family": "Thomas", "given": "Laurent F", "initials": "LF"}, {"family": "Tin", "given": "Adrienne", "initials": "A", "orcid": "0000-0002-4207-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c33ed3b64348be904a14698402445e.json"}}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Tayo", "given": "Bamidele", "initials": "B"}, {"family": "Thio", "given": "Chris H L", "initials": "CHL"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Chai", "given": "Jin-Fang", "initials": "JF"}, {"family": "Sieber", "given": "Karsten B", "initials": "KB"}, {"family": "Horn", "given": "Katrin", "initials": "K"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M", "orcid": "0000-0002-1127-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/86431d25a54645e3988674b5e0ef6a59.json"}}, {"family": "Wuttke", "given": "Matthias", "initials": "M"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ", "orcid": "0000-0001-8450-3518", "researcher": {"href": "https://publications.scilifelab.se/researcher/17cd11842111490ba5460f3093a366f3.json"}}, {"family": "Yang", "given": "Qiong", "initials": "Q", "orcid": "0000-0002-3658-1375", "researcher": {"href": "https://publications.scilifelab.se/researcher/430f81a2a8334a0e887346376b2f530e.json"}}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Li", "given": "Yong", "initials": "Y", "orcid": "0000-0003-2651-8791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c15132ea27d43a097e4f2672f5b00ce.json"}}, {"family": "Pontali", "given": "Giulia", "initials": "G", "orcid": "0000-0002-4521-8981", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1522f9b9c404f7bb1313218a91c6779.json"}}, {"family": "G\u00fcnther", "given": "Felix", "initials": "F"}, {"family": "Dehghan", "given": "Abbas", "initials": "A", "orcid": "0000-0001-6403-016X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a63be46a547c4b99a59d71bf59194790.json"}}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Feresin", "given": "Agnese", "initials": "A"}, {"family": "de Vries", "given": "Aiko P J", "initials": "APJ"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Smith", "given": "Albert V", "initials": "AV", "orcid": "0000-0003-1942-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b28739aa7d746718d670363d7c18a40.json"}}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "De Grandi", "given": "Alessandro", "initials": "A"}, {"family": "Rosenkranz", "given": "Alexander R", "initials": "AR"}, {"family": "Franke", "given": "Andre", "initials": "A", "orcid": "0000-0003-1530-5811", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffe3df068c4283a8b8b583717e6bb6.json"}}, {"family": "Teren", "given": "Andrej", "initials": "A"}, {"family": "Metspalu", "given": "Andres", "initials": "A", "orcid": "0000-0002-3718-796X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd553a77a5a54258b4a4701f0e70a3f8.json"}}, {"family": "Hicks", "given": "Andrew A", "initials": "AA", "orcid": "0000-0001-6320-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/a679db3cfdb6408b8f1a009534d7b902.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Morgan", "given": "Anna", "initials": "A"}, {"family": "Podgornaia", "given": "Anna I", "initials": "AI"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Freedman", "given": "Barry I", "initials": "BI", "orcid": "0000-0003-0275-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/d30522bf1f794a9ab21b5bc757bc9fca.json"}}, {"family": "Spedicati", "given": "Beatrice", "initials": "B", "orcid": "0000-0002-7432-4708", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b182b23b6be49deb7d46b4945474729.json"}}, {"family": "Ponte", "given": "Belen", "initials": "B"}, {"family": "Sch\u00f6ttker", "given": "Ben", "initials": "B"}, {"family": "Brumpton", "given": "Ben", "initials": "B", "orcid": "0000-0002-3058-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9d23aaf1dc4d18a0a13e4847ea9955.json"}}, {"family": "Banas", "given": "Bernhard", "initials": "B"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Jung", "given": "Bettina", "initials": "B"}, {"family": "\u00c5svold", "given": "Bj\u00f8rn Olav", "initials": "BO", "orcid": "0000-0003-3837-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/b75640c684a2457c9e5ebcf472b01dea.json"}}, {"family": "Smith", "given": "Blair H", "initials": "BH", "orcid": "0000-0002-5362-9430", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed343544e1324911931517689ad9ba6b.json"}}, {"family": "Ning", "given": "Boting", "initials": "B"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Vanderwerff", "given": "Brett R", "initials": "BR"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM", "orcid": "0000-0002-7278-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/b18d7cad2e604bcbbb41b8e5d206c22c.json"}}, {"family": "Kammerer", "given": "Candace M", "initials": "CM"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD", "orcid": "0000-0002-4266-6949", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4ca0d34923489785f26c8071a7151d.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Spracklen", "given": "Cassandra N", "initials": "CN", "orcid": "0000-0003-3590-7182", "researcher": {"href": "https://publications.scilifelab.se/researcher/132c3af299ef430294d5d2091f135e90.json"}}, {"family": "Robinson-Cohen", "given": "Cassianne", "initials": "C"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Wang", "given": "Chaolong", "initials": "C", "orcid": "0000-0003-3945-1012", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea6e6c8a06904e3dae39d08efa05234e.json"}}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C", "orcid": "0000-0002-4042-4719", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5ac2397f6b14194949f4dbb92a21eba.json"}}, {"family": "Heng", "given": "Chew-Kiat", "initials": "CK", "orcid": "0000-0002-7309-9473", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4e206bc73574cc1bcb4a9eb6c678d64.json"}}, {"family": "Lanzani", "given": "Chiara", "initials": "C"}, {"family": "Khor", "given": "Chiea-Chuen", "initials": "CC", "orcid": "0000-0002-1128-4729", "researcher": {"href": "https://publications.scilifelab.se/researcher/632dc088fb684153899441da97ec2ccd.json"}}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY", "orcid": "0000-0003-0655-885X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf94723ce7704692ac607327e86d4137.json"}}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Shaffer", "given": "Christian M", "initials": "CM"}, {"family": "Schulz", "given": "Christina-Alexandra", "initials": "CA"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ", "orcid": "0000-0001-5645-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a8e1d33146452b87e7e21eb5339f80.json"}}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Czamara", "given": "Darina", "initials": "D", "orcid": "0000-0001-7381-904X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9a8a7d605d4f63a311fc8a211422a6.json"}}, {"family": "Porteous", "given": "David J", "initials": "DJ", "orcid": "0000-0003-1249-6106", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6e3ae11c02e4cb89e638e1e5ae0f50a.json"}}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Mascalzoni", "given": "Deborah", "initials": "D", "orcid": "0000-0003-4156-1464", "researcher": {"href": "https://publications.scilifelab.se/researcher/0301541bfe5844619d1d0486c58263f5.json"}}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Reilly", "given": "Dermot F", "initials": "DF"}, {"family": "Daw", "given": "E Warwick", "initials": "EW"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Salvi", "given": "Erika", "initials": "E"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Tai", "given": "E-Shyong", "initials": "ES", "orcid": "0000-0003-2929-8966", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d2e26ed9b3848a386b1c6f0359d6917.json"}}, {"family": "Catamo", "given": "Eulalia", "initials": "E"}, {"family": "Rizzi", "given": "Federica", "initials": "F", "orcid": "0000-0002-4606-6553", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dfc1951cef4148a64b4d5270bc97c5.json"}}, {"family": "Guo", "given": "Feng", "initials": "F"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F", "orcid": "0000-0001-9435-9441", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8894904d3cf4671a2e563169829322a.json"}}, {"family": "Guilianini", "given": "Franco", "initials": "F"}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G"}, {"family": "Ehret", "given": "Georg", "initials": "G"}, {"family": "Waeber", "given": "Gerard", "initials": "G"}, {"family": "Biino", "given": "Ginevra", "initials": "G"}, {"family": "Girotto", "given": "Giorgia", "initials": "G"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Nadkarni", "given": "Girish N", "initials": "GN"}, 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"0000-0003-2544-4460", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6b229457c2c4b25ae9c7d2cf029b82b.json"}}, {"family": "Gao", "given": "Xin", "initials": "X"}, {"family": "Sim", "given": "Xueling", "initials": "X", "orcid": "0000-0002-1233-7642", "researcher": {"href": "https://publications.scilifelab.se/researcher/3216a8d2a7264a1390a886fa09d5d648.json"}}, {"family": "Wang", "given": "Ya Xing", "initials": "YX", "orcid": "0000-0003-2749-7793", "researcher": {"href": "https://publications.scilifelab.se/researcher/a335d5361052470689def030e03e597b.json"}}, {"family": "Friedlander", "given": "Yechiel", "initials": "Y"}, {"family": "Tham", "given": "Yih-Chung", "initials": "YC", "orcid": "0000-0002-6752-797X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8175b4e810bb4a1b9448d2e69be60a31.json"}}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y", "orcid": "0000-0001-8748-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf00b09991c4b40bd77a4f2c5bfad97.json"}}, {"family": "Okada", "given": "Yukinori", "initials": "Y", "orcid": "0000-0002-0311-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b13860bfef41959c29be2de853b456.json"}}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications.scilifelab.se/researcher/df8600142a4249b6860fd0cbfa3bda5c.json"}}, {"family": "Lifelines cohort study", "given": "", "initials": ""}, {"family": "DiscovEHR/MyCode study", "given": "", "initials": ""}, {"family": "VA Million Veteran Program", "given": "", "initials": ""}, {"family": "Stark", "given": "Klaus J", "initials": "KJ"}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Hung", "given": "Adriana