{"entity": "publications", "timestamp": "2026-10-17T02:37:09.956Z", "year": "2012", "links": {"self": {"href": "https://publications.scilifelab.se/publications/2012.json"}, "display": {"href": "https://publications.scilifelab.se/publications/2012"}}, "publications_count": 246, "full": true, "publications": [{"entity": "publication", "iuid": "57d11cb6d6af42fa9a9b497a2b9d67da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57d11cb6d6af42fa9a9b497a2b9d67da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57d11cb6d6af42fa9a9b497a2b9d67da"}}, "title": "Powerful identification of cis-regulatory SNPs in human primary monocytes using allele-specific gene expression.", "authors": [{"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Ge", "given": "Bing", "initials": "B"}, {"family": "Maouche", "given": "Seraya", "initials": "S"}, {"family": "G\u00f6ring", "given": "Harald H H", "initials": "HHH"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Enstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Brocheton", "given": "Jessy", "initials": "J"}, {"family": "Proust", "given": "Carole", "initials": "C"}, {"family": "Godefroy", "given": "Tiphaine", "initials": "T"}, {"family": "Sambrook", "given": "Jennifer G", "initials": "JG"}, {"family": "Jolley", "given": "Jennifer", "initials": "J"}, {"family": "Crisp-Hihn", "given": "Abigail", "initials": "A"}, {"family": "Foad", "given": "Nicola", "initials": "N"}, {"family": "Lloyd-Jones", "given": "Heather", "initials": "H"}, {"family": "Stephens", "given": "Jonathan", "initials": "J"}, {"family": "Gwilliam", "given": "Rhian", "initials": "R"}, {"family": "Rice", "given": "Catherine M", "initials": "CM"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Pastinen", "given": "Tomi", "initials": "T"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Cambien", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}], "type": "journal article", "published": "2012-12-26", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "7", "issue": "12", "pages": "e52260"}, "abstract": "A large number of genome-wide association studies have been performed during the past five years to identify associations between SNPs and human complex diseases and traits. The assignment of a functional role for the identified disease-associated SNP is not straight-forward. Genome-wide expression quantitative trait locus (eQTL) analysis is frequently used as the initial step to define a function while allele-specific gene expression (ASE) analysis has not yet gained a wide-spread use in disease mapping studies. We compared the power to identify cis-acting regulatory SNPs (cis-rSNPs) by genome-wide allele-specific gene expression (ASE) analysis with that of traditional expression quantitative trait locus (eQTL) mapping. Our study included 395 healthy blood donors for whom global gene expression profiles in circulating monocytes were determined by Illumina BeadArrays. ASE was assessed in a subset of these monocytes from 188 donors by quantitative genotyping of mRNA using a genome-wide panel of SNP markers. The performance of the two methods for detecting cis-rSNPs was evaluated by comparing associations between SNP genotypes and gene expression levels in sample sets of varying size. We found that up to 8-fold more samples are required for eQTL mapping to reach the same statistical power as that obtained by ASE analysis for the same rSNPs. The performance of ASE is insensitive to SNPs with low minor allele frequencies and detects a larger number of significantly associated rSNPs using the same sample size as eQTL mapping. An unequivocal conclusion from our comparison is that ASE analysis is more sensitive for detecting cis-rSNPs than standard eQTL mapping. Our study shows the potential of ASE mapping in tissue samples and primary cells which are difficult to obtain in large numbers.", "doi": "10.1371/journal.pone.0052260", "pmid": "23300628", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-12-18082"}, {"db": "pmc", "key": "PMC3530574"}], "notes": [], "created": "2017-05-04T15:01:09.875Z", "modified": "2022-03-31T15:21:33.369Z"}, {"entity": "publication", "iuid": "93db6ff10b0f4ed48c3a43f6b7d7a551", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93db6ff10b0f4ed48c3a43f6b7d7a551.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93db6ff10b0f4ed48c3a43f6b7d7a551"}}, "title": "Genomic diversity of the 2011 European outbreaks of Escherichia coli O104:H4.", "authors": [{"family": "Guy", "given": "Lionel", "initials": "L"}, {"family": "Jernberg", "given": "Cecilia", "initials": "C"}, {"family": "Ivarsson", "given": "Sofie", "initials": "S"}, {"family": "Hedenstr\u00f6m", "given": "Ingela", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Siv G E", "initials": "SG"}], "type": "comment", "published": "2012-12-26", "journal": {"volume": "109", "issn": "1091-6490", "issue": "52", "pages": "E3627-E3628", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1206246110", "pmid": "23248326", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1206246110"}, {"db": "pmc", "key": "PMC3535599"}], "notes": [], "created": "2017-05-04T15:01:07.399Z", "modified": "2020-01-21T13:56:03.795Z"}, {"entity": "publication", "iuid": "d94da77410ff4e17a03dcc005cecffe2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d94da77410ff4e17a03dcc005cecffe2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d94da77410ff4e17a03dcc005cecffe2"}}, "title": "Genome-wide sequencing for the identification of rearrangements associated with Tourette syndrome and obsessive-compulsive disorder.", "authors": [{"family": "Hooper", "given": "Sean D", "initials": "SD"}, {"family": "Johansson", "given": "Anna C V", "initials": "AC"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2012-12-19", "journal": {"volume": "13", "issn": "1471-2350", "issue": null, "pages": "123", "title": "BMC Med. Genet.", "issn-l": "1471-2350"}, "abstract": "Tourette Syndrome (TS) is a neuropsychiatric disorder in children characterized by motor and verbal tics. Although several genes have been suggested in the etiology of TS, the genetic mechanisms remain poorly understood.\n\nUsing cytogenetics and FISH analysis, we identified an apparently balanced t(6,22)(q16.2;p13) in a male patient with TS and obsessive-compulsive disorder (OCD). In order to map the breakpoints and to identify additional submicroscopic rearrangements, we performed whole genome mate-pair sequencing and CGH-array analysis on DNA from the proband.\n\nSequence and CGH array analysis revealed a 400 kb deletion located 1.3 Mb telomeric of the chromosome 6q breakpoint, which has not been reported in controls. The deletion affects three genes (GPR63, NDUFA4 and KLHL32) and overlaps a region previously found deleted in a girl with autistic features and speech delay. The proband's mother, also a carrier of the translocation, was diagnosed with OCD and shares the deletion. We also describe a further potentially related rearrangement which, while unmapped in Homo sapiens, was consistent with the chimpanzee genome.\n\nWe conclude that genome-wide sequencing at relatively low resolution can be used for the identification of submicroscopic rearrangements. We also show that large rearrangements may escape detection using standard analysis of whole genome sequencing data. Our findings further provide a candidate region for TS and OCD on chromosome 6q16.", "doi": "10.1186/1471-2350-13-123", "pmid": "23253088", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2350-13-123"}, {"db": "pmc", "key": "PMC3556158"}], "notes": [], "created": "2017-05-04T14:57:31.238Z", "modified": "2021-07-08T12:52:24.439Z"}, {"entity": "publication", "iuid": "9a410aa7c695419782102293becba144", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a410aa7c695419782102293becba144.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a410aa7c695419782102293becba144"}}, "title": "Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.", "authors": [{"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Endlich", "given": "Karlhans", "initials": "K"}, {"family": "Olden", "given": "Matthias", "initials": "M"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Taliun", "given": "Daniel", "initials": "D"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Gao", "given": "Xiaoyi", "initials": "X"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Hundertmark", "given": "Claudia", "initials": "C"}, {"family": "Foster", "given": "Meredith C", "initials": "MC"}, {"family": "O'Seaghdha", "given": "Conall M", "initials": "CM"}, {"family": "Glazer", "given": "Nicole", "initials": "N"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Struchalin", "given": "Maksim", "initials": "M"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Li", "given": "Guo", "initials": "G"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Gierman", "given": "Hinco J", "initials": "HJ"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Atkinson", "given": "Elizabeth J", "initials": "EJ"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "Cornelis", "given": "Marilyn C", "initials": "MC"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Lambert", "given": "Jean-Charles", "initials": "JC"}, {"family": "Holliday", "given": "Elizabeth G", "initials": "EG"}, {"family": "Sorice", "given": "Rossella", "initials": "R"}, {"family": "Kutalik", "given": "Zoltan", "initials": "Z"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Deshmukh", "given": "Harshal", "initials": "H"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Murgia", "given": "Federico", "initials": "F"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "Coassin", "given": "Stefan", "initials": "S"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "CARDIoGRAM Consortium", "given": null, "initials": null}, {"family": "ICBP Consortium", "given": null, "initials": null}, {"family": "CARe Consortium", "given": null, "initials": null}, {"family": "WTCCC2", "given": null, "initials": null}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Cavalieri", "given": "Margherita", "initials": "M"}, {"family": "Rao", "given": "Madhumathi", "initials": "M"}, {"family": "Hu", "given": "Frank", "initials": "F"}, {"family": "Demirkan", "given": "Ayse", "initials": "A"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "de Andrade", "given": "Mariza", "initials": "M"}, {"family": "Turner", "given": "Stephen T", "initials": "ST"}, {"family": "Ding", "given": "Jingzhong", "initials": "J"}, {"family": "Andrews", "given": "Jeanette S", "initials": "JS"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Boban", "given": "Mladen", "initials": "M"}, {"family": "Minelli", "given": "Cosetta", "initials": "C"}, {"family": "Wheeler", "given": "Heather E", "initials": "HE"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Zaboli", "given": "Ghazal", "initials": "G"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Ellinghaus", "given": "David", "initials": "D"}, {"family": "N\u00f6thlings", "given": "Ute", "initials": "U"}, {"family": "Jacobs", "given": "Gunnar", "initials": "G"}, {"family": "Biffar", "given": "Reiner", "initials": "R"}, {"family": "Ernst", "given": "Florian", "initials": "F"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Kroemer", "given": "Heyo K", "initials": "HK"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Stracke", "given": "Sylvia", "initials": "S"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Hastie", "given": "Nick", "initials": "N"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Helmer", "given": "Catherine", "initials": "C"}, {"family": "Wang", "given": "Jie Jin", "initials": "JJ"}, {"family": "Stengel", "given": "B\u00e9n\u00e9dicte", "initials": "B"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Nikopensius", "given": "Tiit", "initials": "T"}, {"family": "Province", "given": "Michael", "initials": "M"}, {"family": "Ketkar", "given": "Shamika", "initials": "S"}, {"family": "Colhoun", "given": "Helen", "initials": "H"}, {"family": "Doney", "given": "Alex", "initials": "A"}, {"family": "Robino", "given": "Antonietta", "initials": "A"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Portas", "given": "Laura", "initials": "L"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Buckley", "given": "Brendan M", "initials": "BM"}, {"family": "Adam", "given": "Martin", "initials": "M"}, {"family": "Thun", "given": "Gian-Andri", "initials": "GA"}, {"family": "Paulweber", "given": "Bernhard", "initials": "B"}, {"family": "Haun", "given": "Margot", "initials": "M"}, {"family": "Sala", "given": "Cinzia", "initials": "C"}, {"family": "Mitchell", "given": "Paul", "initials": "P"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Kim", "given": "Stuart K", "initials": "SK"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Palmer", "given": "Colin", "initials": "C"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Pirastu", "given": "Mario", "initials": "M"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Probst-Hensch", "given": "Nicole M", "initials": "NM"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SL"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Curhan", "given": "Gary C", "initials": "GC"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Witteman", "given": "Jacqueline", "initials": "J"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2012-12-15", "journal": {"volume": "21", "issn": "1460-2083", "issue": "24", "pages": "5329-5343", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 \u00d7 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 \u00d7 10(-4)-2.2 \u00d7 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.", "doi": "10.1093/hmg/dds369", "pmid": "22962313", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "dds369"}, {"db": "pmc", "key": "PMC3607468"}], "notes": [], "created": "2017-05-04T15:02:07.638Z", "modified": "2020-01-21T13:56:03.952Z"}, {"entity": "publication", "iuid": "c8aff4654dd5445e83afbfa1a27e9fa7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8aff4654dd5445e83afbfa1a27e9fa7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8aff4654dd5445e83afbfa1a27e9fa7"}}, "title": "Similar but different: thermodynamic and structural characterization of a pair of enantiomers binding to acetylcholinesterase.", "authors": [{"family": "Berg", "given": "Lotta", "initials": "L"}, {"family": "Niemiec", "given": "Moritz S", "initials": "MS"}, {"family": "Qian", "given": "Weixing", "initials": "W"}, {"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}, {"family": "Ekstr\u00f6m", "given": "Fredrik", "initials": "F"}, {"family": "Linusson", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2012-12-14", "journal": {"volume": "51", "issn": "1521-3773", "issue": "51", "pages": "12716-12720", "title": "Angew. Chem. Int. Ed. Engl.", "issn-l": "1433-7851"}, "abstract": null, "doi": "10.1002/anie.201205113", "pmid": "23161758", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:37.917Z", "modified": "2025-10-17T13:04:30.490Z"}, {"entity": "publication", "iuid": "8a675a9d47874b2ab739dc2952691221", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a675a9d47874b2ab739dc2952691221.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a675a9d47874b2ab739dc2952691221"}}, "title": "Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans.", "authors": [{"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "\u00c5sman", "given": "Anna K M", "initials": "AKM"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Jahan", "given": "Sultana N", "initials": "SN"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Savenkov", "given": "Eugene", "initials": "E"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}, {"family": "Avrova", "given": "Anna O", "initials": "AO"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2012-12-14", "journal": {"volume": "7", "issn": "1932-6203", "issue": "12", "pages": "e51399", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19-40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs.", "doi": "10.1371/journal.pone.0051399", "pmid": "23272103", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-20506"}, {"db": "pmc", "key": "PMC3522703"}], "notes": [], "created": "2017-05-04T14:57:44.513Z", "modified": "2020-01-21T13:56:10.401Z"}, {"entity": "publication", "iuid": "29bdc5e9b91b4b6bb38e0962a385a715", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29bdc5e9b91b4b6bb38e0962a385a715.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29bdc5e9b91b4b6bb38e0962a385a715"}}, "title": "Novel missense mutation in the RSPO4 gene in congenital hyponychia and evidence for a polymorphic initiation codon (p.M1I).", "authors": [{"family": "Khan", "given": "Tahir Naeem", "initials": "TN"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Nawaz", "given": "Sadia", "initials": "S"}, {"family": "Jameel", "given": "Muhammad", "initials": "M"}, {"family": "Tariq", "given": "Muhammad", "initials": "M"}, {"family": "Malik", "given": "Naveed Altaf", "initials": "NA"}, {"family": "Baig", "given": "Shahid M", "initials": "SM"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2012-12-13", "journal": {"volume": "13", "issn": "1471-2350", "issue": null, "pages": "120", "title": "BMC Med. Genet.", "issn-l": "1471-2350"}, "abstract": "Anonychia/hyponychia congenita is a rare autosomal recessive developmental disorder characterized by the absence (anonychia) or hypoplasia (hyponuchia) of finger- and/or toenails frequently caused by mutations in the R-spondin 4 (RSPO4) gene.\n\nThree hypo/anonychia consanguineous Pakistani families were ascertained and genotyped using microsatellite markers spanning the RSPO4 locus on chromosome 20p13. Mutation screening of the RSPO4 gene was carried out by direct sequencing of the entire coding region and all intron-exon boundaries.\n\nMutations in the RSPO4 gene were identified in all families including a novel missense mutation c.178C>T (p.R60W) and two recurrent variants c.353G>A (p.C118Y) and c.3G>A (p.M1I). The c.3G>A variant was identified in unaffected family members and a control sample in a homozygous state.\n\nThis study raises to 17 the number of known RSPO4 mutations and further expands the molecular repertoire causing hypo/anonychia. The c.353G>A emerges as a recurrent change with a possible founder effect in the Pakistani population. Our findings suggest that c.3G>A is not sufficient to cause the disorder and could be considered a polymorphism.", "doi": "10.1186/1471-2350-13-120", "pmid": "23234511", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2350-13-120"}, {"db": "pmc", "key": "PMC3532313"}], "notes": [], "created": "2017-05-04T14:57:31.545Z", "modified": "2020-01-21T13:56:01.193Z"}, {"entity": "publication", "iuid": "e164267f0e424c6aa7552763809abd16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e164267f0e424c6aa7552763809abd16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e164267f0e424c6aa7552763809abd16"}}, "title": "Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors.", "authors": [{"family": "Sur", "given": "Inderpreet Kaur", "initials": "IK"}, {"family": "Hallikas", "given": "Outi", "initials": "O"}, {"family": "V\u00e4h\u00e4rautio", "given": "Anna", "initials": "A"}, {"family": "Yan", "given": "Jian", "initials": "J"}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Karhu", "given": "Auli", "initials": "A"}, {"family": "Aaltonen", "given": "Lauri A", "initials": "LA"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2012-12-07", "journal": {"volume": "338", "issn": "1095-9203", "issue": "6112", "pages": "1360-1363", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Multiple cancer-associated single-nucleotide polymorphisms (SNPs) have been mapped to conserved sequences within a 500-kilobase region upstream of the MYC oncogene on human chromosome 8q24. These SNPs may affect cancer development through altered regulation of MYC expression, but this hypothesis has been difficult to confirm. We generated mice deficient in Myc-335, a putative MYC regulatory element that contains rs6983267, a SNP accounting for more human cancer-related morbidity than any other genetic variant or mutation. In Myc-335 null mice, Myc transcripts were expressed in the intestinal crypts in a pattern similar to that in wild-type mice but at modestly reduced levels. The mutant mice displayed no overt phenotype but were markedly resistant to intestinal tumorigenesis induced by the APCmin mutation. These results establish that a cancer-associated SNP identified in human genome-wide association studies has a functional effect in vivo.", "doi": "10.1126/science.1228606", "pmid": "23118011", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "science.1228606"}], "notes": [], "created": "2017-05-04T14:57:04.565Z", "modified": "2017-05-30T11:44:06.260Z"}, {"entity": "publication", "iuid": "dd5c497e6a6b44708401feadf5e89685", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd5c497e6a6b44708401feadf5e89685.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd5c497e6a6b44708401feadf5e89685"}}, "title": "EGFR gene variants are associated with specific somatic aberrations in glioma.", "authors": [{"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Ghasimi", "given": "Soma", "initials": "S"}, {"family": "Van Loo", "given": "Peter", "initials": "P"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Lau", "given": "Ching", "initials": "C"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Bergenheim", "given": "Tommy", "initials": "T"}, {"family": "Andersson", "given": "Ulrika", "initials": "U"}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P"}, {"family": "Melin", "given": "Beatrice", "initials": "B"}], "type": "journal article", "published": "2012-12-07", "journal": {"volume": "7", "issn": "1932-6203", "issue": "12", "pages": "e47929", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "A number of gene variants have been associated with an increased risk of developing glioma. We hypothesized that the reported risk variants may be associated with tumor genomic instability. To explore potential correlations between germline risk variants and somatic genetic events, we analyzed matched tumor and blood samples from 95 glioma patients by means of SNP genotyping. The generated genotype data was used to calculate genome-wide allele-specific copy number profiles of the tumor samples. We compared the copy number profiles across samples and found two EGFR gene variants (rs17172430 and rs11979158) that were associated with homozygous deletion at the CDKN2A/B locus. One of the EGFR variants (rs17172430) was also associated with loss of heterozygosity at the EGFR locus. Our findings were confirmed in a separate dataset consisting of matched blood and tumor samples from 300 glioblastoma patients, compiled from publically available TCGA data. These results imply there is a functional effect of germline EGFR variants on tumor progression.", "doi": "10.1371/journal.pone.0047929", "pmid": "23236348", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-19282"}, {"db": "pmc", "key": "PMC3517607"}], "notes": [], "created": "2017-05-04T15:01:11.518Z", "modified": "2020-01-21T13:56:05.661Z"}, {"entity": "publication", "iuid": "6cb6fb789ed643b2ab8c7387bb5a3546", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cb6fb789ed643b2ab8c7387bb5a3546.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cb6fb789ed643b2ab8c7387bb5a3546"}}, "title": "Symptomatic atherosclerosis is associated with an altered gut metagenome.", "authors": [{"family": "Karlsson", "given": "Fredrik H", "initials": "FH"}, {"family": "F\u00e5k", "given": "Frida", "initials": "F"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Fagerberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2012-12-06", "journal": {"volume": "3", "issn": "2041-1723", "issue": null, "pages": "1245", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Recent findings have implicated the gut microbiota as a contributor of metabolic diseases through the modulation of host metabolism and inflammation. Atherosclerosis is associated with lipid accumulation and inflammation in the arterial wall, and bacteria have been suggested as a causative agent of this disease. Here we use shotgun sequencing of the gut metagenome to demonstrate that the genus Collinsella was enriched in patients with symptomatic atherosclerosis, defined as stenotic atherosclerotic plaques in the carotid artery leading to cerebrovascular events, whereas Roseburia and Eubacterium were enriched in healthy controls. Further characterization of the functional capacity of the metagenomes revealed that patient gut metagenomes were enriched in genes encoding peptidoglycan synthesis and depleted in phytoene dehydrogenase; patients also had reduced serum levels of \u03b2-carotene. Our findings suggest that the gut metagenome is associated with the inflammatory status of the host and patients with symptomatic atherosclerosis harbor characteristic changes in the gut metagenome.", "doi": "10.1038/ncomms2266", "pmid": "23212374", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ncomms2266"}, {"db": "pmc", "key": "PMC3538954"}], "notes": [], "created": "2017-05-04T14:57:38.926Z", "modified": "2021-07-05T13:05:37.669Z"}, {"entity": "publication", "iuid": "c45be243a5b749b29dd4adaff06f736e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c45be243a5b749b29dd4adaff06f736e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c45be243a5b749b29dd4adaff06f736e"}}, "title": "Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation.", "authors": [{"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Tregouet", "given": "David", "initials": "D"}, {"family": "Shin", "given": "So-Youn", "initials": "SY"}, {"family": "Ding", "given": "Jingzhong", "initials": "J"}, {"family": "Baumert", "given": "Jens", "initials": "J"}, {"family": "Oudot-Mellakh", "given": "Tiphaine", "initials": "T"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Williams", "given": "Scott M", "initials": "SM"}, {"family": "Ikram", "given": "Mohammad A", "initials": "MA"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Truong", "given": "Vinh", "initials": "V"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Moore", "given": "Jason H", "initials": "JH"}, {"family": "Williams", "given": "Frances M K", "initials": "FM"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Silbernagel", "given": "G\u00fcnther", "initials": "G"}, {"family": "Schrijvers", "given": "Elisabeth M C", "initials": "EM"}, {"family": "Smith", "given": "Shelly", "initials": "S"}, {"family": "Karakas", "given": "Mahir", "initials": "M"}, {"family": "Tofler", "given": "Geoffrey H", "initials": "GH"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Navis", "given": "Gerjan J", "initials": "GJ"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO"}, {"family": "Carter", "given": "Angela M", "initials": "AM"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "\u00d6hrvik", "given": "John", "initials": "J"}, {"family": "Taylor", "given": "Kent", "initials": "K"}, {"family": "Franzosi", "given": "Maria Grazia", "initials": "MG"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Collins", "given": "Rory", "initials": "R"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Cushman", "given": "Mary", "initials": "M"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Folsom", "given": "Aaron R", "initials": "AR"}, {"family": "Basu", "given": "Saonli", "initials": "S"}, {"family": "Matijevic", "given": "Nena", "initials": "N"}, {"family": "van Gilst", "given": "Wiek H", "initials": "WH"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "DIAGRAM Consortium", "given": null, "initials": null}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "CARDIoGRAM Consortium", "given": null, "initials": null}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Winkelmann", "given": "Bernhard R", "initials": "BR"}, {"family": "Grant", "given": "Peter J", "initials": "PJ"}, {"family": "Hillege", "given": "Hans L", "initials": "HL"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "C4D Consortium", "given": null, "initials": null}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Becker", "given": "Lewis C", "initials": "LC"}, {"family": "Tracy", "given": "Russell P", "initials": "RP"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Cambien", "given": "Francois", "initials": "F"}, {"family": "CARDIOGENICS Consortium", "given": null, "initials": null}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2012-12-06", "journal": {"volume": "120", "issn": "1528-0020", "issue": "24", "pages": "4873-4881", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "We conducted a genome-wide association study to identify novel associations between genetic variants and circulating plasminogen activator inhibitor-1 (PAI-1) concentration, and examined functional implications of variants and genes that were discovered. A discovery meta-analysis was performed in 19 599 subjects, followed by replication analysis of genome-wide significant (P < 5 \u00d7 10(-8)) single nucleotide polymorphisms (SNPs) in 10 796 independent samples. We further examined associations with type 2 diabetes and coronary artery disease, assessed the functional significance of the SNPs for gene expression in human tissues, and conducted RNA-silencing experiments for one novel association. We confirmed the association of the 4G/5G proxy SNP rs2227631 in the promoter region of SERPINE1 (7q22.1) and discovered genome-wide significant associations at 3 additional loci: chromosome 7q22.1 close to SERPINE1 (rs6976053, discovery P = 3.4 \u00d7 10(-10)); chromosome 11p15.2 within ARNTL (rs6486122, discovery P = 3.0 \u00d7 10(-8)); and chromosome 3p25.2 within PPARG (rs11128603, discovery P = 2.9 \u00d7 10(-8)). Replication was achieved for the 7q22.1 and 11p15.2 loci. There was nominal association with type 2 diabetes and coronary artery disease at ARNTL (P < .05). Functional studies identified MUC3 as a candidate gene for the second association signal on 7q22.1. In summary, SNPs in SERPINE1 and ARNTL and an SNP associated with the expression of MUC3 were robustly associated with circulating levels of PAI-1.", "doi": "10.1182/blood-2012-06-436188", "pmid": "22990020", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "blood-2012-06-436188"}, {"db": "pmc", "key": "PMC3520624"}], "notes": [], "created": "2017-05-04T15:00:55.006Z", "modified": "2021-07-07T15:11:02.727Z"}, {"entity": "publication", "iuid": "3b666b3bfdb241df95e0525cc542eeb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b666b3bfdb241df95e0525cc542eeb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b666b3bfdb241df95e0525cc542eeb8"}}, "title": "Interferometry and Fluorescence Detection for Simultaneous Analysis of Labeled and Unlabeled Nanoparticles in Solution", "authors": [{"family": "Wennmalm", "given": "Stefan", "initials": "S"}, {"family": "Widengren", "given": "Jerker", "initials": "J"}], "type": "journal-article", "published": "2012-12-05", "journal": {"volume": "134", "issn": "1520-5126", "issue": "48", "pages": "19516-19519", "title": "J. Am. Chem. Soc.", "issn-l": "0002-7863"}, "abstract": null, "doi": "10.1021/ja308213q", "pmid": "23157513", "labels": {"Fluorescence Correlation Spectroscopy": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-01T07:07:33.210Z", "modified": "2017-11-02T15:58:20.937Z"}, {"entity": "publication", "iuid": "b5717e1da4704310b8977f7958d2bf33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5717e1da4704310b8977f7958d2bf33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5717e1da4704310b8977f7958d2bf33"}}, "title": "Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles.", "authors": [{"family": "Kanduri", "given": "Meena", "initials": "M"}, {"family": "Marincevic", "given": "Millaray", "initials": "M"}, {"family": "Halld\u00f3rsd\u00f3ttir", "given": "Anna M", "initials": "AM"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Junevik", "given": "Katarina", "initials": "K"}, {"family": "Ntoufa", "given": "Stavroula", "initials": "S"}, {"family": "Kultima", "given": "Hanna G\u00f6ransson", "initials": "HG"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Andersson", "given": "Per-Ola", "initials": "PO"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "journal article", "published": "2012-12-01", "journal": {"volume": "7", "issn": "1559-2308", "issue": "12", "pages": "1435-1442", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "Chronic lymphocytic leukemia (CLL) can be divided into prognostic subgroups based on the IGHV gene mutational status, and is further characterized by multiple subsets of cases with quasi-identical or stereotyped B cell receptors that also share clinical and biological features. We recently reported differential DNA methylation profiles in IGHV-mutated and IGHV-unmutated CLL subgroups. For the first time, we here explore the global methylation profiles of stereotyped subsets with different prognosis, by applying high-resolution methylation arrays on CLL samples from three major stereotyped subsets: the poor-prognostic subsets #1 (n = 15) and #2 (n = 9) and the favorable-prognostic subset #4 (n = 15). Overall, the three subsets exhibited significantly different methylation profiles, which only partially overlapped with those observed in our previous study according to IGHV gene mutational status. Specifically, gene ontology analysis of the differentially methylated genes revealed a clear enrichment of genes involved in immune response, such as B cell activation (e.g., CD80, CD86 and IL10), with higher methylation levels in subset #1 than subsets #2 and #4. Accordingly, higher expression of the co-stimulatory molecules CD80 and CD86 was demonstrated in subset #4 vs. subset #1, pointing to a key role for these molecules in the crosstalk of CLL subset #4 cells with the microenvironment. In summary, investigation of three prototypic, stereotyped CLL subsets revealed distinct DNA methylation profiles for each subset, which suggests subset-biased patterns of transcriptional control and highlights a key role for epigenetics during leukemogenesis.", "doi": "10.4161/epi.22901", "pmid": "23154584", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "22901"}, {"db": "pmc", "key": "PMC3528698"}], "notes": [], "created": "2017-05-04T15:02:56.986Z", "modified": "2017-05-30T12:37:03.981Z"}, {"entity": "publication", "iuid": "c7540c45a2c74038a1abe84eb4313c07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7540c45a2c74038a1abe84eb4313c07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7540c45a2c74038a1abe84eb4313c07"}}, "title": "Transcription factor PROX1: its role in development and cancer.", "authors": [{"family": "Elsir", "given": "Tamador", "initials": "T"}, {"family": "Smits", "given": "Anja", "initials": "A"}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "31", "issn": "1573-7233", "issue": "3-4", "pages": "793-805", "title": "Cancer Metastasis Rev.", "issn-l": "0167-7659"}, "abstract": "The homeobox gene PROX1 is critical for organ development during embryogenesis. The Drosophila homologue, known as prospero has been shown to act as a tumor suppressor by controlling asymmetric cell division of neuroblasts. Likewise, alterations in PROX1 expression and function are associated with a number of human cancers including hematological malignancies, carcinomas of the pancreas, liver and the biliary system, sporadic breast cancer, Kaposiform hemangioendothelioma, colon cancer, and brain tumors. PROX1 is involved in cancer development and progression and has been ascribed both tumor suppressive and oncogenic properties in a variety of different cancer types. However, the exact mechanisms through which PROX1 regulates proliferation, migration, and invasion of cancer cells are by large unknown. This review provides an update on the role of PROX1 in organ development and on its emerging functions in cancer, with special emphasis on the central nervous system and glial brain tumors.", "doi": "10.1007/s10555-012-9390-8", "pmid": "22733308", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:50.261Z", "modified": "2017-05-30T12:57:07.601Z"}, {"entity": "publication", "iuid": "652ff9600fbe4877a6f560a8046f1d99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/652ff9600fbe4877a6f560a8046f1d99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/652ff9600fbe4877a6f560a8046f1d99"}}, "title": "The impact of intronic single nucleotide polymorphisms and ethnic diversity for studies on the obesity gene FTO.", "authors": [{"family": "Jacobsson", "given": "J A", "initials": "JA"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}, {"family": "Fredriksson", "given": "R", "initials": "R"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "13", "issn": "1467-789X", "issue": "12", "pages": "1096-1109", "title": "Obes Rev", "issn-l": "1467-7881"}, "abstract": "In 2007, the first common genetic variants were identified, which undoubtedly affect our susceptibility to obesity. These variants are located in the fat mass and obesity-associated gene FTO. Since then, over 50 loci for common obesity have been identified. As the research on these loci is still at an early stage, there is a great need to review, for clarification purposes, the current research on FTO, as this is likely to influence future studies. Based on the current knowledge, FTO seems to be directly involved in the regulation of energy intake, but there is an urgent need for the identification of regulatory polymorphisms. Thus, herein, we discuss current knowledge and highlight putative functional regions in FTO based on published data and computer-based analysis.", "doi": "10.1111/j.1467-789X.2012.01025.x", "pmid": "22931202", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:06.861Z", "modified": "2020-01-21T13:56:02.748Z"}, {"entity": "publication", "iuid": "ab26b76332524ad58ead61e2ac947af4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab26b76332524ad58ead61e2ac947af4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab26b76332524ad58ead61e2ac947af4"}}, "title": "PCR-based multiparametric assays in single cells.", "authors": [{"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Gallant", "given": "Caroline", "initials": "C"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "comment", "published": "2012-12-00", "journal": {"volume": "58", "issn": "1530-8561", "issue": "12", "pages": "1618-1619", "title": "Clin. Chem.", "issn-l": "0009-9147"}, "abstract": null, "doi": "10.1373/clinchem.2012.195867", "pmid": "23071363", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "clinchem.2012.195867"}], "notes": [], "created": "2017-05-04T14:55:22.863Z", "modified": "2023-04-14T13:56:29.877Z"}, {"entity": "publication", "iuid": "62c4803c14d84c888b82c4e4204c5014", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62c4803c14d84c888b82c4e4204c5014.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62c4803c14d84c888b82c4e4204c5014"}}, "title": "Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age at onset of schizophrenia: no consistent evidence for an association in the Nordic population.", "authors": [{"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Grove", "given": "Jakob", "initials": "J"}, {"family": "B\u00f8rglum", "given": "Anders D", "initials": "AD"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Vares", "given": "Maria", "initials": "M"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "159B", "issn": "1552-485X", "issue": "8", "pages": "981-986", "title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn-l": "1552-4841"}, "abstract": "Methylenetetrahydrofolate reductase (MTHFR) is an enzyme involved in metabolic pathways of importance for nucleotide synthesis and methylation of DNA, membranes, proteins and lipids. The MTHFR gene includes a common polymorphism (rs1801133 or C677T), which is associated with enzyme activity. The T-allele of the C677T polymorphism has been associated with earlier age at onset of schizophrenia in a Scandinavian population, although no association was found in replication attempts in other populations. Extending the study to five Nordic samples consisting of 2,198 patients with schizophrenia, including the original Scandinavian samples, there was no significant association between MTHFR C677T polymorphism and age at onset in schizophrenia. The present results do not suggest that the investigated MTHFR polymorphism has any significant influence on age at onset of schizophrenia in the Nordic population.", "doi": "10.1002/ajmg.b.32104", "pmid": "23076983", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3739001"}], "notes": [], "created": "2017-05-04T15:00:52.874Z", "modified": "2020-01-21T13:56:02.657Z"}, {"entity": "publication", "iuid": "d50ec332292c46de9fbbc0817311ab32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d50ec332292c46de9fbbc0817311ab32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d50ec332292c46de9fbbc0817311ab32"}}, "title": "Integration of genetics into a systems model of electrocardiographic traits using HumanCVD BeadChip.", "authors": [{"family": "Gaunt", "given": "Tom R", "initials": "TR"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Drenos", "given": "Fotios", "initials": "F"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Adeniran", "given": "Ismail", "initials": "I"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Lawlor", "given": "Debbie A", "initials": "DA"}, {"family": "Casas", "given": "Juan-Pablo", "initials": "JP"}, {"family": "Amuzu", "given": "Antoinette", "initials": "A"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Whittaker", "given": "John", "initials": "J"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Zhang", "given": "Henggui", "initials": "H"}, {"family": "Hancox", "given": "Jules C", "initials": "JC"}, {"family": "Tomaszewski", "given": "Maciej", "initials": "M"}, {"family": "Burton", "given": "Paul R", "initials": "PR"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Macfarlane", "given": "Peter W", "initials": "PW"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Day", "given": "Ian N M", "initials": "IN"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "5", "issn": "1942-3268", "issue": "6", "pages": "630-638", "title": "Circ Cardiovasc Genet", "issn-l": null}, "abstract": "Electrocardiographic traits are important, substantially heritable determinants of risk of arrhythmias and sudden cardiac death.\n\nIn this study, 3 population-based cohorts (n=10,526) genotyped with the Illumina HumanCVD Beadchip and 4 quantitative electrocardiographic traits (PR interval, QRS axis, QRS duration, and QTc interval) were evaluated for single-nucleotide polymorphism associations. Six gene regions contained single nucleotide polymorphisms associated with these traits at P<10(-6), including SCN5A (PR interval and QRS duration), CAV1-CAV2 locus (PR interval), CDKN1A (QRS duration), NOS1AP, KCNH2, and KCNQ1 (QTc interval). Expression quantitative trait loci analyses of top associated single-nucleotide polymorphisms were undertaken in human heart and aortic tissues. NOS1AP, SCN5A, IGFBP3, CYP2C9, and CAV1 showed evidence of differential allelic expression. We modeled the effects of ion channel activity on electrocardiographic parameters, estimating the change in gene expression that would account for our observed associations, thus relating epidemiological observations and expression quantitative trait loci data to a systems model of the ECG.\n\nThese association results replicate and refine the mapping of previous genome-wide association study findings for electrocardiographic traits, while the expression analysis and modeling approaches offer supporting evidence for a functional role of some of these loci in cardiac excitation/conduction.", "doi": "10.1161/CIRCGENETICS.112.962852", "pmid": "23139254", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "CIRCGENETICS.112.962852"}], "notes": [], "created": "2017-05-04T15:00:55.940Z", "modified": "2020-01-21T13:56:05.450Z"}, {"entity": "publication", "iuid": "e490d3539f1c41958d66025d3d2768d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e490d3539f1c41958d66025d3d2768d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e490d3539f1c41958d66025d3d2768d9"}}, "title": "Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis.", "authors": [{"family": "Nikulenkov", "given": "F", "initials": "F"}, {"family": "Spinnler", "given": "C", "initials": "C"}, {"family": "Li", "given": "H", "initials": "H"}, {"family": "Tonelli", "given": "C", "initials": "C"}, {"family": "Shi", "given": "Y", "initials": "Y"}, {"family": "Turunen", "given": "M", "initials": "M"}, {"family": "Kivioja", "given": "T", "initials": "T"}, {"family": "Ignatiev", "given": "I", "initials": "I"}, {"family": "Kel", "given": "A", "initials": "A"}, {"family": "Taipale", "given": "J", "initials": "J"}, {"family": "Selivanova", "given": "G", "initials": "G"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "19", "issn": "1476-5403", "issue": "12", "pages": "1992-2002", "title": "Cell Death Differ.", "issn-l": "1350-9047"}, "abstract": "The tumor-suppressor p53 can induce various biological responses. Yet, it is not clear whether it is p53 in vivo promoter selectivity that triggers different transcription programs leading to different outcomes. Our analysis of genome-wide chromatin occupancy by p53 using chromatin immunoprecipitation (ChIP)-seq revealed 'p53 default program', that is, the pattern of major p53-bound sites that is similar upon p53 activation by nutlin3a, reactivation of p53 and induction of tumor cell apoptosis (RITA) or 5-fluorouracil in breast cancer cells, despite different biological outcomes. Parallel analysis of gene expression allowed identification of 280 novel p53 target genes, including p53-repressed AURKA. We identified Sp1 as one of the p53 modulators, which confer specificity to p53-mediated transcriptional response upon RITA. Further, we found that STAT3 antagonizes p53-mediated repression of a subset of genes, including AURKA.", "doi": "10.1038/cdd.2012.89", "pmid": "22790872", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "cdd201289"}, {"db": "pmc", "key": "PMC3504713"}], "notes": [], "created": "2017-05-04T14:57:04.267Z", "modified": "2017-05-30T11:44:02.670Z"}, {"entity": "publication", "iuid": "93e7dc3a2f024c8c938c7baf261838a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93e7dc3a2f024c8c938c7baf261838a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93e7dc3a2f024c8c938c7baf261838a2"}}, "title": "Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk.", "authors": [{"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Ohrvik", "given": "John", "initials": "J"}, {"family": "Zabaneh", "given": "Delilah", "initials": "D"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Fava", "given": "Cristiano", "initials": "C"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "McLachlan", "given": "Stela", "initials": "S"}, {"family": "Kivim\u00e4ki", "given": "Mika", "initials": "M"}, {"family": "Bolton", "given": "Jennifer L", "initials": "JL"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Vikstr\u00f6m", "given": "Max", "initials": "M"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Deanfield", "given": "John", "initials": "J"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Colombo", "given": "Gualtiero I", "initials": "GI"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Wareham", "given": "Nick J", "initials": "NJ"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Gabrielsen", "given": "Anders", "initials": "A"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Nyyss\u00f6nen", "given": "Kristiina", "initials": "K"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Tuomainen", "given": "Tomi-Pekka", "initials": "TP"}, {"family": "Savonen", "given": "Kai", "initials": "K"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Robertson", "given": "Christine M", "initials": "CM"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Hedblad", "given": "Bo", "initials": "B"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Franzosi", "given": "Maria Grazia", "initials": "MG"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Hansson", "given": "G\u00f6ran K", "initials": "GK"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Price", "given": "Jacqueline F", "initials": "JF"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "5", "issn": "1942-3268", "issue": "6", "pages": "656-665", "title": "Circ Cardiovasc Genet", "issn-l": null}, "abstract": "Carotid intima-media thickness (cIMT) is a widely accepted marker of subclinical atherosclerosis. To date, large-scale investigations of genetic determinants of cIMT are sparse.\n\nTo identify cIMT-associated genes and genetic variants, a discovery analysis using the Illumina 200K CardioMetabochip was conducted in 3430 subjects with detailed ultrasonographic determinations of cIMT from the IMPROVE (Carotid Intima Media Thickness [IMT] and IMT-Progression as Predictors of Vascular Events in a High Risk European Population) study. Segment-specific IMT measurements of common carotid, bifurcation, and internal carotid arteries, and composite IMT variables considering the whole carotid tree (IMT(mean), IMT(max), and IMT(mean-max)), were analyzed. A replication stage investigating 42 single-nucleotide polymorphisms for association with common carotid IMT was undertaken in 5 independent European cohorts (total n=11,590). A locus on chromosome 16 (lead single-nucleotide polymorphism rs4888378, intronic in CFDP1) was associated with cIMT at significance levels passing multiple testing correction at both stages (array-wide significant discovery P=6.75 \u00d7 10(-7) for IMT(max); replication P=7.24\u00d710(-6) for common cIMT; adjustments for sex, age, and population substructure where applicable; minor allele frequency 0.43 and 0.41, respectively). The protective minor allele was associated with lower carotid plaque score in a replication cohort (P=0.04, n=2120) and lower coronary artery disease risk in 2 case-control studies of subjects with European ancestry (odds ratio [95% confidence interval] 0.83 [0.77-0.90], P=6.53 \u00d7 10(-6), n=13 591; and 0.95 [0.92-0.98], P=1.83 \u00d7 10(-4), n=82 297, respectively). Queries of human biobank data sets revealed associations of rs4888378 with nearby gene expression in vascular tissues (n=126-138).\n\nThis study identified rs4888378 in the BCAR1-CFDP1-TMEM170A locus as a novel genetic determinant of cIMT and coronary artery disease risk in individuals of European descent.", "doi": "10.1161/CIRCGENETICS.112.963660", "pmid": "23152477", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "CIRCGENETICS.112.963660"}], "notes": [], "created": "2017-05-04T15:00:56.255Z", "modified": "2021-07-07T15:11:02.596Z"}, {"entity": "publication", "iuid": "504f7661fda94a749fe7d389d0bb14fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/504f7661fda94a749fe7d389d0bb14fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/504f7661fda94a749fe7d389d0bb14fe"}}, "title": "High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays.", "authors": [{"family": "Buus", "given": "S\u00f8ren", "initials": "S"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schafer-Nielsen", "given": "Claus", "initials": "C"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "12", "pages": "1790-1800", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Antibodies empower numerous important scientific, clinical, diagnostic, and industrial applications. Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning against unwanted (e.g. autoimmune) reactivities. Antibodies target proteins as either conformational or linear epitopes. The latter are typically probed with peptides, but the cost of peptide screening programs tends to prohibit comprehensive specificity analysis. To perform high-throughput, high-resolution mapping of linear antibody epitopes, we have used ultrahigh-density peptide microarrays generating several hundred thousand different peptides per array. Using exhaustive length and substitution analysis, we have successfully examined the specificity of a panel of polyclonal antibodies raised against linear epitopes of the human proteome and obtained very detailed descriptions of the involved specificities. The epitopes identified ranged from 4 to 12 amino acids in size. In general, the antibodies were of exquisite specificity, frequently disallowing even single conservative substitutions. In several cases, multiple distinct epitopes could be identified for the same target protein, suggesting an efficient approach to the generation of paired antibodies. Two alternative epitope mapping approaches identified similar, although not necessarily identical, epitopes. These results show that ultrahigh-density peptide microarrays can be used for linear epitope mapping. With an upper theoretical limit of 2,000,000 individual peptides per array, these peptide microarrays may even be used for a systematic validation of antibodies at the proteomic level.", "doi": "10.1074/mcp.M112.020800", "pmid": "22984286", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "M112.020800"}, {"db": "pmc", "key": "PMC3518105"}], "notes": [], "created": "2017-05-04T14:55:36.590Z", "modified": "2021-07-08T13:44:33.228Z"}, {"entity": "publication", "iuid": "97cdf4e227d2408a9997d3b5e6f4cebf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97cdf4e227d2408a9997d3b5e6f4cebf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97cdf4e227d2408a9997d3b5e6f4cebf"}}, "title": "High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.", "authors": [{"family": "Eyre", "given": "Steve", "initials": "S"}, {"family": "Bowes", "given": "John", "initials": "J"}, {"family": "Diogo", "given": "Doroth\u00e9e", "initials": "D"}, {"family": "Lee", "given": "Annette", "initials": "A"}, {"family": "Barton", "given": "Anne", "initials": "A"}, {"family": "Martin", "given": "Paul", "initials": "P"}, {"family": "Zhernakova", "given": "Alexandra", "initials": "A"}, {"family": "Stahl", "given": "Eli", "initials": "E"}, {"family": "Viatte", "given": "Sebastien", "initials": "S"}, {"family": "McAllister", "given": "Kate", "initials": "K"}, {"family": "Amos", "given": "Christopher I", "initials": "CI"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Toes", "given": "Rene E M", "initials": "RE"}, {"family": "Huizinga", "given": "Tom W J", "initials": "TW"}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "Trynka", "given": "Gosia", "initials": "G"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Westra", "given": "Harm-Jan", "initials": "HJ"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Hu", "given": "Xinli", "initials": "X"}, {"family": "Sandor", "given": "Cynthia", "initials": "C"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PI"}, {"family": "Davila", "given": "Sonia", "initials": "S"}, {"family": "Khor", "given": "Chiea Chuen", "initials": "CC"}, {"family": "Heng", "given": "Khai Koon", "initials": "KK"}, {"family": "Andrews", "given": "Robert", "initials": "R"}, {"family": "Edkins", "given": "Sarah", "initials": "S"}, {"family": "Hunt", "given": "Sarah E", "initials": "SE"}, {"family": "Langford", "given": "Cordelia", "initials": "C"}, {"family": "Symmons", "given": "Deborah", "initials": "D"}, {"family": "Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate", "given": null, "initials": null}, {"family": "Wellcome Trust Case Control Consortium", "given": null, "initials": null}, {"family": "Concannon", "given": "Pat", "initials": "P"}, {"family": "Onengut-Gumuscu", "given": "Suna", "initials": "S"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Gonzalez-Gay", "given": "Miguel A", "initials": "MA"}, {"family": "Rodriguez-Rodriguez", "given": "Luis", "initials": "L"}, {"family": "\u00c4rlsetig", "given": "Lisbeth", "initials": "L"}, {"family": "Martin", "given": "Javier", "initials": "J"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Plenge", "given": "Robert M", "initials": "RM"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Gregersen", "given": "Peter K", "initials": "PK"}, {"family": "Worthington", "given": "Jane", "initials": "J"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "44", "issn": "1546-1718", "issue": "12", "pages": "1336-1340", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data in a meta-analysis with GWAS data from additional independent cases (n = 2,363) and controls (n = 17,872). We identified 14 new susceptibility loci, 9 of which were associated with rheumatoid arthritis overall and five of which were specifically associated with disease that was positive for anticitrullinated peptide antibodies, bringing the number of confirmed rheumatoid arthritis risk loci in individuals of European ancestry to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at 6 loci and identified association to low-frequency variants at 4 loci. Bioinformatic analyses generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations.", "doi": "10.1038/ng.2462", "pmid": "23143596", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2462"}, {"db": "pmc", "key": "PMC3605761"}, {"db": "mid", "key": "EMS50373"}], "notes": [], "created": "2017-05-04T15:01:04.377Z", "modified": "2020-01-21T13:56:03.912Z"}, {"entity": "publication", "iuid": "441062b272f84356bccf64bd2640e953", "links": {"self": {"href": "https://publications.scilifelab.se/publication/441062b272f84356bccf64bd2640e953.json"}, "display": {"href": "https://publications.scilifelab.se/publication/441062b272f84356bccf64bd2640e953"}}, "title": "Genome sequence of Francisella tularensis subspecies holarctica strain FSC200, isolated from a child with tularemia.", "authors": [{"family": "Svensson", "given": "Kerstin", "initials": "K"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A"}, {"family": "Bystr\u00f6m", "given": "Mona", "initials": "M"}, {"family": "Granberg", "given": "Malin", "initials": "M"}, {"family": "Brittnacher", "given": "Mitchell J", "initials": "MJ"}, {"family": "Rohmer", "given": "Laurence", "initials": "L"}, {"family": "Jacobs", "given": "Michael A", "initials": "MA"}, {"family": "Sims-Day", "given": "Elizabeth H", "initials": "EH"}, {"family": "Levy", "given": "Ruth", "initials": "R"}, {"family": "Zhou", "given": "Yang", "initials": "Y"}, {"family": "Hayden", "given": "Hillary S", "initials": "HS"}, {"family": "Lim", "given": "Regina", "initials": "R"}, {"family": "Chang", "given": "Jean", "initials": "J"}, {"family": "Guenthener", "given": "Donald", "initials": "D"}, {"family": "Kang", "given": "Allison", "initials": "A"}, {"family": "Haugen", "given": "Eric", "initials": "E"}, {"family": "Gillett", "given": "Will", "initials": "W"}, {"family": "Kaul", "given": "Rajinder", "initials": "R"}, {"family": "Forsman", "given": "Mats", "initials": "M"}, {"family": "Larsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-9054-5191", "researcher": {"href": "https://publications.scilifelab.se/researcher/573c6350305a49cba2ac0798dea21ae0.json"}}, {"family": "Johansson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "194", "issn": "1098-5530", "issue": "24", "pages": "6965-6966", "title": "J. Bacteriol.", "issn-l": "0021-9193"}, "abstract": "Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of Francisella and is well-characterized.", "doi": "10.1128/JB.01040-12", "pmid": "23209222", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "194/24/6965"}, {"db": "pmc", "key": "PMC3510583"}, {"db": "GENBANK", "key": "CP003862"}], "notes": [], "created": "2017-05-04T15:01:00.607Z", "modified": "2021-07-08T12:43:38.650Z"}, {"entity": "publication", "iuid": "b56c38a501824beda4557d1adbf34863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b56c38a501824beda4557d1adbf34863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b56c38a501824beda4557d1adbf34863"}}, "title": "Evolution from the prokaryotic to the higher plant chloroplast signal recognition particle: the signal recognition particle RNA is conserved in plastids of a wide range of photosynthetic organisms.", "authors": [{"family": "Tr\u00e4ger", "given": "Chantal", "initials": "C"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Ziehe", "given": "Dominik", "initials": "D"}, {"family": "Garcia-Petit", "given": "Christel", "initials": "C"}, {"family": "Schrader", "given": "Lukas", "initials": "L"}, {"family": "Kock", "given": "Klaus", "initials": "K"}, {"family": "Richter", "given": "Christine Vera", "initials": "CV"}, {"family": "Klinkert", "given": "Birgit", "initials": "B"}, {"family": "Narberhaus", "given": "Franz", "initials": "F"}, {"family": "Herrmann", "given": "Christian", "initials": "C"}, {"family": "Hofmann", "given": "Eckhard", "initials": "E"}, {"family": "Aronsson", "given": "Henrik", "initials": "H"}, {"family": "Sch\u00fcnemann", "given": "Danja", "initials": "D"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "24", "issn": "1532-298X", "issue": "12", "pages": "4819-4836", "title": "Plant Cell", "issn-l": "1040-4651"}, "abstract": "The protein targeting signal recognition particle (SRP) pathway in chloroplasts of higher plants has undergone dramatic evolutionary changes. It disposed of its RNA, which is an essential SRP component in bacteria, and uses a unique chloroplast-specific protein cpSRP43. Nevertheless, homologs of the conserved SRP54 and the SRP receptor, FtsY, are present in higher plant chloroplasts. In this study, we analyzed the phylogenetic distribution of SRP components in photosynthetic organisms to elucidate the evolution of the SRP system. We identified conserved plastid SRP RNAs within all nonspermatophyte land plant lineages and in all chlorophyte branches. Furthermore, we show the simultaneous presence of cpSRP43 in these organisms. The function of this novel SRP system was biochemically and structurally characterized in the moss Physcomitrella patens. We show that P. patens chloroplast SRP (cpSRP) RNA binds cpSRP54 but has lost the ability to significantly stimulate the GTPase cycle of SRP54 and FtsY. Furthermore, the crystal structure at 1.8-\u00c5 resolution and the nucleotide specificity of P. patens cpFtsY was determined and compared with bacterial FtsY and higher plant chloroplast FtsY. Our data lead to the view that the P. patens cpSRP system occupies an intermediate position in the evolution from bacterial-type SRP to higher plant-type cpSRP system.", "doi": "10.1105/tpc.112.102996", "pmid": "23275580", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "tpc.112.102996"}, {"db": "pmc", "key": "PMC3556960"}], "notes": [], "created": "2017-05-04T14:56:19.415Z", "modified": "2020-01-21T13:53:20.795Z"}, {"entity": "publication", "iuid": "c42b4df6aa6a4db9a6b82b4a3a73fd10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c42b4df6aa6a4db9a6b82b4a3a73fd10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c42b4df6aa6a4db9a6b82b4a3a73fd10"}}, "title": "Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties.", "authors": [{"family": "Olsson", "given": "Niclas", "initials": "N"}, {"family": "Wallin", "given": "Stefan", "initials": "S"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CA"}, {"family": "Wingren", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "21", "issn": "1469-896X", "issue": "12", "pages": "1897-1910", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "Protein-peptide interactions are a common occurrence and essential for numerous cellular processes, and frequently explored in broad applications within biology, medicine, and proteomics. Therefore, understanding the molecular mechanism(s) of protein-peptide recognition, specificity, and binding interactions will be essential. In this study, we report the first detailed analysis of antibody-peptide interaction characteristics, by combining large-scale experimental peptide binding data with the structural analysis of eight human recombinant antibodies and numerous peptides, targeting tryptic mammalian and eukaryote proteomes. The results consistently revealed that promiscuous peptide-binding interactions, that is, both specific and degenerate binding, were exhibited by all antibodies, and the discovery was corroborated by orthogonal data, indicating that this might be a general phenomenon for low-affinity antibody-peptide interactions. The molecular mechanism for the degenerate peptide-binding specificity appeared to be executed through the use of 2-3 semi-conserved anchor residues in the C-terminal part of the peptides, in analogue to the mechanism utilized by the major histocompatibility complex-peptide complexes. In the long-term, this knowledge will be instrumental for advancing our fundamental understanding of protein-peptide interactions, as well as for designing, generating, and applying peptide specific antibodies, or peptide-binding proteins in general, in various biotechnical and medical applications.", "doi": "10.1002/pro.2173", "pmid": "23034898", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC3575919"}], "notes": [], "created": "2017-05-04T14:56:20.027Z", "modified": "2020-01-21T13:53:20.850Z"}, {"entity": "publication", "iuid": "e2fb708c0025441abebb4358c4847e66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2fb708c0025441abebb4358c4847e66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2fb708c0025441abebb4358c4847e66"}}, "title": "A genome-wide association study of monozygotic twin-pairs suggests a locus related to variability of serum high-density lipoprotein cholesterol.", "authors": [{"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Falchi", "given": "Mario", "initials": "M"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Rantanen", "given": "Taina", "initials": "T"}, {"family": "Silander", "given": "Kaisa", "initials": "K"}, {"family": "Wid\u00e9n", "given": "Elisabeth", "initials": "E"}, {"family": "Muilu", "given": "Juha", "initials": "J"}, {"family": "Rahman", "given": "Iffat", "initials": "I"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Spector", "given": "Tim", "initials": "T"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "GenomEUtwin Project", "given": "None", "initials": "N"}], "type": "clinical trial", "published": "2012-12-00", "journal": {"title": "Twin Res Hum Genet", "issn": "1832-4274", "issn-l": null, "volume": "15", "issue": "6", "pages": "691-699"}, "abstract": "Genome-wide association analysis on monozygotic twin-pairs offers a route to discovery of gene environment interactions through testing for variability loci associated with sensitivity to individual environment/lifestyle. We present a genome-wide scan of loci associated with intra-pair differences in serum lipid and apolipoprotein levels. We report data for 1,720 monozygotic female twin-pairs from GenomEUtwin project with 2.5 million SNPs, imputed or genotyped, and measured serum lipid fractions for both twins. We found one locus associated with intra-pair differences in high-density lipoprotein cholesterol, rs2483058 in an intron of SRGAP2, where twins carrying the C allele are more sensitive to environmental factors(P=3.98 x 10-8). We followed up the association in further genotyped monozygotic twins (N= 1,261),which showed a moderate association for the variant (P= 0.200, same direction of an effect). In addition,we report a new association on the level of apolipoprotein A-ll (P= 4.03 x 1 o-8).", "doi": "10.1017/thg.2012.63", "pmid": "23031429", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1832427412000631"}, {"db": "pmc", "key": "PMC4333218"}, {"db": "mid", "key": "EMS62065"}], "notes": [], "created": "2017-05-04T15:01:12.732Z", "modified": "2022-03-31T15:22:08.464Z"}, {"entity": "publication", "iuid": "e34eea78ce26495ba3984e5271abacd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e34eea78ce26495ba3984e5271abacd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e34eea78ce26495ba3984e5271abacd9"}}, "title": "Automated analysis and reannotation of subcellular locations in confocal images from the Human Protein Atlas.", "authors": [{"family": "Li", "given": "Jieyue", "initials": "J"}, {"family": "Newberg", "given": "Justin Y", "initials": "JY"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Murphy", "given": "Robert F", "initials": "RF"}], "type": "journal article", "published": "2012-11-30", "journal": {"volume": "7", "issn": "1932-6203", "issue": "11", "pages": "e50514", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. These are currently annotated by visual inspection. In this paper, we describe automated approaches to analyze the images and their use to improve annotation. We began by training classifiers to recognize the annotated patterns. By ranking proteins according to the confidence of the classifier, we generated a list of proteins that were strong candidates for reexamination. In parallel, we applied hierarchical clustering to group proteins and identified proteins whose annotations were inconsistent with the remainder of the proteins in their cluster. These proteins were reexamined by the original annotators, and a significant fraction had their annotations changed. The results demonstrate that automated approaches can provide an important complement to visual annotation.", "doi": "10.1371/journal.pone.0050514", "pmid": "23226299", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-11801"}, {"db": "pmc", "key": "PMC3511558"}], "notes": [], "created": "2017-05-04T14:55:12.577Z", "modified": "2021-07-08T13:44:33.700Z"}, {"entity": "publication", "iuid": "a5d50ee189414344adce46e6fbf8ee82", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5d50ee189414344adce46e6fbf8ee82.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5d50ee189414344adce46e6fbf8ee82"}}, "title": "The genomic landscape of species divergence in Ficedula flycatchers.", "authors": [{"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "K\u00fcnstner", "given": "Axel", "initials": "A"}, {"family": "M\u00e4kinen", "given": "Hannu", "initials": "H"}, {"family": "Nadachowska-Brzyska", "given": "Krystyna", "initials": "K"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JB"}], "type": "journal article", "published": "2012-11-29", "journal": {"volume": "491", "issn": "1476-4687", "issue": "7426", "pages": "756-760", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.", "doi": "10.1038/nature11584", "pmid": "23103876", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "nature11584"}, {"db": "GENBANK", "key": "AGTO00100000"}], "notes": [], "created": "2017-05-04T15:01:06.562Z", "modified": "2020-01-21T13:56:04.272Z"}, {"entity": "publication", "iuid": "d9da21f3e04146d39101398eb31797ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9da21f3e04146d39101398eb31797ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9da21f3e04146d39101398eb31797ef"}}, "title": "Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines.", "authors": [{"family": "Li", "given": "Jieyue", "initials": "J"}, {"family": "Shariff", "given": "Aabid", "initials": "A"}, {"family": "Wiking", "given": "Mikaela", "initials": "M"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Rohde", "given": "Gustavo K", "initials": "GK"}, {"family": "Murphy", "given": "Robert F", "initials": "RF"}], "type": "journal article", "published": "2012-11-28", "journal": {"volume": "7", "issn": "1932-6203", "issue": "11", "pages": "e50292", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Microtubules are filamentous structures that are involved in several important cellular processes, including cell division, cellular structure and mechanics, and intracellular transportation. Little is known about potential differences in microtubule distributions within and across cell lines. Here we describe a method to estimate information pertaining to 3D microtubule distributions from 2D fluorescence images. Our method allows for quantitative comparisons of microtubule distribution parameters (number of microtubules, mean length) between different cell lines. Among eleven cell lines compared, some showed differences that could be accounted for by differences in the total amount of tubulin per cell while others showed statistically significant differences in the balance between number and length of microtubules. We also observed that some cell lines that visually appear different in their microtubule distributions are quite similar when the model parameters are considered. The method is expected to be generally useful for comparing microtubule distributions between cell lines and for a given cell line after various perturbations. The results are also expected to enable analysis of the differences in gene expression underlying the observed differences in microtubule distributions among cell types.", "doi": "10.1371/journal.pone.0050292", "pmid": "23209697", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-11800"}, {"db": "pmc", "key": "PMC3508979"}], "notes": [], "created": "2017-05-04T14:55:12.878Z", "modified": "2021-07-05T16:33:38.769Z"}, {"entity": "publication", "iuid": "3e2a7ef25d704e5587e03e2786f4d552", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e2a7ef25d704e5587e03e2786f4d552.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e2a7ef25d704e5587e03e2786f4d552"}}, "title": "Strong signatures of selection in the domestic pig genome.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Megens", "given": "Hendrik-Jan", "initials": "H"}, {"family": "Martinez Barrio", "given": "Alvaro", "initials": "A"}, {"family": "Maqbool", "given": "Khurram", "initials": "K"}, {"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Wang", "given": "Chao", "initials": "C"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}, {"family": "Jern", "given": "Patric", "initials": "P"}, {"family": "J\u00f8rgensen", "given": "Claus B", "initials": "CB"}, {"family": "Archibald", "given": "Alan L", "initials": "AL"}, {"family": "Fredholm", "given": "Merete", "initials": "M"}, {"family": "Groenen", "given": "Martien A M", "initials": "MAM"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2012-11-27", "journal": {"volume": "109", "issn": "1091-6490", "issue": "48", "pages": "19529-19536", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig--the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.", "doi": "10.1073/pnas.1217149109", "pmid": "23151514", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1217149109"}, {"db": "pmc", "key": "PMC3511700"}], "notes": [], "created": "2017-05-04T14:57:40.051Z", "modified": "2020-01-21T13:56:10.645Z"}, {"entity": "publication", "iuid": "d65fa716349a4deb8347441de3b6d573", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d65fa716349a4deb8347441de3b6d573.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d65fa716349a4deb8347441de3b6d573"}}, "title": "Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements.", "authors": [{"family": "Hooper", "given": "Sean D", "initials": "SD"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Rehman", "given": "Farah L", "initials": "FL"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}], "type": "journal article", "published": "2012-11-22", "journal": {"volume": "5", "issn": "1756-0500", "issue": null, "pages": "648", "title": "BMC Res Notes", "issn-l": "1756-0500"}, "abstract": "Double-hit lymphoma is a complex and highly aggressive sub-type of B-cell lymphoma, which has recently been classified and is an area of active research interest due to the poor prognosis for patients with this disease. It is characterized by the presence of both an activating MYC chromosomal translocation and a simultaneous additional oncogenic translocation, often of the BCL2 gene. Recently, a cell line was established from a patient with this complex lymphoma and analyzed using conventional tools revealing it contains both MYC and BCL2 translocation events.\n\nIn this work, we reanalyzed the genome of the cell line using next generation whole genome sequencing technology in order to catalogue translocations, insertions and deletions which may contribute to the pathology of this lymphoma type.\n\nWe describe the cell line in much greater detail, and pinpoint the exact locations of the chromosomal breakpoints. We also find several rearrangements within cancer-associated genes, which were not found using conventional tools, suggesting that high throughput sequencing may reveal novel targets for therapy, which could be used concurrently with existing treatments.", "doi": "10.1186/1756-0500-5-648", "pmid": "23171647", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1756-0500-5-648"}, {"db": "pmc", "key": "PMC3534606"}], "notes": [], "created": "2017-05-04T14:57:32.158Z", "modified": "2021-07-08T12:52:24.432Z"}, {"entity": "publication", "iuid": "a2e31bb0de974a24a0767b2b43be5e9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2e31bb0de974a24a0767b2b43be5e9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2e31bb0de974a24a0767b2b43be5e9e"}}, "title": "The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns.", "authors": [{"family": "Moummou", "given": "Hanane", "initials": "H"}, {"family": "Kallberg", "given": "Yvonne", "initials": "Y"}, {"family": "Tonfack", "given": "Libert Brice", "initials": "LB"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "van der Rest", "given": "Beno\u00eet", "initials": "B"}], "type": "journal article", "published": "2012-11-20", "journal": {"volume": "12", "issn": "1471-2229", "issue": null, "pages": "219", "title": "BMC Plant Biol.", "issn-l": "1471-2229"}, "abstract": "Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved 'Rossmann-fold' structure, members of the SDR superfamily exhibit low sequence similarities, which constituted a bottleneck in terms of identification. Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce.\n\nWide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types - 'classical', 'extended' and 'divergent' - but a minority (10% of the predicted SDRs) could not be classified into these general types ('unknown' or 'atypical' types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families - tropinone reductase-like proteins (SDR65C), 'ABA2-like'-NAD dehydrogenase (SDR110C), 'salutaridine/menthone-reductase-like' proteins (SDR114C), 'dihydroflavonol 4-reductase'-like proteins (SDR108E) and 'isoflavone-reductase-like' (SDR460A) proteins - have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified.\n\nThe application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms ('higher plants') SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. The multiplicity of SDRs in plant kingdom is mainly explained by the diversification of large families involved in different secondary metabolism pathways, suggesting that the chemical diversification that accompanied the emergence of vascular plants acted as a driving force for SDR evolution.", "doi": "10.1186/1471-2229-12-219", "pmid": "23167570", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2229-12-219"}, {"db": "pmc", "key": "PMC3541173"}], "notes": [], "created": "2017-05-04T14:56:15.150Z", "modified": "2021-07-05T12:34:46.044Z"}, {"entity": "publication", "iuid": "4af187176e06419fbf2e3ef3b9873820", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4af187176e06419fbf2e3ef3b9873820.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4af187176e06419fbf2e3ef3b9873820"}}, "title": "Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring.", "authors": [{"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Martinez Barrio", "given": "Alvaro", "initials": "A"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Gilbert", "given": "Elizabeth R", "initials": "ER"}, {"family": "Berglund", "given": "Jonas", "initials": "J"}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Laikre", "given": "Linda", "initials": "L"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2012-11-20", "journal": {"volume": "109", "issn": "1091-6490", "issue": "47", "pages": "19345-19350", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled a muscle transcriptome and then aligned genomic reads to the transcripts, creating an \"exome assembly,\" capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index F(ST) deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.", "doi": "10.1073/pnas.1216128109", "pmid": "23134729", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1216128109"}, {"db": "pmc", "key": "PMC3511109"}], "notes": [], "created": "2017-05-04T15:01:07.706Z", "modified": "2020-01-21T13:56:02.164Z"}, {"entity": "publication", "iuid": "b8b2b87a0e29439e8aae7eae42a564ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8b2b87a0e29439e8aae7eae42a564ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8b2b87a0e29439e8aae7eae42a564ba"}}, "title": "Polymorphisms in peptidylarginine deiminase associate with rheumatoid arthritis in diverse Asian populations: evidence from MyEIRA study and meta-analysis.", "authors": [{"family": "Too", "given": "Chun Lai", "initials": "CL"}, {"family": "Murad", "given": "Shahnaz", "initials": "S"}, {"family": "Dhaliwal", "given": "Jasbir Singh", "initials": "JS"}, {"family": "Larsson", "given": "Per", "initials": "P"}, {"family": "Jiang", "given": "Xia", "initials": "X"}, {"family": "Ding", "given": "Bo", "initials": "B"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal article", "published": "2012-11-19", "journal": {"volume": "14", "issn": "1478-6362", "issue": "6", "pages": "R250", "title": "Arthritis Res. Ther.", "issn-l": "1478-6354"}, "abstract": "The majority of our knowledge regarding disease-related mechanisms of uncontrolled citrullination and anti-citrullinated protein antibody development in rheumatoid arthritis (RA) was investigated in Caucasian populations. However, peptidylarginine deiminase (PADI) type 4 gene polymorphisms are associated with RA in East Asian populations and weak or no association was found in Caucasian populations. This study explores the association between the PADI4 polymorphisms and RA risk in a multiethnic population residing in South East Asia with the goal of elucidating generalizability of association in non-Caucasian populations.