{"entity": "publications", "timestamp": "2026-08-18T17:01:23.431Z", "year": "2017", "links": {"self": {"href": "https://publications.scilifelab.se/publications/2017.json"}, "display": {"href": "https://publications.scilifelab.se/publications/2017"}}, "publications_count": 681, "full": true, "publications": [{"entity": "publication", "iuid": "eb28ef6a0b2a45cfbb3a285b078eebee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb28ef6a0b2a45cfbb3a285b078eebee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb28ef6a0b2a45cfbb3a285b078eebee"}}, "title": "InSiDDe: A Server for Designing Artificial Disordered Proteins.", "authors": [{"family": "Schramm", "given": "Antoine", "initials": "A"}, {"family": "Lieutaud", "given": "Philippe", "initials": "P"}, {"family": "Gianni", "given": "Stefano", "initials": "S"}, {"family": "Longhi", "given": "Sonia", "initials": "S", "orcid": "0000-0002-6829-6771", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf0f8409acf842f2bcd47219fd02f3fa.json"}}, {"family": "Bignon", "given": "Christophe", "initials": "C"}], "type": "journal article", "published": "2017-12-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "19", "issue": "1", "issn-l": null}, "abstract": "InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0.55 to 0.95 with 0.05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0.6 designed by InSiDDe could be recombinantly expressed in E. coli at high levels without degradation when fused to a natural molecular recognition element (MoRE). In addition, the artificial fusion protein exhibited the expected behavior in terms of binding modulation of the specific partner recognized by the MoRE. To the best of our knowledge, InSiDDe is the first publicly available software for the design of intrinsically disordered protein (IDP) sequences. InSiDDE is publicly available online.", "doi": "10.3390/ijms19010091", "pmid": "29286306", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5796041"}, {"db": "pii", "key": "ijms19010091"}], "notes": [], "created": "2024-04-03T14:50:12.806Z", "modified": "2024-04-03T14:50:12.871Z"}, {"entity": "publication", "iuid": "de5cef0f77da4349b6fd836ac8b9887a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de5cef0f77da4349b6fd836ac8b9887a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de5cef0f77da4349b6fd836ac8b9887a"}}, "title": "Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish.", "authors": [{"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Kurtoglu", "given": "Deniz", "initials": "D"}, {"family": "Armenio", "given": "Miriam", "initials": "M"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Papadogiannakis", "given": "Nikos", "initials": "N"}, {"family": "Gustavsson", "given": "Peter", "initials": "P"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-12-28", "journal": {"volume": null, "issn": "1098-1004", "issue": null, "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Congenital malformations affecting the neural tube can present as isolated malformations or occur in association with other developmental abnormalities and syndromes. Using high resolution copy number screening in 66 fetuses with neural tube defects we identified 6 fetuses with likely pathogenic mutations, three aneuploidies (one trisomy 13 and two trisomy 18) and three deletions previously reported in NTDs (one 22q11.2 deletion and two 1p36 deletions) corresponding to 9% of the cohort. In addition, we identified five rare deletions and two duplications of uncertain significance including a rare intragenic heterozygous in-frame WDR63 deletion in a fetus with occipital encephalocele. Whole genome sequencing verified the deletion and excluded known pathogenic variants. The deletion spans exons 14-17 resulting in the expression of a protein missing the third and fourth WD-repeat domains. These findings were supported by CRISPR/Cas9 mediated somatic deletions in zebrafish. Injection of two different sgRNA-pairs targeting relevant intronic regions resulted in a deletion mimicking the human deletion and a concomitant increase of abnormal embryos with body and brain malformations (41%, n\u00a0=\u00a0161 and 62%, n\u00a0=\u00a0224 respectively), including a sac-like brain protrusion (7% and 9%, p\u00a0<\u00a00.01). Similar results were seen with overexpression of RNA encoding the deleted variant in zebrafish (Total abnormal;46%, n\u00a0=\u00a0255, P\u00a0<\u00a00.001) compared to overexpression of an equivalent amount of wild-type RNA (Total abnormal;3%, n\u00a0=\u00a0177). We predict the in-frame WDR63 deletion to result in a dominant negative or gain of function form of WDR63. These are the first findings supporting a role for WDR63 in encephalocele formation. This article is protected by copyright. All rights reserved.", "doi": "10.1002/humu.23388", "pmid": "29285825", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-10T09:44:17.066Z", "modified": "2020-01-21T13:56:11.002Z"}, {"entity": "publication", "iuid": "999dde89b4de4148b7bf42e4407bdfc3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999dde89b4de4148b7bf42e4407bdfc3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999dde89b4de4148b7bf42e4407bdfc3"}}, "title": "Methylation-based estimated biological age and cardiovascular disease", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Lampa", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2017-12-27", "journal": {"volume": null, "issn": "0014-2972", "issue": null, "pages": "e12872", "title": "Eur J Clin Invest", "issn-l": null}, "abstract": "DNA methylation changes over life at specific sites in the genome, which can be used to estimate \"biological age.\" The aim of this population-based longitudinal cohort study was to investigate the association between estimated biological age and incident cardiovascular disease (CVD).\n\nBased on formulas published by Hannum et\u00a0al and Horvath et\u00a0al, \"biological age\" was calculated using data from the Illumina 450k Bead Methylation chip in 832 participants free from cardiovascular disease in the Prospective Study of the Vasculature in Uppsala Seniors (PIVUS) study (50% women, all aged 70\u00a0years at the examination). The difference between estimated biological and chronological age was calculated (DiffAge).\n\nDuring 10\u00a0years of follow-up, 153 incident cases of cardiovascular disease occurred. In the sex-adjusted analyses, the Horvath estimation of DiffAge was significantly related to incident cardiovascular disease (HR 1.040, 95% CI 1.010-1.071, P\u00a0=\u00a0.0079). Thus, for each year of increased biological age, a 4% increased risk of future cardiovascular disease was observed. This relationship was still significant following adjustment for the traditional risk factors sex, BMI, diabetes, HDL and LDL-cholesterol, systolic blood pressure and smoking (HR 1.033, 95% CI 1.004-1.063, P\u00a0=\u00a0.024). No such significant association was found using the Hannum formula.\n\nDNA methylation-based estimation of \"biological age\" per Horvath was associated with incident cardiovascular disease.", "doi": "10.1111/eci.12872", "pmid": "29231988", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-02T15:37:53.992Z", "modified": "2020-01-21T13:56:13.762Z"}, {"entity": "publication", "iuid": "fef10a717b6948448b27dd4db58ce148", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fef10a717b6948448b27dd4db58ce148.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fef10a717b6948448b27dd4db58ce148"}}, "title": "Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils.", "authors": [{"family": "H\u00f6gfors-R\u00f6nnholm", "given": "Eva", "initials": "E"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Dalhem", "given": "Krister", "initials": "K"}, {"family": "Lillhonga", "given": "Tom", "initials": "T"}, {"family": "Engblom", "given": "Sten", "initials": "S"}, {"family": "\u00d6sterholm", "given": "Peter", "initials": "P"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-12-26", "journal": {"volume": "625", "issn": "1879-1026", "issue": null, "pages": "39-49", "title": "Sci. Total Environ.", "issn-l": "0048-9697"}, "abstract": "Naturally occurring sulfide rich deposits are common along the northern Baltic Sea coast that when exposed to air, release large amounts of acid and metals into receiving water bodies. This causes severe environmental implications for agriculture, forestry, and building of infrastructure. In this study, we investigated the efficiency of ultrafine-grained calcium carbonate and peat (both separately and in combination) to mitigate acid and metal release. The experiments were carried out aerobically that mimicked summer conditions when the groundwater level is low and acid sulfate soils are exposed to oxygen, and anaerobically that is similar to autumn to spring conditions. The ultrafine-grained calcium carbonate dissipated well in the soil and its effect alone and when mixed with peat raised the pH and reduced pyrite dissolution while peat alone was similar to the controls and did not halt metal and acid release. High throughput 16S rRNA gene sequencing identified populations most similar to characterized acidophiles in the control and peat treated incubations while the acidophilic like populations were altered in the calcium carbonate alone and calcium carbonate plus peat treated acid sulfate soils. Coupled with the geochemistry data, it was suggested that the acidophiles were inactivated by the high pH in the presence of calcium carbonate but catalyzed pyrite dissolution in the controls and peat incubations. In conclusion, the anaerobic conditions during winter would likely be sufficient to mitigate acid production and metal release from acid sulfate soils and in the summer, treatment with calcium carbonate was the best mitigation method.", "doi": "10.1016/j.scitotenv.2017.12.287", "pmid": "29287211", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(17)33720-8"}, {"db": "BioProject", "description": "16S rRNA gene raw reads. Community analysis of the microbiome of acid sulfate soils before and after remediation attempts by different treatments.", "key": "PRJNA407753"}], "notes": [], "created": "2018-01-10T09:45:06.241Z", "modified": "2020-01-21T13:56:11.012Z"}, {"entity": "publication", "iuid": "0d4095789678406cba65e6ce25b7b0a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9"}}, "title": "Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.", "authors": [{"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Wang", "given": "Heng", "initials": "H"}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Joven", "given": "Alberto", "initials": "A"}, {"family": "Brito", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2134-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0196703e4df4518b212ed1f3322e811.json"}}, {"family": "Kumar", "given": "Anoop", "initials": "A"}, {"family": "Hameed", "given": "L Shahul", "initials": "LS"}, {"family": "Penrad-Mobayed", "given": "May", "initials": "M"}, {"family": "Yao", "given": "Zeyu", "initials": "Z"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Abbas", "given": "Yamen", "initials": "Y"}, {"family": "Abdullayev", "given": "Ilgar", "initials": "I"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-4624-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85416dce306436ab0c4cdeea22a1f59.