M", "initials": "AM"}, {"family": "Kronenberg", "given": "Florian", "initials": "F", "orcid": "0000-0003-2229-1120", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebc59079554842ecb3512ef90249a2f2.json"}}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}, {"family": "Pattaro", "given": "Cristian", "initials": "C", "orcid": "0000-0002-4119-0109", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a570bbec647b188c4a7a5da03caac.json"}}, {"family": "Heid", "given": "Iris M", "initials": "IM", "orcid": "0000-0002-4122-5308", "researcher": {"href": "https://publications.scilifelab.se/researcher/34990140a9604dd7b61807dafc8fabc6.json"}}], "type": "journal article", "published": "2022-06-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "580", "issn-l": "2399-3642"}, "abstract": "Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (nDM = 178,691, nnoDM = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM.", "doi": "10.1038/s42003-022-03448-z", "pmid": "35697829", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-03448-z"}, {"db": "pmc", "key": "PMC9192715"}], "notes": [], "created": "2022-06-14T13:16:22.813Z", "modified": "2022-11-21T15:40:40.440Z"}, {"entity": "publication", "iuid": "1263db35dcf5464c8840a71f59c535e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1263db35dcf5464c8840a71f59c535e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1263db35dcf5464c8840a71f59c535e6"}}, "title": "Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.", "authors": [{"family": "Srigyan", "given": "Megha", "initials": "M"}, {"family": "Bol\u00edvar", "given": "H\u00e9ctor", "initials": "H", "orcid": "0000-0001-5898-643X", "researcher": {"href": "https://publications.scilifelab.se/researcher/acff178f29e34a368b3f1c0105d473b7.json"}}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I", "orcid": "0000-0001-9724-9977", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b02b033776f4758acc477c75e4ec1ed.json"}}, {"family": "Santana", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9615-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a4f0fc23b847b98e0d57d22a8a756d.json"}}, {"family": "Petersen", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3882-0867", "researcher": {"href": "https://publications.scilifelab.se/researcher/69701b12d455487a9dd1ab55f9904327.json"}}, {"family": "Iriarte", "given": "Eneko", "initials": "E", "orcid": "0000-0001-8365-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/112f0c5761e84deea89b2b7cb68521ce.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "Mora", "given": "Alice", "initials": "A", "orcid": "0000-0002-0313-8545", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ca97200bd0442c3a9d41b84e57c448e.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Abdo", "given": "Khaled", "initials": "K"}, {"family": "Braemer", "given": "Frank", "initials": "F"}, {"family": "Smith", "given": "Colin", "initials": "C"}, {"family": "Iba\u00f1ez", "given": "Juan Jos\u00e9", "initials": "JJ"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}], "type": "journal article", "published": "2022-06-07", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "554"}, "abstract": "The Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here we present a multidisciplinary bioarchaeological analysis of two individuals dated to the late 7th and early 8th centuries, the Umayyad Era, from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates and burial type are consistent with one of the earliest Islamic Arab burials in the Levant. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This study represents the genomic analysis of a secondary use site with characteristics consistent with an early Islamic burial in the Levant. We discuss our findings and possible historic scenarios in the light of forces such as genetic drift and their possible interaction with religious and cultural processes (including diet and subsistence practices).", "doi": "10.1038/s42003-022-03508-4", "pmid": "35672445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9174286"}, {"db": "pii", "key": "10.1038/s42003-022-03508-4"}], "notes": [], "created": "2022-08-19T08:37:53.525Z", "modified": "2024-01-16T13:48:36.218Z"}, {"entity": "publication", "iuid": "63d33ea2899b4d6c88791474991ec2ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63d33ea2899b4d6c88791474991ec2ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63d33ea2899b4d6c88791474991ec2ae"}}, "title": "Speciation and population divergence in a mutualistic seed dispersing bird.", "authors": [{"family": "de Raad", "given": "Jordi", "initials": "J"}, {"family": "P\u00e4ckert", "given": "Martin", "initials": "M"}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Janke", "given": "Axel", "initials": "A", "orcid": "0000-0002-9394-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d649283c9584ff3b6d6415462026721.json"}}, {"family": "Kryukov", "given": "Alexey P", "initials": "AP"}, {"family": "Martens", "given": "Jochen", "initials": "J"}, {"family": "Red'kin", "given": "Yaroslav A", "initials": "YA"}, {"family": "Sun", "given": "Yuehua", "initials": "Y"}, {"family": "T\u00f6pfer", "given": "Till", "initials": "T"}, {"family": "Schleuning", "given": "Matthias", "initials": "M", "orcid": "0000-0001-9426-045X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b928a6bfe0bd467eb84163f4f97efc9a.json"}}, {"family": "Neuschulz", "given": "Eike Lena", "initials": "EL"}, {"family": "Nilsson", "given": "Maria A", "initials": "MA", "orcid": "0000-0002-8136-7263", "researcher": {"href": "https://publications.scilifelab.se/researcher/5073111d83d54096a107ee26e5c1a5b1.json"}}], "type": "journal article", "published": "2022-05-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "429", "issn-l": "2399-3642"}, "abstract": "Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds.", "doi": "10.1038/s42003-022-03364-2", "pmid": "35534538", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-03364-2"}, {"db": "pmc", "key": "PMC9085801"}, {"db": "Dryad", "key": "10.5061/dryad.stqjq2c57"}], "notes": [], "created": "2022-11-09T15:57:44.861Z", "modified": "2024-01-16T13:48:36.574Z"}, {"entity": "publication", "iuid": "18226df579c94c61955019463d361b96", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18226df579c94c61955019463d361b96.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18226df579c94c61955019463d361b96"}}, "title": "Silencing of STE20-type kinase STK25 in human aortic endothelial and smooth muscle cells is atheroprotective.", "authors": [{"family": "Cansby", "given": "Emmelie", "initials": "E", "orcid": "0000-0003-1589-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/48cf95c633c4424ab268f9ecaa311456.json"}}, {"family": "Kumari", "given": "Sima", "initials": "S"}, {"family": "Caputo", "given": "Mara", "initials": "M"}, {"family": "Xia", "given": "Ying", "initials": "Y"}, {"family": "Porosk", "given": "Rando", "initials": "R"}, {"family": "Robinson", "given": "Jonathan", "initials": "J"}, {"family": "Wang", "given": "Hao", "initials": "H", "orcid": "0000-0001-7475-0136", "researcher": {"href": "https://publications.scilifelab.se/researcher/836b4fbf7ebd4f80abc84465c8f29a2e.json"}}, {"family": "Olsson", "given": "Britt-Marie", "initials": "BM"}, {"family": "Vallin", "given": "Josefine", "initials": "J"}, {"family": "Grantham", "given": "Julie", "initials": "J"}, {"family": "Soomets", "given": "Ursel", "initials": "U", "orcid": "0000-0002-3681-188X", "researcher": {"href": "https://publications.scilifelab.se/researcher/72cc178012864ea5a642a15ca1bb6a19.json"}}, {"family": "Svensson", "given": "L Thomas", "initials": "LT"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Marschall", "given": "Hanns-Ulrich", "initials": "HU", "orcid": "0000-0001-7347-3085", "researcher": {"href": "https://publications.scilifelab.se/researcher/82b16fa78a994d12bd49ed280012893c.json"}}, {"family": "Edsfeldt", "given": "Andreas", "initials": "A"}, {"family": "Goncalves", "given": "Isabel", "initials": "I"}, {"family": "Mahlapuu", "given": "Margit", "initials": "M", "orcid": "0000-0001-8740-8874", "researcher": {"href": "https://publications.scilifelab.se/researcher/db46c5dea6e8445888d7cad506d438c8.json"}}], "type": "journal article", "published": "2022-04-19", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "379"}, "abstract": "Recent studies highlight the importance of lipotoxic damage in aortic cells as the major pathogenetic contributor to atherosclerotic disease. Since the STE20-type kinase STK25 has been shown to exacerbate ectopic lipid storage and associated cell injury in several metabolic organs, we here investigate its role in the main cell types of vasculature. We depleted STK25 by small interfering RNA in human aortic endothelial and smooth muscle cells exposed to oleic acid and oxidized LDL. In both cell types, the silencing of STK25 reduces lipid accumulation and suppresses activation of inflammatory and fibrotic pathways as well as lowering oxidative and endoplasmic reticulum stress. Notably, in smooth muscle cells, STK25 inactivation hinders the shift from a contractile to a synthetic phenotype. Together, we provide several lines of evidence that antagonizing STK25 signaling in human aortic endothelial and smooth muscle cells is atheroprotective, highlighting this kinase as a new potential therapeutic target for atherosclerotic disease.", "doi": "10.1038/s42003-022-03309-9", "pmid": "35440683", "labels": {"Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Glycoproteomics and MS Proteomics": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9018782"}, {"db": "pii", "key": "10.1038/s42003-022-03309-9"}], "notes": [], "created": "2022-11-10T17:22:43.040Z", "modified": "2024-01-16T13:46:29.345Z"}, {"entity": "publication", "iuid": "c70668b3d6344353b5fea94523f88e89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c70668b3d6344353b5fea94523f88e89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c70668b3d6344353b5fea94523f88e89"}}, "title": "Peripheral blood CD4+CCR6+ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals.", "authors": [{"family": "Svensson Akusj\u00e4rvi", "given": "Sara", "initials": "S", "orcid": "0000-0002-1086-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3e88a57db14fe0b99dd7b6286f0b81.json"}}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "J\u00fctte", "given": "Bianca B", "initials": "BB"}, {"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Gupta", "given": "Soham", "initials": "S", "orcid": "0000-0003-1136-3010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbd430437164ba38676d7b94e2189ab.json"}}, {"family": "Rodriguez", "given": "Jimmy Esneider", "initials": "JE", "orcid": "0000-0002-6735-3332", "researcher": {"href": "https://publications.scilifelab.se/researcher/48d26949ce194599889ee9fb2a819f2d.