\n\nA total of 320 SNPs from the PADI locus (including PADI1, PADI2, PADI3, PADI4 and PADI6 genes) were genotyped in 1,238 RA cases and 1,571 control subjects from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA) case-control study. Additionally, we conducted meta-analysis of our data together with the previously published studies of RA from East Asian populations.\n\nThe overall odds ratio (ORoverall) for the PADI4 (rs2240340) allelic model was 1.11 (95% confidence interval (CI) = 1.00 to 1.23, P = 0.04) and for the genotypic model was 1.20 (95% CI = 1.01 to 1.44, P = 0.04). Haplotype analysis for four selected PADI4 SNPs revealed a significant association of one with susceptibility (P = 0.001) and of another with a protective effect (P = 0.02). The RA susceptibility was further confirmed when combined meta-analysis was performed using these data together with data from five previously published studies from Asia comprising 5,192 RA cases and 4,317 control subjects (ORoverall = 1.23 (95% CI = 1.16 to 1.31, Pheterogeneity = 0.08) and 1.31 (95% CI = 1.20 to 1.44, Pheterogeneity = 0.32) in allele and genotype-based models, respectively). In addition, we also detected a novel association of PADI2 genetic variant rs1005753 with RA (ORoverall = 0.87 (95% CI = 0.77 to 0.99)).\n\nOur study demonstrates an association between PADI4 and RA in the multiethnic population from South East Asia and suggests additional association with a PADI2 gene. The study thus provides further support for the notion that polymorphisms in genes for enzymes responsible for citrullination contribute to RA development in multiple populations of Asian descent.", "doi": "10.1186/ar4093", "pmid": "23164236", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ar4093"}, {"db": "pmc", "key": "PMC3674620"}], "notes": [], "created": "2017-05-04T15:00:54.090Z", "modified": "2021-07-08T12:43:31.651Z"}, {"entity": "publication", "iuid": "18a47010d25b47b2bb656d6e7d31ffa9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18a47010d25b47b2bb656d6e7d31ffa9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18a47010d25b47b2bb656d6e7d31ffa9"}}, "title": "Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.", "authors": [{"family": "Akan", "given": "Pelin", "initials": "P"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Costea", "given": "Paul Igor", "initials": "PI"}, {"family": "Hedberg", "given": "Lilia", "initials": "L"}, {"family": "Solnestam", "given": "Beata Werne", "initials": "BW"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2012-11-18", "journal": {"volume": "4", "issn": "1756-994X", "issue": "11", "pages": "86", "title": "Genome Med", "issn-l": "1756-994X"}, "abstract": "We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.", "doi": "10.1186/gm387", "pmid": "23158748", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "gm387"}, {"db": "pmc", "key": "PMC3580420"}], "notes": [], "created": "2017-05-04T14:55:10.176Z", "modified": "2021-07-08T13:44:33.049Z"}, {"entity": "publication", "iuid": "30181957b2e34c5288e3afd660451d25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30181957b2e34c5288e3afd660451d25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30181957b2e34c5288e3afd660451d25"}}, "title": "CD99 is a novel prognostic stromal marker in non-small cell lung cancer.", "authors": [{"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Saito", "given": "Akira", "initials": "A"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "G\u00f6ransson-Kultima", "given": "Hanna", "initials": "H"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Planck", "given": "Maria", "initials": "M"}, {"family": "Johansson", "given": "Leif", "initials": "L"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Nyberg", "given": "Fredrik", "initials": "F"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Landelius", "given": "Per", "initials": "P"}, {"family": "Lamberg", "given": "Kristina", "initials": "K"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Ostman", "given": "Arne", "initials": "A"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2012-11-15", "journal": {"volume": "131", "issn": "1097-0215", "issue": "10", "pages": "2264-2273", "title": "Int. J. Cancer", "issn-l": "0020-7136"}, "abstract": "The complex interaction between cancer cells and the microenvironment plays an essential role in all stages of tumourigenesis. Despite the significance of this interplay, alterations in protein composition underlying tumour-stroma interactions are largely unknown. The aim of this study was to identify stromal proteins with clinical relevance in non-small cell lung cancer (NSCLC). A list encompassing 203 stromal candidate genes was compiled based on gene expression array data and available literature. The protein expression of these genes in human NSCLC was screened using the Human Protein Atlas. Twelve proteins were selected that showed a differential stromal staining pattern (BGN, CD99, DCN, EMILIN1, FBN1, PDGFRB, PDLIM5, POSTN, SPARC, TAGLN, TNC and VCAN). The corresponding antibodies were applied on tissue microarrays, including 190 NSCLC samples, and stromal staining was correlated with clinical parameters. Higher stromal expression of CD99 was associated with better prognosis in the univariate (p = 0.037) and multivariate (p = 0.039) analysis. The association was independent from the proportion of tumour stroma, the fraction of inflammatory cells and clinical and pathological parameters like stage, performance status and tumour histology. The prognostic impact of stromal CD99 protein expression was confirmed in an independent cohort of 240 NSCLC patients (p = 0.008). Furthermore, double-staining confocal fluorescence microscopy showed that CD99 was expressed in stromal lymphocytes as well as in cancer-associated fibroblasts. Based on a comprehensive screening strategy the membrane protein CD99 was identified as a novel stromal factor with clinical relevance. The results support the concept that stromal properties have an important impact on tumour progression.", "doi": "10.1002/ijc.27518", "pmid": "22392539", "labels": {"Array and Analysis Facility": null, "Tissue Profiling": null}, "xrefs": [{"db": "GEO", "description": "Expression profiling by array", "key": "GSE33363"}], "notes": [], "created": "2017-05-04T14:55:51.474Z", "modified": "2018-11-14T11:24:08.142Z"}, {"entity": "publication", "iuid": "5575062ad5e64ba5b73244ceee75765f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5575062ad5e64ba5b73244ceee75765f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5575062ad5e64ba5b73244ceee75765f"}}, "title": "Genetic variants and associations of 25-hydroxyvitamin D concentrations with major clinical outcomes.", "authors": [{"family": "Levin", "given": "Gregory P", "initials": "GP"}, {"family": "Robinson-Cohen", "given": "Cassianne", "initials": "C"}, {"family": "de Boer", "given": "Ian H", "initials": "IH"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Cauley", "given": "Jane A", "initials": "JA"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Patel", "given": "Kushang V", "initials": "KV"}, {"family": "Hagstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wang", "given": "Thomas", "initials": "T"}, {"family": "Wolf", "given": "Myles", "initials": "M"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Siscovick", "given": "David", "initials": "D"}, {"family": "Kestenbaum", "given": "Bryan", "initials": "B"}], "type": "journal article", "published": "2012-11-14", "journal": {"volume": "308", "issn": "1538-3598", "issue": "18", "pages": "1898-1905", "title": "JAMA", "issn-l": "0098-7484"}, "abstract": "Lower serum 25-hydroxyvitamin D concentrations are associated with greater risks of many chronic diseases across large, prospective community-based studies. Substrate 25-hydroxyvitamin D must be converted to 1,25-dihydroxyvitamin D for full biological activity, and complex metabolic pathways suggest that interindividual variability in vitamin D metabolism may alter the clinical consequences of measured serum 25-hydroxyvitamin D.\n\nTo investigate whether common variation within genes encoding the vitamin D-binding protein, megalin, cubilin, CYP27B1, CYP24A1, and the vitamin D receptor (VDR) modify associations of low 25-hydroxyvitamin D with major clinical outcomes.\n\nExamination of 141 single-nucleotide polymorphisms in a discovery cohort of 1514 white participants (who were recruited from 4 US regions) from the community-based Cardiovascular Health Study. Participants had serum 25-hydroxyvitamin D measurements in 1992-1993 and were followed up for a median of 11 years (through 2006). Replication meta-analyses were conducted across the independent, community-based US Health, Aging, and Body Composition (n = 922; follow-up: 1998-1999 through 2005), Italian Invecchiare in Chianti (n = 835; follow-up: 1998-2000 through 2006), and Swedish Uppsala Longitudinal Study of Adult Men (n = 970; follow-up: 1991-1995 through 2008) cohort studies.\n\nComposite outcome of incident hip facture, myocardial infarction, cancer, and mortality over long-term follow-up.\n\nInteractions between 5 single-nucleotide polymorphisms and low 25-hydroxyvitamin D concentration were identified in the discovery phase and 1 involving a variant in the VDR gene replicated in independent meta-analysis. Among Cardiovascular Health Study participants, low 25-hydroxyvitamin D concentration was associated with hazard ratios for risk of the composite outcome of 1.40 (95% CI, 1.12-1.74) for those who had 1 minor allele at rs7968585 and 1.82 (95% CI, 1.31-2.54) for those with 2 minor alleles at rs7968585. In contrast, there was no evidence of an association (estimated hazard ratio, 0.93 [95% CI, 0.70-1.24]) among participants who had 0 minor alleles at this single-nucleotide polymorphism.\n\nKnown associations of low 25-hydroxyvitamin D with major health outcomes may vary according to common genetic differences in the vitamin D receptor.", "doi": "10.1001/jama.2012.17304", "pmid": "23150009", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1391914"}, {"db": "pmc", "key": "PMC3645444"}, {"db": "mid", "key": "NIHMS457084"}], "notes": [], "created": "2017-05-04T15:01:01.523Z", "modified": "2020-01-21T13:56:02.361Z"}, {"entity": "publication", "iuid": "df095558e8814454947b6473ce1f0fd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df095558e8814454947b6473ce1f0fd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df095558e8814454947b6473ce1f0fd2"}}, "title": "Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy.", "authors": [{"family": "Neiman", "given": "M\u00e5rten", "initials": "M"}, {"family": "Sundling", "given": "Simon", "initials": "S"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2012-11-05", "journal": {"volume": "7", "issn": "1932-6203", "issue": "11", "pages": "e48616", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "During the recent years, rapid development of sequencing technologies and a competitive market has enabled researchers to perform massive sequencing projects at a reasonable cost. As the price for the actual sequencing reactions drops, enabling more samples to be sequenced, the relative price for preparing libraries gets larger and the practical laboratory work becomes complex and tedious. We present a cost-effective strategy for simplified library preparation compatible with both whole genome- and targeted sequencing experiments. An optimized enzyme composition and reaction buffer reduces the number of required clean-up steps and allows for usage of bulk enzymes which makes the whole process cheap, efficient and simple. We also present a two-tagging strategy, which allows for multiplex sequencing of targeted regions. To prove our concept, we have prepared libraries for low-pass sequencing from 100 ng DNA, performed 2-, 4- and 8-plex exome capture and a 96-plex capture of a 500 kb region. In all samples we see a high concordance (>99.4%) of SNP calls when comparing to commercially available SNP-chip platforms.", "doi": "10.1371/journal.pone.0048616", "pmid": "23139805", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-16041"}, {"db": "pmc", "key": "PMC3489721"}], "notes": [], "created": "2017-05-04T14:57:44.202Z", "modified": "2020-01-21T13:56:05.731Z"}, {"entity": "publication", "iuid": "b1bc27056e554963bd429f1073c6ba5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1bc27056e554963bd429f1073c6ba5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1bc27056e554963bd429f1073c6ba5f"}}, "title": "A 2nd generation linkage map of Heterobasidion annosum s.l. based on in silico anchoring of AFLP markers.", "authors": [{"family": "Lind", "given": "M\u00e5rten", "initials": "M"}, {"family": "van der Nest", "given": "Magriet", "initials": "M"}, {"family": "Olson", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Brandstr\u00f6m-Durling", "given": "Mikael", "initials": "M"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2012-11-05", "journal": {"volume": "7", "issn": "1932-6203", "issue": "11", "pages": "e48347", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "In this study, we present a 2(nd) generation genetic linkage map of a cross between the North American species Heterobasidion irregulare and H. occidentale, based on the alignment of the previously published 1(st) generation map to the parental genomes. We anchored 216 of the original 308 AFLP markers to their respective restriction sites using an in silico-approach. The map resolution was improved by adding 146 sequence-tagged microsatellite markers and 39 sequenced gene markers. The new markers confirmed the positions of the anchored AFLP markers, fused the original 39 linkage groups together into 17, and fully expanded 12 of these to single groups covering entire chromosomes. Map coverage of the genome increased from 55.3% to 92.8%, with 96.3% of 430 markers collinearly aligned with the genome sequence. The anchored map also improved the H. irregulare assembly considerably. It identified several errors in scaffold arrangements and assisted in reducing the total number of major scaffolds from 18 to 15. This denser, more comprehensive map allowed sequence-based mapping of three intersterility loci and one mating type locus. This demonstrates the possibility to utilize an in silico procedure to convert anonymous markers into sequence-tagged ones, as well as the power of a sequence-anchored linkage map and its usefulness in the assembly of a whole genome sequence.", "doi": "10.1371/journal.pone.0048347", "pmid": "23139779", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-15116"}, {"db": "pmc", "key": "PMC3489678"}], "notes": [], "created": "2017-05-04T15:01:12.126Z", "modified": "2020-01-21T13:56:04.691Z"}, {"entity": "publication", "iuid": "ad2c391497fa466d8c3db143b4549e43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad2c391497fa466d8c3db143b4549e43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad2c391497fa466d8c3db143b4549e43"}}, "title": "Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms.", "authors": [{"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Gyllenstrand", "given": "Niclas", "initials": "N"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}], "type": "comparative study", "published": "2012-11-02", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "589", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now simultaneously identify the transcribed part of a species genome and estimate levels of gene expression.\n\nmRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads, together with publicly available expressed sequence tag (EST) data from Norway spruce, was used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 83.5% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression differences between samples collected under dark and light conditions.\n\nOur study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6\u2009\u00d7\u200910-09 and 1.1\u2009\u00d7\u200910-09) is an order of magnitude smaller than values reported for angiosperm herbs. However, if one takes generation time into account, most of this difference disappears. The estimates of the dN/dS ratio (non-synonymous over synonymous divergence) reported here are in general much lower than 1 and only a few genes showed a ratio larger than 1.", "doi": "10.1186/1471-2164-13-589", "pmid": "23122049", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-589"}, {"db": "pmc", "key": "PMC3543189"}], "notes": [], "created": "2017-05-04T15:00:55.331Z", "modified": "2020-01-21T13:56:04.567Z"}, {"entity": "publication", "iuid": "0dc2a140d296454ea162ebc52988e560", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dc2a140d296454ea162ebc52988e560.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dc2a140d296454ea162ebc52988e560"}}, "title": "A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Papini", "given": "Marta", "initials": "M"}, {"family": "Pornputtapong", "given": "Natapol", "initials": "N"}, {"family": "Scalcinati", "given": "Gionata", "initials": "G"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "comparative study", "published": "2012-11-01", "journal": {"volume": "40", "issn": "1362-4962", "issue": "20", "pages": "10084-10097", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the Illumina platform, and to perform a cross-platform comparison based on the results obtained through Affymetrix microarray. As a case study for our work we, used the Saccharomyces cerevisiae strain CEN.PK 113-7D, grown under two different conditions (batch and chemostat). Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation\u22650.99) and high consistency between the two platforms for analysis of gene expression levels (correlation\u22650.91) are reported. The results from differential gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays) for gene expression analysis and addresses the contribution of the different steps involved in the analysis of RNA-seq data.", "doi": "10.1093/nar/gks804", "pmid": "22965124", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "gks804"}, {"db": "pmc", "key": "PMC3488244"}, {"db": "GDB", "key": "SRR453566"}, {"db": "GDB", "key": "SRR453567"}, {"db": "GDB", "key": "SRR453568"}, {"db": "GDB", "key": "SRR453569"}, {"db": "GDB", "key": "SRR453570"}, {"db": "GDB", "key": "SRR453571"}, {"db": "GDB", "key": "SRR453578"}, {"db": "GDB", "key": "SRS307298"}, {"db": "GEO", "key": "GSE37599"}, {"db": "SRA", "description": "Yeast RNA-seq", "key": "SRP012047"}], "notes": [], "created": "2017-05-04T14:56:19.115Z", "modified": "2021-07-08T13:44:33.019Z"}, {"entity": "publication", "iuid": "d86c053b36a54fceb70a026f62cd1db1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d86c053b36a54fceb70a026f62cd1db1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d86c053b36a54fceb70a026f62cd1db1"}}, "title": "Unexpected T-cell recognition of an altered peptide ligand is driven by reversed thermodynamics.", "authors": [{"family": "Allerbring", "given": "Eva B", "initials": "EB"}, {"family": "Duru", "given": "Adil D", "initials": "AD"}, {"family": "Uchtenhagen", "given": "Hannes", "initials": "H"}, {"family": "Madhurantakam", "given": "Chaithanya", "initials": "C"}, {"family": "Tomek", "given": "Markus B", "initials": "MB"}, {"family": "Grimm", "given": "Sebastian", "initials": "S"}, {"family": "Mazumdar", "given": "Pooja A", "initials": "PA"}, {"family": "Friemann", "given": "Rosmarie", "initials": "R"}, {"family": "Uhlin", "given": "Michael", "initials": "M"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P\u00c5"}, {"family": "Achour", "given": "Adnane", "initials": "A"}], "type": "journal article", "published": "2012-11-00", "journal": {"volume": "42", "issn": "1521-4141", "issue": "11", "pages": "2990-3000", "title": "Eur. J. Immunol.", "issn-l": "0014-2980"}, "abstract": "The molecular basis underlying T-cell recognition of MHC molecules presenting altered peptide ligands is still not well-established. A hierarchy of T-cell activation by MHC class I-restricted altered peptide ligands has been defined using the T-cell receptor P14 specific for H-2D(b) in complex with the immunodominant lymphocytic choriomeningitis virus peptide gp33 (KAVYNFATM). While substitution of tyrosine to phenylalanine (Y4F) or serine (Y4S) abolished recognition by P14, the TCR unexpectedly recognized H-2D(b) in complex with the alanine-substituted semiagonist Y4A, which displayed the most significant structural modification. The observed functional hierarchy gp33 > Y4A > Y4S = Y4F was neither due to higher stabilization capacity nor to differences in structural conformation. However, thermodynamic analysis demonstrated that while recognition of the full agonist H-2D(b) /gp33 was strictly enthalpy driven, recognition of the weak agonist H-2D(b) /Y4A was instead entropy driven with a large reduction in the favorable enthalpy term. The fourfold larger negative heat capacity derived for the interaction of P14 with H-2D(b) /gp33 compared with H-2D(b) /Y4A can possibly be explained by higher water entrapment at the TCR/MHC interface, which is also consistent with the measured opposite entropy contributions for the interactions of P14 with both MHCs. In conclusion, this study demonstrates that P14 makes use of different strategies to adapt to structural modifications in the MHC/peptide complex.", "doi": "10.1002/eji.201242588", "pmid": "22837158", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "PDB", "description": "Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 altered peptide ligand (Y4A)", "key": "3QUK"}, {"db": "PDB", "description": "Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 altered peptide ligand (Y4S)", "key": "3QUL"}], "notes": [], "created": "2017-05-04T15:03:44.642Z", "modified": "2018-11-14T16:49:52.759Z"}, {"entity": "publication", "iuid": "7276fd82416646febd7940ca3aa08e4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7276fd82416646febd7940ca3aa08e4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7276fd82416646febd7940ca3aa08e4c"}}, "title": "Transcriptional profiling of human glioblastoma vessels indicates a key role of VEGF-A and TGF\u03b22 in vascular abnormalization.", "authors": [{"family": "Dieterich", "given": "Lothar C", "initials": "LC"}, {"family": "Mellberg", "given": "Sofie", "initials": "S"}, {"family": "Langenkamp", "given": "Elise", "initials": "E"}, {"family": "Zhang", "given": "Lei", "initials": "L"}, {"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Salom\u00e4ki", "given": "Henriikka", "initials": "H"}, {"family": "Teichert", "given": "Martin", "initials": "M"}, {"family": "Huang", "given": "Hua", "initials": "H"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Kraus", "given": "Theo", "initials": "T"}, {"family": "Augustin", "given": "Hellmut G", "initials": "HG"}, {"family": "Olofsson", "given": "Tommie", "initials": "T"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Molema", "given": "Grietje", "initials": "G"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Georgii-Hemming", "given": "Patrik", "initials": "P"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I"}, {"family": "Dimberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2012-11-00", "journal": {"volume": "228", "issn": "1096-9896", "issue": "3", "pages": "378-390", "title": "J. Pathol.", "issn-l": "0022-3417"}, "abstract": "Glioblastoma are aggressive astrocytic brain tumours characterized by microvascular proliferation and an abnormal vasculature, giving rise to brain oedema and increased patient morbidity. Here, we have characterized the transcriptome of tumour-associated blood vessels and describe a gene signature clearly associated with pleomorphic, pathologically altered vessels in human glioblastoma (grade IV glioma). We identified 95 genes differentially expressed in glioblastoma vessels, while no significant differences in gene expression were detected between vessels in non-malignant brain and grade II glioma. Differential vascular expression of ANGPT2, CD93, ESM1, ELTD1, FILIP1L and TENC1 in human glioblastoma was validated by immunohistochemistry, using a tissue microarray. Through qPCR analysis of gene induction in primary endothelial cells, we provide evidence that increased VEGF-A and TGF\u03b22 signalling in the tumour microenvironment is sufficient to invoke many of the changes in gene expression noted in glioblastoma vessels. Notably, we found an enrichment of Smad target genes within the distinct gene signature of glioblastoma vessels and a significant increase of Smad signalling complexes in the vasculature of human glioblastoma in situ. This indicates a key role of TGF\u03b2 signalling in regulating vascular phenotype and suggests that, in addition to VEGF-A, TGF\u03b22 may represent a new target for vascular normalization therapy.", "doi": "10.1002/path.4072", "pmid": "22786655", "labels": {"Array and Analysis Facility": null, "Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:52.086Z", "modified": "2017-05-30T12:54:57.271Z"}, {"entity": "publication", "iuid": "710a176dd95d42f4be0d374a09eb8549", "links": {"self": {"href": "https://publications.scilifelab.se/publication/710a176dd95d42f4be0d374a09eb8549.json"}, "display": {"href": "https://publications.scilifelab.se/publication/710a176dd95d42f4be0d374a09eb8549"}}, "title": "TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression.", "authors": [{"family": "Sillars-Hardebol", "given": "Anke H", "initials": "AH"}, {"family": "Carvalho", "given": "Beatriz", "initials": "B"}, {"family": "Tijssen", "given": "Marianne", "initials": "M"}, {"family": "Beli\u00ebn", "given": "Jeroen A M", "initials": "JA"}, {"family": "de Wit", "given": "Meike", "initials": "M"}, {"family": "Delis-van Diemen", "given": "Pien M", "initials": "PM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "van de Wiel", "given": "Mark A", "initials": "MA"}, {"family": "Fijneman", "given": "Remond J A", "initials": "RJ"}, {"family": "Meijer", "given": "Gerrit A", "initials": "GA"}], "type": "comparative study", "published": "2012-11-00", "journal": {"volume": "61", "issn": "1468-3288", "issue": "11", "pages": "1568-1575", "title": "Gut", "issn-l": "0017-5749"}, "abstract": "Progression of a colorectal adenoma to invasive cancer occurs in a minority of adenomas and is the most crucial step in colorectal cancer pathogenesis. In the majority of cases, this is associated with gain of a substantial part of chromosome 20q, indicating that multiple genes on the 20q amplicon may drive carcinogenesis. The aim of this study was to identify genes located on the 20q amplicon that promote progression of colorectal adenoma to carcinoma.\n\nFunctional assays were performed for 32 candidate driver genes for which a positive correlation between 20q DNA copy number and mRNA expression had been demonstrated. Effects of gene knockdown on cell viability, anchorage-independent growth, and invasion were analysed in colorectal cancer cell lines with 20q gain. Colorectal tumour protein expression was examined by immunohistochemical staining of tissue microarrays.\n\nTPX2, AURKA, CSE1L, DIDO1, HM13, TCFL5, SLC17A9, RBM39 and PRPF6 affected cell viability and/or anchorage-independent growth. Chromosome 20q DNA copy number status correlated significantly with TPX2 and AURKA protein levels in a series of colorectal adenomas and carcinomas. Moreover, downmodulation of TPX2 and AURKA was shown to inhibit invasion.\n\nThese data identify TPX2 (20q11) and AURKA (20q13.2) as two genes located on distinct regions of chromosome 20q that promote 20q amplicon-driven progression of colorectal adenoma to carcinoma. Therefore the selection advantage imposed by 20q gain in tumour progression is achieved by gain-of-function of multiple cancer-related genes-knowledge that can be translated into novel tests for early diagnosis of progressive adenomas.", "doi": "10.1136/gutjnl-2011-301153", "pmid": "22207630", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "gutjnl-2011-301153"}], "notes": [], "created": "2017-05-04T14:55:50.865Z", "modified": "2017-05-30T12:54:52.514Z"}, {"entity": "publication", "iuid": "8db3e39e237348a485c30777a4096144", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8db3e39e237348a485c30777a4096144.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8db3e39e237348a485c30777a4096144"}}, "title": "Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts.", "authors": [{"family": "Cendejas-Bueno", "given": "E", "initials": "E"}, {"family": "Kolecka", "given": "A", "initials": "A"}, {"family": "Alastruey-Izquierdo", "given": "A", "initials": "A"}, {"family": "Theelen", "given": "B", "initials": "B"}, {"family": "Groenewald", "given": "M", "initials": "M"}, {"family": "Kostrzewa", "given": "M", "initials": "M"}, {"family": "Cuenca-Estrella", "given": "M", "initials": "M"}, {"family": "G\u00f3mez-L\u00f3pez", "given": "A", "initials": "A"}, {"family": "Boekhout", "given": "T", "initials": "T"}], "type": "journal article", "published": "2012-11-00", "journal": {"volume": "50", "issn": "1098-660X", "issue": "11", "pages": "3641-3651", "title": "J. Clin. Microbiol.", "issn-l": "0095-1137"}, "abstract": "The Candida haemulonii species complex is currently known as C. haemulonii groups I and II. Here we describe C. haemulonii group II as a new species, Candida duobushaemulonii sp. nov., and C. haemulonii var. vulnera as new a variety of C. haemulonii group I using phenotypic and molecular methods. These taxa and other relatives of C. haemulonii (i.e., Candida auris and Candida pseudohaemulonii) cannot be differentiated by the commercial methods now used for yeast identification. Four isolates (C. haemulonii var. vulnera) differed from the other isolates of C. haemulonii in the sequence of the internal transcribed spacer (ITS) regions of the nuclear rRNA gene operon. The new species and the new variety have a multiresistant antifungal profile, which includes high MICs of amphotericin B (geometric mean MIC, 1.18 mg/liter for C. haemulonii var. vulnera and 2 mg/liter for C. duobushaemulonii sp. nov) and cross-resistance to azole compounds. Identification of these species should be based on molecular methods, such as sequence analysis of ITS regions and matrix-assisted laser desorption ionization-time of flight mass spectrometry.", "doi": "10.1128/JCM.02248-12", "pmid": "22952266", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "JCM.02248-12"}, {"db": "pmc", "key": "PMC3486233"}, {"db": "GENBANK", "key": "JX459660"}, {"db": "GENBANK", "key": "JX459661"}, {"db": "GENBANK", "key": "JX459662"}, {"db": "GENBANK", "key": "JX459663"}, {"db": "GENBANK", "key": "JX459664"}, {"db": "GENBANK", "key": "JX459665"}, {"db": "GENBANK", "key": "JX459666"}, {"db": "GENBANK", "key": "JX459667"}, {"db": "GENBANK", "key": "JX459668"}, {"db": "GENBANK", "key": "JX459669"}, {"db": "GENBANK", "key": "JX459670"}, {"db": "GENBANK", "key": "JX459671"}, {"db": "GENBANK", "key": "JX459672"}, {"db": "GENBANK", "key": "JX459673"}, {"db": "GENBANK", "key": "JX459674"}, {"db": "GENBANK", "key": "JX459675"}, {"db": "GENBANK", "key": "JX459676"}, {"db": "GENBANK", "key": "JX459677"}, {"db": "GENBANK", "key": "JX459678"}, {"db": "GENBANK", "key": "JX459679"}, {"db": "GENBANK", "key": "JX459680"}, {"db": "GENBANK", "key": "JX459681"}, {"db": "GENBANK", "key": "JX459682"}, {"db": "GENBANK", "key": "JX459683"}, {"db": "GENBANK", "key": "JX459684"}, {"db": "GENBANK", "key": "JX459685"}, {"db": "GENBANK", "key": "JX459686"}, {"db": "GENBANK", "key": "JX459687"}, {"db": "GENBANK", "key": "JX459688"}, {"db": "GENBANK", "key": "JX459689"}, {"db": "GENBANK", "key": "JX459690"}, {"db": "GENBANK", "key": "JX459691"}, {"db": "GENBANK", "key": "JX459692"}, {"db": "GENBANK", "key": "JX459693"}, {"db": "GENBANK", "key": "JX459694"}, {"db": "GENBANK", "key": "JX459695"}, {"db": "GENBANK", "key": "JX459696"}, {"db": "GENBANK", "key": "JX459697"}, {"db": "GENBANK", "key": "JX459698"}, {"db": "GENBANK", "key": "JX459699"}, {"db": "GENBANK", "key": "JX459700"}, {"db": "GENBANK", "key": "JX459701"}, {"db": "GENBANK", "key": "JX459702"}, {"db": "GENBANK", "key": "JX459703"}, {"db": "GENBANK", "key": "JX459704"}, {"db": "GENBANK", "key": "JX459705"}, {"db": "GENBANK", "key": "JX459706"}, {"db": "GENBANK", "key": "JX459707"}, {"db": "GENBANK", "key": "JX459708"}, {"db": "GENBANK", "key": "JX459709"}, {"db": "GENBANK", "key": "JX459710"}, {"db": "GENBANK", "key": "JX459711"}, {"db": "GENBANK", "key": "JX459712"}, {"db": "GENBANK", "key": "JX459713"}, {"db": "GENBANK", "key": "JX459714"}, {"db": "GENBANK", "key": "JX459715"}, {"db": "GENBANK", "key": "JX459716"}, {"db": "GENBANK", "key": "JX459717"}, {"db": "GENBANK", "key": "JX459718"}, {"db": "GENBANK", "key": "JX459719"}, {"db": "GENBANK", "key": "JX459720"}, {"db": "GENBANK", "key": "JX459721"}, {"db": "GENBANK", "key": "JX459722"}, {"db": "GENBANK", "key": "JX459723"}, {"db": "GENBANK", "key": "JX459724"}, {"db": "GENBANK", "key": "JX459725"}, {"db": "GENBANK", "key": "JX459726"}, {"db": "GENBANK", 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"JX459753"}, {"db": "GENBANK", "key": "JX459754"}, {"db": "GENBANK", "key": "JX459755"}, {"db": "GENBANK", "key": "JX459756"}, {"db": "GENBANK", "key": "JX459757"}, {"db": "GENBANK", "key": "JX459758"}, {"db": "GENBANK", "key": "JX459759"}, {"db": "GENBANK", "key": "JX459760"}, {"db": "GENBANK", "key": "JX459761"}, {"db": "GENBANK", "key": "JX459762"}, {"db": "GENBANK", "key": "JX459763"}, {"db": "GENBANK", "key": "JX459764"}, {"db": "GENBANK", "key": "JX459765"}, {"db": "GENBANK", "key": "JX459766"}, {"db": "GENBANK", "key": "JX459767"}, {"db": "GENBANK", "key": "JX459768"}, {"db": "GENBANK", "key": "JX459769"}, {"db": "GENBANK", "key": "JX459770"}, {"db": "GENBANK", "key": "JX459771"}, {"db": "GENBANK", "key": "JX459772"}, {"db": "GENBANK", "key": "JX459773"}, {"db": "GENBANK", "key": "JX459774"}, {"db": "GENBANK", "key": "JX459775"}, {"db": "GENBANK", "key": "JX459776"}, {"db": "GENBANK", "key": "JX459777"}, {"db": "GENBANK", "key": "JX459778"}, {"db": "GENBANK", "key": "JX459779"}, {"db": "GENBANK", "key": "JX459780"}, {"db": "GENBANK", "key": "JX459781"}, {"db": "GENBANK", "key": "JX459782"}, {"db": "GENBANK", "key": "JX459783"}, {"db": "GENBANK", "key": "JX459784"}, {"db": "GENBANK", "key": "JX459785"}, {"db": "GENBANK", "key": "JX459786"}, {"db": "GENBANK", "key": "JX459787"}, {"db": "GENBANK", "key": "JX459788"}, {"db": "GENBANK", "key": "JX459789"}, {"db": "GENBANK", "key": "JX459790"}, {"db": "GENBANK", "key": "JX459791"}, {"db": "GENBANK", "key": "JX459792"}], "notes": [], "created": "2017-05-04T14:57:37.189Z", "modified": "2020-01-21T13:56:10.599Z"}, {"entity": "publication", "iuid": "5a6dbca9181a46b196d824946987c4bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a6dbca9181a46b196d824946987c4bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a6dbca9181a46b196d824946987c4bf"}}, "title": "2-[4,5-Difluoro-2-(2-fluorobenzoylamino)-benzoylamino]benzoic acid, an antiviral compound with activity against acyclovir-resistant isolates of herpes simplex virus types 1 and 2.", "authors": [{"family": "Strand", "given": "M\u00e5rten", "initials": "M"}, {"family": "Islam", "given": "Koushikul", "initials": "K"}, {"family": "Edlund", "given": "Karin", "initials": "K"}, {"family": "Oberg", "given": "Christopher T", "initials": "CT"}, {"family": "Allard", "given": "Annika", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "Tomas", "initials": "T"}, {"family": "Mei", "given": "Ya-Fang", "initials": "Y"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Wadell", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2012-11-00", "journal": {"volume": "56", "issn": "1098-6596", "issue": "11", "pages": "5735-5743", "title": "Antimicrob. Agents Chemother.", "issn-l": "0066-4804"}, "abstract": "Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are responsible for lifelong latent infections in humans, with periods of viral reactivation associated with recurring ulcerations in the orofacial and genital tracts. In immunosuppressed patients and neonates, HSV infections are associated with severe morbidity and, in some cases, even mortality. Today, acyclovir is the standard therapy for the management of HSV infections. However, the need for novel antiviral agents is apparent, since HSV isolates resistant to acyclovir therapy are frequently isolated in immunosuppressed patients. In this study, we assessed the anti-HSV activity of the antiadenoviral compounds 2-[2-(2-benzoylamino)-benzoylamino]benzoic acid (benzavir-1) and 2-[4,5-difluoro-2-(2-fluorobenzoylamino)-benzoylamino]benzoic acid (benzavir-2) on HSV-1 and HSV-2. Both compounds were active against both viruses. Importantly, benzavir-2 had potency similar to that of acyclovir against both HSV types, and it was active against clinical acyclovir-resistant HSV isolates.", "doi": "10.1128/AAC.01072-12", "pmid": "22908173", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "AAC.01072-12"}, {"db": "pmc", "key": "PMC3486576"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:38.223Z", "modified": "2025-10-17T13:04:30.508Z"}, {"entity": "publication", "iuid": "ae5c0309da6941ea817f0078274cff36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae5c0309da6941ea817f0078274cff36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae5c0309da6941ea817f0078274cff36"}}, "title": "Human cord blood derived immature basophils show dual characteristics, expressing both basophil and eosinophil associated proteins.", "authors": [{"family": "Grundstr\u00f6m", "given": "Jeanette", "initials": "J"}, {"family": "Reimer", "given": "Jenny M", "initials": "JM"}, {"family": "Magnusson", "given": "Sofia E", "initials": "SE"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Wernersson", "given": "Sara", "initials": "S"}, {"family": "Hellman", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2012-10-31", "journal": {"volume": "7", "issn": "1932-6203", "issue": "10", "pages": "e48308", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Basophils are blood cells of low abundance associated with allergy, inflammation and parasite infections. To study the transcriptome of mature circulating basophils cells were purified from buffy coats by density gradient centrifugations and two-step magnetic cell sorting. However, after extensive analysis the cells were found to be transcriptionally inactive and almost completely lack functional mRNA. In order to obtain transcriptionally active immature basophils for analysis of their transcriptome, umbilical cord blood cells were therefore cultured in the presence of interleukin (IL)-3 for 9 days and basophils were enriched by removing non-basophils using magnetic cell sorting. The majority of purified cells demonstrated typical metachromatic staining with Alcian blue dye (95%) and expression of surface markers Fc\u03b5RI and CD203c, indicating a pure population of cells with basophil-like phenotype. mRNA was extracted from these cells and used to construct a cDNA library with approximately 600 000 independent clones. This library served as tool to determine the mRNA frequencies for a number of hematopoietic marker proteins. It was shown that these cells express basophil/mast cell-specific transcripts, i.e. \u03b2-tryptase, serglycin and Fc\u03b5RI \u03b1-chain, to a relatively low degree. In contrast, the library contained a high number of several eosinophil-associated transcripts such as: major basic protein (MBP), charcot leyden crystal (CLC), eosinophil cationic protein (ECP), eosinophil derived neurotoxin (EDN) and eosinophil peroxidase (EPO). Out of these transcripts, MBP and EPO were the most frequently observed, representing 8% and 3.2% of the total mRNA pool, respectively. Moreover, in a proteome analysis of cultured basophils we identified MBP and EPO as the two most prominent protein bands, suggesting a good correlation between protein and mRNA analyses of these cells. The mixed phenotype observed for these cells strengthens the conclusion that eosinophils and basophils are closely linked during human hematopoietic development. The dual phenotype also indicates that other cytokines than IL-3 or cell surface interactions are needed to obtain the full basophil specific phenotype in vivo.", "doi": "10.1371/journal.pone.0048308", "pmid": "23118978", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-19859"}, {"db": "pmc", "key": "PMC3485157"}], "notes": [], "created": "2017-05-04T14:57:43.302Z", "modified": "2020-01-21T13:56:10.473Z"}, {"entity": "publication", "iuid": "4ac7c51a01b2483582546addacfcc239", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ac7c51a01b2483582546addacfcc239.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ac7c51a01b2483582546addacfcc239"}}, "title": "Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.", "authors": [{"family": "Solnestam", "given": "Beata Werne", "initials": "BW"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Akan", "given": "Pelin", "initials": "P"}], "type": "comparative study", "published": "2012-10-30", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "574", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions from the cytoplasm and from whole cells (total RNA) were prepared from three human cell lines and sequenced using massive parallel sequencing.\n\nFor all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total RNA fractions. Transcripts detected at higher levels in the total RNA fraction had longer coding sequences and higher number of miRNA target sites. Transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. Nuclear retention of transcripts and mRNA degradation via miRNA pathway might contribute to this differential detection of genes. The consequence of the differential detection was further investigated by comparison to proteomics data. Interestingly, the expression profiles of cytoplasmic and total RNA correlated equally well with protein abundance levels indicating regulation at a higher level.\n\nWe conclude that expression levels derived from the total RNA fraction be regarded as an appropriate estimate of the amount of mRNAs present in a given cell population, independent of the coding sequence length or UTRs.", "doi": "10.1186/1471-2164-13-574", "pmid": "23110385", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-574"}, {"db": "pmc", "key": "PMC3495644"}], "notes": [], "created": "2017-05-04T14:55:09.570Z", "modified": "2021-07-08T13:26:08.160Z"}, {"entity": "publication", "iuid": "3d17bf49ee824c219202eacebf916ef0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d17bf49ee824c219202eacebf916ef0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d17bf49ee824c219202eacebf916ef0"}}, "title": "Secretagogin is expressed in sensory CGRP neurons and in spinal cord of mouse and complements other calcium-binding proteins, with a note on rat and human.", "authors": [{"family": "Shi", "given": "Tie-Jun Sten", "initials": "TJ"}, {"family": "Xiang", "given": "Qiong", "initials": "Q"}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD"}, {"family": "Tortoriello", "given": "Giuseppe", "initials": "G"}, {"family": "Hammarberg", "given": "Henrik", "initials": "H"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Wagner", "given": "Ludwig", "initials": "L"}, {"family": "Josephson", "given": "Anna", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Harkany", "given": "Tibor", "initials": "T"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2012-10-29", "journal": {"volume": "8", "issn": "1744-8069", "issue": null, "pages": "80", "title": "Mol Pain", "issn-l": "1744-8069"}, "abstract": "Secretagogin (Scgn), a member of the EF-hand calcium-binding protein (CaBP) superfamily, has recently been found in subsets of developing and adult neurons. Here, we have analyzed the expression of Scgn in dorsal root ganglia (DRGs) and trigeminal ganglia (TGs), and in spinal cord of mouse at the mRNA and protein levels, and in comparison to the well-known CaBPs, calbindin D-28k, parvalbumin and calretinin. Rat DRGs, TGs and spinal cord, as well as human DRGs and spinal cord were used to reveal phylogenetic variations.\n\nWe found Scgn mRNA expressed in mouse and human DRGs and in mouse ventral spinal cord. Our immunohistochemical data showed a complementary distribution of Scgn and the three CaBPs in mouse DRG neurons and spinal cord. Scgn was expressed in ~7% of all mouse DRG neuron profiles, mainly small ones and almost exclusively co-localized with calcitonin gene-related peptide (CGRP). This co-localization was also seen in human, but not in rat DRGs. Scgn could be detected in the mouse sciatic nerve and accumulated proximal to its constriction. In mouse spinal cord, Scgn-positive neuronal cell bodies and fibers were found in gray matter, especially in the dorsal horn, with particularly high concentrations of fibers in the superficial laminae, as well as in cell bodies in inner lamina II and in some other laminae. A dense Scgn-positive fiber network and some small cell bodies were also found in the superficial dorsal horn of humans. In the ventral horn, a small number of neurons were Scgn-positive in mouse but not rat, confirming mRNA distribution. Both in mouse and rat, a subset of TG neurons contained Scgn. Dorsal rhizotomy strongly reduced Scgn fiber staining in the dorsal horn. Peripheral axotomy did not clearly affect Scgn expression in DRGs, dorsal horn or ventral horn neurons in mouse.\n\nScgn is a CaBP expressed in a subpopulation of nociceptive DRG neurons and their processes in the dorsal horn of mouse, human and rat, the former two co-expressing CGRP, as well as in dorsal horn neurons in all three species. Functional implications of these findings include the cellular refinement of sensory information, in particular during the processing of pain.", "doi": "10.1186/1744-8069-8-80", "pmid": "23102406", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1744-8069-8-80"}, {"db": "pmc", "key": "PMC3560279"}], "notes": [], "created": "2017-05-04T14:55:18.337Z", "modified": "2021-07-08T13:44:33.173Z"}, {"entity": "publication", "iuid": "b2e6addab2f24f72a5f8964b5587a900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2e6addab2f24f72a5f8964b5587a900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2e6addab2f24f72a5f8964b5587a900"}}, "title": "Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis.", "authors": [{"family": "Pinto", "given": "Rui C", "initials": "RC"}, {"family": "Gerber", "given": "Lorenz", "initials": "L"}, {"family": "Eliasson", "given": "Mattias", "initials": "M"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Trygg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2012-10-16", "journal": {"volume": "84", "issn": "1520-6882", "issue": "20", "pages": "8675-8681", "title": "Anal. Chem.", "issn-l": "0003-2700"}, "abstract": "We have developed a multistep strategy that integrates data from several large-scale experiments that suffer from systematic between-experiment variation. This strategy removes such variation that would otherwise mask differences of interest. It was applied to the evaluation of wood chemical analysis of 736 hybrid aspen trees: wild-type controls and transgenic trees potentially involved in wood formation. The trees were grown in four different greenhouse experiments imposing significant variation between experiments. Pyrolysis coupled to gas chromatography/mass spectrometry (Py-GC/MS) was used as a high throughput-screening platform for fingerprinting of wood chemotype. Our proposed strategy includes quality control, outlier detection, gene specific classification, and consensus analysis. The orthogonal projections to latent structures discriminant analysis (OPLS-DA) method was used to generate the consensus chemotype profiles for each transgenic line. These were thereafter compiled to generate a global dataset. Multivariate analysis and cluster analysis techniques revealed a drastic reduction in between-experiment variation that enabled a global analysis of all transgenic lines from the four independent experiments. Information from in-depth analysis of specific transgenic lines and independent peak identification validated our proposed strategy.", "doi": "10.1021/ac301869p", "pmid": "22978754", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:14.540Z", "modified": "2020-01-21T13:53:20.782Z"}, {"entity": "publication", "iuid": "75bcf8b81e5448c4b4f8cfded0b0ac72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/75bcf8b81e5448c4b4f8cfded0b0ac72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/75bcf8b81e5448c4b4f8cfded0b0ac72"}}, "title": "Chromosome 1p13 genetic variants antagonize the risk of myocardial infarction associated with high ApoB serum levels.", "authors": [{"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Vikstr\u00f6m", "given": "Max", "initials": "M"}, {"family": "Ye", "given": "Shu", "initials": "S"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2012-10-16", "journal": {"volume": "12", "issn": "1471-2261", "issue": null, "pages": "90", "title": "BMC Cardiovasc Disord", "issn-l": "1471-2261"}, "abstract": "Genetic variation at 1p13 modulates serum lipid levels and the risk of coronary heart disease through the regulation of serum lipid levels. Here we investigate if the interaction between genetic variants at 1p13 and serum lipid levels affects the risk of non-fatal myocardial infarction (MI) in the Stockholm Heart Epidemiology Program (SHEEP), a large population based case control study.\n\nIn the present study only non fatal MI cases (n\u2009=\u20091213, men/women: 852/361) and controls (n\u2009=\u20091516, men/women =1054/507) matched by age, sex and residential area, were included. Three SNPs 12740374\u2009G/T, rs599839A/G and rs646776T/C mapping at 1p13 were analysed for association with serum lipid levels and the risk of MI by a weighted least square regression and logistic regression analyses, respectively. To analyse the effect of the interaction between genetic variants and serum lipid levels on the risk of MI, we applied the biological model of interaction that estimates the difference in risk, expressed as OR (95%CI), observed in the presence and in the absence of both exposures. One derived measure is the Synergy index (S) and 95%CI, where S\u2009>\u20091 indicates synergy and S\u2009<\u20091 antagonism between the two interaction terms.\n\nRs12740374G/T and rs646776T/C were in strong linkage disequilibrium (LD) (r2\u2009=\u20090.99), therefore only rs599839A/G and rs646776 were included in the analysis. Consistently with published data, presence of the rare genotypes was associated with reduced total-, LDL-cholesterol and ApoB serum levels (all p\u2009<\u20090.05) as compared to the reference genotype, but was not associated with the risk of MI.However, the increased risk of MI observed in individual exposed to high (\u226575th percentile) serum lipid levels was offset in subjects carrying the rare alleles G and C. In particular, the risk of MI associated with high ApoB serum levels OR (95%CI) 2.27 (1.86-2.77) was reduced to 1.76 (1.33-2.34) in the presence of the G allele at rs599839 with an S of 0.47 (0.20-0.90).\n\nThese results indicate that an antagonism between ApoB serum levels and genetic variants at 1p13 contributes to reduce the risk of non-fatal MI in the presence of high ApoB serum levels.", "doi": "10.1186/1471-2261-12-90", "pmid": "23067240", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "1471-2261-12-90"}, {"db": "pmc", "key": "PMC3480949"}], "notes": [], "created": "2017-05-04T15:03:33.447Z", "modified": "2017-05-30T14:52:22.877Z"}, {"entity": "publication", "iuid": "c0f68dbcb6cc404990f25cd0cc929989", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0f68dbcb6cc404990f25cd0cc929989.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0f68dbcb6cc404990f25cd0cc929989"}}, "title": "A novel mutation in the Lipase H gene underlies autosomal recessive hypotrichosis and woolly hair.", "authors": [{"family": "Tariq", "given": "Muhammad", "initials": "M"}, {"family": "Azhar", "given": "Aysha", "initials": "A"}, {"family": "Baig", "given": "Shahid Mahmood", "initials": "SM"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Klar", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2012-10-12", "journal": {"volume": "2", "issn": "2045-2322", "issue": null, "pages": "730", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Mutations in the lipase member H (LIPH) gene cause autosomal recessive hypotrichosis with woolly hair. We report herein on five consanguineous families from Pakistan segregating hypotrichosis and woolly hair. Genetic investigation using polymorphic microsatellite markers revealed homozygosity for a region spanning the HYPT7 locus on chromosome 3 in affected individuals of all five families. Sequence analysis of the LIPH gene revealed a novel nonsense mutation (p.Arg260X) associated with hypotrichosis without woolly hair in one family. In the remaining four families we identified previously described mutations in a homozygous state in affected members. These findings extend the spectrum of known LIPH mutations in the Pakistani population.", "doi": "10.1038/srep00730", "pmid": "23066499", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3470015"}], "notes": [], "created": "2017-05-04T14:57:46.321Z", "modified": "2020-01-21T13:56:05.011Z"}, {"entity": "publication", "iuid": "aab1bb0d345742de954ec55b4ff5f7f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aab1bb0d345742de954ec55b4ff5f7f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aab1bb0d345742de954ec55b4ff5f7f4"}}, "title": "The Pseudomonas aeruginosa N-acylhomoserine lactone quorum sensing molecules target IQGAP1 and modulate epithelial cell migration.", "authors": [{"family": "Karlsson", "given": "Thommie", "initials": "T"}, {"family": "Turkina", "given": "Maria V", "initials": "MV"}, {"family": "Yakymenko", "given": "Olena", "initials": "O"}, {"family": "Magnusson", "given": "Karl-Eric", "initials": "K"}, {"family": "Vikstr\u00f6m", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2012-10-11", "journal": {"volume": "8", "issn": "1553-7374", "issue": "10", "pages": "e1002953", "title": "PLoS Pathog.", "issn-l": "1553-7366"}, "abstract": "Quorum sensing (QS) signaling allows bacteria to control gene expression once a critical population density is achieved. The Gram-negative human pathogen Pseudomonas aeruginosa uses N-acylhomoserine lactones (AHL) as QS signals, which coordinate the production of virulence factors and biofilms. These bacterial signals can also modulate human cell behavior. Little is known about the mechanisms of the action of AHL on their eukaryotic targets. Here, we found that N-3-oxo-dodecanoyl-L-homoserine lactone 3O-C(12)-HSL modulates human intestinal epithelial Caco-2 cell migration in a dose- and time-dependent manner. Using new 3O-C(12)-HSL biotin and fluorescently-tagged probes for LC-MS/MS and confocal imaging, respectively, we demonstrated for the first time that 3O-C(12)-HSL interacts and co-localizes with the IQ-motif-containing GTPase-activating protein IQGAP1 in Caco-2 cells. The interaction between IQGAP1 and 3O-C(12)-HSL was further confirmed by pull-down assay using a GST-tagged protein with subsequent Western blot of IQGAP1 and by identifying 3O-C(12)-HSL with a sensor bioassay. Moreover, 3O-C(12)-HSL induced changes in the phosphorylation status of Rac1 and Cdc42 and the localization of IQGAP1 as evidenced by confocal and STED microscopy and Western blots. Our findings suggest that the IQGAP1 is a novel partner for P. aeruginosa 3O-C(12)-HSL and likely the integrator of Rac1 and Cdc42- dependent altered cell migration. We propose that the targeting of IQGAP1 by 3O-C(12)-HSL can trigger essential changes in the cytoskeleton network and be an essential component in bacterial--human cell communication.", "doi": "10.1371/journal.ppat.1002953", "pmid": "23071436", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "PPATHOGENS-D-11-02789"}, {"db": "pmc", "key": "PMC3469656"}], "notes": [], "created": "2017-05-04T14:56:11.216Z", "modified": "2021-05-24T15:33:38.317Z"}, {"entity": "publication", "iuid": "42c6d5252b82437aa9bd3b58c2b7de8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42c6d5252b82437aa9bd3b58c2b7de8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42c6d5252b82437aa9bd3b58c2b7de8c"}}, "title": "Multiply-primed rolling circle amplification of human papillomavirus using sequence-specific primers.", "authors": [{"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Gustavsson", "given": "Inger", "initials": "I"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "comparative study", "published": "2012-10-10", "journal": {"volume": "432", "issn": "1096-0341", "issue": "1", "pages": "57-62", "title": "Virology", "issn-l": "0042-6822"}, "abstract": "Multiply-primed rolling circle amplification (RCA) is a suitable technique for amplification of circular templates and has been used to identify novel human papillomaviruses (HPV). In this study we develop an efficient RCA for whole genome amplification of HPV using HPV-specific primers in clinical samples and establish a protocol for whole genome sequencing using the Sanger method. Amplification of cloned HPV-genomes by RCA was compared using specific primers against random hexamers. Using HPV-specific primers increased the effectiveness on average 15.2 times and the enrichment of HPV relative to human gDNA on average 62.2 times, as compared to using random hexamer. RCA products were sequenced without need for cloning, even when using low-input amounts. The technique was successfully used on 4 patient samples from FTA cards, to generate whole HPV-genome sequences. Degenerated HPV-specific primers for RCA produce DNA of sufficient quality and quantity suitable for sequencing and other potential downstream analyses.", "doi": "10.1016/j.virol.2012.05.030", "pmid": "22739442", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0042-6822(12)00281-4"}, {"db": "GENBANK", "key": "JX129485"}, {"db": "GENBANK", "key": "JX129486"}, {"db": "GENBANK", "key": "JX129487"}, {"db": "GENBANK", "key": "JX129488"}], "notes": [], "created": "2017-05-04T14:57:46.937Z", "modified": "2020-01-21T13:56:10.532Z"}, {"entity": "publication", "iuid": "36aa2c1a1e004c4581aec22ec50609dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36aa2c1a1e004c4581aec22ec50609dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36aa2c1a1e004c4581aec22ec50609dd"}}, "title": "Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae.", "authors": [{"family": "Papini", "given": "Marta", "initials": "M"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2012-10-09", "journal": {"volume": "11", "issn": "1475-2859", "issue": null, "pages": "136", "title": "Microb. Cell Fact.", "issn-l": "1475-2859"}, "abstract": "Scheffersomyces stipitis is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as Saccharomyces cerevisiae, the onset of fermentation in S. stipitis is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations.\n\nStarting from the analysis of physiological data, we confirmed through 13C-based flux analysis the fully respiratory metabolism of S. stipitis when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for S. cerevisiae under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through in silico transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways.\n\nThe work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for S. stipitis under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for S. cerevisiae under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, in silico analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of S. stiptis is investigated in details and is compared to S. cerevisiae. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of S. stipitis as cell factory.", "doi": "10.1186/1475-2859-11-136", "pmid": "23043429", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1475-2859-11-136"}, {"db": "pmc", "key": "PMC3528450"}], "notes": [], "created": "2017-05-04T14:56:17.576Z", "modified": "2021-07-08T13:44:33.145Z"}, {"entity": "publication", "iuid": "c022dd2b61674f24a4e4235c9a1634c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c022dd2b61674f24a4e4235c9a1634c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c022dd2b61674f24a4e4235c9a1634c1"}}, "title": "Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.", "authors": [{"family": "Bock", "given": "Thomas", "initials": "T"}, {"family": "Moest", "given": "Hansjoerg", "initials": "H"}, {"family": "Omasits", "given": "Ulrich", "initials": "U"}, {"family": "Dolski", "given": "Silvia", "initials": "S"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Frei", "given": "Andreas", "initials": "A"}, {"family": "Hofmann", "given": "Andreas", "initials": "A"}, {"family": "Bausch-Fluck", "given": "Damaris", "initials": "D"}, {"family": "Jacobs", "given": "Andrea", "initials": "A"}, {"family": "Krayenbuehl", "given": "Niklaus", "initials": "N"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R"}, {"family": "Frei", "given": "Karl", "initials": "K"}, {"family": "Wollscheid", "given": "Bernd", "initials": "B"}], "type": "journal article", "published": "2012-10-05", "journal": {"volume": "11", "issn": "1535-3907", "issue": "10", "pages": "4885-4893", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Glioblastoma is the most common primary brain tumor in adults with low average survival time after diagnosis. In order to improve glioblastoma treatment, new drug-accessible targets need to be identified. Cell surface glycoproteins are prime drug targets due to their accessibility at the surface of cancer cells. To overcome the limited availability of suitable antibodies for cell surface protein detection, we performed a comprehensive mass spectrometric investigation of the glioblastoma surfaceome. Our combined cell surface capturing analysis of primary ex vivo glioblastoma cell lines in combination with established glioblastoma cell lines revealed 633 N-glycoproteins, which vastly extends the known data of surfaceome drug targets at subcellular resolution. We provide direct evidence of common glioblastoma cell surface glycoproteins and an approximate estimate of their abundances, information that could not be derived from genomic and/or transcriptomic glioblastoma studies. Apart from our pharmaceutically valuable repertoire of already and potentially drug-accessible cell surface glycoproteins, we built a mass-spectrometry-based toolbox enabling directed, sensitive, and repetitive glycoprotein measurements for clinical follow-up studies. The included Skyline Glioblastoma SRM assay library provides an elevated starting point for parallel testing of the abundance level of the detected glioblastoma surfaceome members in future drug perturbation experiments.", "doi": "10.1021/pr300360a", "pmid": "22909291", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:10.473Z", "modified": "2021-07-08T13:44:33.585Z"}, {"entity": "publication", "iuid": "951aea7e94e94e769ea8d79a783a125a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/951aea7e94e94e769ea8d79a783a125a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/951aea7e94e94e769ea8d79a783a125a"}}, "title": "Multiplex epitope mapping using bacterial surface display reveals both linear and conformational epitopes.", "authors": [{"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2012-10-04", "journal": {"volume": "2", "issn": "2045-2322", "issue": null, "pages": "706", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "As antibody-based diagnosis and therapy grow at an increased pace, there is a need for methods which rapidly and accurately determine antibody-antigen interactions. Here, we report a method for the multiplex determination of antibody epitopes using bacterial cell-surface display. A protein-fragment library with 10(7) cell clones, covering 60 clinically-relevant protein targets, was created and characterized with massively parallel sequencing. Using this multi-target fragment library we determined simultaneously epitopes of commercial monoclonal and polyclonal antibodies targeting PSMA, EGFR, and VEGF. Off-target binding was observed for one of the antibodies, which demonstrates the methods ability to reveal cross-reactivity. We exemplify the detection of structural epitopes by mapping the therapeutic antibody Avastin. Based on our findings we suggest this method to be suitable for mapping linear and structural epitopes of monoclonal and polyclonal antibodies in a multiplex fashion and could find applicability in serum profiling as well as other protein-protein interaction studies.", "doi": "10.1038/srep00706", "pmid": "23050090", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3463815"}], "notes": [], "created": "2017-05-04T14:57:46.018Z", "modified": "2021-07-08T13:44:33.449Z"}, {"entity": "publication", "iuid": "122807c9966645f3ba82349bf707f5eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/122807c9966645f3ba82349bf707f5eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/122807c9966645f3ba82349bf707f5eb"}}, "title": "The science of librarianship. University of Wales at Aberystwyth, July 31, 1917.", "authors": [{"family": "Osler", "given": "William", "initials": "W"}], "type": "biography", "published": "2012-10-00", "journal": {"title": "J Med Libr Assoc", "issn": "1558-9439", "volume": "100", "issue": "4 Suppl", "pages": "A", "issn-l": null}, "abstract": null, "doi": null, "pmid": "23509423", "labels": {"Clinical Genomics Link\u00f6ping": "Service", "Clinical Genomics": "Service", "Clinical Genomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC3571674"}, {"db": "sici", "key": "i1536-5050-100-4s-70"}], "notes": [], "created": "2024-12-10T08:20:39.447Z", "modified": "2026-08-30T17:45:12.165Z"}, {"entity": "publication", "iuid": "3ea7e4059caf4dd8bc31c45a4a1cba86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ea7e4059caf4dd8bc31c45a4a1cba86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ea7e4059caf4dd8bc31c45a4a1cba86"}}, "title": "Selected polymorphisms in sex hormone-related genes, circulating sex hormones and risk of endometrial cancer.", "authors": [{"family": "Lundin", "given": "Eva", "initials": "E"}, {"family": "Wirgin", "given": "Isaac", "initials": "I"}, {"family": "Lukanova", "given": "Annekatrin", "initials": "A"}, {"family": "Afanasyeva", "given": "Yelena", "initials": "Y"}, {"family": "Krogh", "given": "Vittorio", "initials": "V"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Hemminki", "given": "Kari", "initials": "K"}, {"family": "Clendenen", "given": "Tess V", "initials": "TV"}, {"family": "Arslan", "given": "Alan A", "initials": "AA"}, {"family": "Ohlson", "given": "Nina", "initials": "N"}, {"family": "Sieri", "given": "Sabina", "initials": "S"}, {"family": "Roy", "given": "Nirmal", "initials": "N"}, {"family": "Koenig", "given": "Karen L", "initials": "KL"}, {"family": "Idahl", "given": "Annika", "initials": "A"}, {"family": "Berrino", "given": "Franco", "initials": "F"}, {"family": "Toniolo", "given": "Paolo", "initials": "P"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "F\u00f6rsti", "given": "Asta", "initials": "A"}, {"family": "Muti", "given": "Paola", "initials": "P"}, {"family": "Lenner", "given": "Per", "initials": "P"}, {"family": "Shore", "given": "Roy E", "initials": "RE"}, {"family": "Zeleniuch-Jacquotte", "given": "Anne", "initials": "A"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "36", "issn": "1877-783X", "issue": "5", "pages": "445-452", "title": "Cancer Epidemiol", "issn-l": "1877-7821"}, "abstract": "The role of estrogen and progesterone in the development of endometrial cancer is well documented. Few studies have examined the association of genetic variants in sex hormone-related genes with endometrial cancer risk.\n\nWe conducted a case-control study nested within three cohorts to examine the association of endometrial cancer risk with polymorphisms in hormone-related genes among 391 cases (92% postmenopausal at diagnosis) and 712 individually-matched controls. We also examined the association of these polymorphisms with circulating levels of sex hormones and SHBG in a cross-sectional analysis including 596 healthy postmenopausal women at blood donation (controls from this nested case-control study and from a nested case-control study of breast cancer in one of the three cohorts).\n\nAdjusting for endometrial cancer risk factors, the A allele of rs4775936 in CYP19 was significantly associated (OR(per allele)=1.22, 95% CI=1.01-1.47, p(trend)=0.04), while the T allele of rs10046 was marginally associated with increased risk of endometrial cancer (OR(per allele)=1.20, 95% CI=0.99-1.45, p(trend)=0.06). PGR rs1042838 was also marginally associated with risk (OR(per allele)=1.25, 95% CI=0.96-1.61, p(trend)=0.09). No significant association was found for the other polymorphisms, i.e. CYP1B1 rs1800440 and rs1056836, UGT1A1 rs8175347, SHBG rs6259 and ESR1 rs2234693. Rs8175347 was significantly associated with postmenopausal levels of estradiol, free estradiol and estrone and rs6259 with SHBG and estradiol.\n\nOur findings support an association between genetic variants in CYP19, and possibly PGR, and risk of endometrial cancer.", "doi": "10.1016/j.canep.2012.04.006", "pmid": "22633539", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S1877-7821(12)00059-8"}, {"db": "pmc", "key": "PMC3663487"}, {"db": "mid", "key": "NIHMS380895"}], "notes": [], "created": "2017-05-04T15:00:55.632Z", "modified": "2020-01-21T13:56:01.833Z"}, {"entity": "publication", "iuid": "f19861f2021c485c8460562c82beb902", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f19861f2021c485c8460562c82beb902.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f19861f2021c485c8460562c82beb902"}}, "title": "MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs.", "authors": [{"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "18", "issn": "1469-9001", "issue": "10", "pages": "1771-1782", "title": "RNA", "issn-l": "1355-8382"}, "abstract": "The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.", "doi": "10.1261/rna.033175.112", "pmid": "22875808", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "rna.033175.112"}, {"db": "pmc", "key": "PMC3446702"}], "notes": [], "created": "2017-05-04T14:57:45.715Z", "modified": "2020-01-21T13:56:10.526Z"}, {"entity": "publication", "iuid": "0edbe032b8224c3792b76ee929764468", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0edbe032b8224c3792b76ee929764468.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0edbe032b8224c3792b76ee929764468"}}, "title": "Mapping QTL affecting a systemic sclerosis-like disorder in a cross between UCD-200 and red jungle fowl chickens.", "authors": [{"family": "Ek", "given": "Weronica", "initials": "W"}, {"family": "Sahlqvist", "given": "Anna-Stina", "initials": "AS"}, {"family": "Crooks", "given": "Lucy", "initials": "L"}, {"family": "Sgonc", "given": "Roswitha", "initials": "R"}, {"family": "Dietrich", "given": "Hermann", "initials": "H"}, {"family": "Wick", "given": "Georg", "initials": "G"}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Kerje", "given": "Susanne", "initials": "S", "orcid": "0000-0002-2944-9288", "researcher": {"href": "https://publications.scilifelab.se/researcher/078ca525f2cc4a68a430f2655e45efce.json"}}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "38", "issn": "1879-0089", "issue": "2", "pages": "352-359", "title": "Dev. Comp. Immunol.", "issn-l": "0145-305X"}, "abstract": "Systemic sclerosis (SSc) or scleroderma is a rare, autoimmune, multi-factorial disease characterized by early microvascular alterations, inflammation, and fibrosis. Chickens from the UCD-200 line develop a hereditary SSc-like disease, showing all the hallmarks of the human disorder, which makes this line a promising model to study genetic factors underlying the disease. A backcross was generated between UCD-200 chickens and its wild ancestor - the red jungle fowl and a genome-scan was performed to identify loci affecting early (21 days of age) and late (175 days of age) ischemic lesions of the comb. A significant difference in frequency of disease was observed between sexes in the BC population, where the homogametic males were more affected than females, and there was evidence for a protective W chromosome effect. Three suggestive disease predisposing loci were mapped to chromosomes 2, 12 and 14. Three orthologues of genes implicated in human SSc are located in the QTL region on chromosome 2, TGFRB1, EXOC2-IRF4 and COL1A2, as well as CCR8, which is more generally related to immune function. IGFBP3 is also located within the QTL on chromosome 2 and earlier studies have showed increased IGFBP3 serum levels in SSc patients. To our knowledge, this study is the first to reveal a potential genetic association between IGFBP3 and SSc. Another gene with an immunological function, SOCS1, is located in the QTL region on chromosome 14. These results illustrate the usefulness of the UCD-200 chicken as a model of human SSc and motivate further in-depth functional studies of the implicated candidate genes.", "doi": "10.1016/j.dci.2012.06.006", "pmid": "22796227", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0145-305X(12)00134-6"}], "notes": [], "created": "2017-05-04T15:00:56.573Z", "modified": "2021-07-07T15:26:06.496Z"}, {"entity": "publication", "iuid": "8b71d3a19f64447c9276a24ac68c8035", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b71d3a19f64447c9276a24ac68c8035.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b71d3a19f64447c9276a24ac68c8035"}}, "title": "Lack of association between the regulator of G-protein signaling 4 (RGS4) rs951436 polymorphism and schizophrenia.", "authors": [{"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Nyholm", "given": "Helena", "initials": "H"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Skj\u00f8dt", "given": "Celina", "initials": "C"}, {"family": "Thygesen", "given": "Johan H", "initials": "JH"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Hall", "given": "H\u00e5kan", "initials": "H"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Terenius", "given": "Lars", "initials": "L"}], "type": "letter", "published": "2012-10-00", "journal": {"volume": "22", "issn": "1473-5873", "issue": "5", "pages": "263-264", "title": "Psychiatr. Genet.", "issn-l": "0955-8829"}, "abstract": null, "doi": "10.1097/YPG.0b013e32834f3558", "pmid": "22157635", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:12.425Z", "modified": "2020-01-21T13:56:03.603Z"}, {"entity": "publication", "iuid": "1072983f8b93466785ba4465cb7e7555", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1072983f8b93466785ba4465cb7e7555.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1072983f8b93466785ba4465cb7e7555"}}, "title": "High-resolution insights into binding of unfolded polypeptides by the PPIase chaperone SlpA.", "authors": [{"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "26", "issn": "1530-6860", "issue": "10", "pages": "4003-4013", "title": "FASEB J.", "issn-l": "0892-6638"}, "abstract": "SlpA is a 2-domain protein consisting of an FK506-binding protein (FKBP) domain that harbors the peptidyl-prolyl cis/trans-isomerase (PPIase) active site and a small insert-in-flap (IF) domain that endows the protein with chaperone activity. We have determined the structure of SlpA from Escherichia coli at 1.35-\u00c5 resolution. The overall structure is similar to other known structures of the FKBP-IF subfamily. However, by serendipity, the linker region of the purification tag binds in the chaperone binding groove of the IF domain, making this the first structure of an FKBP-IF protein in complex with a mimic of an unfolded chaperone substrate. The linker binds by \u03b2-sheet augmentation, thus completing the incomplete \u03b2 barrel of the IF domain and shielding a considerable hydrophobic surface area from the solvent. Interestingly, a proline residue in trans configuration appears to be specifically recognized in a small pocket within the binding groove. Hence, the IF domain can preselect and prealign substrates with proline residues, which may explain how it enhances the catalytic efficiency and modulates the specificity of the FKBP domain in addition to its chaperone function. Based on pulldown results, we suggest that SlpA is likely to be involved in ribosome assembly.", "doi": "10.1096/fj.12-208397", "pmid": "22735173", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "fj.12-208397"}, {"db": "PDB", "description": "Crystal structure of the PPIase-chaperone SlpA with the chaperone binding site occupied by the linker of the purification tag", "key": "4DT4"}], "notes": [], "created": "2017-05-04T15:03:44.941Z", "modified": "2018-11-14T16:48:21.324Z"}, {"entity": "publication", "iuid": "b3810b588dc44c6d844d91549e756a3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3810b588dc44c6d844d91549e756a3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3810b588dc44c6d844d91549e756a3b"}}, "title": "Genetic variation in Puccinia graminis collected from oats, rye, and barberry.", "authors": [{"family": "Berlin", "given": "Anna", "initials": "A"}, {"family": "Djurle", "given": "Annika", "initials": "A"}, {"family": "Samils", "given": "Berit", "initials": "B"}, {"family": "Yuen", "given": "Jonathan", "initials": "J"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "102", "issn": "0031-949X", "issue": "10", "pages": "1006-1012", "title": "Phytopathology", "issn-l": null}, "abstract": "Puccinia graminis, the causal agent of stem rust, was collected from its alternate host barberry (Berberis spp.) and two different uredinial hosts, oats (Avena sativa) and rye (Secale cereale). The samples were analyzed using 11 polymorphic simple sequence repeat (SSR) markers. There were large differences between fungal populations on oats (P. graminis f. sp. avenae) and rye (P. graminis f. sp. secalis), and the genetic variation within the different formae speciales was also high. It was possible to distinguish between the two formae speciales on barberry. Additional genotypic groups not present in the field samples from oats and rye were also identified on barberry. Our results confirm the importance of barberry in maintaining the populations of P. graminis in Sweden and the importance of the sexual stage for the survival of the pathogen.", "doi": "10.1094/PHYTO-03-12-0041-R", "pmid": "22734559", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:40.560Z", "modified": "2020-01-21T13:56:10.455Z"}, {"entity": "publication", "iuid": "c67d9089e33d40b9aac44fbafaebc131", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c67d9089e33d40b9aac44fbafaebc131.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c67d9089e33d40b9aac44fbafaebc131"}}, "title": "Evaluating the effectiveness of clinical medical librarian programs: a systematic review of the literature. J Med Libr Assoc 92(1) January 2004.", "authors": [{"family": "Wagner", "given": "Kay Cimpl", "initials": "KC"}, {"family": "Byrd", "given": "Gary D", "initials": "GD"}], "type": "journal article", "published": "2012-10-00", "journal": {"title": "J Med Libr Assoc", "issn": "1558-9439", "volume": "100", "issue": "4 Suppl", "pages": "J", "issn-l": null}, "abstract": "Objective: This study was undertaken to determine if a systematic review of the evidence from thirty years of literature evaluating clinical medical librarian (CML) programs could help clarify the effectiveness of this outreach service model. Methods: A descriptive review of the CML literature describes the general characteristics of these services as they have been implemented, primarily in teaching-hospital settings. Comprehensive searches for CML studies using quantitative or qualitative evaluation methods were conducted in the medical, allied health, librarianship, and social sciences literature. Findings: Thirty-five studies published between 1974 and 2001 met the review criteria. Most (30) evaluated single, active programs and used descriptive research methods (e.g., use statistics or surveys/ questionnaires). A weighted average of 89% of users in twelve studies found CML services useful and of high quality, and 65% of users in another overlapping, but not identical, twelve studies said these services contributed to improved patient care. Conclusions: The total amount of research evidence for CML program effectiveness is not great and most of it is descriptive rather than comparative or analytically qualitative. Standards are needed to consistently evaluate CML or informationist programs in the future. A carefully structured multiprogram study including three to five of the best current programs is needed to define the true value of these services.", "doi": null, "pmid": "23509432", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC3571670"}, {"db": "sici", "key": "i1536-5050-92-1-14"}], "notes": [], "created": "2023-06-01T06:57:43.092Z", "modified": "2023-06-01T06:57:43.096Z"}, {"entity": "publication", "iuid": "2bbe0fe4a34842559adbcfa051baa28a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bbe0fe4a34842559adbcfa051baa28a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bbe0fe4a34842559adbcfa051baa28a"}}, "title": "D-amino acid oxidase activator gene (DAOA) variation affects cerebrospinal fluid homovanillic acid concentrations in healthy Caucasians.", "authors": [{"family": "Andreou", "given": "Dimitrios", "initials": "D"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Sedvall", "given": "G\u00f6ran C", "initials": "GC"}, {"family": "Hall", "given": "H\u00e5kan", "initials": "H"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "262", "issn": "1433-8491", "issue": "7", "pages": "549-556", "title": "Eur Arch Psychiatry Clin Neurosci", "issn-l": "0940-1334"}, "abstract": "The D-amino acid oxidase activator (DAOA) protein regulates the function of D-amino oxidase (DAO), an enzyme that catalyzes the oxidative deamination of D-3,4-dihydroxyphenylalanine (D-DOPA) and D-serine. D-DOPA is converted to L-3,4-DOPA, a precursor of dopamine, whereas D-serine participates in glutamatergic transmission. We hypothesized that DAOA polymorphisms are associated with dopamine, serotonin and noradrenaline turnover in the human brain. Four single-nucleotide polymorphisms, previously reported to be associated with schizophrenia, were genotyped. Cerebrospinal fluid (CSF) samples were drawn by lumbar puncture, and the concentrations of the major dopamine metabolite homovanillic acid (HVA), the major serotonin metabolite 5-hydroxyindoleacetic acid (5-HIAA) and the major noradrenaline metabolite 3-methoxy-4-hydroxyphenylglycol (MHPG) were measured. Two of the investigated polymorphisms, rs3918342 and rs1421292, were significantly associated with CSF HVA concentrations. Rs3918342 was found to be nominally associated with CSF 5-HIAA concentrations. None of the polymorphisms were significantly associated with MHPG concentrations. Our results indicate that DAOA gene variation affects dopamine turnover in healthy individuals, suggesting that disturbed dopamine turnover is a possible mechanism behind the observed associations between genetic variation in DAOA and behavioral phenotypes in humans.", "doi": "10.1007/s00406-012-0313-z", "pmid": "22454242", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3464385"}], "notes": [], "created": "2017-05-04T15:00:58.151Z", "modified": "2020-01-21T13:56:01.239Z"}, {"entity": "publication", "iuid": "203794e7c78d43e991933db58e49f6d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/203794e7c78d43e991933db58e49f6d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/203794e7c78d43e991933db58e49f6d5"}}, "title": "Consistent mutation status within histologically heterogeneous lung cancer lesions.", "authors": [{"family": "Mattsson", "given": "Johanna Sofia Margareta", "initials": "JS"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "61", "issn": "1365-2559", "issue": "4", "pages": "744-748", "title": "Histopathology", "issn-l": "0309-0167"}, "abstract": "Activating epidermal growth factor receptor (EGFR) and KRAS mutations characterize molecular subgroups of non-small-cell lung cancer (NSCLC) with a strong predictive value for response to EGFR inhibitor therapy. However, the temporal occurrence and clonal stability of these mutations during the course of cancer progression are debated. The aim of this study was to characterize the presence of EGFR and KRAS mutations in histologically different areas of primary NSCLC lesions.