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A"}], "type": "journal article", "published": "2017-12-22", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "2286", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome of the Iberian ribbed newt Pleurodeles waltl, a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b and mir-427/430/302, as well as Harbinger DNA transposons carrying the Myb-like proto-oncogene have expanded dramatically in the Pleurodeles waltl genome and are co-expressed during limb regeneration. Moreover, we find that a family of salamander methyltransferases is expressed specifically in adult appendages. Using CRISPR/Cas9 technology to perturb transcription factors, we demonstrate that, unlike the axolotl, Pax3 is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional Pax7 gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates.", "doi": "10.1038/s41467-017-01964-9", "pmid": "29273779", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-01964-9"}, {"db": "pmc", "key": "PMC5741667"}], "notes": [], "created": "2018-01-10T09:44:17.789Z", "modified": "2021-07-07T11:44:07.846Z"}, {"entity": "publication", "iuid": "9ae9f569627e48c0865040cae25491e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ae9f569627e48c0865040cae25491e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ae9f569627e48c0865040cae25491e5"}}, "title": "Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms.", "authors": [{"family": "Pandit", "given": "Santosh", "initials": "S"}, {"family": "Ravikumar", "given": "Vaishnavi", "initials": "V"}, {"family": "Abdel-Haleem", "given": "Alyaa M", "initials": "AM"}, {"family": "Derouiche", "given": "Abderahmane", "initials": "A"}, {"family": "Mokkapati", "given": "V R S S", "initials": "VRSS"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Mineta", "given": "Katsuhiko", "initials": "K"}, {"family": "Gojobori", "given": "Takashi", "initials": "T"}, {"family": "Gao", "given": "Xin", "initials": "X"}, {"family": "Westerlund", "given": "Fredrik", "initials": "F"}, {"family": "Mijakovic", "given": "Ivan", "initials": "I"}], "type": "journal article", "published": "2017-12-22", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": "2599", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Extracellular polymeric substances (EPS) produced by bacteria form a matrix supporting the complex three-dimensional architecture of biofilms. This EPS matrix is primarily composed of polysaccharides, proteins and extracellular DNA. In addition to supporting the community structure, the EPS matrix protects bacterial biofilms from the environment. Specifically, it shields the bacterial cells inside the biofilm, by preventing antimicrobial agents from getting in contact with them, thereby reducing their killing effect. New strategies for disrupting the formation of the EPS matrix can therefore lead to a more efficient use of existing antimicrobials. Here we examined the mechanism of the known effect of vitamin C (sodium ascorbate) on enhancing the activity of various antibacterial agents. Our quantitative proteomics analysis shows that non-lethal concentrations of vitamin C inhibit bacterial quorum sensing and other regulatory mechanisms underpinning biofilm development. As a result, the EPS biosynthesis in reduced, and especially the polysaccharide component of the matrix is depleted. Once the EPS content is reduced beyond a critical point, bacterial cells get fully exposed to the medium. At this stage, the cells are more susceptible to killing, either by vitamin C-induced oxidative stress as reported here, or by other antimicrobials or treatments.", "doi": "10.3389/fmicb.2017.02599", "pmid": "29317857", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5748153"}], "notes": [], "created": "2020-01-27T22:43:58.690Z", "modified": "2024-01-16T13:46:32.429Z"}, {"entity": "publication", "iuid": "dac2b3f82e9044b1a7d6ab522e8b03f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dac2b3f82e9044b1a7d6ab522e8b03f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dac2b3f82e9044b1a7d6ab522e8b03f6"}}, "title": "Common founder effects of hereditary hemochromatosis, Wilson\u00b4s disease, the long QT syndrome and autosomal recessive deafness caused by two novel mutations in the WHRN and TMC1 genes.", "authors": [{"family": "Olsson", "given": "K Sigvard", "initials": "KS"}, {"family": "W\u00e5linder", "given": "Olof", "initials": "O"}, {"family": "Jansson", "given": "Ulf", "initials": "U"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Raha-Chowdhury", "given": "Ruma", "initials": "R"}, {"family": "Williams", "given": "Roger", "initials": "R"}], "type": "journal article", "published": "2017-12-19", "journal": {"title": "Hereditas", "issn": "1601-5223", "volume": "154", "issue": "1", "pages": "16", "issn-l": "0018-0661"}, "abstract": "Genealogy and molecular genetic studies of a Swedish river valley population resulted in a large pedigree, showing that the hereditary hemochromatosis (HH) HFE/p.C282Y mutation is inherited with other recessive disorders such as Wilson\u00b4s disease (WND), a rare recessive disorder of copper overload. The population also contain individuals with the Swedish long QT syndrome (LQTS1) founder mutation (KCNQ1/p.Y111C) which in homozygotes causes the Jervell & Lange Nielsen syndrome (JLNS) and hearing loss (HL).Aims of the study were to test whether the Swedish long QT founder mutation originated in an ancestral HFE family and if carriers had an increased risk for hemochromatosis (HH), a treatable disorder. We also aimed to identify the pathogenic mutation causing the hearing loss disorder segregating in the pedigree.\n\nLQTS patients were asked about their ancestry and possible origin in a HH family. They were also offered a predictive testing for the HFE genotype. Church books were screened for families with hearing loss. One HH family had two members with hearing loss, who underwent molecular genetic analysis of the LQTS founder mutation, connexin 26 and thereafter exome sequencing. Another family with hearing loss in repeat generations was also analyzed for connexin 26 and underwent exome sequencing.\n\nOf nine LQTS patients studied, four carried a HFE mutation (two p.C282Y, two p.H63D), none was homozygous. Three LQTS patients confirmed origin in a female founder ( b 1694, identical to AJ b 1694, a HFE pedigree member from the Fax river. Her descent of 44 HH families, included also 29 families with hearing loss (HL) suggesting JLNS. Eleven LQTS probands confirmed origin in a second founder couple (b 1614/1605) in which the woman b 1605 was identical to a HFE pedigree member from the Fj\u00e4llsj\u00f6 river. In her descent there were not only 64 HH, six WND families, one JLNS, but also 48 hearing loss families. Most hearing loss was non syndromic and caused by founder effects of the late 16 th century. One was of Swedish origin carrying the WHRN, c.1977delC, (p.S660Afs*30) mutation, the other was a TMC1(NM_138691),c.1814T>C,(p.L605P) mutation, possibly of Finnish origin.\n\nDeep human HFE genealogies show HFE to be associated with other genetic disorders like Wilson\u00b4s disease, LQTS, JLNS, and autosomal recessive hearing loss. Two new homozygous HL mutations in WHRN/p.S660Afs*30 and TMC1/p.L605P were identified,none of them previously reported from Scandinavia. The rarity of JLNS was possibly caused by miscarriage or intrauterine death. Most hearing loss (81.7%) was seen after 1844 when first cousin marriages were permitted. However, only 10 (10.3%) came from 1st cousin unions and only 2 (2.0 %) was born out of wedlock.", "doi": "10.1186/s41065-017-0052-2", "pmid": "29270100", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "52"}, {"db": "pmc", "key": "PMC5735936"}], "notes": [], "created": "2018-10-29T14:32:23.507Z", "modified": "2021-06-21T14:58:04.795Z"}, {"entity": "publication", "iuid": "63ef8af7a9eb43c2837e989c5f0510a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63ef8af7a9eb43c2837e989c5f0510a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63ef8af7a9eb43c2837e989c5f0510a5"}}, "title": "A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis", "authors": [{"family": "Bohman", "given": "Anton", "initials": "A"}, {"family": "Juodakis", "given": "Julius", "initials": "J"}, {"family": "Oscarsson", "given": "Martin", "initials": "M"}, {"family": "Bacelis", "given": "Jonas", "initials": "J"}, {"family": "Bende", "given": "Mats", "initials": "M"}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2017-12-18", "journal": {"volume": "12", "issn": "1932-6203", "issue": "12", "pages": "e0185244", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0185244", "pmid": "29253858", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "EGA", "description": "sequence reads", "key": "EGAD00010001447"}], "notes": [], "created": "2018-01-02T15:37:55.021Z", "modified": "2020-01-21T13:56:12.063Z"}, {"entity": "publication", "iuid": "80ee676ab40e477a82e1d09e11627d6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80ee676ab40e477a82e1d09e11627d6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80ee676ab40e477a82e1d09e11627d6b"}}, "title": "A chemical screen identifies trifluoperazine as an inhibitor of glioblastoma growth.", "authors": [{"family": "Pinheiro", "given": "Tiago", "initials": "T"}, {"family": "Otrocka", "given": "Magdalena", "initials": "M"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Rraklli", "given": "Vilma", "initials": "V"}, {"family": "Holmberg", "given": "Johan", "initials": "J"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K"}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Kirkham", "given": "Matthew", "initials": "M"}], "type": "journal article", "published": "2017-12-16", "journal": {"title": "Biochem. Biophys. Res. Commun.", "issn": "1090-2104", "issn-l": "0006-291X", "volume": "494", "issue": "3-4", "pages": "477-483"}, "abstract": "Glioblastoma (GBM) is regarded as the most common malignant brain tumor but treatment options are limited. Thus, there is an unmet clinical need for compounds and corresponding targets that could inhibit GBM growth. We screened a library of 80 dopaminergic ligands with the aim of identifying compounds capable of inhibiting GBM cell line proliferation and survival. Out of 45 active compounds, 8 were further validated. We found that the dopamine receptor D2 antagonist trifluoperazine 2HCl inhibits growth and proliferation of GBM cells in a dose dependent manner. Trifluoperazine's inhibition of GBM cells is cell line dependent and correlates with variations in dopamine receptor expression profile. We conclude that components of the dopamine receptor signaling pathways are potential targets for pharmacological interventions of GBM