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Svensson", "given": "J Peter", "initials": "JP", "orcid": "0000-0002-5863-6250", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c226ba652024fdabbbf9203e1edb5d1.json"}}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U", "orcid": "0000-0002-0844-3338", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8094017c2a4d0a94d72813cab526f7.json"}}], "type": "journal article", "published": "2022-04-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "357", "issn-l": "2399-3642"}, "abstract": "HIV-1 infection induces a chronic inflammatory environment not restored by suppressive antiretroviral therapy (ART). As of today, the effect of viral suppression and immune reconstitution in people living with HIV-1 (PLWH) has been well described but not completely understood. Herein, we show how PLWH who naturally control the virus (PLWHEC) have a reduced proportion of CD4+CCR6+ and CD8+CCR6+ cells compared to PLWH on suppressive ART (PLWHART) and HIV-1 negative controls (HC). Expression of CCR2 was reduced on both CD4+, CD8+ and classical monocytes in PLWHEC compared to PLWHART and HC. Longer suppressive therapy, measured in the same patients, decreased number of cells expressing CCR2 on all monocytic cell populations while expression on CD8+ T cells increased. Furthermore, the CD4+CCR6+/CCR6- cells exhibited a unique proteomic profile with a modulated energy metabolism in PLWHEC compared to PLWHART independent of CCR6 status. The CD4+CCR6+ cells also showed an enrichment in proteins involved in apoptosis and p53 signalling in PLWHEC compared to PLWHART, indicative of increased sensitivity towards cell death mechanisms. Collectively, this data shows how PLWHEC have a unique chemokine receptor profile that may aid in facilitating natural control of HIV-1 infection.", "doi": "10.1038/s42003-022-03315-x", "pmid": "35418589", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9008025"}, {"db": "pii", "key": "10.1038/s42003-022-03315-x"}], "notes": [], "created": "2022-12-02T08:49:45.869Z", "modified": "2022-12-02T08:49:45.999Z"}, {"entity": "publication", "iuid": "b1a6f3fb64d34dc5b599349bc378a722", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1a6f3fb64d34dc5b599349bc378a722.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1a6f3fb64d34dc5b599349bc378a722"}}, "title": "Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Schapiro", "given": "Denis", "initials": "D", "orcid": "0000-0002-9391-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ebb422a68344362a76e1bd23bfb5b49.json"}}, {"family": "Carlberg", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-1774-6058", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e018cce30794ae08a4d7b5096914169.json"}}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Hildebrandt", "given": "Franziska", "initials": "F"}, {"family": "Korotkova", "given": "Marina", "initials": "M"}, {"family": "Hensvold", "given": "Aase H", "initials": "AH"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Sorger", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-3364-1838", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c63ad2d92e943b89ea7590c8a928ad9.json"}}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "129"}, "abstract": "The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area. Rheumatoid arthritis synovium has primarily been studied either by immunostaining or by molecular profiling after tissue homogenization. Here, we use Spatial Transcriptomics, where tissue-resident RNA is spatially labeled in situ with barcodes in a transcriptome-wide fashion, to study local tissue interactions at the site of chronic synovial inflammation. We report comprehensive spatial RNA-Seq data coupled to cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium. Combining morphological features and high-throughput spatially resolved transcriptomics may be able to provide higher statistical power and more insights into monitoring disease severity and treatment-specific responses in seropositive and seronegative rheumatoid arthritis.", "doi": "10.1038/s42003-022-03050-3", "pmid": "35149753", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-03050-3"}, {"db": "pmc", "key": "PMC8837632"}], "notes": [], "created": "2022-03-29T13:47:26.413Z", "modified": "2022-08-19T09:06:49.671Z"}, {"entity": "publication", "iuid": "2b5a77cf1023482b9a4307217fcfb0aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b5a77cf1023482b9a4307217fcfb0aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b5a77cf1023482b9a4307217fcfb0aa"}}, "title": "Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection.", "authors": [{"family": "Mikaeloff", "given": "Flora", "initials": "F"}, {"family": "Svensson Akusj\u00e4rvi", "given": "Sara", "initials": "S", "orcid": "0000-0002-1086-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3e88a57db14fe0b99dd7b6286f0b81.json"}}, {"family": "Ikomey", "given": "George Mondinde", "initials": "GM"}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "Gupta", "given": "Soham", "initials": "S", "orcid": "0000-0003-1136-3010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbd430437164ba38676d7b94e2189ab.json"}}, {"family": "Magdaleno", "given": "Gustavo Daniel Vega", "initials": "GDV"}, {"family": "Esc\u00f3s", "given": "Alejandra", "initials": "A", "orcid": "0000-0002-2990-7920", "researcher": {"href": "https://publications.scilifelab.se/researcher/7344a932be1649418f7de419efe98bd3.json"}}, {"family": "Lyonga", "given": "Emilia", "initials": "E"}, {"family": "Okomo", "given": "Marie Claire", "initials": "MC"}, {"family": "Tagne", "given": "Claude Tayou", "initials": "CT"}, {"family": "Babu", "given": "Hemalatha", "initials": "H"}, {"family": "Lorson", "given": "Christian L", "initials": "CL"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Banerjea", "given": "Akhil C", "initials": "AC"}, {"family": "Kele", "given": "Julianna", "initials": "J"}, {"family": "Hanna", "given": "Luke Elizabeth", "initials": "LE"}, {"family": "Singh", "given": "Kamal", "initials": "K", "orcid": "0000-0001-6153-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ce44cd68d68429195bd05741b1a01ac.json"}}, {"family": "de Magalh\u00e3es", "given": "Jo\u00e3o Pedro", "initials": "JP", "orcid": "0000-0002-6363-2465", "researcher": {"href": "https://publications.scilifelab.se/researcher/2008de4aab5e4559891581b28d1b7163.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U", "orcid": "0000-0002-0844-3338", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8094017c2a4d0a94d72813cab526f7.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "27", "issn-l": "2399-3642"}, "abstract": "Despite successful combination antiretroviral therapy (cART), persistent low-grade immune activation together with inflammation and toxic antiretroviral drugs can lead to long-lasting metabolic flexibility and adaptation in people living with HIV (PLWH). Our study investigated alterations in the plasma metabolic profiles by comparing PLWH on long-term cART(>5 years) and matched HIV-negative controls (HC) in two cohorts from low- and middle-income countries (LMIC), Cameroon, and India, respectively, to understand the system-level dysregulation in HIV-infection. Using untargeted and targeted LC-MS/MS-based metabolic profiling and applying advanced system biology methods, an altered amino acid metabolism, more specifically to glutaminolysis in PLWH than HC were reported. A significantly lower level of neurosteroids was observed in both cohorts and could potentiate neurological impairments in PLWH. Further, modulation of cellular glutaminolysis promoted increased cell death and latency reversal in pre-monocytic HIV-1 latent cell model U1, which may be essential for the clearance of the inducible reservoir in HIV-integrated cells.", "doi": "10.1038/s42003-021-02985-3", "pmid": "35017663", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8752762"}, {"db": "pii", "key": "10.1038/s42003-021-02985-3"}], "notes": [], "created": "2022-12-05T08:10:43.650Z", "modified": "2025-10-17T13:03:15.416Z"}, {"entity": "publication", "iuid": "d1c02b37ff1e42cf98540d9d4d2e9035", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1c02b37ff1e42cf98540d9d4d2e9035.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1c02b37ff1e42cf98540d9d4d2e9035"}}, "title": "Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.", "authors": [{"family": "Westmeijer", "given": "George", "initials": "G", "orcid": "0000-0002-5529-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2146c3e286d4f858efb5787cb3c74a2.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Alakangas", "given": "Linda", "initials": "L"}, {"family": "Sachpazidou", "given": "Varvara", "initials": "V"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Ketzer", "given": "Marcelo", "initials": "M", "orcid": "0000-0003-4796-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/5224e1bded3a4866802b863ed32cb10e.json"}}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "37"}, "abstract": "The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the \u00c4sp\u00f6 Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions.", "doi": "10.1038/s42003-021-02980-8", "pmid": "35017653", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8752596"}, {"db": "pii", "key": "10.1038/s42003-021-02980-8"}], "notes": [], "created": "2022-03-29T13:47:23.684Z", "modified": "2024-01-16T13:48:37.771Z"}, {"entity": "publication", "iuid": "960433d0e9d14c7baf59a3e9a519d1db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/960433d0e9d14c7baf59a3e9a519d1db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/960433d0e9d14c7baf59a3e9a519d1db"}}, "title": "A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.", "authors": [{"family": "Powell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-6323-7791", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8.json"}}, {"family": "Gro\u03b2e-Wilde", "given": "Ewald", "initials": "E"}, {"family": "Krokene", "given": "Paal", "initials": "P"}, {"family": "Roy", "given": "Amit", "initials": "A"}, {"family": "Chakraborty", "given": "Amrita", "initials": "A"}, {"family": "L\u00f6fstedt", "given": "Christer", "initials": "C", "orcid": "0000-0002-3116-6922", "researcher": {"href": "https://publications.scilifelab.se/researcher/68150ac5a3d44f26af3fa81a5209c535.json"}}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "Andersson", "given": "Martin N", "initials": "MN", "orcid": "0000-0001-9807-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/42bc7f90fad040c292fceed405df5ac3.json"}}, {"family": "Schlyter", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-1244-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/38df140cdd0e4a1693da808131833114.json"}}], "type": "journal