\n\nFormalin-fixed paraffin-embedded cancer specimens from six cases with EGFR mutations and five cases with KRAS mutations were selected from a pool of primary resected NSCLC patients. From each tumour, three morphologically distinct areas were manually microdissected and analysed for the presence of mutations. The results demonstrated consistent EGFR and KRAS mutation status in the different histological areas of all primary tumours.\n\nThe results support the concept that activating EGFR and KRAS mutations are oncogenic events that are consistently present throughout the primary tumour independently of histological heterogeneity. Thus, for molecular diagnostics, any part of the tumour is likely to be representative for EGFR and KRAS mutation testing.", "doi": "10.1111/j.1365-2559.2012.04245.x", "pmid": "22458769", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:51.165Z", "modified": "2017-05-30T12:52:02.512Z"}, {"entity": "publication", "iuid": "42070e69ed294acf80bae18014583638", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42070e69ed294acf80bae18014583638.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42070e69ed294acf80bae18014583638"}}, "title": "Chemosensory proteins, major salivary factors in caterpillar mandibular glands.", "authors": [{"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "Mde L"}, {"family": "Sundmalm", "given": "Sara M", "initials": "SM"}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}, {"family": "Ytterberg", "given": "A Jimmy", "initials": "AJ"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Janz", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2012-10-00", "journal": {"volume": "42", "issn": "1879-0240", "issue": "10", "pages": "796-805", "title": "Insect Biochem. Mol. Biol.", "issn-l": "0965-1748"}, "abstract": "Research in the field of insect-host plant interactions has indicated that constituents of insect saliva play an important role in digestion and affect host chemical defense responses. However, most efforts have focused on studying the composition and function of regurgitant or saliva produced in the labial glands. Acknowledging the need for understanding the role of the mandibular glands in herbivory, we sought to make a qualitative and semi-quantitative comparison of soluble luminal protein fractions between mandibular and labial glands of Vanessa gonerilla butterfly larvae. Amylase and lysozyme were inspected as possible major enzymatic activities in the mandibular glands aiding in pre-digestion and antimicrobial defense. Although detected, neither of these enzymatic activities was prominent in the luminal protein preparation of a particular type of gland. Proteins isolated from the glands were identified by mass spectrometry and by searching an EST-library database generated for four other nymphalid butterfly species, in addition to the public NCBI database. The identified proteins were also quantified from the data using \"Quanty\", an in-house program. The proteomic analysis detected chemosensory proteins as the most abundant luminal proteins in the mandibular glands. In comparison to these proteins, the relative amounts of amylase and lysozyme were much lower in both gland types. Therefore, we speculate that the primary role of the mandibular glands in Lepidopteran larvae is chemoreception which may include the detection of microorganisms on plant surfaces, host plant recognition and communication with conspecifics.", "doi": "10.1016/j.ibmb.2012.07.008", "pmid": "22885177", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pii", "key": "S0965-1748(12)00097-5"}], "notes": [], "created": "2017-05-04T15:02:42.769Z", "modified": "2021-07-08T08:58:46.759Z"}, {"entity": "publication", "iuid": "cf3147fb7dd441a683f167b38270fb8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf3147fb7dd441a683f167b38270fb8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf3147fb7dd441a683f167b38270fb8d"}}, "title": "A suggestion to the medical librarians. 1920.", "authors": [{"family": "Smith", "given": "Laura E", "initials": "LE"}], "type": "biography", "published": "2012-10-00", "journal": {"title": "J Med Libr Assoc", "issn": "1558-9439", "volume": "100", "issue": "4 Suppl", "pages": "B", "issn-l": null}, "abstract": null, "doi": null, "pmid": "23509424", "labels": {"Clinical Genomics": "Service", "Clinical Genomics \u00d6rebro": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC3571666"}, {"db": "sici", "key": "i1536-5050-100-4s-30"}], "notes": [], "created": "2025-11-19T15:13:42.127Z", "modified": "2025-11-19T15:14:49.894Z"}, {"entity": "publication", "iuid": "f51ca77cdbe64ad19435f4e55f6cac26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f51ca77cdbe64ad19435f4e55f6cac26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f51ca77cdbe64ad19435f4e55f6cac26"}}, "title": "On the roles and regulation of chondroitin sulfate and heparan sulfate in zebrafish pharyngeal cartilage morphogenesis.", "authors": [{"family": "Holmborn", "given": "Katarina", "initials": "K"}, {"family": "Habicher", "given": "Judith", "initials": "J"}, {"family": "Kasza", "given": "Zsolt", "initials": "Z"}, {"family": "Eriksson", "given": "Anna S", "initials": "AS"}, {"family": "Filipek-Gorniok", "given": "Beata", "initials": "B", "orcid": "0000-0002-6757-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f0b7b3e0b045f082d2aff1dd23ec0e.json"}}, {"family": "Gopal", "given": "Sandeep", "initials": "S"}, {"family": "Couchman", "given": "John R", "initials": "JR"}, {"family": "Ahlberg", "given": "Per E", "initials": "PE"}, {"family": "Wiweger", "given": "Malgorzata", "initials": "M"}, {"family": "Spillmann", "given": "Dorothe", "initials": "D"}, {"family": "Kreuger", "given": "Johan", "initials": "J"}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}], "type": "journal article", "published": "2012-09-28", "journal": {"volume": "287", "issn": "1083-351X", "issue": "40", "pages": "33905-33916", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The present study addresses the roles of heparan sulfate (HS) proteoglycans and chondroitin sulfate (CS) proteoglycans in the development of zebrafish pharyngeal cartilage structures. uxs1 and b3gat3 mutants, predicted to have impaired biosynthesis of both HS and CS because of defective formation of the common proteoglycan linkage tetrasaccharide were analyzed along with ext2 and extl3 mutants, predicted to have defective HS polymerization. Notably, the effects on HS and CS biosynthesis in the respective mutant strains were shown to differ from what had been hypothesized. In uxs1 and b3gat3 mutant larvae, biosynthesis of CS was shown to be virtually abolished, whereas these mutants still were capable of synthesizing 50% of the HS produced in control larvae. extl3 and ext2 mutants on the other hand were shown to synthesize reduced amounts of hypersulfated HS. Further, extl3 mutants produced higher levels of CS than control larvae, whereas morpholino-mediated suppression of csgalnact1/csgalnact2 resulted in increased HS biosynthesis. Thus, the balance of the Extl3 and Csgalnact1/Csgalnact2 proteins influences the HS/CS ratio. A characterization of the pharyngeal cartilage element morphologies in the single mutant strains, as well as in ext2;uxs1 double mutants, was conducted. A correlation between HS and CS production and phenotypes was found, such that impaired HS biosynthesis was shown to affect chondrocyte intercalation, whereas impaired CS biosynthesis inhibited formation of the extracellular matrix surrounding chondrocytes.", "doi": "10.1074/jbc.M112.401646", "pmid": "22869369", "labels": {"Genome Engineering Zebrafish": null}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)62888-5"}, {"db": "pmc", "key": "PMC3460485"}], "notes": [], "created": "2017-05-04T15:03:43.219Z", "modified": "2021-07-06T16:05:51.263Z"}, {"entity": "publication", "iuid": "9f43b71e36324575a326615b0bbc41a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f43b71e36324575a326615b0bbc41a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f43b71e36324575a326615b0bbc41a6"}}, "title": "Genome-wide and locus specific alterations in CDC73/HRPT2-mutated parathyroid tumors.", "authors": [{"family": "Sulaiman", "given": "Luqman", "initials": "L"}, {"family": "Haglund", "given": "Felix", "initials": "F"}, {"family": "Hashemi", "given": "Jamileh", "initials": "J"}, {"family": "Obara", "given": "Takao", "initials": "T"}, {"family": "Nordenstr\u00f6m", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC"}], "type": "journal article", "published": "2012-09-28", "journal": {"volume": "7", "issn": "1932-6203", "issue": "9", "pages": "e46325", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Mutations in the hyperparathyroidism type 2 (HRPT2/CDC73) gene and alterations in the parafibromin protein have been established in the majority of parathyroid carcinomas and in subsets of parathyroid adenomas. While it is known that CDC73-mutated parathyroid tumors display specific gene expression changes compared to CDC73 wild-type cases, the molecular cytogenetic profile in CDC73-mutated cases compared to unselected adenomas (with an expected very low frequency of CDC73 mutations) remains unknown. For this purpose, nine parathyroid tumors with established CDC73 gene inactivating mutations (three carcinomas, one atypical adenoma and five adenomas) were analyzed for copy number alterations and loss of heterozygosity using array-comparative genomic hybridization (a-CGH) and single nucleotide polymorphism (SNP) microarrays, respectively. Furthermore, CDC73 gene promoter methylation levels were assessed using bisulfite Pyrosequencing. The panel included seven tumors with single mutation and three with double mutations of the CDC73 gene. The carcinomas displayed copy number alterations in agreement with previous studies, whereas the CDC73-mutated adenomas did not display the same pattern of alterations at loci frequently deleted in unselected parathyroid tumors. Furthermore, gross losses of chromosomal material at 1p and 13 were significantly (p\u200a=\u200a0.012) associated with parathyroid carcinomas as opposed to adenomas. Quantitative PCR-based copy number loss regarding CDC73 was observed in three adenomas, while all the carcinomas were diploid or showed copy number gain for CDC73 gene. Hypermethylation of the CDC73 gene promoter was not observed. Our data could suggest that CDC73-mutated parathyroid adenomas exhibit a partly unique cytogenetic profile in addition to that of carcinomas and unselected adenomas. Furthermore, CDC73-mutated carcinomas displayed losses at 1p and 13 which are not seen in CDC73-mutated adenomas, making these regions of interest for further studies regarding malignant properties in tumors from CDC73-mutated cases. However, due to the small sample size, validation of the results in a larger cohort is warranted.", "doi": "10.1371/journal.pone.0046325", "pmid": "23029479", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-17703"}, {"db": "pmc", "key": "PMC3460869"}], "notes": [], "created": "2017-05-04T15:03:13.632Z", "modified": "2017-05-30T14:51:02.573Z"}, {"entity": "publication", "iuid": "ec5f7932f2b14a41b2fe9c78d368743f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec5f7932f2b14a41b2fe9c78d368743f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec5f7932f2b14a41b2fe9c78d368743f"}}, "title": "Gene expression profiles in paired gingival biopsies from periodontitis-affected and healthy tissues revealed by massively parallel sequencing.", "authors": [{"family": "Davanian", "given": "Haleh", "initials": "H"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "B\u00e5ge", "given": "Tove", "initials": "T"}, {"family": "Lagervall", "given": "Maria", "initials": "M"}, {"family": "Jansson", "given": "Leif", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2012-09-28", "journal": {"volume": "7", "issn": "1932-6203", "issue": "9", "pages": "e46440", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Periodontitis is a chronic inflammatory disease affecting the soft tissue and bone that surrounds the teeth. Despite extensive research, distinctive genes responsible for the disease have not been identified. The objective of this study was to elucidate transcriptome changes in periodontitis, by investigating gene expression profiles in gingival tissue obtained from periodontitis-affected and healthy gingiva from the same patient, using RNA-sequencing. Gingival biopsies were obtained from a disease-affected and a healthy site from each of 10 individuals diagnosed with periodontitis. Enrichment analysis performed among uniquely expressed genes for the periodontitis-affected and healthy tissues revealed several regulated pathways indicative of inflammation for the periodontitis-affected condition. Hierarchical clustering of the sequenced biopsies demonstrated clustering according to the degree of inflammation, as observed histologically in the biopsies, rather than clustering at the individual level. Among the top 50 upregulated genes in periodontitis-affected tissues, we investigated two genes which have not previously been demonstrated to be involved in periodontitis. These included interferon regulatory factor 4 and chemokine (C-C motif) ligand 18, which were also expressed at the protein level in gingival biopsies from patients with periodontitis. In conclusion, this study provides a first step towards a quantitative comprehensive insight into the transcriptome changes in periodontitis. We demonstrate for the first time site-specific local variation in gene expression profiles of periodontitis-affected and healthy tissues obtained from patients with periodontitis, using RNA-seq. Further, we have identified novel genes expressed in periodontitis tissues, which may constitute potential therapeutic targets for future treatment strategies of periodontitis.", "doi": "10.1371/journal.pone.0046440", "pmid": "23029519", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-17275"}, {"db": "pmc", "key": "PMC3460903"}], "notes": [], "created": "2017-05-04T14:57:43.000Z", "modified": "2021-07-08T13:26:08.387Z"}, {"entity": "publication", "iuid": "c5b9166df38348bba44240b73c6168ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5b9166df38348bba44240b73c6168ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5b9166df38348bba44240b73c6168ae"}}, "title": "Microscopic particles in two fractions of fresh cerebrospinal fluid in twins with schizophrenia or bipolar disorder and in healthy controls.", "authors": [{"family": "Johansson", "given": "Viktoria", "initials": "V"}, {"family": "Nybom", "given": "Rolf", "initials": "R"}, {"family": "Wetterberg", "given": "Lennart", "initials": "L"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Cannon", "given": "Tyrone D", "initials": "TD"}, {"family": "Johansson", "given": "Anette G M", "initials": "AG"}, {"family": "Ekman", "given": "Carl Johan", "initials": "CJ"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2012-09-25", "journal": {"volume": "7", "issn": "1932-6203", "issue": "9", "pages": "e45994", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Using scanning electron microscopy, microscopic structures have been identified in fresh cerebrospinal fluid (CSF) in patients with schizophrenia and bipolar disorder, but only rarely in control subjects. However, it has not been determined whether these microscopic particles represent state or trait markers, i.e. if their presence is related to clinical manifestations of the disease or if they also can be found in as yet asymptomatic individuals with a genetic liability. This question can be addressed by studying twins discordant or concordant for schizophrenia or bipolar disorder.\n\nWe investigated microscopic structures in CSF in 102 individuals: 21 monozygotic and 16 dizygotic twins affected or not affected with schizophrenia, schizoaffective disorder or bipolar disorder and in 65 healthy singleton controls. A first and a second fraction of CSF was freshly applied on filters and examined by scanning electron microscopy technique. Spherical particles with lipid appearance averaging between 0.1 to 8.0 \u00b5m in diameter were detected in the center of the filter as well as located in the margins of larger aggregates binding in a viscous state. Structures were found in 12 of 17 probands, 5 of 12 healthy co-twins and 3 of 73 healthy controls. Thus, a positive microscopic finding significantly increased the likelihood of belonging to the proband group (OR=48, 95% CL: 8.2-550, p<0.0001) and the co-twin-group (OR=16, 95% CL: 2.0-218, p=0.006). Age, sex, history of alcohol abuse or anxiety syndrome, somatic disorder and markers of acute inflammatory activity did not account for group differences; nor did exposure to psychotropic medication.\n\nPresence of microscopic particles in CSF may possibly reflect trait dependent genetic or environmental vulnerability in patients with schizophrenia, schizoaffective disorder or bipolar disorder.", "doi": "10.1371/journal.pone.0045994", "pmid": "23049916", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-13597"}, {"db": "pmc", "key": "PMC3457946"}], "notes": [], "created": "2017-05-04T15:03:34.994Z", "modified": "2017-05-30T14:52:41.419Z"}, {"entity": "publication", "iuid": "b0c867e7f2f34e78939fd064ec6fe602", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c867e7f2f34e78939fd064ec6fe602.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c867e7f2f34e78939fd064ec6fe602"}}, "title": "Elevated MARK2-dependent phosphorylation of Tau in Alzheimer's disease.", "authors": [{"family": "Gu", "given": "Gucci Jijuan", "initials": "GJ"}, {"family": "Wu", "given": "Di", "initials": "D"}, {"family": "Lund", "given": "Harald", "initials": "H"}, {"family": "Sunnemark", "given": "Dan", "initials": "D"}, {"family": "Kvist", "given": "Alexander J", "initials": "AJ"}, {"family": "Milner", "given": "Roy", "initials": "R"}, {"family": "Eckersley", "given": "Sonia", "initials": "S"}, {"family": "Nilsson", "given": "Lars N G", "initials": "LN"}, {"family": "Agerman", "given": "Karin", "initials": "K"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2012-09-25", "journal": {"volume": "33", "issn": "1875-8908", "issue": "3", "pages": "699-713", "title": "J. Alzheimers Dis.", "issn-l": "1387-2877"}, "abstract": "The appearance of neurofibrillary tangles (NFT), one of the major hallmarks of Alzheimer's disease (AD), is most likely caused by inappropriate phosphorylation and/or dephosphorylation of tau, eventually leading to the accumulation of NFTs. Enhanced phosphorylation of tau on Ser(262) is detected early in the course of the disease and may have a role in the formation of tangles. Several kinases such as microtubule-affinity regulating kinase (MARK), protein kinase A, calcium calmodulin kinase II, and checkpoint kinase 2 are known to phosphorylate tau on Ser(262) in vitro. In this study, we took advantage of the in situ proximity ligation assay to investigate the role of MARK2, one of the four MARK isoforms, in AD. We demonstrate that MARK2 interacts with tau and phosphorylates tau at Ser(262) in stably transfected NIH/3T3 cells expressing human recombinant tau. Staurosporine, a protein kinase inhibitor, significantly reduced the interaction between MARK2 and tau, and also phosphorylation of tau at Ser(262). Furthermore, we observed elevated interactions between MARK2 and tau in post-mortem human AD brains, compared to samples from non-demented elderly controls. Our results from transfected cells demonstrate a specific interaction between MARK2 and tau, as well as MARK2-dependent phosphorylation of tau at Ser(262). Furthermore, the elevated interactions between MARK2 and tau in AD brain sections suggests that MARK2 may play an important role in early phosphorylation of tau in AD, possibly qualifying as a therapeutic target for intervention to prevent disease progression.", "doi": "10.3233/JAD-2012-121357", "pmid": "23001711", "labels": {"Clinical Biomarkers": "", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "C06R73LN268U5222"}], "notes": [], "created": "2017-05-04T14:55:24.349Z", "modified": "2023-04-14T13:56:30.059Z"}, {"entity": "publication", "iuid": "754ed0ecba204bbab89683565893e3ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/754ed0ecba204bbab89683565893e3ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/754ed0ecba204bbab89683565893e3ab"}}, "title": "Comprehensive exploration of the effects of miRNA SNPs on monocyte gene expression.", "authors": [{"family": "Greliche", "given": "Nicolas", "initials": "N"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Rotival", "given": "Maxime", "initials": "M"}, {"family": "Schillert", "given": "Arne", "initials": "A"}, {"family": "Ziegler", "given": "Andreas", "initials": "A"}, {"family": "Cardiogenics Consortium", "given": null, "initials": null}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Munzel", "given": "Thomas", "initials": "T"}, {"family": "Lackner", "given": "Karl J", "initials": "KJ"}, {"family": "Cambien", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Tiret", "given": "Laurence", "initials": "L"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA"}], "type": "journal article", "published": "2012-09-21", "journal": {"volume": "7", "issn": "1932-6203", "issue": "9", "pages": "e45863", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "We aimed to assess whether pri-miRNA SNPs (miSNPs) could influence monocyte gene expression, either through marginal association or by interacting with polymorphisms located in 3'UTR regions (3utrSNPs). We then conducted a genome-wide search for marginal miSNPs effects and pairwise miSNPs \u00d7 3utrSNPs interactions in a sample of 1,467 individuals for which genome-wide monocyte expression and genotype data were available. Statistical associations that survived multiple testing correction were tested for replication in an independent sample of 758 individuals with both monocyte gene expression and genotype data. In both studies, the hsa-mir-1279 rs1463335 was found to modulate in cis the expression of LYZ and in trans the expression of CNTN6, CTRC, COPZ2, KRT9, LRRFIP1, NOD1, PCDHA6, ST5 and TRAF3IP2 genes, supporting the role of hsa-mir-1279 as a regulator of several genes in monocytes. In addition, we identified two robust miSNPs \u00d7 3utrSNPs interactions, one involving HLA-DPB1 rs1042448 and hsa-mir-219-1 rs107822, the second the H1F0 rs1894644 and hsa-mir-659 rs5750504, modulating the expression of the associated genes.As some of the aforementioned genes have previously been reported to reside at disease-associated loci, our findings provide novel arguments supporting the hypothesis that the genetic variability of miRNAs could also contribute to the susceptibility to human diseases.", "doi": "10.1371/journal.pone.0045863", "pmid": "23029284", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-13025"}, {"db": "pmc", "key": "PMC3448685"}], "notes": [], "created": "2017-05-04T15:01:10.489Z", "modified": "2020-01-21T13:56:03.043Z"}, {"entity": "publication", "iuid": "60af987d1dab4b67b147feb04b723afe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60af987d1dab4b67b147feb04b723afe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60af987d1dab4b67b147feb04b723afe"}}, "title": "Role of sepsis in the development of limb muscle weakness in a porcine intensive care unit model.", "authors": [{"family": "Aare", "given": "Sudhakar", "initials": "S"}, {"family": "Radell", "given": "Peter", "initials": "P"}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}, {"family": "Chen", "given": "Yi-Wen", "initials": "YW"}, {"family": "Hoffman", "given": "Eric P", "initials": "EP"}, {"family": "Larsson", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2012-09-18", "journal": {"volume": "44", "issn": "1531-2267", "issue": "18", "pages": "865-877", "title": "Physiol. Genomics", "issn-l": "1094-8341"}, "abstract": "Severe muscle wasting and loss of muscle function in critically ill mechanically ventilated intensive care unit (ICU) patients have significant negative consequences on their recovery and rehabilitation that persist long after their hospital discharge; moreover, the underlying mechanisms are unclear. Mechanical ventilation (MV) and immobilization-induced modifications play an important role in these consequences, including endotoxin-induced sepsis. The present study aims to investigate how sepsis aggravates ventilator and immobilization-related limb muscle dysfunction. Hence, biceps femoris muscle gene expression was investigated in pigs exposed to ICU intervention, i.e., immobilization, sedation, and MV, alone or in combination with sepsis, for 5 days. In previous studies, we have shown that ICU intervention alone or in combination with sepsis did not affect muscle fiber size on day 5, but a significant decrease was observed in single fiber maximal force normalized to cross-sectional area (specific force) when sepsis was added to the ICU intervention. According to microarray data, the addition of sepsis to the ICU intervention induced a deregulation of > 500 genes, such as an increased expression of genes involved in chemokine activity, kinase activity, and transcriptional regulation. Genes involved in the regulation of the oxidative stress response and cytoskeletal/sarcomeric and heat shock proteins were on the other hand downregulated when sepsis was added to the ICU intervention. Thus, sepsis has a significant negative effect on muscle function in critically ill ICU patients, and chemokine activity and heat shock protein genes are forwarded to play an instrumental role in this specific muscle wasting condition.", "doi": "10.1152/physiolgenomics.00031.2012", "pmid": "22851759", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "physiolgenomics.00031.2012"}], "notes": [], "created": "2017-05-04T15:03:00.265Z", "modified": "2017-05-30T12:37:41.547Z"}, {"entity": "publication", "iuid": "fb17b979742c40ea9a8bf301f79059ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb17b979742c40ea9a8bf301f79059ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb17b979742c40ea9a8bf301f79059ca"}}, "title": "Molecular tools for companion diagnostics.", "authors": [{"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Grannas", "given": "Karin", "initials": "K"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Gullberg", "given": "Mats", "initials": "M"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2012-09-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "6", "pages": "634-640", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "The heterogeneous nature of cancer results in highly variable therapeutic responses even among patients with identical stages and grades of a malignancy. The move towards personalised medicine in cancer therapy has therefore been motivated by a need to customise therapy according to molecular features of individual tumours. Companion diagnostics serves to support early drug development, it can provide surrogate markers in clinical trials, and also guide selection of individual therapies and monitoring of responses in routine clinical care. The era of companion diagnostics can be said to have begun with the introduction of the HercepTest - a first-of-a-kind diagnostic tool developed by DakoCytomation in 1998 to select patients for therapy with the anticancer drug Herceptin (trastuzumab). Herceptin and the paired test proved that companion diagnostics can help guide patient-tailored therapies. We will discuss herein technologies to analyse companion diagnostics markers at the level of DNA, RNA or protein, focusing on a series of methods developed in our laboratory that can facilitate drug development and help stratify patients for therapy.", "doi": "10.1016/j.nbt.2012.05.004", "pmid": "22634023", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(12)00088-X"}], "notes": [], "created": "2017-05-04T14:55:23.461Z", "modified": "2023-04-14T13:56:30.201Z"}, {"entity": "publication", "iuid": "2fdedc5402bb4246846cf6da7baf1e53", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fdedc5402bb4246846cf6da7baf1e53.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fdedc5402bb4246846cf6da7baf1e53"}}, "title": "Catalytic convergence of manganese and iron lipoxygenases by replacement of a single amino acid.", "authors": [{"family": "Wennman", "given": "Anneli", "initials": "A"}, {"family": "Jerner\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Hamberg", "given": "Mats", "initials": "M"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "journal article", "published": "2012-09-14", "journal": {"volume": "287", "issn": "1083-351X", "issue": "38", "pages": "31757-31765", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Lipoxygenases (LOXs) contain a hydrophobic substrate channel with the conserved Gly/Ala determinant of regio- and stereospecificity and a conserved Leu residue near the catalytic non-heme iron. Our goal was to study the importance of this region (Gly(332), Leu(336), and Phe(337)) of a lipoxygenase with catalytic manganese (13R-MnLOX). Recombinant 13R-MnLOX oxidizes 18:2n-6 and 18:3n-3 to 13R-, 11(S or R)-, and 9S-hydroperoxy metabolites (\u223c80-85, 15-20, and 2-3%, respectively) by suprafacial hydrogen abstraction and oxygenation. Replacement of Phe(337) with Ile changed the stereochemistry of the 13-hydroperoxy metabolites of 18:2n-6 and 18:3n-3 (from \u223c100% R to 69-74% S) with little effect on regiospecificity. The abstraction of the pro-S hydrogen of 18:2n-6 was retained, suggesting antarafacial hydrogen abstraction and oxygenation. Replacement of Leu(336) with smaller hydrophobic residues (Val, Ala, and Gly) shifted the oxygenation from C-13 toward C-9 with formation of 9S- and 9R-hydroperoxy metabolites of 18:2n-6 and 18:3n-3. Replacement of Gly(332) and Leu(336) with larger hydrophobic residues (G332A and L336F) selectively augmented dehydration of 13R-hydroperoxyoctadeca-9Z,11E,15Z-trienoic acid and increased the oxidation at C-13 of 18:1n-6. We conclude that hydrophobic replacements of Leu(336) can modify the hydroperoxide configurations at C-9 with little effect on the R configuration at C-13 of the 18:2n-6 and 18:3n-3 metabolites. Replacement of Phe(337) with Ile changed the stereospecific oxidation of 18:2n-6 and 18:3n-3 with formation of 13S-hydroperoxides by hydrogen abstraction and oxygenation in analogy with soybean LOX-1.", "doi": "10.1074/jbc.M112.364331", "pmid": "22822060", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "M112.364331"}, {"db": "pmc", "key": "PMC3442510"}], "notes": [], "created": "2017-05-04T14:57:36.883Z", "modified": "2020-01-21T13:56:10.330Z"}, {"entity": "publication", "iuid": "4e1fec29eb984ccabfd6ac098c12e8e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e1fec29eb984ccabfd6ac098c12e8e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e1fec29eb984ccabfd6ac098c12e8e7"}}, "title": "Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening", "authors": [{"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Ekblad", "given": "Torun", "initials": "T"}, {"family": "Lindgren", "given": "Anders E G", "initials": "AEG"}, {"family": "Thorsell", "given": "Ann Gerd", "initials": "AG"}, {"family": "Spjut", "given": "Sara", "initials": "S"}, {"family": "Uciechowska", "given": "Urszula", "initials": "U"}, {"family": "Niemiec", "given": "Moritz S", "initials": "MS"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}, {"family": "Weigelt", "given": "Johan", "initials": "J"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}, {"family": "Linusson", "given": "Anna", "initials": "A"}], "type": "journal-article", "published": "2012-09-13", "journal": {"volume": "55", "issn": "1520-4804", "issue": "17", "pages": "7706-7718", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": null, "doi": "10.1021/jm300746d", "pmid": "22823910", "labels": {"Protein Science Facility (PSF)": null, "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "PDB", "description": "Human ADP-RIBOSYLTRANSFERASE 7 (ARTD7/PARP15), CATALYTIC DOMAIN IN COMPLEX WITH STO1102", "key": "4F0E"}, {"db": "PDB", "description": "Human Artd8 (Parp14, Bal2) - catalytic domain in complex with inhibitor A16(Z)", "key": "4F1L"}, {"db": "PDB", "description": "Human Artd8 (Parp14, Bal2) - catalytic domain in complex with A16(E)", "key": "4F1Q"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:39.125Z", "modified": "2025-10-17T13:04:30.521Z"}, {"entity": "publication", "iuid": "71c62030cc0446d5b86aff2877a1836b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71c62030cc0446d5b86aff2877a1836b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71c62030cc0446d5b86aff2877a1836b"}}, "title": "Loss-of-heterozygosity on chromosome 19q in early-stage serous ovarian cancer is associated with recurrent disease.", "authors": [{"family": "Skirnisdottir", "given": "Ingiridur", "initials": "I"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Ryd\u00e5ker", "given": "Maria", "initials": "M"}, {"family": "Akerud", "given": "Helena", "initials": "H"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2012-09-12", "journal": {"volume": "12", "issn": "1471-2407", "issue": null, "pages": "407", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Ovarian cancer is a heterogeneous disease and prognosis for apparently similar cases of ovarian cancer varies. Recurrence of the disease in early stage (FIGO-stages I-II) serous ovarian cancer results in survival that is comparable to those with recurrent advanced-stage disease. The aim of this study was to investigate if there are specific genomic aberrations that may explain recurrence and clinical outcome.\n\nFifty-one women with early stage serous ovarian cancer were included in the study. DNA was extracted from formalin fixed samples containing tumor cells from ovarian tumors. Tumor samples from thirty-seven patients were analysed for allele-specific copy numbers using OncoScan single nucleotide polymorphism arrays from Affymetrix and the bioinformatic tool Tumor Aberration Prediction Suite. Genomic gains, losses, and loss-of-heterozygosity that associated with recurrent disease were identified.\n\nThe most significant differences (p\u2009<\u20090.01) in Loss-of-heterozygosity (LOH) were identified in two relatively small regions of chromosome 19; 8.0-8,8\u2009Mbp (19 genes) and 51.5-53.0\u2009Mbp (37 genes). Thus, 56 genes on chromosome 19 were potential candidate genes associated with clinical outcome. LOH at 19q (51-56\u2009Mbp) was associated with shorter disease-free survival and was an independent prognostic factor for survival in a multivariate Cox regression analysis. In particular LOH on chromosome 19q (51-56\u2009Mbp) was significantly (p\u2009<\u20090.01) associated with loss of TP53 function.\n\nThe results of our study indicate that presence of two aberrations in TP53 on 17p and LOH on 19q in early stage serous ovarian cancer is associated with recurrent disease. Further studies related to the findings of chromosomes 17 and 19 are needed to elucidate the molecular mechanism behind the recurring genomic aberrations and the poor clinical outcome.", "doi": "10.1186/1471-2407-12-407", "pmid": "22967087", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "1471-2407-12-407"}, {"db": "pmc", "key": "PMC3495882"}], "notes": [], "created": "2017-05-04T15:02:55.178Z", "modified": "2017-05-30T14:49:43.224Z"}, {"entity": "publication", "iuid": "9f3eac7955274b349e93cf9948fbee23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f3eac7955274b349e93cf9948fbee23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f3eac7955274b349e93cf9948fbee23"}}, "title": "GCH1-polymorphism and pain sensitivity among women with provoked vestibulodynia.", "authors": [{"family": "Heddini", "given": "Ulrika", "initials": "U"}, {"family": "Bohm-Starke", "given": "Nina", "initials": "N"}, {"family": "Gr\u00f6nbladh", "given": "Alfhild", "initials": "A"}, {"family": "Nyberg", "given": "Fred", "initials": "F"}, {"family": "Nilsson", "given": "Kent W", "initials": "KW"}, {"family": "Johannesson", "given": "Ulrika", "initials": "U"}], "type": "journal article", "published": "2012-09-12", "journal": {"volume": "8", "issn": "1744-8069", "issue": null, "pages": "68", "title": "Mol Pain", "issn-l": "1744-8069"}, "abstract": "Provoked vestibulodynia (PVD) is a pain disorder localized in the vestibular mucosa. It is the most common cause of dyspareunia among young women and it is associated with general pain hypersensitivity and other chronic pain conditions. Polymorphism in the guanosine triphosphate cyclohydrolase (GCH1) gene has been found to influence general pain sensitivity and the risk of developing a longstanding pain condition. The aim of this study was to investigate GCH1-polymorphism in women with PVD and healthy controls, in correlation to pain sensitivity.\r\n\r\nWe found no correlation between the previously defined pain-protective GCH1-SNP combination and the diagnosis of PVD. Nor any correlation with pain sensitivity measured as pressure pain thresholds on the arm, leg and in the vestibule, coital pain scored on a visual analog scale and prevalence of other bodily pain conditions among women with PVD (n\u2009=\u200998) and healthy controls (n\u2009=\u2009102). However, among patients with current treatment (n\u2009=\u200936), there was a significant interaction effect of GCH1-gene polymorphism and hormonal contraceptive (HC) therapy on coital pain (p\u2009=\u20090.04) as well as on pressure pain thresholds on the arm (p\u2009=\u20090.04). PVD patients carrying the specified SNP combination and using HCs had higher pain sensitivity compared to non-carriers. In non-HC-users, carriers had lower pain sensitivity.\r\n\r\nThe results of this study gave no support to the hypothesis that polymorphism in the GCH1-gene contributes to the etiology of PVD. However, among patients currently receiving treatment an interaction effect of the defined SNP combination and use of hormonal contraceptives on pain sensitivity was found. This finding offers a possible explanation to the clinically known fact that some PVD patients improve after cessation of hormonal contraceptives, indicating that PVD patients carrying the defined SNP combination of GCH1 would benefit from this intervention.", "doi": "10.1186/1744-8069-8-68", "pmid": "22971341", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1744-8069-8-68"}, {"db": "pmc", "key": "PMC3489821"}], "notes": [], "created": "2017-05-04T14:57:38.626Z", "modified": "2020-01-21T13:56:10.442Z"}, {"entity": "publication", "iuid": "fd5339728a92423293ad65afe5cbdb19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd5339728a92423293ad65afe5cbdb19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd5339728a92423293ad65afe5cbdb19"}}, "title": "Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function.", "authors": [{"family": "Kallberg", "given": "Yvonne", "initials": "Y"}, {"family": "Segerstolpe", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Lackmann", "given": "Fredrik", "initials": "F"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Wieslander", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2012-09-12", "journal": {"volume": "7", "issn": "1932-6203", "issue": "9", "pages": "e43786", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Ribosome biogenesis in eukaryotes requires coordinated folding and assembly of a pre-rRNA into sequential pre-rRNA-protein complexes in which chemical modifications and RNA cleavages occur. These processes require many small nucleolar RNAs (snoRNAs) and proteins. Rbm19/Mrd1 is one such protein that is built from multiple RNA-binding domains (RBDs). We find that Rbm19/Mrd1 with five RBDs is present in all branches of the eukaryotic phylogenetic tree, except in animals and Choanoflagellates, that instead have a version with six RBDs and Microsporidia which have a minimal Rbm19/Mrd1 protein with four RBDs. Rbm19/Mrd1 therefore evolved as a multi-RBD protein very early in eukaryotes. The linkers between the RBDs have conserved properties; they are disordered, except for linker 3, and position the RBDs at conserved relative distances from each other. All but one of the RBDs have conserved properties for RNA-binding and each RBD has a specific consensus sequence and a conserved position in the protein, suggesting a functionally important modular design. The patterns of evolutionary conservation provide information for experimental analyses of the function of Rbm19/Mrd1. In vivo mutational analysis confirmed that a highly conserved loop 5-\u03b24-strand in RBD6 is essential for function.", "doi": "10.1371/journal.pone.0043786", "pmid": "22984444", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-14217"}, {"db": "pmc", "key": "PMC3440411"}], "notes": [], "created": "2017-05-04T14:56:19.726Z", "modified": "2021-07-05T12:34:46.059Z"}, {"entity": "publication", "iuid": "5af2b1cc2957448da246fde20468dff6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5af2b1cc2957448da246fde20468dff6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5af2b1cc2957448da246fde20468dff6"}}, "title": "A tool to facilitate clinical biomarker studies--a tissue dictionary based on the Human Protein Atlas.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Wiking", "given": "Mikaela", "initials": "M"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-09-12", "journal": {"volume": "10", "issn": "1741-7015", "issue": null, "pages": "103", "title": "BMC Med", "issn-l": "1741-7015"}, "abstract": "The complexity of tissue and the alterations that distinguish normal from cancer remain a challenge for translating results from tumor biological studies into clinical medicine. This has generated an unmet need to exploit the findings from studies based on cell lines and model organisms to develop, validate and clinically apply novel diagnostic, prognostic and treatment predictive markers. As one step to meet this challenge, the Human Protein Atlas project has been set up to produce antibodies towards human protein targets corresponding to all human protein coding genes and to map protein expression in normal human tissues, cancer and cells. Here, we present a dictionary based on microscopy images created as an amendment to the Human Protein Atlas. The aim of the dictionary is to facilitate the interpretation and use of the image-based data available in the Human Protein Atlas, but also to serve as a tool for training and understanding tissue histology, pathology and cell biology. The dictionary contains three main parts, normal tissues, cancer tissues and cells, and is based on high-resolution images at different magnifications of full tissue sections stained with H & E. The cell atlas is centered on immunofluorescence and confocal microscopy images, using different color channels to highlight the organelle structure of a cell. Here, we explain how this dictionary can be used as a tool to aid clinicians and scientists in understanding the use of tissue histology and cancer pathology in diagnostics and biomarker studies.", "doi": "10.1186/1741-7015-10-103", "pmid": "22971420", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1741-7015-10-103"}, {"db": "pmc", "key": "PMC3523031"}], "notes": [], "created": "2017-05-04T14:55:09.873Z", "modified": "2021-07-08T13:44:33.290Z"}, {"entity": "publication", "iuid": "a27ba07d898841af81503f9d61dee5e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a27ba07d898841af81503f9d61dee5e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a27ba07d898841af81503f9d61dee5e4"}}, "title": "Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues.", "authors": [{"family": "Hasmats", "given": "Johanna", "initials": "J"}, {"family": "Kupershmidt", "given": "Ilya", "initials": "I"}, {"family": "Rodr\u00edguez-Antona", "given": "Cristina", "initials": "C"}, {"family": "Su", "given": "Qiaojuan Jane", "initials": "QJ"}, {"family": "Khan", "given": "Muhammad Suleman", "initials": "MS"}, {"family": "Jara", "given": "Carlos", "initials": "C"}, {"family": "Mielgo", "given": "Xabier", "initials": "X"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Green", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2012-09-10", "journal": {"volume": "506", "issn": "1879-0038", "issue": "1", "pages": "62-68", "title": "Gene", "issn-l": "0378-1119"}, "abstract": "The growing collection of publicly available high-throughput data provides an invaluable resource for generating preliminary in silico data in support of novel hypotheses. In this study we used a cross-dataset meta-analysis strategy to identify novel candidate genes and genetic variations relevant to paclitaxel/carboplatin-induced myelosuppression and neuropathy. We identified genes affected by drug exposure and present in tissues associated with toxicity. From ten top-ranked genes 42 non-synonymous single nucleotide polymorphisms (SNPs) were identified in silico and genotyped in 94 cancer patients treated with carboplatin/paclitaxel. We observed variations in 11 SNPs, of which seven were present in a sufficient frequency for statistical evaluation. Of these seven SNPs, three were present in ABCA1 and ATM, and showed significant or borderline significant association with either myelosuppression or neuropathy. The strikingly high number of associations between genotype and clinically observed toxicity provides support for our data-driven computations strategy to identify biomarkers for drug toxicity.", "doi": "10.1016/j.gene.2012.06.053", "pmid": "22759513", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0378-1119(12)00763-9"}], "notes": [], "created": "2017-05-04T14:57:34.566Z", "modified": "2021-07-08T13:26:08.268Z"}, {"entity": "publication", "iuid": "b659c386f09242aca02397820ed956c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b659c386f09242aca02397820ed956c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b659c386f09242aca02397820ed956c9"}}, "title": "Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Abarenkov", "given": "Kessy", "initials": "K"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Hartmann", "given": "Martin", "initials": "M"}, {"family": "Schoch", "given": "Conrad L", "initials": "CL"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}, {"family": "Porter", "given": "Teresita M", "initials": "TM"}, {"family": "Jumpponen", "given": "Ari", "initials": "A"}, {"family": "Vaishampayan", "given": "Parag", "initials": "P"}, {"family": "Ovaskainen", "given": "Otso", "initials": "O"}, {"family": "Hallenberg", "given": "Nils", "initials": "N"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Larsson", "given": "Karl Henrik", "initials": "KH"}, {"family": "Larsson", "given": "Ellen", "initials": "E"}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}], "type": "journal-article", "published": "2012-09-05", "journal": {"volume": "4", "issn": "1314-4049", "issue": null, "pages": "37-63", "title": "MycoKeys", "issn-l": null}, "abstract": null, "doi": "10.3897/mycokeys.4.3606", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:18.543Z", "modified": "2021-06-22T12:06:26.068Z"}, {"entity": "publication", "iuid": "29494054d8cb4115b87b74c2d166a6f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29494054d8cb4115b87b74c2d166a6f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29494054d8cb4115b87b74c2d166a6f2"}}, "title": "Improved gap size estimation for scaffolding algorithms.", "authors": [{"family": "Sahlin", "given": "Kristoffer", "initials": "K"}, {"family": "Street", "given": "Nathaniel", "initials": "N"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Arvestad", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2012-09-01", "journal": {"volume": "28", "issn": "1367-4811", "issue": "17", "pages": "2215-2222", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "One of the important steps of genome assembly is scaffolding, in which contigs are linked using information from read-pairs. Scaffolding provides estimates about the order, relative orientation and distance between contigs. We have found that contig distance estimates are generally strongly biased and based on false assumptions. Since erroneous distance estimates can mislead in subsequent analysis, it is important to provide unbiased estimation of contig distance.\n\nIn this article, we show that state-of-the-art programs for scaffolding are using an incorrect model of gap size estimation. We discuss why current maximum likelihood estimators are biased and describe what different cases of bias we are facing. Furthermore, we provide a model for the distribution of reads that span a gap and derive the maximum likelihood equation for the gap length. We motivate why this estimate is sound and show empirically that it outperforms gap estimators in popular scaffolding programs. Our results have consequences both for scaffolding software, structural variation detection and for library insert-size estimation as is commonly performed by read aligners.\n\nA reference implementation is provided at https://github.com/SciLifeLab/gapest.\n\nSupplementary data are availible at Bioinformatics online.", "doi": "10.1093/bioinformatics/bts441", "pmid": "22923455", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "bts441"}], "notes": [], "created": "2017-05-04T14:57:30.125Z", "modified": "2021-07-08T13:26:08.126Z"}, {"entity": "publication", "iuid": "8ac40d6bdf594ad68f2c6a1b5740ee67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ac40d6bdf594ad68f2c6a1b5740ee67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ac40d6bdf594ad68f2c6a1b5740ee67"}}, "title": "The evolution of filamin-a protein domain repeat perspective.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Sagit", "given": "Rauan", "initials": "R"}, {"family": "Ithychanda", "given": "Sujay S", "initials": "SS"}, {"family": "Qin", "given": "Jun", "initials": "J"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2012-09-00", "journal": {"volume": "179", "issn": "1095-8657", "issue": "3", "pages": "289-298", "title": "J. Struct. Biol.", "issn-l": "1047-8477"}, "abstract": "Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin \u03b23, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates.", "doi": "10.1016/j.jsb.2012.02.010", "pmid": "22414427", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1047-8477(12)00063-9"}, {"db": "pmc", "key": "PMC3728663"}, {"db": "mid", "key": "NIHMS470530"}], "notes": [], "created": "2017-05-04T14:56:17.274Z", "modified": "2020-01-21T13:53:20.651Z"}, {"entity": "publication", "iuid": "5bdc7539193a467f8a0341e810f73305", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bdc7539193a467f8a0341e810f73305.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bdc7539193a467f8a0341e810f73305"}}, "title": "Stepping stones in DNA sequencing.", "authors": [{"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2012-09-00", "journal": {"volume": "7", "issn": "1860-7314", "issue": "9", "pages": "1063-1073", "title": "Biotechnol J", "issn-l": "1860-6768"}, "abstract": "In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid technological advances have enormously expanded sequencing opportunities and applications, but also imposed strains and challenges on steps prior to sequencing and in the downstream process of handling and analysis of these massive amounts of sequence data. Traditionally, sequencing has been limited to small DNA fragments of approximately one thousand bases (derived from the organism's genome) due to issues in maintaining a high sequence quality and accuracy for longer read lengths. Although many technological breakthroughs have been made, currently the commercially available massively parallel sequencing methods have not been able to resolve this issue. However, recent announcements in nanopore sequencing hold the promise of removing this read-length limitation, enabling sequencing of larger intact DNA fragments. The ability to sequence longer intact DNA with high accuracy is a major stepping stone towards greatly simplifying the downstream analysis and increasing the power of sequencing compared to today. This review covers some of the technical advances in sequencing that have opened up new frontiers in genomics.", "doi": "10.1002/biot.201200153", "pmid": "22887891", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3472021"}], "notes": [], "created": "2017-05-04T14:57:30.422Z", "modified": "2021-07-08T13:26:08.190Z"}, {"entity": "publication", "iuid": "3e9d49562b634d1cad36e79e7c808957", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e9d49562b634d1cad36e79e7c808957.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e9d49562b634d1cad36e79e7c808957"}}, "title": "Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.", "authors": [{"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Voight", "given": "Benjamin F", 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"Boehnke", "given": "Michael", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium", "given": null, "initials": null}], "type": "journal article", "published": "2012-09-00", "journal": {"volume": "44", "issn": "1546-1718", "issue": "9", "pages": "981-990", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.", "doi": "10.1038/ng.2383", "pmid": "22885922", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2383"}, {"db": "pmc", "key": "PMC3442244"}, {"db": "mid", "key": "UKMS49214"}], "notes": [], "created": "2017-05-04T15:01:05.103Z", "modified": "2021-07-07T15:57:26.586Z"}, {"entity": "publication", "iuid": "1be58909f2c94e9eafec9ea12a96aa7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1be58909f2c94e9eafec9ea12a96aa7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1be58909f2c94e9eafec9ea12a96aa7c"}}, "title": "Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological 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"TV"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Oksa", "given": "Heikki", "initials": "H"}, {"family": "Antonella", "given": "Mulas", "initials": "M"}, {"family": "Nagaraja", "given": "Ramaiah", "initials": "R"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJ"}, {"family": "Kong", "given": "Augustine", "initials": "A"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Herder", "given": "Christian", "initials": "C"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Caulfield", "given": "Mark", "initials": "M"}, {"family": "Antti", "given": "Jula", "initials": "J"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Small", "given": "Kerrin", "initials": "K"}, {"family": "Miljkovic", "given": "Iva", "initials": "I"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Atalay", "given": "Mustafa", "initials": "M"}, {"family": "Kiess", "given": "Wieland", "initials": "W"}, {"family": "James", "given": "Alan L", "initials": "AL"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Palmer", "given": "Colin N A", "initials": "CN"}, {"family": "Doney", "given": "Alex S F", "initials": "AS"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Campbell", "given": "Susan", "initials": "S"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Hercberg", "given": "Serge", "initials": "S"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Bolton", "given": "Jennifer L", "initials": "JL"}, {"family": "Fowkes", "given": "Gerard R", "initials": "GR"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Lindstr\u00f6m", "given": "Jaana", "initials": "J"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Basart", "given": "Hanneke V", "initials": "HV"}, {"family": "Rathmann", "given": "Wolfgang", "initials": "W"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "DIAbetes Genetics Replication and Meta-analysis (DIAGRAM) Consortium", "given": null, "initials": null}, {"family": "Maerz", "given": "Winfried", "initials": "W"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Hastie", "given": "Nicholas D", "initials": "ND"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Price", "given": "Jackie F", "initials": "JF"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Meneton", "given": "Pierre", "initials": "P"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Toenjes", "given": "Anke", "initials": "A"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Beilby", "given": "John P", "initials": "JP"}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Schwarz", "given": "Peter E H", "initials": "PE"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Adair", "given": "Linda S", "initials": "LS"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Keinanen-Kiukaanniemi", "given": "Sirkka M", "initials": "SM"}, {"family": "Saaristo", "given": "Timo E", "initials": "TE"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}], "type": "journal article", "published": "2012-09-00", "journal": {"volume": "44", "issn": "1546-1718", "issue": "9", "pages": "991-1005", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control.", "doi": "10.1038/ng.2385", "pmid": "22885924", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2385"}, {"db": "pmc", "key": "PMC3433394"}, {"db": "mid", "key": "UKMS49338"}], "notes": [], "created": "2017-05-04T15:01:05.501Z", "modified": "2020-01-21T13:56:00.962Z"}, {"entity": "publication", "iuid": "febbdae8a9934f24b045fce3a12cd7ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/febbdae8a9934f24b045fce3a12cd7ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/febbdae8a9934f24b045fce3a12cd7ce"}}, "title": "Global transcriptional response to ISCOM-Matrix adjuvant at the site of administration and in the draining lymph node early after intramuscular injection in pigs.", "authors": [{"family": "Ahlberg", "given": "Viktor", "initials": "V"}, {"family": "L\u00f6vgren Bengtsson", "given": "Karin", "initials": "K"}, {"family": "Wallgren", "given": "Per", "initials": "P"}, {"family": "Fossum", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2012-09-00", "journal": {"volume": "38", "issn": "1879-0089", "issue": "1", "pages": "17-26", "title": "Dev. Comp. Immunol.", "issn-l": "0145-305X"}, "abstract": "ISCOM vaccines induce a balanced Th1/Th2 response, long-lasting antibody responses and cytotoxic T lymphocytes. The mode of action for the adjuvant component, the ISCOM-Matrix, is known to some extent but questions remain regarding its mechanism of action. The Affymetrix GeneChip\u00ae Porcine Genome Array was applied to study the global transcriptional response to ISCOM-Matrix in pigs at the injection site and in the draining lymph node 24h after i.m. injection. Gene enrichment analysis revealed inflammation, innate immunity and antigen processing to be central in the ISCOM-Matrix response. At the injection site, 594 genes were differentially expressed, including up-regulation of the cytokines osteopontin (SPP1), IL-10 and IL-18 and the chemokines CCL2, CCL19 and CXCL16. Of the 362 genes differentially expressed in the lymph node, IL-1\u03b2 and CXCL11 were up-regulated whereas IL18, CCL15 and CXCL12 were down-regulated. ISCOM-Matrix also modulated genes for pattern recognition receptors at the injection site (TLR2, TLR4, MRC1, PTX3, LGALS3) and in the lymph node (TLR4, RIG-I, MDA5, OAS1, EIF2AK2, LGALS3). A high proportion of up-regulated interferon-regulated genes indicated an interferon response. Thus, several genes, genetic pathways and biological processes were identified that are likely to shape the early immune response elicited by ISCOM-based vaccines.", "doi": "10.1016/j.dci.2012.03.005", "pmid": "22426325", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "S0145-305X(12)00043-2"}], "notes": [], "created": "2017-05-04T15:02:56.385Z", "modified": "2017-05-30T12:36:54.617Z"}, {"entity": "publication", "iuid": "560722ee21fc442eac3da8f4565bc1a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/560722ee21fc442eac3da8f4565bc1a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/560722ee21fc442eac3da8f4565bc1a2"}}, "title": "Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice.", "authors": [{"family": "Andersson", "given": "Lisa S", "initials": "LS"}, {"family": "Larhammar", "given": "Martin", "initials": "M"}, {"family": "Memic", "given": "Fatima", "initials": "F"}, {"family": "Wootz", "given": "Hanna", "initials": "H"}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Patra", "given": "Kalicharan", "initials": "K"}, {"family": "Arnason", "given": "Thorvaldur", "initials": "T"}, {"family": "Wellbring", "given": "Lisbeth", "initials": "L"}, {"family": "Hj\u00e4lm", "given": "G\u00f6ran", "initials": "G"}, {"family": "Imsland", "given": "Freyja", "initials": "F"}, {"family": "Petersen", "given": "Jessica L", "initials": "JL"}, {"family": "McCue", "given": "Molly E", "initials": "ME"}, {"family": "Mickelson", "given": "James R", "initials": "JR"}, {"family": "Cothran", "given": "Gus", "initials": "G"}, {"family": "Ahituv", "given": "Nadav", "initials": "N"}, {"family": "Roepstorff", "given": "Lars", "initials": "L"}, {"family": "Mikko", "given": "Sofia", "initials": "S"}, {"family": "Vallstedt", "given": "Anna", "initials": "A"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Kullander", "given": "Klas", "initials": "K"}], "type": "journal article", "published": "2012-08-30", "journal": {"volume": "488", "issn": "1476-4687", "issue": "7413", "pages": "642-646", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement. These networks produce left-right alternation of limbs as well as coordinated activation of flexor and extensor muscles. Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favourable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is expressed in the dI6 subdivision of spinal cord neurons, takes part in neuronal specification within this subdivision, and is critical for the normal development of a coordinated locomotor network controlling limb movements. Our discovery positions Dmrt3 in a pivotal role for configuring the spinal circuits controlling stride in vertebrates. The DMRT3 mutation has had a major effect on the diversification of the domestic horse, as the altered gait characteristics of a number of breeds apparently require this mutation.", "doi": "10.1038/nature11399", "pmid": "22932389", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "nature11399"}, {"db": "pmc", "key": "PMC3523687"}, {"db": "mid", "key": "NIHMS404855"}, {"db": "GENBANK", "key": "JQ922365"}, {"db": "GENBANK", "key": "JQ922366"}, {"db": "GENBANK", "key": "JQ922367"}, {"db": "GENBANK", "key": "JQ922368"}, {"db": "GENBANK", "key": "JQ922369"}, {"db": "GENBANK", "key": "JQ922370"}, {"db": "GENBANK", "key": "JQ922371"}, {"db": "GENBANK", "key": "JQ922372"}, {"db": "GENBANK", "key": "JQ922373"}, {"db": "GENBANK", "key": "JQ922374"}, {"db": "GENBANK", "key": "JQ922375"}, {"db": "GENBANK", "key": "JQ922376"}, {"db": "GENBANK", "key": "JQ922377"}, {"db": "GENBANK", "key": "JQ922378"}, {"db": "GENBANK", "key": "JQ922379"}, {"db": "GENBANK", "key": "JQ922380"}, {"db": "GENBANK", "key": "JQ922381"}, {"db": "GENBANK", "key": "JQ922382"}, {"db": "GENBANK", "key": "JQ922383"}, {"db": "GENBANK", "key": "JQ922384"}, {"db": "GENBANK", "key": "JQ922385"}, {"db": "GENBANK", "key": "JQ922386"}, {"db": "GENBANK", "key": "JQ922387"}, {"db": "GENBANK", "key": "JQ922388"}, {"db": "GENBANK", "key": "JQ922389"}, {"db": "GENBANK", "key": "JQ922390"}, {"db": "GENBANK", "key": "JQ922391"}, {"db": "GENBANK", "key": "JQ922392"}, {"db": "GENBANK", "key": "JQ922393"}, {"db": "GENBANK", "key": "JQ922394"}, {"db": "GENBANK", "key": "JQ922395"}], "notes": [], "created": "2017-05-04T15:01:06.255Z", "modified": "2020-01-21T13:56:02.368Z"}, {"entity": "publication", "iuid": "ed7ca330bc1648809214958a4f049387", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed7ca330bc1648809214958a4f049387.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed7ca330bc1648809214958a4f049387"}}, "title": "A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during domestication.", "authors": [{"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Gustafson", "given": "Ida", "initials": "I"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Sahlqvist", "given": "Anna-Stina", "initials": "A"}, {"family": "Jonsson", "given": "Kenneth B", "initials": "KB"}, {"family": "Kerje", "given": "Susanne", "initials": "S", "orcid": "0000-0002-2944-9288", "researcher": {"href": "https://publications.scilifelab.se/researcher/078ca525f2cc4a68a430f2655e45efce.json"}}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D"}], "type": "journal article", "published": "2012-08-30", "journal": {"volume": "8", "issn": "1553-7404", "issue": "8", "pages": "e1002914", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Domestication is one of the strongest forms of short-term, directional selection. Although selection is typically only exerted on one or a few target traits, domestication can lead to numerous changes in many seemingly unrelated phenotypes. It is unknown whether such correlated responses are due to pleiotropy or linkage between separate genetic architectures. Using three separate intercrosses between wild and domestic chickens, a locus affecting comb mass (a sexual ornament in the chicken) and several fitness traits (primarily medullary bone allocation and fecundity) was identified. This locus contains two tightly-linked genes, BMP2 and HAO1, which together produce the range of pleiotropic effects seen. This study demonstrates the importance of pleiotropy (or extremely close linkage) in domestication. The nature of this pleiotropy also provides insights into how this sexual ornament could be maintained in wild populations.", "doi": "10.1371/journal.pgen.1002914", "pmid": "22956912", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-02811"}, {"db": "pmc", "key": "PMC3431302"}], "notes": [], "created": "2017-05-04T14:57:42.391Z", "modified": "2021-07-07T15:26:06.527Z"}, {"entity": "publication", "iuid": "8b64f9961f7f47f7aeda2a732f724fe1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b64f9961f7f47f7aeda2a732f724fe1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b64f9961f7f47f7aeda2a732f724fe1"}}, "title": "Validation of whole genome amplification for analysis of the p53 tumor suppressor gene in limited amounts of tumor samples.", "authors": [{"family": "Hasmats", "given": "Johanna", "initials": "J"}, {"family": "Green", "given": "Henrik", "initials": "H"}, {"family": "Solnestam", "given": "Beata Werne", "initials": "BW"}, {"family": "Zajac", "given": "Pawel", "initials": "P"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Orear", "given": "Cedric", "initials": "C"}, {"family": "Validire", "given": "Pierre", "initials": "P"}, {"family": "Bjursell", "given": "Magnus", "initials": "M"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2012-08-24", "journal": {"volume": "425", "issn": "1090-2104", "issue": "2", "pages": "379-383", "title": "Biochem. Biophys. Res. Commun.", "issn-l": "0006-291X"}, "abstract": "Personalized cancer treatment requires molecular characterization of individual tumor biopsies. These samples are frequently only available in limited quantities hampering genomic analysis. Several whole genome amplification (WGA) protocols have been developed with reported varying representation of genomic regions post amplification. In this study we investigate region dropout using a \u03c629 polymerase based WGA approach. DNA from 123 lung cancers specimens and corresponding normal tissue were used and evaluated by Sanger sequencing of the p53 exons 5-8. To enable comparative analysis of this scarce material, WGA samples were compared with unamplified material using a pooling strategy of the 123 samples. In addition, a more detailed analysis of exon 7 amplicons were performed followed by extensive cloning and Sanger sequencing. Interestingly, by comparing data from the pooled samples to the individually sequenced exon 7, we demonstrate that mutations are more easily recovered from WGA pools and this was also supported by simulations of different sequencing coverage. Overall this data indicate a limited random loss of genomic regions supporting the use of whole genome amplification for genomic analysis.", "doi": "10.1016/j.bbrc.2012.07.101", "pmid": "22842464", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0006-291X(12)01408-8"}], "notes": [], "created": "2017-05-04T14:57:29.825Z", "modified": "2021-07-08T13:26:08.241Z"}, {"entity": "publication", "iuid": "de1f1172b5fa4a0a94e02ce36e84a68e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de1f1172b5fa4a0a94e02ce36e84a68e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de1f1172b5fa4a0a94e02ce36e84a68e"}}, "title": "MicroRNA-125b down-regulates matrix metallopeptidase 13 and inhibits cutaneous squamous cell carcinoma cell proliferation, migration, and invasion.", "authors": [{"family": "Xu", "given": "Ning", "initials": "N"}, {"family": "Zhang", "given": "Lingyun", "initials": "L"}, {"family": "Meisgen", "given": "Florian", "initials": "F"}, {"family": "Harada", "given": "Masako", "initials": "M"}, {"family": "Heilborn", "given": "Johan", "initials": "J"}, {"family": "Homey", "given": "Bernhard", "initials": "B"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "St\u00e5hle", "given": "Mona", "initials": "M"}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E"}, {"family": "Pivarcsi", "given": "Andor", "initials": "A"}], "type": "clinical trial", "published": "2012-08-24", "journal": {"volume": "287", "issn": "1083-351X", "issue": "35", "pages": "29899-29908", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Cutaneous squamous cell carcinoma (cSCC) is the second most common human cancer. Although dysregulation of microRNAs (miRNAs) is known to be involved in a variety of cancers, the role of miRNAs in cSCC is unclear. In this study, we aimed to identify tumor suppressive and oncogenic miRNAs involved in the pathogenesis of cSCC. MiRNA expression profiles in healthy skins (n = 4) and cSCCs (n = 4) were analyzed using MicroRNA Low Density Array. MiR-125b expression was analyzed by quantitative real-time PCR and in situ hybridization in skin biopsies from 40 healthy donors, 13 actinic keratosis, and 74 cSCC patients. The effect of miR-125b was analyzed in wound closure, colony formation, migration, and invasion assays in two cSCC cell lines, UT-SCC-7 and A431. The genes regulated by miR-125b in cSCC were identified by microarray analysis and its direct target was validated by luciferase reporter assay. Comparing cSCC with healthy skin, we identified four up-regulated miRNAs (miR-31, miR-135b, miR-21, and miR-223) and 54 down-regulated miRNAs, including miR-125b, whose function was further examined. We found that miR-125b suppressed proliferation, colony formation, migratory, and invasive capacity of cSCC cells. Matrix metallopeptidase 13 (MMP13) was identified as a direct target suppressed by miR-125b, and there was an inverse relationship between the expression of miR-125b and MMP13 in cSCC. Knockdown of MMP13 expression phenocopied the effects of miR-125b overexpression. These findings provide a novel molecular mechanism by which MMP13 is up-regulated in cSCCs and indicate that miR-125b plays a tumor suppressive role in cSCC.", "doi": "10.1074/jbc.M112.391243", "pmid": "22782903", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "M112.391243"}, {"db": "pmc", "key": "PMC3436131"}], "notes": [], "created": "2017-05-04T15:03:11.960Z", "modified": "2017-05-30T12:40:35.114Z"}, {"entity": "publication", "iuid": "63137bd2dbd243c5bef74e7e647c8cb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63137bd2dbd243c5bef74e7e647c8cb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63137bd2dbd243c5bef74e7e647c8cb0"}}, "title": "Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays.", "authors": [{"family": "Smith", "given": "Andrew J P", "initials": "AJ"}, {"family": "Howard", "given": "Philip", "initials": "P"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Stender", "given": "Stefan", "initials": "S"}, {"family": "Giambartolomei", "given": "Claudia", "initials": "C"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Tybj\u00e6rg-Hansen", "given": "Anne", "initials": "A"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Palmen", "given": "Jutta", "initials": "J"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}], "type": "journal article", "published": "2012-08-16", "journal": {"volume": "8", "issn": "1553-7404", "issue": "8", "pages": "e1002908", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Following the widespread use of genome-wide association studies (GWAS), focus is turning towards identification of causal variants rather than simply genetic markers of diseases and traits. As a step towards a high-throughput method to identify genome-wide, non-coding, functional regulatory variants, we describe the technique of allele-specific FAIRE, utilising large-scale genotyping technology (FAIRE-gen) to determine allelic effects on chromatin accessibility and regulatory potential. FAIRE-gen was explored using lymphoblastoid cells and the 50,000 SNP Illumina CVD BeadChip. The technique identified an allele-specific regulatory polymorphism within NR1H3 (coding for LXR-\u03b1), rs7120118, coinciding with a previously GWAS-identified SNP for HDL-C levels. This finding was confirmed using FAIRE-gen with the 200,000 SNP Illumina Metabochip and verified with the established method of TaqMan allelic discrimination. Examination of this SNP in two prospective Caucasian cohorts comprising 15,000 individuals confirmed the association with HDL-C levels (combined beta\u200a=\u200a0.016; p\u200a=\u200a0.0006), and analysis of gene expression identified an allelic association with LXR-\u03b1 expression in heart tissue. Using increasingly comprehensive genotyping chips and distinct tissues for examination, FAIRE-gen has the potential to aid the identification of many causal SNPs associated with disease from GWAS.", "doi": "10.1371/journal.pgen.1002908", "pmid": "22916038", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-00477"}, {"db": "pmc", "key": "PMC3420950"}], "notes": [], "created": "2017-05-04T15:01:09.240Z", "modified": "2020-01-21T13:56:02.677Z"}, {"entity": "publication", "iuid": "1bc6175eacc84744aafca007e4d5f81a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1bc6175eacc84744aafca007e4d5f81a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1bc6175eacc84744aafca007e4d5f81a"}}, "title": "Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse with implications for therapy.", "authors": [{"family": "Roberts", "given": "Thomas C", "initials": "TC"}, {"family": "Blomberg", "given": "K Emelie M", "initials": "KE"}, {"family": "McClorey", "given": "Graham", "initials": "G"}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}, {"family": "Godfrey", "given": "Caroline", "initials": "C"}, {"family": "Betts", "given": "Corinne", "initials": "C"}, {"family": "Coursindel", "given": "Thibault", "initials": "T"}, {"family": "Gait", "given": "Michael J", "initials": "MJ"}, {"family": "Smith", "given": "C I Edvard", "initials": "CI"}, {"family": "Wood", "given": "Matthew J A", "initials": "MJ"}], "type": "journal article", "published": "2012-08-14", "journal": {"volume": "1", "issn": "2162-2531", "issue": null, "pages": "e39", "title": "Mol Ther Nucleic Acids", "issn-l": "2162-2531"}, "abstract": "MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression and are implicated in wide-ranging cellular processes and pathological conditions including Duchenne muscular dystrophy (DMD). We have compared differential miRNA expression in proximal and distal limb muscles, diaphragm, heart and serum in the mdx mouse relative to wild-type controls. Global transcriptome analysis revealed muscle-specific patterns of differential miRNA expression as well as a number of changes common between tissues, including previously identified dystromirs. In the case of miR-31 and miR-34c, upregulation of primary-miRNA transcripts, precursor hairpins and all mature miRNAs derived from the same transcript or miRNA cluster, strongly suggests transcriptional regulation of these miRNAs. The most striking differences in differential miRNA expression were between muscle tissue and serum. Specifically, miR-1, miR-133a, and miR-206 were highly abundant in mdx serum but downregulated or modestly upregulated in muscle, suggesting that these miRNAs are promising disease biomarkers. Indeed, the relative serum levels of these miRNAs were normalized in response to peptide-phosphorodiamidate morpholino oligonucleotide (PMO) mediated dystrophin restoration therapy. This study has revealed further complexity in the miRNA transcriptome of the mdx mouse, an understanding of which will be valuable in the development of novel therapeutics and for monitoring their efficacy.", "doi": "10.1038/mtna.2012.26", "pmid": "23344181", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "mtna201226"}, {"db": "pmc", "key": "PMC3437806"}], "notes": [], "created": "2017-05-04T15:03:13.026Z", "modified": "2017-05-30T14:50:53.146Z"}, {"entity": "publication", "iuid": "83a7c3d0d4b2472999439d435c32214f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83a7c3d0d4b2472999439d435c32214f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83a7c3d0d4b2472999439d435c32214f"}}, "title": "Evidence of association between interferon regulatory factor 5 gene polymorphisms and asthma.", "authors": [{"family": "Wang", "given": "Chuan", "initials": "C"}, {"family": "Rose-Zerilli", "given": "Matthew J", "initials": "MJ"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Holloway", "given": "John W", "initials": "JW"}, {"family": "Postma", "given": "Dirkje S", "initials": "DS"}, {"family": "Holgate", "given": "Stephen T", "initials": "ST"}, {"family": "Bours", "given": "Vincent", "initials": "V"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Dideberg", "given": "Vinciane", "initials": "V"}], "type": "journal article", "published": "2012-08-10", "journal": {"volume": "504", "issn": "1879-0038", "issue": "2", "pages": "220-225", "title": "Gene", "issn-l": "0378-1119"}, "abstract": "Asthma is a heterogeneous disorder hallmarked by chronic inflammation in the respiratory system. Exacerbations of asthma are correlated with respiratory infections. Considering the implication of interferon regulatory factor 5 (IRF5) in innate and adaptive immunity, we investigated the preferential transmission patterns of ten IRF5 gene polymorphisms in two asthmatic family cohorts. A common IRF5 haplotype was found to be associated with asthma and the severity of asthmatic symptoms. Stratified analysis of subgroups of asthmatic individuals revealed that the associations were more pronounced in nonatopic asthmatic individuals. In addition, the risk alleles of IRF5 polymorphisms for asthma were almost completely opposite to those for autoimmune disorders. Our study provides the first evidence of association between IRF5 and asthma, and sheds light on the related but potentially distinct roles of IRF5 alleles in the pathogenesis of asthma and autoimmune disorders.", "doi": "10.1016/j.gene.2012.05.021", "pmid": "22613848", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0378-1119(12)00596-3"}], "notes": [], "created": "2017-05-04T15:00:58.762Z", "modified": "2021-07-07T15:11:02.555Z"}, {"entity": "publication", "iuid": "2e8a48c6bcb0435e81f13645120db225", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e8a48c6bcb0435e81f13645120db225"}}, "title": "Proteomic screen reveals Fbw7 as a modulator of the NF-\u03baB pathway.", "authors": [{"family": "Arabi", "given": "Azadeh", "initials": "A"}, {"family": "Ullah", "given": "Karim", "initials": "K"}, {"family": "Branca", "given": "Rui M M", "initials": "RM"}, {"family": "Johansson", "given": "Johan", "initials": "J"}, {"family": "Bandarra", "given": "Daniel", "initials": "D"}, {"family": "Haneklaus", "given": "Moritz", "initials": "M"}, {"family": "Fu", "given": "Jing", "initials": "J"}, {"family": "Ari\u00ebs", "given": "Ingrid", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Den Boer", "given": "Monique L", "initials": "ML"}, {"family": "Pokrovskaja", "given": "Katja", "initials": "K"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Xiao", "given": "Gutian", "initials": "G"}, {"family": "Rocha", "given": "Sonia", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2012-08-07", "journal": {"volume": "3", "issn": "2041-1723", "issue": null, "pages": "976", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fbw7 is a ubiquitin-ligase that targets several oncoproteins for proteolysis, but the full range of Fbw7 substrates is not known. Here we show that by performing quantitative proteomics combined with degron motif searches, we effectively screened for a more complete set of Fbw7 targets. We identify 89 putative Fbw7 substrates, including several disease-associated proteins. The transcription factor NF-\u03baB2 (p100/p52) is one of the candidate Fbw7 substrates. We show that Fbw7 interacts with p100 via a conserved degron and that it promotes degradation of p100 in a GSK3\u03b2 phosphorylation-dependent manner. Fbw7 inactivation increases p100 levels, which in the presence of NF-\u03baB pathway stimuli, leads to increased p52 levels and activity. Accordingly, the apoptotic threshold can be increased by loss of Fbw7 in a p100-dependent manner. In conclusion, Fbw7-mediated destruction of p100 is a regulatory component restricting the response to NF-\u03baB2 pathway stimulation.", "doi": "10.1038/ncomms1975", "pmid": "22864569", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "ncomms1975"}, {"db": "pmc", "key": "PMC4354031"}], "notes": [], "created": "2017-05-04T14:56:18.815Z", "modified": "2021-07-08T11:36:15.152Z"}, {"entity": "publication", "iuid": "e742938350ca4f2dacb0e778af86d501", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e742938350ca4f2dacb0e778af86d501.