growth.", "doi": "10.1016/j.bbrc.2017.10.106", "pmid": "29066348", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0006-291X(17)32084-3"}], "notes": [], "created": "2017-11-14T12:36:05.553Z", "modified": "2025-10-17T13:04:29.061Z"}, {"entity": "publication", "iuid": "6322930a56bd4c78bf88ce2ea9b3ab7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6322930a56bd4c78bf88ce2ea9b3ab7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6322930a56bd4c78bf88ce2ea9b3ab7f"}}, "title": "Targeting tumor cells based on Phosphodiesterase 3A expression.", "authors": [{"family": "Nazir", "given": "Madiha", "initials": "M"}, {"family": "Senkowski", "given": "Wojciech", "initials": "W"}, {"family": "Nyberg", "given": "Frida", "initials": "F"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}], "type": "journal article", "published": "2017-12-15", "journal": {"title": "Exp. Cell Res.", "issn": "1090-2422", "volume": "361", "issue": "2", "pages": "308-315", "issn-l": "0014-4827"}, "abstract": "We and others have previously reported a correlation between high phosphodiesterase 3A (PDE3A) expression and selective sensitivity to phosphodiesterase (PDE) inhibitors. This indicates that PDE3A could serve both as a drug target and a biomarker of sensitivity to PDE3 inhibition. In this report, we explored publicly available mRNA gene expression data to identify cell lines with different PDE3A expression. Cell lines with high PDE3A expression showed marked in vitro sensitivity to PDE inhibitors zardaverine and quazinone, when compared with those having low PDE3A expression. Immunofluorescence and immunohistochemical stainings were in agreement with PDE3A mRNA expression, providing suitable alternatives for biomarker analysis of clinical tissue specimens. Moreover, we here demonstrate that tumor cells from patients with ovarian carcinoma show great variability in PDE3A protein expression and that level of PDE3A expression is correlated with sensitivity to PDE inhibition. Finally, we demonstrate that PDE3A is highly expressed in subsets of patient tumor cell samples from different solid cancer diagnoses and expressed at exceptional levels in gastrointestinal stromal tumor (GIST) specimens. Importantly, vulnerability to PDE3 inhibitors has recently been associated with co-expression of PDE3A and Schlafen family member 12 (SLFN12). We here demonstrate that high expression of PDE3A in clinical specimens, at least on the mRNA level, seems to be frequently associated with high SLFN12 expression. In conclusion, PDE3A seems to be both a promising biomarker and drug target for individualized drug treatment of various cancers.", "doi": "10.1016/j.yexcr.2017.10.032", "pmid": "29107068", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4827(17)30580-3"}], "notes": [], "created": "2020-12-10T12:22:27.451Z", "modified": "2025-10-17T13:05:08.630Z"}, {"entity": "publication", "iuid": "a2f292fd15964c09bf55b71f9a64af47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2f292fd15964c09bf55b71f9a64af47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2f292fd15964c09bf55b71f9a64af47"}}, "title": "Discovery of the fourth mobile sulfonamide resistance gene.", "authors": [{"family": "Razavi", "given": "Mohammad", "initials": "M"}, {"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "Gillings", "given": "Michael R", "initials": "MR"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Joakim Larsson", "given": "D G", "initials": "DG"}], "type": "journal article", "published": "2017-12-15", "journal": {"volume": "5", "issn": "2049-2618", "issue": "1", "pages": "160", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Over the past 75\u00a0years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.\n\nUp to 89% of identified open reading frames encode known resistance genes, or variations thereof (>\u20091000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.\n\nOur findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.", "doi": "10.1186/s40168-017-0379-y", "pmid": "29246178", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0379-y"}, {"db": "pmc", "key": "PMC5732528"}, {"db": "BioProject", "description": "Sediment metagenome. Amplicon sequencing of gene cassettes from polluted sediments.", "key": "PRJNA400874"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv2 dihydropteroate synthase (sul4) and quaternary ammonium compound efflux genes, complete cds", "key": "MG649394"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv3 OXA-2-like protein gene, complete cds; and QacE delta gene, partial cds", "key": "MG649395"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv4 dihydrofolate reductase (drfb2) gene, partial cds; arr-6-like protein gene, complete cds; and class 1 integron integrase gene, partial cds", "key": "MG649396"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv5 class 1 integron integrase gene, partial cds; and OXA-10-like protein gene, complete cds", "key": "MG649397"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv6 chloramphenicol O-acetyltransferase gene, complete cds", "key": "MG649398"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv7 QacE delta gene, partial cds; and OXA-46-like protein gene, complete cds", "key": "MG649399"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv9 OXA-2-like protein gene, complete cds; and QacE delta gene, partial cds", "key": "MG649400"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv10 CARB-PSE gene, partial cds; and dfrA-like protein gene, complete cds", "key": "MG649401"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv8 ISCR20-like protein, dihydropteroate synthase (sul4), and hypothetical protein genes, complete cds", "key": "MG649402"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv11 qacE gene, partial cds; and molecular chaperone, qacE, and aminoglycoside nucleotidyltransferase AadA genes, complete cds", "key": "MG649403"}], "notes": [], "created": "2018-01-10T09:45:03.356Z", "modified": "2020-01-21T13:56:11.019Z"}, {"entity": "publication", "iuid": "fe02c4674f4d493aa4b9f694a14029a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe02c4674f4d493aa4b9f694a14029a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe02c4674f4d493aa4b9f694a14029a8"}}, "title": "Cancer risk susceptibility loci in a Swedish population.", "authors": [{"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Mahdessian", "given": "Hovsep", "initials": "H"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2017-12-15", "journal": {"volume": "8", "issn": "1949-2553", "issue": "66", "pages": "110300-110310", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "A germline mutation in cancer predisposing genes is known to increase the risk of more than one tumor type. In order to find loci associated with many types of cancer, a genome-wide association study (GWAS) was conducted, and 3,555 Swedish cancer cases and 15,581 controls were analyzed for 226,883 SNPs. The study used haplotype analysis instead of single SNP analysis in order to find putative founder effects. Haplotype association studies identified seven risk loci associated with cancer risk, on chromosomes 1, 7, 11, 14, 16, 17 and 21. Four of the haplotypes, on chromosomes 7, 14, 16 and 17, were confirmed in Swedish familial cancer cases. It was possible to perform exome sequencing in one patient for each of those four loci. No clear disease-causing exonic mutation was found in any of the four loci. Some of the candidate loci hold several cancer genes, suggesting that the risk associated with one locus could involve more than one gene associated with cancer risk. In summary, this study identified seven novel candidate loci associated with cancer risk. It was also suggested that cancer risk at one locus could depend on multiple contributing risk mutations/genes.", "doi": "10.18632/oncotarget.22687", "pmid": "29299148", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "22687"}, {"db": "pmc", "key": "PMC5746383"}], "notes": [], "created": "2018-01-09T13:55:52.931Z", "modified": "2021-06-21T15:01:18.619Z"}, {"entity": "publication", "iuid": "ee0a6224e2a94d9ab542f3537deca12a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee0a6224e2a94d9ab542f3537deca12a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee0a6224e2a94d9ab542f3537deca12a"}}, "title": "Gene expression and risk of leukemic transformation in myelodysplasia.", "authors": [{"family": "Shiozawa", "given": "Yusuke", "initials": "Y", "orcid": "0000-0001-9814-9230", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dc8c5586f854ce38bd2671a7e93285b.json"}}, {"family": "Malcovati", "given": "Luca", "initials": "L", "orcid": "0000-0002-1460-1611", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac37858898774ff29209add33a79fd48.json"}}, {"family": "Gall\u00ec", "given": "Anna", "initials": "A", "orcid": "0000-0002-7912-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2e7029ae6f442b2a8ea6947f9f1989e.json"}}, {"family": "Pellagatti", "given": "Andrea", "initials": "A", "orcid": "0000-0002-6122-0221", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f0150ad6f456bb79b30f7acb2ed2a.json"}}, {"family": "Karimi", "given": "Mohsen", "initials": "M", "orcid": "0000-0002-8946-6944", "researcher": {"href": "https://publications.scilifelab.se/researcher/8353eda283bb4e1391261269d80f9f7f.json"}}, {"family": "Sato-Otsubo", "given": "Aiko", "initials": "A"}, {"family": "Sato", "given": "Yusuke", "initials": "Y", "orcid": "0000-0003-0913-7815", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9da90ff6344440cba83f530ffcddf8e.json"}}, {"family": "Suzuki", "given": "Hiromichi", "initials": "H", "orcid": "0000-0003-1434-7104", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ff5a7c284d4ebea1a03fc0948cc27d.json"}}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T"}, {"family": "Yoshida", "given": "Kenichi", "initials": "K", "orcid": "0000-0001-5189-5105", "researcher": {"href": "https://publications.scilifelab.se/researcher/c92b02588d804081a867f4489139affd.json"}}, {"family": "Shiraishi", "given": "Yuichi", "initials": "Y", "orcid": "0000-0001-6144-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/a807a9117617477196d55d150e62b437.json"}}, {"family": "Chiba", "given": "Kenichi", "initials": "K"}, {"family": "Makishima", "given": "Hideki", "initials": "H"}, {"family": "Boultwood", "given": "Jacqueline", "initials": "J", "orcid": "0000-0002-4330-2928", "researcher": {"href": "https://publications.scilifelab.se/researcher/389b184fad7048daaa8bd0466b298374.