{"entity": "journal", "iuid": "49c1a907a9d049f1aa0e7e70f68f8fef", "timestamp": "2026-08-09T07:25:57.645Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Proc%20Natl%20Acad%20Sci%20USA.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Proc%20Natl%20Acad%20Sci%20USA"}}, "title": "Proc Natl Acad Sci USA", "issn": "0027-8424", "issn-l": "0027-8424", "publications_count": 9, "publications": [{"entity": "publication", "iuid": "868204592395423f990c951ba83d71d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/868204592395423f990c951ba83d71d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/868204592395423f990c951ba83d71d3"}}, "title": "Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard", "authors": [{"family": "Andrade", "given": "Pedro", "initials": "P"}, {"family": "Pinho", "given": "Catarina", "initials": "C"}, {"family": "P\u00e9rez i de Lanuza", "given": "Guillem", "initials": "G"}, {"family": "Afonso", "given": "Sandra", "initials": "S"}, {"family": "Brejcha", "given": "Jind\u0159ich", "initials": "J"}, {"family": "Rubin", "given": "Carl Johan", "initials": "CJ"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Pereira", "given": "Paulo", "initials": "P"}, {"family": "Sabatino", "given": "Stephen J", "initials": "SJ"}, {"family": "Bellati", "given": "Adriana", "initials": "A"}, {"family": "Pellitteri-Rosa", "given": "Daniele", "initials": "D"}, {"family": "Bosakova", "given": "Zuzana", "initials": "Z"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Carretero", "given": "Miguel A", "initials": "MA"}, {"family": "Feiner", "given": "Nathalie", "initials": "N"}, {"family": "Marsik", "given": "Petr", "initials": "P"}, {"family": "Paup\u00e9rio", "given": "Francisco", "initials": "F"}, {"family": "Salvi", "given": "Daniele", "initials": "D"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "While", "given": "Geoffrey M", "initials": "GM"}, {"family": "Uller", "given": "Tobias", "initials": "T"}, {"family": "Font", "given": "Enrique", "initials": "E"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Carneiro", "given": "Miguel", "initials": "M"}], "type": "journal-article", "published": "2019-02-28", "journal": {"volume": null, "issn": "0027-8424", "issue": null, "pages": "201820320", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": "Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard ( Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.", "doi": "10.1073/pnas.1820320116", "pmid": "30819892", "labels": {"National Genomics Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-03-08T07:59:28.818Z", "modified": "2024-01-16T13:48:44.663Z"}, {"entity": "publication", "iuid": "7b9a4b3254e04ef1aa2d5b21da472e47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b9a4b3254e04ef1aa2d5b21da472e47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b9a4b3254e04ef1aa2d5b21da472e47"}}, "title": "Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen", "authors": [{"family": "Lin", "given": "Yao Cheng", "initials": "YC"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "de la Torre", "given": "Amanda", "initials": "A"}, {"family": "Cossu", "given": "Rosa M", "initials": "RM"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Leitch", "given": "Ilia J", "initials": "IJ"}, {"family": "Pellicer", "given": "Jaume", "initials": "J"}, {"family": "Park", "given": "Eung Jun", "initials": "EJ"}, {"family": "Van Montagu", "given": "Marc", "initials": "M"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal-article", "published": "2018-10-29", "journal": {"volume": null, "issn": "0027-8424", "issue": null, "pages": "201801437", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1801437115", "pmid": "30373829", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "European Nucleotide Archive", "description": "GENOME AND POPULATION SEQUENCING OF ASPEN ADVANCES POPULUS AS A MODEL SYSTEM FOR PLANT RESEARCH", "key": "PRJEB23585"}, {"db": "PlantGenie.org", "description": "ftp://plantgenie.org/Publications/Lin2018/pnas201801437/", "key": "pnas201801437"}], "notes": [], "created": "2018-10-31T12:03:08.142Z", "modified": "2024-01-16T13:48:45.277Z"}, {"entity": "publication", "iuid": "7a6564ec50de477397922fc916950f25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a6564ec50de477397922fc916950f25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a6564ec50de477397922fc916950f25"}}, "title": "Molecular mechanism of ATP versus GTP selectivity of adenylate kinase", "authors": [{"family": "Rogne", "given": "Per", "initials": "P"}, {"family": "Rosselin", "given": "Marie", "initials": "M"}, {"family": "Grundstr\u00f6m", "given": "Christin", "initials": "C"}, {"family": "Hedberg", "given": "Christian", "initials": "C"}, {"family": "Sauer", "given": "Uwe