article", "published": "2021-09-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "1059", "issn-l": "2399-3642"}, "abstract": "Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy >100 million m3 of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N50 of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome sequence from the genus Ips provides timely resources to address questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. In forests of today, increasingly stressed by global warming, this draft genome may assist in developing pest control strategies to mitigate outbreaks.", "doi": "10.1038/s42003-021-02602-3", "pmid": "34504275", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02602-3"}, {"db": "pmc", "key": "PMC8429705"}, {"db": "figshare", "key": "10.6084/m9.figshare.14503065"}], "notes": [], "created": "2021-09-22T15:33:20.295Z", "modified": "2024-01-16T13:48:38.511Z"}, {"entity": "publication", "iuid": "151d85634a7c4b3f91ab1db716346e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/151d85634a7c4b3f91ab1db716346e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/151d85634a7c4b3f91ab1db716346e7f"}}, "title": "Comprehensive in situ mapping of human cortical transcriptomic cell types.", "authors": [{"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5c0db7c1c9b474b8726fbd44d530330.json"}}, {"family": "Miller", "given": "Jeremy A", "initials": "JA", "orcid": "0000-0003-4549-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa758938d296460c8066cc14376896d3.json"}}, {"family": "Close", "given": "Jennie L", "initials": "JL"}, {"family": "Long", "given": "Brian", "initials": "B", "orcid": "0000-0002-7793-5969", "researcher": {"href": "https://publications.scilifelab.se/researcher/19069749bcda42d683765351e485d984.json"}}, {"family": "Lein", "given": "Ed S", "initials": "ES", "orcid": "0000-0001-9012-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd450c764a4431aa798630053343cd6.json"}}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2021-08-24", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "998", "issn-l": "2399-3642"}, "abstract": "The ability to spatially resolve the cellular architecture of human cortical cell types over informative areas is essential to understanding brain function. We combined in situ sequencing gene expression data and single-nucleus RNA-sequencing cell type definitions to spatially map cells in sections of the human cortex via probabilistic cell typing. We mapped and classified a total of 59,816 cells into all 75 previously defined subtypes to create a first spatial atlas of human cortical cells in their native position, their abundances and genetic signatures. We also examined the precise within- and across-layer distributions of all the cell types and provide a resource for the cell atlas community. The abundances and locations presented here could serve as a reference for further studies, that include human brain tissues and disease applications at the cell type level.", "doi": "10.1038/s42003-021-02517-z", "pmid": "34429496", "labels": {"In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02517-z"}, {"db": "pmc", "key": "PMC8384853"}], "notes": [], "created": "2021-12-10T17:13:17.226Z", "modified": "2025-10-17T13:02:17.907Z"}, {"entity": "publication", "iuid": "e0aeef535c474932927ea3ec20227770", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0aeef535c474932927ea3ec20227770.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0aeef535c474932927ea3ec20227770"}}, "title": "Complex population structure of the Atlantic puffin revealed by whole genome analyses.", "authors": [{"family": "Kersten", "given": "Oliver", "initials": "O", "orcid": "0000-0001-9304-2493", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b317e145ab940a2a612b38ddb698e79.json"}}, {"family": "Star", "given": "Bastiaan", "initials": "B", "orcid": "0000-0003-0235-9810", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4edcdfadd284a8e9b6b474ff34fd424.json"}}, {"family": "Leigh", "given": "Deborah M", "initials": "DM", "orcid": "0000-0003-3902-2568", "researcher": {"href": "https://publications.scilifelab.se/researcher/48b5deef5a7444109a5e490e267e8c72.json"}}, {"family": "Anker-Nilssen", "given": "Tycho", "initials": "T", "orcid": "0000-0002-1030-5524", "researcher": {"href": "https://publications.scilifelab.se/researcher/35855a3c33304060ba5c3f660079e484.json"}}, {"family": "Str\u00f8m", "given": "Hallvard", "initials": "H"}, {"family": "Danielsen", "given": "J\u00f3hannis", "initials": "J", "orcid": "0000-0002-9775-4786", "researcher": {"href": "https://publications.scilifelab.se/researcher/2074ae819cd84f839fed587ae95807a3.json"}}, {"family": "Descamps", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0003-0590-9013", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf274a4bdbac47cca89bd922c977b1e0.json"}}, {"family": "Erikstad", "given": "Kjell E", "initials": "KE"}, {"family": "Fitzsimmons", "given": "Michelle G", "initials": "MG", "orcid": "0000-0002-1749-3695", "researcher": {"href": "https://publications.scilifelab.se/researcher/572fce1630a9444684e3080555907207.json"}}, {"family": "Fort", "given": "J\u00e9r\u00f4me", "initials": "J", "orcid": "0000-0002-0860-6707", "researcher": {"href": "https://publications.scilifelab.se/researcher/232a039a62754c6dbcc98497a243e92a.json"}}, {"family": "Hansen", "given": "Erpur S", "initials": "ES", "orcid": "0000-0001-6899-2817", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c3158ad44124231804b993ce046fbb4.json"}}, {"family": "Harris", "given": "Mike P", "initials": "MP"}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Kleven", "given": "Oddmund", "initials": "O", "orcid": "0000-0003-0267-6795", "researcher": {"href": "https://publications.scilifelab.se/researcher/77abc47074084d85af635520a118143e.json"}}, {"family": "Mallory", "given": "Mark L", "initials": "ML", "orcid": "0000-0003-2744-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8fda3f16774feeb99eb4209a18f013.json"}}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce6b0ca9c5224a26947b5f941d75f039.json"}}, {"family": "Boessenkool", "given": "Sanne", "initials": "S", "orcid": "0000-0001-8033-1165", "researcher": {"href": "https://publications.scilifelab.se/researcher/49f2aaa706b446bca8e44c639fcbd0a8.json"}}], "type": "journal article", "published": "2021-07-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "922", "issn-l": "2399-3642"}, "abstract": "The factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.", "doi": "10.1038/s42003-021-02415-4", "pmid": "34326442", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02415-4"}, {"db": "pmc", "key": "PMC8322098"}], "notes": [], "created": "2021-10-01T09:03:20.955Z", "modified": "2024-01-16T13:48:39.060Z"}, {"entity": "publication", "iuid": "47e2059a8c6d4ea5aefb39c53bc5c234", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234"}}, "title": "Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.", "authors": [{"family": "Chen", "given": "Junfeng", "initials": "J", "orcid": "0000-0001-6155-411X", "researcher": {"href": "https://publications.scilifelab.se/researcher/270488419b56484993472f518ba1d286.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sato", "given": "Daiki X", "initials": "DX", "orcid": "0000-0002-9527-8253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad2eafb0bce4d2ba7c4f9cf7ed05eac.json"}}, {"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Mo", "given": "Chunheng", "initials": "C"}, {"family": "Younis", "given": "Shady", "initials": "S", "orcid": "0000-0002-4319-1738", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b77c6e3ed14b9ba2e10132f89ef781.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Mol\u00e9s", "given": "Gregorio", "initials": "G", "orcid": "0000-0001-5762-6993", "researcher": {"href": "https://publications.scilifelab.se/researcher/26c43e28a3fa49ccad6c77ae61f87777.json"}}, {"family": "G\u00f3mez", "given": "Ana", "initials": "A"}, {"family": "Kleinau", "given": "Gunnar", "initials": "G"}, {"family": "Scheerer", "given": "Patrick", "initials": "P", "orcid": "0000-0001-5028-2075", "researcher": {"href": "https://publications.scilifelab.se/researcher/50350a6ed93442f38ea62edb86eaa99b.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "795", "issn-l": "2399-3642"}, "abstract": "The underlying molecular mechanisms that determine long day versus short day breeders remain unknown in any organism. Atlantic herring provides a unique opportunity to examine the molecular mechanisms involved in reproduction timing, because both spring and autumn spawners exist within the same species. Although our previous whole genome comparisons revealed a strong association of TSHR alleles with spawning seasons, the functional consequences of these variants remain unknown. Here we examined the functional significance of six candidate TSHR mutations strongly associated with herring reproductive seasonality. We show that the L471M missense mutation in the spring-allele causes enhanced cAMP signaling. The best candidate non-coding mutation is a 5.2 kb retrotransposon insertion upstream of the TSHR transcription start site, near an open chromatin region, which is likely to affect TSHR expression. The insertion occurred prior to the split between Pacific and Atlantic herring and was lost in the autumn-allele. Our study shows that strongly associated coding and non-coding variants at the TSHR locus may both contribute to the regulation of seasonal reproduction in herring.", "doi": "10.1038/s42003-021-02307-7", "pmid": "34172814", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02307-7"}, {"db": "pmc", "key": "PMC8233318"}, {"db": "Dryad", "key": "10.5061/dryad.pnvx0k6kr"}], "notes": [], "created": "2021-12-07T21:41:02.372Z", "modified": "2024-01-16T13:48:39.437Z"}, {"entity": "publication", "iuid": "588c74de2d17433bb685094ea5947079", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588c74de2d17433bb685094ea5947079.