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-0602-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/f28d2116631f4f4cb286be690e0cf896.json"}}, {"family": "Miyano", "given": "Satoru", "initials": "S", "orcid": "0000-0002-1753-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e65512044c4965863ed41ef8aadd31.json"}}, {"family": "Cazzola", "given": "Mario", "initials": "M", "orcid": "0000-0001-6984-8817", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85ab5f89c604aad824a42107184f196.json"}}, {"family": "Ogawa", "given": "Seishi", "initials": "S", "orcid": "0000-0002-7778-5374", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcc3b1b5f3045a7acd123222445449d.json"}}], "type": "journal article", "published": "2017-12-14", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "130", "issue": "24", "pages": "2642-2653", "issn-l": "0006-4971"}, "abstract": "Myelodysplastic syndromes (MDSs) are a heterogeneous group of clonal hematopoietic disorders with a highly variable prognosis. To identify a gene expression-based classification of myelodysplasia with biological and clinical relevance, we performed a comprehensive transcriptomic analysis of myeloid neoplasms with dysplasia using transcriptome sequencing. Unsupervised clustering of gene expression data of bone marrow CD34 + cells from 100 patients identified 2 subgroups. The first subtype was characterized by increased expression of genes related to erythroid/megakaryocytic (EMK) lineages, whereas the second subtype showed upregulation of genes related to immature progenitor (IMP) cells. Compared with the first so-called EMK subtype, the IMP subtype showed upregulation of many signaling pathways and downregulation of several pathways related to metabolism and DNA repair. The IMP subgroup was associated with a significantly shorter survival in both univariate (hazard ratio [HR], 5.0; 95% confidence interval [CI], 1.8-14; P = .002) and multivariate analysis (HR, 4.9; 95% CI, 1.3-19; P = .02). Leukemic transformation was limited to the IMP subgroup. The prognostic significance of our classification was validated in an independent cohort of 183 patients. We also constructed a model to predict the subgroups using gene expression profiles of unfractionated bone marrow mononuclear cells (BMMNCs). The model successfully predicted clinical outcomes in a test set of 114 patients with BMMNC samples. The addition of our classification to the clinical model improved prediction of patient outcomes. These results indicated biological and clinical relevance of our gene expression-based classification, which will improve risk prediction and treatment stratification of MDS.", "doi": "10.1182/blood-2017-05-783050", "pmid": "29097382", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)32644-6"}], "notes": [], "created": "2018-10-31T13:09:22.884Z", "modified": "2021-06-21T14:57:20.742Z"}, {"entity": "publication", "iuid": "105ffce64b2d49f09088d4300f162663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/105ffce64b2d49f09088d4300f162663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/105ffce64b2d49f09088d4300f162663"}}, "title": "CELSR2 is a candidate susceptibility gene in idiopathic scoliosis", "authors": [{"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Grauers", "given": "Anna", "initials": "A"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Escher", "given": "Stefan A", "initials": "SA"}, {"family": "Danielsson", "given": "Aina", "initials": "A"}, {"family": "Simony", "given": "Ane", "initials": "A"}, {"family": "Andersen", "given": "Mikkel", "initials": "M"}, {"family": "Christensen", "given": "Steen Bach", "initials": "SB"}, {"family": "\u00c5kesson", "given": "Kristina", "initials": "K"}, {"family": "Kou", "given": "Ikuyo", "initials": "I"}, {"family": "Khanshour", "given": "Anas M", "initials": "AM"}, {"family": "Ohlin", "given": "Acke", "initials": "A"}, {"family": "Wise", "given": "Carol", "initials": "C"}, {"family": "Ikegawa", "given": "Shiro", "initials": "S"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}], "type": "journal-article", "published": "2017-12-14", "journal": {"volume": "12", "issn": "1932-6203", "issue": "12", "pages": "e0189591", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0189591", "pmid": "29240829", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "ENA", "description": "sequences", "key": "PRJEB22953"}], "notes": [], "created": "2018-01-02T15:37:54.529Z", "modified": "2020-01-21T13:56:12.055Z"}, {"entity": "publication", "iuid": "8f6ae3f4a79d4fa49e24d158da645cd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f6ae3f4a79d4fa49e24d158da645cd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f6ae3f4a79d4fa49e24d158da645cd7"}}, "title": "Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.", "authors": [{"family": "Zhang", "given": "Wang", "initials": "W"}, {"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "van Domselaar", "given": "Robert", "initials": "R"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Noyan", "given": "Kajsa", "initials": "K"}, {"family": "Russom", "given": "Aman", "initials": "A"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U"}], "type": "journal article", "published": "2017-12-12", "journal": {"volume": null, "issn": "2352-3964", "issue": null, "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "A small subset of HIV-1 infected individuals, the \"Elite Controllers\" (EC), can control viral replication and restrain progression to immunodeficiency without antiretroviral therapy (ART). In this study, a cross-sectional transcriptomics and targeted proteomics analysis were performed in a well-defined Swedish cohort of untreated EC (n=19), treatment na\u00efve patients with viremia (VP, n=32) and HIV-1-negative healthy controls (HC, n=23). The blood transcriptome identified 151 protein-coding genes that were differentially expressed (DE) in VP compared to EC. Genes like CXCR6 and SIGLEC1 were downregulated in EC compared to VP. A definite distinction in gene expression between males and females among all patient-groups were observed. The gene expression profile between female EC and the healthy females was similar but did differ between male EC and healthy males. At targeted proteomics analysis, 90% (29/32) of VPs clustered together while EC and HC clustered separately from VP. Among the soluble factors, 33 were distinctive to be statistically significant (False discovery rate=0.02). Cell surface receptor signaling pathway, programmed cell death, response to cytokine and cytokine-mediated signaling seem to synergistically play an essential role in HIV-1 control in EC.", "doi": "10.1016/j.ebiom.2017.11.031", "pmid": "29269040", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(17)30473-5"}, {"db": "BioProject", "description": "Transcriptomic analysis to map mechanisms of viral replication control in HIV-1 positive Elite Controllers", "key": "PRJNA420459"}, {"db": "SRA", "description": "Transcriptomic analysis to map mechanisms of viral replication control in HIV-1 positive Elite Controllers", "key": "SRP125882"}], "notes": [], "created": "2018-01-10T09:45:01.949Z", "modified": "2020-01-21T13:56:11.033Z"}, {"entity": "publication", "iuid": "1bc051a18e1844c1bab6b323a7d23dc3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1bc051a18e1844c1bab6b323a7d23dc3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1bc051a18e1844c1bab6b323a7d23dc3"}}, "title": "Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells", "authors": [{"family": "Bostr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Sramkova", "given": "Zuzana", "initials": "Z"}, {"family": "Sala\u0161ov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Johard", "given": "Helena", "initials": "H"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Fedr", "given": "Radek", "initials": "R"}, {"family": "Marks", "given": "Carolyn", "initials": "C"}, {"family": "Medalov\u00e1", "given": "Ji\u0159ina", "initials": "J"}, {"family": "Sou\u010dek", "given": "Karel", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Bryja", "given": "V\u00edt\u011bzslav", "initials": "V"}, {"family": "Sekyrova", "given": "Petra", "initials": "P"}, {"family": "Altun", "given": "Mikael", "initials": "M"}, {"family": "And\u00e4ng", "given": "Michael", "initials": "M"}], "type": "journal-article", "published": "2017-12-11", "journal": {"volume": "12", "issn": "1932-6203", "issue": "12", "pages": "e0188772", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0188772", "pmid": "29228002", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "GEO", "description": "sequences", "key": "GSE104736"}], "notes": [], "created": "2018-01-10T19:44:34.675Z", "modified": "2021-07-05T16:23:51.093Z"}, {"entity": "publication", "iuid": "24b048c24f744e429bced723b28876bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24b048c24f744e429bced723b28876bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24b048c24f744e429bced723b28876bc"}}, "title": "Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells", "authors": [{"family": "Ma\u2019ayeh", "given": "Showgy Y", "initials": "SY"}, {"family": "Liu", "given": "Jingyi", "initials": "J"}, {"family": "Peirasmaki", "given": "Dimitra", "initials": "D"}, {"family": "H\u00f6rnaeus", "given": "Katarina", "initials": "K"}, {"family": "Bergstr\u00f6m Lind", "given": "Sara", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal-article", "published": "2017-12-11", "journal": {"volume": "11", "issn": "1935-2735", "issue": "12", "pages": "e0006120", "title": "PLoS Negl Trop Dis", "issn-l": "1935-2727"}, "abstract": null, "doi": "10.1371/journal.pntd.0006120", "pmid": "29228011", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:27:01.260Z", "modified": "2020-01-21T13:56:12.047Z"}, {"entity": "publication", "iuid": "8ed0fa619a97453eb7cbae0f3f3c69bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed0fa619a97453eb7cbae0f3f3c69bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed0fa619a97453eb7cbae0f3f3c69bc"}}, "title": "Genomic and phenotypic characteristics of Swedish C. jejuni water isolates.", "authors": [{"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Johansson", "given": "Cecilia", "initials": "C"}, {"family": "Skarp", "given": "Astrid", "initials": "A"}, {"family": "Kaden", "given": "Ren\u00e9", "initials": "R"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Rautelin", "given": "Hilpi", "initials": "H"}], "type": "journal article", "published": "2017-12-07", "journal": {"volume": "12", "issn": "1932-6203", "issue": "12", "pages": "e0189222", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens. Further genomic characterization revealed that these isolates had potential for arsenic resistance (due to presence of arsB gene in all isolates), an anaerobic dimethyl sulfoxide oxidoreductase (in three isolates) and lacked the MarR-type transcriptional regulator gene rrpB (in all but one isolate) earlier shown to be involved in better survival under oxidative and aerobic stress. As putative virulence factors were concerned, there were differences between the water isolates in the presence of genes coding for cytolethal distending toxin (cdtABC), Type VI secretion system and sialylated LOS, as well as in biofilm formation. However, all isolates were motile and could adhere to and invade the human HT-29 colon cancer cell line in vitro and induce IL-8 secretion suggesting potential to infect humans. This is, to the best of our knowledge, the first study where C. jejuni water isolates have been characterized using whole genome sequencing and phenotypical assays. We found differences and shared traits among the isolates but also potential to infect humans.", "doi": "10.1371/journal.pone.0189222", "pmid": "29216271", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-22124"}, {"db": "pmc", "key": "PMC5720728"}], "notes": [], "created": "2018-10-29T09:14:49.934Z", "modified": "2018-11-14T09:45:09.488Z"}, {"entity": "publication", "iuid": "a1e96d19911348b0881541e490d67a58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1e96d19911348b0881541e490d67a58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1e96d19911348b0881541e490d67a58"}}, "title": "A