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e742938350ca4f2dacb0e778af86d501"}}, "title": "Platelet-derived growth factor over-expression in retinal progenitors results in abnormal retinal vessel formation.", "authors": [{"family": "Edqvist", "given": "Per-Henrik D", "initials": "PH"}, {"family": "Niklasson", "given": "Mia", "initials": "M"}, {"family": "Vidal-Sanz", "given": "Manuel", "initials": "M"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2012-08-03", "journal": {"volume": "7", "issn": "1932-6203", "issue": "8", "pages": "e42488", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Platelet-derived growth factor (PDGF) plays an important role in development of the central nervous system, including the retina. Excessive PDGF signaling is associated with proliferative retinal disorders. We reported previously that transgenic mice in which PDGF-B was over-expressed under control of the nestin enhancer, nes/tk-PdgfB-lacZ, exhibited enhanced apoptosis in the developing corpus striatum. These animals display enlarged lateral ventricles after birth as well as behavioral aberrations as adults. Here, we report that in contrast to the relatively mild central nervous system phenotype, development of the retina is severely disturbed in nes/tk-PdgfB-lacZ mice. In transgenic retinas all nuclear layers were disorganized and photoreceptor segments failed to develop properly. Since astrocyte precursor cells did not populate the retina, retinal vascular progenitors could not form a network of vessels. With time, randomly distributed vessels resembling capillaries formed, but there were no large trunk vessels and the intraocular pressure was reduced. In addition, we observed a delayed regression of the hyaloid vasculature. The prolonged presence of this structure may contribute to the other abnormalities observed in the retina, including the defective lamination.", "doi": "10.1371/journal.pone.0042488", "pmid": "22880002", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-21303"}, {"db": "pmc", "key": "PMC3411765"}], "notes": [], "created": "2017-05-04T14:55:53.804Z", "modified": "2017-05-30T14:56:07.385Z"}, {"entity": "publication", "iuid": "bf093dd596d340b098fd79e5c82b6af4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf093dd596d340b098fd79e5c82b6af4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf093dd596d340b098fd79e5c82b6af4"}}, "title": "Erlin-2 is associated with active \u03b3-secretase in brain and affects amyloid \u03b2-peptide production.", "authors": [{"family": "Teranishi", "given": "Yasuhiro", "initials": "Y"}, {"family": "Hur", "given": "Ji-Yeun", "initials": "JY"}, {"family": "Gu", "given": "Gucci Jijuan", "initials": "GJ"}, {"family": "Kihara", "given": "Takahiro", "initials": "T"}, {"family": "Ishikawa", "given": "Taizo", "initials": "T"}, {"family": "Nishimura", "given": "Takeshi", "initials": "T"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Behbahani", "given": "Homira", "initials": "H"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Frykman", "given": "Susanne", "initials": "S"}, {"family": "Tjernberg", "given": "Lars O", "initials": "LO"}], "type": "journal article", "published": "2012-08-03", "journal": {"volume": "424", "issn": "1090-2104", "issue": "3", "pages": "476-481", "title": "Biochem. Biophys. Res. Commun.", "issn-l": "0006-291X"}, "abstract": "The transmembrane protease complex \u03b3-secretase is responsible for the generation of the neurotoxic amyloid \u03b2-peptide (A\u03b2) from its precursor (APP). A\u03b2 has a causative role in Alzheimer disease, and thus, \u03b3-secretase is a therapeutic target. However, since there are more than 70 \u03b3-secretase substrates besides APP, selective inhibition of APP processing is required. Recent data indicates the existence of several \u03b3-secretase associated proteins (GSAPs) that affect the selection and processing of substrates. Here, we use a \u03b3-secretase inhibitor for affinity purification of \u03b3-secretase and associated proteins from microsomes and detergent resistant membranes (DRMs) prepared from rat or human brain. By tandem mass spectrometry we identified a novel brain GSAP; erlin-2. This protein was recently reported to reside in DRMs in the ER. A proximity ligation assay, as well as co-immunoprecipitation, confirmed the association of erlin-2 with \u03b3-secretase. We found that a higher proportion of erlin-2 was associated with \u03b3-secretase in DRMs than in soluble membranes. siRNA experiments indicated that reduced levels of erlin-2 resulted in a decreased A\u03b2 production, whereas the effect on Notch processing was limited. In summary, we have found a novel brain GSAP, erlin-2, that resides in DRMs and affects A\u03b2 production.", "doi": "10.1016/j.bbrc.2012.06.137", "pmid": "22771797", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0006-291X(12)01239-9"}], "notes": [], "created": "2017-05-04T14:55:22.562Z", "modified": "2023-04-14T13:56:30.420Z"}, {"entity": "publication", "iuid": "679f970f91c14171b9ebc9c804976e4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/679f970f91c14171b9ebc9c804976e4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/679f970f91c14171b9ebc9c804976e4e"}}, "title": "Loss of cancer drug activity in colon cancer HCT-116 cells during spheroid formation in a new 3-D spheroid cell culture system.", "authors": [{"family": "Karlsson", "given": "Henning", "initials": "H"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Nygren", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2012-08-01", "journal": {"volume": "318", "issn": "1090-2422", "issue": "13", "pages": "1577-1585", "title": "Exp. Cell Res.", "issn-l": "0014-4827"}, "abstract": "Clinically relevant in vitro methods are needed to identify new cancer drugs for solid tumors. We report on a new 3-D spheroid cell culture system aimed to mimic the properties of solid tumors in vivo. The colon cancer cell lines HCT-116 wt and HCT-116 wt/GFP were grown as monolayers and for 3 or 6 days on 96-well NanoCulture\u00ae plates to form spheroids. Expression of surface markers, genes and hypoxia were assessed to characterize the spheroids and drug induced cytotoxicity was evaluated based on fluorescein diacetate (FDA) conversion by viable cells to fluorescent fluorescein or by direct measurement of fluorescence of GFP marked cells after a 72 h drug incubation. The cells reproducibly formed spheroids in the NanoCulture\u00ae plates with tight cell-attachment after 6 days. Cells in spheroids showed geno- and phenotypical properties reminiscent of hypoxic stem cells. Monolayer cultured cells were sensitive to standard and investigational drugs, whereas the spheroids gradually turned resistant. Similar results for cytotoxicity were observed using simplified direct measurement of fluorescence of GFP marked cells compared with FDA incubation. In conclusion, this new 3-D spheroid cell culture system provides a convenient and clinically relevant model for the identification and characterization of cancer drugs for solid tumors.", "doi": "10.1016/j.yexcr.2012.03.026", "pmid": "22487097", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "S0014-4827(12)00162-0"}], "notes": [], "created": "2017-05-04T15:02:58.085Z", "modified": "2017-05-30T12:37:13.364Z"}, {"entity": "publication", "iuid": "47542fb5f19943c8b2dfa59a9cc833fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47542fb5f19943c8b2dfa59a9cc833fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47542fb5f19943c8b2dfa59a9cc833fc"}}, "title": "Unraveling assembly of stream biofilm communities.", "authors": [{"family": "Besemer", "given": "Katharina", "initials": "K"}, {"family": "Peter", "given": "Hannes", "initials": "H"}, {"family": "Logue", "given": "J\u00fcrg B", "initials": "JB"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}, {"family": "Tranvik", "given": "Lars J", "initials": "LJ"}, {"family": "Battin", "given": "Tom J", "initials": "TJ"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "6", "issn": "1751-7370", "issue": "8", "pages": "1459-1468", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Microbial biofilms assemble from cells that attach to a surface, where they develop into matrix-enclosed communities. Mechanistic insights into community assembly are crucial to better understand the functioning of natural biofilms, which drive key ecosystem processes in numerous aquatic habitats. We studied the role of the suspended microbial community as the source of the biofilm community in three streams using terminal-restriction fragment length polymorphism and 454 pyrosequencing of the 16S ribosomal RNA (rRNA) and the 16S rRNA gene (as a measure for the active and the bulk community, respectively). Diversity was consistently lower in the biofilm communities than in the suspended stream water communities. We propose that the higher diversity in the suspended communities is supported by continuous inflow from various sources within the catchment. Community composition clearly differed between biofilms and suspended communities, whereas biofilm communities were similar in all three streams. This suggests that biofilm assembly did not simply reflect differences in the source communities, but that certain microbial groups from the source community proliferate in the biofilm. We compared the biofilm communities with random samples of the respective community suspended in the stream water. This analysis confirmed that stochastic dispersal from the source community was unlikely to shape the observed community composition of the biofilms, in support of species sorting as a major biofilm assembly mechanism. Bulk and active populations generated comparable patterns of community composition in the biofilms and the suspended communities, which suggests similar assembly controls on these populations.", "doi": "10.1038/ismej.2011.205", "pmid": "22237539", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ismej2011205"}, {"db": "pmc", "key": "PMC3400417"}], "notes": [], "created": "2017-05-04T14:57:35.682Z", "modified": "2020-01-21T13:56:10.740Z"}, {"entity": "publication", "iuid": "0a5e834e0fd44a66adb019f865df9aa5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a5e834e0fd44a66adb019f865df9aa5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a5e834e0fd44a66adb019f865df9aa5"}}, "title": "The novel tyrosine kinase inhibitor AKN-028 has significant antileukemic activity in cell lines and primary cultures of acute myeloid leukemia", "authors": [{"family": "Eriksson", "given": "A", "initials": "A"}, {"family": "Hermanson", "given": "M", "initials": "M"}, {"family": "Wickstr\u00f6m", "given": "M", "initials": "M"}, {"family": "Lindhagen", "given": "E", "initials": "E"}, {"family": "Ekholm", "given": "C", "initials": "C"}, {"family": "Jenmalm Jensen", "given": "A", "initials": "A"}, {"family": "L\u00f6thgren", "given": "A", "initials": "A"}, {"family": "Lehmann", "given": "F", "initials": "F"}, {"family": "Larsson", "given": "R", "initials": "R"}, {"family": "Parrow", "given": "V", "initials": "V"}, {"family": "H\u00f6glund", "given": "M", "initials": "M"}], "type": "journal-article", "published": "2012-08-00", "journal": {"volume": "2", "issn": "2044-5385", "issue": "8", "pages": "e81", "title": "Blood Cancer J", "issn-l": "2044-5385"}, "abstract": null, "doi": "10.1038/bcj.2012.28", "pmid": "22864397", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T11:49:04.973Z", "modified": "2025-10-17T13:04:30.532Z"}, {"entity": "publication", "iuid": "5b6f8762d73149dbb537f991932a7fbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b6f8762d73149dbb537f991932a7fbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b6f8762d73149dbb537f991932a7fbc"}}, "title": "Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry.", "authors": [{"family": "Olsson", "given": "Niclas", "initials": "N"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CA"}, {"family": "Wingren", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "8", "pages": "342-354", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The development of high-performance technology platforms for generating detailed protein expression profiles, or protein atlases, is essential. Recently, we presented a novel platform that we termed global proteome survey, where we combined the best features of affinity proteomics and mass spectrometry, to probe any proteome in a species independent manner while still using a limited set of antibodies. We used so called context-independent-motif-specific antibodies, directed against short amino acid motifs. This enabled enrichment of motif-containing peptides from a digested proteome, which then were detected and identified by mass spectrometry. In this study, we have demonstrated the quantitative capability, reproducibility, sensitivity, and coverage of the global proteome survey technology by targeting stable isotope labeling with amino acids in cell culture-labeled yeast cultures cultivated in glucose or ethanol. The data showed that a wide range of motif-containing peptides (proteins) could be detected, identified, and quantified in a highly reproducible manner. On average, each of six different motif-specific antibodies was found to target about 75 different motif-containing proteins. Furthermore, peptides originating from proteins spanning in abundance from over a million down to less than 50 copies per cell, could be targeted. It is worth noting that a significant set of peptides previously not reported in the PeptideAtlas database was among the profiled targets. The quantitative data corroborated well with the corresponding data generated after conventional strong cation exchange fractionation of the same samples. Finally, several differentially expressed proteins, with both known and unknown functions, many relevant for the central carbon metabolism, could be detected in the glucose- versus ethanol-cultivated yeast. Taken together, the study demonstrated the potential of our immunoaffinity-based mass spectrometry platform for reproducible quantitative proteomics targeting classes of motif-containing peptides.", "doi": "10.1074/mcp.M111.016238", "pmid": "22543061", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "M111.016238"}, {"db": "pmc", "key": "PMC3412966"}], "notes": [], "created": "2017-05-04T14:56:17.870Z", "modified": "2020-01-21T13:53:20.530Z"}, {"entity": "publication", "iuid": "771b158dba864bfaa57b06f6c1e81c1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/771b158dba864bfaa57b06f6c1e81c1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/771b158dba864bfaa57b06f6c1e81c1e"}}, "title": "QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch.", "authors": [{"family": "Knief", "given": "Ulrich", "initials": "U"}, {"family": "Schielzeth", "given": "Holger", "initials": "H"}, {"family": "Kempenaers", "given": "Bart", "initials": "B"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "21", "issn": "1365-294X", "issue": "15", "pages": "3704-3717", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak have also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now, no genomic polymorphisms have been identified, which are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here, we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1404 informative single-nucleotide polymorphisms genotyped in a four-generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of 11 genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.", "doi": "10.1111/j.1365-294X.2012.05661.x", "pmid": "22694741", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:03.453Z", "modified": "2020-01-21T13:56:03.092Z"}, {"entity": "publication", "iuid": "f472ac24452340228a47ab7ed26e3be4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f472ac24452340228a47ab7ed26e3be4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f472ac24452340228a47ab7ed26e3be4"}}, "title": "Polymorphisms in sh2b1 and spns1 loci are associated with triglyceride levels in a healthy population in northern Sweden.", "authors": [{"family": "V\u00e4stermark", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Jacobsson", "given": "Josefin A", "initials": "JA"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "91", "issn": "0973-7731", "issue": "2", "pages": "237-240", "title": "J. Genet.", "issn-l": "0022-1333"}, "abstract": null, "doi": "10.1007/s12041-012-0167-1", "pmid": "22942098", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:37.494Z", "modified": "2021-06-22T12:16:46.077Z"}, {"entity": "publication", "iuid": "b8bdac96b3dc42e4999d3bb061ede430", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8bdac96b3dc42e4999d3bb061ede430.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8bdac96b3dc42e4999d3bb061ede430"}}, "title": "Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing.", "authors": [{"family": "Mohammad", "given": "Faizaan", "initials": "F"}, {"family": "Pandey", "given": "Gaurav Kumar", "initials": "GK"}, {"family": "Mondal", "given": "Tanmoy", "initials": "T"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Redrup", "given": "Lisa", "initials": "L"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Kanduri", "given": "Chandrasekhar", "initials": "C"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "139", "issn": "1477-9129", "issue": "15", "pages": "2792-2803", "title": "Development", "issn-l": "0950-1991"}, "abstract": "Establishment of silencing by noncoding RNAs (ncRNAs) via targeting of chromatin remodelers is relatively well investigated; however, their role in the maintenance of silencing is poorly understood. Here, we explored the functional role of the long ncRNA Kcnq1ot1 in the maintenance of transcriptional gene silencing in the one mega-base Kcnq1 imprinted domain in a transgenic mouse model. By conditionally deleting the Kcnq1ot1 ncRNA at different stages of mouse development, we suggest that Kcnq1ot1 ncRNA is required for the maintenance of the silencing of ubiquitously imprinted genes (UIGs) at all developmental stages. In addition, Kcnq1ot1 ncRNA is also involved in guiding and maintaining the CpG methylation at somatic differentially methylated regions flanking the UIGs, which is a hitherto unknown role for a long ncRNA. On the other hand, silencing of some of the placental-specific imprinted genes (PIGs) is maintained independently of Kcnq1ot1 ncRNA. Interestingly, the non-imprinted genes (NIGs) that escape RNA-mediated silencing are enriched with enhancer-specific modifications. Taken together, this study illustrates the gene-specific maintenance mechanisms operational at the Kcnq1 locus for tissue-specific transcriptional gene silencing and activation.", "doi": "10.1242/dev.079566", "pmid": "22721776", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "dev.079566"}], "notes": [], "created": "2017-05-04T14:57:32.757Z", "modified": "2020-01-21T13:56:10.518Z"}, {"entity": "publication", "iuid": "23f07fa1366140489ae6b485aefa3f41", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23f07fa1366140489ae6b485aefa3f41.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23f07fa1366140489ae6b485aefa3f41"}}, "title": "Intractable epilepsy of infancy due to homozygous mutation in the EFHC1 gene.", "authors": [{"family": "Berger", "given": "Itai", "initials": "I"}, {"family": "Dor", "given": "Talya", "initials": "T"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Edvardson", "given": "Simon", "initials": "S"}, {"family": "Shaag", "given": "Avraham", "initials": "A"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Elpeleg", "given": "Orly", "initials": "O"}], "type": "case reports", "published": "2012-08-00", "journal": {"volume": "53", "issn": "1528-1167", "issue": "8", "pages": "1436-1440", "title": "Epilepsia", "issn-l": "0013-9580"}, "abstract": "The molecular etiology of primary intractable epilepsy in infancy is largely unknown. We studied a nonconsanguineous Moroccan-Jewish family, where three of their seven children presented with intractable seizures and died at 18-36 months.\n\nHomozygous regions were searched using 250 K DNA single nucleotide polymorphism (SNP) array. The sequence of 50 Mb exome of a single patient was determined using SOLiD 5500XL deep sequencing analyzer.\n\nA single homozygous 11.3 Mb genomic region on chromosome 6 was linked to the disease in this family. This region contained 110 genes encoding a total of 1,000 exons. Whole exome sequencing revealed a single pathogenic homozygous variant within the critical region. The mutation, Phe229Leu in the EFHC1 gene was previously shown, in a carrier state, to be associated with juvenile myoclonic epilepsy.\n\nAlthough heterozygosity for the Phe229Leu mutation is known to be associated with a relatively benign form of epilepsy in adolescence; homozygosity for the same mutation is associated with lethal epilepsy of infancy. Given the considerable carrier rate of this mutation worldwide, the sequence of the EFHC1 gene should be determined in all patients with primary intractable epilepsy in infancy.", "doi": "10.1111/j.1528-1167.2012.03536.x", "pmid": "22690745", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:33.057Z", "modified": "2021-07-07T14:15:07.510Z"}, {"entity": "publication", "iuid": "cb9001009ccd408da98ec3d253f84c03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb9001009ccd408da98ec3d253f84c03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb9001009ccd408da98ec3d253f84c03"}}, "title": "Impact of common variation in bone-related genes on type 2 diabetes and related traits.", "authors": [{"family": "Billings", "given": "Liana K", "initials": "LK"}, {"family": "Hsu", "given": "Yi-Hsiang", "initials": "YH"}, {"family": "Ackerman", "given": "Rachel J", "initials": "RJ"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Hercberg", "given": "Serge", "initials": "S"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Barnes", "given": "Daniel", "initials": "D"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Hui", "given": "Jennie", "initials": "J"}, {"family": "Fu", "given": "Mao", "initials": "M"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C"}, {"family": "An", "given": "Ping", "initials": "P"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Christiansen", "given": "Lene", "initials": "L"}, {"family": "Dalg\u00e5rd", "given": "Christine", "initials": "C"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Grundberg", "given": "Elin", "initials": "E"}, {"family": "MAGIC Investigators", "given": null, "initials": null}, {"family": "DIAGRAM + Consortium", "given": null, "initials": null}, {"family": "MuTHER Consortium", "given": null, "initials": null}, {"family": "ASCOT Investigators", "given": null, "initials": null}, {"family": "GEFOS Consortium", "given": null, "initials": null}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Ohm Kyvik", "given": "Kirsten", "initials": "K"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Wareham", "given": "Nick", "initials": "N"}, {"family": "Meneton", "given": "Pierre", "initials": "P"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "61", "issn": "1939-327X", "issue": "8", "pages": "2176-2186", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "Exploring genetic pleiotropy can provide clues to a mechanism underlying the observed epidemiological association between type 2 diabetes and heightened fracture risk. We examined genetic variants associated with bone mineral density (BMD) for association with type 2 diabetes and glycemic traits in large well-phenotyped and -genotyped consortia. We undertook follow-up analysis in \u223c19,000 individuals and assessed gene expression. We queried single nucleotide polymorphisms (SNPs) associated with BMD at levels of genome-wide significance, variants in linkage disequilibrium (r(2) > 0.5), and BMD candidate genes. SNP rs6867040, at the ITGA1 locus, was associated with a 0.0166 mmol/L (0.004) increase in fasting glucose per C allele in the combined analysis. Genetic variants in the ITGA1 locus were associated with its expression in the liver but not in adipose tissue. ITGA1 variants appeared among the top loci associated with type 2 diabetes, fasting insulin, \u03b2-cell function by homeostasis model assessment, and 2-h post-oral glucose tolerance test glucose and insulin levels. ITGA1 has demonstrated genetic pleiotropy in prior studies, and its suggested role in liver fibrosis, insulin secretion, and bone healing lends credence to its contribution to both osteoporosis and type 2 diabetes. These findings further underscore the link between skeletal and glucose metabolism and highlight a locus to direct future investigations.", "doi": "10.2337/db11-1515", "pmid": "22698912", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "db11-1515"}, {"db": "pmc", "key": "PMC3402303"}], "notes": [], "created": "2017-05-04T15:00:56.888Z", "modified": "2020-01-21T13:56:05.199Z"}, {"entity": "publication", "iuid": "268592580d41462595a2fbda90be239b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/268592580d41462595a2fbda90be239b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/268592580d41462595a2fbda90be239b"}}, "title": "Evidence-based approach to assess passive diffusion and carrier-mediated drug transport", "authors": [{"family": "Di", "given": "Li", "initials": "L"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Avdeef", "given": "Alex", "initials": "A"}, {"family": "Ecker", "given": "Gerhard F", "initials": "GF"}, {"family": "Faller", "given": "Bernard", "initials": "B"}, {"family": "Fischer", "given": "Holger", "initials": "H"}, {"family": "Houston", "given": "J Brian", "initials": "JB"}, {"family": "Kansy", "given": "Manfred", "initials": "M"}, {"family": "Kerns", "given": "Edward H", "initials": "EH"}, {"family": "Kr\u00e4mer", "given": "Stefanie D", "initials": "SD"}, {"family": "Lennern\u00e4s", "given": "Hans", "initials": "H"}, {"family": "Sugano", "given": "Kiyohiko", "initials": "K"}], "type": "journal-article", "published": "2012-08-00", "journal": {"volume": "17", "issn": "1359-6446", "issue": "15-16", "pages": "905-912", "title": "Drug Discovery Today", "issn-l": "1359-6446"}, "abstract": null, "doi": "10.1016/j.drudis.2012.03.015", "pmid": "22507594", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T11:54:02.806Z", "modified": "2025-10-17T13:04:30.542Z"}, {"entity": "publication", "iuid": "c1da6f26337743248fa21813da97231f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1da6f26337743248fa21813da97231f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1da6f26337743248fa21813da97231f"}}, "title": "Design, synthesis and evaluation of triazole functionalized ring-fused 2-pyridones as antibacterial agents.", "authors": [{"family": "Bengtsson", "given": "Christoffer", "initials": "C"}, {"family": "Lindgren", "given": "Anders E G", "initials": "AEG"}, {"family": "Uvell", "given": "Hanna", "initials": "H"}, {"family": "Almqvist", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "54", "issn": "1768-3254", "issue": null, "pages": "637-646", "title": "Eur J Med Chem", "issn-l": "0223-5234"}, "abstract": "Antibacterial resistance is today a worldwide problem and the demand for new classes of antibacterial agents with new mode of action is enormous. In the strive for new antibacterial agents that inhibit pilus assembly, an important virulence factor, routes to introduce triazoles in position 8 and 2 of ring-fused bicyclic 2-pyridones have been developed. This was made via Sonogashira couplings followed by Huisgen 1,3-dipolar cycloadditions. The method development made it possible to introduce a diverse series of substituted triazoles and their antibacterial properties were tested in a whole cell pili-dependent biofilm assay. Most of the twenty four candidates tested showed low to no activity but interestingly three compounds, one 8-substituted and two 2-substituted, showed promising activities with EC(50)'s between 9 and 50 \u03bcM.", "doi": "10.1016/j.ejmech.2012.06.018", "pmid": "22749393", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0223-5234(12)00370-4"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:38.825Z", "modified": "2025-10-17T13:04:30.552Z"}, {"entity": "publication", "iuid": "efcfa6f2bdab4562bcd84c278dbb3622", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efcfa6f2bdab4562bcd84c278dbb3622.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efcfa6f2bdab4562bcd84c278dbb3622"}}, "title": "Compensatory mutations in agrC partly restore fitness in vitro to peptide deformylase inhibitor-resistant Staphylococcus aureus.", "authors": [{"family": "Zorzet", "given": "Anna", "initials": "A"}, {"family": "Andersen", "given": "Jytte Mark", "initials": "JM"}, {"family": "Nilsson", "given": "Annika I", "initials": "AI"}, {"family": "M\u00f8ller", "given": "Niels Frimodt", "initials": "NF"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "67", "issn": "1460-2091", "issue": "8", "pages": "1835-1842", "title": "J. Antimicrob. Chemother.", "issn-l": "0305-7453"}, "abstract": "To determine how the fitness cost of deformylase inhibitor resistance conferred by fmt mutations can be genetically compensated.\n\nResistant mutants were isolated and characterized with regard to their growth rates in vitro and in neutropenic mice, MIC and DNA sequence. Faster-growing compensated mutants were isolated by serial passage in culture medium, and for a subset of the resistant and compensated mutants whole-genome sequencing was performed.\n\nStaphylococcus aureus mutants resistant to the peptide deformylase inhibitor actinonin had mutations in the fmt gene that conferred high-level actinonin resistance and reduced bacterial growth rate. Compensated mutants that remained fully resistant to actinonin and showed increased growth rates appeared within 30-60 generations of growth. Whole-genome sequencing and localized DNA sequencing of mutated candidate genes showed that alterations in the gene agrC were present in the majority of compensated strains. Resistant and compensated mutants grew at similar rates as the wild-type in a mouse thigh infection model.\n\nResistance to deformylase inhibitors due to fmt mutations reduces bacterial growth rates, but these costs can be reduced by mutations in the agrC gene. Mutants defective in fmt (with or without compensatory agrC mutations) grew well in an animal model, implying that they can also cause infection in a host.", "doi": "10.1093/jac/dks168", "pmid": "22577101", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "dks168"}], "notes": [], "created": "2017-05-04T15:01:00.305Z", "modified": "2020-01-21T13:56:06.140Z"}, {"entity": "publication", "iuid": "d9a1ef3628bb47d99c4d4fcdf663680c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9a1ef3628bb47d99c4d4fcdf663680c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9a1ef3628bb47d99c4d4fcdf663680c"}}, "title": "A-to-I editing of microRNAs in the mammalian brain increases during development.", "authors": [{"family": "Ekdahl", "given": "Ylva", "initials": "Y"}, {"family": "Farahani", "given": "Hossein Shahrabi", "initials": "HS"}, {"family": "Behm", "given": "Mikaela", "initials": "M"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "\u00d6hman", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "22", "issn": "1549-5469", "issue": "8", "pages": "1477-1487", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "Adenosine-to-inosine (A-to-I) RNA editing targets double-stranded RNA stem-loop structures in the mammalian brain. It has previously been shown that miRNAs are substrates for A-to-I editing. For the first time, we show that for several definitions of edited miRNA, the level of editing increases with development, thereby indicating a regulatory role for editing during brain maturation. We use high-throughput RNA sequencing to determine editing levels in mature miRNA, from the mouse transcriptome, and compare these with the levels of editing in pri-miRNA. We show that increased editing during development gradually changes the proportions of the two miR-376a isoforms, which previously have been shown to have different targets. Several other miRNAs that also are edited in the seed sequence show an increased level of editing through development. By comparing editing of pri-miRNA with editing and expression of the corresponding mature miRNA, we also show an editing-induced developmental regulation of miRNA expression. Taken together, our results imply that RNA editing influences the miRNA repertoire during brain maturation.", "doi": "10.1101/gr.131912.111", "pmid": "22645261", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "gr.131912.111"}, {"db": "pmc", "key": "PMC3409261"}], "notes": [], "created": "2017-05-04T14:57:35.081Z", "modified": "2020-01-21T13:56:10.278Z"}, {"entity": "publication", "iuid": "f3a5d8a2efa1444794240df1cde7dfb1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a5d8a2efa1444794240df1cde7dfb1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a5d8a2efa1444794240df1cde7dfb1"}}, "title": "A genome-wide association study identifies KNG1 as a genetic determinant of plasma factor XI Level and activated partial thromboplastin time.", "authors": [{"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Martinez-Perez", "given": "Angel", "initials": "A"}, {"family": "Buil", "given": "Alfonso", "initials": "A"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Souto", "given": "Juan Carlos", "initials": "JC"}, {"family": "Bruzelius", "given": "Maria", "initials": "M"}, {"family": "Borrell", "given": "Montserrat", "initials": "M"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Almasy", "given": "Laura", "initials": "L"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Soria", "given": "Jos\u00e9 Manuel", "initials": "JM"}], "type": "journal article", "published": "2012-08-00", "journal": {"volume": "32", "issn": "1524-4636", "issue": "8", "pages": "2008-2016", "title": "Arterioscler. Thromb. Vasc. Biol.", "issn-l": "1079-5642"}, "abstract": "Elevated plasma levels of coagulation factor XI (FXI) are implicated in the pathogenesis of venous thromboembolism and ischemic stroke, and polymorphisms in the F11 gene are associated both with risk of venous thromboembolism and an elevated plasma FXI level.\n\nHere, we report the first hypothesis-free genome-wide genetic analysis of plasma FXI levels. Two genome-wide significant loci were detected in the family-based Genetic Analysis of Idiopathic Thrombophilia 1 cohort: one located in the kininogen 1 gene (KNG1) (rs710446; P=7.98 \u00d7 10(-10)) and one located in the structural F11 gene (rs4241824; P=1.16 \u00d7 10(-8)). Both associations were replicated in a second population-based Swedish cohort. A significant effect on KNG1 mRNA expression was also seen for the 2 most robustly FXI-associated single nucleotide polymorphisms located in KNG1. Furthermore, both KNG1 single nucleotide polymorphisms were associated with activated partial thromboplastin time, suggesting that FXI may be the main mechanistic pathway by which KNG1 and F11 influence activated partial thromboplastin time and risk of thrombosis.\n\nThese findings contribute to the emerging molecular basis of venous thromboembolism and, more importantly, help in understanding the biological regulation of a phenotype that has proved to have promising therapeutic properties in relation to thrombosis.", "doi": "10.1161/ATVBAHA.112.248492", "pmid": "22701019", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ATVBAHA.112.248492"}], "notes": [], "created": "2017-05-04T15:00:53.785Z", "modified": "2020-01-21T13:56:06.301Z"}, {"entity": "publication", "iuid": "867161b23dec4def849ff5da517f7aae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/867161b23dec4def849ff5da517f7aae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/867161b23dec4def849ff5da517f7aae"}}, "title": "Polyploidy and the evolution of complex traits.", "authors": [{"family": "Huminiecki", "given": "Lukasz", "initials": "L"}, {"family": "Conant", "given": "Gavin C", "initials": "GC"}], "type": "journal article", "published": "2012-07-30", "journal": {"volume": "2012", "issn": "2090-052X", "issue": null, "pages": "292068", "title": "Int J Evol Biol", "issn-l": null}, "abstract": "We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers' yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.", "doi": "10.1155/2012/292068", "pmid": "22900230", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC3413983"}], "notes": [], "created": "2017-05-04T14:56:15.763Z", "modified": "2020-01-21T13:53:20.637Z"}, {"entity": "publication", "iuid": "b2e641ad43514c72a5da8dc05a7d921a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2e641ad43514c72a5da8dc05a7d921a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2e641ad43514c72a5da8dc05a7d921a"}}, "title": "Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility.", "authors": [{"family": "Reinius", "given": "Lovisa E", "initials": "LE"}, {"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Joerink", "given": "Maaike", "initials": "M"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Dahl\u00e9n", "given": "Sven-Erik", "initials": "SE"}, {"family": "Greco", "given": "Dario", "initials": "D"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "clinical trial", "published": "2012-07-25", "journal": {"volume": "7", "issn": "1932-6203", "issue": "7", "pages": "e41361", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Methylation of cytosines at CpG sites is a common epigenetic DNA modification that can be measured by a large number of methods, now even in a genome-wide manner for hundreds of thousands of sites. The application of DNA methylation analysis is becoming widely popular in complex disorders, for example, to understand part of the \"missing heritability\". The DNA samples most readily available for methylation studies are derived from whole blood. However, blood consists of many functionally and developmentally distinct cell populations in varying proportions. We studied whether such variation might affect the interpretation of methylation studies based on whole blood DNA. We found in healthy male blood donors there is important variation in the methylation profiles of whole blood, mononuclear cells, granulocytes, and cells from seven selected purified lineages. CpG methylation between mononuclear cells and granulocytes differed for 22% of the 8252 probes covering the selected 343 genes implicated in immune-related disorders by genome-wide association studies, and at least one probe was differentially methylated for 85% of the genes, indicating that whole blood methylation results might be unintelligible. For individual genes, even if the overall methylation patterns might appear similar, a few CpG sites in the regulatory regions may have opposite methylation patterns (i.e., hypo/hyper) in the main blood cell types. We conclude that interpretation of whole blood methylation profiles should be performed with great caution and for any differences implicated in a disorder, the differences resulting from varying proportions of white blood cell types should be considered.", "doi": "10.1371/journal.pone.0041361", "pmid": "22848472", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-05695"}, {"db": "pmc", "key": "PMC3405143"}], "notes": [], "created": "2017-05-04T15:03:13.942Z", "modified": "2017-05-30T14:51:07.222Z"}, {"entity": "publication", "iuid": "2206ea195bdb4024815aa4e0581e3f73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2206ea195bdb4024815aa4e0581e3f73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2206ea195bdb4024815aa4e0581e3f73"}}, "title": "The presence of tumor associated macrophages in tumor stroma as a prognostic marker for breast cancer patients.", "authors": [{"family": "Medrek", "given": "Catharina", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Leandersson", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2012-07-23", "journal": {"volume": "12", "issn": "1471-2407", "issue": null, "pages": "306", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Tumor associated macrophages (TAMs) are alternatively activated macrophages that enhance tumor progression by promoting tumor cell invasion, migration and angiogenesis. TAMs have an anti-inflammatory function resembling M2 macrophages. CD163 is regarded as a highly specific monocyte/macrophage marker for M2 macrophages. In this study we evaluated the specificity of using the M2 macrophage marker CD163 as a TAM marker and compared its prognostic value with the more frequently used pan-macrophage marker CD68. We also analyzed the prognostic value of the localization of CD163(+) and CD68(+) myeloid cells in human breast cancer.\n\nThe extent of infiltrating CD163(+) or CD68(+) myeloid cells in tumor nest versus tumor stroma was evaluated by immunohistochemistry in tissue microarrays with tumors from 144 breast cancer cases. Spearman's Rho and \u03c7(2) tests were used to examine the correlations between CD163(+) or CD68(+) myeloid cells and clinicopathological parameters. Kaplan Meier analysis and Cox proportional hazards modeling were used to assess the impact of CD163(+) and CD68(+) myeloid cells in tumor stroma and tumor nest, respectively, on recurrence free survival, breast cancer specific and overall survival.\n\nWe found that infiltration of CD163(+) and CD68(+) macrophages into tumor stroma, but not into tumor nest, were of clinical relevance. CD163(+) macrophages in tumor stroma positively correlated with higher grade, larger tumor size, Ki67 positivity, estrogen receptor negativity, progesterone receptor negativity, triple-negative/basal-like breast cancer and inversely correlated with luminal A breast cancer. Some CD163(+) areas lacked CD68 expression, suggesting that CD163 could be used as a general anti-inflammatory myeloid marker with prognostic impact. CD68(+) macrophages in tumor stroma positively correlated to tumor size and inversely correlated to luminal A breast cancer. More importantly, CD68 in tumor stroma was an independent prognostic factor for reduced breast cancer specific survival.\n\nThese findings highlight the importance of analyzing the localization rather than merely the presence of TAMs as a prognostic marker for breast cancer patients.", "doi": "10.1186/1471-2407-12-306", "pmid": "22824040", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1471-2407-12-306"}, {"db": "pmc", "key": "PMC3414782"}], "notes": [], "created": "2017-05-04T14:55:49.746Z", "modified": "2017-05-30T14:54:43.506Z"}, {"entity": "publication", "iuid": "815a472b1ede4289b7872379d1eb350b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/815a472b1ede4289b7872379d1eb350b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/815a472b1ede4289b7872379d1eb350b"}}, "title": "Functional analysis of two PLA2G2A variants associated with secretory phospholipase A2-IIA levels.", "authors": [{"family": "Exeter", "given": "Holly J", "initials": "HJ"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Palmen", "given": "Jutta", "initials": "J"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Cooper", "given": "Jackie A", "initials": "JA"}, {"family": "Kalea", "given": "Anastasia Z", "initials": "AZ"}, {"family": "Hooft", "given": "Ferdinand Van't", "initials": "FV"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}], "type": "journal article", "published": "2012-07-17", "journal": {"volume": "7", "issn": "1932-6203", "issue": "7", "pages": "e41139", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Secretory phospholipase A2 group IIA (sPLA2-IIA) has been identified as a biomarker of atherosclerosis in observational and animal studies. The protein is encoded by the PLA2G2A gene and the aim of this study was to test the functionality of two PLA2G2A non-coding SNPs, rs11573156 C>G and rs3767221 T>G where the rare alleles have been previously associated with higher and lower sPLA2-IIA levels respectively.\n\nLuciferase assays, electrophoretic mobility shift assays (EMSA), and RNA expression by RT-PCR were used to examine allelic differences. For rs3767221 the G allele showed \u223c55% lower luciferase activity compared to the T allele (T\u200a=\u200a62.1 (95% CI 59.1 to 65.1) G\u200a=\u200a27.8 (95% CI 25.0 to 30.6), p\u200a=\u200a1.22\u00d710\u207b\u00b3\u2075, and stronger EMSA binding of a nuclear protein compared to the T-allele. For rs11573156 C >G there were no luciferase or EMSA allelic differences seen. In lymphocyte cell RNA, from individuals of known rs11573156 genotype, there was no allelic RNA expression difference for exons 5 and 6, but G allele carriers (n\u200a=\u200a7) showed a trend to lower exon 1-2 expression compared to CC individuals. To take this further, in the ASAP study (n\u200a=\u200a223), an rs11573156 proxy (r\u00b2\u200a=\u200a0.91) showed \u223c25% higher liver expression of PLA2G2A (1.67\u00d710\u207b\u00b9\u2077) associated with the G allele. However, considering exon specific expression, the association was greatly reduced for exon 2 (4.5\u00d710\u207b\u2075) compared to exons 3-6 (10\u207b\u00b9\u2070 to 10\u207b\u00b2\u2070), suggesting rs11573156 G allele-specific exon 2 skipping.\n\nBoth SNPs are functional and provide useful tools for Mendelian Randomisation to determine whether the relationship between sPLA2-IIA and coronary heart disease is causal.", "doi": "10.1371/journal.pone.0041139", "pmid": "22879865", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-11961"}, {"db": "pmc", "key": "PMC3412631"}], "notes": [], "created": "2017-05-04T15:01:10.186Z", "modified": "2020-01-21T13:56:03.368Z"}, {"entity": "publication", "iuid": "94208020417e409086bbd8fe9ba46ad9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94208020417e409086bbd8fe9ba46ad9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94208020417e409086bbd8fe9ba46ad9"}}, "title": "Small molecule screening for inhibitors of the YopH phosphatase of Yersinia pseudotuberculosis.", "authors": [{"family": "Eriksson", "given": "Jonas", "initials": "J"}, {"family": "Grundstr\u00f6m", "given": "Christin", "initials": "C"}, {"family": "Sauer-Eriksson", "given": "A Elisabeth", "initials": "AE"}, {"family": "Sauer", "given": "Uwe H", "initials": "UH"}, {"family": "Wolf-Watz", "given": "Hans", "initials": "H"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2012-07-12", "journal": {"volume": "954", "issn": "0065-2598", "issue": null, "pages": "357-363", "title": "Adv. Exp. Med. Biol.", "issn-l": null}, "abstract": null, "doi": "10.1007/978-1-4614-3561-7_43", "pmid": "22782782", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:37.621Z", "modified": "2025-10-17T13:04:30.563Z"}, {"entity": "publication", "iuid": "dc5853e1c9694941a377fbc6a057c489", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc5853e1c9694941a377fbc6a057c489.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc5853e1c9694941a377fbc6a057c489"}}, "title": "Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.", "authors": [{"family": "Hammond", "given": "Maria", "initials": "M", "orcid": "0000-0002-8375-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/78703c93891e4827aabb35c2011be9f2.json"}}, {"family": "Nong", "given": "Rachel Yuan", "initials": "RY"}, {"family": "Ericsson", "given": "Olle", "initials": "O"}, {"family": "Pardali", "given": "Katerina", "initials": "K"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2012-07-10", "journal": {"volume": "7", "issn": "1932-6203", "issue": "7", "pages": "e40405", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.", "doi": "10.1371/journal.pone.0040405", "pmid": "22808155", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "PONE-D-12-05955"}, {"db": "pmc", "key": "PMC3393744"}], "notes": [], "created": "2017-05-04T14:55:24.055Z", "modified": "2023-04-14T13:56:30.628Z"}, {"entity": "publication", "iuid": "cf46f4fc293f4987b7abe9996f9626c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf46f4fc293f4987b7abe9996f9626c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf46f4fc293f4987b7abe9996f9626c9"}}, "title": "Automated selected reaction monitoring software for accurate label-free protein quantification.", "authors": [{"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Waldemarson", "given": "Sofia", "initials": "S"}, {"family": "Hansson", "given": "Karin", "initials": "K"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-07-06", "journal": {"volume": "11", "issn": "1535-3907", "issue": "7", "pages": "3766-3773", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.", "doi": "10.1021/pr300256x", "pmid": "22658081", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC3426189"}], "notes": [], "created": "2017-05-04T14:56:16.974Z", "modified": "2020-01-21T13:53:20.874Z"}, {"entity": "publication", "iuid": "9c03ca6098d34e65a2be5a046c08844c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c03ca6098d34e65a2be5a046c08844c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c03ca6098d34e65a2be5a046c08844c"}}, "title": "Ethanol effects on apparent solubility of poorly soluble drugs in simulated intestinal fluid.", "authors": [{"family": "Fagerberg", "given": "Jonas H", "initials": "JH"}, {"family": "Al-Tikriti", "given": "Yassir", "initials": "Y"}, {"family": "Ragnarsson", "given": "Gert", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Christel A S", "initials": "CAS"}], "type": "journal article", "published": "2012-07-02", "journal": {"volume": "9", "issn": "1543-8392", "issue": "7", "pages": "1942-1952", "title": "Mol. Pharm.", "issn-l": "1543-8384"}, "abstract": "Ethanol intake can lead to an unexpected and possibly problematic increase in the bioavailability of druglike compounds. In this work we investigated the effect of ethanol on the apparent solubility and dissolution rate of poorly soluble compounds in simulated intestinal fluid representing a preprandial state. A series of 22 structurally diverse, poorly soluble compounds were measured for apparent solubility and intrinsic dissolution rate (37 \u00b0C) in phosphate buffer pH 6.5 (PhB6.5) and fasted state simulated intestinal fluid (FaSSIF, pH 6.5) with and without ethanol at 5% v/v or 20% v/v. The obtained data were used to understand for which molecules ethanol results in an increased apparent solubility and, therefore, may increase the amount of drug absorbed. In FaSSIF20%ethanol 59% of the compounds displayed >3-fold higher apparent solubility than in pure FaSSIF, whereas the effects of 5% ethanol on solubility, in most cases, were negligible. Acidic and neutral compounds were more solubilized by the addition of ethanol than by lecithin/taurocholate aggregates, whereas bases showed a more substance-specific response to the additives in the buffer. The stronger solubilizing capacity of ethanol as compared to the mixed lipid aggregates in FaSSIF was further identified through Spearman rank analyses, which showed a stronger relationship between FaSSIF20%ethanol and PhB6.5,20%ethanol (rS of 0.97) than FaSSIF20%ethanol and FaSSIF (rS of 0.86). No relationships were found between solubility changes in media containing ethanol and single physicochemical properties, but multivariate data analysis showed that inclusion of ethanol significantly reduced the negative effect of compound lipophilicity on solubility. For this data set the higher concentration of ethanol gave a dose number (Do) <1 for 30% of the compounds that showed incomplete dissolution in FaSSIF. Significant differences were shown in the melting point, lipophilicity, and dose profiles between the compounds having a Do < 1 and Do > 1, with the latter having higher absolute values in all three parameters. In conclusion, this study showed that significant effects of ethanol on apparent solubility in the preprandial state can be expected for lipophilic compounds. The results herein indicate that acidic and neutral compounds are more sensitive to the addition of ethanol than to the mixed lipid aggregates present in the fasted intestine.", "doi": "10.1021/mp2006467", "pmid": "22651218", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-04T14:56:45.297Z", "modified": "2025-10-17T13:04:30.579Z"}, {"entity": "publication", "iuid": "9717935191f64e5688d7f2ab0b015919", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9717935191f64e5688d7f2ab0b015919.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9717935191f64e5688d7f2ab0b015919"}}, "title": "Polymorphisms and variants in the prion protein sequence of European moose (Alces alces), reindeer (Rangifer tarandus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) in Scandinavia.", "authors": [{"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Mikko", "given": "Sofia", "initials": "S"}, {"family": "Klingeborn", "given": "Mikael", "initials": "M"}, {"family": "St\u00e9en", "given": "Margareta", "initials": "M"}, {"family": "Simonsson", "given": "Magnus", "initials": "M"}, {"family": "Linn\u00e9", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2012-07-01", "journal": {"volume": "6", "issn": "1933-690X", "issue": "3", "pages": "256-260", "title": "Prion", "issn-l": "1933-6896"}, "abstract": "The prion protein (PrP) sequence of European moose, reindeer, roe deer and fallow deer in Scandinavia has high homology to the PrP sequence of North American cervids. Variants in the European moose PrP sequence were found at amino acid position 109 as K or Q. The 109Q variant is unique in the PrP sequence of vertebrates. During the 1980s a wasting syndrome in Swedish moose, Moose Wasting Syndrome (MWS), was described. SNP analysis demonstrated a difference in the observed genotype proportions of the heterozygous Q/K and homozygous Q/Q variants in the MWS animals compared with the healthy animals. In MWS moose the allele frequencies for 109K and 109Q were 0.73 and 0.27, respectively, and for healthy animals 0.69 and 0.31. Both alleles were seen as heterozygotes and homozygotes. In reindeer, PrP sequence variation was demonstrated at codon 176 as D or N and codon 225 as S or Y. The PrP sequences in roe deer and fallow deer were identical with published GenBank sequences.", "doi": "10.4161/pri.19641", "pmid": "22441661", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "19641"}, {"db": "pmc", "key": "PMC3399539"}], "notes": [], "created": "2017-05-04T14:57:45.115Z", "modified": "2020-01-21T13:56:10.566Z"}, {"entity": "publication", "iuid": "9d0b3263877c406a863f351a4ddaeaac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d0b3263877c406a863f351a4ddaeaac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d0b3263877c406a863f351a4ddaeaac"}}, "title": "The role of obesity-related genetic loci in insulin sensitivity.", "authors": [{"family": "Fall", "given": "T", "initials": "T"}, {"family": "Arnl\u00f6v", "given": "J", "initials": "J"}, {"family": "Berne", "given": "C", "initials": "C"}, {"family": "Ingelsson", "given": "E", "initials": "E"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "29", "issn": "1464-5491", "issue": "7", "pages": "e62-e66", "title": "Diabet. Med.", "issn-l": "0742-3071"}, "abstract": "Despite rapid advancements and many new diabetes susceptibility loci found in the past few years, few genetic variants associated with insulin sensitivity have been described, potentially attributable to the lack of larger cohorts examined with gold standard methods for insulin sensitivity assessment. There is a strong link between obesity and insulin sensitivity, and we hypothesized that known obesity susceptibility loci may act via effects on insulin sensitivity.\n\nA cohort of 71-year-old men without diabetes (Uppsala Longitudinal Study of Adult Men) underwent a euglycaemic-hyperinsulinaemic clamp and genotyping for genetic variants representing 32 loci recently reported to be associated with BMI (n = 926). The effect of these loci on the insulin sensitivity index (M/I ratio) was examined using linear regression. An in silico replication was performed in publically available data for the three top single-nucleotide polymorphisms from the Meta-Analyses of Glucose and Insulin-related traits Consortium analyses of homeostasis model assessment of insulin resistance (n = 37,037).\n\nThree loci (SH2B1, MTCH2 and NEGR1) were associated with decreased insulin sensitivity at a nominal significance (P \u2264 0.05) after adjustment for BMI, but did not hold for multiple comparison correction. SH2B1 rs7359397 was also associated with homeostasis model assessment of insulin resistance in the Meta-Analyses of Glucose and Insulin-related traits Consortium data set (P = 3.9 \u00d7 10(-3)).\n\nOur study supports earlier reports of SH2B1 to be of importance in insulin sensitivity and, in addition, suggests potential roles of NEGR1 and MTCH2.", "doi": "10.1111/j.1464-5491.2012.03665.x", "pmid": "22443470", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:57.547Z", "modified": "2020-01-21T13:56:04.076Z"}, {"entity": "publication", "iuid": "a8a647fae4e14476b12653f6b774884b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8a647fae4e14476b12653f6b774884b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8a647fae4e14476b12653f6b774884b"}}, "title": "Pain sensitivity and opioid analgesia: a pharmacogenomic twin study.", "authors": [{"family": "Angst", "given": "Martin S", "initials": "MS"}, {"family": "Phillips", "given": "Nicholas G", "initials": "NG"}, {"family": "Drover", "given": "David R", "initials": "DR"}, {"family": "Tingle", "given": "Martha", "initials": "M"}, {"family": "Ray", "given": "Amrita", "initials": "A"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "Lazzeroni", "given": "Laura C", "initials": "LC"}, {"family": "Clark", "given": "J David", "initials": "JD"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "153", "issn": "1872-6623", "issue": "7", "pages": "1397-1409", "title": "Pain", "issn-l": "0304-3959"}, "abstract": "Opioids are the cornerstone medication for the management of moderate to severe pain. Unfortunately, vast inter-individual differences in dose requirements complicate their effective and safe clinical use. Mechanisms underlying such differences are incompletely understood, are likely multifactorial, and include genetic and environmental contributions. While accumulating evidence suggests that variants of several genes account for some of the observed response variance, the relative contribution of these factors remains unknown. This study used a twin paradigm to provide a global estimate of the genetic and environmental contributions to inter-individual differences in pain sensitivity and analgesic opioid effects. Eighty one monozygotic and 31 dizygotic twin pairs successfully underwent a computer-controlled infusion with the \u03bc-opioid agonist alfentanil in a single occasion, randomized, double-blind and placebo-controlled study design. Pain sensitivity and analgesic effects were assessed with experimental heat and cold pressor pain models along with important covariates including demographic factors, depression, anxiety, and sleep quality. Significant heritability was detected for cold pressor pain tolerance and opioid-mediated elevations in heat and cold pressor pain thresholds. Genetic effects accounted for 12-60% of the observed response variance. Significant familial effects accounting for 24-32% of observed variance were detected for heat and cold pressor pain thresholds and opioid-mediated elevation in cold pressor pain tolerance. Significant covariates included age, gender, race, education, and anxiety. Results provide a strong rationale for more detailed molecular genetic studies to elucidate mechanisms underlying inter-individual differences in pain sensitivity and analgesic opioid responses. Such studies will require careful consideration of the studied pain phenotype.", "doi": "10.1016/j.pain.2012.02.022", "pmid": "22444188", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "S0304-3959(12)00098-X"}, {"db": "pmc", "key": "PMC3377769"}, {"db": "mid", "key": "NIHMS365869"}], "notes": [], "created": "2017-05-04T15:03:33.760Z", "modified": "2017-05-30T12:45:10.575Z"}, {"entity": "publication", "iuid": "cb3714bba2054d88a6db98b25edb4c9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb3714bba2054d88a6db98b25edb4c9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb3714bba2054d88a6db98b25edb4c9c"}}, "title": "Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia.", "authors": [{"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Gunnarsson", "given": "Rebeqa", "initials": "R"}, {"family": "Sutton", "given": "Lesley-Ann", "initials": "LA"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Hooper", "given": "Sean D", "initials": "SD"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "comparative study", "published": "2012-07-00", "journal": {"volume": "87", "issn": "1096-8652", "issue": "7", "pages": "737-740", "title": "Am. J. Hematol.", "issn-l": "0361-8609"}, "abstract": "Advances in next-generation RNA-sequencing have revealed the complexity of transcriptomes by allowing both coding and noncoding(nc)RNAs to be analyzed. However, limited data exist regarding the whole transcriptional landscape of chronic lymphocytic leukemia(CLL). In this pilot-study, we evaluated RNA-sequencing in CLL by comparing two subsets which carry almost identical or \"stereotyped\" B-cell receptors with distinct clinical outcome, that is the poor-prognostic subset #1 (n 5 4) and the more favorable-prognostic subset #4(n 5 4). Our analysis revealed that 156 genes (e.g. LPL, WNT9A) and 76 ncRNAs, (e.g. SNORD48, SNORD115) were differentially expressed between the subsets. This technology also enabled us to identify numerous subset-specific splice variants (n 5 406), which were predominantly expressed in subset #1, including a splice-isoform of MSI2 with a novel start exon. A further important application of RNA-sequencing was for mutation detection and revealed 16\u201330 missense mutations per sample; notably many of these changes were found in genes with a strong potential for involvement in CLL pathogenesis, e.g., ATM and NOTCH2.This study not only demonstrates the effectiveness of RNA-sequencing for identifying mutations, quantifying gene expression and detecting splicing events, but also highlights the potential such global approaches have to significantly advance our understanding of the molecular mechanisms behind CLL development.", "doi": "10.1002/ajh.23227", "pmid": "22674506", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:27.993Z", "modified": "2021-07-07T14:37:06.614Z"}, {"entity": "publication", "iuid": "2dcdb8e3c2f24c5b99d98055a892c20f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2dcdb8e3c2f24c5b99d98055a892c20f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2dcdb8e3c2f24c5b99d98055a892c20f"}}, "title": "Intercellular variation in signaling through the TGF-\u03b2 pathway and its relation to cell density and cell cycle phase.", "authors": [{"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Pardali", "given": "Katerina", "initials": "K"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Lindbom", "given": "Lena", "initials": "L"}, {"family": "Nystr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A"}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "7", "pages": "M111.013482", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Fundamental open questions in signal transduction remain concerning the sequence and distribution of molecular signaling events among individual cells. In this work, we have characterized the intercellular variability of transforming growth factor \u03b2-induced Smad interactions, providing essential information about TGF-\u03b2 signaling and its dependence on the density of cell populations and the cell cycle phase. By employing the recently developed in situ proximity ligation assay, we investigated the dynamics of interactions and modifications of Smad proteins and their partners under native and physiological conditions. We analyzed the kinetics of assembly of Smad complexes and the influence of cellular environment and relation to mitosis. We report rapid kinetics of formation of Smad complexes, including native Smad2-Smad3-Smad4 trimeric complexes, in a manner influenced by the rate of proteasomal degradation of these proteins, and we found a striking cell to cell variation of signaling complexes. The single-cell analysis of TGF-\u03b2 signaling in genetically unmodified cells revealed previously unknown aspects of regulation of this pathway, and it provided a basis for analysis of these signaling events to diagnose pathological perturbations in patient samples and to evaluate their susceptibility to drug treatment.", "doi": "10.1074/mcp.M111.013482", "pmid": "22442258", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "M111.013482"}, {"db": "pmc", "key": "PMC3394940"}], "notes": [], "created": "2017-05-04T14:55:23.162Z", "modified": "2023-04-14T13:56:30.884Z"}, {"entity": "publication", "iuid": "a89a4f4347a64c159d56300081f3b1d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a89a4f4347a64c159d56300081f3b1d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a89a4f4347a64c159d56300081f3b1d0"}}, "title": "Ichthyin/NIPAL4 localizes to keratins and desmosomes in epidermis and Ichthyin mutations affect epidermal lipid metabolism.", "authors": [{"family": "Dahlqvist", "given": "Johanna", "initials": "J"}, {"family": "Westermark", "given": "Gunilla T", "initials": "GT"}, {"family": "Vahlquist", "given": "Anders", "initials": "A"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "304", "issn": "1432-069X", "issue": "5", "pages": "377-386", "title": "Arch. Dermatol. Res.", "issn-l": "0340-3696"}, "abstract": "Autosomal recessive congenital ichthyosis (ARCI) is a group of disorders characterized by abnormal desquamation of the skin and a disrupted epidermal water barrier. Ichthyin/NIPAL4 gene mutations have been identified in a subgroup of ARCI patients, but the role of ichthyin in epidermis remains elusive. In order to obtain new insights concerning the characteristics of ichthyin and the ARCI pathogenesis, we studied the expression and localization of ichthyin and related epidermal components in cultured keratinocytes and skin sections from patients with Ichthyin mutations and healthy controls. We observed an up-regulation of Ichthyin mRNA levels after in vitro differentiation of keratinocytes from both a patient with Ichthyin mutations and controls. Confocal and electron microscopy analyses of immunolabeled skin sections revealed that ichthyin localizes to desmosomes and keratins in both patients with mutant Ichthyin and controls, with an increased immunolabeling in patients. Nile red lipid analysis of skin sections exposed intra-cellular lipid accumulations in cells of the granular and cornified layers in patients but not in controls, consistent with the pathognomonic lipid membrane structures previously identified in epidermis from patients. Our combined findings indicate that ichthyin is associated with keratins and desmosomes in epidermis and is involved in lipid metabolism, possibly through processing of lamellar bodies. These results provide new clues to the understanding of the epidermal water barrier and the pathogenesis in ARCI.", "doi": "10.1007/s00403-012-1207-7", "pmid": "22258272", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:29.505Z", "modified": "2020-01-21T13:56:04.394Z"}, {"entity": "publication", "iuid": "efe49673e51f460dbdd00db39b1312a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efe49673e51f460dbdd00db39b1312a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efe49673e51f460dbdd00db39b1312a0"}}, "title": "Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation.", "authors": [{"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}, {"family": "Schielzeth", "given": "Holger", "initials": "H"}, {"family": "Mueller", "given": "Jakob C", "initials": "JC"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Kempenaers", "given": "Bart", "initials": "B"}], "type": "comparative study", "published": "2012-07-00", "journal": {"volume": "21", "issn": "1365-294X", "issue": "13", "pages": "3237-3249", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Numerous studies have reported associations between heterozygosity in microsatellite markers and fitness-related traits (heterozygosity-fitness correlations, HFCs). However, it has often been questioned whether HFCs reflect general inbreeding depression, because a small panel of microsatellite markers does not reflect very well an individual's inbreeding coefficient (F) as calculated from a pedigree. Here, we challenge this prevailing view. Because of chance events during Mendelian segregation, an individual's realized proportion of the genome that is identical by descent (IBD) may substantially deviate from the pedigree-based expectation (i.e. F). This Mendelian noise may result in a weak correlation between F and multi-locus heterozygosity, but this does not imply that multi-locus heterozygosity is a bad estimator of realized IBD. We examined correlations between 11 fitness-related traits measured in up to 1192 captive zebra finches and three measures of inbreeding: (i) heterozygosity across 11 microsatellite markers, (ii) heterozygosity across 1359 single-nucleotide polymorphism (SNP) markers and (iii) F, based on a 5th-generation pedigree. All 11 phenotypic traits showed positive relationships with measures of heterozygosity, especially traits that are most closely related to fitness. Remarkably, the small panel of microsatellite markers produced equally strong HFCs as the large panel of SNP markers. Both marker-based approaches produced stronger correlations with phenotypes than the pedigree-based F, and this did not seem to result from the shortness of our pedigree. We argue that a small panel of microsatellites with high allelic richness may better reflect an individual's realized IBD than previously appreciated, especially in species like the zebra finch, where much of the genome is inherited in large blocks that rarely experience cross-over during meiosis.", "doi": "10.1111/j.1365-294X.2012.05593.x", "pmid": "22554318", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:03.149Z", "modified": "2020-01-21T13:56:06.147Z"}, {"entity": "publication", "iuid": "07171d4ce6724a6598e447a657b526fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07171d4ce6724a6598e447a657b526fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07171d4ce6724a6598e447a657b526fc"}}, "title": "Effects of redox modulation by inhibition of thioredoxin reductase on radiosensitivity and gene expression.", "authors": [{"family": "Selenius", "given": "Markus", "initials": "M"}, {"family": "Hedman", "given": "Mattias", "initials": "M"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Gandin", "given": "Valentina", "initials": "V"}, {"family": "Rigobello", "given": "Maria Pia", "initials": "MP"}, {"family": "Flygare", "given": "Jenny", "initials": "J"}, {"family": "Marzano", "given": "Christine", "initials": "C"}, {"family": "Bindoli", "given": "Alberto", "initials": "A"}, {"family": "Brodin", "given": "Ola", "initials": "O"}, {"family": "Bj\u00f6rnstedt", "given": "Mikael", "initials": "M"}, {"family": "Fernandes", "given": "Aristi P", "initials": "AP"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "16", "issn": "1582-4934", "issue": "7", "pages": "1593-1605", "title": "J. Cell. Mol. Med.", "issn-l": "1582-1838"}, "abstract": "The thioredoxin system is a promising target when aiming to overcome the problem of clinical radiation resistance. Altered cellular redox status and redox sensitive thiols contributing to induction of resistance strongly connect the ubiquitous redox enzyme thioredoxin reductase (TrxR) to the cellular response to ionizing radiation. To further investigate possible strategies in combating clinical radiation resistance, human radio-resistant lung cancer cells were subjected to a combination of single fractions of \u03b3-radiation at clinically relevant doses and non-toxic levels of a well-characterized thioredoxin reductase inhibitor, the phosphine gold(I) compound [Au(SCN)(PEt(3))]. The combination of the TrxR-inhibitor and ionizing radiation reduced the surviving fractions and impaired the ability of the U1810 cells to repopulate by approximately 50%. In addition, inhibition of thioredoxin reductase caused changes in the cell cycle distribution, suggesting a disturbance of the mitotic process. Global gene expression analysis also revealed clustered genetic expression changes connected to several major cellular pathways such as cell cycle, cellular response to stress and DNA damage. Specific TrxR-inhibition as a factor behind the achieved results was confirmed by correlation of gene expression patterns between gold and siRNA treatment. These results clearly demonstrate TrxR as an important factor conferring resistance to irradiation and the use of [Au(SCN)(PEt(3))] as a promising radiosensitizing agent.", "doi": "10.1111/j.1582-4934.2011.01469.x", "pmid": "22003958", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pmc", "key": "PMC3823227"}], "notes": [], "created": "2017-05-04T15:03:12.270Z", "modified": "2017-05-30T12:40:39.730Z"}, {"entity": "publication", "iuid": "1c8a41436f684808b7311863612b92d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c8a41436f684808b7311863612b92d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c8a41436f684808b7311863612b92d7"}}, "title": "Aversive and reinforcing opioid effects: a pharmacogenomic twin study.", "authors": [{"family": "Angst", "given": "Martin S", "initials": "MS"}, {"family": "Lazzeroni", "given": "Laura C", "initials": "LC"}, {"family": "Phillips", "given": "Nicholas G", "initials": "NG"}, {"family": "Drover", "given": "David R", "initials": "DR"}, {"family": "Tingle", "given": "Martha", "initials": "M"}, {"family": "Ray", "given": "Amrita", "initials": "A"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "Clark", "given": "J David", "initials": "JD"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "117", "issn": "1528-1175", "issue": "1", "pages": "22-37", "title": "Anesthesiology", "issn-l": "0003-3022"}, "abstract": "The clinical utility of opioids is limited by adverse drug effects including respiratory depression, sedation, nausea, and pruritus. In addition, abuse of prescription opioids is problematic. Gaining a better understanding of the genetic and environmental mechanisms contributing to an individual's susceptibility to adverse opioid effects is essential to identify patients at risk.\n\nA classic twin study paradigm provided estimates for the genetic and familial (genetic and/or shared environment) contribution to acute adverse and affective opioid responses, all secondary outcomes of a larger dataset. One hundred twenty-one twin pairs were recruited in a single occasion, randomized, double-blind, and placebo-controlled study. The \u03bc-opioid receptor agonist alfentanil and saline placebo were administered as target-controlled infusions under carefully monitored laboratory conditions. Measured outcomes included respiratory depression, sedation, nausea, pruritus, drug liking, and drug disliking. Demographic information was collected, and aspects of mood and sleep were evaluated.\n\nSignificant heritability was detected for respiratory depression (30%), nausea (59%), and drug disliking (36%). Significant familial effects were detected for sedation (29%), pruritus (38%), dizziness (32%), and drug liking (26%). Significant covariates included age, sex, race, ethnicity, education, mood, and depression. Covariates affected sedation, pruritus, drug liking and disliking, and dizziness.\n\nThis study demonstrates that large-scale efforts to collect quantitative and well-defined opioid response data are not only feasible but also produce data that are suitable for genetic analysis. Genetic, environmental, and demographic factors work together to control adverse and reinforcing opioid responses, but contribute differently to specific responses.", "doi": "10.1097/ALN.0b013e31825a2a4e", "pmid": "22713632", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "00000542-201207000-00012"}, {"db": "pmc", "key": "PMC3428265"}, {"db": "mid", "key": "NIHMS386120"}], "notes": [], "created": "2017-05-04T15:03:33.147Z", "modified": "2017-05-30T12:45:01.208Z"}, {"entity": "publication", "iuid": "a4e87d7afcb74dcab930371d037b5828", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4e87d7afcb74dcab930371d037b5828.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4e87d7afcb74dcab930371d037b5828"}}, "title": "Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research.", "authors": [{"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Edqvist", "given": "Per-Henrik D", "initials": "PH"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "12", "issn": "1615-9861", "issue": "13", "pages": "2067-2077", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "In this review, we present an update on the progress of the Human Protein Atlas, with an emphasis on strategies for validating immunohistochemistry-based protein expression patterns and on the possibilities to extend the map of protein expression patterns for cancer research projects. The objectives underlying the Human Protein Atlas include (i) the generation of validated antibodies toward a major isoform of all proteins encoded by the human genome, (ii) creating an information database of protein expression patterns in normal human tissues, in cells, and in cancer, and (iii) utilizing generated antibodies and protein expression data as tools to identify clinically useful biomarkers. The success of such an effort is dependent on the validity of antibodies as specific binders of intended targets in applications used to map protein expression patterns. The development of strategies to support specific target binding is crucial and remains a challenge as a large fraction of proteins encoded by the human genome is poorly characterized, including the approximately one-third of all proteins lacking evidence of existence. Conceivable methods for validation include the use of paired antibodies, i.e. two independent antibodies targeting different and nonoverlapping epitopes on the same protein as well as comparative analysis of mRNA expression patterns with corresponding proteins.", "doi": "10.1002/pmic.201100504", "pmid": "22623277", "labels": {"Tissue Profiling": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:54.101Z", "modified": "2021-07-08T12:07:34.209Z"}, {"entity": "publication", "iuid": "0d57c18748214d2ebfcfa7819a6aafe6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d57c18748214d2ebfcfa7819a6aafe6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d57c18748214d2ebfcfa7819a6aafe6"}}, "title": "1012 Synergistic Effects of PI3K or P38 MAPK Inhibition in Combination With Vandetanib Treatment in Glioblastoma Cells", "authors": [{"family": "Sooman", "given": "L", "initials": "L"}, {"family": "Ekman", "given": "S", "initials": "S"}, {"family": "Andersson", "given": "C", "initials": "C"}, {"family": "Johansson", "given": "F", "initials": "F"}, {"family": "Goransson-Kultima", "given": "H", "initials": "H"}, {"family": "Isaksson", "given": "A", "initials": "A"}, {"family": "Bergqvist", "given": "M", "initials": "M"}, {"family": "Blomquist", "given": "E", "initials": "E"}, {"family": "Lennartsson", "given": "J", "initials": "J"}, {"family": "Gullbo", "given": "J", "initials": "J"}], "type": "journal-article", "published": "2012-07-00", "journal": {"volume": "48", "issn": "0959-8049", "issue": null, "pages": "S244", "title": "European Journal of Cancer", "issn-l": "0959-8049"}, "abstract": null, "doi": "10.1016/s0959-8049(12)71629-5", "pmid": null, "labels": {"Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:57.525Z", "modified": "2021-06-22T12:06:35.202Z"}, {"entity": "publication", "iuid": "8d686769990245d6bee2d1286d5dd436", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d686769990245d6bee2d1286d5dd436.