H", "initials": "UH"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}], "type": "journal-article", "published": "2018-03-20", "journal": {"volume": "115", "issn": "0027-8424", "issue": "12", "pages": "3012-3017", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1721508115", "pmid": "29507216", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T14:46:24.210Z", "modified": "2025-10-17T13:03:58.809Z"}, {"entity": "publication", "iuid": "d293ef3dac5449d5933f54ff50b164bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d293ef3dac5449d5933f54ff50b164bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d293ef3dac5449d5933f54ff50b164bb"}}, "title": "The ZBED6\u2013IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals", "authors": [{"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Sch\u00f6nke", "given": "Milena", "initials": "M"}, {"family": "Massart", "given": "Julie", "initials": "J"}, {"family": "Hjortebjerg", "given": "Rikke", "initials": "R"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Gustafson", "given": "Ulla", "initials": "U"}, {"family": "Bj\u00f6rnholm", "given": "Marie", "initials": "M"}, {"family": "Krook", "given": "Anna", "initials": "A"}, {"family": "Frystyk", "given": "Jan", "initials": "J"}, {"family": "Zierath", "given": "Juleen R", "initials": "JR"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal-article", "published": "2018-02-27", "journal": {"volume": "115", "issn": "0027-8424", "issue": "9", "pages": "E2048-E2057", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": "A single nucleotide substitution in the third intron of insulin-like growth factor 2 (\n                IGF2) is associated with increased muscle mass and reduced subcutaneous fat in domestic pigs. This mutation disrupts the binding of the ZBED6 transcription factor and leads to a threefold up-regulation of IGF2 expression in pig skeletal muscle. Here, we investigated the biological significance of ZBED6-IGF2 interaction in the growth of placental mammals using two mouse models, ZBED6 knock-out (Zbed6-/-) and Igf2 knock-in mice that carry the pig IGF2 mutation. These transgenic mice exhibit markedly higher serum IGF2 concentrations, higher growth rate, increased lean mass, and larger heart, kidney, and liver; no significant changes were observed for white adipose tissues. The changes in body and lean mass were most pronounced in female mice. The phenotypic changes were concomitant with a remarkable up-regulation of Igf2 expression in adult tissues. Transcriptome analysis of skeletal muscle identified differential expression of genes belonging to the extracellular region category. Expression analysis using fetal muscles indicated a minor role of ZBED6 in regulating Igf2 expression prenatally. Furthermore, transcriptome analysis of the adult skeletal muscle revealed that this elevated expression of Igf2 was derived from the P1 and P2 promoters. The results revealed very similar phenotypic effects in the Zbed6 knock-out mouse and in the Igf2 knock-in mouse, showing that the effect of ZBED6 on growth of muscle and internal organs is mediated through the binding site in the Igf2 gene. The results explain why this ZBED6 binding site is extremely well conserved among placental mammals.", "doi": "10.1073/pnas.1719278115", "pmid": "29440408", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP128271"}], "notes": [], "created": "2018-04-04T11:30:57.231Z", "modified": "2024-01-16T13:48:46.876Z"}, {"entity": "publication", "iuid": "0e3e496b27f34d6982c9309b7afed7c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e3e496b27f34d6982c9309b7afed7c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e3e496b27f34d6982c9309b7afed7c3"}}, "title": "Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery", "authors": [{"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Gordon", "given": "Laurie J", "initials": "LJ"}, {"family": "Wayne", "given": "Gareth J", "initials": "GJ"}, {"family": "Almqvist", "given": "Helena", "initials": "H"}, {"family": "Axelsson", "given": "Hanna", "initials": "H"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Treyer", "given": "Andrea", "initials": "A"}, {"family": "Matsson", "given": "P\u00e4r", "initials": "P"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "West", "given": "Andy", "initials": "A"}, {"family": "Hann", "given": "Michael M", "initials": "MM"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal-article", "published": "2017-07-25", "journal": {"volume": "114", "issn": "0027-8424", "issue": "30", "pages": "E6231-E6239", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1701848114", "pmid": "28701380", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T13:33:31.528Z", "modified": "2025-10-17T13:04:29.208Z"}, {"entity": "publication", "iuid": "f46452abecc647e3bb3780c1224e3e42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f46452abecc647e3bb3780c1224e3e42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f46452abecc647e3bb3780c1224e3e42"}}, "title": "Haploid selection within a single ejaculate increases offspring fitness", "authors": [{"family": "Alavioon", "given": "Ghazal", "initials": "G"}, {"family": "Hotzy", "given": "Cosima", "initials": "C"}, {"family": "Nakhro", "given": "Khriezhanuo", "initials": "K"}, {"family": "Rudolf", "given": "Sandra", "initials": "S"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Zajitschek", "given": "Susanne", "initials": "S"}, {"family": "Maklakov", "given": "Alexei