Unique ISR Program Determines Cellular Responses to Chronic Stress.", "authors": [{"family": "Guan", "given": "Bo-Jhih", "initials": "BJ"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Jobava", "given": "Raul", "initials": "R"}, {"family": "Elroy-Stein", "given": "Orna", "initials": "O"}, {"family": "Valasek", "given": "Leos S", "initials": "LS"}, {"family": "Cargnello", "given": "Marie", "initials": "M"}, {"family": "Gao", "given": "Xing-Huang", "initials": "XH"}, {"family": "Krokowski", "given": "Dawid", "initials": "D"}, {"family": "Merrick", "given": "William C", "initials": "WC"}, {"family": "Kimball", "given": "Scot R", "initials": "SR"}, {"family": "Komar", "given": "Anton A", "initials": "AA"}, {"family": "Koromilas", "given": "Antonis E", "initials": "AE"}, {"family": "Wynshaw-Boris", "given": "Anthony", "initials": "A"}, {"family": "Topisirovic", "given": "Ivan", "initials": "I"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Hatzoglou", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2017-12-07", "journal": {"volume": "68", "issn": "1097-4164", "issue": "5", "pages": "885-900.e6", "title": "Mol. Cell", "issn-l": "1097-2765"}, "abstract": "The integrated stress response (ISR) is a homeostatic mechanism induced by endoplasmic reticulum (ER) stress. In acute/transient ER stress, decreased global protein synthesis and increased uORF mRNA translation are followed by normalization of protein synthesis. Here, we report a dramatically different response during chronic ER stress. This chronic ISR program is characterized by persistently elevated uORF mRNA translation and concurrent gene expression reprogramming, which permits simultaneous stress sensing and proteostasis. The program includes PERK-dependent switching to an eIF3-dependent translation initiation mechanism, resulting in partial, but not complete, translational recovery, which, together with transcriptional reprogramming, selectively bolsters expression of proteins with ER functions. Coordination of transcriptional and translational reprogramming prevents ER dysfunction and inhibits \"foamy cell\" development, thus establishing a molecular basis for understanding human diseases associated with ER dysfunction.", "doi": "10.1016/j.molcel.2017.11.007", "pmid": "29220654", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(17)30842-0"}, {"db": "pmc", "key": "PMC5730339"}, {"db": "mid", "key": "NIHMS919694"}, {"db": "GEO", "description": "A unique ISR Program Determines Cellular Responses to Chronic Stress", "key": "GSE90070"}], "notes": [], "created": "2018-01-10T09:45:07.638Z", "modified": "2020-01-21T13:56:11.026Z"}, {"entity": "publication", "iuid": "a7236b8ef8c24dd4b49db1bbbcd151a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7236b8ef8c24dd4b49db1bbbcd151a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7236b8ef8c24dd4b49db1bbbcd151a6"}}, "title": "Magnesium induces preconditioning of the neonatal brain via profound mitochondrial protection", "authors": [{"family": "Koning", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-9521-2994", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6ad14f86e5d40b4ae6c17cd70b5568a.json"}}, {"family": "Leverin", "given": "Anna Lena", "initials": "AL"}, {"family": "Nair", "given": "Syam", "initials": "S"}, {"family": "Schwendimann", "given": "Leslie", "initials": "L"}, {"family": "Ek", "given": "Joakim", "initials": "J"}, {"family": "Carlsson", "given": "Ylva", "initials": "Y"}, {"family": "Gressens", "given": "Pierre", "initials": "P"}, {"family": "Thornton", "given": "Claire", "initials": "C"}, {"family": "Wang", "given": "Xiaoyang", "initials": "X"}, {"family": "Mallard", "given": "Carina", "initials": "C"}, {"family": "Hagberg", "given": "Henrik", "initials": "H"}], "type": "journal-article", "published": "2017-12-05", "journal": {"volume": "39", "issn": "0271-678X", "issue": "6", "pages": "1038-1055", "title": "J Cereb Blood Flow Metab", "issn-l": "0271-678X"}, "abstract": "Magnesium sulphate (MgSO4) given to women in preterm labor reduces cerebral palsy in their offspring but the mechanism behind this protection is unclear, limiting its effective, safe clinical implementation. Previous studies suggest that MgSO4 is not neuroprotective if administered during or after the insult, so we hypothesised that MgSO4 induces preconditioning in the immature brain. Therefore, we administered MgSO4 at various time-points before/after unilateral hypoxia-ischemia (HI) in seven-day-old rats. We found that MgSO4 treatment administered as a bolus between 6 days and 12\u2009h prior to HI markedly reduced the brain injury, with maximal protection achieved by 1.1\u2009mg/g MgSO4 administered 24\u2009h before HI. As serum magnesium levels returned to baseline before the induction of HI, we ascribed this reduction in brain injury to preconditioning. Cerebral blood flow was unaffected, but mRNAs/miRNAs involved in mitochondrial function and metabolism were modulated by MgSO4. Metabolomic analysis (H+-NMR) disclosed that MgSO4 attenuated HI-induced increases in succinate and prevented depletion of high-energy phosphates. MgSO4 pretreatment preserved mitochondrial respiration, reducing ROS production and inflammation after HI. Therefore, we propose that MgSO4 evokes preconditioning via induction of mitochondrial resistance and attenuation of inflammation.", "doi": "10.1177/0271678x17746132", "pmid": "29206066", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:31:28.630Z", "modified": "2025-10-17T13:03:59.228Z"}, {"entity": "publication", "iuid": "812369ae8ecd493db7a2b7cb3c8387f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/812369ae8ecd493db7a2b7cb3c8387f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/812369ae8ecd493db7a2b7cb3c8387f9"}}, "title": "Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff ( Phylloscopus collybita abietinus/P. tristis).", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Kalsoom", "given": "Faheema", "initials": "F"}, {"family": "Shipilina", "given": "Daria", "initials": "D"}, {"family": "Marova", "given": "Irina", "initials": "I"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2017-12-04", "journal": {"volume": "7", "issn": "2160-1836", "issue": "12", "pages": "3983-3998", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European ( Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)-two recently diverged species which differ in morphology, plumage, song, habitat, and migration-to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that postdivergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species.", "doi": "10.1534/g3.117.300152", "pmid": "29054864", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "g3.117.300152"}, {"db": "pmc", "key": "PMC5714495"}], "notes": [], "created": "2017-11-03T16:22:15.701Z", "modified": "2021-06-21T14:59:08.098Z"}, {"entity": "publication", "iuid": "f51fe47e221a40f89e4936c9689a725c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f51fe47e221a40f89e4936c9689a725c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f51fe47e221a40f89e4936c9689a725c"}}, "title": "The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/c434ae7226ff49e8b00a33c37a46dd60.json"}}, {"family": "Sun", "given": "Zhi", "initials": "Z"}, {"family": "Campbell", "given": "David S", "initials": "DS"}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}}, {"family": "Overall", "given": "Christopher M", "initials": "CM"}, {"family": "Aebersold", "given": "Ruedi", "initials": "R"}, {"family": "Moritz", "given": "Robert L", "initials": "RL", "orcid": "0000-0002-3216-9447", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aaa7d54f7de41cf915b47e8037c15cf.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications.scilifelab.se/researcher/aada71c99b5b4364855e193e3a719d39.json"}}], "type": "historical article", "published": "2017-12-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "16", "issue": "12", "pages": "4299-4310", "issn-l": "1535-3893"}, "abstract": "Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields \u223c43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely mapping peptides of nine amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target \u223c2000 proteins. Finally, we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.", "doi": "10.1021/acs.jproteome.7b00467", "pmid": "28938075", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5864247"}, {"db": "mid", "key": "NIHMS950847"}], "notes": [], "created": "2018-10-31T09:22:30.694Z", "modified": "2021-07-08T12:07:34.326Z"}, {"entity": "publication", "iuid": "ded108dcb61c4041ae82cdc1a250c08a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ded108dcb61c4041ae82cdc1a250c08a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ded108dcb61c4041ae82cdc1a250c08a"}}, "title": "Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies).", "authors": [{"family": "Dobrowolska", "given": "Izabela", "initials": "I"}, {"family": "Businge", "given": "Edward", "initials": "E"}, {"family": "Abreu", "given": "Ilka N", "initials": "IN"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Egertsdotter", "given": "Ulrika", "initials": "U"}], "type": "journal article", "published": "2017-12-01", "journal": {"title": "Tree Physiol", "issn": "1758-4469", "volume": "37", "issue": "12", "pages": "1752-1766", "issn-l": "0829-318X"}, "abstract": "Transcriptome, metabolome and histological profiling were performed on normal and aberrant somatic embryo germinants of Norway spruce (Picea abies L. Karst) providing a simplistic systems biology description of conifer germination. Aberrant germinants (AGs) formed periderm-like tissue at the apical pole and lacked shoot growth above the cotyledons. Transcriptome profiling (RNA-Sequencing) revealed a total of 370 differentially expressed genes at \u22651 or \u2264-1 log2-fold change, where 92% were down-regulated in AGs compared with normal germinants (NGs). Genes associated with shoot apical meristem formation were down-regulated in AGs, or not differentially expressed between AGs and NGs. Genes involved in hormone signaling and transport were also down-regulated. Metabolite profiling by gas chromatography-mass spectrometry (MS) and liquid chromatography-MS revealed biochemical difference between AGs and NGs, notably increased levels of sugars including glucose in AGs. Genes involved in glucose signaling were down-regulated and genes involved in starch biosynthesis were up-regulated, suggesting involvement of sugar signaling during late embryo development and germination. The overall results provide new data enabling further studies to confirm potential markers for a normal germination process in conifers.", "doi": "10.1093/treephys/tpx078", "pmid": "28985382", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "3896382"}], "notes": [], "created": "2018-01-09T12:30:08.698Z", "modified": "2025-10-17T13:03:18.419Z"}, {"entity": "publication", "iuid": "69a62f2d2e814f84b417bac2bff59c70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69a62f2d2e814f84b417bac2bff59c70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69a62f2d2e814f84b417bac2bff59c70"}}, "title": "Towards