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d686769990245d6bee2d1286d5dd436"}}, "title": "Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos.", "authors": [{"family": "Holmqvist", "given": "Per-Henrik", "initials": "P"}, {"family": "Boija", "given": "Ann", "initials": "A"}, {"family": "Philip", "given": "Philge", "initials": "P"}, {"family": "Crona", "given": "Filip", "initials": "F"}, {"family": "Stenberg", "given": "Per", "initials": "P"}, {"family": "Mannervik", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2012-06-21", "journal": {"volume": "8", "issn": "1553-7404", "issue": "6", "pages": "e1002769", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "CBP and the related p300 protein are widely used transcriptional co-activators in metazoans that interact with multiple transcription factors. Whether CBP/p300 occupies the genome equally with all factors or preferentially binds together with some factors is not known. We therefore compared Drosophila melanogaster CBP (nejire) ChIP-seq peaks with regions bound by 40 different transcription factors in early embryos, and we found high co-occupancy with the Rel-family protein Dorsal. Dorsal is required for CBP occupancy in the embryo, but only at regions where few other factors are present. CBP peaks in mutant embryos lacking nuclear Dorsal are best correlated with TGF-\u00df/Dpp-signaling and Smad-protein binding. Differences in CBP occupancy in mutant embryos reflect gene expression changes genome-wide, but CBP also occupies some non-expressed genes. The presence of CBP at silent genes does not result in histone acetylation. We find that Polycomb-repressed H3K27me3 chromatin does not preclude CBP binding, but restricts histone acetylation at CBP-bound genomic sites. We conclude that CBP occupancy in Drosophila embryos preferentially overlaps factors controlling dorso-ventral patterning and that CBP binds silent genes without causing histone hyperacetylation.", "doi": "10.1371/journal.pgen.1002769", "pmid": "22737084", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-00343"}, {"db": "pmc", "key": "PMC3380834"}], "notes": [], "created": "2017-05-04T14:57:41.775Z", "modified": "2020-01-21T13:56:10.579Z"}, {"entity": "publication", "iuid": "c1d946b9f3d94a48bb6bb42aa2eac167", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1d946b9f3d94a48bb6bb42aa2eac167.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1d946b9f3d94a48bb6bb42aa2eac167"}}, "title": "Geographic differences in genetic susceptibility to IgA nephropathy: GWAS replication study and geospatial risk analysis.", "authors": [{"family": "Kiryluk", "given": "Krzysztof", "initials": "K"}, {"family": "Li", "given": "Yifu", "initials": "Y"}, {"family": "Sanna-Cherchi", "given": "Simone", "initials": "S"}, {"family": "Rohanizadegan", "given": "Mersedeh", "initials": "M"}, {"family": "Suzuki", "given": "Hitoshi", "initials": "H"}, {"family": "Eitner", "given": "Frank", "initials": "F"}, {"family": "Snyder", "given": "Holly J", "initials": "HJ"}, {"family": "Choi", "given": "Murim", "initials": "M"}, {"family": "Hou", "given": "Ping", "initials": "P"}, {"family": "Scolari", "given": "Francesco", "initials": "F"}, {"family": "Izzi", "given": "Claudia", "initials": "C"}, {"family": "Gigante", "given": "Maddalena", "initials": "M"}, {"family": "Gesualdo", "given": "Loreto", "initials": "L"}, {"family": "Savoldi", "given": "Silvana", "initials": "S"}, {"family": "Amoroso", "given": "Antonio", "initials": "A"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Zamboli", "given": "Pasquale", "initials": "P"}, {"family": "Julian", "given": "Bruce A", "initials": "BA"}, {"family": "Novak", "given": "Jan", "initials": "J"}, {"family": "Wyatt", "given": "Robert J", "initials": "RJ"}, {"family": "Mucha", "given": "Krzysztof", "initials": "K"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Viktorin", "given": "Alexander", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Boland", "given": "Anne", "initials": "A"}, {"family": "Metzger", "given": "Marie", "initials": "M"}, {"family": "Thibaudin", "given": "Lise", "initials": "L"}, {"family": "Wanner", "given": "Christoph", "initials": "C"}, {"family": "Jager", "given": "Kitty J", "initials": "KJ"}, {"family": "Goto", "given": "Shin", "initials": "S"}, {"family": "Maixnerova", "given": "Dita", "initials": "D"}, {"family": "Karnib", "given": "Hussein H", "initials": "HH"}, {"family": "Nagy", "given": "Judit", "initials": "J"}, {"family": "Panzer", "given": "Ulf", "initials": "U"}, {"family": "Xie", "given": "Jingyuan", "initials": "J"}, {"family": "Chen", "given": "Nan", "initials": "N"}, {"family": "Tesar", "given": "Vladimir", "initials": "V"}, {"family": "Narita", "given": "Ichiei", "initials": "I"}, {"family": "Berthoux", "given": "Francois", "initials": "F"}, {"family": "Floege", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Stengel", "given": "Benedicte", "initials": "B"}, {"family": "Zhang", "given": "Hong", "initials": "H"}, {"family": "Lifton", "given": "Richard P", "initials": "RP"}, {"family": "Gharavi", "given": "Ali G", "initials": "AG"}], "type": "journal article", "published": "2012-06-21", "journal": {"volume": "8", "issn": "1553-7404", "issue": "6", "pages": "e1002765", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "IgA nephropathy (IgAN), major cause of kidney failure worldwide, is common in Asians, moderately prevalent in Europeans, and rare in Africans. It is not known if these differences represent variation in genes, environment, or ascertainment. In a recent GWAS, we localized five IgAN susceptibility loci on Chr.6p21 (HLA-DQB1/DRB1, PSMB9/TAP1, and DPA1/DPB2 loci), Chr.1q32 (CFHR3/R1 locus), and Chr.22q12 (HORMAD2 locus). These IgAN loci are associated with risk of other immune-mediated disorders such as type I diabetes, multiple sclerosis, or inflammatory bowel disease. We tested association of these loci in eight new independent cohorts of Asian, European, and African-American ancestry (N\u200a=\u200a4,789), followed by meta-analysis with risk-score modeling in 12 cohorts (N\u200a=\u200a10,755) and geospatial analysis in 85 world populations. Four susceptibility loci robustly replicated and all five loci were genome-wide significant in the combined cohort (P\u200a=\u200a5\u00d710\u207b\u00b3\u00b2-3\u00d710\u207b\u00b9\u2070), with heterogeneity detected only at the PSMB9/TAP1 locus (I\u00b2\u200a=\u200a0.60). Conditional analyses identified two new independent risk alleles within the HLA-DQB1/DRB1 locus, defining multiple risk and protective haplotypes within this interval. We also detected a significant genetic interaction, whereby the odds ratio for the HORMAD2 protective allele was reversed in homozygotes for a CFHR3/R1 deletion (P\u200a=\u200a2.5\u00d710\u207b\u2074). A seven-SNP genetic risk score, which explained 4.7% of overall IgAN risk, increased sharply with Eastward and Northward distance from Africa (r\u200a=\u200a0.30, P\u200a=\u200a3\u00d710\u207b\u00b9\u00b2\u2078). This model paralleled the known East-West gradient in disease risk. Moreover, the prediction of a South-North axis was confirmed by registry data showing that the prevalence of IgAN-attributable kidney failure is increased in Northern Europe, similar to multiple sclerosis and type I diabetes. Variation at IgAN susceptibility loci correlates with differences in disease prevalence among world populations. These findings inform genetic, biological, and epidemiological investigations of IgAN and permit cross-comparison with other complex traits that share genetic risk loci and geographic patterns with IgAN.", "doi": "10.1371/journal.pgen.1002765", "pmid": "22737082", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-02636"}, {"db": "pmc", "key": "PMC3380840"}], "notes": [], "created": "2017-10-30T13:48:14.214Z", "modified": "2020-01-21T13:56:08.412Z"}, {"entity": "publication", "iuid": "c715d94addb8457fb349e441761e4094", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c715d94addb8457fb349e441761e4094.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c715d94addb8457fb349e441761e4094"}}, "title": "Visualising individual sequence-specific protein-DNA interactions in situ.", "authors": [{"family": "Weibrecht", "given": "Irene", "initials": "I"}, {"family": "Gavrilovic", "given": "Milan", "initials": "M"}, {"family": "Lindbom", "given": "Lena", "initials": "L"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2012-06-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "5", "pages": "589-598", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "Gene expression - a key feature for modulating cell fate-is regulated in part by histone modifications, which modulate accessibility of the chromatin to transcription factors. Until now, protein-DNA interactions (PDIs) have mostly been studied in bulk without retrieving spatial information from the sample or with poor sequence resolution. New tools are needed to reveal proteins interacting with specific DNA sequences in situ for further understanding of the orchestration of transcriptional control within the nucleus. We present herein an approach to visualise individual PDIs within cells, based on the in situ proximity ligation assay (PLA). This assay, previously used for the detection of protein-protein interactions in situ, was adapted for analysis of target PDIs, using padlock probes to identify unique DNA sequences in complex genomes. As a proof-of-principle we detected histone H3 interacting with a 26 bp consensus sequence of the Alu-repeat abundantly expressed in the human genome, but absent in mice. However, the mouse genome contains a highly similar sequence, providing a model system to analyse the selectivity of the developed methods. Although efficiency of detection currently is limiting, we conclude that in situ PLA can be used to achieve a highly selective analysis of PDIs in single cells.", "doi": "10.1016/j.nbt.2011.08.002", "pmid": "21906700", "labels": {"BioImage Informatics": "Collaborative", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1871-6784(11)00186-5"}], "notes": [], "created": "2017-05-04T14:55:23.757Z", "modified": "2023-04-14T13:56:31.053Z"}, {"entity": "publication", "iuid": "1c65428b58d9411b8a95e81e4cab18b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c65428b58d9411b8a95e81e4cab18b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c65428b58d9411b8a95e81e4cab18b5"}}, "title": "Validation of affinity reagents using antigen microarrays.", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Sundberg", "given": "M\u00e5rten", "initials": "M"}, {"family": "Gundberg", "given": "Anna", "initials": "A"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2012-06-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "5", "pages": "555-563", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.", "doi": "10.1016/j.nbt.2011.11.009", "pmid": "22134247", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(11)00257-3"}], "notes": [], "created": "2017-05-04T14:55:37.189Z", "modified": "2021-07-08T13:44:33.060Z"}, {"entity": "publication", "iuid": "0224e341360f4089a0ae4444c38f10ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0224e341360f4089a0ae4444c38f10ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0224e341360f4089a0ae4444c38f10ef"}}, "title": "Local contamination in relation to population genetic diversity and resilience of an arctic marine amphipod.", "authors": [{"family": "Bach", "given": "Lis", "initials": "L"}, {"family": "Dahll\u00f6f", "given": "Ingela", "initials": "I"}], "type": "journal article", "published": "2012-06-15", "journal": {"volume": "114-115", "issn": "1879-1514", "issue": null, "pages": "58-66", "title": "Aquat. Toxicol.", "issn-l": "0166-445X"}, "abstract": "The objective of this study was to investigate whether populations inhabiting a contaminated environment are affected in terms of decreased genetic diversity due to selection of tolerant genotypes and if such effect carries a cost. Marine arctic amphipod populations (Orchomenella pinguis) were collected from sites within a contaminated fjord, as well as from sites outside the fjord on the west-coast of Greenland over three years (2006-2008). Impacts on genetic diversity, effects on resilience such as development of tolerance and cost were determined. AFLP-analysis was used to explore within and between population genetic diversity, and exposure studies were performed where the populations were subjected to known and unknown stressors to assess resilience. Populations collected at three contaminated sites all had reduced genetic diversity in 2007 compared to populations outside the fjord. This pattern was different in 2008 as all contaminated site populations increased in diversity, whereas a decrease in diversity occurred at the outer sites. However, tolerance, but even more so, cost, was related to contamination exposure in 2008, in spite of the shift in genetic diversity. We suggest that contamination rapidly induces effects that can be captured as tolerance and associated cost, whereas effects on genetic diversity can be difficult to separate from recent migration events that dilute eventual decreases in diversity due to contamination pressure. As long as impacted populations can be influenced by migration events that increase the genetic diversity and add health to an affected population, populations in contaminated areas may have enhanced probability of survival.", "doi": "10.1016/j.aquatox.2012.02.003", "pmid": "22421731", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0166-445X(12)00053-7"}], "notes": [], "created": "2017-05-04T14:57:29.209Z", "modified": "2020-01-21T13:56:10.510Z"}, {"entity": "publication", "iuid": "5baa7889c10943b3a05a955706c46c32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5baa7889c10943b3a05a955706c46c32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5baa7889c10943b3a05a955706c46c32"}}, "title": "Classification of protein profiles from antibody microarrays using heat and detergent treatment.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2012-06-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "5", "pages": "564-570", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "Antibody microarrays offer new opportunities for exploring the proteome and to identify biomarker candidates in human serum and plasma. Here, we have investigated the effect of heat and detergents on an antibody-based suspension bead array (SBA) assay using polyclonal antibodies and biotinylated plasma samples. With protein profiles from more than 2300 antibodies generated in 384-plex antibody SBAs, three major classes of heat and detergent susceptibility could be described. The results show that washing of the beads with SDS (rather than Tween) after target binding lowered intensity levels of basically all profiles and that about 50% of the profiles appeared to be lowered to a similar extent by heating of the sample. About 33% of the profiles appeared to be insensitive to heat treatment while another 17% showed a positive influence of heat to yield elevated profiles. The results suggest that the classification of antibodies is driven by the molecular properties of the antibody-antigen interaction and can generally not be predicted based on protein class or Western blot data. The experimental scheme presented here can be used to systematically categorize antibodies and thereby combine antibodies with similar properties into targeted arrays for analysis of plasma and serum.", "doi": "10.1016/j.nbt.2011.10.005", "pmid": "22023822", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(11)00225-1"}], "notes": [], "created": "2017-05-04T14:55:36.890Z", "modified": "2021-07-08T13:44:33.296Z"}, {"entity": "publication", "iuid": "4cdcfeca87f34f2f822ceb9860f55d36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4cdcfeca87f34f2f822ceb9860f55d36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4cdcfeca87f34f2f822ceb9860f55d36"}}, "title": "Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors.", "authors": [{"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Leroy", "given": "Bernard", "initials": "B"}, {"family": "Sundstr\u00f6m", "given": "Magnus", "initials": "M"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Soussi", "given": "Thierry", "initials": "T"}], "type": "journal article", "published": "2012-06-12", "journal": {"volume": "109", "issn": "1091-6490", "issue": "24", "pages": "9551-9556", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Cancer mutation databases are expected to play central roles in personalized medicine by providing targets for drug development and biomarkers to tailor treatments to each patient. The accuracy of reported mutations is a critical issue that is commonly overlooked, which leads to mutation databases that include a sizable number of spurious mutations, either sequencing errors or passenger mutations. Here we report an analysis of the latest version of the TP53 mutation database, including 34,453 mutations. By using several data-driven methods on multiple independent quality criteria, we obtained a quality score for each report contributing to the database. This score can now be used to filter for high-confidence mutations and reports within the database. Sequencing the entire TP53 gene from various types of cancer using next-generation sequencing with ultradeep coverage validated our approach for curation. In summary, 9.7% of all collected studies, mostly comprising numerous tumors with multiple infrequent TP53 mutations, should be excluded when analyzing TP53 mutations. Thus, by combining statistical and experimental analyses, we provide a curated mutation database for TP53 mutations and a framework for mutation database analysis.", "doi": "10.1073/pnas.1200019109", "pmid": "22628563", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1200019109"}, {"db": "pmc", "key": "PMC3386058"}], "notes": [], "created": "2017-05-04T14:57:39.750Z", "modified": "2021-07-07T14:37:06.445Z"}, {"entity": "publication", "iuid": "a63099587354485e85c31f1d7da135b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a63099587354485e85c31f1d7da135b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a63099587354485e85c31f1d7da135b0"}}, "title": "Integrative approach to pain genetics identifies pain sensitivity loci across diseases.", "authors": [{"family": "Ruau", "given": "David", "initials": "D"}, {"family": "Dudley", "given": "Joel T", "initials": "JT"}, {"family": "Chen", "given": "Rong", "initials": "R"}, {"family": "Phillips", "given": "Nicholas G", "initials": "NG"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "Lazzeroni", "given": "Laura C", "initials": "LC"}, {"family": "Clark", "given": "J David", "initials": "JD"}, {"family": "Butte", "given": "Atul J", "initials": "AJ"}, {"family": "Angst", "given": "Martin S", "initials": "MS"}], "type": "journal article", "published": "2012-06-07", "journal": {"volume": "8", "issn": "1553-7358", "issue": "6", "pages": "e1002538", "title": "PLoS Comput. Biol.", "issn-l": "1553-734X"}, "abstract": "Identifying human genes relevant for the processing of pain requires difficult-to-conduct and expensive large-scale clinical trials. Here, we examine a novel integrative paradigm for data-driven discovery of pain gene candidates, taking advantage of the vast amount of existing disease-related clinical literature and gene expression microarray data stored in large international repositories. First, thousands of diseases were ranked according to a disease-specific pain index (DSPI), derived from Medical Subject Heading (MESH) annotations in MEDLINE. Second, gene expression profiles of 121 of these human diseases were obtained from public sources. Third, genes with expression variation significantly correlated with DSPI across diseases were selected as candidate pain genes. Finally, selected candidate pain genes were genotyped in an independent human cohort and prospectively evaluated for significant association between variants and measures of pain sensitivity. The strongest signal was with rs4512126 (5q32, ABLIM3, P\u200a=\u200a1.3\u00d710\u207b\u00b9\u2070) for the sensitivity to cold pressor pain in males, but not in females. Significant associations were also observed with rs12548828, rs7826700 and rs1075791 on 8q22.2 within NCALD (P\u200a=\u200a1.7\u00d710\u207b\u2074, 1.8\u00d710\u207b\u2074, and 2.2\u00d710\u207b\u2074 respectively). Our results demonstrate the utility of a novel paradigm that integrates publicly available disease-specific gene expression data with clinical data curated from MEDLINE to facilitate the discovery of pain-relevant genes. This data-derived list of pain gene candidates enables additional focused and efficient biological studies validating additional candidates.", "doi": "10.1371/journal.pcbi.1002538", "pmid": "22685391", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PCOMPBIOL-D-12-00028"}, {"db": "pmc", "key": "PMC3369906"}], "notes": [], "created": "2017-05-04T15:03:34.063Z", "modified": "2017-05-30T14:52:27.480Z"}, {"entity": "publication", "iuid": "ede8b83029ae429f9d2c02612ae27f3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ede8b83029ae429f9d2c02612ae27f3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ede8b83029ae429f9d2c02612ae27f3d"}}, "title": "Which sequencing depth is sufficient to describe patterns in bacterial \u03b1- and \u03b2-diversity?", "authors": [{"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Severin", "given": "Ina", "initials": "I"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Ostman", "given": "Orjan", "initials": "O"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "4", "issn": "1758-2229", "issue": "3", "pages": "367-372", "title": "Environ Microbiol Rep", "issn-l": "1758-2229"}, "abstract": "The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 6-15 communities from which 15\u2003000-20\u2003000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in \u03b2-diversity (Bray-Curtis index) among samples observed for 15\u2003000-20\u2003000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in \u03b1-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.", "doi": "10.1111/j.1758-2229.2012.00345.x", "pmid": "23760801", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:15.460Z", "modified": "2020-01-21T13:53:20.940Z"}, {"entity": "publication", "iuid": "f2d694c8ca48410a9c6ffc35c151d0a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2d694c8ca48410a9c6ffc35c151d0a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2d694c8ca48410a9c6ffc35c151d0a1"}}, "title": "The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility.", "authors": [{"family": "Imsland", "given": "Freyja", "initials": "F"}, {"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Boije", "given": "Henrik", "initials": "H"}, {"family": "Bed'hom", "given": "Bertrand", "initials": "B"}, {"family": "Fillon", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Dorshorst", "given": "Ben", "initials": "B"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Liu", "given": "Ranran", "initials": "R"}, {"family": "Gao", "given": "Yu", "initials": "Y"}, {"family": "Gu", "given": "Xiaorong", "initials": "X"}, {"family": "Wang", "given": "Yanqiang", "initials": "Y"}, {"family": "Gourichon", "given": "David", "initials": "D"}, {"family": "Zody", "given": "Michael C", "initials": "MC"}, {"family": "Zecchin", "given": "William", "initials": "W"}, {"family": "Vieaud", "given": "Agathe", "initials": "A"}, {"family": "Tixier-Boichard", "given": "Mich\u00e8le", "initials": "M"}, {"family": "Hu", "given": "Xiaoxiang", "initials": "X"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}, {"family": "Li", "given": "Ning", "initials": "N"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "8", "issn": "1553-7404", "issue": "6", "pages": "e1002775", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Rose-comb, a classical monogenic trait of chickens, is characterized by a drastically altered comb morphology compared to the single-combed wild-type. Here we show that Rose-comb is caused by a 7.4 Mb inversion on chromosome 7 and that a second Rose-comb allele arose by unequal crossing over between a Rose-comb and wild-type chromosome. The comb phenotype is caused by the relocalization of the MNR2 homeodomain protein gene leading to transient ectopic expression of MNR2 during comb development. We also provide a molecular explanation for the first example of epistatic interaction reported by Bateson and Punnett 104 years ago, namely that walnut-comb is caused by the combined effects of the Rose-comb and Pea-comb alleles. Transient ectopic expression of MNR2 and SOX5 (causing the Pea-comb phenotype) occurs in the same population of mesenchymal cells and with at least partially overlapping expression in individual cells in the comb primordium. Rose-comb has pleiotropic effects, as homozygosity in males has been associated with poor sperm motility. We postulate that this is caused by the disruption of the CCDC108 gene located at one of the inversion breakpoints. CCDC108 is a poorly characterized protein, but it contains a MSP (major sperm protein) domain and is expressed in testis. The study illustrates several characteristic features of the genetic diversity present in domestic animals, including the evolution of alleles by two or more consecutive mutations and the fact that structural changes have contributed to fast phenotypic evolution.", "doi": "10.1371/journal.pgen.1002775", "pmid": "22761584", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-00059"}, {"db": "pmc", "key": "PMC3386170"}], "notes": [], "created": "2017-05-04T14:57:42.079Z", "modified": "2020-01-21T13:56:10.708Z"}, {"entity": "publication", "iuid": "2e18ae153fca422fab75e7d5adab2544", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e18ae153fca422fab75e7d5adab2544.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e18ae153fca422fab75e7d5adab2544"}}, "title": "Selection-driven gene loss in bacteria.", "authors": [{"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "Sun", "given": "Song", "initials": "S"}, {"family": "Berg", "given": "Otto G", "initials": "OG"}, {"family": "Andersson", "given": "Dan I", "initials": "DI"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "8", "issn": "1553-7404", "issue": "6", "pages": "e1002787", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Gene loss by deletion is a common evolutionary process in bacteria, as exemplified by bacteria with small genomes that have evolved from bacteria with larger genomes by reductive processes. The driving force(s) for genome reduction remains unclear, and here we examined the hypothesis that gene loss is selected because carriage of superfluous genes confers a fitness cost to the bacterium. In the bacterium Salmonella enterica, we measured deletion rates at 11 chromosomal positions and the fitness effects of several spontaneous deletions. Deletion rates varied over 200-fold between different regions with the replication terminus region showing the highest rates. Approximately 25% of the examined deletions caused an increase in fitness under one or several growth conditions, and after serial passage of wild-type bacteria in rich medium for 1,000 generations we observed fixation of deletions that substantially increased bacterial fitness when reconstructed in a non-evolved bacterium. These results suggest that selection could be a significant driver of gene loss and reductive genome evolution.", "doi": "10.1371/journal.pgen.1002787", "pmid": "22761588", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-00783"}, {"db": "pmc", "key": "PMC3386194"}], "notes": [], "created": "2017-05-04T15:01:09.579Z", "modified": "2020-01-21T13:56:01.299Z"}, {"entity": "publication", "iuid": "758e1c055935406dad8dddc45a6c2d60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/758e1c055935406dad8dddc45a6c2d60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/758e1c055935406dad8dddc45a6c2d60"}}, "title": "Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships.", "authors": [{"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Drakare", "given": "Stina", "initials": "S"}, {"family": "Lanz\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "6", "issn": "1751-7370", "issue": "6", "pages": "1127-1136", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine the bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22,669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few 'laws' in ecology.", "doi": "10.1038/ismej.2011.184", "pmid": "22170419", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ismej2011184"}, {"db": "pmc", "key": "PMC3358030"}], "notes": [], "created": "2017-05-04T14:57:35.982Z", "modified": "2020-01-21T13:56:03.068Z"}, {"entity": "publication", "iuid": "9674d68c923b43cea1ce8b3b2ac0dc9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9674d68c923b43cea1ce8b3b2ac0dc9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9674d68c923b43cea1ce8b3b2ac0dc9b"}}, "title": "Digital gene expression profiling of primary acute lymphoblastic leukemia cells.", "authors": [{"family": "Nordlund", "given": "J", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Kiialainen", "given": "A", "initials": "A"}, {"family": "Karlberg", "given": "O", "initials": "O"}, {"family": "Berglund", "given": "E C", "initials": "EC"}, {"family": "G\u00f6ransson-Kultima", "given": "H", "initials": "H"}, {"family": "S\u00f8nderk\u00e6r", "given": "M", "initials": "M"}, {"family": "Nielsen", "given": "K L", "initials": "KL"}, {"family": "Gustafsson", "given": "M G", "initials": "MG"}, {"family": "Behrendtz", "given": "M", "initials": "M"}, {"family": "Forestier", "given": "E", "initials": "E"}, {"family": "Perkki\u00f6", "given": "M", "initials": "M"}, {"family": "S\u00f6derh\u00e4ll", "given": "S", "initials": "S"}, {"family": "L\u00f6nnerholm", "given": "G", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "A-C", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "26", "issn": "1476-5551", "issue": "6", "pages": "1218-1227", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "We determined the genome-wide digital gene expression (DGE) profiles of primary acute lymphoblastic leukemia (ALL) cells from 21 patients taking advantage of 'second-generation' sequencing technology. Patients included in this study represent four cytogenetically distinct subtypes of B-cell precursor (BCP) ALL and T-cell lineage ALL (T-ALL). The robustness of DGE combined with supervised classification by nearest shrunken centroids (NSC) was validated experimentally and by comparison with published expression data for large sets of ALL samples. Genes that were differentially expressed between BCP ALL subtypes were enriched to distinct signaling pathways with dic(9;20) enriched to TP53 signaling, t(9;22) to interferon signaling, as well as high hyperdiploidy and t(12;21) to apoptosis signaling. We also observed antisense tags expressed from the non-coding strand of ~50% of annotated genes, many of which were expressed in a subtype-specific pattern. Antisense tags from 17 gene regions unambiguously discriminated between the BCP ALL and T-ALL subtypes, and antisense tags from 76 gene regions discriminated between the 4 BCP subtypes. We observed a significant overlap of gene regions with alternative polyadenylation and antisense transcription (P<1 \u00d7 10(-15)). Our study using DGE profiling provided new insights into the RNA expression patterns in ALL cells.", "doi": "10.1038/leu.2011.358", "pmid": "22173241", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "leu2011358"}, {"db": "pmc", "key": "PMC3377998"}, {"db": "GEO", "key": "GSE26878"}], "notes": [], "created": "2017-05-04T15:01:02.547Z", "modified": "2021-07-07T15:11:02.260Z"}, {"entity": "publication", "iuid": "7b404f49104f43e8920d6cbca0d50c4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b404f49104f43e8920d6cbca0d50c4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b404f49104f43e8920d6cbca0d50c4a"}}, "title": "Common and low-frequency genetic variants in the PCSK9 locus influence circulating PCSK9 levels.", "authors": [{"family": "Chernogubova", "given": "Ekaterina", "initials": "E"}, {"family": "Strawbridge", "given": "Rona", "initials": "R"}, {"family": "Mahdessian", "given": "Hovsep", "initials": "H"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Krapivner", "given": "Sergey", "initials": "S"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Hell\u00e9nius", "given": "Mai-Lis", "initials": "ML"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Troutt", "given": "Jason S", "initials": "JS"}, {"family": "Konrad", "given": "Robert J", "initials": "RJ"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "van 't Hooft", "given": "Ferdinand M", "initials": "FM"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "32", "issn": "1524-4636", "issue": "6", "pages": "1526-1534", "title": "Arterioscler. Thromb. Vasc. Biol.", "issn-l": "1079-5642"}, "abstract": "Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a circulating protein that influences plasma low-density lipoprotein concentration and susceptibility to coronary heart disease. Circulating PCSK9 levels show considerable interindividual differences, but the factors responsible for this variation are largely unknown.\n\nWe analyzed circulating PCSK9 levels in 4 cohorts of healthy, middle-aged Swedes (n=5722) and found that PCSK9 levels varied over \u224850-fold range, showed a positive relationship with plasma low-density lipoprotein-cholesterol concentration, and were associated with plasma triglyceride, fibrinogen, insulin, and glucose concentrations. A genome-wide association study conducted in 2 cohorts (n=1215) failed to uncover common genetic variants robustly associated with variation in circulating PCSK9 level. As expected, the minor allele of the PCSK9 R46L variant was in all cohorts associated with reduced PCSK9 levels and decreased plasma low-density lipoprotein-cholesterol concentrations, but no relationship was observed with the plasma triglyceride concentration. Further mapping of the PCSK9 locus revealed a common polymorphism (rs2479415, minor allele frequency 43.9%), located \u22486 kb upstream from PCSK9, which is independently associated with increased circulating PCSK9 levels.\n\nCommon and low-frequency genetic variants in the PCSK9 locus influence the pronounced interindividual variation in circulating PCSK9 levels in healthy, middle-aged white (predominantly Swedish) subjects.", "doi": "10.1161/ATVBAHA.111.240549", "pmid": "22460556", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ATVBAHA.111.240549"}], "notes": [], "created": "2017-05-04T15:00:53.483Z", "modified": "2021-07-07T15:11:02.530Z"}, {"entity": "publication", "iuid": "139c08524b4c4aad918a0b84fd25f836", "links": {"self": {"href": "https://publications.scilifelab.se/publication/139c08524b4c4aad918a0b84fd25f836.json"}, "display": {"href": "https://publications.scilifelab.se/publication/139c08524b4c4aad918a0b84fd25f836"}}, "title": "Association between genetic variants in the tumour necrosis factor/lymphotoxin \u03b1/lymphotoxin \u03b2 locus and primary Sjogren's syndrome in Scandinavian samples.", "authors": [{"family": "Bolstad", "given": "Anne Isine", "initials": "AI"}, {"family": "Le Hellard", "given": "Stephanie", "initials": "S"}, {"family": "Kristjansdottir", "given": "Gudlaug", "initials": "G"}, {"family": "Vasaitis", "given": "Lilian", "initials": "L"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Johnsen", "given": "Svein Joar Augl\u00e6nd", "initials": "SJ"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Theander", "given": "Elke", "initials": "E"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "71", "issn": "1468-2060", "issue": "6", "pages": "981-988", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "Lymphotoxin \u03b2 (LTB) has been found to be upregulated in salivary glands of patients with primary Sj\u00f6gren's syndrome (pSS). An animal model of pSS also showed ablation of the lymphoid organisation and a marked improvement in salivary gland function on blocking the LTB receptor pathway. This study aimed to investigate whether single-nucleotide polymorphisms (SNP) in the lymphotoxin \u03b1 (LTA)/LTB/tumour necrosis factor (TNF) gene clusters are associated with pSS.\n\n527 pSS patients and 532 controls participated in the study, all of Caucasian origin from Sweden and Norway. 14 SNP markers were genotyped and after quality control filtering, 12 SNP were analysed for their association with pSS using single marker and haplotype tests, and corrected by permutation testing.\n\nNine markers showed significant association with pSS at the p=0.05 level. Markers rs1800629 and rs909253 showed the strongest genotype association (p=1.64E-11 and p=4.42E-08, respectively, after correcting for sex and country of origin). When the analysis was conditioned for the effect of rs1800629, only the association with rs909253 remained nominally significant (p=0.027). In haplotype analyses the strongest effect was observed for the haplotype rs909253G_rs1800629A (p=9.14E-17). The associations were mainly due to anti-Ro/SSA and anti-La/SSB antibody-positive pSS.\n\nA strong association was found between several SNP in the LTA/LTB/TNF\u03b1 locus and pSS, some of which led to amino acid changes. These data suggest a role for this locus in the development of pSS. Further studies are needed to examine if the genetic effect described here is independent of the known genetic association between HLA and pSS.", "doi": "10.1136/annrheumdis-2011-200446", "pmid": "22294627", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "annrheumdis-2011-200446"}], "notes": [], "created": "2017-05-04T15:00:53.178Z", "modified": "2021-07-07T15:11:02.297Z"}, {"entity": "publication", "iuid": "f514e4bc75ea468aa19f05ee6aeec896", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f514e4bc75ea468aa19f05ee6aeec896.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f514e4bc75ea468aa19f05ee6aeec896"}}, "title": "Accelerated proliferation and differential global gene expression in pancreatic islets of five-week-old heterozygous Men1 mice: Men1 is a haploinsufficient suppressor.", "authors": [{"family": "Lejonklou", "given": "Margareta H", "initials": "MH"}, {"family": "Barbu", "given": "Andreea", "initials": "A"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Skogseid", "given": "Britt", "initials": "B"}], "type": "journal article", "published": "2012-06-00", "journal": {"volume": "153", "issn": "1945-7170", "issue": "6", "pages": "2588-2598", "title": "Endocrinology", "issn-l": "0013-7227"}, "abstract": "Individuals carrying heterozygous (hz) MEN1 (Multiple Endocrine Neoplasia Syndrome Type 1) germ line mutations develop endocrine tumors as a result of somatic loss of the wild-type (wt) allele. However, endocrine cell proliferation has been observed despite wt allele retention, indicating haploinsufficiency. To study downstream molecular effects of the hz haplotype, a germ line Men1 hz mouse model was used to explore differences in global endocrine pancreatic gene expression. Because islet cells of 5-wk-old hz mice express Menin from the retained wt Men1 allele, these were isolated after collagenase digestion of the pancreas, and used for global gene expression array. Wild-type littermates were used for comparison. Array findings were corroborated by quantitative PCR, Western blotting, in situ proximity ligation assay, and immunohistochemistry. The hz islets show increased proliferation: the Ki-67 index was twice as high as in wt islets (3.48 vs. 1.74%; P = 0.024). The microarray results demonstrated that several genes were differentially expressed. Some selected genes were studied on the protein level, e.g. the cytoskeletal regulator myristoylated alanine-rich protein kinase C substrate (Marcks) was significantly less expressed in hz islets, using in situ proximity ligation assay and Western blotting (P < 0.001 and P < 0.01, respectively). Further, gene ontology analysis showed that genes with higher mRNA expression in the hz endocrine pancreas were associated with e.g. chromatin maintenance and apoptosis. Lower mRNA was observed for genes involved in growth factor binding. In conclusion, despite retained Menin expression, proliferation was accelerated, and numerous genes were differentially expressed in the endocrine pancreas of 5-wk-old hz Men1 mice, corroborating the hypothesis that MEN1 is a haploinsufficient suppressor.", "doi": "10.1210/en.2011-1924", "pmid": "22492302", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "en.2011-1924"}, {"db": "GEO", "key": "GSE29674"}], "notes": [], "created": "2017-05-04T15:02:56.685Z", "modified": "2017-05-30T12:36:59.271Z"}, {"entity": "publication", "iuid": "6febd91cfc7343b3ab701b87788adbc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6febd91cfc7343b3ab701b87788adbc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6febd91cfc7343b3ab701b87788adbc9"}}, "title": "A novel variant in plakophilin-2 gene detected in a family with arrhythmogenic right ventricular cardiomyopathy.", "authors": [{"family": "Ostrowska Dahlgren", "given": "Bozena", "initials": "B"}, {"family": "Allen", "given": "Marie", "initials": "M"}, {"family": "Lindstr\u00f6m", "given": "Anne-Cristine", "initials": "AC"}, {"family": "Bjerke", "given": "Mia", "initials": "M"}, {"family": "Blomstr\u00f6m-Lundqvist", "given": "Carina", "initials": "C"}], "type": "case reports", "published": "2012-06-00", "journal": {"volume": "34", "issn": "1572-8595", "issue": "1", "pages": "11-18", "title": "J Interv Card Electrophysiol", "issn-l": "1383-875X"}, "abstract": "Arrhythmogenic right ventricular cardiomyopathy (ARVC) is characterized by fibrofatty replacement of muscular fibers predominantly in the right ventricle and with ventricular arrhythmias as the main clinical manifestation. Mutations in several components of the desmosome genes have been identified and mutations of the plakophilin-2 (PKP-2) gene are a common cause of ARVC. The aim of this study is to investigate the correlation between genotype and phenotype in a family with a novel PKP-2 variant.\n\nThis study describes the clinical findings and genetic analysis in a family with ARVC. A part of the family has been followed clinically long term for up to 27 years. Two not previously reported PKP-2 variants (L506P and T526A) have been identified in this family. Even though all members of this family share the novel variant L506P, the clinical features, i.e., their phenotypes are different. The L506P variant is located in exon 7 and affects a highly conserved residue. The same amino acid, leucine, is present in all species evaluated, indicating a functional importance and the variant is predicted to be damaging. The novel L506P variant in the PKP-2 gene is thus a possible pathogenic alteration in the described family with ARVC. In contrast, the T526A variant is weakly conserved and predicted to be tolerated.\n\nWhile many of the reported ARVC mutations are truncating mutations, the possibly damaging variant found in this family, is a missense alteration affecting a highly conserved residue 506 located in exon 7.", "doi": "10.1007/s10840-011-9643-4", "pmid": "22170284", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:37.793Z", "modified": "2020-01-21T13:56:02.931Z"}, {"entity": "publication", "iuid": "8f44f12eedf540b28ebffd763b0558e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f44f12eedf540b28ebffd763b0558e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f44f12eedf540b28ebffd763b0558e4"}}, "title": "A non-peptide receptor inhibitor with selectivity for one of the neutrophil formyl peptide receptors, FPR 1", "authors": [{"family": "\u00c7evik-Aras", "given": "H\u00fclya", "initials": "H"}, {"family": "Kalder\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Jenmalm Jensen", "given": "Annika", "initials": "A"}, {"family": "Oprea", "given": "Tudor", "initials": "T"}, {"family": "Dahlgren", "given": "Claes", "initials": "C"}, {"family": "Forsman", "given": "Huamei", "initials": "H"}], "type": "journal-article", "published": "2012-06-00", "journal": {"volume": "83", "issn": "0006-2952", "issue": "12", "pages": "1655-1662", "title": "Biochemical Pharmacology", "issn-l": "0006-2952"}, "abstract": null, "doi": "10.1016/j.bcp.2012.02.024", "pmid": "22410002", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T11:51:00.867Z", "modified": "2025-10-17T13:04:30.603Z"}, {"entity": "publication", "iuid": "7a04598235434276bde1de8902aecc37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a04598235434276bde1de8902aecc37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a04598235434276bde1de8902aecc37"}}, "title": "Production of tissue microarrays, immunohistochemistry staining and digitalization within the human protein atlas.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Olsson", "given": "Ingmarie", "initials": "I"}, {"family": "Ryberg", "given": "Urban", "initials": "U"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-05-31", "journal": {"volume": null, "issn": "1940-087X", "issue": "63", "title": "J Vis Exp", "issn-l": "1940-087X"}, "abstract": "The tissue microarray (TMA) technology provides the means for high-throughput analysis of multiple tissues and cells. The technique is used within the Human Protein Atlas project for global analysis of protein expression patterns in normal human tissues, cancer and cell lines. Here we present the assembly of 1 mm cores, retrieved from microscopically selected representative tissues, into a single recipient TMA block. The number and size of cores in a TMA block can be varied from approximately forty 2 mm cores to hundreds of 0.6 mm cores. The advantage of using TMA technology is that large amount of data can rapidly be obtained using a single immunostaining protocol to avoid experimental variability. Importantly, only limited amount of scarce tissue is needed, which allows for the analysis of large patient cohorts (1 2). Approximately 250 consecutive sections (4 \u03bcm thick) can be cut from a TMA block and used for immunohistochemical staining to determine specific protein expression patterns for 250 different antibodies. In the Human Protein Atlas project, antibodies are generated towards all human proteins and used to acquire corresponding protein profiles in both normal human tissues from 144 individuals and cancer tissues from 216 different patients, representing the 20 most common forms of human cancer. Immunohistochemically stained TMA sections on glass slides are scanned to create high-resolution images from which pathologists can interpret and annotate the outcome of immunohistochemistry. Images together with corresponding pathology-based annotation data are made publically available for the research community through the Human Protein Atlas portal (www.proteinatlas.org) (Figure 1) (3 4). The Human Protein Atlas provides a map showing the distribution and relative abundance of proteins in the human body. The current version contains over 11 million images with protein expression data for 12.238 unique proteins, corresponding to more than 61% of all proteins encoded by the human genome.", "doi": "10.3791/3620", "pmid": "22688270", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "3620"}, {"db": "pmc", "key": "PMC3468196"}], "notes": [], "created": "2017-05-04T14:55:52.693Z", "modified": "2017-05-30T14:55:25.250Z"}, {"entity": "publication", "iuid": "bd6cc0589fdb4e1d93caa541c88748eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd6cc0589fdb4e1d93caa541c88748eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd6cc0589fdb4e1d93caa541c88748eb"}}, "title": "Evidence for a negative association between schizophrenia and a polymorphism in the insulin receptor substrate-3 (IRS-3) gene.", "authors": [{"family": "Melkersson", "given": "Kristina", "initials": "K"}, {"family": "Persson", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2012-05-29", "journal": {"volume": "33", "issn": "0172-780X", "issue": "3", "pages": "321-330", "title": "Neuro Endocrinol. Lett.", "issn-l": null}, "abstract": "Since there are clear indications that schizophrenia is a systemic disorder, we sought for a common molecular basis for schizophrenia abnormalities in brain and body. Our hypothesis was that an impaired insulin and insulin-like growth factor signalling in cells might underlie changes in both brain and body in schizophrenia. In this regard, the insulin receptor substrates 1-4, linking both the insulin and insulin-like growth factor-1 receptors with intracellular pathways, might be of interest to study genetically. In the present study, we chose to study the insulin receptor substrate-3 (IRS-3) gene as a candidate gene in schizophrenia.\r\n\r\nThe IRS-3 gene of 93 patients with the diagnosis of schizophrenia according to DSM-IV criteria and 57 healthy control subjects was screened for DNA sequence variations, followed by case-control analyses of total 10 detected polymorphisms.\r\n\r\nThe A/G genotype of the single nucleotide polymorphism (SNP) rs117078492 in the IRS-3 gene occurred in 5.3% of the control subjects compared with in 0% of the patients (p=0.05). Similarly, the haplotypes 5 and 3X, constructed from polymorphisms in the IRS-3 gene and including the A allele of this A/G SNP, occurred only in the control subjects and not in the patients (5.3% vs 0%, p=0.05).\r\n\r\nOur findings suggest that individuals carrying the A allele of this A/G SNP in the IRS-3 gene as well as the estimated haplotypes 5 or 3X including this A allele, have a protection against schizophrenia development.", "doi": "10.1016/S0924-9338(13)77131-1", "pmid": "22635093", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "NEL330312A01"}], "notes": [], "created": "2017-05-04T14:57:39.236Z", "modified": "2020-01-21T13:56:10.388Z"}, {"entity": "publication", "iuid": "bd5b16445ce74721bc53e6cef5718b08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd5b16445ce74721bc53e6cef5718b08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd5b16445ce74721bc53e6cef5718b08"}}, "title": "Classification of Inhibitors of Hepatic Organic Anion Transporting Polypeptides (OATPs): Influence of Protein Expression on Drug\u2013Drug Interactions", "authors": [{"family": "Karlgren", "given": "Maria", "initials": "M"}, {"family": "Vildhede", "given": "Anna", "initials": "A"}, {"family": "Norinder", "given": "Ulf", "initials": "U"}, {"family": "Wisniewski", "given": "Jacek R", "initials": "JR"}, {"family": "Kimoto", "given": "Emi", "initials": "E"}, {"family": "Lai", "given": "Yurong", "initials": "Y"}, {"family": "Haglund", "given": "Ulf", "initials": "U"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal-article", "published": "2012-05-24", "journal": {"volume": "55", "issn": "0022-2623", "issue": "10", "pages": "4740-4763", "title": "J. Med. Chem.", "issn-l": null}, "abstract": null, "doi": "10.1021/jm300212s", "pmid": "22541068", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T11:47:16.325Z", "modified": "2025-10-17T13:04:30.649Z"}, {"entity": "publication", "iuid": "d01d2834e0694ec0aa8169038b729eeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d01d2834e0694ec0aa8169038b729eeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d01d2834e0694ec0aa8169038b729eeb"}}, "title": "The MAP2K5-linked SNP rs2241423 is associated with BMI and obesity in two cohorts of Swedish and Greek children.", "authors": [{"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Jacobsson", "given": "Josefin A", "initials": "JA"}, {"family": "Moschonis", "given": "George", "initials": "G"}, {"family": "Ek", "given": "Anna E", "initials": "AE"}, {"family": "Chrousos", "given": "George P", "initials": "GP"}, {"family": "Marcus", "given": "Claude", "initials": "C"}, {"family": "Manios", "given": "Yannis", "initials": "Y"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2012-05-17", "journal": {"volume": "13", "issn": "1471-2350", "issue": null, "pages": "36", "title": "BMC Med. Genet.", "issn-l": "1471-2350"}, "abstract": "Recent genome-wide association studies have identified a single nucleotide polymorphism within the last intron of MAP2K5 associated with a higher body mass index (BMI) in adults. MAP2K5 is a component of the MAPK-family intracellular signaling pathways, responding to extracellular growth factors such as brain derived neurotrophic factor (BDNF) and nerve growth factor (NGF). In this study, we examined the association of this variant in two cohorts of children from Sweden and Greece.\r\n\r\nWe examine the association of rs2241423 to BMI in a cohort of 474 Swedish children admitted for treatment of childhood obesity and 519 children matched for gender, ethnicity and socioeconomic background from the Stockholm area, as well as a cross-sectional cohort of 2308 Greek school children (Healthy Growth Study). Children were genotyped using a predesigned TaqMan polymorphism assay. Logistic regression was used to test for an association of rs2241423 to obesity in the cohort of Swedish children. Linear regression was used to test for an association of rs2241423 to BMI z-score and phenotypic measurements of body adiposity in the cohort of Greek children. Models were adjusted for age and gender. In the cohort of Greek children the model was also adjusted for stage of pubertal development.\r\n\r\nThe minor allele of rs2241423, allele A, was associated with a protective effect against obesity in the cohort of Swedish children (p = 0.029, OR = 0.79 (95% CI: 0.64-0.98)), and with a lower BMI z-score in the cohort of Greek children (p = 0.028, \u03b2 =\u2009-0.092). No association to phenotypic measurements of body fat distribution could be observed in our study.\r\n\r\nrs2241423 was associated with BMI and obesity in two independent European cohorts suggesting a role for MAP2K5 in early weight regulation.", "doi": "10.1186/1471-2350-13-36", "pmid": "22594783", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2350-13-36"}, {"db": "pmc", "key": "PMC3459804"}], "notes": [], "created": "2017-05-04T14:57:31.854Z", "modified": "2020-01-21T13:56:10.677Z"}, {"entity": "publication", "iuid": "a580c7a5d0084601a61580195b1fe625", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a580c7a5d0084601a61580195b1fe625.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a580c7a5d0084601a61580195b1fe625"}}, "title": "Novel pancreatic beta cell-specific proteins: antibody-based proteomics for identification of new biomarker candidates.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}], "type": "journal article", "published": "2012-05-17", "journal": {"volume": "75", "issn": "1876-7737", "issue": "9", "pages": "2611-2620", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Beta cell-specific surface targets are required for non-invasive monitoring of beta cell mass, which could be used for evaluation of new diabetes treatments as well as to help unravel pathogenic mechanisms underlying beta cell dysfunction. By antibody-based proteomics, we have identified and explored a set of islet cell-specific proteins. A search algorithm in the Human Protein Atlas was set up for identification of islet-specific proteins that yielded 27 hits, of which twelve showed a clear membranous expression pattern or had predicted transmembrane regions. The specificity of the identified proteins was investigated by immunohistochemical staining of pancreas sections from diabetic and non-diabetic subjects. No expression of these antigens could be detected in the exocrine pancreas. Colocalization with insulin and glucagon was further determined by confocal microscopy using isolated human islets. All antibodies specifically stained human islets and colocalization analysis revealed that four proteins were exclusively expressed in beta cells. Importantly, these antibodies were negative in sections from subjects with long-standing type 1 diabetes. In the present study, we present four proteins; DGCR2, GBF1, GPR44 and SerpinB10, the expression of which has not previously been described in beta cells.", "doi": "10.1016/j.jprot.2012.03.008", "pmid": "22465717", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(12)00141-8"}], "notes": [], "created": "2017-05-04T14:55:52.393Z", "modified": "2017-05-30T12:55:57.867Z"}, {"entity": "publication", "iuid": "30fdfaa075dc4fb989512e63e2e06a13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30fdfaa075dc4fb989512e63e2e06a13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30fdfaa075dc4fb989512e63e2e06a13"}}, "title": "GABA-A channel subunit expression in human glioma correlates with tumor histology and clinical outcome.", "authors": [{"family": "Smits", "given": "Anja", "initials": "A"}, {"family": "Jin", "given": "Zhe", "initials": "Z"}, {"family": "Elsir", "given": "Tamador", "initials": "T"}, {"family": "Pedder", "given": "Hugo", "initials": "H"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I"}, {"family": "Dimberg", "given": "Anna", "initials": "A"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Aronica", "given": "Eleonora", "initials": "E"}, {"family": "Birnir", "given": "Bryndis", "initials": "B"}], "type": "journal article", "published": "2012-05-17", "journal": {"volume": "7", "issn": "1932-6203", "issue": "5", "pages": "e37041", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "GABA (\u03b3-aminobutyric acid) is the main inhibitory neurotransmitter in the CNS and is present in high concentrations in presynaptic terminals of neuronal cells. More recently, GABA has been ascribed a more widespread role in the control of cell proliferation during development where low concentrations of extrasynaptic GABA induce a tonic activation of GABA receptors. The GABA-A receptor consists of a ligand-gated chloride channel, formed by five subunits that are selected from 19 different subunit isoforms. The functional and pharmacological properties of the GABA-A channels are dictated by their subunit composition. Here we used qRT-PCR to compare mRNA levels of all 19 GABA-A channel subunits in samples of human glioma (n = 29) and peri-tumoral tissue (n = 5). All subunits except the \u03c11 and \u03c13 subunit were consistently detected. Lowest mRNA levels were found in glioblastoma compared to gliomas of lower malignancy, except for the \u03b8 subunit. The expression and cellular distribution of the \u03b11, \u03b31, \u03c12 and \u03b8 subunit proteins was investigated by immunohistochemistry on tissue microarrays containing 87 gliomas grade II. We found a strong co-expression of \u03c12 and \u03b8 subunits in both astrocytomas (r = 0.86, p<0.0001) and oligodendroglial tumors (r = 0.66, p<0.0001). Kaplan-Meier analysis and Cox proportional hazards modeling to estimate the impact of GABA-A channel subunit expression on survival identified the \u03c12 subunit (p = 0.043) but not the \u03b8 subunit (p = 0.64) as an independent predictor of improved survival in astrocytomas, together with established prognostic factors. Our data give support for the presence of distinct GABA-A channel subtypes in gliomas and provide the first link between specific composition of the A-channel and patient survival.", "doi": "10.1371/journal.pone.0037041", "pmid": "22615883", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-03413"}, {"db": "pmc", "key": "PMC3355166"}], "notes": [], "created": "2017-05-04T14:55:53.503Z", "modified": "2017-05-30T14:54:52.781Z"}, {"entity": "publication", "iuid": "e449c00db18f42919a98ddd7b5c19260", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e449c00db18f42919a98ddd7b5c19260.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e449c00db18f42919a98ddd7b5c19260"}}, "title": "Association between a genetic variant in the serotonin transporter gene (SLC6A4) and suicidal behavior in patients with schizophrenia.", "authors": [{"family": "Lindholm Carlstr\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Rosengren", "given": "Anders", "initials": "A"}, {"family": "Thygesen", "given": "Johan H", "initials": "JH"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Hall", "given": "H\u00e5kan", "initials": "H"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}], "type": "journal article", "published": "2012-05-17", "journal": {"volume": "8", "issn": "1744-9081", "issue": null, "pages": "24", "title": "Behav Brain Funct", "issn-l": "1744-9081"}, "abstract": "The serotonin (5-hydroxytryptamin; 5-HT) system has a central role in the circuitry of cognition and emotions. Multiple lines of evidence suggest that genetic variation in the serotonin transporter gene (SLC6A4; 5-HTT) is associated with schizophrenia and suicidal behavior. In this study, we wanted to elucidate whether SLC6A4 variations is involved in attempted suicide among patients with schizophrenia in a Scandinavian case-control sample.\n\nPatients diagnosed with schizophrenia from three Scandinavian samples were assessed for presence or absence of suicide attempts, based on record reviews and interview data. Seven SLC6A4 single nucleotide polymorphisms (SNPs) were genotyped in 837 schizophrenia patients and 1,473 control individuals. Association analyses and statistical evaluations were performed with the program UNPHASED (version 3.0.9).\n\nWe observed an allele association between the SNP rs16965628, located in intron one of SLC6A4, and attempted suicide (adjusted p-value 0.01), among patients with schizophrenia. No association was found to a diagnosis of schizophrenia, when patients were compared to healthy control individuals.\n\nThe gene SLC6A4 appears to be involved in suicidal ideation among patients with schizophrenia. Independent replication is needed before more firm conclusions can be drawn.", "doi": "10.1186/1744-9081-8-24", "pmid": "22594806", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1744-9081-8-24"}, {"db": "pmc", "key": "PMC3527134"}], "notes": [], "created": "2017-05-04T15:00:54.396Z", "modified": "2020-01-21T13:56:05.868Z"}, {"entity": "publication", "iuid": "cd1de4f3c7744ffaa632497dcbbca399", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd1de4f3c7744ffaa632497dcbbca399.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd1de4f3c7744ffaa632497dcbbca399"}}, "title": "MAGI1 copy number variation in bipolar affective disorder and schizophrenia.", "authors": [{"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Graae", "given": "Lisette", "initials": "L"}, {"family": "Lekman", "given": "Magnus", "initials": "M"}, {"family": "Wang", "given": "Dai", "initials": "D"}, {"family": "Favis", "given": "Reyna", "initials": "R"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Galter", "given": "Dagmar", "initials": "D"}, {"family": "Belin", "given": "Andrea Carmine", "initials": "AC"}, {"family": "Paddock", "given": "Silvia", "initials": "S"}], "type": "journal article", "published": "2012-05-15", "journal": {"volume": "71", "issn": "1873-2402", "issue": "10", "pages": "922-930", "title": "Biol. Psychiatry", "issn-l": "0006-3223"}, "abstract": "Bipolar affective disorder (BPAD) and schizophrenia (SZ) are devastating psychiatric disorders that each affect about 1% of the population worldwide. Identification of new drug targets is an important step toward better treatment of these poorly understood diseases.\n\nGenome-wide copy number variation (CNV) was assessed and variants were ranked by co-occurrence with disease in 48 BPAD families. Additional support for involvement of the highest-ranking CNV from the family-based analysis in psychiatric disease was obtained through analysis of 4084 samples with BPAD, SZ, or schizoaffective disorder. Finally, a pooled analysis of in-house and published datasets was carried out including 10,925 cases with BPAD, SZ, or schizoaffective disorder and 16,747 controls.\n\nIn the family-based analysis, an approximately 200 kilobase (kb) deletion in the first intron of the MAGI1 gene was identified that segregated with BPAD in a pedigree (six out of six affected individuals; parametric logarithm of the odds score = 1.14). In the pooled analysis, seven additional insertions or deletions over 100 kb were identified in MAGI1 in cases, while only two such CNV events were identified in the same gene in controls (p = .023; Fisher's exact test). Because earlier work had identified a CNV in the close relative MAGI2 in SZ, the study was extended to include MAGI2. In the pooled analysis of MAGI2, two large deletions were found in cases, and two duplications were detected in controls.\n\nResults presented herein provide further evidence for a role of MAGI1 and MAGI2 in BPAD and SZ etiology.", "doi": "10.1016/j.biopsych.2012.01.020", "pmid": "22381734", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0006-3223(12)00086-8"}], "notes": [], "created": "2017-05-04T15:00:54.693Z", "modified": "2020-01-21T13:56:05.227Z"}, {"entity": "publication", "iuid": "39ea1e478b8241e280e93e84e39c1fc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39ea1e478b8241e280e93e84e39c1fc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39ea1e478b8241e280e93e84e39c1fc8"}}, "title": "Derivatives of 8-hydroxyquinoline--antibacterial agents that target intra- and extracellular Gram-negative pathogens.", "authors": [{"family": "Enquist", "given": "Per-Anders", "initials": "P"}, {"family": "Gylfe", "given": "Asa", "initials": "A"}, {"family": "H\u00e4gglund", "given": "Ulrik", "initials": "U"}, {"family": "Lindstr\u00f6m", "given": "Pia", "initials": "P"}, {"family": "Norberg-Scherman", "given": "Henrik", "initials": "H"}, {"family": "Sundin", "given": "Charlotta", "initials": "C"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2012-05-15", "journal": {"volume": "22", "issn": "1464-3405", "issue": "10", "pages": "3550-3553", "title": "Bioorg. Med. Chem. Lett.", "issn-l": "0960-894X"}, "abstract": "Small molecule screening identified 5-nitro-7-((4-phenylpiperazine-1-yl-)methyl)quinolin-8-ol INP1750 as a putative inhibitor of type III secretion (T3S) in the Gram-negative pathogen Yersinia pseudotuberculosis. In this study we report structure-activity relationships for inhibition of T3S and show that the most potent compounds target both the extracellular bacterium Y. pseudotuberculosis and the intracellular pathogen Chlamydia trachomatis in cell-based infection models.", "doi": "10.1016/j.bmcl.2012.03.096", "pmid": "22525317", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-894X(12)00426-X"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:38.521Z", "modified": "2025-10-17T13:04:30.666Z"}, {"entity": "publication", "iuid": "f0e0cef839d34873ae951bfee93463bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0e0cef839d34873ae951bfee93463bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0e0cef839d34873ae951bfee93463bd"}}, "title": "A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.", "authors": [{"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Grimsby", "given": "Jonna L", "initials": "JL"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Chen", "given": "Han", "initials": "H"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Barnes", "given": "Daniel", "initials": "D"}, {"family": "Cadby", "given": "Gemma", "initials": "G"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Martinez-Larrad", "given": "Maria Teresa", "initials": "MT"}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Perry", "given": "John R B", "initials": "JR"}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "An", "given": "Ping", "initials": "P"}, {"family": "de Andrade", "given": "Mariza", "initials": "M"}, {"family": "Andrews", "given": "Jeanette S", "initials": "JS"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Atalay", "given": "Mustafa", "initials": "M"}, {"family": "Aulchenko", "given": "Yurii", "initials": "Y"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Beilby", "given": "John P", "initials": "JP"}, {"family": "Bellis", "given": "Claire", "initials": "C"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "Boban", "given": "Mladen", "initials": "M"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "B\u00f6ttcher", "given": "Yvonne", "initials": "Y"}, {"family": "Bouchard", "given": "Claude", "initials": "C"}, {"family": "Brunner", "given": "Eric", "initials": "E"}, {"family": "Budimir", "given": "Danijela", "initials": "D"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Carlson", "given": "Olga", "initials": "O"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Corbat\u00f3n-Anchuelo", "given": "Arturo", "initials": "A"}, {"family": "Couper", "given": "David", "initials": "D"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Egan", "given": "Josephine M", "initials": "JM"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Erdos", "given": "Michael R", "initials": "MR"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Eury", "given": "Elodie", "initials": "E"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Franzosi", "given": "Maria Grazia", "initials": "MG"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Galan", "given": "Pilar", "initials": "P"}, {"family": "de Geus", "given": "Eco", "initials": "E"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hansson", "given": "Ola", "initials": "O"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "Hercberg", "given": "Serge", "initials": "S"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hui", "given": "Jennie", "initials": "J"}, {"family": "Hung", "given": "Joseph", "initials": "J"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Jhun", "given": "Min A", "initials": "MA"}, {"family": "Johnson", "given": "Paul C D", "initials": "PC"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Kao", "given": "W H", "initials": "WH"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SL"}, {"family": "Keinanen-Kiukaanniemi", "given": "Sirkka", "initials": "S"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Kyvik", "given": "Kirsten Ohm", "initials": "KO"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lakka", "given": "Timo", "initials": "T"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Lathrop", "given": "G Mark", "initials": "GM"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Li", "given": "Guo", "initials": "G"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindstrom", "given": "Jaana", "initials": "J"}, {"family": "Lobbens", "given": "St\u00e9phane", "initials": "S"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Marmot", "given": "Michael", "initials": "M"}, {"family": "Meneton", "given": "Pierre", "initials": "P"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Morken", "given": "Mario A", "initials": "MA"}, {"family": "Miljkovic", "given": "Iva", "initials": "I"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "O'Connell", "given": "Jeff", "initials": "J"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pehlic", "given": "Marina", "initials": "M"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Penninx", "given": "Brenda", "initials": "B"}, {"family": "Pericic", "given": "Marijana", "initials": "M"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Perusse", "given": "Louis", "initials": "L"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Rehnberg", "given": "Emil", "initials": "E"}, {"family": "Rice", "given": "Ken", "initials": "K"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Ruokonen", "given": "Aimo", "initials": "A"}, {"family": "Saaristo", "given": "Timo", "initials": "T"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Savage", "given": "David B", "initials": "DB"}, {"family": "Saxena", "given": "Richa", "initials": "R"}, {"family": "Schwarz", "given": "Peter", "initials": "P"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Serrano-Rios", "given": "Manuel", "initials": "M"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Sijbrands", "given": "Eric J G", "initials": "EJ"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Sun", "given": "Yan V", "initials": "YV"}, {"family": "Swift", "given": "Amy J", "initials": "AJ"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "Vikstr\u00f6m", "given": "Max", "initials": "M"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Vohl", "given": "Marie-Claude", "initials": "MC"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "Gerard", "initials": "G"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "Zelenika", "given": "Diana", "initials": "D"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium", "given": null, "initials": null}, {"family": "Multiple Tissue Human Expression Resource (MUTHER) Consortium", "given": null, "initials": null}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Barroso", "given": "Ines", "initials": "I"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}], "type": "journal article", "published": "2012-05-13", "journal": {"volume": "44", "issn": "1546-1718", "issue": "6", "pages": "659-669", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and \u03b2-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 \u00d7 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.", "doi": "10.1038/ng.2274", "pmid": "22581228", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2274"}, {"db": "pmc", "key": "PMC3613127"}, {"db": "mid", "key": "NIHMS430753"}], "notes": [], "created": "2017-05-04T15:01:04.720Z", "modified": "2020-01-21T13:56:06.200Z"}, {"entity": "publication", "iuid": "2d993ff940d6424da8381b7fe881e7d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d993ff940d6424da8381b7fe881e7d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d993ff940d6424da8381b7fe881e7d2"}}, "title": "Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.", "authors": [{"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "White", "given": "Charles C", "initials": "CC"}, {"family": "Feitosa", "given": "Mary", "initials": "M"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Heard-Costa", "given": "Nancy", "initials": "N"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "GIANT Consortium", "given": null, "initials": null}, {"family": "MAGIC Consortium", "given": null, "initials": null}, {"family": "GLGC Consortium", "given": null, "initials": null}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Foster", "given": "Meredith C", "initials": "MC"}, {"family": "Greenawalt", "given": "Danielle M", "initials": "DM"}, {"family": "Griffin", "given": "Paula", "initials": "P"}, {"family": "Ding", "given": "Jinghong", "initials": "J"}, {"family": "Newman", "given": "Anne B", "initials": "AB"}, {"family": "Tylavsky", "given": "Fran", "initials": "F"}, {"family": "Miljkovic", "given": "Iva", "initials": "I"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Launer", "given": "Lenore", "initials": "L"}, {"family": "Garcia", "given": "Melissa", "initials": "M"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Carr", "given": "J Jeffrey", "initials": "JJ"}, {"family": "Gudnason", "given": "Vilmunder", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}], "type": "journal article", "published": "2012-05-10", "journal": {"volume": "8", "issn": "1553-7404", "issue": "5", "pages": "e1002695", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Body fat distribution, particularly centralized obesity, is associated with metabolic risk above and beyond total adiposity. We performed genome-wide association of abdominal adipose depots quantified using computed tomography (CT) to uncover novel loci for body fat distribution among participants of European ancestry. Subcutaneous and visceral fat were quantified in 5,560 women and 4,997 men from 4 population-based studies. Genome-wide genotyping was performed using standard arrays and imputed to ~2.5 million Hapmap SNPs. Each study performed a genome-wide association analysis of subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT), VAT adjusted for body mass index, and VAT/SAT ratio (a metric of the propensity to store fat viscerally as compared to subcutaneously) in the overall sample and in women and men separately. A weighted z-score meta-analysis was conducted. For the VAT/SAT ratio, our most significant p-value was rs11118316 at LYPLAL1 gene (p = 3.1 \u00d7 10E-09), previously identified in association with waist-hip ratio. For SAT, the most significant SNP was in the FTO gene (p = 5.9 \u00d7 10E-08). Given the known gender differences in body fat distribution, we performed sex-specific analyses. Our most significant finding was for VAT in women, rs1659258 near THNSL2 (p = 1.6 \u00d7 10-08), but not men (p = 0.75). Validation of this SNP in the GIANT consortium data demonstrated a similar sex-specific pattern, with observed significance in women (p = 0.006) but not men (p = 0.24) for BMI and waist circumference (p = 0.04 [women], p = 0.49 [men]). Finally, we interrogated our data for the 14 recently published loci for body fat distribution (measured by waist-hip ratio adjusted for BMI); associations were observed at 7 of these loci. In contrast, we observed associations at only 7/32 loci previously identified in association with BMI; the majority of overlap was observed with SAT. Genome-wide association for visceral and subcutaneous fat revealed a SNP for VAT in women. More refined phenotypes for body composition and fat distribution can detect new loci not previously uncovered in large-scale GWAS of anthropometric traits.", "doi": "10.1371/journal.pgen.1002695", "pmid": "22589738", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-02103"}, {"db": "pmc", "key": "PMC3349734"}], "notes": [], "created": "2017-05-04T15:01:08.488Z", "modified": "2020-01-21T13:56:01.293Z"}, {"entity": "publication", "iuid": "6f0e491f6b594d1da9ec15e23f884d5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f0e491f6b594d1da9ec15e23f884d5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f0e491f6b594d1da9ec15e23f884d5f"}}, "title": "Prediction of ischemic events on the basis of transcriptomic and genomic profiling in patients undergoing carotid endarterectomy.", "authors": [{"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Persson", "given": "Jonas", "initials": "J"}, {"family": "Ekstrand", "given": "Johan", "initials": "J"}, {"family": "Agardh", "given": "Hanna E", "initials": "HE"}, {"family": "Hansson", "given": "G\u00f6ran K", "initials": "GK"}, {"family": "Gabrielsen", "given": "Anders", "initials": "A"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}, {"family": "Paulsson-Berne", "given": "Gabrielle", "initials": "G"}], "type": "journal article", "published": "2012-05-09", "journal": {"volume": "18", "issn": "1528-3658", "issue": null, "pages": "669-675", "title": "Mol. Med.", "issn-l": "1076-1551"}, "abstract": "Classic risk factors, including age, smoking, serum cholesterol, diabetes and blood pressure, constitute the basis of present risk prediction models but fail to identify all individuals at risk. The objective of this study was to investigate if genomic and transcriptional patterns improve prediction of ischemic events in patients with established carotid artery disease. Genotype and gene expression profiles were obtained from carotid plaque tissue (n = 126) and peripheral blood mononuclear cells (n = 97) of patients undergoing carotid endarterectomy. Patients were followed for an average of 44 months, and 25 ischemic events occurred (18 ischemic strokes and 7 myocardial infarctions). Blinded leave-one-out cross-validation on Cox regression coefficients was used to assign gene expression-based risk scores to each patient. When compared with classic risk factors, addition of carotid plaque gene expression-based risk score improved the prediction of future ischemic events from an area under the curve (AUC) of 0.66 to an AUC of 0.79. The inclusion of gene expression risk score from peripheral blood mononuclear cells or from 25 established myocardial infarction risk single nucleotide polymorphisms only exhibited marginal effects on the prediction of ischemic events. Prediction of ischemic events is improved by inclusion of gene expression profiling from carotid endarterectomy tissue compared with prediction on the basis of classic risk markers alone in patients with atherosclerosis. The method may be developed to identify subjects at very high risk of ischemic events.", "doi": "10.2119/molmed.2011.00479", "pmid": "22371308", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "molmed.2011.00479"}, {"db": "pmc", "key": "PMC3388132"}], "notes": [], "created": "2017-05-04T15:01:04.054Z", "modified": "2020-01-21T13:56:02.893Z"}, {"entity": "publication", "iuid": "f9228292f20d4e1995524fc30991b78e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9228292f20d4e1995524fc30991b78e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9228292f20d4e1995524fc30991b78e"}}, "title": "Multimodel pathway enrichment methods for functional evaluation of expression regulation.", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Cifani", "given": "Paolo", "initials": "P"}, {"family": "Albrekt", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Lindstedt", "given": "Malin", "initials": "M"}, {"family": "Heyden", "given": "Anders", "initials": "A"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-05-04", "journal": {"volume": "11", "issn": "1535-3907", "issue": "5", "pages": "2955-2967", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Functional analysis of quantitative expression data is becoming common practice within the proteomics and transcriptomics fields; however, a gold standard for this type of analysis has yet not emerged. To grasp the systemic changes in biological systems, efficient and robust methods are needed for data analysis following expression regulation experiments. We discuss several conceptual and practical challenges potentially hindering the emergence of such methods and present a novel method, called FEvER, that utilizes two enrichment models in parallel. We also present analysis of three disparate differential expression data sets using our method and compare our results to other established methods. With many useful features such as pathway hierarchy overview, we believe the FEvER method and its software implementation will provide a useful tool for peers in the field of proteomics. Furthermore, we show that the method is also applicable to other types of expression data.", "doi": "10.1021/pr300038b", "pmid": "22471554", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:16.365Z", "modified": "2020-01-21T13:53:20.975Z"}, {"entity": "publication", "iuid": "77b8c1e7b0a14bd4940ea15e8f8ed19a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77b8c1e7b0a14bd4940ea15e8f8ed19a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77b8c1e7b0a14bd4940ea15e8f8ed19a"}}, "title": "Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Zaboli", "given": "Ghazal", "initials": "G"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Johansson", "given": "Anna C V", "initials": "AC"}, {"family": "Rivas", "given": "Manuel A", "initials": "MA"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}, {"family": "Schmitz", "given": "Gerd", "initials": "G"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "van Duijn", "given": "Cornelia", "initials": "C"}, {"family": "Oostra", "given": "Ben", "initials": "B"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2012-05-04", "journal": {"volume": "90", "issn": "1537-6605", "issue": "5", "pages": "809-820", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Omega-3 and omega-6 long-chain polyunsaturated fatty acids (LC-PUFAs) are essential for the development and function of the human brain. They can be obtained directly from food, e.g., fish, or synthesized from precursor molecules found in vegetable oils. To determine the importance of genetic variability to fatty-acid biosynthesis, we studied FADS1 and FADS2, which encode rate-limiting enzymes for fatty-acid conversion. We performed genome-wide genotyping (n = 5,652 individuals) and targeted resequencing (n = 960 individuals) of the FADS region in five European population cohorts. We also analyzed available genomic data from human populations, archaic hominins, and more distant primates. Our results show that present-day humans have two common FADS haplotypes-defined by 28 closely linked SNPs across 38.9 kb-that differ dramatically in their ability to generate LC-PUFAs. No independent effects on FADS activity were seen for rare SNPs detected by targeted resequencing. The more efficient, evolutionarily derived haplotype appeared after the lineage split leading to modern humans and Neanderthals and shows evidence of positive selection. This human-specific haplotype increases the efficiency of synthesizing essential long-chain fatty acids from precursors and thereby might have provided an advantage in environments with limited access to dietary LC-PUFAs. In the modern world, this haplotype has been associated with lifestyle-related diseases, such as coronary artery disease.", "doi": "10.1016/j.ajhg.2012.03.014", "pmid": "22503634", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(12)00158-9"}, {"db": "pmc", "key": "PMC3376635"}], "notes": [], "created": "2017-05-04T14:57:28.310Z", "modified": "2021-07-07T14:37:06.520Z"}, {"entity": "publication", "iuid": "ff433a09d59b40f384ae09e8d57426af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff433a09d59b40f384ae09e8d57426af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff433a09d59b40f384ae09e8d57426af"}}, "title": "Differential evolutionary wiring of the tyrosine kinase Btk.", "authors": [{"family": "Nawaz", "given": "Hossain M", "initials": "HM"}, {"family": "Kylsten", "given": "Per", "initials": "P"}, {"family": "Hamada", "given": "Noriko", "initials": "N"}, {"family": "Yamamoto", "given": "Daisuke", "initials": "D"}, {"family": "Smith", "given": "C I Edvard", "initials": "CI"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}], "type": "journal article", "published": "2012-05-04", "journal": {"volume": "7", "issn": "1932-6203", "issue": "5", "pages": "e35640", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "A central question within biology is how intracellular signaling pathways are maintained throughout evolution. Btk29A is considered to be the fly-homolog of the mammalian Bruton's tyrosine kinase (Btk), which is a non-receptor tyrosine-kinase of the Tec-family. In mammalian cells, there is a single transcript splice-form and the corresponding Btk-protein plays an important role for B-lymphocyte development with alterations within the human BTK gene causing the immunodeficiency disease X-linked agammaglobulinemia in man and a related disorder in mice. In contrast, the Drosophila Btk29A locus encodes two splice-variants, where the type 2-form is the more related to the mammalian Btk gene product displaying more than 80% homology. In Drosophila, Btk29A displays a dynamic pattern of expression through the embryonic to adult stages. Complete loss-of-function of both splice-forms is lethal, whereas selective absence of the type 2-form reduces the adult lifespan of the fly and causes developmental abnormalities in male genitalia.