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588c74de2d17433bb685094ea5947079"}}, "title": "The \u03b3-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells.", "authors": [{"family": "Corvaisier", "given": "Matthieu", "initials": "M"}, {"family": "Zhou", "given": "Jingkai", "initials": "J"}, {"family": "Malycheva", "given": "Darina", "initials": "D"}, {"family": "Cornella", "given": "Nicola", "initials": "N"}, {"family": "Chioureas", "given": "Dimitrios", "initials": "D"}, {"family": "Gustafsson", "given": "Nina M S", "initials": "NMS", "orcid": "0000-0001-6401-0548", "researcher": {"href": "https://publications.scilifelab.se/researcher/4484176c6d67435d9564a5fb65319e24.json"}}, {"family": "Rossell\u00f3", "given": "Catalina Ana", "initials": "CA", "orcid": "0000-0002-8977-607X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e30f3fde2ced4d9aad8810029b7fc68e.json"}}, {"family": "Ayora", "given": "Silvia", "initials": "S", "orcid": "0000-0003-3121-1786", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a4fa4ad7b244faa96b5b9460fea933.json"}}, {"family": "Li", "given": "Tongbin", "initials": "T"}, {"family": "Ekstr\u00f6m-Holka", "given": "Kristina", "initials": "K"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0598-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ee81797eff452fa037821f293d8673.json"}}], "type": "journal article", "published": "2021-06-22", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "767", "issn-l": "2399-3642"}, "abstract": "Changes in the location of \u03b3-tubulin ensure cell survival and preserve genome integrity. We investigated whether the nuclear accumulation of \u03b3-tubulin facilitates the transport of proliferating cell nuclear antigen (PCNA) between the cytosolic and the nuclear compartment in mammalian cells. We found that the \u03b3-tubulin meshwork assists in the recruitment of PCNA to chromatin. Also, decreased levels of \u03b3-tubulin reduce the nuclear pool of PCNA. In addition, the \u03b3-tubulin C terminus encodes a PCNA-interacting peptide (PIP) motif, and a \u03b3-tubulin-PIP-mutant affects the nuclear accumulation of PCNA. In a cell-free system, PCNA and \u03b3-tubulin formed a complex. In tumors, there is a significant positive correlation between TUBG1 and PCNA expression. Thus, we report a novel mechanism that constitutes the basis for tumor growth by which the \u03b3-tubulin meshwork maintains indefinite proliferation by acting as an opportune scaffold for the transport of PCNA from the cytosol to the chromatin.", "doi": "10.1038/s42003-021-02280-1", "pmid": "34158617", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02280-1"}, {"db": "pmc", "key": "PMC8219688"}], "notes": [], "created": "2021-11-03T15:39:48.182Z", "modified": "2021-11-10T12:23:58.806Z"}, {"entity": "publication", "iuid": "d6a88ec152fc41aa9cd664708fc3c565", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6a88ec152fc41aa9cd664708fc3c565.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6a88ec152fc41aa9cd664708fc3c565"}}, "title": "A combined approach for single-cell mRNA and intracellular protein expression analysis.", "authors": [{"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Danielsson", "given": "Marcus", "initials": "M", "orcid": "0000-0003-4418-0165", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6b237ce613e4ef8a6d7ab2654c2c41e.json"}}, {"family": "Schuster", "given": "Jens", "initials": "J", "orcid": "0000-0002-4383-9880", "researcher": {"href": "https://publications.scilifelab.se/researcher/a194d037b21c47a2926b082e9e79de31.json"}}, {"family": "Baskaran", "given": "Sathishkumar", "initials": "S"}, {"family": "Panagiotou", "given": "Styliani", "initials": "S"}, {"family": "Dahl", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8122-0800", "researcher": {"href": "https://publications.scilifelab.se/researcher/689e06ddc001490a8cb891050ba5a732.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ", "orcid": "0000-0002-1499-8444", "researcher": {"href": "https://publications.scilifelab.se/researcher/b11c1c853309426faed0af716f1288cd.json"}}], "type": "journal article", "published": "2021-05-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "4", "issue": "1", "pages": "624"}, "abstract": "Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.", "doi": "10.1038/s42003-021-02142-w", "pmid": "34035432", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Technology development", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02142-w"}, {"db": "pmc", "key": "PMC8149646"}], "notes": [], "created": "2021-06-02T12:38:48.106Z", "modified": "2024-01-16T13:48:39.677Z"}, {"entity": "publication", "iuid": "35be6ff1f4b1470dbb8b410f7082b5c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35be6ff1f4b1470dbb8b410f7082b5c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35be6ff1f4b1470dbb8b410f7082b5c7"}}, "title": "Neutron reflectometry and NMR spectroscopy of full-length Bcl-2 protein reveal its membrane localization and conformation.", "authors": [{"family": "Mushtaq", "given": "Ameeq Ul", "initials": "AU", "orcid": "0000-0002-5636-2567", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b77280f8a9463a9af768275bc80ae9.json"}}, {"family": "\u00c5d\u00e9n", "given": "J\u00f6rgen", "initials": "J", "orcid": "0000-0002-4480-1219", "researcher": {"href": "https://publications.scilifelab.se/researcher/00206abad0de45eb90dc6bd3d5f3cf22.json"}}, {"family": "Clifton", "given": "Luke A", "initials": "LA", "orcid": "0000-0001-8754-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e26f83508bc7451a9d66123eb9ea747c.json"}}, {"family": "Wacklin-Knecht", "given": "Hanna", "initials": "H"}, {"family": "Campana", "given": "Mario", "initials": "M"}, {"family": "Dingeldein", "given": "Artur P G", "initials": "APG"}, {"family": "Persson", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-6663-6536", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fb6fe3555374aec90b2a8b9dfd8016b.json"}}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-7380-8797", "researcher": {"href": "https://publications.scilifelab.se/researcher/85bd86ebc85d4653bc880bc9be25bc80.json"}}], "type": "journal article", "published": "2021-04-27", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "507", "issn-l": "2399-3642"}, "abstract": "B-cell lymphoma 2 (Bcl-2) proteins are the main regulators of mitochondrial apoptosis. Anti-apoptotic Bcl-2 proteins possess a hydrophobic tail-anchor enabling them to translocate to their target membrane and to shift into an active conformation where they inhibit pro-apoptotic Bcl-2 proteins to ensure cell survival. To address the unknown molecular basis of their cell-protecting functionality, we used intact human Bcl-2 protein natively residing at the mitochondrial outer membrane and applied neutron reflectometry and NMR spectroscopy. Here we show that the active full-length protein is entirely buried into its target membrane except for the regulatory flexible loop domain (FLD), which stretches into the aqueous exterior. The membrane location of Bcl-2 and its conformational state seems to be important for its cell-protecting activity, often infamously upregulated in cancers. Most likely, this situation enables the Bcl-2 protein to sequester pro-apoptotic Bcl-2 proteins at the membrane level while sensing cytosolic regulative signals via its FLD region.", "doi": "10.1038/s42003-021-02032-1", "pmid": "33907308", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02032-1"}, {"db": "pmc", "key": "PMC8079415"}], "notes": [], "created": "2021-07-02T14:10:45.578Z", "modified": "2025-10-17T13:03:55.993Z"}, {"entity": "publication", "iuid": "598bd6b5445f44679e26ebb6cb896fe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5"}}, "title": "The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.", "authors": [{"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "de Bruijn", "given": "Ino", "initials": "I", "orcid": "0000-0001-5427-4750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c71c59a5f064f4c84150c7b5cd366ac.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2021-03-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "307", "issn-l": "2399-3642"}, "abstract": "The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.", "doi": "10.1038/s42003-021-01810-1", "pmid": "33686191", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01810-1"}, {"db": "pmc", "key": "PMC7940616"}], "notes": [], "created": "2021-06-09T12:14:33.814Z", "modified": "2024-01-16T13:48:40.474Z"}, {"entity": "publication", "iuid": "15c10995ae464830a4c3608c5f24bdb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15c10995ae464830a4c3608c5f24bdb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15c10995ae464830a4c3608c5f24bdb8"}}, "title": "Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses.", "authors": [{"family": "Flatt", "given": "Justin W", "initials": "JW", "orcid": "0000-0001-5406-8156", "researcher": {"href": "https://publications.scilifelab.se/researcher/482e1659c59c441883228d50d051dacc.json"}}, {"family": "Domanska", "given": "Au\u0161ra", "initials": "A", "orcid": "0000-0002-3772-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b6fec96ed5c4cd88389e71a4fa2412b.json"}}, {"family": "Sepp\u00e4l\u00e4", "given": "Alma L", "initials": "AL", "orcid": "0000-0002-0534-246X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0199c8e9b184f9cacdc5c0009c63cd0.json"}}, {"family": "Butcher", "given": "Sarah J", "initials": "SJ", "orcid": "0000-0001-7060-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7076e70172b45d7ab9de4ab86775ae9.json"}}], "type": "journal article", "published": "2021-02-26", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "250", "issn-l": "2399-3642"}, "abstract": "Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals that prevent virus attachment and entry into host cells. To aid with broad-range drug development, we report here structures of coxsackieviruses B3 and B4 bound to different interprotomer-targeting capsid binders using single-particle cryo-EM. The EM density maps are beyond 3 \u00c5 resolution, providing detailed information about interactions in the ligand-binding pocket. Comparative analysis revealed the residues that form a conserved virion-stabilizing network at the interprotomer site, and showed the small molecule properties that allow anchoring in the pocket to inhibit virus disassembly.", "doi": "10.1038/s42003-021-01779-x", "pmid": "33637854", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01779-x"}, {"db": "pmc", "key": "PMC7910612"}], "notes": [], "created": "2021-02-26T16:17:20.469Z", "modified": "2021-11-10T12:26:46.984Z"}, {"entity": "publication", "iuid": "e5924e2e04a64152ac970d7f2353229e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e"}}, "title": "A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.", "authors": [{"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Arendt", "given": "Maja-Louise", "initials": "ML"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "M\u00e4kel\u00e4inen", "given": "Suvi", "initials": "S", "orcid": "0000-0001-7378-4991", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b1f91bf7dcd466a9814effddf67976e.json"}}, {"family": "Pielberg", "given": "Gerli Rosengren", "initials": "GR"}, {"family": "Hanson", "given": "Jeanette", "initials": "J"}, {"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Saellstr\u00f6m", "given": "Sara", "initials": "S", "orcid": "0000-0001-5253-5830", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac98530437d4d6890dffcbd31eabde0.json"}}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H", "orcid": "0000-0001-6098-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8783f23d664f4b98ef8f6ff03b6693.json"}}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF", "orcid": "0000-0002-7480-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/b590797209ee4feab6302920621fc621.