repositioning of quinacrine for treatment of acute myeloid leukemia - Promising synergies and in vivo effects.", "authors": [{"family": "Eriksson", "given": "Anna", "initials": "A"}, {"family": "Chantzi", "given": "Efthymia", "initials": "E"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Gustafsson", "given": "Mats", "initials": "M"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "Leuk Res", "issn": "1873-5835", "volume": "63", "issue": null, "pages": "41-46", "issn-l": null}, "abstract": "We previously reported that the anti-malarial drug quinacrine has potential to be repositioned for treatment of acute myeloid leukemia (AML). As a next step towards clinical use, we assessed the efficacy of quinacrine in an AML-PS mouse model and investigated possible synergistic effects when combining quinacrine with nine other antileukemic compounds in two AML cell lines. Furthermore, we explored the in vivo activity of quinacrine in combination with the widely used AML agent cytarabine. The in vivo use of quinacrine (100mg/kg three times per week for two consecutive weeks) significantly suppressed circulating blast cells at days 30/31 and increased the median survival time (MST). The in vitro drug combination analysis yielded promising synergistic interactions when combining quinacrine with cytarabine, azacitidine and geldanamycin. Finally, combining quinacrine with cytarabine in vivo showed a significant decrease in circulating leukemic blast cells and increased MST compared to the effect of either drug used alone, thus supporting the findings from the in vitro combination experiments. Taken together, the repositioning potential of quinacrine for treatment of AML is reinforced by demonstrating significant in vivo activity and promising synergies when quinacrine is combined with different agents, including cytarabine, the hypomethylating agent azacitidine and HSP-90 inhibitor geldanamycin.", "doi": "10.1016/j.leukres.2017.10.012", "pmid": "29100024", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "S0145-2126(17)30565-9"}], "notes": [], "created": "2020-12-10T12:20:36.874Z", "modified": "2025-10-17T13:05:08.641Z"}, {"entity": "publication", "iuid": "f006469155d6463596d06eebc5f81ae0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f006469155d6463596d06eebc5f81ae0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f006469155d6463596d06eebc5f81ae0"}}, "title": "The oxylipin and endocannabidome responses in acute phase Plasmodium falciparum malaria in children", "authors": [{"family": "Surowiec", "given": "Izabella", "initials": "I"}, {"family": "Gouveia-Figueira", "given": "Sandra", "initials": "S"}, {"family": "Orikiiriza", "given": "Judy", "initials": "J"}, {"family": "Lindquist", "given": "Elisabeth", "initials": "E"}, {"family": "Bonde", "given": "Mari", "initials": "M"}, {"family": "Magambo", "given": "Jimmy", "initials": "J"}, {"family": "Muhinda", "given": "Charles", "initials": "C"}, {"family": "Bergstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Normark", "given": "Johan", "initials": "J"}, {"family": "Trygg", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "16", "issn": "1475-2875", "issue": "1", "pages": null, "title": "Malar. J.", "issn-l": "1475-2875"}, "abstract": null, "doi": "10.1186/s12936-017-2001-y", "pmid": "28886714", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:35:35.894Z", "modified": "2025-10-17T13:03:18.426Z"}, {"entity": "publication", "iuid": "36b0ab5dc4b2438a83cf7164999249d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36b0ab5dc4b2438a83cf7164999249d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36b0ab5dc4b2438a83cf7164999249d8"}}, "title": "The dynamic dimer structure of the chaperone Trigger Factor", "authors": [{"family": "Morgado", "given": "Leonor", "initials": "L"}, {"family": "Burmann", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Sharpe", "given": "Timothy", "initials": "T"}, {"family": "Mazur", "given": "Adam", "initials": "A"}, {"family": "Hiller", "given": "Sebastian", "initials": "S"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-02196-7", "pmid": "29222465", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:31:30.436Z", "modified": "2025-10-17T13:03:59.239Z"}, {"entity": "publication", "iuid": "4b838933f7564dbcbb8d65bfc4f78b19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b838933f7564dbcbb8d65bfc4f78b19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b838933f7564dbcbb8d65bfc4f78b19"}}, "title": "Structural basis for dolichylphosphate mannose biosynthesis", "authors": [{"family": "Gandini", "given": "Rosaria", "initials": "R"}, {"family": "Reichenbach", "given": "Tom", "initials": "T"}, {"family": "Tan", "given": "Tien Chye", "initials": "TC"}, {"family": "Divne", "given": "Christina", "initials": "C"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-00187-2", "pmid": "28743912", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:20.090Z", "modified": "2017-11-09T13:21:29.760Z"}, {"entity": "publication", "iuid": "a3142a603e7a4accb9d367851765f150", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3142a603e7a4accb9d367851765f150.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3142a603e7a4accb9d367851765f150"}}, "title": "Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.", "authors": [{"family": "Ferreira", "given": "Manuel A", "initials": "MA", "orcid": "0000-0001-9059-1825", "researcher": {"href": "https://publications.scilifelab.se/researcher/d27aef5015494b018b22352125c0225d.json"}}, {"family": "Vonk", "given": "Judith M", "initials": "JM"}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H"}, {"family": "Marenholz", "given": "Ingo", "initials": "I"}, {"family": "Tian", "given": "Chao", "initials": "C"}, {"family": "Hoffman", "given": "Joshua D", "initials": "JD"}, {"family": "Helmer", "given": "Quinta", "initials": "Q"}, {"family": "Tillander", "given": "Annika", "initials": "A"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "R\u00fcschendorf", "given": "Franz", "initials": "F", "orcid": "0000-0001-5640-810X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02ac817ef224343ba9d9a9ac7cdc43e.json"}}, {"family": "Esparza-Gordillo", "given": "Jorge", "initials": "J"}, {"family": "Medway", "given": "Chris W", "initials": "CW"}, {"family": "Mountjoy", "given": "Edward", "initials": "E", "orcid": "0000-0002-0626-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/16fc9f5da5c34418a207b9bd468a0403.json"}}, {"family": "Burrows", "given": "Kimberley", "initials": "K"}, {"family": "Hummel", "given": "Oliver", "initials": "O"}, {"family": "Grosche", "given": "Sarah", "initials": "S"}, {"family": "Brumpton", "given": "Ben M", "initials": "BM"}, {"family": "Witte", "given": "John S", "initials": "JS"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Zheng", "given": "Jie", "initials": "J"}, {"family": "Rodr\u00edguez", "given": "Elke", "initials": "E"}, {"family": "Hotze", "given": "Melanie", "initials": "M"}, {"family": "Franke", "given": "Andre", "initials": "A", "orcid": "0000-0003-1530-5811", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffe3df068c4283a8b8b583717e6bb6.json"}}, {"family": "Revez", "given": "Joana A", "initials": "JA"}, {"family": "Beesley", "given": "Jonathan", "initials": "J"}, {"family": "Matheson", "given": "Melanie C", "initials": "MC"}, {"family": "Dharmage", "given": "Shyamali C", "initials": "SC"}, {"family": "Bain", "given": "Lisa M", "initials": "LM"}, {"family": "Fritsche", "given": "Lars G", "initials": "LG"}, {"family": "Gabrielsen", "given": "Maiken E", "initials": "ME"}, {"family": "Balliu", "given": "Brunilda", "initials": "B"}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "AAGC collaborators", "given": "", "initials": ""}, {"family": "BIOS consortium", "given": "", "initials": ""}, {"family": "LifeLines Cohort Study", "given": "", "initials": ""}, {"family": "Nielsen", "given": "Jonas B", "initials": "JB", "orcid": "0000-0002-6654-2852", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e2c20e3817a4c79b8ae7110d197e69d.json"}}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Langhammer", "given": "Arnulf", "initials": "A"}, {"family": "Holmen", "given": "Oddgeir L", "initials": "OL"}, {"family": "L\u00f8set", "given": "Mari", "initials": "M"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ", "orcid": "0000-0001-5645-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a8e1d33146452b87e7e21eb5339f80.json"}}, {"family": "Arnold", "given": "Andreas", "initials": "A"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Schmidt", "given": "Carsten O", "initials": "CO"}, {"family": "Thompson", "given": "Philip J", "initials": "PJ"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Duffy", "given": "David L", "initials": "DL", "orcid": "0000-0002-8875-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/dce1a0fd17154c73b30f23c2a58bd390.json"}}, {"family": "Novak", "given": "Natalija", "initials": "N"}, {"family": "Schulz", "given": "Holger", "initials": "H"}, {"family": "Karrasch", "given": "Stefan", "initials": "S"}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Melles", "given": "Ronald B", "initials": "RB"}, {"family": "Hinds", "given": "David A", "initials": "DA", "orcid": "0000-0002-4911-803X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba56969917d14df0bd923a54ce9f911d.json"}}, {"family": "H\u00fcbner", "given": "Norbert", "initials": "N", "orcid": "0000-0002-1218-6223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84f34739c743838cea107286522e42.json"}}, {"family": "Weidinger", "given": "Stephan", "initials": "S"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Jorgenson", "given": "Eric", "initials": "E", "orcid": "0000-0002-5829-8191", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ef095c3de94bbc884d80c8949d16f5.json"}}, {"family": "Lee", "given": "Young-Ae", "initials": "YA"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Almqvist", "given": "Catarina", "initials": "C", "orcid": "0000-0002-1045-1898", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7b0899897f046499272a916fd0c6ba5.