\n\nOut of 7004-7979 transcripts expressed in the four sample groups, 5587 (70-79%) were found in all four tissues and strains. Here, we investigated the role of Btk29A type 2 on a transcriptomic level in larval CNS and adult heads. We used samples either selectively defective in Btk29A type 2 (Btk29A(ficP)) or revertant flies with restored Btk29A type 2-function (Btk29A(fic Exc1-16)). The whole transcriptomic profile for the different sample groups revealed Gene Ontology patterns reflecting lifespan abnormalities in adult head neuronal tissue, but not in larvae.\n\nIn the Btk29A type 2-deficient strains there was no significant overlap between transcriptomic alterations in adult heads and larvae neuronal tissue, respectively. Moreover, there was no significant overlap of the transcriptomic changes between flies and mammals, suggesting that the evolutionary conservation is confined to components of the proximal signaling, whereas the corresponding, downstream transcriptional regulation has been differentially wired.", "doi": "10.1371/journal.pone.0035640", "pmid": "22574122", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-01915"}, {"db": "pmc", "key": "PMC3344829"}], "notes": [], "created": "2017-05-04T15:03:13.330Z", "modified": "2021-07-05T12:48:16.058Z"}, {"entity": "publication", "iuid": "65f3916f49f14417a25de1d57057d0ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65f3916f49f14417a25de1d57057d0ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65f3916f49f14417a25de1d57057d0ef"}}, "title": "A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin \u03ba C as a compatible prognostic marker in human solid tumors.", "authors": [{"family": "Schmidt", "given": "Marcus", "initials": "M"}, {"family": "Hellwig", "given": "Birte", "initials": "B"}, {"family": "Hammad", "given": "Seddik", "initials": "S"}, {"family": "Othman", "given": "Amnah", "initials": "A"}, {"family": "Lohr", "given": "Miriam", "initials": "M"}, {"family": "Chen", "given": "Zonglin", "initials": "Z"}, {"family": "Boehm", "given": "Daniel", "initials": "D"}, {"family": "Gebhard", "given": "Susanne", "initials": "S"}, {"family": "Petry", "given": "Ilka", "initials": "I"}, {"family": "Lebrecht", "given": "Antje", "initials": "A"}, {"family": "Cadenas", "given": "Cristina", "initials": "C"}, {"family": "Marchan", "given": "Rosemarie", "initials": "R"}, {"family": "Stewart", "given": "Joanna D", "initials": "JD"}, {"family": "Solbach", "given": "Christine", "initials": "C"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Kultima", "given": "Hanna G\u00f6ransson", "initials": "HG"}, {"family": "Rody", "given": "Achim", "initials": "A"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Karn", "given": "Thomas", "initials": "T"}, {"family": "M\u00fcller", "given": "Volkmar", "initials": "V"}, {"family": "Gerhold-Ay", "given": "Aslihan", "initials": "A"}, {"family": "Cotarelo", "given": "Christina", "initials": "C"}, {"family": "Sebastian", "given": "Martin", "initials": "M"}, {"family": "Kronenwett", "given": "Ralf", "initials": "R"}, {"family": "Bojar", "given": "Hans", "initials": "H"}, {"family": "Lehr", "given": "Hans-Anton", "initials": "HA"}, {"family": "Sahin", "given": "Ugur", "initials": "U"}, {"family": "Koelbl", "given": "Heinz", "initials": "H"}, {"family": "Gehrmann", "given": "Mathias", "initials": "M"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Hengstler", "given": "Jan G", "initials": "JG"}], "type": "journal article", "published": "2012-05-01", "journal": {"volume": "18", "issn": "1078-0432", "issue": "9", "pages": "2695-2703", "title": "Clin. Cancer Res.", "issn-l": null}, "abstract": "Although the central role of the immune system for tumor prognosis is generally accepted, a single robust marker is not yet available.\n\nOn the basis of receiver operating characteristic analyses, robust markers were identified from a 60-gene B cell-derived metagene and analyzed in gene expression profiles of 1,810 breast cancer; 1,056 non-small cell lung carcinoma (NSCLC); 513 colorectal; and 426 ovarian cancer patients. Protein and RNA levels were examined in paraffin-embedded tissue of 330 breast cancer patients. The cell types were identified with immunohistochemical costaining and confocal fluorescence microscopy.\n\nWe identified immunoglobulin \u03ba C (IGKC) which as a single marker is similarly predictive and prognostic as the entire B-cell metagene. IGKC was consistently associated with metastasis-free survival across different molecular subtypes in node-negative breast cancer (n = 965) and predicted response to anthracycline-based neoadjuvant chemotherapy (n = 845; P < 0.001). In addition, IGKC gene expression was prognostic in NSCLC and colorectal cancer. No association was observed in ovarian cancer. IGKC protein expression was significantly associated with survival in paraffin-embedded tissues of 330 breast cancer patients. Tumor-infiltrating plasma cells were identified as the source of IGKC expression.\n\nOur findings provide IGKC as a novel diagnostic marker for risk stratification in human cancer and support concepts to exploit the humoral immune response for anticancer therapy. It could be validated in several independent cohorts and carried out similarly well in RNA from fresh frozen as well as from paraffin tissue and on protein level by immunostaining.", "doi": "10.1158/1078-0432.CCR-11-2210", "pmid": "22351685", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "1078-0432.CCR-11-2210"}], "notes": [], "created": "2017-05-04T15:02:56.079Z", "modified": "2017-05-30T12:36:49.862Z"}, {"entity": "publication", "iuid": "997d4ba8a0914edfa6226639e802cf57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/997d4ba8a0914edfa6226639e802cf57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/997d4ba8a0914edfa6226639e802cf57"}}, "title": "Transgenerational effects of early experience on behavioral, hormonal and gene expression responses to acute stress in the precocial chicken.", "authors": [{"family": "Goerlich", "given": "Vivian C", "initials": "VC"}, {"family": "N\u00e4tt", "given": "Daniel", "initials": "D"}, {"family": "Elfwing", "given": "Magnus", "initials": "M"}, {"family": "Macdonald", "given": "Barry", "initials": "B"}, {"family": "Jensen", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2012-05-00", "journal": {"volume": "61", "issn": "1095-6867", "issue": "5", "pages": "711-718", "title": "Horm Behav", "issn-l": "0018-506X"}, "abstract": "Stress during early life can profoundly influence an individual's phenotype. Effects can manifest in the short-term as well as later in life and even in subsequent generations. Transgenerational effects of stress are potentially mediated via modulation of the hypothalamic-pituitary-adrenal axis (HPA) as well as epigenetic mechanisms causing heritable changes in gene expression. To investigate these pathways we subjected domestic chicken (Gallus gallus) to intermittent social isolation for the first three weeks of life. The early life stress resulted in a dampened corticosterone response to restraint stress in affected birds and in their male offspring. Stress-specific genes, such as early growth response 1 (EGR1) and corticotropin releasing hormone receptor 1 (CRHR1), were upregulated immediately after restraint stress, but not under baseline conditions. Treatment differences in gene expression were also correlated across generations which indicate transgenerational epigenetic inheritance. In an associative learning test early stressed birds made more correct choices suggesting a higher coping ability in stressful situations. This study is the first to show transgenerational effects of early life stress in a precocial species by combining behavioral, endocrinological, and transcriptomic measurements.", "doi": "10.1016/j.yhbeh.2012.03.006", "pmid": "22465454", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "S0018-506X(12)00083-9"}], "notes": [], "created": "2017-05-04T15:02:58.391Z", "modified": "2017-05-30T12:37:18.223Z"}, {"entity": "publication", "iuid": "f70af08792374bcdbd4ac9d80b8e4f7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f70af08792374bcdbd4ac9d80b8e4f7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f70af08792374bcdbd4ac9d80b8e4f7e"}}, "title": "No interactions between previously associated 2-hour glucose gene variants and physical activity or BMI on 2-hour glucose levels.", "authors": [{"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Yesupriya", "given": "Ajay", "initials": "A"}, {"family": "Barnes", "given": "Daniel", "initials": "D"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "Marek", "given": "Diana", "initials": "D"}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Aadahl", "given": "Mette", "initials": "M"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Brunner", "given": "Eric", "initials": "E"}, {"family": "Bumpstead", "given": "Suzannah J", "initials": "SJ"}, {"family": "Brage", "given": "Soren", "initials": "S"}, {"family": "Carlson", "given": "Olga D", "initials": "OD"}, {"family": "Chen", "given": "Han", "initials": "H"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YD"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Couper", "given": "David J", "initials": "DJ"}, {"family": "Dennison", "given": "Elaine M", "initials": "EM"}, {"family": "Dowling", "given": "Nicole F", "initials": "NF"}, {"family": "Egan", "given": "Josephine S", "initials": "JS"}, {"family": "Ekelund", "given": "Ulf", "initials": "U"}, {"family": "Erdos", "given": "Michael R", "initials": "MR"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Gr\u00e4ssler", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Holloway", "given": "John W", "initials": "JW"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Jameson", "given": "Karen A", "initials": "KA"}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}, {"family": "Jonsson", "given": "Anna", "initials": "A"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lecoeur", "given": "C\u00e9cile", "initials": "C"}, {"family": "L\u00e9vy-Marchal", "given": "Claire", "initials": "C"}, {"family": "Li", "given": "Guo", "initials": "G"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Lyssenko", "given": "Valeri", "initials": "V"}, {"family": "Marmot", "given": "Michael", "initials": "M"}, {"family": "Marques-Vidal", "given": "Pedro", "initials": "P"}, {"family": "Morken", "given": "Mario A", "initials": "MA"}, {"family": "M\u00fcller", "given": "Gabriele", "initials": "G"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Payne", "given": "Felicity", "initials": "F"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Rice", "given": "Ken", "initials": "K"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Sandholt", "given": "Camilla H", "initials": "CH"}, {"family": "Sayer", "given": "Avan A", "initials": "AA"}, {"family": "Shrader", "given": "Peter", "initials": "P"}, {"family": "Schwarz", "given": "Peter E H", "initials": "PE"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Stanc\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Williams", "given": "Gordon H", "initials": "GH"}, {"family": "Witte", "given": "Daniel R", "initials": "DR"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Xie", "given": "Weijia", "initials": "W"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Cooper", "given": "Cyrus", "initials": "C"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}], "type": "journal article", "published": "2012-05-00", "journal": {"volume": "61", "issn": "1939-327X", "issue": "5", "pages": "1291-1296", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "Gene-lifestyle interactions have been suggested to contribute to the development of type 2 diabetes. Glucose levels 2 h after a standard 75-g glucose challenge are used to diagnose diabetes and are associated with both genetic and lifestyle factors. However, whether these factors interact to determine 2-h glucose levels is unknown. We meta-analyzed single nucleotide polymorphism (SNP) \u00d7 BMI and SNP \u00d7 physical activity (PA) interaction regression models for five SNPs previously associated with 2-h glucose levels from up to 22 studies comprising 54,884 individuals without diabetes. PA levels were dichotomized, with individuals below the first quintile classified as inactive (20%) and the remainder as active (80%). BMI was considered a continuous trait. Inactive individuals had higher 2-h glucose levels than active individuals (\u03b2 = 0.22 mmol/L [95% CI 0.13-0.31], P = 1.63 \u00d7 10(-6)). All SNPs were associated with 2-h glucose (\u03b2 = 0.06-0.12 mmol/allele, P \u2264 1.53 \u00d7 10(-7)), but no significant interactions were found with PA (P > 0.18) or BMI (P \u2265 0.04). In this large study of gene-lifestyle interaction, we observed no interactions between genetic and lifestyle factors, both of which were associated with 2-h glucose. It is perhaps unlikely that top loci from genome-wide association studies will exhibit strong subgroup-specific effects, and may not, therefore, make the best candidates for the study of interactions.", "doi": "10.2337/db11-0973", "pmid": "22415877", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "db11-0973"}, {"db": "pmc", "key": "PMC3331745"}], "notes": [], "created": "2017-05-04T15:00:57.213Z", "modified": "2020-01-21T13:56:06.375Z"}, {"entity": "publication", "iuid": "bc76c405ba714dfab0af893783def1b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc76c405ba714dfab0af893783def1b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc76c405ba714dfab0af893783def1b2"}}, "title": "A novel mutation in lysophosphatidic acid receptor 6 gene in autosomal recessive hypotrichosis and evidence for a founder effect.", "authors": [{"family": "Azhar", "given": "Aysha", "initials": "A"}, {"family": "Tariq", "given": "Muhammad", "initials": "M"}, {"family": "Baig", "given": "Shahid Mahmood", "initials": "SM"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Klar", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2012-04-26", "journal": {"volume": "22", "issn": "1952-4013", "issue": "4", "pages": "464-466", "title": "Eur J Dermatol", "issn-l": "1167-1122"}, "abstract": "Mutations in the lysophosphatidic acid receptor 6 (LPAR6) gene cause localized autosomal recessive hypotrichosis. We report six consanguineous families from Pakistan with segregating hypotrichosis localized to the scalp. Genetic investigation using polymorphic microsatellite markers revealed homozygosity spanning the LAH3 locus on chromosome\u00a013 in affected individuals of all six families. Sequence analysis of the LPAR6 gene showed a novel insertion resulting in a frameshift and a premature termination (p.I194FfsX11) in affected members of one family. In the remaining five families we identified a previously described missense mutation (p.G146R) in a homozygous state in affected members. The closest flanking polymorphic marker showed an identical allele size in the five families segregating with the p.G146R mutation, supporting a single origin of this variation. These findings extend the spectrum of known LPAR6 mutations and suggest a founder effect of the p.G146R mutation in the Pakistani population.", "doi": "10.1684/ejd.2012.1731", "pmid": "22531990", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ejd.2012.1731"}], "notes": [], "created": "2017-05-04T14:57:33.362Z", "modified": "2020-01-21T13:56:04.919Z"}, {"entity": "publication", "iuid": "ec90e115ccd04a53be01f112704a09a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec90e115ccd04a53be01f112704a09a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec90e115ccd04a53be01f112704a09a8"}}, "title": "Common SNPs explain some of the variation in the personality dimensions of neuroticism and extraversion.", "authors": [{"family": "Vinkhuyzen", "given": "A A E", "initials": "AA"}, {"family": "Pedersen", "given": "N L", "initials": "NL"}, {"family": "Yang", "given": "J", "initials": "J"}, {"family": "Lee", "given": "S H", "initials": "SH"}, {"family": "Magnusson", "given": "P K E", "initials": "PK"}, {"family": "Iacono", "given": "W G", "initials": "WG"}, {"family": "McGue", "given": "M", "initials": "M"}, {"family": "Madden", "given": "P A F", "initials": "PA"}, {"family": "Heath", "given": "A C", "initials": "AC"}, {"family": "Luciano", "given": "M", "initials": "M"}, {"family": "Payton", "given": "A", "initials": "A"}, {"family": "Horan", "given": "M", "initials": "M"}, {"family": "Ollier", "given": "W", "initials": "W"}, {"family": "Pendleton", "given": "N", "initials": "N"}, {"family": "Deary", "given": "I J", "initials": "IJ"}, {"family": "Montgomery", "given": "G W", "initials": "GW"}, {"family": "Martin", "given": "N G", "initials": "NG"}, {"family": "Visscher", "given": "P M", "initials": "PM"}, {"family": "Wray", "given": "N R", "initials": "NR"}], "type": "journal article", "published": "2012-04-17", "journal": {"volume": "2", "issn": "2158-3188", "issue": null, "pages": "e102", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "The personality traits of neuroticism and extraversion are predictive of a number of social and behavioural outcomes and psychiatric disorders. Twin and family studies have reported moderate heritability estimates for both traits. Few associations have been reported between genetic variants and neuroticism/extraversion, but hardly any have been replicated. Moreover, the ones that have been replicated explain only a small proportion of the heritability (<~2%). Using genome-wide single-nucleotide polymorphism (SNP) data from ~12,000 unrelated individuals we estimated the proportion of phenotypic variance explained by variants in linkage disequilibrium with common SNPs as 0.06 (s.e. = 0.03) for neuroticism and 0.12 (s.e. = 0.03) for extraversion. In an additional series of analyses in a family-based sample, we show that while for both traits ~45% of the phenotypic variance can be explained by pedigree data (that is, expected genetic similarity) one third of this can be explained by SNP data (that is, realized genetic similarity). A part of the so-called 'missing heritability' has now been accounted for, but some of the reported heritability is still unexplained. Possible explanations for the remaining missing heritability are that: (i) rare variants that are not captured by common SNPs on current genotype platforms make a major contribution; and/ or (ii) the estimates of narrow sense heritability from twin and family studies are biased upwards, for example, by not properly accounting for nonadditive genetic factors and/or (common) environmental factors.", "doi": "10.1038/tp.2012.27", "pmid": "22832902", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "tp201227"}, {"db": "pmc", "key": "PMC3337075"}], "notes": [], "created": "2017-10-30T13:48:14.902Z", "modified": "2020-01-21T13:56:08.419Z"}, {"entity": "publication", "iuid": "5aa2459f7f9e4644aac608d937002bce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5aa2459f7f9e4644aac608d937002bce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5aa2459f7f9e4644aac608d937002bce"}}, "title": "Synthesis, biological evaluation, and structure-activity relationships of 2-[2-(benzoylamino)benzoylamino]benzoic acid analogues as inhibitors of adenovirus replication.", "authors": [{"family": "\u00d6berg", "given": "Christopher T", "initials": "CT"}, {"family": "Strand", "given": "M\u00e5rten", "initials": "M"}, {"family": "Andersson", "given": "Emma K", "initials": "EK"}, {"family": "Edlund", "given": "Karin", "initials": "K"}, {"family": "Tran", "given": "Nam Phuong Nguyen", "initials": "NPN"}, {"family": "Mei", "given": "Ya-Fang", "initials": "Y"}, {"family": "Wadell", "given": "G\u00f6ran", "initials": "G"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2012-04-12", "journal": {"volume": "55", "issn": "1520-4804", "issue": "7", "pages": "3170-3181", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "2-[2-Benzoylamino)benzoylamino]benzoic acid (1) was previously identified as a potent and nontoxic antiadenoviral compound (Antimicrob. Agents Chemother. 2010, 54, 3871). Here, the potency of 1 was improved over three generations of compounds. We found that the ortho, ortho substituent pattern and the presence of the carboxylic acid of 1 are favorable for this class of compounds and that the direction of the amide bonds (as in 1) is obligatory. Some variability in the N-terminal moiety was tolerated, but benzamides appear to be preferred. The substituents on the middle and C-terminal rings were varied, resulting in two potent inhibitors, 35g and 35j, with EC(50) = 0.6 \u03bcM and low cell toxicity.", "doi": "10.1021/jm201636v", "pmid": "22369233", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:39.425Z", "modified": "2025-10-17T13:04:30.679Z"}, {"entity": "publication", "iuid": "60e1ceb883e64a2da56ae31f5bb7c414", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60e1ceb883e64a2da56ae31f5bb7c414.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60e1ceb883e64a2da56ae31f5bb7c414"}}, "title": "DNA methylation analysis of bone marrow cells at diagnosis of acute lymphoblastic leukemia and at remission.", "authors": [{"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2012-04-06", "journal": {"volume": "7", "issn": "1932-6203", "issue": "4", "pages": "e34513", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "To detect genes with CpG sites that display methylation patterns that are characteristic of acute lymphoblastic leukemia (ALL) cells, we compared the methylation patterns of cells taken at diagnosis from 20 patients with pediatric ALL to the methylation patterns in mononuclear cells from bone marrow of the same patients during remission and in non-leukemic control cells from bone marrow or blood. Using a custom-designed assay, we measured the methylation levels of 1,320 CpG sites in regulatory regions of 413 genes that were analyzed because they display allele-specific gene expression (ASE) in ALL cells. The rationale for our selection of CpG sites was that ASE could be the result of allele-specific methylation in the promoter regions of the genes. We found that the ALL cells had methylation profiles that allowed distinction between ALL cells and control cells. Using stringent criteria for calling differential methylation, we identified 28 CpG sites in 24 genes with recurrent differences in their methylation levels between ALL cells and control cells. Twenty of the differentially methylated genes were hypermethylated in the ALL cells, and as many as nine of them (AMICA1, CPNE7, CR1, DBC1, EYA4, LGALS8, RYR3, UQCRFS1, WDR35) have functions in cell signaling and/or apoptosis. The methylation levels of a subset of the genes were consistent with an inverse relationship with the mRNA expression levels in a large number of ALL cells from published data sets, supporting a potential biological effect of the methylation signatures and their application for diagnostic purposes.", "doi": "10.1371/journal.pone.0034513", "pmid": "22493696", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-01632"}, {"db": "pmc", "key": "PMC3321015"}], "notes": [], "created": "2017-05-04T15:01:10.800Z", "modified": "2021-07-07T15:11:02.477Z"}, {"entity": "publication", "iuid": "32ee13d08d2f4563bbbdb19dff26644c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32ee13d08d2f4563bbbdb19dff26644c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32ee13d08d2f4563bbbdb19dff26644c"}}, "title": "Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy.", "authors": [{"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Neumann", "given": "Beate", "initials": "B"}, {"family": "Jonasson", "given": "Kalle", "initials": "K"}, {"family": "Pepperkok", "given": "Rainer", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2012-04-03", "journal": {"volume": "75", "issn": "1876-7737", "issue": "7", "pages": "2236-2251", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "We have developed a platform for validation of antibody binding and protein subcellular localization data obtained from immunofluorescence using siRNA technology combined with automated confocal microscopy and image analysis. By combining the siRNA technology with automated sample preparation, automated imaging and quantitative image analysis, a high-throughput assay has been set-up to enable confirmation of accurate protein binding and localization in a systematic manner. Here, we describe the analysis and validation of the subcellular location of 65 human proteins, targeted by 75 antibodies and silenced by 130 siRNAs. A large fraction of (80%) the subcellular locations, including locations of several previously uncharacterized proteins, could be confirmed by the significant down-regulation of the antibody signal after the siRNA silencing. A quantitative analysis was set-up using automated image analysis to facilitate studies of targets found in more than one compartment. The results obtained using the platform demonstrate that siRNA silencing in combination with quantitative image analysis of antibody signals in different compartments of the cells is an attractive approach for ensuring accurate protein localization as well as antibody binding using immunofluorescence. With a large fraction of the human proteome still unexplored, we suggest this approach to be of great importance under the continued work of mapping the human proteome on a subcellular level.", "doi": "10.1016/j.jprot.2012.01.030", "pmid": "22361696", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(12)00070-X"}], "notes": [], "created": "2017-05-04T14:55:10.773Z", "modified": "2021-07-08T13:44:33.123Z"}, {"entity": "publication", "iuid": "10cde2acbb4747dab0b852f5fad4d773", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10cde2acbb4747dab0b852f5fad4d773.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10cde2acbb4747dab0b852f5fad4d773"}}, "title": "Tumor-mast cell interactions: induction of pro-tumorigenic genes and anti-tumorigenic 4-1BB in MCs in response to Lewis Lung Carcinoma.", "authors": [{"family": "Wensman", "given": "Helena", "initials": "H"}, {"family": "Kamgari", "given": "Nona", "initials": "N"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Grujic", "given": "Mirjana", "initials": "M"}, {"family": "Calounova", "given": "Gabriela", "initials": "G"}, {"family": "Lundequist", "given": "Anders", "initials": "A"}, {"family": "R\u00f6nnberg", "given": "Elin", "initials": "E"}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "50", "issn": "1872-9142", "issue": "4", "pages": "210-219", "title": "Mol. Immunol.", "issn-l": "0161-5890"}, "abstract": "Mast cells (MCs) can have either detrimental or beneficial effects on malignant processes but the underlying mechanisms are poorly understood. Here we addressed this issue by examining the interaction between Lewis Lung Carcinoma (LLC) cells and MCs. In vivo, LLC tumors caused a profound accumulation of MCs, suggesting that LLC tumors have the capacity to attract MCs. Indeed, transwell migration assays showed that LLC-conditioned medium had chemotactic activity towards MCs, which was blocked by an antibody towards stem cell factor. In order to gain insight into the molecular mechanisms operative in tumor-MC interactions, the effect of LLC on the MC gene expression pattern was examined. As judged by gene array analysis, conditioned medium from LLC cells caused significant upregulation of numerous cell surface receptors and a pro-angiogenic Runx2/VEGF/Dusp5 axis in MCs, the latter in line with a role for MCs in promoting tumor angiogenesis. Among the genes showing the highest extent of upregulation was Tnfrsf9, encoding the anti-tumorigenic protein 4-1BB, suggesting that also anti-tumorigenic factors are induced. Quantitative RT-PCR analysis showed that 4-1BB was upregulated in a transient manner, and it was also shown that tumor cells induce 4-1BB in human MCs. Immunohistochemical analysis showed that LLC-conditioned medium induced 4-1BB also at the protein level. Together, this study provides novel insight into the molecular events associated with MC-tumor interactions and suggests that tumor cells induce both pro- and anti-tumorigenic responses in MCs.", "doi": "10.1016/j.molimm.2012.01.009", "pmid": "22343053", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "S0161-5890(12)00010-7"}], "notes": [], "created": "2017-05-04T15:02:59.661Z", "modified": "2017-05-30T12:37:32.226Z"}, {"entity": "publication", "iuid": "5ebd38fdc77348bd9ee901fff7f987e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ebd38fdc77348bd9ee901fff7f987e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ebd38fdc77348bd9ee901fff7f987e4"}}, "title": "The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus.", "authors": [{"family": "Kindgren", "given": "Peter", "initials": "P"}, {"family": "Kremnev", "given": "Dmitry", "initials": "D"}, {"family": "Blanco", "given": "Nicol\u00e1s E", "initials": "NE"}, {"family": "de Dios Barajas L\u00f3pez", "given": "Juan", "initials": "J"}, {"family": "Fern\u00e1ndez", "given": "Aurora Pi\u00f1as", "initials": "AP"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Kleine", "given": "Tatjana", "initials": "T"}, {"family": "Small", "given": "Ian", "initials": "I"}, {"family": "Strand", "given": "Asa", "initials": "A"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "70", "issn": "1365-313X", "issue": "2", "pages": "279-291", "title": "Plant J.", "issn-l": "0960-7412"}, "abstract": "The photosynthetic apparatus is composed of proteins encoded by genes from both the nuclear and the chloroplastic genomes. The activities of the nuclear and chloroplast genomes must therefore be closely coordinated through intracellular signalling. The plastids produce multiple retrograde signals at different times of their development, and in response to changes in the environment. These signals regulate the expression of nuclear-encoded photosynthesis genes to match the current status of the plastids. Using forward genetics we identified PLASTID REDOX INSENSITIVE 2 (PRIN2), a chloroplast component involved in redox-mediated retrograde signalling. The allelic mutants prin2-1 and prin2-2 demonstrated a misregulation of photosynthesis-associated nuclear gene expression in response to excess light, and an inhibition of photosynthetic electron transport. As a consequence of the misregulation of LHCB1.1 and LHCB2.4, the prin2 mutants displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by a reduced variable to maximal fluorescence ratio (F(v) /F(m) ). PRIN2 is localized to the nucleoids, and plastid transcriptome analyses demonstrated that PRIN2 is required for full expression of genes transcribed by the plastid-encoded RNA polymerase (PEP). Similarly to the prin2 mutants, the ys1 mutant with impaired PEP activity also demonstrated a misregulation of LHCB1.1 and LHCB2.4 expression in response to excess light, suggesting a direct role for PEP activity in redox-mediated retrograde signalling. Taken together, our results indicate that PRIN2 is part of the PEP machinery, and that the PEP complex responds to photosynthetic electron transport and generates a retrograde signal, enabling the plant to synchronize the expression of photosynthetic genes from both the nuclear and plastidic genomes.", "doi": "10.1111/j.1365-313X.2011.04865.x", "pmid": "22211401", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:41.474Z", "modified": "2020-01-21T13:56:10.683Z"}, {"entity": "publication", "iuid": "899c6c42cf0f43beba9c286b08fbfb10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/899c6c42cf0f43beba9c286b08fbfb10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/899c6c42cf0f43beba9c286b08fbfb10"}}, "title": "Proteinase production in Pseudomonas fluorescens ON2 is affected by carbon sources and allows surface-attached but not planktonic cells to utilize protein for growth in lake water.", "authors": [{"family": "Nicolaisen", "given": "Mette H", "initials": "MH"}, {"family": "Worm", "given": "Jakob", "initials": "J"}, {"family": "J\u00f8rgensen", "given": "Niels O G", "initials": "NOG"}, {"family": "Middelboe", "given": "Mathias", "initials": "M"}, {"family": "Nybroe", "given": "Ole", "initials": "O"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "80", "issn": "1574-6941", "issue": "1", "pages": "168-178", "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": "Proteins may be an important carbon and nitrogen source to bacteria in aquatic habitats, yet knowledge on the actual utilization of this substrate by proteolytic bacteria is scarce. In this study, Pseudomonas fluorescens ON2 produced an alkaline proteinase (AprX) during growth, and there was no evidence for cell density-regulated or starvation-induced proteinase production. Proteinase was produced in the absence of an organic nitrogen source, and citrate had a negative while glucose had a positive effect on the production. Hence, P.\u00a0fluorescens ON2 seems to exploit protein sources by expressing the proteinase during growth unless a preferred carbon source such as citrate is present. Lake water model systems were subsequently used to investigate the ability of proteolytic vs. nonproteolytic ON2 strains to utilize protein for growth at moderate cell densities. Only cells forming surface-attached microcolonies were able to utilize this resource, while planktonic cells were not. Our experiments are the first to experimentally support models predicting that production of extracellular enzymes in dilute environments may be a waste of resources, whereas it represents a favorable feeding strategy in organic matrices such as detritus, microcolonies, or biofilm.", "doi": "10.1111/j.1574-6941.2011.01285.x", "pmid": "22224410", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:34.265Z", "modified": "2020-01-21T13:56:10.592Z"}, {"entity": "publication", "iuid": "a20dbc6d35db44d4afa14c5092534c01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a20dbc6d35db44d4afa14c5092534c01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a20dbc6d35db44d4afa14c5092534c01"}}, "title": "Prevalence of Rickettsia spp., Anaplasma phagocytophilum, and Coxiella burnetii in adult Ixodes ricinus ticks from 29 study areas in central and southern Sweden.", "authors": [{"family": "Wallm\u00e9nius", "given": "Katarina", "initials": "K"}, {"family": "Pettersson", "given": "John H-O", "initials": "JH"}, {"family": "Jaenson", "given": "Thomas G T", "initials": "TGT"}, {"family": "Nilsson", "given": "Kenneth", "initials": "K"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "3", "issn": "1877-9603", "issue": "2", "pages": "100-106", "title": "Ticks Tick Borne Dis", "issn-l": "1877-959X"}, "abstract": "A total of 887 adult Ixodes ricinus ticks (469 females and 418 males) from 29 different localities in Sweden were screened for Rickettsia, Anaplasma, and Coxiella DNA using PCR and then subjected to gene sequencing. Rickettsial DNA was detected in 9.5-9.6% of the ticks. Most of the positive ticks were infected with Rickettsia helvetica. One tick harbored another spotted fever rickettsia, closely related to or identical with R. sibirica not previously found in I. ricinus nor in Sweden. Six of the ticks (0.7%) were infected with an Anaplasma sp., presumably A. phagocytophilum. Coxiella burnetii DNA was not detected in any of the ticks. The detection of R. helvetica and A. phagocytophilum in several of the localities sampled suggests that these potentially human-pathogenic agents are common in Sweden.", "doi": "10.1016/j.ttbdis.2011.11.003", "pmid": "22487426", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S1877-959X(11)00090-2"}], "notes": [], "created": "2017-05-04T14:57:46.622Z", "modified": "2020-01-21T13:56:10.585Z"}, {"entity": "publication", "iuid": "c22b835311824bd09b34696240694a83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c22b835311824bd09b34696240694a83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c22b835311824bd09b34696240694a83"}}, "title": "Mutational analysis of human glutathione transferase A2-2 identifies structural elements supporting high activity with the prodrug azathioprine.", "authors": [{"family": "Mod\u00e9n", "given": "Olof", "initials": "O"}, {"family": "Zhang", "given": "Wei", "initials": "W"}, {"family": "Mannervik", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "25", "issn": "1741-0134", "issue": "4", "pages": "189-197", "title": "Protein Eng. Des. Sel.", "issn-l": "1741-0126"}, "abstract": "Glutathione transferase (GST) A2-2 is the human enzyme displaying the highest catalytic activity with the prodrug azathioprine (Aza). The reaction releases pharmacologically active 6-mercaptopurine by displacing the imidazole moiety from the Aza molecule. The GST-catalyzed reaction is of medical significance, since high rates of Aza activation may lead to adverse side effects in treated patients. The present study involves structure-activity relationships in GST A2-2 variants. Chimeric GSTs were previously generated by DNA shuffling and two peptide segments, one N-terminal and one C-terminal, were identified as primary determinants of Aza activity. The segments contain several residues of the substrate-binding H-site and their significance for supporting high Aza activity was investigated. Substitution of the corresponding two small regions in the low-activity human GST A3-3 or rat GST A3-3 by the human GST A2-2 segments generated chimeras with \u223c10-fold enhanced Aza activity. The H-site residues Met208 and Leu213 in the C-terminal segment of GST A2-2 were mutated to produce a library with all possible residue combinations. At a calculated 93% library coverage, all of the 1880 mutants examined showed wild-type or decreased Aza activity, even though some retained activities with alternative substrates, further emphasizing the importance of this region for the targeted activity.", "doi": "10.1093/protein/gzs006", "pmid": "22334756", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "gzs006"}], "notes": [], "created": "2017-05-04T14:57:45.413Z", "modified": "2020-01-21T13:56:10.538Z"}, {"entity": "publication", "iuid": "b839da82b5ed42dfa4c08eb8f18be674", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b839da82b5ed42dfa4c08eb8f18be674.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b839da82b5ed42dfa4c08eb8f18be674"}}, "title": "Mantle cell lymphoma displays a homogenous methylation profile: a comparative analysis with chronic lymphocytic leukemia.", "authors": [{"family": "Halld\u00f3rsd\u00f3ttir", "given": "Anna Margr\u00e9t", "initials": "AM"}, {"family": "Kanduri", "given": "Meena", "initials": "M"}, {"family": "Marincevic", "given": "Millaray", "initials": "M"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Agarwal", "given": "Prasoon", "initials": "P"}, {"family": "Jernberg-Wiklund", "given": "Helena", "initials": "H"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}, {"family": "Sander", "given": "Birgitta", "initials": "B"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "comparative study", "published": "2012-04-00", "journal": {"volume": "87", "issn": "1096-8652", "issue": "4", "pages": "361-367", "title": "Am. J. Hematol.", "issn-l": "0361-8609"}, "abstract": "Mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL) are mature CD5(+) B-cell malignancies with different biological/clinical characteristics. We recently reported an association between different prognostic subgroups of CLL (i.e., IGHV mutated and unmutated) and genomic methylation pattern. However, the relationship between DNA methylation and prognostic markers, such as the proliferation gene expression signature, has not been investigated in MCL. We applied high-resolution methylation microarrays (27,578 CpG sites) to assess the global DNA methylation profiles in 20 MCL (10 each with high/low proliferation signature) and 30 CLL (15 poor-prognostic IGHV unmutated subset #1 and 15 good-prognostic IGHV mutated subset #4) samples. Notably, MCL and each CLL subset displayed distinct genomic methylation profiles. After unsupervised hierarchical clustering, 17/20 MCL cases formed a cluster separate from CLL, while CLL subsets #1 and #4 formed subclusters. Surprisingly, few differentially methylated genes (n = 6) were identified between high vs. low proliferation MCL. In contrast, distinct methylation profiles were demonstrated for MCL and CLL. Importantly, certain functional classes of genes were preferentially methylated in either disease. For instance, developmental genes, in particular homeobox transcription factor genes (e.g., HLXB9, HOXA13), were more highly methylated in MCL, whereas apoptosis-related genes were enriched among targets methylated in CLL (e.g., CYFIP2, NR4A1). Results were validated using pyrosequencing, RQ-PCR and reexpression of specific genes. In summary, the methylation profile of MCL was homogeneous and no correlation with the proliferation signature was observed. Compared to CLL, however, marked differences were discovered such as the preferential methylation of homeobox genes in MCL.", "doi": "10.1002/ajh.23115", "pmid": "22374828", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:52.258Z", "modified": "2020-01-21T13:56:04.843Z"}, {"entity": "publication", "iuid": "0dbbf8978547434d8ec6c1926d36edeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dbbf8978547434d8ec6c1926d36edeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dbbf8978547434d8ec6c1926d36edeb"}}, "title": "Manipulating the genetic code for membrane protein production: what have we learnt so far?", "authors": [{"family": "N\u00f8rholm", "given": "Morten H H", "initials": "MH"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Virkki", "given": "Minttu T I", "initials": "MT"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Daley", "given": "Daniel O", "initials": "DO"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "1818", "issn": "0006-3002", "issue": "4", "pages": "1091-1096", "title": "Biochim. Biophys. Acta", "issn-l": null}, "abstract": "With synthetic gene services, molecular cloning is as easy as ordering a pizza. However choosing the right RNA code for efficient protein production is less straightforward, more akin to deciding on the pizza toppings. The possibility to choose synonymous codons in the gene sequence has ignited a discussion that dates back 50 years: Does synonymous codon use matter? Recent studies indicate that replacement of particular codons for synonymous codons can improve expression in homologous or heterologous hosts, however it is not always successful. Furthermore it is increasingly apparent that membrane protein biogenesis can be codon-sensitive. Single synonymous codon substitutions can influence mRNA stability, mRNA structure, translational initiation, translational elongation and even protein folding. Synonymous codon substitutions therefore need to be carefully evaluated when membrane proteins are engineered for higher production levels and further studies are needed to fully understand how to select the codons that are optimal for higher production. This article is part of a Special Issue entitled: Protein Folding in Membranes.", "doi": "10.1016/j.bbamem.2011.08.018", "pmid": "21884679", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0005-2736(11)00280-X"}, {"db": "pmc", "key": "PMC3288168"}, {"db": "mid", "key": "NIHMS328986"}], "notes": [], "created": "2017-05-04T14:56:14.844Z", "modified": "2021-06-16T15:21:58.633Z"}, {"entity": "publication", "iuid": "5742a85722674d7db890394136a8ac05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5742a85722674d7db890394136a8ac05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5742a85722674d7db890394136a8ac05"}}, "title": "Can weed hosts increase aggressiveness of Phytophthora infestans on potato?", "authors": [{"family": "Gr\u00f6nberg", "given": "L", "initials": "L"}, {"family": "Andersson", "given": "B", "initials": "B"}, {"family": "Yuen", "given": "J", "initials": "J"}], "type": "journal article", "published": "2012-04-00", "journal": {"volume": "102", "issn": "0031-949X", "issue": "4", "pages": "429-433", "title": "Phytopathology", "issn-l": null}, "abstract": "Potato late blight, caused by Phytophthora infestans, is a major disease in potato production throughout the world. In southern Sweden, hairy nightshade (Solanum physalifolium), an alternative non-crop host to the pathogen, is an increasing weed problem. Single-lesion leaves infected by P. infestans were collected from potato and hairy nightshade to determine phenotypic and genotypic population differentiation of P. infestans between the two hosts. Genotypic variation was estimated using microsatellites as markers. The results showed no genotypic differentiation in the samples between the two hosts. Aggressiveness tests were performed using the sampled isolates to cross-inoculate potato and hairy nightshade. The proportion of infected leaves, latency period, lesion growth rate, and sporulation capacity were measured. For isolates from hairy nightshade, the odds of infection were higher on both hosts combined. When tested on potato leaves, isolates from hairy nightshade showed a significantly shorter latency period and higher sporulation capacity compared with isolates from potato. This indicates that an alternative host can filter populations of P. infestans toward a higher aggressiveness, which could lead to increasing problems in controlling potato late blight.", "doi": "10.1094/PHYTO-07-11-0192", "pmid": "22185335", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:41.173Z", "modified": "2020-01-21T13:56:10.316Z"}, {"entity": "publication", "iuid": "778e3c31f0464468972d8821d2a48636", "links": {"self": {"href": "https://publications.scilifelab.se/publication/778e3c31f0464468972d8821d2a48636.json"}, "display": {"href": "https://publications.scilifelab.se/publication/778e3c31f0464468972d8821d2a48636"}}, "title": "The interleukin-6 receptor as a target for prevention of coronary heart disease: a mendelian randomisation analysis.", "authors": [{"family": "Interleukin-6 Receptor Mendelian Randomisation Analysis (IL6R MR) Consortium", "given": null, "initials": null}, {"family": "Swerdlow", "given": "Daniel I", "initials": "DI"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Kuchenbaecker", "given": "Karoline B", "initials": "KB"}, {"family": "Engmann", "given": "Jorgen E L", "initials": "JE"}, {"family": "Shah", "given": "Tina", "initials": "T"}, {"family": "Sofat", "given": "Reecha", "initials": "R"}, {"family": "Guo", "given": "Yiran", "initials": "Y"}, {"family": "Chung", "given": "Christina", "initials": "C"}, {"family": "Peasey", "given": "Anne", "initials": "A"}, {"family": "Pfister", "given": "Roman", "initials": "R"}, {"family": "Mooijaart", "given": "Simon P", "initials": "SP"}, {"family": "Ireland", "given": "Helen A", "initials": "HA"}, {"family": "Leusink", "given": "Maarten", "initials": "M"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Li", "given": "Ka Wah", "initials": "KW"}, {"family": "Palmen", "given": "Jutta", "initials": "J"}, {"family": "Howard", "given": "Philip", "initials": "P"}, {"family": "Cooper", "given": "Jackie A", "initials": "JA"}, {"family": "Drenos", "given": "Fotios", "initials": "F"}, {"family": "Hardy", "given": "John", "initials": "J"}, {"family": "Nalls", "given": "Michael A", "initials": "MA"}, {"family": "Li", "given": "Yun Rose", "initials": "YR"}, {"family": "Lowe", "given": "Gordon", "initials": "G"}, {"family": "Stewart", "given": "Marlene", "initials": "M"}, {"family": "Bielinski", "given": "Suzette J", "initials": "SJ"}, {"family": "Peto", "given": "Julian", "initials": "J"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Gallacher", "given": "John", "initials": "J"}, {"family": "Dunlop", "given": "Malcolm", "initials": "M"}, {"family": "Houlston", "given": "Richard", "initials": "R"}, {"family": "Tomlinson", "given": "Ian", "initials": "I"}, {"family": "Tzoulaki", "given": "Ioanna", "initials": "I"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Boer", "given": "Jolanda M A", "initials": "JM"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Onland-Moret", "given": "N Charlotte", "initials": "NC"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "Schnabel", "given": "Renate B", "initials": "RB"}, {"family": "Hubacek", "given": "Jaroslav A", "initials": "JA"}, {"family": "Kubinova", "given": "Ruzena", "initials": "R"}, {"family": "Baceviciene", "given": "Migle", "initials": "M"}, {"family": "Tamosiunas", "given": "Abdonas", "initials": "A"}, {"family": "Pajak", "given": "Andrzej", "initials": "A"}, {"family": "Topor-Madry", "given": "Roman", "initials": "R"}, {"family": "Malyutina", "given": "Sofia", "initials": "S"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Bandenelli", "given": "Stefania", "initials": "S"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Meschia", "given": "James F", "initials": "JF"}, {"family": "Singleton", "given": "Andrew", "initials": "A"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "Mateo Leach", "given": "Irene", "initials": "I"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJ"}, {"family": "Gansevoort", "given": "Ron T", "initials": "RT"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Epstein", "given": "Stephen E", "initials": "SE"}, {"family": "Burnett", "given": "Mary Susan", "initials": "MS"}, {"family": "Devaney", "given": "Joe M", "initials": "JM"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Westendorp", "given": "Rudi G J", "initials": "RG"}, {"family": "Jan de Borst", "given": "Gert", "initials": "G"}, {"family": "van der Graaf", "given": "Yolanda", "initials": "Y"}, {"family": "de Jong", "given": "Pim A", "initials": "PA"}, {"family": "Mailand-van der Zee", "given": "Anke-Hilse", "initials": "AH"}, {"family": "Klungel", "given": "Olaf H", "initials": "OH"}, {"family": "de Boer", "given": "Anthonius", "initials": "A"}, {"family": "Doevendans", "given": "Pieter A", "initials": "PA"}, {"family": "Stephens", "given": "Jeffrey W", "initials": "JW"}, {"family": "Eaton", "given": "Charles B", "initials": "CB"}, {"family": "Robinson", "given": "Jennifer G", "initials": "JG"}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Fowkes", "given": "F Gerry", "initials": "FG"}, {"family": "Frayling", "given": "Timonthy M", "initials": "TM"}, {"family": "Price", "given": "Jackie F", "initials": "JF"}, {"family": "Whincup", "given": "Peter H", "initials": "PH"}, {"family": "Morris", "given": "Richard W", "initials": "RW"}, {"family": "Lawlor", "given": "Debbie A", "initials": "DA"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Ben-Shlomo", "given": "Yoav", "initials": "Y"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Wareham", "given": "Nick J", "initials": "NJ"}, {"family": "Verschuren", "given": "W M Monique", "initials": "WM"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ"}, {"family": "Whittaker", "given": "John C", "initials": "JC"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Dudbridge", "given": "Frank", "initials": "F"}, {"family": "Delaney", "given": "J A Chris", "initials": "JA"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Hardy", "given": "Rebecca", "initials": "R"}, {"family": "Castillo", "given": "Berta Almoguera", "initials": "BA"}, {"family": "Connolly", "given": "John J", "initials": "JJ"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Brunner", "given": "Eric J", "initials": "EJ"}, {"family": "Marmot", "given": "Michael G", "initials": "MG"}, {"family": "Wassel", "given": "Christina L", "initials": "CL"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Voevoda", "given": "Mikhail", "initials": "M"}, {"family": "Bobak", "given": "Martin", "initials": "M"}, {"family": "Pikhart", "given": "Hynek", "initials": "H"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Hakonarson", "given": "Hakon", "initials": "H"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Keating", "given": "Brendan J", "initials": "BJ"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Casas", "given": "Juan Pablo", "initials": "JP"}], "type": "journal article", "published": "2012-03-31", "journal": {"volume": "379", "issn": "1474-547X", "issue": "9822", "pages": "1214-1224", "title": "Lancet", "issn-l": "0140-6736"}, "abstract": "A high circulating concentration of interleukin 6 is associated with increased risk of coronary heart disease. Blockade of the interleukin-6 receptor (IL6R) with a monoclonal antibody (tocilizumab) licensed for treatment of rheumatoid arthritis reduces systemic and articular inflammation. However, whether IL6R blockade also reduces risk of coronary heart disease is unknown.\n\nApplying the mendelian randomisation principle, we used single nucleotide polymorphisms (SNPs) in the gene IL6R to evaluate the likely efficacy and safety of IL6R inhibition for primary prevention of coronary heart disease. We compared genetic findings with the effects of tocilizumab reported in randomised trials in patients with rheumatoid arthritis.\n\nIn 40 studies including up to 133,449 individuals, an IL6R SNP (rs7529229) marking a non-synonymous IL6R variant (rs8192284; p.Asp358Ala) was associated with increased circulating log interleukin-6 concentration (increase per allele 9\u00b745%, 95% CI 8\u00b734-10\u00b757) as well as reduced C-reactive protein (decrease per allele 8\u00b735%, 95% CI 7\u00b731-9\u00b738) and fibrinogen concentrations (decrease per allele 0\u00b785%, 95% CI 0\u00b760-1\u00b710). This pattern of effects was consistent with IL6R blockade from infusions of tocilizumab (4-8 mg/kg every 4 weeks) in patients with rheumatoid arthritis studied in randomised trials. In 25,458 coronary heart disease cases and 100,740 controls, the IL6R rs7529229 SNP was associated with a decreased odds of coronary heart disease events (per allele odds ratio 0\u00b795, 95% CI 0\u00b793-0\u00b797, p=1\u00b753\u00d710(-5)).\n\nOn the basis of genetic evidence in human beings, IL6R signalling seems to have a causal role in development of coronary heart disease. IL6R blockade could provide a novel therapeutic approach to prevention of coronary heart disease that warrants testing in suitably powered randomised trials. Genetic studies in populations could be used more widely to help to validate and prioritise novel drug targets or to repurpose existing agents and targets for new therapeutic uses.\n\nUK Medical Research Council; British Heart Foundation; Rosetrees Trust; US National Heart, Lung, and Blood Institute; Du Pont Pharma; Chest, Heart and Stroke Scotland; Wellcome Trust; Coronary Thrombosis Trust; Northwick Park Institute for Medical Research; UCLH/UCL Comprehensive Medical Research Centre; US National Institute on Aging; Academy of Finland; Netherlands Organisation for Health Research and Development; SANCO; Dutch Ministry of Public Health, Welfare and Sports; World Cancer Research Fund; Agentschap NL; European Commission; Swedish Heart-Lung Foundation; Swedish Research Council; Strategic Cardiovascular Programme of the Karolinska Institutet; Stockholm County Council; US National Institute of Neurological Disorders and Stroke; MedStar Health Research Institute; GlaxoSmithKline; Dutch Kidney Foundation; US National Institutes of Health; Netherlands Interuniversity Cardiology Institute of the Netherlands; Diabetes UK; European Union Seventh Framework Programme; National Institute for Healthy Ageing; Cancer Research UK; MacArthur Foundation.", "doi": "10.1016/S0140-6736(12)60110-X", "pmid": "22421340", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0140-6736(12)60110-X"}, {"db": "pmc", "key": "PMC3316968"}, {"db": "ClinicalTrials.gov", "key": "NCT00000611"}], "notes": [], "created": "2017-05-04T15:01:02.211Z", "modified": "2020-01-21T13:56:03.100Z"}, {"entity": "publication", "iuid": "8be046b833e64c9cb161275cf6da40a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8be046b833e64c9cb161275cf6da40a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8be046b833e64c9cb161275cf6da40a6"}}, "title": "Interleukin-6 receptor pathways in coronary heart disease: a collaborative meta-analysis of 82 studies.", "authors": [{"family": "IL6R Genetics Consortium Emerging Risk Factors Collaboration", "given": null, "initials": null}, {"family": "Sarwar", "given": "Nadeem", "initials": "N"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Freitag", "given": "Daniel F", "initials": "DF"}, {"family": "Gregson", "given": "John", "initials": "J"}, {"family": "Willeit", "given": "Peter", "initials": "P"}, {"family": "Gorman", "given": "Donal N", "initials": "DN"}, {"family": "Gao", "given": "Pei", "initials": "P"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Rendon", "given": "Augusto", "initials": "A"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Tybj\u00e6rg-Hansen", "given": "Anne", "initials": "A"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Wilde", "given": "Arthur A M", "initials": "AA"}, {"family": "Trip", "given": "Mieke D", "initials": "MD"}, {"family": "Steri", "given": "Maristella", "initials": "M"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "van der Schoot", "given": "C Ellen", "initials": "CE"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Melzer", "given": "David", "initials": "D"}, {"family": "Reich", "given": "David", "initials": "D"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Panagiotakos", "given": "Demosthenes B", "initials": "DB"}, {"family": "Willeit", "given": "Johann", "initials": "J"}, {"family": "Wennberg", "given": "Patrik", "initials": "P"}, {"family": "Woodward", "given": "Mark", "initials": "M"}, {"family": "Adamovic", "given": "Svetlana", "initials": "S"}, {"family": "Rimm", "given": "Eric B", "initials": "EB"}, {"family": "Meade", "given": "Tom W", "initials": "TW"}, {"family": "Gillum", "given": "Richard F", "initials": "RF"}, {"family": "Shaffer", "given": "Jonathan A", "initials": "JA"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Onat", "given": "Altan", "initials": "A"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Wassertheil-Smoller", "given": "Sylvia", "initials": "S"}, {"family": "Mellstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Gallacher", "given": "John", "initials": "J"}, {"family": "Cushman", "given": "Mary", "initials": "M"}, {"family": "Tracy", "given": "Russell P", "initials": "RP"}, {"family": "Kauhanen", "given": "Jussi", "initials": "J"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Salonen", "given": "Jukka T", "initials": "JT"}, {"family": "Wilhelmsen", "given": "Lars", "initials": "L"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Cantin", "given": "Bernard", "initials": "B"}, {"family": "Best", "given": "Lyle G", "initials": "LG"}, {"family": "Ben-Shlomo", "given": "Yoav", "initials": "Y"}, {"family": "Manson", "given": "JoAnn E", "initials": "JE"}, {"family": "Davey-Smith", "given": "George", "initials": "G"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PI"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wilson", "given": "Anthony G", "initials": "AG"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Jansson", "given": "John-Olov", "initials": "JO"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Tivesten", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Ljunggren", "given": "\u00d6sten", "initials": "\u00d6"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Cambien", "given": "Francois", "initials": "F"}, {"family": "Hung", "given": "Joseph", "initials": "J"}, {"family": "Thomas", "given": "G Neil", "initials": "GN"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Kastelein", "given": "John J P", "initials": "JJ"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Allin", "given": "Kristine H", "initials": "KH"}, {"family": "Nordestgaard", "given": "B\u00f8rge G", "initials": "BG"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "H\u00f3lm", "given": "Hilma", "initials": "H"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Kaptoge", "given": "Stephen", "initials": "S"}, {"family": "Di Angelantonio", "given": "Emanuele", "initials": "E"}, {"family": "Harari", "given": "Olivier", "initials": "O"}, {"family": "Danesh", "given": "John", "initials": "J"}], "type": "journal article", "published": "2012-03-31", "journal": {"volume": "379", "issn": "1474-547X", "issue": "9822", "pages": "1205-1213", "title": "Lancet", "issn-l": "0140-6736"}, "abstract": "Persistent inflammation has been proposed to contribute to various stages in the pathogenesis of cardiovascular disease. Interleukin-6 receptor (IL6R) signalling propagates downstream inflammation cascades. To assess whether this pathway is causally relevant to coronary heart disease, we studied a functional genetic variant known to affect IL6R signalling.\n\nIn a collaborative meta-analysis, we studied Asp358Ala (rs2228145) in IL6R in relation to a panel of conventional risk factors and inflammation biomarkers in 125,222 participants. We also compared the frequency of Asp358Ala in 51,441 patients with coronary heart disease and in 136,226 controls. To gain insight into possible mechanisms, we assessed Asp358Ala in relation to localised gene expression and to postlipopolysaccharide stimulation of interleukin 6.\n\nThe minor allele frequency of Asp358Ala was 39%. Asp358Ala was not associated with lipid concentrations, blood pressure, adiposity, dysglycaemia, or smoking (p value for association per minor allele \u22650\u00b704 for each). By contrast, for every copy of 358Ala inherited, mean concentration of IL6R increased by 34\u00b73% (95% CI 30\u00b74-38\u00b72) and of interleukin 6 by 14\u00b76% (10\u00b77-18\u00b74), and mean concentration of C-reactive protein was reduced by 7\u00b75% (5\u00b79-9\u00b71) and of fibrinogen by 1\u00b70% (0\u00b77-1\u00b73). For every copy of 358Ala inherited, risk of coronary heart disease was reduced by 3\u00b74% (1\u00b78-5\u00b70). Asp358Ala was not related to IL6R mRNA levels or interleukin-6 production in monocytes.\n\nLarge-scale human genetic and biomarker data are consistent with a causal association between IL6R-related pathways and coronary heart disease.\n\nBritish Heart Foundation; UK Medical Research Council; UK National Institute of Health Research, Cambridge Biomedical Research Centre; BUPA Foundation.", "doi": "10.1016/S0140-6736(11)61931-4", "pmid": "22421339", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0140-6736(11)61931-4"}, {"db": "pmc", "key": "PMC3316940"}], "notes": [], "created": "2017-05-04T15:01:01.867Z", "modified": "2020-01-21T13:56:03.619Z"}, {"entity": "publication", "iuid": "b05375bb734f442bb7ab24d76b38f38b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b05375bb734f442bb7ab24d76b38f38b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b05375bb734f442bb7ab24d76b38f38b"}}, "title": "Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.", "authors": [{"family": "Dastani", "given": "Zari", "initials": "Z"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Timpson", "given": "Nicholas", "initials": "N"}, {"family": "Perry", "given": "John R B", "initials": "JR"}, {"family": "Yuan", "given": "Xin", "initials": "X"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Henneman", "given": "Peter", "initials": "P"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Kizer", "given": "Jorge R", "initials": "JR"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Small", "given": "Kerrin", "initials": "K"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "Coassin", "given": "Stefan", "initials": "S"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Uh", "given": "Hae-Won", "initials": "HW"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Bidulescu", "given": "Aurelian", "initials": "A"}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Greenwood", "given": "Celia M T", "initials": "CM"}, {"family": "Ladouceur", "given": "Martin", "initials": "M"}, {"family": "Grimsby", "given": "Jonna", "initials": "J"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Kooner", "given": "Jaspal", "initials": "J"}, {"family": "Mooser", "given": "Vincent E", "initials": "VE"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Kapur", "given": "Karen A", "initials": "KA"}, {"family": "Chambers", "given": "John", "initials": "J"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Frants", "given": "Rune", "initials": "R"}, {"family": "Willems-Vandijk", "given": "Ko", "initials": "K"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Lamina", "given": "Claudia", "initials": "C"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Tracy", "given": "Russell P", "initials": "RP"}, {"family": "Brody", "given": "Jennifer", "initials": "J"}, {"family": "Chen", "given": "Ida", "initials": "I"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Evans", "given": "David M", "initials": "DM"}, {"family": "St Pourcain", "given": "Beate", "initials": "B"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Carlson", "given": "Olga D", "initials": "OD"}, {"family": "Egan", "given": "Josephine M", "initials": "JM"}, {"family": "B\u00f6hringer", "given": "Stefan", "initials": "S"}, {"family": "van Heemst", "given": "Diana", "initials": "D"}, {"family": "Kedenko", "given": "Lyudmyla", "initials": "L"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Nuotio", "given": "Marja-Liisa", "initials": "ML"}, {"family": "Loo", "given": "Britt-Marie", "initials": "BM"}, {"family": "Harris", "given": "Tamara", "initials": "T"}, {"family": "Garcia", "given": "Melissa", "initials": "M"}, {"family": "Kanaya", "given": "Alka", "initials": "A"}, {"family": "Haun", "given": "Margot", "initials": "M"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Katsareli", "given": "Efi", "initials": "E"}, {"family": "Couper", "given": "David J", "initials": "DJ"}, {"family": "Duncan", "given": "Bruce B", "initials": "BB"}, {"family": "Kloppenburg", "given": "Margreet", "initials": "M"}, {"family": "Adair", "given": "Linda S", "initials": "LS"}, {"family": "Borja", "given": "Judith B", "initials": "JB"}, {"family": "DIAGRAM+ Consortium", "given": null, "initials": null}, {"family": "MAGIC Consortium", "given": null, "initials": null}, {"family": "GLGC Investigators", "given": null, "initials": null}, {"family": "MuTHER Consortium", "given": null, "initials": null}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Musani", "given": "Solomon", "initials": "S"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Semple", "given": "Robert", "initials": "R"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Allison", "given": "Matthew A", "initials": "MA"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "Buxbaum", "given": "Sarah G", "initials": "SG"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Meulenbelt", "given": "Ingrid", "initials": "I"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Paulweber", "given": "Bernhard", "initials": "B"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Slagboom", "given": "P Eline", "initials": "PE"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "van Duijn", "given": "Cornelia", "initials": "C"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Dupuis", "given": "Josee", "initials": "J"}, {"family": "Richards", "given": "J Brent", "initials": "JB"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "Welch", "given": "Ryan P", "initials": "RP"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Huth", "given": "Cornelia", "initials": "C"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "McCulloch", "given": "Laura J", "initials": "LJ"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Wu", "given": "Guanming", "initials": "G"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "McCarroll", "given": "Steve A", "initials": "SA"}, {"family": "Hofmann", "given": "Oliver M", "initials": "OM"}, {"family": "Segr\u00e8", "given": "Ayellet V", "initials": "AV"}, {"family": "van Hoek", "given": "Mandy", "initials": "M"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Ardlie", "given": "Kristin", "initials": "K"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Benediktsson", "given": "Rafn", "initials": "R"}, {"family": "Bennett", "given": "Amanda J", "initials": "AJ"}, {"family": "Blagieva", "given": "Roza", "initials": "R"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Bostr\u00f6m", "given": "Kristina Bengtsson", "initials": "KB"}, {"family": "Bravenboer", "given": "Bert", "initials": "B"}, {"family": "Bumpstead", "given": "Suzannah", "initials": "S"}, {"family": "Burtt", "given": "No\u00ebl P", "initials": "NP"}, {"family": "Charpentier", "given": "Guillaume", "initials": "G"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Cornelis", "given": "Marilyn", "initials": "M"}, {"family": "Crawford", "given": "Gabe", "initials": "G"}, {"family": "Doney", "given": "Alex S F", "initials": "AS"}, {"family": "Elliott", "given": "Katherine S", "initials": "KS"}, {"family": "Elliott", "given": "Amanda L", "initials": "AL"}, {"family": "Erdos", "given": "Michael R", "initials": "MR"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Franklin", "given": "Christopher S", "initials": "CS"}, {"family": "Ganser", "given": 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"initials": "A"}, {"family": "Dominiczak", "given": "Anna F", "initials": "AF"}, {"family": "Demissie", "given": "Serkalem", "initials": "S"}, {"family": "Deloukas", "given": "Panagiotis", "initials": "P"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Crawford", "given": "Gabriel", "initials": "G"}, {"family": "Chen", "given": "Yii-der I", "initials": "YD"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Boekholdt", "given": "S Matthijs", "initials": "SM"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Seielstad", "given": "Mark", "initials": "M"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}, {"family": "Tai", "given": "E-Shyong", "initials": "ES"}, {"family": "Feranil", "given": "Alan B", "initials": "AB"}, {"family": "Kuzawa", "given": "Christopher W", "initials": "CW"}, {"family": "Taylor", "given": "Herman A", "initials": "HA"}, {"family": "Gabriel", "given": "Stacey B", "initials": "SB"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Krauss", "given": "Ronald M", "initials": "RM"}, {"family": "Ordovas", "given": "Jose M", "initials": "JM"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Tall", "given": "Alan R", "initials": "AR"}, {"family": "Hegele", "given": "Robert A", "initials": "RA"}, {"family": "Kastelein", "given": "John J P", "initials": "JJ"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Sandhu", "given": "Manjinder S", "initials": "MS"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}], "type": "journal article", "published": "2012-03-29", "journal": {"volume": "8", "issn": "1553-7404", "issue": "3", "pages": "e1002607", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Circulating levels of adiponectin, a hormone produced predominantly by adipocytes, are highly heritable and are inversely associated with type 2 diabetes mellitus (T2D) and other metabolic traits. We conducted a meta-analysis of genome-wide association studies in 39,883 individuals of European ancestry to identify genes associated with metabolic disease. We identified 8 novel loci associated with adiponectin levels and confirmed 2 previously reported loci (P\u200a=\u200a4.5\u00d710(-8)-1.2\u00d710(-43)). Using a novel method to combine data across ethnicities (N\u200a=\u200a4,232 African Americans, N\u200a=\u200a1,776 Asians, and N\u200a=\u200a29,347 Europeans), we identified two additional novel loci. Expression analyses of 436 human adipocyte samples revealed that mRNA levels of 18 genes at candidate regions were associated with adiponectin concentrations after accounting for multiple testing (p<3\u00d710(-4)). We next developed a multi-SNP genotypic risk score to test the association of adiponectin decreasing risk alleles on metabolic traits and diseases using consortia-level meta-analytic data. This risk score was associated with increased risk of T2D (p\u200a=\u200a4.3\u00d710(-3), n\u200a=\u200a22,044), increased triglycerides (p\u200a=\u200a2.6\u00d710(-14), n\u200a=\u200a93,440), increased waist-to-hip ratio (p\u200a=\u200a1.8\u00d710(-5), n\u200a=\u200a77,167), increased glucose two hours post oral glucose tolerance testing (p\u200a=\u200a4.4\u00d710(-3), n\u200a=\u200a15,234), increased fasting insulin (p\u200a=\u200a0.015, n\u200a=\u200a48,238), but with lower in HDL-cholesterol concentrations (p\u200a=\u200a4.5\u00d710(-13), n\u200a=\u200a96,748) and decreased BMI (p\u200a=\u200a1.4\u00d710(-4), n\u200a=\u200a121,335). These findings identify novel genetic determinants of adiponectin levels, which, taken together, influence risk of T2D and markers of insulin resistance.", "doi": "10.1371/journal.pgen.1002607", "pmid": "22479202", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-02099"}, {"db": "pmc", "key": "PMC3315470"}], "notes": [], "created": "2017-05-04T15:01:08.057Z", "modified": "2021-07-07T15:57:26.550Z"}, {"entity": "publication", "iuid": "3aeb72d8a2c24525bbb894283e1184b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3aeb72d8a2c24525bbb894283e1184b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3aeb72d8a2c24525bbb894283e1184b6"}}, "title": "Genome-wide association and functional follow-up reveals new loci for kidney function.", "authors": [{"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Garnaas", "given": "Maija", "initials": "M"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Olden", "given": "Matthias", "initials": "M"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Taliun", "given": "Daniel", "initials": "D"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Gao", "given": "Xiaoyi", "initials": "X"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Hundertmark", "given": "Claudia", "initials": "C"}, {"family": "Foster", "given": "Meredith C", "initials": "MC"}, {"family": "O'Seaghdha", "given": "Conall M", "initials": "CM"}, {"family": "Glazer", 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"initials": "AF"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Ellinghaus", "given": "David", "initials": "D"}, {"family": "N\u00f6thlings", "given": "Ute", "initials": "U"}, {"family": "Jacobs", "given": "Gunnar", "initials": "G"}, {"family": "Biffar", "given": "Reiner", "initials": "R"}, {"family": "Endlich", "given": "Karlhans", "initials": "K"}, {"family": "Ernst", "given": "Florian", "initials": "F"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Kroemer", "given": "Heyo K", "initials": "HK"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Stracke", "given": "Sylvia", "initials": "S"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Hastie", "given": "Nick", "initials": "N"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Helmer", "given": "Catherine", "initials": "C"}, {"family": "Wang", "given": "Jie Jin", "initials": "JJ"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Nikopensius", "given": "Tiit", "initials": "T"}, {"family": "Province", "given": "Michael", "initials": "M"}, {"family": "Ketkar", "given": "Shamika", "initials": "S"}, {"family": "Colhoun", "given": "Helen", "initials": "H"}, {"family": "Doney", "given": "Alex", "initials": "A"}, {"family": "Robino", "given": "Antonietta", "initials": "A"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Portas", "given": "Laura", "initials": "L"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Buckley", "given": "Brendan M", "initials": "BM"}, {"family": "Adam", "given": "Martin", "initials": "M"}, {"family": "Thun", "given": "Gian-Andri", "initials": "GA"}, {"family": "Paulweber", "given": "Bernhard", "initials": "B"}, {"family": "Haun", "given": "Margot", "initials": "M"}, {"family": "Sala", "given": "Cinzia", "initials": "C"}, {"family": "Metzger", "given": "Marie", "initials": "M"}, {"family": "Mitchell", "given": "Paul", "initials": "P"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Kim", "given": "Stuart