A", "initials": "AA"}, {"family": "Immler", "given": "Simone", "initials": "S"}], "type": "journal-article", "published": "2017-07-25", "journal": {"volume": "114", "issn": "0027-8424", "issue": "30", "pages": "8053-8058", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1705601114", "pmid": "28698378", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Genome Engineering Zebrafish": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-26T09:20:47.508Z", "modified": "2020-01-21T13:56:11.851Z"}, {"entity": "publication", "iuid": "0e8332d687b24f6a84e890ecb7fbb1f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e8332d687b24f6a84e890ecb7fbb1f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e8332d687b24f6a84e890ecb7fbb1f3"}}, "title": "Regulating plant physiology with organic electronics", "authors": [{"family": "Poxson", "given": "David J", "initials": "DJ"}, {"family": "Karady", "given": "Michal", "initials": "M"}, {"family": "Gabrielsson", "given": "Roger", "initials": "R"}, {"family": "Alkattan", "given": "Aziz Y", "initials": "AY"}, {"family": "Gustavsson", "given": "Anna", "initials": "A"}, {"family": "Doyle", "given": "Siamsa M", "initials": "SM"}, {"family": "Robert", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Grebe", "given": "Markus", "initials": "M"}, {"family": "Simon", "given": "Daniel T", "initials": "DT"}, {"family": "Berggren", "given": "Magnus", "initials": "M"}], "type": "journal-article", "published": "2017-05-02", "journal": {"volume": "114", "issn": "0027-8424", "issue": "18", "pages": "4597-4602", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1617758114", "pmid": "28420793", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:34:50.023Z", "modified": "2025-10-17T13:03:18.833Z"}, {"entity": "publication", "iuid": "74c4f22cfa234ed1bb280bbb9b4d8518", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74c4f22cfa234ed1bb280bbb9b4d8518.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74c4f22cfa234ed1bb280bbb9b4d8518"}}, "title": "Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean", "authors": [{"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "McCracken", "given": "Gregory R", "initials": "GR"}, {"family": "Bourne", "given": "Christina", "initials": "C"}, {"family": "Singh", "given": "Rabindra", "initials": "R"}, {"family": "Ruzzante", "given": "Daniel E", "initials": "DE"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal-article", "published": "2017-04-25", "journal": {"volume": "114", "issn": "0027-8424", "issue": "17", "pages": "E3452-E3461", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1617728114", "pmid": "28389569", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Comparison of herring populations across the North Atlantic Ocean", "key": "PRJNA338612"}], "notes": [], "created": "2017-10-19T20:43:11.214Z", "modified": "2024-01-16T13:48:48.086Z"}, {"entity": "publication", "iuid": "3ab189fbee87422abd559ff87c88dd32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ab189fbee87422abd559ff87c88dd32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ab189fbee87422abd559ff87c88dd32"}}, "title": "Microbial community assembly and evolution in subseafloor sediment", "authors": [{"family": "Starnawski", "given": "Piotr", "initials": "P"}, {"family": "Bataillon", "given": "Thomas", "initials": "T"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Jochum", "given": "Lara M", "initials": "LM"}, {"family": "Schreiber", "given": "Lars", "initials": "L"}, {"family": "Chen", "given": "Xihan", "initials": "X"}, {"family": "Lever", "given": "Mark A", "initials": "MA"}, {"family": "Polz", "given": "Martin F", "initials": "MF"}, {"family": "J\u00f8rgensen", "given": "Bo B", "initials": "BB"}, {"family": "Schramm", "given": "Andreas", "initials": "A"}, {"family": "Kjeldsen", "given": "Kasper U", "initials": "KU"}], "type": "journal-article", "published": "2017-03-14", "journal": {"volume": "114", "issn": "0027-8424", "issue": "11", "pages": "2940-2945", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1614190114", "pmid": "28242677", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Marine sediment amplicon Targeted loci environmental", "key": "PRJNA308429"}, {"db": "BioProject", "description": "Marine sediment communities", "key": "PRJNA305566"}, {"db": "img.jgi.doe.gov", "description": "2606217225, 2626541591, 2606217224, 2609459604, 2606217227, 2606217228, 2609459605, 2626541542, 2626541544, 2626541633, 2626541550, 2626541552, 2626541551, 2609459610, 2609459611, 2609459606, 2609459607, 2626541553, 2615840654 and 2615840655", "key": "https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2615840655"}], "notes": [], "created": "2017-10-19T20:12:08.593Z", "modified": "2024-01-16T13:48:48.315Z"}], "created": "2017-08-23T14:19:03.186Z", "modified": "2020-11-27T13:13:58.624Z"}