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH", "orcid": "0000-0001-8567-3252", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd7e0158050a4ab3860e288c4eb9ae87.json"}}, {"family": "Paternoster", "given": "Lavinia", "initials": "L", "orcid": "0000-0003-2514-0889", "researcher": {"href": "https://publications.scilifelab.se/researcher/826f9852c56d4922ab255ab83d26faa8.json"}}], "type": "journal article", "published": "2017-12-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "12", "title": "Nat. Genet.", "pages": "1752-1757", "issn-l": "1061-4036"}, "abstract": "Asthma, hay fever (or allergic rhinitis) and eczema (or atopic dermatitis) often coexist in the same individuals, partly because of a shared genetic origin. To identify shared risk variants, we performed a genome-wide association study (GWAS; n = 360,838) of a broad allergic disease phenotype that considers the presence of any one of these three diseases. We identified 136 independent risk variants (P < 3 \u00d7 10-8), including 73 not previously reported, which implicate 132 nearby genes in allergic disease pathophysiology. Disease-specific effects were detected for only six variants, confirming that most represent shared risk factors. Tissue-specific heritability and biological process enrichment analyses suggest that shared risk variants influence lymphocyte-mediated immunity. Six target genes provide an opportunity for drug repositioning, while for 36 genes CpG methylation was found to influence transcription independently of genetic effects. Asthma, hay fever and eczema partly coexist because they share many genetic risk variants that dysregulate the expression of immune-related genes.", "doi": "10.1038/ng.3985", "pmid": "29083406", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "mid", "key": "EMS74439"}, {"db": "pmc", "key": "PMC5989923"}, {"db": "pii", "key": "ng.3985"}], "notes": [], "created": "2017-11-09T16:02:23.965Z", "modified": "2023-06-19T10:57:00.779Z"}, {"entity": "publication", "iuid": "b0c456eb98294268808bdeeb2a0263c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c456eb98294268808bdeeb2a0263c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c456eb98294268808bdeeb2a0263c0"}}, "title": "Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells", "authors": [{"family": "Piltti", "given": "Juha", "initials": "J"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Fern\u00e1ndez-Echevarr\u00eda", "given": "Cecilia", "initials": "C"}, {"family": "Marcellino", "given": "Daniel", "initials": "D"}, {"family": "Lammi", "given": "Mikko J", "initials": "MJ"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-03958-5", "pmid": "28623370", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:54:58.518Z", "modified": "2020-01-21T13:53:21.859Z"}, {"entity": "publication", "iuid": "772771bb3bbc4cbcb15ffb55d59a1acb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/772771bb3bbc4cbcb15ffb55d59a1acb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/772771bb3bbc4cbcb15ffb55d59a1acb"}}, "title": "RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study", "authors": [{"family": "Berghoff", "given": "Bork A", "initials": "BA"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "10", "issn": "1756-0381", "issue": "1", "pages": null, "title": "BioData Mining", "issn-l": "1756-0381"}, "abstract": "Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes. Existing methods thus either normalize on selected known reference genes that are invariant in expression across the experiment, assume that the majority of genes are invariant, or that the effects of up- and down-regulated genes cancel each other out during the normalization.\n\nHere, we present a novel method, \n                moose\n                         , which predicts invariant genes in silico through a dynamic programming (DP) scheme and applies a quadratic normalization based on this subset. The method allows for specifying a set of known or experimentally validated invariant genes, which guides the DP. We experimentally verified the predictions of this method in the bacterium 2\n                    Escherichia coli, and show how moose\n                         is able to (i) estimate the expression value distances between RNA-seq samples, (ii) reduce the variation of expression values across all samples, and (iii) to subsequently reveal new functional groups of genes during the late stages of DNA damage. We further applied the method to three eukaryotic data sets, on which its performance compares favourably to other methods. The software is implemented in C++ and is publicly available from http://grabherr.github.io/moose2/.2\n\nThe proposed RNA-seq normalization method, \n            moose\n                         , is a valuable alternative to existing methods, with two major advantages: (i) in silico prediction of invariant genes provides a list of potential reference genes for downstream analyses, and (ii) non-linear artefacts in RNA-seq data are handled adequately to minimize variations between replicates.2", "doi": "10.1186/s13040-017-0150-8", "pmid": "28878825", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:45.065Z", "modified": "2024-01-16T13:48:47.258Z"}, {"entity": "publication", "iuid": "c6761f62f1d9488ca64f266cef67224a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6761f62f1d9488ca64f266cef67224a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6761f62f1d9488ca64f266cef67224a"}}, "title": "Plasma stem cell factor levels are associated with risk of cardiovascular disease and death.", "authors": [{"family": "Bj\u00f6rkbacka", "given": "H", "initials": "H"}, {"family": "Yao Mattisson", "given": "I", "initials": "I"}, {"family": "Wigren", "given": "M", "initials": "M"}, {"family": "Melander", "given": "O", "initials": "O"}, {"family": "Fredrikson", "given": "G N", "initials": "GN"}, {"family": "Bengtsson", "given": "E", "initials": "E"}, {"family": "Gon\u00e7alves", "given": "I", "initials": "I"}, {"family": "Almgren", "given": "P", "initials": "P"}, {"family": "Lagerstedt", "given": "J O", "initials": "JO"}, {"family": "Orho-Melander", "given": "M", "initials": "M"}, {"family": "Engstr\u00f6m", "given": "G", "initials": "G"}, {"family": "Nilsson", "given": "J", "initials": "J", "orcid": "0000-0002-9752-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8777140448bc47f0a7984db3c15c0e23.json"}}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "issn-l": "0954-6820", "volume": "282", "issue": "6", "pages": "508-521"}, "abstract": "Stem cell factor (SCF) is a key growth factor for several types of stem and progenitor cells. There is experimental evidence that such cells are of importance for maintaining the integrity of the cardiovascular system. We investigated the association between circulating levels of SCF and risk for development of cardiovascular events and death.\n\nSCF was analysed by the proximity extension assay technique in plasma from 4742 subjects participating in the Malm\u00f6 Diet and Cancer Study. Cardiovascular events and death were monitored through national registers with a mean follow-up time of 19.2 years.\n\nSubjects with high baseline levels of SCF had lower cardiovascular (n = 340) and all-cause mortality (n = 1159) as well as a lower risk of heart failure (n = 177), stroke (n = 318) and myocardial infarction (n = 452). Smoking, diabetes and high alcohol consumption were associated with lower levels of SCF. Single nucleotide polymorphisms in the gene region encoding PDX1 C-terminal inhibiting factor 1 (PCIF1) and matrix metalloproteinase-9 were associated with plasma SCF levels. The highest SCF quartile remained independently associated with a lower risk of a lower risk of cardiovascular [hazard ratio and 95% confidence interval 0.59 (0.43-0.81)] and all-cause mortality [0.68 (0.57-0.81)], heart failure [0.50 (0.31-0.80)] and stroke [0.66 (0.47-0.92)], but not with MI [0.96 (0.72-1.27)] as compared with the lowest quartile when adjusting for traditional cardiovascular risk factors in Cox proportional hazard regression models.\n\nThis prospective population-based study demonstrates that subjects with high levels of SCF have a lower risk of cardiovascular events and death. The findings provide clinical support for a protective role of SCF in maintaining cardiovascular integrity.", "doi": "10.1111/joim.12675", "pmid": "28842933", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T12:14:15.657Z", "modified": "2023-04-14T13:56:08.176Z"}, {"entity": "publication", "iuid": "21aaff4ed48e45438079d2d7652600df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21aaff4ed48e45438079d2d7652600df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21aaff4ed48e45438079d2d7652600df"}}, "title": "Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development", "authors": [{"family": "Dalman", "given": "Kerstin", "initials": "K"}, {"family": "Wind", "given": "Julia Johanna", "initials": "JJ"}, {"family": "Nemesio-Gorriz", "given": "Miguel", "initials": "M"}, {"family": "Hammerbacher", "given": "Almuth", "initials": "A"}, {"family": "Lund\u00e9n", "given": "Karl", "initials": "K"}, {"family": "Ezcurra", "given": "Ines", "initials": "I"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "17", "issn": "1471-2229", "issue": "1", "pages": null, "title": "BMC Plant Biol.", "issn-l": "1471-2229"}, "abstract": null, "doi": "10.1186/s12870-016-0952-8", "pmid": "28061815", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Picea abies cell lines transcriptome project", "key": "PRJNA350779"}, {"db": "SRA", "description": null, "key": "SRP093366"}], "notes": [], "created": "2018-01-09T20:49:55.957Z", "modified": "2020-01-21T13:56:11.999Z"}, {"entity": "publication", "iuid": "8be977a6fe724420894f3df784d9aff1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8be977a6fe724420894f3df784d9aff1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8be977a6fe724420894f3df784d9aff1"}}, "title": "Novel risk genes for systemic lupus erythematosus predicted by random forest classification", "authors": [{"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Sylwan", "given": "Lina", "initials": "L"}, {"family": "B\u00e4cklin", "given": "Christofer", "initials": "C"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Eloranta", "given": "Maija Leena", "initials": "ML"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Bengtsson", "given": "Christine", "initials": "C"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Dahlqvist", "given": "Solbritt Rantap\u00e4\u00e4", "initials": "SR"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Syv\u00e4nen", "given": "Ann Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-06516-1", "pmid": "28740209", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:02.637Z", "modified": "2024-01-16T13:48:47.265Z"}, {"entity": "publication", "iuid": "13b158b1f8104b7f8cf82c52e803ff32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13b158b1f8104b7f8cf82c52e803ff32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13b158b1f8104b7f8cf82c52e803ff32"}}, "title": "Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma", "authors": [{"family": "Lauss", "given": "Martin", "initials": "M"}, {"family": "Donia", "given": "Marco", "initials": "M"}, {"family": "Harbst", "given": "Katja", "initials": "K"}, {"family": "Andersen", "given": "Rikke", "initials": "R"}, {"family": "Mitra", "given": "Shamik", "initials": "S"}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Salim", "given": "Maryem", "initials": "M"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J"}, {"family": "T\u00f6rngren", "given": "Therese", "initials": "T"}, {"family": "Kvist", "given": "Anders", "initials": "A"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Svane", "given": "Inge