K", "initials": "SK"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Palmer", "given": "Colin", "initials": "C"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Pirastu", "given": "Mario", "initials": "M"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Probst-Hensch", "given": "Nicole M", "initials": "NM"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Borecki", "given": "Ingrid", "initials": "I"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SL"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Curhan", "given": "Gary C", "initials": "GC"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Ridker", "given": "Paul", "initials": "P"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Goessling", "given": "Wolfram", "initials": "W"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}], "type": "journal article", "published": "2012-03-29", "journal": {"volume": "8", "issn": "1553-7404", "issue": "3", "pages": "e1002584", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.", "doi": "10.1371/journal.pgen.1002584", "pmid": "22479191", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-02100"}, {"db": "pmc", "key": "PMC3315455"}], "notes": [], "created": "2017-05-04T15:02:15.020Z", "modified": "2020-01-21T13:56:01.649Z"}, {"entity": "publication", "iuid": "1321ac0506224598ad24c5cb410e276b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1321ac0506224598ad24c5cb410e276b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1321ac0506224598ad24c5cb410e276b"}}, "title": "Toward the single-hour high-quality genome.", "authors": [{"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2012-03-20", "journal": {"volume": "81", "issn": "1545-4509", "issue": null, "pages": "359-378", "title": "Annu. Rev. Biochem.", "issn-l": "0066-4154"}, "abstract": "Today, resequencing of a human genome can be performed in approximately a week using a single instrument. Thanks to a steady logarithmic rate of increase in performance for DNA sequencing platforms over the past seven years, DNA sequencing is one of the fastest developing technology fields. As the process becomes faster, it opens up possibilities within health care, diagnostics, and entirely new fields of research. Immediate genetic characterization of contagious outbreaks has been exemplified, and with such applications for the direct benefit of human health, expectations of future sensitive, rapid, high-throughput, and cost-effective technologies are steadily growing. Simultaneously, some of the limitations of a rapidly growing field have become apparent, and questions regarding the quality of some of the data deposited into databases have been raised. A human genome sequenced in only an hour is likely to become a reality in the future, but its definition may not be as certain.", "doi": "10.1146/annurev-biochem-060410-094158", "pmid": "22443932", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:28.913Z", "modified": "2021-07-08T13:26:08.092Z"}, {"entity": "publication", "iuid": "47589549f1f34f26aaf1da50af5214d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47589549f1f34f26aaf1da50af5214d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47589549f1f34f26aaf1da50af5214d1"}}, "title": "The transcriptome of the adenovirus infected cell.", "authors": [{"family": "Zhao", "given": "Hongxing", "initials": "H"}, {"family": "Dahl\u00f6", "given": "Martin", "initials": "M"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2012-03-15", "journal": {"volume": "424", "issn": "1096-0341", "issue": "2", "pages": "115-128", "title": "Virology", "issn-l": "0042-6822"}, "abstract": "Alternations of cellular gene expression following an adenovirus type 2 infection of human primary cells were studied by using superior sensitive cDNA sequencing. In total, 3791 cellular genes were identified as differentially expressed more than 2-fold. Genes involved in DNA replication, RNA transcription and cell cycle regulation were very abundant among the up-regulated genes. On the other hand, genes involved in various signaling pathways including TGF-\u03b2, Rho, G-protein, Map kinase, STAT and NF-\u03baB stood out among the down-regulated genes. Binding sites for E2F, ATF/CREB and AP2 were prevalent in the up-regulated genes, whereas binding sites for SRF and NF-\u03baB were dominant among the down-regulated genes. It is evident that the adenovirus has gained a control of the host cell cycle, growth, immune response and apoptosis at 24 h after infection. However, efforts from host cell to block the cell cycle progression and activate an antiviral response were also observed.", "doi": "10.1016/j.virol.2011.12.006", "pmid": "22236370", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "S0042-6822(11)00564-2"}], "notes": [], "created": "2017-05-04T15:01:13.042Z", "modified": "2021-07-07T15:11:02.422Z"}, {"entity": "publication", "iuid": "38929e26c17b490e84391fdab6e52d1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38929e26c17b490e84391fdab6e52d1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38929e26c17b490e84391fdab6e52d1a"}}, "title": "Neurobeachin, a regulator of synaptic protein targeting, is associated with body fat mass and feeding behavior in mice and body-mass index in humans.", "authors": [{"family": "Olszewski", "given": "Pawel K", "initials": "PK"}, {"family": "Rozman", "given": "Jan", "initials": "J"}, {"family": "Jacobsson", "given": "Josefin A", "initials": "JA"}, {"family": "Rathkolb", "given": "Birgit", "initials": "B"}, {"family": "Str\u00f6mberg", "given": "Siv", "initials": "S"}, {"family": "Hans", "given": "Wolfgang", "initials": "W"}, {"family": "Klockars", "given": "Anica", "initials": "A"}, {"family": "Alsi\u00f6", "given": "Johan", "initials": "J"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Becker", "given": "Lore", "initials": "L"}, {"family": "H\u00f6lter", "given": "Sabine M", "initials": "SM"}, {"family": "Elvert", "given": "Ralf", "initials": "R"}, {"family": "Ehrhardt", "given": "Nicole", "initials": "N"}, {"family": "Gailus-Durner", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Fuchs", "given": "Helmut", "initials": "H"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Wolf", "given": "Eckhard", "initials": "E"}, {"family": "Klopstock", "given": "Thomas", "initials": "T"}, {"family": "Wurst", "given": "Wolfgang", "initials": "W"}, {"family": "Levine", "given": "Allen S", "initials": "AS"}, {"family": "Marcus", "given": "Claude", "initials": "C"}, {"family": "de Angelis", "given": "Martin Hrab\u011b", "initials": "MH"}, {"family": "Klingenspor", "given": "Martin", "initials": "M"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Kilimann", "given": "Manfred W", "initials": "MW"}], "type": "journal article", "published": "2012-03-15", "journal": {"volume": "8", "issn": "1553-7404", "issue": "3", "pages": "e1002568", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Neurobeachin (Nbea) regulates neuronal membrane protein trafficking and is required for the development and functioning of central and neuromuscular synapses. In homozygous knockout (KO) mice, Nbea deficiency causes perinatal death. Here, we report that heterozygous KO mice haploinsufficient for Nbea have higher body weight due to increased adipose tissue mass. In several feeding paradigms, heterozygous KO mice consumed more food than wild-type (WT) controls, and this consumption was primarily driven by calories rather than palatability. Expression analysis of feeding-related genes in the hypothalamus and brainstem with real-time PCR showed differential expression of a subset of neuropeptide or neuropeptide receptor mRNAs between WT and Nbea+/- mice in the sated state and in response to food deprivation, but not to feeding reward. In humans, we identified two intronic NBEA single-nucleotide polymorphisms (SNPs) that are significantly associated with body-mass index (BMI) in adult and juvenile cohorts. Overall, data obtained in mice and humans suggest that variation of Nbea abundance or activity critically affects body weight, presumably by influencing the activity of feeding-related neural circuits. Our study emphasizes the importance of neural mechanisms in body weight control and points out NBEA as a potential risk gene in human obesity.", "doi": "10.1371/journal.pgen.1002568", "pmid": "22438821", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-00029"}, {"db": "pmc", "key": "PMC3305408"}], "notes": [], "created": "2017-05-04T14:57:42.692Z", "modified": "2020-01-21T13:56:08.540Z"}, {"entity": "publication", "iuid": "547988f4d8724956a59d84137668d1ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/547988f4d8724956a59d84137668d1ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/547988f4d8724956a59d84137668d1ff"}}, "title": "Inflammation-associated nitrotyrosination affects TCR recognition through reduced stability and alteration of the molecular surface of the MHC complex.", "authors": [{"family": "Madhurantakam", "given": "Chaithanya", "initials": "C"}, {"family": "Duru", "given": "Adil D", "initials": "AD"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Webb", "given": "John R", "initials": "JR"}, {"family": "Achour", "given": "Adnane", "initials": "A"}], "type": "journal article", "published": "2012-03-14", "journal": {"volume": "7", "issn": "1932-6203", "issue": "3", "pages": "e32805", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Nitrotyrosination of proteins, a hallmark of inflammation, may result in the production of MHC-restricted neoantigens that can be recognized by T cells and bypass the constraints of immunological self-tolerance. Here we biochemically and structurally assessed how nitrotyrosination of the lymphocytic choriomeningitis virus (LCMV)-associated immunodominant MHC class I-restricted epitopes gp33 and gp34 alters T cell recognition in the context of both H-2D(b) and H-2K(b). Comparative analysis of the crystal structures of H-2K(b)/gp34 and H-2K(b)/NY-gp34 demonstrated that nitrotyrosination of p3Y in gp34 abrogates a hydrogen bond interaction formed with the H-2K(b) residue E152. As a consequence the conformation of the TCR-interacting E152 was profoundly altered in H-2K(b)/NY-gp34 when compared to H-2K(b)/gp34, thereby modifying the surface of the nitrotyrosinated MHC complex. Furthermore, nitrotyrosination of gp34 resulted in structural over-packing, straining the overall conformation and considerably reducing the stability of the H-2K(b)/NY-gp34 MHC complex when compared to H-2K(b)/gp34. Our structural analysis also indicates that nitrotyrosination of the main TCR-interacting residue p4Y in gp33 abrogates recognition of H-2D(b)/gp33-NY complexes by H-2D(b)/gp33-specific T cells through sterical hindrance. In conclusion, this study provides the first structural and biochemical evidence for how MHC class I-restricted nitrotyrosinated neoantigens may enable viral escape and break immune tolerance.", "doi": "10.1371/journal.pone.0032805", "pmid": "22431983", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-25869"}, {"db": "pmc", "key": "PMC3303804"}], "notes": [], "created": "2017-05-04T15:03:46.072Z", "modified": "2018-11-14T16:51:39.153Z"}, {"entity": "publication", "iuid": "9d69998ae15a4878bf629d13abaec2be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d69998ae15a4878bf629d13abaec2be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d69998ae15a4878bf629d13abaec2be"}}, "title": "Antibiotic-induced change of bacterial communities associated with the copepod Nitocra spinipes.", "authors": [{"family": "Edlund", "given": "Anna", "initials": "A"}, {"family": "Ek", "given": "Karin", "initials": "K"}, {"family": "Breitholtz", "given": "Magnus", "initials": "M"}, {"family": "Gorokhova", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2012-03-12", "journal": {"volume": "7", "issn": "1932-6203", "issue": "3", "pages": "e33107", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Environmental pressures, such as physical factors, diet and contaminants may affect interactions between microbial symbionts and their multicellular hosts. Despite obvious relevance, effects of antimicrobial contaminants on host-symbiont relations in non-target aquatic organisms are largely unknown. We show that exposure to antibiotics had negative effects on survival and juvenile development of the copepod Nitocra spinipes and caused significant alterations in copepod-associated bacterial communities. The significant positive correlations between indices of copepod development and bacterial diversity indicate that disruption of the microflora was likely to be an important factor behind retarded juvenile development in the experimental animals. Moreover, as evidenced by ribotype distribution in the bacterial clone libraries, the exposure to antibiotics caused a shift in dominance from Betaproteobacteria to Cardinium bacteria; the latter have been shown to cause reproductive manipulations in various terrestrial arthropods. Thus, in addition to providing evidence that the antibiotic-induced perturbation of the microbial community associates with reductions in fitness-related traits of the host, this study is the first record of a copepod serving as a host for endosymbiotic Cardinium. Taken together, our results suggest that (1) antimicrobial substances and possibly other stressors can affect micobiome and symbiont-mediated interactions in copepods and other hosts, and (2) Cardinium endosymbionts may occur in other copepods and affect reproduction of their hosts.", "doi": "10.1371/journal.pone.0033107", "pmid": "22427962", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-22380"}, {"db": "pmc", "key": "PMC3299745"}], "notes": [], "created": "2017-05-04T14:57:43.606Z", "modified": "2020-01-21T13:56:10.295Z"}, {"entity": "publication", "iuid": "586f6b11de1d47dba7ce229c441380b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/586f6b11de1d47dba7ce229c441380b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/586f6b11de1d47dba7ce229c441380b4"}}, "title": "Infantile cerebellar-retinal degeneration associated with a mutation in mitochondrial aconitase, ACO2.", "authors": [{"family": "Spiegel", "given": "Ronen", "initials": "R"}, {"family": "Pines", "given": "Ophry", "initials": "O"}, {"family": "Ta-Shma", "given": "Asaf", "initials": "A"}, {"family": "Burak", "given": "Efrat", "initials": "E"}, {"family": "Shaag", "given": "Avraham", "initials": "A"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Edvardson", "given": "Shimon", "initials": "S"}, {"family": "Mahajna", "given": "Muhammad", "initials": "M"}, {"family": "Zenvirt", "given": "Shamir", "initials": "S"}, {"family": "Saada", "given": "Ann", "initials": "A"}, {"family": "Shalev", "given": "Stavit", "initials": "S"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Elpeleg", "given": "Orly", "initials": "O"}], "type": "journal article", "published": "2012-03-09", "journal": {"volume": "90", "issn": "1537-6605", "issue": "3", "pages": "518-523", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Degeneration of the cerebrum, cerebellum, and retina in infancy is part of the clinical spectrum of lysosomal storage disorders, mitochondrial respiratory chain defects, carbohydrate glycosylation defects, and infantile neuroaxonal dystrophy. We studied eight individuals from two unrelated families who presented at 2-6 months of age with truncal hypotonia and athetosis, seizure disorder, and ophthalmologic abnormalities. Their course was characterized by failure to acquire developmental milestones and culminated in profound psychomotor retardation and progressive visual loss, including optic nerve and retinal atrophy. Despite their debilitating state, the disease was compatible with survival of up to 18 years. Laboratory investigations were normal, but the oxidation of glutamate by muscle mitochondria was slightly reduced. Serial brain MRI displayed progressive, prominent cerebellar atrophy accompanied by thinning of the corpus callosum, dysmyelination, and frontal and temporal cortical atrophy. Homozygosity mapping followed by whole-exome sequencing disclosed a Ser112Arg mutation in ACO2, encoding mitochondrial aconitase, a component of the Krebs cycle. Specific aconitase activity in the individuals' lymphoblasts was severely reduced. Under restrictive conditions, the mutant human ACO2 failed to complement a yeast ACO1 deletion strain, whereas the wild-type human ACO2 succeeded, indicating that this mutation is pathogenic. Thus, a defect in mitochondrial aconitase is associated with an infantile neurodegenerative disorder affecting mainly the cerebellum and retina. In the absence of noninvasive biomarkers, determination of the ACO2 sequence or of aconitase activity in lymphoblasts are warranted in similarly affected individuals, based on clinical and neuroradiologic grounds.", "doi": "10.1016/j.ajhg.2012.01.009", "pmid": "22405087", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(12)00043-2"}, {"db": "pmc", "key": "PMC3309186"}], "notes": [], "created": "2017-05-04T14:57:28.614Z", "modified": "2021-07-07T14:15:07.577Z"}, {"entity": "publication", "iuid": "0b13ffd149d140ffb85af4300f0afaca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b13ffd149d140ffb85af4300f0afaca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b13ffd149d140ffb85af4300f0afaca"}}, "title": "Scalable in situ hybridization on tissue arrays for validation of novel cancer and tissue-specific biomarkers.", "authors": [{"family": "Kiflemariam", "given": "Sara", "initials": "S"}, {"family": "Andersson", "given": "Sandra", "initials": "S"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2012-03-08", "journal": {"volume": "7", "issn": "1932-6203", "issue": "3", "pages": "e32927", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Tissue localization of gene expression is increasingly important for accurate interpretation of large scale datasets from expression and mutational analyses. To this end, we have (1) developed a robust and scalable procedure for generation of mRNA hybridization probes, providing >95% first-pass success rate in probe generation to any human target gene and (2) adopted an automated staining procedure for analyses of formalin-fixed paraffin-embedded tissues and tissue microarrays. The in situ mRNA and protein expression patterns for genes with known as well as unknown tissue expression patterns were analyzed in normal and malignant tissues to assess procedure specificity and whether in situ hybridization can be used for validating novel antibodies. We demonstrate concordance between in situ transcript and protein expression patterns of the well-known pathology biomarkers KRT17, CHGA, MKI67, PECAM1 and VIL1, and provide independent validation for novel antibodies to the biomarkers BRD1, EZH2, JUP and SATB2. The present study provides a foundation for comprehensive in situ gene set or transcriptome analyses of human normal and tumor tissues.", "doi": "10.1371/journal.pone.0032927", "pmid": "22412953", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-18464"}, {"db": "pmc", "key": "PMC3297615"}], "notes": [], "created": "2017-05-04T14:55:53.205Z", "modified": "2017-05-30T14:54:29.464Z"}, {"entity": "publication", "iuid": "f4948203b9ef4c60bd5b7876c2fc4a5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4948203b9ef4c60bd5b7876c2fc4a5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4948203b9ef4c60bd5b7876c2fc4a5c"}}, "title": "Ecosystem effects of materials proposed for thin\u2011layer capping of contaminated sediments", "authors": [{"family": "N\u00e4slund", "given": "J", "initials": "J"}, {"family": "Samuelsson", "given": "GS", "initials": "G"}, {"family": "Gunnarsson", "given": "JS", "initials": "J"}, {"family": "Nascimento", "given": "FJA", "initials": "F"}, {"family": "Nilsson", "given": "HC", "initials": "H"}, {"family": "Cornelissen", "given": "G", "initials": "G"}, {"family": "Schaanning", "given": "MT", "initials": "M"}], "type": "journal-article", "published": "2012-03-08", "journal": {"volume": "449", "issn": "0171-8630", "issue": null, "pages": "27-40", "title": "Mar. Ecol. Prog. Ser.", "issn-l": null}, "abstract": null, "doi": "10.3354/meps09546", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:10.279Z", "modified": "2021-06-22T12:06:54.904Z"}, {"entity": "publication", "iuid": "0ccc26616b0544a8b463101d454548ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ccc26616b0544a8b463101d454548ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ccc26616b0544a8b463101d454548ad"}}, "title": "Variation in the oxytocin receptor gene is associated with pair-bonding and social behavior.", "authors": [{"family": "Walum", "given": "Hasse", "initials": "H"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Neiderhiser", "given": "Jenae M", "initials": "JM"}, {"family": "Reiss", "given": "David", "initials": "D"}, {"family": "Ganiban", "given": "Jody M", "initials": "JM"}, {"family": "Spotts", "given": "Erica L", "initials": "EL"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Anckars\u00e4ter", "given": "Henrik", "initials": "H"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Westberg", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2012-03-01", "journal": {"volume": "71", "issn": "1873-2402", "issue": "5", "pages": "419-426", "title": "Biol. Psychiatry", "issn-l": "0006-3223"}, "abstract": "In specific vole and primate species the neuropeptide oxytocin plays a central role in the regulation of pair-bonding behavior. Here we investigate the extent to which genetic variants in the oxytocin receptor gene (OXTR) are associated with pair-bonding and related social behaviors in humans.\n\nWe first genotyped twelve single nucleotide polymorphisms (SNPs) in the TOSS (Twin and Offspring Study in Sweden) (n = 2309) and the TCHAD (Swedish Twin Study of Child and Adolescent Development) (n = 1240), comprising measures of self-reported pair-bonding behavior. In the TOSS sample we further investigated one of the SNPs for measures of marital status and quality. Moreover, in the TCHAD sample we explored the longitudinal relationship between precursors of pair-bonding during childhood and subsequent behavior in romantic relationships. Finally, in the TCHAD study and in the Child and Adolescent Twin Study of Sweden (CATSS) (n = 1771), the association between the same SNP and childhood behaviors was investigated.\n\nOne SNP (rs7632287) in OXTR was associated with traits reflecting pair-bonding in women in the TOSS and TCHAD samples. In girls the rs7632287 SNP was further associated with childhood social problems, which longitudinally predicted pair-bonding behavior in the TCHAD sample. This association was replicated in the CATSS sample in which an association between the same SNP and social interaction deficit symptoms from the autism spectrum was detected.\n\nThese results suggest an association between variation in OXTR and human pair-bonding and other social behaviors, possibly indicating that the well-described influence of oxytocin on affiliative behavior in voles could also be of importance for humans.", "doi": "10.1016/j.biopsych.2011.09.002", "pmid": "22015110", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "S0006-3223(11)00860-2"}, {"db": "pmc", "key": "PMC3266986"}, {"db": "mid", "key": "NIHMS325804"}], "notes": [], "created": "2017-05-04T15:03:29.879Z", "modified": "2017-05-30T12:44:09.587Z"}, {"entity": "publication", "iuid": "63270c2f3dda4f3a8a91c059f512d840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63270c2f3dda4f3a8a91c059f512d840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63270c2f3dda4f3a8a91c059f512d840"}}, "title": "Can silencing of transposons contribute to variation in effector gene expression in Phytophthora infestans?", "authors": [{"family": "Whisson", "given": "Stephen", "initials": "S"}, {"family": "Vetukuri", "given": "Ramesh", "initials": "R"}, {"family": "Avrova", "given": "Anna", "initials": "A"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2012-03-01", "journal": {"volume": "2", "issn": "2159-2543", "issue": "2", "pages": "110-114", "title": "Mob Genet Elements", "issn-l": null}, "abstract": "Transposable elements are ubiquitous residents in eukaryotic genomes. Often considered to be genomic parasites, they can lead to dramatic changes in genome organization, gene expression, and gene evolution. The oomycete plant pathogen Phytophthora infestans has evolved a genome organization where core biology genes are predominantly located in genome regions that have relatively few resident transposons. In contrast, disease effector-encoding genes are most frequently located in rapidly evolving genomic regions that are rich in transposons. P. infestans, as a eukaryote, likely uses RNA silencing to minimize the activity of transposons. We have shown that fusion of a short interspersed element (SINE) to an effector gene in P. infestans leads to the silencing of both the introduced fusion and endogenous homologous sequences. This is also likely to occur naturally in the genome of P. infestans, as transcriptional inactivation of effectors is known to occur, and over half of the translocated \"RXLR class\" of effectors are located within 2 kb of transposon sequences in the P. infestans genome. In this commentary, we review the diverse transposon inventory of P. infestans, its control by RNA silencing, and consequences for expression modulation of nearby effector genes in this economically important plant pathogen.", "doi": "10.4161/mge.20265", "pmid": "22934246", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "2012MGE0014R"}, {"db": "pmc", "key": "PMC3429519"}], "notes": [], "created": "2017-05-04T14:57:38.325Z", "modified": "2020-01-21T13:56:02.683Z"}, {"entity": "publication", "iuid": "a19edf0632554037ad7018099f0fc4c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a19edf0632554037ad7018099f0fc4c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a19edf0632554037ad7018099f0fc4c1"}}, "title": "Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.", "authors": [{"family": "Ahmad", "given": "Yasmeen", "initials": "Y"}, {"family": "Boisvert", "given": "Francois-Michel", "initials": "FM"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lamond", "given": "Angus I", "initials": "AI"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "M111.013680", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "In higher eukaryotes many genes encode protein isoforms whose properties and biological roles are often poorly characterized. Here we describe systematic approaches for detection of either distinct isoforms, or separate pools of the same isoform, with differential biological properties. Using information from ion intensities we have estimated protein abundance levels and using rates of change in stable isotope labeling with amino acids in cell culture isotope ratios we measured turnover rates and subcellular distribution for the HeLa cell proteome. Protein isoforms were detected using three data analysis strategies that evaluate differences between stable isotope labeling with amino acids in cell culture isotope ratios for specific groups of peptides within the total set of peptides assigned to a protein. The candidate approach compares stable isotope labeling with amino acids in cell culture isotope ratios for predicted isoform-specific peptides, with ratio values for peptides shared by all the isoforms. The rule of thirds approach compares the mean isotope ratio values for all peptides in each of three equal segments along the linear length of the protein, assessing differences between segment values. The three in a row approach compares mean isotope ratio values for each sequential group of three adjacent peptides, assessing differences with the mean value for all peptides assigned to the protein. Protein isoforms were also detected and their properties evaluated by fractionating cell extracts on one-dimensional SDS-PAGE prior to trypsin digestion and MS analysis and independently evaluating isotope ratio values for the same peptides isolated from different gel slices. The effect of protein phosphorylation on turnover rates was analyzed by comparing mean turnover values calculated for all peptides assigned to a protein, either including, or excluding, values for cognate phosphopeptides. Collectively, these experimental and analytical approaches provide a framework for expanding the functional annotation of the genome.", "doi": "10.1074/mcp.M111.013680", "pmid": "22002106", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "M111.013680"}, {"db": "pmc", "key": "PMC3316725"}], "notes": [], "created": "2017-05-04T14:55:11.982Z", "modified": "2021-07-08T13:44:33.497Z"}, {"entity": "publication", "iuid": "f03ca5da7a6b4192b05897baafae8a2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f03ca5da7a6b4192b05897baafae8a2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f03ca5da7a6b4192b05897baafae8a2b"}}, "title": "Signaling pathways involved in the regulation of TNF\u03b1-induced toll-like receptor 2 expression in human gingival fibroblasts.", "authors": [{"family": "Davanian", "given": "Haleh", "initials": "H"}, {"family": "B\u00e5ge", "given": "Tove", "initials": "T"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Concha", "given": "Hernan Q", "initials": "HQ"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M"}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "57", "issn": "1096-0023", "issue": "3", "pages": "406-416", "title": "Cytokine", "issn-l": "1043-4666"}, "abstract": "Periodontitis is a chronic inflammatory disease characterized by a host inflammatory response against bacteria that leads to destruction of the supporting structures of the teeth. Bacterial components of pathogens in the periodontal pocket are recognized by toll-like receptors (TLRs) that trigger an inflammatory response. In this study, we investigated the effects of the pro-inflammatory cytokine tumor necrosis factor \u03b1 (TNF\u03b1) on TLR2 expression in human gingival fibroblasts. In addition, we examined the signaling pathways involved in the regulation of TNF\u03b1-induced TLR2 expression. Our results showed that TNF\u03b1 increased TLR2 mRNA and protein expression. Microarray analysis and the inhibition of specific signaling pathways demonstrated that c-Jun N-terminal kinases (JNK) and nuclear factor kappa B (NF-\u03baB) were involved in the regulation of TNF\u03b1-induced TLR2 expression in gingival fibroblasts. Furthermore, the prostaglandin E(2) (PGE(2)) regulatory enzyme cytosolic phospholipase A(2) (cPLA(2)) and the anti-inflammatory prostaglandin 15-deoxy-\u0394(12,14)-prostaglandin J(2) (15d-PGJ(2)), were found to regulate TLR2 mRNA expression stimulated by TNF\u03b1. Our findings suggest that these pathways and mediators, through the regulation of TLR2 expression in gingival fibroblasts, may be involved in the pathogenesis of periodontitis. The study provides new insights into the molecular mechanisms underlying the regulation of TLR2, implicated in the chronic inflammatory disease periodontitis.", "doi": "10.1016/j.cyto.2011.12.008", "pmid": "22227093", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1043-4666(11)00860-X"}], "notes": [], "created": "2017-05-04T14:57:32.457Z", "modified": "2021-07-08T13:26:08.398Z"}, {"entity": "publication", "iuid": "f0d112a2276442afae025866d9acbb19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0d112a2276442afae025866d9acbb19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0d112a2276442afae025866d9acbb19"}}, "title": "Phenotypic variation within a clonal lineage of Phytophthora infestans infecting both tomato and potato in Nicaragua.", "authors": [{"family": "Bland\u00f3n-D\u00edaz", "given": "J U", "initials": "JU"}, {"family": "Widmark", "given": "A-K", "initials": "A"}, {"family": "Hannukkala", "given": "A", "initials": "A"}, {"family": "Andersson", "given": "B", "initials": "B"}, {"family": "H\u00f6gberg", "given": "N", "initials": "N"}, {"family": "Yuen", "given": "J E", "initials": "JE"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "102", "issn": "0031-949X", "issue": "3", "pages": "323-330", "title": "Phytopathology", "issn-l": null}, "abstract": "Late blight caused by Phytophthora infestans (Mont.) de Bary is a constraint to both potato and tomato crops in Nicaragua. The hypothesis that the Nicaraguan population of P. infestans is genotypically and phenotypically diverse and potentially subdivided based on host association was tested. A collection of isolates was analyzed using genotypic markers (microsatellites and mitochondrial DNA haplotype) and phenotypic markers (mating type, virulence, and fungicide sensitivity). The genotypic analysis revealed no polymorphism in 121 of 132 isolates of P. infestans tested. Only the Ia haplotype and the A2 mating type were detected. Most of the tested isolates were resistant to metalaxyl. The virulence testing showed variation among isolates of P. infestans. No evidence was found of population differentiation among potato and tomato isolates of P. infestans based on the genotypic and phenotypic analysis. We conclude that the Nicaraguan population of P. infestans consists of a single clonal lineage (NI-1) which belongs to the A2 mating type and the Ia mitochondrial DNA haplotype. Moreover, based on the markers used, this population of P. infestans does not resemble the population in countries from which potato seed is imported to Nicaragua or the population in neighboring countries. The data presented here indicate that the NI-1 clonal lineage is the primary pathogen on both potato and tomato, and its success on both host species is unique in a South American context.", "doi": "10.1094/PHYTO-02-11-0033", "pmid": "22085300", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:40.868Z", "modified": "2020-01-21T13:56:10.559Z"}, {"entity": "publication", "iuid": "7b1a3ad72f1d482ba65db8b617b2ce4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b1a3ad72f1d482ba65db8b617b2ce4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b1a3ad72f1d482ba65db8b617b2ce4c"}}, "title": "Oral contraceptive and progestin-only use correlates to tissue tumor marker expression in women with cervical intraepithelial neoplasia.", "authors": [{"family": "Samir", "given": "Raghad", "initials": "R"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Tot", "given": "Tibor", "initials": "T"}, {"family": "Pekar", "given": "Gyula", "initials": "G"}, {"family": "Hellberg", "given": "Dan", "initials": "D"}], "type": "comparative study", "published": "2012-03-00", "journal": {"volume": "85", "issn": "1879-0518", "issue": "3", "pages": "288-293", "title": "Contraception", "issn-l": "0010-7824"}, "abstract": "The study was conducted to investigate correlations between combined oral contraceptive (COC), any progestin-only contraceptive, medicated intrauterine device (MID) or systemic progestin-only (Syst-P) use and tumor marker expression in cervical intraepithelial neoplasia compared to nonusers.\n\nOne-hundred ninety-five women of fertile age with cervical biopsies ranging histologically from normal epithelium to carcinoma in situ were recruited consecutively. Combined oral contraceptive, Syst-P and MID users were investigated according to the expression of 11 tumor markers.\n\nOverexpression of cyclooxygenase-2 (Cox-2) was observed in COC users, while interleukin 10 was underexpressed. When users of progestogen-only contraceptives were analyzed, there was a lower expression of cytokeratin 10 and interleukin 10. When only MID users were analyzed, a high expression of p53 was found. Expression of Cox-2, p53 and retinoblastoma protein differed between COC and MID\u00a0users.\n\nThe study showed molecular alterations, which, in general, have not been studied previously in COC users and have never been studied in progestogen-only users. These biological events might be involved in epidemiological correlations found between hormonal contraceptive use and cervical neoplasms.", "doi": "10.1016/j.contraception.2011.09.001", "pmid": "22067748", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S0010-7824(11)00520-8"}], "notes": [], "created": "2017-05-04T14:55:50.557Z", "modified": "2017-05-30T12:55:16.066Z"}, {"entity": "publication", "iuid": "88b5fd89159c45bfaf3217e1dd5ec375", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88b5fd89159c45bfaf3217e1dd5ec375.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88b5fd89159c45bfaf3217e1dd5ec375"}}, "title": "Novel amplifications in pediatric medulloblastoma identified by genome-wide copy number profiling.", "authors": [{"family": "Nord", "given": "Helena", "initials": "H"}, {"family": "Pfeifer", "given": "Susan", "initials": "S"}, {"family": "Nilsson", "given": "Pelle", "initials": "P"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "Popova", "given": "Svetlana", "initials": "S"}, {"family": "Str\u00f6mberg", "given": "Bo", "initials": "B"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M"}, {"family": "D\u00edaz de St\u00e5hl", "given": "Teresita", "initials": "T"}], "type": "comparative study", "published": "2012-03-00", "journal": {"volume": "107", "issn": "1573-7373", "issue": "1", "pages": "37-49", "title": "J. Neurooncol.", "issn-l": "0167-594X"}, "abstract": "Medulloblastoma (MB) is a WHO grade IV, invasive embryonal CNS tumor that mainly affects children. The aggressiveness and response to therapy can vary considerably between cases, and despite treatment, ~30% of patients die within 2 years from diagnosis. Furthermore, the majority of survivors suffer long-term side-effects due to severe management modalities. Several distinct morphological features have been associated with differences in biological behavior, but improved molecular-based criteria that better reflect the underlying tumor biology are in great demand. In this study, we profiled a series of 25 MB with a 32K BAC array covering 99% of the current assembly of the human genome for the identification of genetic copy number alterations possibly important in MB. Previously known aberrations as well as several novel focally amplified loci could be identified. As expected, the most frequently observed alteration was the combination of 17p loss and 17q gain, which was detected in both high- and standard-risk patients. We also defined minimal overlapping regions of aberrations, including 16 regions of gain and 18 regions of loss in various chromosomes. A few noteworthy narrow amplified loci were identified on autosomes 1 (38.89-41.97 and 84.89-90.76 Mb), 3 (27.64-28.20 and 35.80-43.50 Mb), and 8 (119.66-139.79 Mb), aberrations that were verified with an alternative platform (Illumina 610Q chips). Gene expression levels were also established for these samples using Affymetrix U133Plus2.0 arrays. Several interesting genes encompassed within the amplified regions and presenting with transcript upregulation were identified. These data contribute to the characterization of this malignant childhood brain tumor and confirm its genetic heterogeneity.", "doi": "10.1007/s11060-011-0716-0", "pmid": "21979893", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:00.909Z", "modified": "2020-01-21T13:56:03.485Z"}, {"entity": "publication", "iuid": "0cc8e86f74674b16a843ca1093c66d28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cc8e86f74674b16a843ca1093c66d28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cc8e86f74674b16a843ca1093c66d28"}}, "title": "Microarray profiling of diaphyseal bone of rats suffering from hypervitaminosis A.", "authors": [{"family": "Lind", "given": "Thomas", "initials": "T"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Lind", "given": "P Monica", "initials": "PM"}, {"family": "Sugars", "given": "Rachael", "initials": "R"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Jacobson", "given": "Annica", "initials": "A"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "90", "issn": "1432-0827", "issue": "3", "pages": "219-229", "title": "Calcif. Tissue Int.", "issn-l": "0171-967X"}, "abstract": "Vitamin A is the only known compound that produces spontaneous fractures in rats. In an effort to resolve the molecular mechanism behind this effect, we fed young male rats high doses of vitamin A and performed microarray analysis of diaphyseal bone with and without marrow after 1 week, i.e., just before the first fractures appeared. Of the differentially expressed genes in cortical bone, including marrow, 98% were upregulated. In contrast, hypervitaminotic cortical bone without marrow showed reduced expression of 37% of differentially expressed genes. Gene ontology (GO) analysis revealed that only samples containing bone marrow were associated with a GO term, which principally represented extracellular matrix. This is consistent with the histological findings of increased endosteal/marrow osteoblast number. Fourteen genes, including Cyp26b1, which is known to be upregulated by vitamin A, were selected and verified by real-time PCR. In addition, immunohistochemical staining of bone sections confirmed that the bone-specific molecule osteoadherin was upregulated. Further analysis of the major gene-expression changes revealed apparent augmented Wnt signaling in the sample containing bone marrow but reduced Wnt signaling in cortical bone. Moreover, induced expression of hypoxia-associated genes was found only in samples containing bone marrow. Together, these results highlight the importance of compartment-specific analysis of bone and corroborate previous observations of compartment-specific effects of vitamin A, with reduced activity in cortical bone but increased activity in the endosteal/marrow compartment. We specifically identify potential key osteoblast-, Wnt signaling-, and hypoxia-associated genes in the processes leading to spontaneous fractures.", "doi": "10.1007/s00223-011-9561-6", "pmid": "22215263", "labels": {"Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:55.777Z", "modified": "2017-05-30T12:36:45.142Z"}, {"entity": "publication", "iuid": "14d3e80ce02d49e099343751042aacb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14d3e80ce02d49e099343751042aacb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14d3e80ce02d49e099343751042aacb4"}}, "title": "Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens.", "authors": [{"family": "Dengjel", "given": "J\u00f6rn", "initials": "J"}, {"family": "H\u00f8yer-Hansen", "given": "Maria", "initials": "M"}, {"family": "Nielsen", "given": "Maria O", "initials": "MO"}, {"family": "Eisenberg", "given": "Tobias", "initials": "T"}, {"family": "Harder", "given": "Lea M", "initials": "LM"}, {"family": "Schandorff", "given": "S\u00f8ren", "initials": "S"}, {"family": "Farkas", "given": "Thomas", "initials": "T"}, {"family": "Kirkegaard", "given": "Thomas", "initials": "T"}, {"family": "Becker", "given": "Andrea C", "initials": "AC"}, {"family": "Schroeder", "given": "Sabrina", "initials": "S"}, {"family": "Vanselow", "given": "Katja", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Nielsen", "given": "Mogens M", "initials": "MM"}, {"family": "Kristensen", "given": "Anders R", "initials": "AR"}, {"family": "Akimov", "given": "Vyacheslav", "initials": "V"}, {"family": "Bunkenborg", "given": "Jakob", "initials": "J"}, {"family": "Madeo", "given": "Frank", "initials": "F"}, {"family": "J\u00e4\u00e4ttel\u00e4", "given": "Marja", "initials": "M"}, {"family": "Andersen", "given": "Jens S", "initials": "JS"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "M111.014035", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Autophagy is one of the major intracellular catabolic pathways, but little is known about the composition of autophagosomes. To study the associated proteins, we isolated autophagosomes from human breast cancer cells using two different biochemical methods and three stimulus types: amino acid deprivation or rapamycin or concanamycin A treatment. The autophagosome-associated proteins were dependent on stimulus, but a core set of proteins was stimulus-independent. Remarkably, proteasomal proteins were abundant among the stimulus-independent common autophagosome-associated proteins, and the activation of autophagy significantly decreased the cellular proteasome level and activity supporting interplay between the two degradation pathways. A screen of yeast strains defective in the orthologs of the human genes encoding for a common set of autophagosome-associated proteins revealed several regulators of autophagy, including subunits of the retromer complex. The combined spatiotemporal proteomic and genetic data sets presented here provide a basis for further characterization of autophagosome biogenesis and cargo selection.", "doi": "10.1074/mcp.M111.014035", "pmid": "22311637", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "S1535-9476(20)30499-0"}, {"db": "pmc", "key": "PMC3316729"}], "notes": [], "created": "2017-05-04T14:55:11.076Z", "modified": "2021-07-05T16:33:38.552Z"}, {"entity": "publication", "iuid": "dda66f63a7244599ba409cca419b8f75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dda66f63a7244599ba409cca419b8f75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dda66f63a7244599ba409cca419b8f75"}}, "title": "Genome-wide and gene-based association implicates FRMD6 in alzheimer disease", "authors": [{"family": "Hong", "given": "Mun Gwan", "initials": "MG"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Feldman", "given": "Adina L", "initials": "AL"}, {"family": "Kallin", "given": "Mikael", "initials": "M"}, {"family": "Lambert", "given": "Jean Charles", "initials": "JC"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}], "type": "journal-article", "published": "2012-03-00", "journal": {"volume": "33", "issn": "1059-7794", "issue": "3", "pages": "521-529", "title": "Human Mutation", "issn-l": "1059-7794"}, "abstract": "Genome-wide association studies (GWAS) that allow for allelic heterogeneity may facilitate the discovery of novel genes not detectable by models that require replication of a single variant site. One strategy to accomplish this is to focus on genes rather than markers as units of association, and so potentially capture a spectrum of causal alleles that differ across populations. Here, we conducted a GWAS of Alzheimer disease (AD) in 2,586 Swedes and performed gene-based meta-analysis with three additional studies from France, Canada, and the United States, in total encompassing 4,259 cases and 8,284 controls. Implementing a newly designed gene-based algorithm, we identified two loci apart from the region around APOE that achieved study-wide significance in combined samples, the strongest finding being for FRMD6 on chromosome 14q (P = 2.6 \u00d7 10(-14)) and a weaker signal for NARS2 that is immediately adjacent to GAB2 on chromosome 11q (P = 7.8 \u00d7 10(-9)). Ontology-based pathway analyses revealed significant enrichment of genes involved in glycosylation. Results suggest that gene-based approaches that accommodate allelic heterogeneity in GWAS can provide a complementary avenue for gene discovery and may help to explain a portion of the missing heritability not detectable with single nucleotide polymorphisms (SNPs) derived from marker-specific meta-analysis.", "doi": "10.1002/humu.22009", "pmid": "22190428", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "mid", "key": "NIHMS344656"}, {"db": "pmc", "key": "PMC3326347"}], "notes": [], "created": "2017-05-04T15:00:59.693Z", "modified": "2023-06-19T11:48:51.655Z"}, {"entity": "publication", "iuid": "d9589f25b8934fc2b36bab354043125a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9589f25b8934fc2b36bab354043125a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9589f25b8934fc2b36bab354043125a"}}, "title": "Genome wide analysis reveals association of a FTO gene variant with epigenetic changes.", "authors": [{"family": "Alm\u00e9n", "given": "Markus S\u00e4llman", "initials": "MS"}, {"family": "Jacobsson", "given": "Josefin A", "initials": "JA"}, {"family": "Moschonis", "given": "George", "initials": "G"}, {"family": "Benedict", "given": "Christian", "initials": "C"}, {"family": "Chrousos", "given": "George P", "initials": "GP"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "99", "issn": "1089-8646", "issue": "3", "pages": "132-137", "title": "Genomics", "issn-l": "0888-7543"}, "abstract": "Variants of the FTO gene show strong association with obesity, but the mechanisms behind this association remain unclear. We determined the genome wide DNA methylation profile in blood from 47 female preadolescents. We identified sites associated with the genes KARS, TERF2IP, DEXI, MSI1, STON1 and BCAS3 that had a significant differential methylation level in the carriers of the FTO risk allele (rs9939609). In addition, we identified 20 differentially methylated sites associated with obesity. Our findings suggest that the effect of the FTO obesity risk allele may be mediated through epigenetic changes. Further, these sites might prove to be valuable biomarkers for the understanding of obesity and its comorbidites.", "doi": "10.1016/j.ygeno.2011.12.007", "pmid": "22234326", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0888-7543(11)00281-3"}], "notes": [], "created": "2017-05-04T15:00:59.065Z", "modified": "2020-01-21T13:56:05.590Z"}, {"entity": "publication", "iuid": "c76cc56dd91f4a708ab21d5a78761a7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c76cc56dd91f4a708ab21d5a78761a7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c76cc56dd91f4a708ab21d5a78761a7b"}}, "title": "Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.", "authors": [{"family": "Larance", "given": "Mark", "initials": "M"}, {"family": "Kirkwood", "given": "Kathryn J", "initials": "KJ"}, {"family": "Xirodimas", "given": "Dimitris P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lamond", "given": "Angus I", "initials": "AI"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "M111.014407", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The NEDD8-Cullin E3 ligase pathway plays an important role in protein homeostasis, in particular the degradation of cell cycle regulators and transcriptional control networks. To characterize NEDD8-cullin target proteins, we performed a quantitative proteomic analysis of cells treated with MLN4924, a small molecule inhibitor of the NEDD8 conjugation pathway. MRFAP1 and its interaction partner, MORF4L1, were among the most up-regulated proteins after NEDD8 inhibition in multiple human cell lines. We show that MRFAP1 has a fast turnover rate in the absence of MLN4924 and is degraded via the ubiquitin-proteasome system. The increased abundance of MRFAP1 after MLN4924 treatment results from a decreased rate of degradation. Characterization of the binding partners of both MRFAP1 and MORF4L1 revealed a complex protein-protein interaction network. MRFAP1 bound to a number of E3 ubiquitin ligases, including CUL4B, but not to components of the NuA4 complex, including MRGBP, which bound to MORF4L1. These data indicate that MRFAP1 may regulate the ability of MORF4L1 to interact with chromatin-modifying enzymes by binding to MORF4L1 in a mutually exclusive manner with MRGBP. Analysis of MRFAP1 expression in human tissues by immunostaining with a MRFAP1-specific antibody revealed that it was detectable in only a small number of tissues, in particular testis and brain. Strikingly, analysis of the seminiferous tubules of the testis showed the highest nuclear staining in the spermatogonia and much weaker staining in the spermatocytes and spermatids. MRGBP was inversely correlated with MRFAP1 expression in these cell types, consistent with an exchange of MORF4L1 interaction partners as cells progress through meiosis in the testis. These data highlight an important new arm of the NEDD8-cullin pathway.", "doi": "10.1074/mcp.M111.014407", "pmid": "22038470", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "S1535-9476(20)30503-X"}, {"db": "pmc", "key": "PMC3316733"}], "notes": [], "created": "2017-05-04T14:55:11.687Z", "modified": "2021-07-08T13:44:33.624Z"}, {"entity": "publication", "iuid": "5488813a095a489d96085f5df73da1f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5488813a095a489d96085f5df73da1f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5488813a095a489d96085f5df73da1f8"}}, "title": "Antibody-based protein profiling of the human chromosome 21.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "\u00c4lgen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Kondo", "given": "Tadashi", "initials": "T"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "M111.013458", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The Human Proteome Project has been proposed to create a knowledge-based resource based on a systematical mapping of all human proteins, chromosome by chromosome, in a gene-centric manner. With this background, we here describe the systematic analysis of chromosome 21 using an antibody-based approach for protein profiling using both confocal microscopy and immunohistochemistry, complemented with transcript profiling using next generation sequencing data. We also describe a new approach for protein isoform analysis using a combination of antibody-based probing and isoelectric focusing. The analysis has identified several genes on chromosome 21 with no previous evidence on the protein level, and the isoform analysis indicates that a large fraction of human proteins have multiple isoforms. A chromosome-wide matrix is presented with status for all chromosome 21 genes regarding subcellular localization, tissue distribution, and molecular characterization of the corresponding proteins. The path to generate a chromosome-specific resource, including integrated data from complementary assay platforms, such as mass spectrometry and gene tagging analysis, is discussed.", "doi": "10.1074/mcp.M111.013458", "pmid": "22042635", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "M111.013458"}, {"db": "pmc", "key": "PMC3316724"}], "notes": [], "created": "2017-05-04T14:55:11.382Z", "modified": "2021-07-08T13:44:33.262Z"}, {"entity": "publication", "iuid": "7d06fc08dada4b148a9d889a8ed92d01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d06fc08dada4b148a9d889a8ed92d01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d06fc08dada4b148a9d889a8ed92d01"}}, "title": "A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.", "authors": [{"family": "Zeiler", "given": "Marlis", "initials": "M"}, {"family": "Straube", "given": "Werner L", "initials": "WL"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "O111.009613", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Mass spectrometry-based proteomics increasingly relies on relative or absolute quantification. In relative quantification, stable isotope based methods often allow mixing at early stages of sample preparation, whereas for absolute quantification this has generally required recombinant expression of full length, labeled protein standards. Here we make use of a very large library of Protein Epitope Signature Tags (PrESTs) that has been developed in the course of the Human Protein Atlas Project. These PrESTs are expressed recombinantly in E. coli and they consist of a short and unique region of the protein of interest as well as purification and solubility tags. We first quantify a highly purified, stable isotope labeling of amino acids in cell culture (SILAC)-labeled version of the solubility tag and use it determine the precise amount of each PrEST by its SILAC ratios. The PrESTs are then spiked into cell lysates and the SILAC ratios of PrEST peptides to peptides from endogenous target proteins yield their cellular quantities. The procedure can readily be multiplexed, as we demonstrate by simultaneously determining the copy number of 40 proteins in HeLa cells. Among the proteins analyzed, the cytoskeletal protein vimentin was found to be most abundant with 20 million copies per cell, while the transcription factor and oncogene FOS only had 6000 copies. Direct quantification of the absolute amount of single proteins is possible via a SILAC experiment in which labeled cell lysate is mixed both with the heavy labeled solubility tag and with the corresponding PrEST. The SILAC-PrEST combination allows accurate and streamlined quantification of the absolute or relative amount of proteins of interest in a wide variety of applications.", "doi": "10.1074/mcp.O111.009613", "pmid": "21964433", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "O111.009613"}, {"db": "pmc", "key": "PMC3316735"}], "notes": [], "created": "2017-05-04T14:55:12.279Z", "modified": "2021-07-08T13:44:33.380Z"}, {"entity": "publication", "iuid": "6435cce794dd4d8bbeb5a4dc74edbc9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6435cce794dd4d8bbeb5a4dc74edbc9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6435cce794dd4d8bbeb5a4dc74edbc9c"}}, "title": "A dimerized single-chain variable fragment system for the assessment of neutralizing activity of phage display-selected antibody fragments specific for cytomegalovirus.", "authors": [{"family": "Carlsson", "given": "Fredrika", "initials": "F"}, {"family": "Trilling", "given": "Mirko", "initials": "M"}, {"family": "Perez", "given": "Franck", "initials": "F"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2012-02-28", "journal": {"volume": "376", "issn": "1872-7905", "issue": "1-2", "pages": "69-78", "title": "J. Immunol. Methods", "issn-l": "0022-1759"}, "abstract": "Cytomegalovirus (CMV) causes severe sequelae in congenitally infected newborns and may cause life-threatening disease in immuno-deficient patients. Recent findings demonstrate the possibility to alleviate the disease by infusing intravenous immunoglobulin G (IgG) preparations, indicating that antibodies are an effective therapeutic option. Modern molecular methodologies, like phage display, allow for the development of specific antibodies targeting virtually any antigen, including those of CMV. However, such methodologies do not in general result in products that by themselves mediate biological activity. To facilitate a semi-high-throughput approach for functional screening in future efforts to develop efficacious antibodies against CMV, we have integrated two different approaches to circumvent potential bottlenecks in such efforts. Firstly, we explored an approach that permits easy transfer of antibody fragment encoding genes from commonly used phage display vectors into vectors for the production of divalent immunoglobulins. Secondly, we demonstrate that such proteins can be applied in a novel reporter-based neutralization assay to establish a proof-of-concept workflow for the generation of neutralizing antibodies against CMV. We validated our approach by showing that divalent antibodies raised against the antigenic domain (AD)-2 region of gB effectively neutralized three different CMV strains (AD169, Towne and TB40/E), whereas two antibodies against the AD-1 region of gB displayed minor neutralizing capabilities. In conclusion, the methods investigated in this proof-of-concept study enables for a semi-high-throughput workflow in the screening and investigation of biological active antibodies.", "doi": "10.1016/j.jim.2011.11.010", "pmid": "22154743", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0022-1759(11)00316-4"}], "notes": [], "created": "2017-05-04T14:56:16.057Z", "modified": "2020-01-21T13:53:20.565Z"}, {"entity": "publication", "iuid": "3c2e1ee6240f42f8a471580f651f3a81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c2e1ee6240f42f8a471580f651f3a81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c2e1ee6240f42f8a471580f651f3a81"}}, "title": "Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.", "authors": [{"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Jesus Iglesias", "given": "Maria", "initials": "M"}, {"family": "Reilly", "given": "Sarah-Jayne", "initials": "SJ"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Pirmoradian Najafabadi", "given": "Mohammad", "initials": "M"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2012-02-27", "journal": {"volume": "7", "issn": "1932-6203", "issue": "2", "pages": "e32306", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS).To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches--gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. We examined the effect of 2 hrs LPS stimulation on early gene expression and its relation to chromatin remodeling (H3 acetylation; H3Ac) and promoter binding of Sp1 and RNA polymerase II phosphorylated at serine 5 (S5P RNAPII), which is a marker for transcriptional initiation. Our results indicate novel and alternative gene regulatory mechanisms for certain proinflammatory genes. We identified two groups of up-regulated inflammatory genes with respect to chromatin modification and promoter features. One group, including highly up-regulated genes such as tumor necrosis factor (TNF), was characterized by H3Ac, high CpG content and lack of TATA boxes. The second group, containing inflammatory mediators (interleukins and CCL chemokines), was up-regulated upon LPS stimulation despite lacking H3Ac in their annotated promoters, which were low in CpG content but did contain TATA boxes. Genome-wide analysis showed that few H3Ac peaks were unique to either +/-LPS condition. However, within these, an unpacking/expansion of already existing H3Ac peaks was observed upon LPS stimulation. In contrast, a significant proportion of S5P RNAPII peaks (approx 40%) was unique to either condition. Furthermore, data indicated a large portion of previously unannotated TSSs, particularly in LPS-stimulated macrophages, where only 28% of unique S5P RNAPII peaks overlap annotated promoters. The regulation of the inflammatory response appears to occur in a very specific manner at the chromatin level for specific genes and this study highlights the level of fine-tuning that occurs in the immune response.", "doi": "10.1371/journal.pone.0032306", "pmid": "22384210", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-18710"}, {"db": "pmc", "key": "PMC3288078"}], "notes": [], "created": "2017-05-04T15:01:11.818Z", "modified": "2020-01-21T13:56:01.691Z"}, {"entity": "publication", "iuid": "8e81fe1748214647aebe420e8df0726f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e81fe1748214647aebe420e8df0726f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e81fe1748214647aebe420e8df0726f"}}, "title": "Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes.", "authors": [{"family": "Min", "given": "Josine L", "initials": "JL"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Halgrimsdottir", "given": "Ingileif", "initials": "I"}, {"family": "Almstrup", "given": "Kristian", "initials": "K"}, {"family": "Petri", "given": "Andreas", "initials": "A"}, {"family": "Barrett", "given": "Amy", "initials": "A"}, {"family": "Travers", "given": "Mary", "initials": "M"}, {"family": "Rayner", "given": "Nigel W", "initials": "NW"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Pettersson", "given": "Fredrik H", "initials": "FH"}, {"family": "Broxholme", "given": "John", "initials": "J"}, {"family": "Neville", "given": "Matt J", "initials": "MJ"}, {"family": "Wills", "given": "Quin F", "initials": "QF"}, {"family": "Cheeseman", "given": "Jane", "initials": "J"}, {"family": "GIANT Consortium", "given": null, "initials": null}, {"family": "MolPAGE Consortium", "given": null, "initials": null}, {"family": "Allen", "given": "Maxine", "initials": "M"}, {"family": "Holmes", "given": "Chris C", "initials": "CC"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Fleckner", "given": "Jan", "initials": "J"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Zondervan", "given": "Krina T", "initials": "KT"}], "type": "journal article", "published": "2012-02-23", "journal": {"volume": "8", "issn": "1553-7404", "issue": "2", "pages": "e1002505", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, and whole blood (WB), from 29 MetS cases and 44 controls. Co-expression network analysis for each tissue independently identified nine, six, and zero MetS-associated modules of coexpressed genes in ABD, GLU, and WB, respectively. Of 8,992 probesets expressed in ABD or GLU, 685 (7.6%) were expressed in ABD and 51 (0.6%) in GLU only. Differential eigengene network analysis of 8,256 shared probesets detected 22 shared modules with high preservation across adipose depots (D(ABD-GLU)\u200a=\u200a0.89), seven of which were associated with MetS (FDR P<0.01). The strongest associated module, significantly enriched for immune response-related processes, contained 94/620 (15%) genes with inter-depot differences. In an independent cohort of 145/141 twins with ABD and WB longitudinal expression data, median variability in ABD due to familiality was greater for MetS-associated versus un-associated modules (ABD: 0.48 versus 0.18, P\u200a=\u200a0.08; GLU: 0.54 versus 0.20, P\u200a=\u200a7.8\u00d710(-4)). Cis-eQTL analysis of probesets associated with MetS (FDR P<0.01) and/or inter-depot differences (FDR P<0.01) provided evidence for 32 eQTLs. Corresponding eSNPs were tested for association with MetS-related phenotypes in two GWAS of >100,000 individuals; rs10282458, affecting expression of RARRES2 (encoding chemerin), was associated with body mass index (BMI) (P\u200a=\u200a6.0\u00d710(-4)); and rs2395185, affecting inter-depot differences of HLA-DRB1 expression, was associated with high-density lipoprotein (P\u200a=\u200a8.7\u00d710(-4)) and BMI-adjusted waist-to-hip ratio (P\u200a=\u200a2.4\u00d710(-4)). Since many genes and their interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations.", "doi": "10.1371/journal.pgen.1002505", "pmid": "22383892", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-00968"}, {"db": "pmc", "key": "PMC3285582"}], "notes": [], "created": "2017-05-04T15:03:34.376Z", "modified": "2017-05-30T14:52:32.118Z"}, {"entity": "publication", "iuid": "cbb7722cd0744c16832bc2353473107e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbb7722cd0744c16832bc2353473107e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbb7722cd0744c16832bc2353473107e"}}, "title": "Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.", "authors": [{"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Oehlmann", "given": "Wulf", "initials": "W"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Braun", "given": "Yvonne", "initials": "Y"}, {"family": "Huck", "given": "Carmen", "initials": "C"}, {"family": "Maringer", "given": "Marko", "initials": "M"}, {"family": "Singh", "given": "Mahavir", "initials": "M"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}], "type": "journal article", "published": "2012-02-16", "journal": {"volume": "7", "issn": "1932-6203", "issue": "2", "pages": "e31133", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The diaminopimelic acid pathway of lysine biosynthesis has been suggested to provide attractive targets for the development of novel antibacterial drugs. Here we report the characterization of two enzymes from this pathway in the human pathogen Pseudomonas aeruginosa, utilizing structural biology, biochemistry and genetics. We show that tetrahydrodipicolinate N-succinyltransferase (DapD) from P. aeruginosa is specific for the L-stereoisomer of the amino substrate L-2-aminopimelate, and its D-enantiomer acts as a weak inhibitor. The crystal structures of this enzyme with L-2-aminopimelate and D-2-aminopimelate, respectively, reveal that both compounds bind at the same site of the enzyme. Comparison of the binding interactions of these ligands in the enzyme active site suggests misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition. P. aeruginosa mutants where the dapA gene had been deleted were viable and able to grow in a mouse lung infection model, suggesting that DapA is not an optimal target for drug development against this organism. Structure-based sequence alignments, based on the DapA crystal structure determined to 1.6 \u00c5 resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1\u0394dapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA activity.", "doi": "10.1371/journal.pone.0031133", "pmid": "22359568", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-20225"}, {"db": "pmc", "key": "PMC3281039"}, {"db": "PDB", "description": "Crystal structure of a putative 2,3,4,5-tetrahydropyridine-2-carboxylate n-succinyltransferase (cj1605c, dapd) from campylobacter jejuni at 1.90 A resolution", "key": "2RIJ"}, {"db": "PDB", "description": "Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Enterococcus faecalis V583", "key": "3CJ8"}, {"db": "PDB", "description": "Crystal structure of 2,3,4,5-Tetrahydropyridine-2-carboxylate N-Succinyltransferase from Brucella melitensis biovar abortus 2308", "key": "3EG4"}, {"db": "PDB", "description": "The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Yersinia pestis CO92", "key": "3GOS"}], "notes": [], "created": "2017-05-04T15:03:45.763Z", "modified": "2018-11-14T16:54:16.239Z"}, {"entity": "publication", "iuid": "d913f4e0a88f4baf8d66d6748998b637", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d913f4e0a88f4baf8d66d6748998b637.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d913f4e0a88f4baf8d66d6748998b637"}}, "title": "Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.", "authors": [{"family": "Demirkan", "given": "Ay\u015fe", "initials": "A"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Ugocsai", "given": "Peter", "initials": "P"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Liebisch", "given": "Gerhard", "initials": "G"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Kirichenko", "given": "Anatoly V", "initials": "AV"}, {"family": "Janssens", "given": "A Cecile J W", "initials": "AC"}, {"family": "Jansen", "given": "Ritsert C", "initials": "RC"}, {"family": "Gnewuch", "given": "Carsten", "initials": "C"}, {"family": "Domingues", "given": "Francisco S", "initials": "FS"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Jonasson", "given": "Inger", "initials": "I"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Zorkoltseva", "given": "Irina V", "initials": "IV"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Karssen", "given": "Lennart C", "initials": "LC"}, {"family": "Struchalin", "given": "Maksim", "initials": "M"}, {"family": "Floyd", "given": "James", "initials": "J"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Biloglav", "given": "Zrinka", "initials": "Z"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Pfeufer", "given": "Arne", "initials": "A"}, {"family": "Pichler", "given": "Irene", "initials": "I"}, {"family": "Campbell", "given": "Susan", "initials": "S"}, {"family": "Zaboli", "given": "Ghazal", "initials": "G"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Huffman", "given": "Jennifer", "initials": "J"}, {"family": "Hastie", "given": "Nicholas D", "initials": "ND"}, {"family": "Uitterlinden", "given": "Andre", "initials": "A"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Franklin", "given": "Christopher S", "initials": "CS"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "DIAGRAM Consortium", "given": null, "initials": null}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Preuss", "given": "Michael", "initials": "M"}, {"family": "CARDIoGRAM Consortium", "given": null, "initials": null}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "CHARGE Consortium", "given": null, "initials": null}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Axenovich", "given": "Tatiana", "initials": "T"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Schmitz", "given": "Gerd", "initials": "G"}, {"family": "EUROSPAN consortium", "given": null, "initials": null}], "type": "journal article", "published": "2012-02-16", "journal": {"volume": "8", "issn": "1553-7404", "issue": "2", "pages": "e1002490", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Phospho- and sphingolipids are crucial cellular and intracellular compounds. These lipids are required for active transport, a number of enzymatic processes, membrane formation, and cell signalling. Disruption of their metabolism leads to several diseases, with diverse neurological, psychiatric, and metabolic consequences. A large number of phospholipid and sphingolipid species can be detected and measured in human plasma. We conducted a meta-analysis of five European family-based genome-wide association studies (N\u200a=\u200a4034) on plasma levels of 24 sphingomyelins (SPM), 9 ceramides (CER), 57 phosphatidylcholines (PC), 20 lysophosphatidylcholines (LPC), 27 phosphatidylethanolamines (PE), and 16 PE-based plasmalogens (PLPE), as well as their proportions in each major class. This effort yielded 25 genome-wide significant loci for phospholipids (smallest P-value\u200a=\u200a9.88\u00d710(-204)) and 10 loci for sphingolipids (smallest P-value\u200a=\u200a3.10\u00d710(-57)). After a correction for multiple comparisons (P-value<2.2\u00d710(-9)), we observed four novel loci significantly associated with phospholipids (PAQR9, AGPAT1, PKD2L1, PDXDC1) and two with sphingolipids (PLD2 and APOE) explaining up to 3.1% of the variance. Further analysis of the top findings with respect to within class molar proportions uncovered three additional loci for phospholipids (PNLIPRP2, PCDH20, and ABDH3) suggesting their involvement in either fatty acid elongation/saturation processes or fatty acid specific turnover mechanisms. Among those, 14 loci (KCNH7, AGPAT1, PNLIPRP2, SYT9, FADS1-2-3, DLG2, APOA1, ELOVL2, CDK17, LIPC, PDXDC1, PLD2, LASS4, and APOE) mapped into the glycerophospholipid and 12 loci (ILKAP, ITGA9, AGPAT1, FADS1-2-3, APOA1, PCDH20, LIPC, PDXDC1, SGPP1, APOE, LASS4, and PLD2) to the sphingolipid pathways. In large meta-analyses, associations between FADS1-2-3 and carotid intima media thickness, AGPAT1 and type 2 diabetes, and APOA1 and coronary artery disease were observed. In conclusion, our study identified nine novel phospho- and sphingolipid loci, substantially increasing our knowledge of the genetic basis for these traits.", "doi": "10.1371/journal.pgen.1002490", "pmid": "22359512", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-11-01673"}, {"db": "pmc", "key": "PMC3280968"}], "notes": [], "created": "2017-05-04T15:02:15.360Z", "modified": "2020-01-21T13:56:05.564Z"}, {"entity": "publication", "iuid": "f1676e871bb6465a964c7904f8023a23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1676e871bb6465a964c7904f8023a23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1676e871bb6465a964c7904f8023a23"}}, "title": "Syntheses of pseudoceramines A-D and a new synthesis of spermatinamine, bromotyrosine natural products from marine sponges.", "authors": [{"family": "Hillgren", "given": "J Mikael", "initials": "JM"}, {"family": "Oberg", "given": "Christopher T", "initials": "CT"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2012-02-14", "journal": {"volume": "10", "issn": "1477-0539", "issue": "6", "pages": "1246-1254", "title": "Org. Biomol. Chem.", "issn-l": "1477-0520"}, "abstract": "Herein we report the total syntheses of pseudoceramine A-D (2-5) and spermatinamine (1) isolated from the marine sponge Pseudoceratina sp. Direct acyl substitution of \u03b1-hydroxyiminoesters with amine nucleophiles was developed as a key transformation. The synthetic compounds confirm the reported structures and importantly gives access to non-symmetrical spermine based natural products carrying two different bromotyrosine building blocks. Our new synthesis of spermatinamine is two steps shorter and more efficient than the previously reported sequence.", "doi": "10.1039/c1ob06722b", "pmid": "22179542", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:39.726Z", "modified": "2025-10-17T13:04:30.691Z"}, {"entity": "publication", "iuid": "94a5f4debb6349c8bc0051217bd7d8a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94a5f4debb6349c8bc0051217bd7d8a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94a5f4debb6349c8bc0051217bd7d8a8"}}, "title": "High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C.", "authors": [{"family": "Willander", "given": "Hanna", "initials": "H"}, {"family": "Askarieh", "given": "Glareh", "initials": "G"}, {"family": "Landreh", "given": "Michael", "initials": "M"}, {"family": "Westermark", "given": "Per", "initials": "P"}, {"family": "Nordling", "given": "Kerstin", "initials": "K"}, {"family": "Ker\u00e4nen", "given": "Henrik", "initials": "H"}, {"family": "Hermansson", "given": "Erik", "initials": "E"}, {"family": "Hamvas", "given": "Aaron", "initials": "A"}, {"family": "Nogee", "given": "Lawrence M", "initials": "LM"}, {"family": "Bergman", "given": "Tomas", "initials": "T"}, {"family": "Saenz", "given": "Alejandra", "initials": "A"}, {"family": "Casals", "given": "Cristina", "initials": "C"}, {"family": "\u00c5qvistg", "given": "Johan", "initials": "J"}, {"family": "J\u00f6rnvall", "given": "Hans", "initials": "H"}, {"family": "Berglund", "given": "Helena", "initials": "H"}, {"family": "Presto", "given": "Jenny", "initials": "J"}, {"family": "Knight", "given": "Stefan D", "initials": "SD"}, {"family": "Johansson", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2012-02-14", "journal": {"volume": "109", "issn": "1091-6490", "issue": "7", "pages": "2325-2329", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "BRICHOS domains are encoded in > 30 human genes, which are associated with cancer, neurodegeneration, and interstitial lung disease (ILD). The BRICHOS domain from lung surfactant protein C proprotein (proSP-C) is required for membrane insertion of SP-C and has anti-amyloid activity in vitro. Here, we report the 2.1 \u212b crystal structure of the human proSP-C BRICHOS domain, which, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry, reveals how BRICHOS domains may mediate chaperone activity. Observation of amyloid deposits composed of mature SP-C in lung tissue samples from ILD patients with mutations in the BRICHOS domain or in its peptide-binding linker region supports the in vivo relevance of the proposed mechanism. The results indicate that ILD mutations interfering with proSP-C BRICHOS activity cause amyloid disease secondary to intramolecular chaperone malfunction.", "doi": "10.1073/pnas.1114740109", "pmid": "22308375", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "1114740109"}, {"db": "pmc", "key": "PMC3289314"}, {"db": "PDB", "key": "2YAD"}], "notes": [], "created": "2017-05-04T15:03:45.459Z", "modified": "2017-09-06T11:42:09.198Z"}, {"entity": "publication", "iuid": "7175ee02a0724c8ebeeb6f7ba3ac27f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7175ee02a0724c8ebeeb6f7ba3ac27f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7175ee02a0724c8ebeeb6f7ba3ac27f0"}}, "title": "Age-related somatic structural changes in the nuclear genome of human blood cells.", "authors": [{"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "Rasi", "given": "Chiara", "initials": "C"}, {"family": "Razzaghian", "given": "Hamid R", "initials": "HR"}, {"family": "Pakalapati", "given": "Geeta", "initials": "G"}, {"family": "Waite", "given": "Lindsay", "initials": "L"}, {"family": "Thilbeault", "given": "Krista Stanton", "initials": "KS"}, {"family": "Ronowicz", "given": "Anna", "initials": "A"}, {"family": "Wineinger", "given": "Nathan E", "initials": "NE"}, {"family": "Tiwari", "given": "Hemant K", "initials": "HK"}, {"family": "Boomsma", "given": "Dorret", "initials": "D"}, {"family": "Westerman", "given": "Maxwell P", "initials": "MP"}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Lyle", "given": "Robert", "initials": "R"}, {"family": "Essand", "given": "Magnus", "initials": "M"}, {"family": "Eriksson", "given": "Fredrik", "initials": "F"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Iribarren", "given": "Carlos", "initials": "C"}, {"family": "Strachan", "given": "Eric", "initials": "E"}, {"family": "O'Hanlon", "given": "Terrance P", "initials": "TP"}, {"family": "Rider", "given": "Lisa G", "initials": "LG"}, {"family": "Miller", "given": "Frederick W", "initials": "FW"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}], "type": "journal article", "published": "2012-02-10", "journal": {"volume": "90", "issn": "1537-6605", "issue": "2", "pages": "217-228", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Structural variations are among the most frequent interindividual genetic differences in the human genome. The frequency and distribution of de novo somatic structural variants in normal cells is, however, poorly explored. Using age-stratified cohorts of 318 monozygotic (MZ) twins and 296 single-born subjects, we describe age-related accumulation of copy-number variation in the nuclear genomes in vivo and frequency changes for both megabase- and kilobase-range variants. Megabase-range aberrations were found in 3.4% (9 of 264) of subjects \u226560 years old; these subjects included 78 MZ twin pairs and 108 single-born individuals. No such findings were observed in 81 MZ pairs or 180 single-born subjects who were \u226455 years old. Recurrent region- and gene-specific mutations, mostly deletions, were observed. Longitudinal analyses of 43 subjects whose data were collected 7-19 years apart suggest considerable variation in the rate of accumulation of clones carrying structural changes. Furthermore, the longitudinal analysis of individuals with structural aberrations suggests that there is a natural self-removal of aberrant cell clones from peripheral blood. In three healthy subjects, we detected somatic aberrations characteristic of patients with myelodysplastic syndrome. The recurrent rearrangements uncovered here are candidates for common age-related defects in human blood cells. We anticipate that extension of these results will allow determination of the genetic age of different somatic-cell lineages and estimation of possible individual differences between genetic and chronological age. Our work might also help to explain the cause of an age-related reduction in the number of cell clones in the blood; such a reduction is one of the hallmarks of immunosenescence.", "doi": "10.1016/j.ajhg.2011.12.009", "pmid": "22305530", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(11)00544-1"}, {"db": "pmc", "key": "PMC3276669"}], "notes": [], "created": "2017-05-04T15:00:52.563Z", "modified": "2020-01-21T13:56:02.985Z"}, {"entity": "publication", "iuid": "3d819b5b85db45f89c7d9a7b3d3ce4f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d819b5b85db45f89c7d9a7b3d3ce4f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d819b5b85db45f89c7d9a7b3d3ce4f7"}}, "title": "Genetic and environmental contributions to weight, height, and BMI from birth to 19 years of age: an international study of over 12,000 twin pairs.", "authors": [{"family": "Dubois", "given": "Lise", "initials": "L"}, {"family": "Ohm Kyvik", "given": "Kirsten", "initials": "K"}, {"family": "Girard", "given": "Manon", "initials": "M"}, {"family": "Tatone-Tokuda", "given": "Fabiola", "initials": "F"}, {"family": "P\u00e9russe", "given": "Daniel", "initials": "D"}, {"family": "Hjelmborg", "given": "Jacob", "initials": "J"}, {"family": "Skytthe", "given": "Axel", "initials": "A"}, {"family": "Rasmussen", "given": "Finn", "initials": "F"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}], "type": "journal article", "published": "2012-02-08", "journal": {"volume": "7", "issn": "1932-6203", "issue": "2", "pages": "e30153", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "To examine the genetic and environmental influences on variances in weight, height, and BMI, from birth through 19 years of age, in boys and girls from three continents.