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "comparative study", "published": "2021-02-10", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "4", "issue": "1", "pages": "185"}, "abstract": "We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine \"dark\" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.", "doi": "10.1038/s42003-021-01698-x", "pmid": "33568770", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01698-x"}, {"db": "pmc", "key": "PMC7875987"}], "notes": [], "created": "2021-02-17T19:15:39.689Z", "modified": "2024-01-16T13:48:40.742Z"}, {"entity": "publication", "iuid": "af9a1d63cb8445088a21a8b5498b3f5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af9a1d63cb8445088a21a8b5498b3f5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af9a1d63cb8445088a21a8b5498b3f5a"}}, "title": "Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide.", "authors": [{"family": "Heidler", "given": "Thomas V", "initials": "TV", "orcid": "0000-0002-5997-3945", "researcher": {"href": "https://publications.scilifelab.se/researcher/54d1a40e92fc4128ab2477ccc717e7d8.json"}}, {"family": "Ernits", "given": "Karin", "initials": "K"}, {"family": "Ziolkowska", "given": "Agnieszka", "initials": "A"}, {"family": "Claesson", "given": "Rolf", "initials": "R"}, {"family": "Persson", "given": "Karina", "initials": "K", "orcid": "0000-0003-0807-0348", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b999cf004141468eefb2504b7c5b99.json"}}], "type": "journal article", "published": "2021-01-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "106", "issn-l": "2399-3642"}, "abstract": "The Gram-negative bacterium Porphyromonas gingivalis is a secondary colonizer of the oral biofilm and is involved in the onset and progression of periodontitis. Its fimbriae, of type-V, are important for attachment to other microorganisms in the biofilm and for adhesion to host cells. The fimbriae are assembled from five proteins encoded by the mfa1 operon, of which Mfa5 is one of the ancillary tip proteins. Here we report the X-ray structure of the N-terminal half of Mfa5, which reveals a von Willebrand factor domain and two IgG-like domains. One of the IgG-like domains is stabilized by an intramolecular isopeptide bond, which is the first such bond observed in a Gram-negative bacterium. These features make Mfa5 structurally more related to streptococcal adhesins than to the other P. gingivalis Mfa proteins. The structure reported here indicates that horizontal gene transfer has occurred among the bacteria within the oral biofilm.", "doi": "10.1038/s42003-020-01621-w", "pmid": "33495563", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-01621-w"}, {"db": "pmc", "key": "PMC7835359"}], "notes": [], "created": "2021-12-13T21:53:45.043Z", "modified": "2021-12-13T21:53:45.135Z"}, {"entity": "publication", "iuid": "2c302588fb0a42b3be111c75c663961d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c302588fb0a42b3be111c75c663961d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c302588fb0a42b3be111c75c663961d"}}, "title": "LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.", "authors": [{"family": "Herdenberg", "given": "Carl", "initials": "C"}, {"family": "Mutie", "given": "Pascal M", "initials": "PM"}, {"family": "Billing", "given": "Ola", "initials": "O", "orcid": "0000-0001-5824-6263", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c9507722d964ce9a32a6cd3c6d80b2c.json"}}, {"family": "Abdullah", "given": "Ahmad", "initials": "A", "orcid": "0000-0003-3502-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/dca27d1581fc4760b2b8a34f6f53e6f6.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Tuck", "given": "Simon", "initials": "S"}, {"family": "Holmlund", "given": "Camilla", "initials": "C"}, {"family": "Arner", "given": "Peter", "initials": "P", "orcid": "0000-0002-6208-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b10e9b283e4806a8d97755a43e4cec.json"}}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.json"}}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-6891-6996", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b1b2d57a55e415aa17acbd0318a019e.json"}}], "type": "journal article", "published": "2021-01-19", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "90", "issn-l": "2399-3642"}, "abstract": "Leucine-rich repeats and immunoglobulin-like domains (LRIG) proteins have been implicated as regulators of growth factor signaling; however, the possible redundancy among mammalian LRIG1, LRIG2, and LRIG3 has hindered detailed elucidation of their physiological functions. Here, we show that Lrig-null mouse embryonic fibroblasts (MEFs) are deficient in adipogenesis and bone morphogenetic protein (BMP) signaling. In contrast, transforming growth factor-beta (TGF-\u03b2) and receptor tyrosine kinase (RTK) signaling appeared unaltered in Lrig-null cells. The BMP signaling defect was rescued by ectopic expression of LRIG1 or LRIG3 but not by expression of LRIG2. Caenorhabditis elegans with mutant LRIG/sma-10 variants also exhibited a lipid storage defect. Human LRIG1 variants were strongly associated with increased body mass index (BMI) yet protected against type 2 diabetes; these effects were likely mediated by altered adipocyte morphology. These results demonstrate that LRIG proteins function as evolutionarily conserved regulators of lipid metabolism and BMP signaling and have implications for human disease.", "doi": "10.1038/s42003-020-01613-w", "pmid": "33469151", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-01613-w"}, {"db": "pmc", "key": "PMC7815736"}], "notes": [], "created": "2021-12-09T20:01:11.461Z", "modified": "2025-10-17T13:03:16.382Z"}, {"entity": "publication", "iuid": "c46844a0633944c99b1408c2c833442e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c46844a0633944c99b1408c2c833442e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c46844a0633944c99b1408c2c833442e"}}, "title": "UvrD helicase-RNA polymerase interactions are governed by UvrD's carboxy-terminal Tudor domain.", "authors": [{"family": "Kawale", "given": "Ashish A", "initials": "AA", "orcid": "0000-0002-5074-680X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b286129785b441c793dc1ba8f1d09dd2.json"}}, {"family": "Burmann", "given": "Bj\u00f6rn M", "initials": "BM", "orcid": "0000-0002-3135-7964", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a6d61fc1a64677874973c3247b1eb4.json"}}], "type": "journal article", "published": "2020-10-23", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "607", "issn-l": "2399-3642"}, "abstract": "All living organisms have to cope with the constant threat of genome damage by UV light and other toxic reagents. To maintain the integrity of their genomes, organisms developed a variety of DNA repair pathways. One of these, the Transcription Coupled DNA-Repair (TCR) pathway, is triggered by stalled RNA Polymerase (RNAP) complexes at DNA damage sites on actively transcribed genes. A recently elucidated bacterial TCR pathway employs the UvrD helicase pulling back stalled RNAP complexes from the damage, stimulating recruitment of the DNA-repair machinery. However, structural and functional aspects of UvrD's interaction with RNA Polymerase remain elusive. Here we used advanced solution NMR spectroscopy to investigate UvrD's role within the TCR, identifying that the carboxy-terminal region of the UvrD helicase facilitates RNAP interactions by adopting a Tudor-domain like fold. Subsequently, we functionally analyzed this domain, identifying it as a crucial component for the UvrD-RNAP interaction besides having nucleic-acid affinity.", "doi": "10.1038/s42003-020-01332-2", "pmid": "33097771", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-01332-2"}, {"db": "pmc", "key": "PMC7585439"}], "notes": [], "created": "2020-12-11T09:10:27.274Z", "modified": "2025-10-17T13:03:56.528Z"}, {"entity": "publication", "iuid": "f0dc43b7323e459ca55148bf15d20642", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0dc43b7323e459ca55148bf15d20642.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0dc43b7323e459ca55148bf15d20642"}}, "title": "Genome sequence of segmented filamentous bacteria present in the human intestine.", "authors": [{"family": "Jonsson", "given": "Hans", "initials": "H"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dfdcf0109a942228d35d8dbfdede585.json"}}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Lundin", "given": "Eva", "initials": "E"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "485", "issn-l": "2399-3642"}, "abstract": "Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host's intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.", "doi": "10.1038/s42003-020-01214-7", "pmid": "32887924", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-01214-7"}, {"db": "pmc", "key": "PMC7474095"}], "notes": [], "created": "2020-11-16T08:52:13.095Z", "modified": "2024-01-16T13:48:41.758Z"}, {"entity": "publication", "iuid": "011596f9427341e9be5a619b81b0b796", "links": {"self": {"href": "https://publications.scilifelab.se/publication/011596f9427341e9be5a619b81b0b796.json"}, "display": {"href": "https://publications.scilifelab.se/publication/011596f9427341e9be5a619b81b0b796"}}, "title": "Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing.", "authors": [{"family": "Brofelth", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1187-4005", "researcher": {"href": "https://publications.scilifelab.se/researcher/d07ff976b577400788e60a42a1a7bb5c.json"}}, {"family": "Ekstrand", "given": "Anna