\n\nCross-sectional twin study. Data obtained from a total of 23 twin birth-cohorts from four countries: Canada, Sweden, Denmark, and Australia. Participants were Monozygotic (MZ) and dizygotic (DZ) (same- and opposite-sex) twin pairs with data available for both height and weight at a given age, from birth through 19 years of age. Approximately 24,036 children were included in the analyses.\n\nHeritability for body weight, height, and BMI was low at birth (between 6.4 and 8.7% for boys, and between 4.8 and 7.9% for girls) but increased over time, accounting for close to half or more of the variance in body weight and BMI after 5 months of age in both sexes. Common environmental influences on all body measures were high at birth (between 74.1-85.9% in all measures for boys, and between 74.2 and 87.3% in all measures for girls) and markedly reduced over time. For body height, the effect of the common environment remained significant for a longer period during early childhood (up through 12 years of age). Sex-limitation of genetic and shared environmental effects was observed.\n\nGenetics appear to play an increasingly important role in explaining the variation in weight, height, and BMI from early childhood to late adolescence, particularly in boys. Common environmental factors exert their strongest and most independent influence specifically in pre-adolescent years and more significantly in girls. These findings emphasize the need to target family and social environmental interventions in early childhood years, especially for females. As gene-environment correlation and interaction is likely, it is also necessary to identify the genetic variants that may predispose individuals to obesity.", "doi": "10.1371/journal.pone.0030153", "pmid": "22347368", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-14346"}, {"db": "pmc", "key": "PMC3275599"}], "notes": [], "created": "2017-05-04T15:03:34.689Z", "modified": "2017-05-30T14:52:36.770Z"}, {"entity": "publication", "iuid": "0ccfaf0b5fba4e478a018931b547b6fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ccfaf0b5fba4e478a018931b547b6fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ccfaf0b5fba4e478a018931b547b6fb"}}, "title": "Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.", "authors": [{"family": "N\u00e4tt", "given": "Daniel", "initials": "D"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Belt\u00e9ky", "given": "Johan", "initials": "J"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Jensen", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2012-02-04", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "59", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Variations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, such as patterns of DNA methylation, are transferred across generations, and therefore it is uncertain what role epigenetic variation may play in adaptation.\n\nIn Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differed substantially from that of a domesticated egg laying breed. Expression as well as methylation differences were largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation. Some of the inherited methylation differences were tissue-specific, and the differential methylation at specific loci were little changed after eight generations of intercrossing between Red Junglefowl and domesticated laying hens. There was an over-representation of differentially expressed and methylated genes in selective sweep regions associated with chicken domestication.\n\nOur results show that epigenetic variation is inherited in chickens, and we suggest that selection of favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation states which are inherited independently of sequence differences, may have been an important aspect of chicken domestication.", "doi": "10.1186/1471-2164-13-59", "pmid": "22305654", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-59"}, {"db": "pmc", "key": "PMC3297523"}], "notes": [], "created": "2017-05-04T15:02:55.478Z", "modified": "2017-05-30T14:49:47.817Z"}, {"entity": "publication", "iuid": "d790487ea34c4b10bdd4b71b2e32c46f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d790487ea34c4b10bdd4b71b2e32c46f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d790487ea34c4b10bdd4b71b2e32c46f"}}, "title": "Characterization of the lipid droplet proteome of a clonal insulin-producing \u03b2-cell line (INS-1 832/13).", "authors": [{"family": "Larsson", "given": "Sara", "initials": "S"}, {"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Gomez", "given": "Maria F", "initials": "MF"}, {"family": "James", "given": "Peter", "initials": "P"}, {"family": "Holm", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2012-02-03", "journal": {"volume": "11", "issn": "1535-3907", "issue": "2", "pages": "1264-1273", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Lipids are known to play a crucial role both in the normal control of insulin release and in the deterioration of \u03b2-cell function, as observed in type 2 diabetes. Despite this established dual role of lipids, little is known about lipid storage and handling in \u03b2-cells. Here, we isolated lipid droplets from oleate-incubated INS-1 832/13 cells and characterized the lipid droplet proteome. In a total of four rounds of droplet isolation and proteomic analysis by HPLC-MS/MS, we identified 96 proteins that were specific to droplets. The proteins fall into six categories based on function or previously observed localization: metabolism, endoplasmic reticulum/ribosomes, mitochondria, vesicle formation and transport, signaling, and miscellaneous. The protein profile reinforces the emerging picture of the lipid droplet as an active and dynamic organelle involved in lipid homeostasis and intracellular trafficking. Proteins belonging to the category mitochondria were highly represented, suggesting that the \u03b2-cell mitochondria and lipid droplets form a metabolic unit of potential relevance for insulin secretion.", "doi": "10.1021/pr200957p", "pmid": "22268682", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:16.669Z", "modified": "2020-01-21T13:53:20.903Z"}, {"entity": "publication", "iuid": "008c29bc02ef4c5681e916c21de6b778", "links": {"self": {"href": "https://publications.scilifelab.se/publication/008c29bc02ef4c5681e916c21de6b778.json"}, "display": {"href": "https://publications.scilifelab.se/publication/008c29bc02ef4c5681e916c21de6b778"}}, "title": "Sequential closure of the cytoplasm and then the periplasm during cell division in Escherichia coli.", "authors": [{"family": "Skoog", "given": "Karl", "initials": "K"}, {"family": "S\u00f6derstr\u00f6m", "given": "Bill", "initials": "B"}, {"family": "Widengren", "given": "Jerker", "initials": "J"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Daley", "given": "Daniel O", "initials": "DO"}], "type": "journal article", "published": "2012-02-00", "journal": {"volume": "194", "issn": "1098-5530", "issue": "3", "pages": "584-586", "title": "J. Bacteriol.", "issn-l": "0021-9193"}, "abstract": "To visualize the latter stages of cell division in live Escherichia coli, we have carried out fluorescence recovery after photobleaching (FRAP) on 121 cells expressing cytoplasmic green fluorescent protein and periplasmic mCherry. Our data show conclusively that the cytoplasm is sealed prior to the periplasm during the division event.", "doi": "10.1128/JB.06091-11", "pmid": "22101847", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "JB.06091-11"}, {"db": "pmc", "key": "PMC3264074"}], "notes": [], "created": "2017-05-04T14:56:10.917Z", "modified": "2021-06-16T15:21:58.624Z"}, {"entity": "publication", "iuid": "fd27b826e237424b8522a24356fd977a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd27b826e237424b8522a24356fd977a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd27b826e237424b8522a24356fd977a"}}, "title": "Low diversity of the gut microbiota in infants with atopic eczema.", "authors": [{"family": "Abrahamsson", "given": "Thomas R", "initials": "TR"}, {"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bj\u00f6rkst\u00e9n", "given": "Bengt", "initials": "B"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC"}], "type": "controlled clinical trial", "published": "2012-02-00", "journal": {"volume": "129", "issn": "1097-6825", "issue": "2", "pages": "434-40, 440.e1-2", "title": "J. Allergy Clin. Immunol.", "issn-l": "0091-6749"}, "abstract": "It is debated whether a low total diversity of the gut microbiota in early childhood is more important than an altered prevalence of particular bacterial species for the increasing incidence of allergic disease. The advent of powerful, cultivation-free molecular methods makes it possible to characterize the total microbiome down to the genus level in large cohorts.\n\nWe sought to assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to atopic eczema development.\n\nMicrobial diversity and composition were analyzed with barcoded 16S rDNA 454-pyrosequencing in stool samples at 1 week, 1 month, and 12 months of age in 20 infants with IgE-associated eczema and 20 infants without any allergic manifestation until 2 years of age (ClinicalTrials.gov ID NCT01285830).\n\nInfants with IgE-associated eczema had a lower diversity of the total microbiota at 1 month (P\u00a0= .004) and a lower diversity of the bacterial phylum Bacteroidetes and the genus Bacteroides at 1 month (P\u00a0= .02 and P\u00a0= .01) and the phylum Proteobacteria at 12 months of age (P\u00a0= .02). The microbiota was less uniform at 1 month than at 12 months of age, with a high interindividual variability. At 12 months, when the microbiota had stabilized, Proteobacteria, comprising gram-negative organisms, were more abundant in infants without allergic manifestation (Empirical Analysis of Digital Gene Expression in R [edgeR] test: P\u00a0= .008, q\u00a0= 0.02).\n\nLow intestinal microbial diversity during the first month of life was associated with subsequent atopic eczema.", "doi": "10.1016/j.jaci.2011.10.025", "pmid": "22153774", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0091-6749(11)01657-5"}, {"db": "ClinicalTrials.gov", "key": "NCT01285830"}], "notes": [], "created": "2017-05-04T14:57:36.581Z", "modified": "2020-01-21T13:56:06.506Z"}, {"entity": "publication", "iuid": "0a5ff77ed5a64120a326dfff0f0282be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a5ff77ed5a64120a326dfff0f0282be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a5ff77ed5a64120a326dfff0f0282be"}}, "title": "In vitro and in silico strategies to identify OATP1B1 inhibitors and predict clinical drug-drug interactions.", "authors": [{"family": "Karlgren", "given": "Maria", "initials": "M"}, {"family": "Ahlin", "given": "Gustav", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Christel A S", "initials": "CA"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Palm", "given": "Johan", "initials": "J"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2012-02-00", "journal": {"volume": "29", "issn": "1573-904X", "issue": "2", "pages": "411-426", "title": "Pharm. Res.", "issn-l": "0724-8741"}, "abstract": "To establish in vitro and in silico models that predict clinical drug-drug interactions (DDIs) with the OATP1B1 (SLCO1B1) transporter.\n\nThe inhibitory effect of 146 drugs and drug-like compounds on OATP1B1-mediated transport was studied in HEK293 cells. A computational model was developed to predict OATP1B1 inhibition. Concentration-dependent effects were investigated for six compounds; clinical DDIs were predicted by calculating change in exposure (i.e. R-values) in eight different ways.\n\nSixty-five compounds were identified as OATP1B1 inhibitors at 20 \u03bcM. The computational model predicted the test set with 80% accuracy for inhibitors and 91% for non-inhibitors. In vitro-in vivo comparisons underscored the importance of using drugs with known clinical effects as references. Thus, reference drugs, cyclosporin A, gemfibrozil, and fenofibrate, provided an inhibition interval to which three antiviral drugs, atazanavir, lopinavir, and amprenavir, could be compared and their clinical DDIs with OATP1B1 classified.\n\nTwenty-two new OATP1B1 inhibitors were identified, a predictive OATP1B1 inhibition in silico model was developed, and successful predictions of clinical DDIs were obtained with OATP1B1.", "doi": "10.1007/s11095-011-0564-9", "pmid": "21861202", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC3264873"}], "notes": [], "created": "2017-10-31T11:58:50.878Z", "modified": "2025-10-17T13:04:30.716Z"}, {"entity": "publication", "iuid": "62ea024c7e40454e83d316fcf1300f49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62ea024c7e40454e83d316fcf1300f49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62ea024c7e40454e83d316fcf1300f49"}}, "title": "Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?", "authors": [{"family": "Strand", "given": "Tanja M", "initials": "TM"}, {"family": "Segelbacher", "given": "Gernot", "initials": "G"}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Xiao", "given": "Lingyun", "initials": "L"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2012-02-00", "journal": {"volume": "2", "issn": "2045-7758", "issue": "2", "pages": "341-353", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": "The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here, we use both neutral and major histocompatibility complex (MHC) markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled 11 different populations; five continuous, three isolated, and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs) which both were found to be neutral, and two functional MHC genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented.", "doi": "10.1002/ece3.86", "pmid": "22423328", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3298947"}], "notes": [], "created": "2017-05-04T15:00:57.850Z", "modified": "2020-01-21T13:56:02.670Z"}, {"entity": "publication", "iuid": "a9b4a8bb765945cb93d750e492d52952", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9b4a8bb765945cb93d750e492d52952.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9b4a8bb765945cb93d750e492d52952"}}, "title": "BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain.", "authors": [{"family": "Sillars-Hardebol", "given": "Anke H", "initials": "AH"}, {"family": "Carvalho", "given": "Beatriz", "initials": "B"}, {"family": "Beli\u00ebn", "given": "Jeroen Am", "initials": "JA"}, {"family": "de Wit", "given": "Meike", "initials": "M"}, {"family": "Delis-van Diemen", "given": "Pien M", "initials": "PM"}, {"family": "Tijssen", "given": "Marianne", "initials": "M"}, {"family": "van de Wiel", "given": "Mark A", "initials": "MA"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Fijneman", "given": "Remond Ja", "initials": "RJ"}, {"family": "Meijer", "given": "Gerrit A", "initials": "GA"}], "type": "journal article", "published": "2012-02-00", "journal": {"volume": "226", "issn": "1096-9896", "issue": "3", "pages": "442-450", "title": "J. Pathol.", "issn-l": "0022-3417"}, "abstract": "Colorectal cancer (CRC) is the second leading cause of cancer death in the western world. The majority of CRCs, which develop from adenoma precursor lesions, show gain of chromosome arm 20q, where BCL2L1 is located. BCL2L1 is an important apoptosis regulating gene that codes for both an anti-apoptotic (Bcl-x(L)) and a pro-apoptotic (Bcl-x(S)) splice variant. The aim of the present study was to investigate whether BCL2L1 contributes to 20q gain-driven colorectal adenoma-to-carcinoma progression. To this end, the functional role of BCL2L1 in cancer-related processes was investigated, and differences in BCL2L1 DNA, mRNA, and protein levels were compared between colorectal adenomas and CRCs, as well as between tumours with and without 20q gain. Down-modulation of BCL2L1 inhibited cell viability and anchorage-independent growth of CRC cells, while invasion was not affected. BCL2L1 DNA copy number and protein expression were increased in CRCs compared to adenomas (p = 0.00005 and p = 0.03, respectively), while mRNA expression was not. Differences in BCL2L1 protein expression were even more pronounced between tumours with and without 20q gain (p = 0.0001). In conclusion, BCL2L1 is functionally involved in several cancer-related processes and its protein expression is associated with 20q gain. This supports a role for 20q gain-dependent expression of BCL2L1 in colorectal adenoma-to-carcinoma progression. However, the absence of a direct correlation between BCL2L1 mRNA and protein expression implies that BCL2L1 protein expression is regulated at the post-transcriptional level by a distinct factor on the 20q amplicon (eg ZNF217, AURKA or miRNAs). Therefore, even though BCL2L1 affects CRC biology in a 20q gain-dependent manner, it is not likely to be a driver of chromosome 20q gain associated adenoma-to-carcinoma progression.", "doi": "10.1002/path.2983", "pmid": "22009326", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:51.785Z", "modified": "2017-05-30T12:56:07.201Z"}, {"entity": "publication", "iuid": "0ccfa327678647ed926ff8312b803d72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ccfa327678647ed926ff8312b803d72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ccfa327678647ed926ff8312b803d72"}}, "title": "Association of TMEM18 variants with BMI and waist circumference in children and correlation of mRNA expression in the PFC with body weight in rats.", "authors": [{"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Jacobsson", "given": "Josefin A", "initials": "JA"}, {"family": "Moschonis", "given": "George", "initials": "G"}, {"family": "Chavan", "given": "Rohit A", "initials": "RA"}, {"family": "Sikder", "given": "Md Abu Noman", "initials": "MA"}, {"family": "Allz\u00e9n", "given": "Elin", "initials": "E"}, {"family": "Alsi\u00f6", "given": "Johan", "initials": "J"}, {"family": "Chrousos", "given": "George P", "initials": "GP"}, {"family": "Manios", "given": "Yannis", "initials": "Y"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2012-02-00", "journal": {"volume": "20", "issn": "1476-5438", "issue": "2", "pages": "192-197", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Genome-wide association studies have shown a strong association of single-nucleotide polymorphisms (SNPs) in the near vicinity of the TMEM18 gene. The effects of the TMEM18-associated variants are more readily observed in children. TMEM18 encodes a 3TM protein, which locates to the nuclear membrane. The functional context of TMEM18 and the effects of its associated variants are as of yet undetermined. To further explore the effects of near-TMEM18 variants, we have genotyped two TMEM18-associated SNPs, rs6548238 and rs4854344, in a cohort of 2352 Greek children (Healthy Growth Study). Included in this study are data on anthropomorphic traits body weight, BMI z-score and waist circumference. Also included are dietary energy and macronutrient intake as measured via 24-h recall interviews. Major alleles of rs6548238 and rs4854344 were significantly associated with an increased risk of obesity (odds ratio = 1.489 (1.161-1.910) and 1.494 (1.165-1.917), respectively), and positively correlated to body weight (P = 0.017, P = 0.010) and waist circumference (P = 0.003, P = 0.003). An association to energy and macronutrient intake was not observed in this cohort. We also correlated food intake and body weight in a food choice model in rats to Tmem18 expression in central regions involved in feeding behavior. We observed a strong positive correlation between TMEM18 expression and body weight in the prefrontal cortex (PFC) (r = 0.5694, P = 0.0003) indicating a potential role for TMEM18 in higher functions related to feeding involving the PFC.", "doi": "10.1038/ejhg.2011.176", "pmid": "21952719", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ejhg2011176"}, {"db": "pmc", "key": "PMC3262189"}], "notes": [], "created": "2017-05-04T15:01:56.958Z", "modified": "2020-01-21T13:56:00.670Z"}, {"entity": "publication", "iuid": "5b0676260c644fe786a633d08cdc3fc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b0676260c644fe786a633d08cdc3fc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b0676260c644fe786a633d08cdc3fc4"}}, "title": "Mutations in CTC1, encoding conserved telomere maintenance component 1, cause Coats plus.", "authors": [{"family": "Anderson", "given": "Beverley H", "initials": "BH"}, {"family": "Kasher", "given": "Paul R", "initials": "PR"}, {"family": "Mayer", "given": "Josephine", "initials": "J"}, {"family": "Szynkiewicz", "given": "Marcin", "initials": "M"}, {"family": "Jenkinson", "given": "Emma M", "initials": "EM"}, {"family": "Bhaskar", "given": "Sanjeev S", "initials": "SS"}, {"family": "Urquhart", "given": "Jill E", "initials": "JE"}, {"family": "Daly", "given": "Sarah B", "initials": "SB"}, {"family": "Dickerson", "given": "Jonathan E", "initials": "JE"}, {"family": "O'Sullivan", "given": "James", "initials": "J"}, {"family": "Leibundgut", "given": "Elisabeth Oppliger", "initials": "EO"}, {"family": "Muter", "given": "Joanne", "initials": "J"}, {"family": "Abdel-Salem", "given": "Ghada M H", "initials": "GM"}, {"family": "Babul-Hirji", "given": "Riyana", "initials": "R"}, {"family": "Baxter", "given": "Peter", "initials": "P"}, {"family": "Berger", "given": "Andrea", "initials": "A"}, {"family": "Bonaf\u00e9", "given": "Luisa", "initials": "L"}, {"family": "Brunstom-Hernandez", "given": "Janice E", "initials": "JE"}, {"family": "Buckard", "given": "Johannes A", "initials": "JA"}, {"family": "Chitayat", "given": "David", "initials": "D"}, {"family": "Chong", "given": "Wui K", "initials": "WK"}, {"family": "Cordelli", "given": "Duccio M", "initials": "DM"}, {"family": "Ferreira", "given": "Patrick", "initials": "P"}, {"family": "Fluss", "given": "Joel", "initials": "J"}, {"family": "Forrest", "given": "Ewan H", "initials": "EH"}, {"family": "Franzoni", "given": "Emilio", "initials": "E"}, {"family": "Garone", "given": "Caterina", "initials": "C"}, {"family": "Hammans", "given": "Simon R", "initials": "SR"}, {"family": "Houge", "given": "Gunnar", "initials": "G"}, {"family": "Hughes", "given": "Imelda", "initials": "I"}, {"family": "Jacquemont", "given": "Sebastien", "initials": "S"}, {"family": "Jeannet", "given": "Pierre-Yves", "initials": "PY"}, {"family": "Jefferson", "given": "Rosalind J", "initials": "RJ"}, {"family": "Kumar", "given": "Ram", "initials": "R"}, {"family": "Kutschke", "given": "Georg", "initials": "G"}, {"family": "Lundberg", "given": "Staffan", "initials": "S"}, {"family": "Louren\u00e7o", "given": "Charles M", "initials": "CM"}, {"family": "Mehta", "given": "Ramesh", "initials": "R"}, {"family": "Naidu", "given": "Sakkubai", "initials": "S"}, {"family": "Nischal", "given": "Ken K", "initials": "KK"}, {"family": "Nunes", "given": "Lu\u00eds", "initials": "L"}, {"family": "Ounap", "given": "Katrin", "initials": "K"}, {"family": "Philippart", "given": "Michel", "initials": "M"}, {"family": "Prabhakar", "given": "Prab", "initials": "P"}, {"family": "Risen", "given": "Sarah R", "initials": "SR"}, {"family": "Schiffmann", "given": "Raphael", "initials": "R"}, {"family": "Soh", "given": "Calvin", "initials": "C"}, {"family": "Stephenson", "given": "John B P", "initials": "JB"}, {"family": "Stewart", "given": "Helen", "initials": "H"}, {"family": "Stone", "given": "Jon", "initials": "J"}, {"family": "Tolmie", "given": "John L", "initials": "JL"}, {"family": "van der Knaap", "given": "Marjo S", "initials": "MS"}, {"family": "Vieira", "given": "Jose P", "initials": "JP"}, {"family": "Vilain", "given": "Catheline N", "initials": "CN"}, {"family": "Wakeling", "given": "Emma L", "initials": "EL"}, {"family": "Wermenbol", "given": "Vanessa", "initials": "V"}, {"family": "Whitney", "given": "Andrea", "initials": "A"}, {"family": "Lovell", "given": "Simon C", "initials": "SC"}, {"family": "Meyer", "given": "Stefan", "initials": "S"}, {"family": "Livingston", "given": "John H", "initials": "JH"}, {"family": "Baerlocher", "given": "Gabriela M", "initials": "GM"}, {"family": "Black", "given": "Graeme C M", "initials": "GC"}, {"family": "Rice", "given": "Gillian I", "initials": "GI"}, {"family": "Crow", "given": "Yanick J", "initials": "YJ"}], "type": "journal article", "published": "2012-01-22", "journal": {"volume": "44", "issn": "1546-1718", "issue": "3", "pages": "338-342", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Coats plus is a highly pleiotropic disorder particularly affecting the eye, brain, bone and gastrointestinal tract. Here, we show that Coats plus results from mutations in CTC1, encoding conserved telomere maintenance component 1, a member of the mammalian homolog of the yeast heterotrimeric CST telomeric capping complex. Consistent with the observation of shortened telomeres in an Arabidopsis CTC1 mutant and the phenotypic overlap of Coats plus with the telomeric maintenance disorders comprising dyskeratosis congenita, we observed shortened telomeres in three individuals with Coats plus and an increase in spontaneous \u03b3H2AX-positive cells in cell lines derived from two affected individuals. CTC1 is also a subunit of the \u03b1-accessory factor (AAF) complex, stimulating the activity of DNA polymerase-\u03b1 primase, the only enzyme known to initiate DNA replication in eukaryotic cells. Thus, CTC1 may have a function in DNA metabolism that is necessary for but not specific to telomeric integrity.", "doi": "10.1038/ng.1084", "pmid": "22267198", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ng.1084"}], "notes": [], "created": "2017-05-04T15:02:11.241Z", "modified": "2020-01-21T13:56:02.498Z"}, {"entity": "publication", "iuid": "3580eee5e5764b258963f38120f577a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3580eee5e5764b258963f38120f577a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3580eee5e5764b258963f38120f577a3"}}, "title": "Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.", "authors": [{"family": "Stolk", "given": "Lisette", "initials": "L"}, {"family": "Perry", "given": "John R B", "initials": "JR"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "He", "given": "Chunyan", "initials": "C"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Sulem", "given": "Patrick", "initials": "P"}, {"family": "Barbalic", "given": "Maja", "initials": "M"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Ernst", "given": "Florian", "initials": "F"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "McArdle", "given": "Patrick F", "initials": "PF"}, {"family": "Porcu", "given": "Eleonora", "initials": "E"}, {"family": "Shin", "given": "So-Youn", "initials": "SY"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "van Wingerden", "given": "Sophie", "initials": "S"}, {"family": "Zhai", "given": "Guangju", "initials": "G"}, {"family": "Zhuang", "given": "Wei V", "initials": "WV"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Lauc", "given": "Lovorka Barac", "initials": "LB"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Boban", "given": "Mladen", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Broekmans", "given": "Frank J", "initials": "FJ"}, {"family": "Burri", "given": "Andrea", "initials": "A"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Chen", "given": "Constance", "initials": "C"}, {"family": "Cornelis", "given": "Marilyn C", "initials": "MC"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Coviello", "given": "Andrea D", "initials": "AD"}, {"family": "d'Adamo", "given": "Pio", "initials": "P"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Dedoussis", "given": "George V Z", "initials": "GV"}, {"family": "Deloukas", "given": "Panagiotis", "initials": "P"}, {"family": "Ebrahim", "given": "Shah", "initials": "S"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Emilsson", "given": "Valur", "initials": "V"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Fauser", "given": "Bart C J M", "initials": "BC"}, {"family": "Ferreli", "given": "Liana", "initials": "L"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Folsom", "given": "Aaron R", "initials": "AR"}, {"family": "Garcia", "given": "Melissa E", "initials": "ME"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Glazer", "given": "Nicole", "initials": "N"}, {"family": "Grobbee", "given": "Diederick E", "initials": "DE"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Haller", "given": "Toomas", "initials": "T"}, {"family": "Hankinson", "given": "Susan E", "initials": "SE"}, {"family": "Hass", "given": "Merli", "initials": "M"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Janssens", "given": "A Cecile J W", "initials": "AC"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SL"}, {"family": "Keyzer", "given": "Jules", "initials": "J"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Lai", "given": "Sandra", "initials": "S"}, {"family": "Laisk", "given": "Triin", "initials": "T"}, {"family": "Laven", "given": "Joop S E", "initials": "JS"}, {"family": "Lawlor", "given": "Debbie A", "initials": "DA"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "Louwers", "given": "Yvonne V", "initials": "YV"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Marongiu", "given": "Mara", "initials": "M"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Klaric", "given": "Irena Martinovic", "initials": "IM"}, {"family": "Masciullo", "given": "Corrado", "initials": "C"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Melzer", "given": "David", "initials": "D"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Newman", "given": "Anne B", "initials": "AB"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Onland-Moret", "given": "N Charlotte", "initials": "NC"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Parker", "given": "Alex N", "initials": "AN"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Peeters", "given": "Petra H M", "initials": "PH"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Plump", "given": "Andrew S", "initials": "AS"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Pop", "given": "Victor J M", "initials": "VJ"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Rehnberg", "given": "Emil", "initials": "E"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Sala", "given": "Cinzia", "initials": "C"}, {"family": "Salumets", "given": "Andres", "initials": "A"}, {"family": "Scuteri", "given": "Angelo", "initials": "A"}, {"family": "Singleton", "given": "Andrew", "initials": "A"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Stacey", "given": "Simon N", "initials": "SN"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Stathopoulou", "given": "Maria G", "initials": "MG"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "Stolk", "given": "Ronald P", "initials": "RP"}, {"family": "Styrkarsdottir", "given": "Unnur", "initials": "U"}, {"family": "Sun", "given": "Yan V", "initials": "YV"}, {"family": "Tenesa", "given": "Albert", "initials": "A"}, {"family": "Thorand", "given": "Barbara", "initials": "B"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Tryggvadottir", "given": "Laufey", "initials": "L"}, {"family": "Tsui", "given": "Kim", "initials": "K"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "van Gils", "given": "Carla H", "initials": "CH"}, {"family": "van Nierop", "given": "Peter", "initials": "P"}, {"family": "Vink", "given": "Jacqueline M", "initials": "JM"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Voorhuis", "given": "Marlies", "initials": "M"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "Wichmann", "given": "H Erich", "initials": "HE"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Wijnands-van Gent", "given": "Colette J M", "initials": "CJ"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BH"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Zygmunt", "given": "Marek", "initials": "M"}, {"family": "LifeLines Cohort Study", "given": null, "initials": null}, {"family": "Arnold", "given": "Alice M", "initials": "AM"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Buring", "given": "Julie E", "initials": "JE"}, {"family": "Crisponi", "given": "Laura", "initials": "L"}, {"family": "Demerath", "given": "Ellen W", "initials": "EW"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Hunter", "given": "David J", "initials": "DJ"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Streeten", "given": "Elizabeth A", "initials": "EA"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Murray", "given": "Anna", "initials": "A"}, {"family": "Murabito", "given": "Joanne M", "initials": "JM"}, {"family": "Visser", "given": "Jenny A", "initials": "JA"}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}], "type": "journal article", "published": "2012-01-22", "journal": {"volume": "44", "issn": "1546-1718", "issue": "3", "pages": "260-268", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P < 5 \u00d7 10(-8)). Candidate genes located at these newly associated loci include genes implicated in DNA repair (EXO1, HELQ, UIMC1, FAM175A, FANCI, TLK1, POLG and PRIM1) and immune function (IL11, NLRP11 and PRRC2A (also known as BAT2)). Gene-set enrichment pathway analyses using the full GWAS data set identified exoDNase, NF-\u03baB signaling and mitochondrial dysfunction as biological processes related to timing of menopause.", "doi": "10.1038/ng.1051", "pmid": "22267201", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.1051"}, {"db": "pmc", "key": "PMC3288642"}, {"db": "mid", "key": "NIHMS342040"}], "notes": [], "created": "2017-05-04T15:01:05.893Z", "modified": "2020-01-21T13:56:01.543Z"}, {"entity": "publication", "iuid": "9bba61f40cc44974ac4937eabecd119b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bba61f40cc44974ac4937eabecd119b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bba61f40cc44974ac4937eabecd119b"}}, "title": "Non-bullous congentital ichthyosiform erythroderma associated with homozygosity for a novel missense mutation in an ATP binding domain of ABCA12.", "authors": [{"family": "Nawaz", "given": "Sadia", "initials": "S"}, {"family": "Tariq", "given": "Muhammad", "initials": "M"}, {"family": "Ahmad", "given": "Ilyas", "initials": "I"}, {"family": "Malik", "given": "Naveed Altaf", "initials": "NA"}, {"family": "Baig", "given": "Shahid Mahmood", "initials": "SM"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Klar", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2012-01-20", "journal": {"volume": "22", "issn": "1952-4013", "issue": "2", "pages": "178-181", "title": "Eur J Dermatol", "issn-l": "1167-1122"}, "abstract": "A Mutations in the gene encoding the ABCA12 protein are associated with different subtypes of autosomal recessive congenital ichthyosis (ARCI), including Harlequin ichthyosis (HI), lamellar ichthyosis (LI) and non-bullous congenital ichthyosiform erythroderma (NCIE). Disruption of ABCA12 lead to perturbed lipid transport in lamellar granules and a defective intercellular lipid layer of the stratum corneum. We have identified a large consanguineous Pakistani family affected by NCIE. Autozygosity mapping showed that affected individuals are homozygous for the ABCA12 gene region. Subsequent mutation screening revealed a homozygous c.4676G>T transition in all five affected family members. The mutation results in a novel p.G1559V substitution within the first nucleotide binding domain of ABCA12. The combined results support that an ABCA12 missense mutation, despite its location in a functional domain, may be associated with a mild ichthyosis phenotype. Furthermore, our findings increase the mutational spectrum in ABCA12 associated with ARCI of diagnostic and prognostic importance.", "doi": "10.1684/ejd.2011.1638", "pmid": "22257947", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ejd.2011.1638"}], "notes": [], "created": "2017-05-04T14:57:33.661Z", "modified": "2020-01-21T13:56:04.044Z"}, {"entity": "publication", "iuid": "058c0df5115246479cdb4f237646a8f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/058c0df5115246479cdb4f237646a8f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/058c0df5115246479cdb4f237646a8f1"}}, "title": "A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.", "authors": [{"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Andersson", "given": "Claes R", "initials": "CR"}, {"family": "Andersson", "given": "Robin", "initials": "R"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2012-01-16", "journal": {"volume": "7", "issn": "1748-7188", "issue": "1", "pages": "2", "title": "Algorithms Mol Biol", "issn-l": "1748-7188"}, "abstract": "High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e.g. repetitive regions or non-specific antibody interactions. The noise will appear in the form of a background distribution of reads that must be taken into account in the downstream analysis, for example when detecting enriched regions (peak-calling). Several reported peak-callers can take experimental measurements of background tag distribution into account when analysing a data set. Unfortunately, the background is only used to adjust peak calling and not as a pre-processing step that aims at discerning the signal from the background noise. A normalization procedure that extracts the signal of interest would be of universal use when investigating genomic patterns.\r\n\r\nWe formulated such a normalization method based on linear regression and made a proof-of-concept implementation in R and C++. It was tested on simulated as well as on publicly available ChIP-seq data on binding sites for two transcription factors, MAX and FOXA1 and two control samples, Input and IgG. We applied three different peak-callers to (i) raw (un-normalized) data using statistical background models and (ii) raw data with control samples as background and (iii) normalized data without additional control samples as background. The fraction of called regions containing the expected transcription factor binding motif was largest for the normalized data and evaluation with qPCR data for FOXA1 suggested higher sensitivity and specificity using normalized data over raw data with experimental background.\r\n\r\nThe proposed method can handle several control samples allowing for correction of multiple sources of bias simultaneously. Our evaluation on both synthetic and experimental data suggests that the method is successful in removing background noise.", "doi": "10.1186/1748-7188-7-2", "pmid": "22248020", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1748-7188-7-2"}, {"db": "pmc", "key": "PMC3371767"}], "notes": [], "created": "2017-05-04T14:57:27.693Z", "modified": "2020-01-21T13:56:10.271Z"}, {"entity": "publication", "iuid": "a424339a9d0e407da321b590561dbb24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a424339a9d0e407da321b590561dbb24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a424339a9d0e407da321b590561dbb24"}}, "title": "Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene.", "authors": [{"family": "Davison", "given": "Lucy J", "initials": "LJ"}, {"family": "Wallace", "given": "Chris", "initials": "C"}, {"family": "Cooper", "given": "Jason D", "initials": "JD"}, {"family": "Cope", "given": "Nathan F", "initials": "NF"}, {"family": "Wilson", "given": "Nicola K", "initials": "NK"}, {"family": "Smyth", "given": "Deborah J", "initials": "DJ"}, {"family": "Howson", "given": "Joanna M M", "initials": "JM"}, {"family": "Saleh", "given": "Nada", "initials": "N"}, {"family": "Al-Jeffery", "given": "Abdullah", "initials": "A"}, {"family": "Angus", "given": "Karen L", "initials": "KL"}, {"family": "Stevens", "given": "Helen E", "initials": "HE"}, {"family": "Nutland", "given": "Sarah", "initials": "S"}, {"family": "Duley", "given": "Simon", "initials": "S"}, {"family": "Coulson", "given": "Richard M R", "initials": "RM"}, {"family": "Walker", "given": "Neil M", "initials": "NM"}, {"family": "Burren", "given": "Oliver S", "initials": "OS"}, {"family": "Rice", "given": "Catherine M", "initials": "CM"}, {"family": "Cambien", "given": "Francois", "initials": "F"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Munzel", "given": "Thomas", "initials": "T"}, {"family": "Lackner", "given": "Karl", "initials": "K"}, {"family": "Blakenberg", "given": "Stefan", "initials": "S"}, {"family": "Cardiogenics Consortium", "given": null, "initials": null}, {"family": "Fraser", "given": "Peter", "initials": "P"}, {"family": "Gottgens", "given": "Berthold", "initials": "B"}, {"family": "Todd", "given": "John A", "initials": "JA"}, {"family": "Attwood", "given": "Tony", "initials": "T"}, {"family": "Belz", "given": "Stephanie", "initials": "S"}, {"family": "Braund", "given": "Peter", "initials": "P"}, {"family": "Cambien", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Cooper", "given": "Jason", "initials": "J"}, {"family": "Crisp-Hihn", "given": "Abi", "initials": "A"}, {"family": "Diemert", "given": "Patrick", "initials": "P"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Foad", "given": "Nicola", "initials": "N"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Gracey", "given": "Jay", "initials": "J"}, {"family": "Gray", "given": "Emma", "initials": "E"}, {"family": "Williams", "given": "Rhian G", "initials": "RG"}, {"family": "Heimerl", "given": "Susanne", "initials": "S"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Jolley", "given": "Jennifer", "initials": "J"}, {"family": "Krishnan", "given": "Unni", "initials": "U"}, {"family": "Lloyd-Jones", "given": "Heather", "initials": "H"}, {"family": "Lugauer", "given": "Ingrid", "initials": "I"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Maouche", "given": "Seraya", "initials": "S"}, {"family": "Moore", "given": "Jasbir S", "initials": "JS"}, {"family": "Muir", "given": "David", "initials": "D"}, {"family": "Murray", "given": "Elizabeth", "initials": "E"}, {"family": "Nelson", "given": "Chris P", "initials": "CP"}, {"family": "Neudert", "given": "Jessica", "initials": "J"}, {"family": "Niblett", "given": "David", "initials": "D"}, {"family": "O'Leary", "given": "Karen", "initials": "K"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Pollard", "given": "Helen", "initials": "H"}, {"family": "Rankin", "given": "Angela", "initials": "A"}, {"family": "Sager", "given": "Hendrik", "initials": "H"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Sambrook", "given": "Jennifer", "initials": "J"}, {"family": "Schmitz", "given": "Gerd", "initials": "G"}, {"family": "Scholz", "given": "Michael", "initials": "M"}, {"family": "Schroeder", "given": "Laura", "initials": "L"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Syvannen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Tennstedt", "given": "Stefanie", "initials": "S"}], "type": "journal article", "published": "2012-01-15", "journal": {"volume": "21", "issn": "1460-2083", "issue": "2", "pages": "322-333", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes.", "doi": "10.1093/hmg/ddr468", "pmid": "21989056", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ddr468"}, {"db": "pmc", "key": "PMC3276289"}], "notes": [], "created": "2017-05-04T15:00:59.375Z", "modified": "2020-01-21T13:56:04.228Z"}, {"entity": "publication", "iuid": "4e29f3d9ea9a44c1bc81f0adee660b0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e29f3d9ea9a44c1bc81f0adee660b0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e29f3d9ea9a44c1bc81f0adee660b0b"}}, "title": "Deregulation of the A-to-I RNA editing mechanism in psychiatric disorders.", "authors": [{"family": "Silberberg", "given": "Gilad", "initials": "G"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Navon", "given": "Ruth", "initials": "R"}, {"family": "\u00d6hman", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2012-01-15", "journal": {"volume": "21", "issn": "1460-2083", "issue": "2", "pages": "311-321", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Schizophrenia and bipolar disorder (BPD) are common neurodevelopmental disorders, characterized by various life-crippling symptoms and high suicide rates. Multiple studies support a strong genetic involvement in the etiology of these disorders, although patterns of inheritance are variable and complex. Adenosine-to-inosine RNA editing is a cellular mechanism, which has been implicated in mental disorders and suicide. To examine the involvement of altered RNA editing in these disorders, we: (i) quantified the mRNA levels of the adenosine deaminase acting on RNA (ADAR) editing enzymes by real-time quantitative polymerase chain reaction, and (ii) measured the editing levels in transcripts of several neuroreceptors using 454 high-throughput sequencing, in dorsolateral-prefrontal cortices of schizophrenics, BPD patients and controls. Increased expression of specific ADAR2 variants with diminished catalytic activity was observed in schizophrenia. Our results also indicate that the I/V editing site in the glutamate receptor, ionotropic kainate 2 (GRIK2) transcript is under-edited in BPD (type I) patients (45.8 versus 53.9%, P= 0.023). GRIK2 has been implicated in mood disorders, and editing of its I/V site can modulate Ca(+2) permeability of the channel, consistent with numerous observations of elevated intracellular Ca(+2) levels in BPD patients. Our findings may therefore, at least partly, explain a molecular mechanism underlying the disorder. In addition, an intriguing correlation was found between editing events on separate exons of GRIK2. Finally, multiple novel editing sites were detected near previously known sites, albeit most with very low editing rates. This supports the hypothesis raised previously regarding the existence of wide-spread low-level 'background' editing as a mechanism that enhances adaptation and evolvability.", "doi": "10.1093/hmg/ddr461", "pmid": "21984433", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ddr461"}], "notes": [], "created": "2017-05-04T14:57:35.380Z", "modified": "2020-01-21T13:56:02.229Z"}, {"entity": "publication", "iuid": "167e14d4c9514936905ce24bf6eb8776", "links": {"self": {"href": "https://publications.scilifelab.se/publication/167e14d4c9514936905ce24bf6eb8776.json"}, "display": {"href": "https://publications.scilifelab.se/publication/167e14d4c9514936905ce24bf6eb8776"}}, "title": "Contribution of TMC6 and TMC8 (EVER1 and EVER2) variants to cervical cancer susceptibility.", "authors": [{"family": "Castro", "given": "Felipe A", "initials": "FA"}, {"family": "Ivansson", "given": "Emma L", "initials": "EL"}, {"family": "Schmitt", "given": "Markus", "initials": "M"}, {"family": "Juko-Pecirep", "given": "Ivana", "initials": "I"}, {"family": "Kjellberg", "given": "Lennart", "initials": "L"}, {"family": "Hildesheim", "given": "Allan", "initials": "A"}, {"family": "Gyllensten", "given": "Ulf B", "initials": "UB"}, {"family": "Pawlita", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2012-01-15", "journal": {"volume": "130", "issn": "1097-0215", "issue": "2", "pages": "349-355", "title": "Int. J. Cancer", "issn-l": "0020-7136"}, "abstract": "Cervical cancer (CxCa) is caused by persistent human papillomavirus (HPV) infection; genetic predisposition is also suspected to play a role. Our study is a targeted candidate gene follow-up based on: (i) strong clinical evidence demonstrating that mutations in the TMC6 and TMC8 (EVER1 and EVER2) genes associate with the HPV-associated disease epidermodysplasia verruciformis (EV) and (ii) recent epidemiological data suggesting a genetic susceptibility conferred by polymorphisms in such genes for skin and CxCa. Clarifying the association of the TMC6/8 genes with risk of CxCa will help in understanding why some HPV-infected women develop persistent infection, cervical lesions and eventually cancer while others do not. Twenty-two single nucleotide polymorphisms (SNPs) harboring the TMC6/8 genes were genotyped in 2,989 cases with cervical intraepithelial neoplasia grade III or invasive CxCa and 2,281 controls from the Swedish population. Association was evaluated in logistic regression models. Two SNPs displayed association with cervical disease: rs2290907 [odds ratio (OR)(GGvsAA) = 0.6, 95% confidence interval (95% CI): 0.3-0.9, p = 0.02)] and rs16970849 (OR(AGvsGG) = 0.8, 95% CI: 0.66-0.98, p = 0.03). The present data support the involvement of the TMC6/8 region in CxCa susceptibility but further analyses are needed to replicate our findings, fully characterize the region and understand the function of the genetic variants involved.", "doi": "10.1002/ijc.26016", "pmid": "21387292", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC3530613"}, {"db": "mid", "key": "NIHMS428292"}], "notes": [], "created": "2017-05-04T15:02:07.986Z", "modified": "2020-01-21T13:56:00.878Z"}, {"entity": "publication", "iuid": "758b525b3955477e8f58d7cc2c603d38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/758b525b3955477e8f58d7cc2c603d38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/758b525b3955477e8f58d7cc2c603d38"}}, "title": "Structural genetic variation in the context of somatic mosaicism.", "authors": [{"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A"}], "type": "journal article", "published": "2012-01-10", "journal": {"volume": "838", "issn": "1940-6029", "issue": null, "pages": "249-272", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Somatic mosaicism is the result of postzygotic de novo mutation occurring in a portion of the cells making up an organism. Structural genetic variation is a very heterogeneous group of changes, in terms of numerous types of aberrations that are included in this category, involvement of many mechanisms behind the generation of structural variants, and because structural variation can encompass genomic regions highly variable in size. Structural variation rapidly evolved as the dominating type of changes behind human genetic diversity, and the importance of this variation in biology and medicine is continuously increasing. In this review, we combine the evidence of structural variation in the context of somatic cells. We discuss the normal and disease-related somatic structural variation. We review the recent advances in the field of monozygotic twins and other models that have been studied for somatic mutations, including other vertebrates. We also discuss chromosomal mosaicism in a few prime examples of disease genes that contributed to understanding of the importance of somatic heterogeneity. We further highlight challenges and opportunities related to this field, including methodological and practical aspects of detection of somatic mosaicism. The literature devoted to interindividual variation versus papers reporting on somatic variation suggests that the latter is understudied and underestimated. It is important to increase our awareness about somatic mosaicism, in particular, related to structural variation. We believe that further research of somatic mosaicism will prove beneficial for better understanding of common sporadic disorders.", "doi": "10.1007/978-1-61779-507-7_12", "pmid": "22228016", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:02.848Z", "modified": "2020-01-21T13:56:03.060Z"}, {"entity": "publication", "iuid": "b0c9cd20e86541bcbd1cc2c3211c019d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c9cd20e86541bcbd1cc2c3211c019d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c9cd20e86541bcbd1cc2c3211c019d"}}, "title": "Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development.", "authors": [{"family": "Bizuayehu", "given": "Teshome T", "initials": "TT"}, {"family": "Lanes", "given": "Carlos F C", "initials": "CFC"}, {"family": "Furmanek", "given": "Tomasz", "initials": "T"}, {"family": "Karlsen", "given": "B\u00e5rd O", "initials": "BO"}, {"family": "Fernandes", "given": "Jorge M O", "initials": "JMO"}, {"family": "Johansen", "given": "Steinar D", "initials": "SD"}, {"family": "Babiak", "given": "Igor", "initials": "I"}], "type": "journal article", "published": "2012-01-10", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "11", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Developmental profiles of miRNAs have been reported in few fish species only and, to our knowledge, differential expressions of isomiRs have not yet been shown during fish development. Atlantic halibut, Hippoglossus hippoglossus L., undergoes dramatic metamorphosis during early development from symmetrical pelagic larval stage to unsymmetrical flatfish. No data exist on role of miRNAs in halibut metamorphosis.\r\n\r\nmiRNA profiling using SOLiD deep sequencing technology revealed a total of 199 conserved, one novel antisense, and one miRNA* mature form. Digital expression profiles of selected miRNAs were validated using reverse transcription quantitative PCR. We found developmental transition-specific miRNA expression. Expression of some miRNA* exceeded the guide strand miRNA. We revealed that nucleotide truncations and/or additions at the 3' end of mature miRNAs resulted in size variants showing differential expression patterns during the development in a number of miRNA families. We confirmed the presence of isomiRs by cloning and Sanger sequencing. Also, we found inverse relationship between expression levels of sense/antisense miRNAs during halibut development.\r\n\r\nDevelopmental transitions during early development of Atlantic halibut are associated with expression of certain miRNA types. IsomiRs are abundant and often show differential expression during the development.", "doi": "10.1186/1471-2164-13-11", "pmid": "22233483", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-11"}, {"db": "pmc", "key": "PMC3398304"}], "notes": [], "created": "2017-05-04T14:57:30.723Z", "modified": "2020-01-21T13:56:10.369Z"}, {"entity": "publication", "iuid": "b7b2d26caba640baae9e6a6c706360c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7b2d26caba640baae9e6a6c706360c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7b2d26caba640baae9e6a6c706360c1"}}, "title": "Combinations of histone modifications mark exon inclusion levels.", "authors": [{"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2012-01-05", "journal": {"volume": "7", "issn": "1932-6203", "issue": "1", "pages": "e29911", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Splicing is a complex process regulated by sequence at the classical splice sites and other motifs in exons and introns with an enhancing or silencing effect. In addition, specific histone modifications on nucleosomes positioned over the exons have been shown to correlate both positively and negatively with exon expression. Here, we trained a model of \"IF \u2026 THEN \u2026\" rules to predict exon inclusion levels in a transcript from histone modification patterns. Furthermore, we showed that combinations of histone modifications, in particular those residing on nucleosomes preceding or succeeding the exon, are better predictors of exon inclusion levels than single modifications. The resulting model was evaluated with cross validation and had an average accuracy of 72% for 27% of the exons, which demonstrates that epigenetic signals substantially mark alternative splicing.", "doi": "10.1371/journal.pone.0029911", "pmid": "22242188", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-10-01654"}, {"db": "pmc", "key": "PMC3252363"}], "notes": [], "created": "2017-05-04T14:57:43.905Z", "modified": "2020-01-21T13:56:04.791Z"}, {"entity": "publication", "iuid": "9ba3e0d7fbbe42d39db7c4cd21315b59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ba3e0d7fbbe42d39db7c4cd21315b59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ba3e0d7fbbe42d39db7c4cd21315b59"}}, "title": "A genome-wide association search for type 2 diabetes genes in African Americans.", "authors": [{"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "McDonough", "given": "Caitrin W", "initials": "CW"}, {"family": "Hicks", "given": "Pamela J", "initials": "PJ"}, {"family": "Roh", "given": "Bong H", "initials": "BH"}, {"family": "Wing", "given": "Maria R", "initials": "MR"}, {"family": "An", "given": "S Sandy", "initials": "SS"}, {"family": "Hester", "given": "Jessica M", "initials": "JM"}, {"family": "Cooke", "given": "Jessica N", "initials": "JN"}, {"family": "Bostrom", "given": "Meredith A", "initials": "MA"}, {"family": "Rudock", "given": "Megan E", "initials": "ME"}, {"family": "Talbert", "given": "Matthew E", "initials": "ME"}, {"family": "Lewis", "given": "Joshua P", "initials": "JP"}, {"family": "DIAGRAM Consortium", "given": null, "initials": null}, {"family": "MAGIC Investigators", "given": null, "initials": null}, {"family": "Ferrara", "given": "Assiamira", "initials": "A"}, {"family": "Lu", "given": "Lingyi", "initials": "L"}, {"family": "Ziegler", "given": 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{"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Cooper", "given": "Cyrus", "initials": "C"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Serrano-R\u00edos", "given": "Manuel", "initials": "M"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Ebrahim", "given": "Shah", "initials": "S"}, {"family": "Marmot", "given": "Michael", "initials": "M"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Pramstaller", "given": "Peter Paul", "initials": "PP"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA"}, {"family": "Valle", "given": "Timo T", "initials": "TT"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BW"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Cao", "given": "Antonio", "initials": "A"}, {"family": "Scuteri", "given": "Angelo", "initials": "A"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "Ruokonen", "given": "Aimo", "initials": "A"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Sladek", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2012-01-04", "journal": {"volume": "7", "issn": "1932-6203", "issue": "1", "pages": "e29202", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n\u200a=\u200a550 independent loci) were genotyped in a replication cohort and 122 SNPs (n\u200a=\u200a98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5\u00d710(-8)). SNP rs7560163 (P\u200a=\u200a7.0\u00d710(-9), OR (95% CI)\u200a=\u200a0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5\u00d710(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.", "doi": "10.1371/journal.pone.0029202", "pmid": "22238593", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-17050"}, {"db": "pmc", "key": "PMC3251563"}], "notes": [], "created": "2017-05-04T15:01:11.133Z", "modified": "2021-07-07T15:57:26.534Z"}, {"entity": "publication", "iuid": "a95d3f8a7bd640d0814032bf7ddf636d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a95d3f8a7bd640d0814032bf7ddf636d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a95d3f8a7bd640d0814032bf7ddf636d"}}, "title": "siRNA silencing of proteasome maturation protein (POMP) activates the unfolded protein response and constitutes a model for KLICK genodermatosis.", "authors": [{"family": "Dahlqvist", "given": "Johanna", "initials": "J"}, {"family": "T\u00f6rm\u00e4", "given": "Hans", "initials": "H"}, {"family": "Badhai", "given": "Jitendra", "initials": "J"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2012-01-03", "journal": {"volume": "7", "issn": "1932-6203", "issue": "1", "pages": "e29471", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Keratosis linearis with ichthyosis congenita and keratoderma (KLICK) is an autosomal recessive skin disorder associated with a single-nucleotide deletion in the 5'untranslated region of the proteasome maturation protein (POMP) gene. The deletion causes a relative switch in transcription start sites for POMP, predicted to decrease levels of POMP protein in terminally differentiated keratinocytes. To investigate the pathophysiology behind KLICK we created an in vitro model of the disease using siRNA silencing of POMP in epidermal air-liquid cultures. Immunohistochemical analysis of the tissue constructs revealed aberrant staining of POMP, proteasome subunits and the skin differentiation marker filaggrin when compared to control tissue constructs. The staining patterns of POMP siRNA tissue constructs showed strong resemblance to those observed in skin biopsies from KLICK patients. Western blot analysis of lysates from the organotypic tissue constructs revealed an aberrant processing of profilaggrin to filaggrin in samples transfected with siRNA against POMP. Knock-down of POMP expression in regular cell cultures resulted in decreased amounts of proteasome subunits. Prolonged silencing of POMP in cultured cells induced C/EBP homologous protein (CHOP) expression consistent with an activation of the unfolded protein response and increased endoplasmic reticulum (ER) stress. The combined results indicate that KLICK is caused by reduced levels of POMP, leading to proteasome insufficiency in differentiating keratinocytes. Proteasome insufficiency disturbs terminal epidermal differentiation, presumably by increased ER stress, and leads to perturbed processing of profilaggrin. Our findings underline a critical role for the proteasome in human epidermal differentiation.", "doi": "10.1371/journal.pone.0029471", "pmid": "22235297", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-09470"}, {"db": "pmc", "key": "PMC3250448"}], "notes": [], "created": "2017-05-04T14:57:44.814Z", "modified": "2020-01-21T13:56:04.419Z"}, {"entity": "publication", "iuid": "d373e71c06094217863b00c08b3b5ee2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d373e71c06094217863b00c08b3b5ee2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d373e71c06094217863b00c08b3b5ee2"}}, "title": "Lymphoblastoid cell line with B1 cell characteristics established from a chronic lymphocytic leukemia clone by in vitro EBV infection.", "authors": [{"family": "Ros\u00e9n", "given": "Anders", "initials": "A"}, {"family": "Bergh", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Gogok", "given": "Peter", "initials": "P"}, {"family": "Evaldsson", "given": "Chamilly", "initials": "C"}, {"family": "Myhrinder", "given": "Anna Lanemo", "initials": "AL"}, {"family": "Hellqvist", "given": "Eva", "initials": "E"}, {"family": "Rasul", "given": "Abu", "initials": "A"}, {"family": "Bj\u00f6rkholm", "given": "Magnus", "initials": "M"}, {"family": "Jansson", "given": "Mattias", "initials": "M"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Liu", "given": "Anquan", "initials": "A"}, {"family": "Teh", "given": "Bin Tean", "initials": "BT"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Klein", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2012-01-01", "journal": {"volume": "1", "issn": "2162-4011", "issue": "1", "pages": "18-27", "title": "Oncoimmunology", "issn-l": null}, "abstract": "Chronic lymphocytic leukemia (CLL) cells express the receptor for Epstein-Barr virus (EBV) and can be infected in vitro. Infected cells do not express the growth-promoting set of EBV-encoded genes and therefore they do not yield LCLs, in most experiments. With exceptional clones, lines were obtained however. We describe a new line, HG3, established by in vitro EBV-infection from an IGHV1-2 unmutated CLL patient clone. All cells expressed EBNA-2 and LMP-1, the EBV-encoded genes pivotal for transformation. The karyotype, FISH cytogenetics and SNP-array profile of the line and the patient's ex vivo clone showed biallelic 13q14 deletions with genomic loss of DLEU7, miR15a/miR16-1, the two micro-RNAs that are deleted in 50% of CLL cases. Further features of CLL cells were: expression of CD5/CD20/CD27/CD43 and release of IgM natural antibodies reacting with oxLDL-like epitopes on apoptotic cells (cf. stereotyped subset-1). Comparison with two LCLs established from normal B cells showed 32 genes expressed at higher levels (> 2-fold). Among these were LHX2 and LILRA. These genes may play a role in the development of the disease. LHX2 expression was shown in self-renewing multipotent hematopoietic stem cells, and LILRA4 codes for a receptor for bone marrow stromal cell antigen-2 that contributes to B cell development. Twenty-four genes were expressed at lower levels, among these PARD3 that is essential for asymmetric cell division. These genes may contribute to establish precursors of CLL clones by regulation of cellular phenotype in the hematopoietic compartment. Expression of CD5/CD20/CD27/CD43 and spontaneous production of natural antibodies may identify the CLL cell as a self-renewing B1 lymphocyte.", "doi": "10.4161/onci.1.1.18400", "pmid": "22720208", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "2011ONCOIMM0075"}, {"db": "pmc", "key": "PMC3376971"}], "notes": [], "created": "2017-05-04T15:02:59.963Z", "modified": "2017-05-31T08:17:05.183Z"}, {"entity": "publication", "iuid": "675ada456452400aabae4ca754bf7f9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/675ada456452400aabae4ca754bf7f9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/675ada456452400aabae4ca754bf7f9b"}}, "title": "Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.", "authors": [{"family": "Zaboli", "given": "Ghazal", "initials": "G"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Campbell", "given": "Susan", "initials": "S"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Schmitz", "given": "Gerd", "initials": "G"}, {"family": "van Duijn", "given": "Cornelia", "initials": "C"}, {"family": "Oostra", "given": "Ben", "initials": "B"}, {"family": "Pramstaller", "given": "Peter", "initials": "P"}, {"family": "Hicks", "given": "Andrew", "initials": "A"}, {"family": "Meitinger", "given": "Tomas", "initials": "T"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Wright", "given": "Alan", "initials": "A"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "EUROSPAN Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2012-01-00", "journal": {"volume": "20", "issn": "1476-5438", "issue": "1", "pages": "77-83", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "We have used targeted genomic sequencing of high-complexity DNA pools based on long-range PCR and deep DNA sequencing by the SOLiD technology. The method was used for sequencing of 286 kb from four chromosomal regions with quantitative trait loci (QTL) influencing blood plasma lipid and uric acid levels in DNA pools of 500 individuals from each of five European populations. The method shows very good precision in estimating allele frequencies as compared with individual genotyping of SNPs (r(2) = 0.95, P < 10(-16)). Validation shows that the method is able to identify novel SNPs and estimate their frequency in high-complexity DNA pools. In our five populations, 17% of all SNPs and 61% of structural variants are not available in the public databases. A large fraction of the novel variants show a limited geographic distribution, with 62% of the novel SNPs and 59% of novel structural variants being detected in only one of the populations. The large number of population-specific novel SNPs underscores the need for comprehensive sequencing of local populations in order to identify the causal variants of human traits.", "doi": "10.1038/ejhg.2011.138", "pmid": "21811304", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ejhg2011138"}, {"db": "pmc", "key": "PMC3234506"}], "notes": [], "created": "2017-05-04T14:57:33.963Z", "modified": "2021-07-07T14:37:06.488Z"}, {"entity": "publication", "iuid": "a937595f131842ae948b3394fe05cf30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a937595f131842ae948b3394fe05cf30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a937595f131842ae948b3394fe05cf30"}}, "title": "QTL linkage mapping of zebra finch beak color shows an oligogenic control of a sexually selected trait.", "authors": [{"family": "Schielzeth", "given": "Holger", "initials": "H"}, {"family": "Kempenaers", "given": "Bart", "initials": "B"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}], "type": "journal article", "published": "2012-01-00", "journal": {"volume": "66", "issn": "1558-5646", "issue": "1", "pages": "18-30", "title": "Evolution", "issn-l": "0014-3820"}, "abstract": "Mate choice based on sexual ornaments can impose strong selection, which raises the question of how genetic variation in ornaments is maintained. One mechanism that has been proposed is genic capture. If ornament expression is influenced by general condition and condition is under polygenic control, selection will be inefficient in removing genetic variation. Here we analyze whether the genetic architecture of beak color in a population of zebra finches supports this hypothesis. Zebra finch beak color is commonly assumed to be under strong selection by mate choice, although some of the evidence is ambiguous. We show that beak redness has a heritability of 34% in our population and that it is strongly genetically correlated between the sexes, suggesting that it is largely controlled by the same genes in males and females. We mapped variation in beak redness based on 1404 single-nucleotide polymorphism (SNP) markers genotyped in a large pedigree. We find evidence for linkage on four chromosomes (Tgu1, Tgu5, Tgu13, Tgu21), which together explain a large part of the additive genetic variance. Our finding of genomic regions with major additive effects is not consistent with directional selection and genic capture, but rather suggests a role of antagonistic pleiotropy in maintaining genetic variation.", "doi": "10.1111/j.1558-5646.2011.01431.x", "pmid": "22220861", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:58.460Z", "modified": "2020-01-21T13:56:04.412Z"}, {"entity": "publication", "iuid": "3254c495191d4eb6a408bc2f88e9c98b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3254c495191d4eb6a408bc2f88e9c98b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3254c495191d4eb6a408bc2f88e9c98b"}}, "title": "QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers.", "authors": [{"family": "Schielzeth", "given": "Holger", "initials": "H"}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}, {"family": "Kempenaers", "given": "Bart", "initials": "B"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2012-01-00", "journal": {"volume": "21", "issn": "1365-294X", "issue": "2", "pages": "329-339", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Avian wing length is an important trait that covaries with the ecology and migratory behaviour of a species and tends to change rapidly when the conditions are altered. Long-distance migrants typically have longer wings than short-distance migrants and sedentary species, and long-winged species also tend to be more dispersive. Although the substantial heritability of avian wing length is well established, the identification of causal genes has remained elusive. Based on large-scale genotyping of 1404 informative single nucleotide polymorphisms (SNP) in a captive population of 1067 zebra finches, we here show that the within-population variation of relative wing length (h(2) = 0.74 \u00b1 0.05) is associated with standing genetic variation in at least six genomic regions (one genome-wide significant and five suggestive). The variance explained by these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic variance (half of the additive genetic variance), although this likely is an overestimate attributable to the Beavis effect. As avian wing length is primarily determined by the length of the primary feathers, we then searched for candidate genes that are related to feather growth. Interestingly, all of the QTL signals co-locate with Wnt growth factors and closely interacting genes (Wnt3a, Wnt5a, Wnt6, Wnt7a, Wnt9a, RhoU and RhoV). Our findings therefore suggest that standing genetic variation in the Wnt genes might be linked to avian wing morphology, although there are many other genes that also fall within the confidence regions.", "doi": "10.1111/j.1365-294X.2011.05365.x", "pmid": "22111790", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:03.752Z", "modified": "2020-01-21T13:56:01.402Z"}, {"entity": "publication", "iuid": "5debdccd950549b0a5d75b2a49c85939", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5debdccd950549b0a5d75b2a49c85939.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5debdccd950549b0a5d75b2a49c85939"}}, "title": "Kynurenine 3-monooxygenase polymorphisms: relevance for kynurenic acid synthesis in patients with schizophrenia and healthy controls.", "authors": [{"family": "Holtze", "given": "Maria", "initials": "M"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Engberg", "given": "G\u00f6ran", "initials": "G"}, {"family": "Schwieler", "given": "Lilly", "initials": "L"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Hall", "given": "H\u00e5kan", "initials": "H"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Schalling", "given": "Martin", "initials": "M"}, {"family": "Erhardt", "given": "Sophie", "initials": "S"}], "type": "journal article", "published": "2012-01-00", "journal": {"volume": "37", "issn": "1488-2434", "issue": "1", "pages": "53-57", "title": "J Psychiatry Neurosci", "issn-l": "1180-4882"}, "abstract": "Patients with schizophrenia show increased brain and cerebrospinal fluid (CSF) concentrations of the endogenous N-methyl-D-aspartate receptor antagonist kynurenic acid (KYNA). This compound is an end-metabolite of the kynurenine pathway, and its formation indirectly depends on the activity of kynurenine 3-monooxygenase (KMO), the enzyme converting kynurenine to 3-hydroxykynurenine.\n\nWe analyzed the association between KMO gene polymorphisms and CSF concentrations of KYNA in patients with schizophrenia and healthy controls. Fifteen single nucleotide polymorphisms (SNPs) were selected covering KMO and were analyzed in UNPHASED.\n\nWe included 17 patients with schizophrenia and 33 controls in our study. We found an association between a KMO SNP (rs1053230), encoding an amino acid change of potential importance for substrate interaction, and CSF concentrations of KYNA.\n\nGiven the limited sample size, the results are tentative until replication.\n\nOur results suggest that the nonsynonymous KMO SNP rs1053230 influences CSF concentrations of KYNA.", "doi": "10.1503/jpn.100175", "pmid": "21693093", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "10.1503/jpn.100175"}, {"db": "pmc", "key": "PMC3244499"}], "notes": [], "created": "2017-05-04T15:01:01.214Z", "modified": "2020-01-21T13:56:02.547Z"}, {"entity": "publication", "iuid": "bc1e3776d31d4aeb994e45d42f982b6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc1e3776d31d4aeb994e45d42f982b6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc1e3776d31d4aeb994e45d42f982b6f"}}, "title": "High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.", "authors": [{"family": "Martinez-Garcia", "given": "Manuel", "initials": "M"}, {"family": "Swan", "given": "Brandon K", "initials": "BK"}, {"family": "Poulton", "given": "Nicole J", "initials": "NJ"}, {"family": "Gomez", "given": "Monica Lluesma", "initials": "ML"}, {"family": "Masland", "given": "Dashiell", "initials": "D"}, {"family": "Sieracki", "given": "Michael E", "initials": "ME"}, {"family": "Stepanauskas", "given": "Ramunas", "initials": "R"}], "type": "journal article", "published": "2012-01-00", "journal": {"volume": "6", "issn": "1751-7370", "issue": "1", "pages": "113-123", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10-23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma- and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments.", "doi": "10.1038/ismej.2011.84", "pmid": "21716306", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ismej201184"}, {"db": "pmc", "key": "PMC3246240"}], "notes": [], "created": "2017-05-04T14:57:36.282Z", "modified": "2020-01-21T13:56:04.913Z"}, {"entity": "publication", "iuid": "c20e44ab50be452e92a86a18ed45a06c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c20e44ab50be452e92a86a18ed45a06c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c20e44ab50be452e92a86a18ed45a06c"}}, "title": "Genetic variants near the MGAT1 gene are associated with body weight, BMI and fatty acid metabolism among adults and children.", "authors": [{"family": "Jacobsson", "given": "J A", "initials": "JA"}, {"family": "Rask-Andersen", "given": "M", "initials": "M"}, {"family": "Ris\u00e9rus", "given": "U", "initials": "U"}, {"family": "Moschonis", "given": "G", "initials": "G"}, {"family": "Koumpitski", "given": "A", "initials": "A"}, {"family": "Chrousos", "given": "G P", "initials": "GP"}, {"family": "Lannfelt", "given": "L", "initials": "L"}, {"family": "Marcus", "given": "C", "initials": "C"}, {"family": "Gyllensten", "given": "U", "initials": "U"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}, {"family": "Fredriksson", "given": "R", "initials": "R"}], "type": "journal article", "published": "2012-01-00", "journal": {"volume": "36", "issn": "1476-5497", "issue": "1", "pages": "119-129", "title": "Int J Obes (Lond)", "issn-l": "0307-0565"}, "abstract": "Recently a genome-wide association analysis from five European populations identified a polymorphism located downstream of the mannosyl-(\u03b1-1,3)-glycoprotein-\u03b2-1,2-N-acetylglucosaminyltransferase (MGAT1) gene that was associated with body-weight. In the present study, associations between MGAT1 variants combined with obesity and insulin measurements were investigated in three cohorts. Levels of fatty acids and estimated measures of \u0394 desaturases were also investigated among adult men.\n\nSix polymorphisms downstream of MGAT1 were genotyped in a cross-sectional cohort of 1152 Swedish men. Three polymorphisms were further analyzed in a case-control study of 1076 Swedish children and in a cross-sectional study of 2249 Greek children.\n\nThree polymorphisms, rs12186500 (odds ratio (OR): 1.892, 95% confidence interval (CI): 1.237-2.895, P=0.003), rs1021001 (OR: 2.102, 95% CI: 1.280-3.455, P=0.003) and rs4285184 (OR: 1.587, 95% CI: 1.024-2.459, P=0.038) were associated with a higher prevalence of obesity among the adult men and a trend for obesity was observed for rs4285184 among the Swedish (OR: 1.205, 95% CI: 0.987-1.471, P=0.067) and Greek children (OR: 1.192, 95%CI: 0.978-1.454, P=0.081). Association with body weight was observed for rs12186500 (P=0.017) and rs4285184 (P=0.024) among the men. The rs1021001 and rs4285184 were also associated with body mass index (BMI) in the two Swedish cohorts and similar trends were observed among the Greek children. The combined effect size for rs1021001 and rs4285184 on BMI z-score from a meta-analysis was 0.233 (95% CI:0.093-0.373, P=0.001) and 0.147 (95% CI:0.057-0.236, P=0.001), respectively. We further observed associations between the genetic variants and fatty acids (P<0.039) and estimated measures of \u0394 desaturases (P<0.040), as well as interactions for rs12186500 (P<0.019) with an effect on BMI. No association was found with homeostatic model assessment-insulin resistance in any cohort but increased insulin levels, insulin response and decreased insulin sensitivity were observed among the children (P<0.038).\n\nGenetic variants downstream MGAT1 seem to influence susceptibility to obesity. Moreover, these genetic variants affect the levels of serum unsaturated fatty acids and \u0394 desaturase indices, variables previously shown to correlate with obesity.", "doi": "10.1038/ijo.2011.11", "pmid": "21304485", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ijo201111"}, {"db": "pmc", "key": "PMC3255099"}], "notes": [], "created": "2017-05-04T15:00:59.999Z", "modified": "2020-01-21T13:56:05.032Z"}, {"entity": "publication", "iuid": "5ee700805e74435b81a690144c426c34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ee700805e74435b81a690144c426c34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ee700805e74435b81a690144c426c34"}}, "title": "Biosensor Based Protein Profiling on Reverse Phase Serum Microarray", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal-article", "published": "2012-00-00", "journal": {"title": "JPB", "issn": "0974-276X", "issn-l": "0974-276X", "volume": "05", "issue": "08", "pages": null}, "abstract": null, "doi": "10.4172/jpb.1000233", "pmid": null, "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:36.331Z", "modified": "2021-07-07T15:55:05.825Z"}]}