Isinger", "initials": "AI"}, {"family": "Gour", "given": "Shashank", "initials": "S"}, {"family": "Jansson", "given": "Ronnie", "initials": "R"}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Elleby", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Kvist", "given": "Anders", "initials": "A", "orcid": "0000-0002-1358-0695", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e6b39bdc00c442f94caed782772a278.json"}}, {"family": "Wingren", "given": "Christer", "initials": "C"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-3712-4897", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c96993814854e10b98890f952ba1151.json"}}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CAK", "orcid": "0000-0003-2461-2354", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fabeaf17da24138990ee896281fc4d5.json"}}], "type": "journal article", "published": "2020-07-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "339", "issn-l": "2399-3642"}, "abstract": "The composition of serum proteins is reflecting the current health status and can, with the right tools, be used to detect early signs of disease, such as an emerging cancer. An earlier diagnosis of cancer would greatly increase the chance of an improved outcome for the patients. However, there is still an unmet need for proficient tools to decipher the information in the blood proteome, which calls for further technological development. Here, we present a proof-of-concept study that demonstrates an alternative approach for multiplexed protein profiling of serum samples in solution, using DNA barcoded scFv antibody fragments and next generation sequencing. The outcome shows high accuracy when discriminating samples derived from pancreatic cancer patients and healthy controls and represents a scalable alternative for serum analysis.", "doi": "10.1038/s42003-020-1068-0", "pmid": "32620783", "labels": {"Clinical Genomics Lund": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-1068-0"}, {"db": "pmc", "key": "PMC7334203"}, {"db": "figshare", "key": "10.6084/m9.figshare.12370106"}], "notes": [], "created": "2020-12-01T18:13:15.627Z", "modified": "2021-11-10T12:49:31.330Z"}, {"entity": "publication", "iuid": "5d10760287d3464a96f10a51a55e9a7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d10760287d3464a96f10a51a55e9a7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d10760287d3464a96f10a51a55e9a7c"}}, "title": "Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.", "authors": [{"family": "Wall\u00e9n-Mackenzie", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-8713-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeda951c090846008ee77d1aa28e5fe1.json"}}, {"family": "Dumas", "given": "Sylvie", "initials": "S", "orcid": "0000-0002-4415-9924", "researcher": {"href": "https://publications.scilifelab.se/researcher/0393bec924d24ecfaa75cd77062b7231.json"}}, {"family": "Papathanou", "given": "Maria", "initials": "M", "orcid": "0000-0002-0845-9831", "researcher": {"href": "https://publications.scilifelab.se/researcher/281c8a847ca64d50988627c9d92f5b8a.json"}}, {"family": "Martis Thiele", "given": "Mihaela M", "initials": "MM"}, {"family": "Vlcek", "given": "Bianca", "initials": "B", "orcid": "0000-0001-5442-2303", "researcher": {"href": "https://publications.scilifelab.se/researcher/7afc70325f904d95b16a5e0fc9179e4b.json"}}, {"family": "K\u00f6nig", "given": "Niclas", "initials": "N", "orcid": "0000-0003-0899-046X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7def2d96c45b462fa50a6579ad1dad97.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}], "type": "journal article", "published": "2020-07-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "3", "issue": "1", "pages": "338"}, "abstract": "The subthalamic nucleus (STN) is crucial for normal motor, limbic and associative function. STN dysregulation is correlated with several brain disorders, including Parkinson's disease and obsessive compulsive disorder (OCD), for which high-frequency stimulation of the STN is increasing as therapy. However, clinical progress is hampered by poor knowledge of the anatomical-functional organization of the STN. Today, experimental mouse genetics provides outstanding capacity for functional decoding, provided selective promoters are available. Here, we implemented single-nuclei RNA sequencing (snRNASeq) of the mouse STN followed through with histological analysis of 16 candidate genes of interest. Our results demonstrate that the mouse STN is composed of at least four spatio-molecularly defined domains, each distinguished by defined sets of promoter activities. Further, molecular profiles dissociate the STN from the adjoining para-STN (PSTN) and neighboring structures of the hypothalamus, mammillary nuclei and zona incerta. Enhanced knowledge of STN\u00b4s internal organization should prove useful towards genetics-based functional decoding of this clinically relevant brain structure.", "doi": "10.1038/s42003-020-1028-8", "pmid": "32620779", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-1028-8"}, {"db": "pmc", "key": "PMC7334224"}], "notes": [], "created": "2020-08-10T12:44:57.714Z", "modified": "2024-01-16T13:48:42.209Z"}, {"entity": "publication", "iuid": "b666d402dd5343929e0fbb695aca0efe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe"}}, "title": "Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2467-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d517d4f20046c08405f8aeecf4ad2a.json"}}, {"family": "Bennke", "given": "Christin", "initials": "C"}, {"family": "Beier", "given": "Sara", "initials": "S", "orcid": "0000-0003-3707-4487", "researcher": {"href": "https://publications.scilifelab.se/researcher/5358a1e162474073a69b08c32e7c5420.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Quince", "given": "Christopher", "initials": "C"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2020-03-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "119", "issn-l": "2399-3642"}, "abstract": "The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.", "doi": "10.1038/s42003-020-0856-x", "pmid": "32170201", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0856-x"}, {"db": "pmc", "key": "PMC7070063"}], "notes": [], "created": "2020-07-08T13:04:08.349Z", "modified": "2024-01-16T13:48:42.773Z"}, {"entity": "publication", "iuid": "6ef6a5481f8043e3a6bd28a7ef84d080", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ef6a5481f8043e3a6bd28a7ef84d080.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ef6a5481f8043e3a6bd28a7ef84d080"}}, "title": "Uncovering diversity and metabolic spectrum of animals in dead zone sediments.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Bonaglia", "given": "Stefano", "initials": "S", "orcid": "0000-0003-4366-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02dd99f9fd14dd89d5c231260806720.json"}}, {"family": "Holovachov", "given": "Oleksandr", "initials": "O", "orcid": "0000-0002-4285-0754", "researcher": {"href": "https://publications.scilifelab.se/researcher/7887fd76b35c47aaa67ac8ab7a1d07d5.json"}}, {"family": "Marzocchi", "given": "Ugo", "initials": "U", "orcid": "0000-0002-4746-9944", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d1ad4b2b3e48db9cc591f4574cb848.json"}}, {"family": "Hall", "given": "Per O J", "initials": "POJ"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}], "type": "journal article", "published": "2020-03-06", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "106", "issn-l": "2399-3642"}, "abstract": "Ocean deoxygenation driven by global warming and eutrophication is a primary concern for marine life. Resistant animals may be present in dead zone sediments, however there is lack of information on their diversity and metabolism. Here we combined geochemistry, microscopy, and RNA-seq for estimating taxonomy and functionality of micrometazoans along an oxygen gradient in the largest dead zone in the world. Nematodes are metabolically active at oxygen concentrations below 1.8 \u00b5mol L-1, and their diversity and community structure are different between low oxygen areas. This is likely due to toxic hydrogen sulfide and its potential to be oxidized by oxygen or nitrate. Zooplankton resting stages dominate the metazoan community, and these populations possibly use cytochrome c oxidase as an oxygen sensor to exit dormancy. Our study sheds light on mechanisms of animal adaptation to extreme environments. These biological resources can be essential for recolonization of dead zones when oxygen conditions improve.", "doi": "10.1038/s42003-020-0822-7", "pmid": "32144383", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0822-7"}, {"db": "pmc", "key": "PMC7060179"}], "notes": [], "created": "2020-07-08T13:05:16.537Z", "modified": "2024-01-16T13:48:42.803Z"}, {"entity": "publication", "iuid": "35806cca1dd04fef9c3505fa53346c1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35806cca1dd04fef9c3505fa53346c1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35806cca1dd04fef9c3505fa53346c1e"}}, "title": "Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Gill", "given": "Jacquelyn", "initials": "J"}, {"family": "Fisher", "given": "Daniel C", "initials": "DC"}, {"family": "Protopopov", "given": "Albert V", "initials": "AV"}, {"family": "Herridge", "given": "Victoria L", "initials": "VL"}, {"family": "Plotnikov", "given": "Valery", "initials": "V", "orcid": "0000-0002-4870-3499", "researcher": {"href": "https://publications.scilifelab.se/researcher/378b10136be74923bff019375f5d6c91.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "historical article", "published": "2020-02-21", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "84", "issn-l": "2399-3642"}, "abstract": "Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44-49 ka BP, and was genetically identified as a female horned lark. This is a species that usually inhabits open habitat, such as the steppe environment that existed in Siberia at the time. This near-intact carcass highlights the potential of permafrost remains for evolutionary studies that combine both morphology and ancient nucleic acids.", "doi": "10.1038/s42003-020-0806-7", "pmid": "32081985", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0806-7"}, {"db": "pmc", "key": "PMC7035339"}], "notes": [], "created": "2020-07-08T13:04:57.570Z", "modified": "2024-01-16T13:48:42.909Z"}, {"entity": "publication", "iuid": "17ab6ae7353b461ab314603a3d7cf0e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17ab6ae7353b461ab314603a3d7cf0e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17ab6ae7353b461ab314603a3d7cf0e1"}}, "title": "Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.", "authors": [{"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Dahl", "given": "Martin", "initials": "M"}, {"family": "Deyanova", "given": "Diana", "initials": "D"}, {"family": "Lyimo", "given": "Liberatus D", "initials": "LD"}, {"family": "Bik", "given": "Holly M", "initials": "HM"}, {"family": "Schuelke", "given": "Taruna", "initials": "T"}, {"family": "Pereira", "given": "Tiago Jos\u00e9", "initials": "TJ"}, {"family": "Bj\u00f6rk", "given": "Mats", "initials": "M"}, {"family": "Creer", "given": "Simon", "initials": "S"}, {"family": "Gullstr\u00f6m", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-10-04", "journal": {"volume": "2", "issn": "2399-3642", "issue": null, "pages": "362", "title": "Commun Biol", "issn-l": "2399-3642"}, "abstract": "Ecological interactions between aquatic plants and sediment communities can shape the structure and function of natural systems. Currently, we do not fully understand how seagrass habitat degradation impacts the biodiversity of belowground sediment communities. Here, we evaluated indirect effects of disturbance of seagrass meadows on meiobenthic community composition, with a five-month in situ experiment in a tropical seagrass meadow. Disturbance was created by reducing light availability (two levels of shading), and by mimicking grazing events (two levels) to assess impacts on meiobenthic diversity using high-throughput sequencing of 18S rRNA amplicons. Both shading and simulated grazing had an effect on meiobenthic community structure, mediated by seagrass-associated biotic drivers and sediment abiotic variables. Additionally, shading substantially altered the trophic structure of the nematode community. Our findings show that degradation of seagrass meadows can alter benthic community structure in coastal areas with potential impacts to ecosystem functions mediated by meiobenthos in marine sediments.", "doi": "10.1038/s42003-019-0610-4", "pmid": "31602411", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "610"}, {"db": "pmc", "key": "PMC6778119"}], "notes": [], "created": "2019-12-02T17:20:31.307Z", "modified": "2024-01-16T13:48:43.707Z"}, {"entity": "publication", "iuid": "74d4aa31e7774b5d81c9f6b39c75f31c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74d4aa31e7774b5d81c9f6b39c75f31c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74d4aa31e7774b5d81c9f6b39c75f31c"}}, "title": "Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.", "authors": [{"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Damlien", "given": "Hege", "initials": "H"}, {"family": "Manninen", "given": "Mikael A", "initials": "MA", "orcid": "0000-0002-8906-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce8d3c355c374e8794526fdfeb1c87e8.json"}}, {"family": "Nordqvist", "given": "Bengt", "initials": "B"}, {"family": "Persson", "given": "Per", "initials": "P"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2019-05-15", "journal": {"volume": "2", "issn": "2399-3642", "issue": null, "pages": "185", "title": "Commun Biol", "issn-l": "2399-3642"}, "abstract": "Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.", "doi": "10.1038/s42003-019-0399-1", "pmid": "31123709", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "399"}, {"db": "pmc", "key": "PMC6520363"}, {"db": "Dryad", "key": "10.5061/dryad.j3k19p9"}], "notes": [], "created": "2019-12-02T17:20:27.160Z", "modified": "2024-01-16T13:48:44.340Z"}, {"entity": "publication", "iuid": "42facd6bed944bae835b71cba9824a4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42facd6bed944bae835b71cba9824a4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42facd6bed944bae835b71cba9824a4f"}}, "title": "Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells.", "authors": [{"family": "Mehmeti", "given": "Meliha", "initials": "M"}, {"family": "Bergenfelz", "given": "Caroline", "initials": "C"}, {"family": "K\u00e4llberg", "given": "Eva", "initials": "E"}, {"family": "Millrud", "given": "Camilla Rydberg", "initials": "CR"}, {"family": "Bj\u00f6rk", "given": "Per", "initials": "P"}, {"family": "Ivars", "given": "Fredrik", "initials": "F"}, {"family": "Johansson-Lindbom", "given": "Bengt", "initials": "B"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Andr\u00e9", "given": "Ingemar", "initials": "I"}, {"family": "Leandersson", "given": "Karin", "initials": "K", "orcid": "0000-0001-8254-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/4736923f382845c2990efb251340bfb4.json"}}], "type": "journal article", "published": "2019-05-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "2", "issue": "1", "pages": "176", "issn-l": "2399-3642"}, "abstract": "Innate immune responses are rapid, dynamic and highly regulated to avoid overt reactions. This regulation is executed by innate immune tolerance mechanisms that remain obscure. Wnt5a is a signalling protein mainly involved in developmental processes and cancer. The effect of Wnt5a on inflammatory myeloid cells is controversial. Here, we combine primary cell cultures, in vitro binding studies, mass spectrometry and Drosophila protein modelling to show that Wnt5a is a direct ligand of toll-like receptor (TLR) 2 and 4. The binding promotes a MyD88-non-canonical nuclear factor of kappa B (NF\u03baB) and AP-1 signalling cascade, with contradictory profiles in mouse (pro-inflammatory) and human (anti-inflammatory) myeloid immune cells. These data reveal that the true nature of Wnt5a in inflammatory cells, is to regulate TLR signals, and in human myeloid cells it acts as an endogenous, tolerance-associated molecular pattern (TAMP), inducing IL-10 and innate immune tolerance.", "doi": "10.1038/s42003-019-0432-4", "pmid": "31098409", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "432"}, {"db": "pmc", "key": "PMC6509336"}], "notes": [], "created": "2020-01-27T10:00:20.654Z", "modified": "2021-06-16T14:55:04.785Z"}, {"entity": "publication", "iuid": "c7414fa518d74fd0a11e89491b445b95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7414fa518d74fd0a11e89491b445b95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7414fa518d74fd0a11e89491b445b95"}}, "title": "RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples.", "authors": [{"family": "Wu", "given": "Chenglin", "initials": "C"}, {"family": "Simonetti", "given": "Michele", "initials": "M"}, {"family": "Rossell", "given": "Carla", "initials": "C"}, {"family": "Mignardi", "given": "Marco", "initials": "M"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Annaratone", "given": "Laura", "initials": "L", "orcid": "0000-0001-5750-1445", "researcher": {"href": "https://publications.scilifelab.se/researcher/d341ea28491445688116796fc15f53ae.json"}}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2018-11-28", "journal": {"volume": "1", "issn": "2399-3642", "issue": null, "pages": "209", "title": "Commun Biol", "issn-l": "2399-3642"}, "abstract": "Single-molecule RNA fluorescence in situ hybridization (smFISH) represents a promising approach to quantify the expression of clinically useful biomarkers in tumor samples. However, routine application of smFISH to formalin-fixed, paraffin-embedded (FFPE) samples is challenging due to the low signal intensity and high background noise. Here we present RollFISH, a method combining the specificity of smFISH with the signal boosting of rolling circle amplification. We apply RollFISH to quantify widely used breast cancer biomarkers in cell lines and FFPE samples. Thanks to the high signal-to-noise ratio, we can visualize selected biomarkers at low magnification (20 \u00d7 ) across entire tissue sections, and thus assess their spatial heterogeneity. Lastly, we apply RollFISH to quantify HER2 mRNA in 150 samples on a single tissue microarray, achieving a sensitivity and specificity of detection of HER2-positive samples of ~90%. RollFISH is a robust method for quantifying the expression and intratumor heterogeneity of biomarkers in FFPE tissues.", "doi": "10.1038/s42003-018-0218-0", "pmid": "30511022", "labels": {"Advanced FISH Technologies": "Technology development", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "218"}, {"db": "pmc", "key": "PMC6262000"}], "notes": [], "created": "2020-01-21T12:30:17.817Z", "modified": "2025-10-17T13:02:18.566Z"}, {"entity": "publication", "iuid": "c3dcf2e9bf1d4382866d6a7c7b6018f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3dcf2e9bf1d4382866d6a7c7b6018f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3dcf2e9bf1d4382866d6a7c7b6018f7"}}, "title": "The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization.", "authors": [{"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Li", "given": "Tongbin", "initials": "T"}, {"family": "Malycheva", "given": "Darina", "initials": "D"}, {"family": "Kancharla", "given": "Arun", "initials": "A"}, {"family": "Nilsson", "given": "Hel\u00e9n", "initials": "H"}, {"family": "Vishnu", "given": "Neelanjan", "initials": "N"}, {"family": "Mulder", "given": "Hindrik", "initials": "H"}, {"family": "Johansson", "given": "Martin", "initials": "M"}, {"family": "Rossell\u00f3", "given": "Catalina Ana", "initials": "CA"}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0598-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ee81797eff452fa037821f293d8673.json"}}], "type": "journal article", "published": "2018-05-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "1", "issue": "1", "pages": "37", "issn-l": "2399-3642"}, "abstract": "In the cell, \u03b3-tubulin establishes a cellular network of threads named the \u03b3-string meshwork. However, the functions of this meshwork remain to be determined. We investigated the traits of the meshwork and show that \u03b3-strings have the ability to connect the cytoplasm and the mitochondrial DNA together. We also show that \u03b3-tubulin has a role in the maintenance of the mitochondrial network and functions as reduced levels of \u03b3-tubulin or impairment of its GTPase domain disrupts the mitochondrial network and alters both their respiratory capacity and the expression of mitochondrial-related genes. By contrast, reduced mitochondrial number or increased protein levels of \u03b3-tubulin DNA-binding domain enhanced the association of \u03b3-tubulin with mitochondria. Our results demonstrate that \u03b3-tubulin is an important mitochondrial structural component that maintains the mitochondrial network, providing mitochondria with a cellular infrastructure. We propose that \u03b3-tubulin provides a cytoskeletal element that gives form to the mitochondrial network.", "doi": "10.1038/s42003-018-0037-3", "pmid": "30271923", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-018-0037-3"}, {"db": "pmc", "key": "PMC6123723"}], "notes": [], "created": "2020-01-23T16:26:11.434Z", "modified": "2021-11-03T15:41:13.583Z"}], "created": "2019-12-02T17:20:27.175Z", "modified": "2020-11-27T13:14:10.166Z"}