Marie", "initials": "IM"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-01460-0", "pmid": "29170503", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-24T11:50:36.213Z", "modified": "2020-01-21T13:53:22.045Z"}, {"entity": "publication", "iuid": "6fa4d2ff4f9e44c5ad4978a084dea8b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fa4d2ff4f9e44c5ad4978a084dea8b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fa4d2ff4f9e44c5ad4978a084dea8b3"}}, "title": "Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi", "authors": [{"family": "Berlin", "given": "Anna", "initials": "A"}, {"family": "Samils", "given": "Berit", "initials": "B"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "4", "issn": "2054-3085", "issue": "1", "pages": null, "title": "Fungal Biol Biotechnol", "issn-l": "2054-3085"}, "abstract": null, "doi": "10.1186/s40694-017-0032-3", "pmid": "28955472", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T16:06:55.721Z", "modified": "2024-01-16T13:48:47.272Z"}, {"entity": "publication", "iuid": "9ad388cd6d244508a84f9856b409965a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ad388cd6d244508a84f9856b409965a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ad388cd6d244508a84f9856b409965a"}}, "title": "Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size.", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "van der Plicht", "given": "Johannes", "initials": "J"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2017-12-00", "journal": {"volume": "1", "issn": "2056-3744", "issue": "6", "pages": "292-303", "title": "Evolution Letters", "issn-l": "2056-3744"}, "abstract": "The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high-quality mitogenomes from 21 radiocarbon-dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.", "doi": "10.1002/evl3.33", "pmid": "30283657", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "EVL333"}, {"db": "pmc", "key": "PMC6121868"}], "notes": [], "created": "2017-11-29T17:49:46.201Z", "modified": "2021-07-07T20:31:10.875Z"}, {"entity": "publication", "iuid": "eafab88fefb94d66b47cebbd0ea62bd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eafab88fefb94d66b47cebbd0ea62bd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eafab88fefb94d66b47cebbd0ea62bd2"}}, "title": "Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1", "authors": [{"family": "Lehmann", "given": "Laura C", "initials": "LC", "orcid": "0000-0003-2518-5606", "researcher": {"href": "https://publications.scilifelab.se/researcher/e73ae6d30ebe4c68971f3b0908d061c6.json"}}, {"family": "Hewitt", "given": "Graeme", "initials": "G"}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Leitner", "given": "Alexander", "initials": "A"}, {"family": "Marklund", "given": "Emil", "initials": "E", "orcid": "0000-0002-1150-7304", "researcher": {"href": "https://publications.scilifelab.se/researcher/67842d62534d4612a5e92f7a275df4dc.json"}}, {"family": "Maslen", "given": "Sarah L", "initials": "SL"}, {"family": "Maturi", "given": "Varun", "initials": "V", "orcid": "0000-0003-1177-0839", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd84539b66b4e79964ec0330f1aefd7.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "van der Spoel", "given": "David", "initials": "D", "orcid": "0000-0002-7659-8526", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf896790b2f844f181e60f3b01d7ae0f.json"}}, {"family": "Skehel", "given": "J Mark", "initials": "JM"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}, {"family": "Boulton", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-6936-6834", "researcher": {"href": "https://publications.scilifelab.se/researcher/8be210bb12b54a19b4020803fa0c3357.json"}}, {"family": "Deindl", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6807-8654", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e45e8288a3445e2b346f29b73141738.json"}}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "68", "issn": "1097-2765", "issue": "5", "pages": "847-859.e7", "title": "Molecular Cell", "issn-l": "1097-2765"}, "abstract": "Human ALC1 is an oncogene-encoded chromatin-remodeling enzyme required for DNA repair that possesses a poly(ADP-ribose) (PAR)-binding macro domain. Its engagement with PARylated PARP1 activates ALC1 at sites of DNA damage, but the underlying mechanism remains unclear. Here, we establish a dual role for the macro domain in autoinhibition of ALC1 ATPase activity and coupling to nucleosome mobilization. In the absence of DNA damage, an inactive conformation of the ATPase is maintained by juxtaposition of the macro domain against predominantly the C-terminal ATPase lobe through conserved electrostatic interactions. Mutations within this interface displace the macro domain, constitutively activate the ALC1 ATPase independent of PARylated PARP1, and alter the dynamics of ALC1 recruitment at DNA damage sites. Upon DNA damage, binding of PARylated PARP1 by the macro domain induces a conformational change that relieves autoinhibitory interactions with the ATPase motor, which selectively activates ALC1 remodeling upon recruitment to sites of DNA damage.", "doi": "10.1016/j.molcel.2017.10.017", "pmid": "29220652", "labels": {"Protein Science Facility (PSF)": "Service", "Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5745148"}, {"db": "pii", "key": "S1097-2765(17)30792-X"}], "notes": [], "created": "2018-04-11T08:26:47.042Z", "modified": "2023-12-04T10:12:26.534Z"}, {"entity": "publication", "iuid": "6fa53d5882bc44ccb2d2078ffadb5c1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fa53d5882bc44ccb2d2078ffadb5c1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fa53d5882bc44ccb2d2078ffadb5c1e"}}, "title": "Mapping of leptin and its syntenic genes to chicken chromosome 1p", "authors": [{"family": "Seroussi", "given": "Eyal", "initials": "E"}, {"family": "Pitel", "given": "Fr\u00e9d\u00e9rique", "initials": "F"}, {"family": "Leroux", "given": "Sophie", "initials": "S"}, {"family": "Morisson", "given": "Mireille", "initials": "M"}, {"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Miyara", "given": "Shoval", "initials": "S"}, {"family": "Yosefi", "given": "Sara", "initials": "S"}, {"family": "Cogburn", "given": "Larry A", "initials": "LA"}, {"family": "Burt", "given": "David W", "initials": "DW"}, {"family": "Anderson", "given": "Leif", "initials": "L"}, {"family": "Friedman-Einat", "given": "Miriam", "initials": "M"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "18", "issn": "1471-2156", "issue": "1", "pages": null, "title": "BMC Genet.", "issn-l": "1471-2156"}, "abstract": null, "doi": "10.1186/s12863-017-0543-1", "pmid": "28793857", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Mapping of leptin and its syntenic genes to chicken chromosome 1p", "key": "PRJEB18741"}], "notes": [], "created": "2017-11-02T18:42:15.441Z", "modified": "2020-01-21T13:56:11.270Z"}, {"entity": "publication", "iuid": "9d75b5479e9e4b7d9b24207f5240a1a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d75b5479e9e4b7d9b24207f5240a1a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d75b5479e9e4b7d9b24207f5240a1a5"}}, "title": "MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis.", "authors": [{"family": "Jagadeesan", "given": "Kishore Kumar", "initials": "KK"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "SLAS DISCOVERY: Advancing Life Sciences R&D", "issn": "2472-5560", "volume": "22", "issue": "10", "pages": "1246-1252", "issn-l": "2472-5552"}, "abstract": "Recently, mass spectrometry (MS) has emerged as an important tool for high-throughput screening (HTS) providing a direct and label-free detection method, complementing traditional fluorescent and colorimetric methodologies. Among the various MS techniques used for HTS, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) provides many of the characteristics required for high-throughput analyses, such as low cost, speed, and automation. However, visualization and analysis of the large datasets generated by HTS MALDI-MS can pose significant challenges, especially for multiparametric experiments. The datasets can be generated fast, and the complexity of the experimental data (e.g., screening many different sorbent phases, the sorbent mass, and the load, wash, and elution conditions) makes manual data analysis difficult. To address these challenges, a comprehensive informatics tool called MALDIViz was developed. This tool is an R-Shiny-based web application, accessible independently of the operating system and without the need to install any program locally. It has been designed to facilitate easy analysis and visualization of MALDI-MS datasets, comparison of multiplex experiments, and export of the analysis results to high-quality images.", "doi": "10.1177/2472555217727517", "pmid": "28825969", "labels": {"Structural Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-27T10:07:31.455Z", "modified": "2021-06-21T14:58:27.910Z"}, {"entity": "publication", "iuid": "ea6804e42c5e4575803e5bfb736058af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea6804e42c5e4575803e5bfb736058af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea6804e42c5e4575803e5bfb736058af"}}, "title": "Low-dose \u03b3-secretase inhibition increases secretion of A\u03b2 peptides and intracellular oligomeric A\u03b2.", "authors": [{"family": "Agholme", "given": "Lotta", "initials": "L", "orcid": "0000-0003-3816-7474", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7034ae6b9644a6fabd3bfb6d719459b.json"}}, {"family": "Clarin", "given": "Marcus", "initials": "M"}, {"family": "Gkanatsiou", "given": "Eleni", "initials": "E", "orcid": "0000-0003-4443-2836", "researcher": {"href": "https://publications.scilifelab.se/researcher/021f4c0da3ee408999103c7504e39170.json"}}, {"family": "Kettunen", "given": "Petronella", "initials": "P"}, {"family": "Chebli", "given": "Jasmine", "initials": "J"}, {"family": "Brinkmalm", "given": "Gunnar", "initials": "G"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Bergstr\u00f6m", "given": "Petra", "initials": "P"}, {"family": "Portelius", "given": "Erik", "initials": "E"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "Molecular and Cellular Neuroscience", "issn": "1095-9327", "volume": "85", "issue": null, "pages": "211-219", "issn-l": "1044-7431"}, "abstract": "\u03b3-Secretase inhibitors have been considered promising drug candidates against Alzheimer's disease (AD) due to their ability to reduce amyloid-\u03b2 (A\u03b2) production. However, clinical trials have been halted due to lack of clinical efficacy and/or side effects. Recent in vitro studies suggest that low doses of \u03b3-secretase inhibitors may instead increase A\u03b2 production. Using a stem cell-derived human model of cortical neurons and low doses of the \u03b3-secretase inhibitor DAPT, the effects on a variety of A\u03b2 peptides were studied using mass spectrometry. One major focus was to develop a novel method for specific detection of oligomeric A\u03b2 (oA\u03b2), and this was used to study the effects of low-dose \u03b3-secretase inhibitor treatment on intracellular oA\u03b2 accumulation. Low-dose treatment (2 and 20nM) with DAPT increased the secretion of several A\u03b2 peptides, especially A\u03b2x-42. Furthermore, using the novel method for oA\u03b2 detection, we found that 2nM DAPT treatment of cortical neurons resulted in increased oA\u03b2 accumulation. Thus, low dose-treatment with DAPT causes both increased production of long, aggregation-prone A\u03b2 peptides and accumulation of intracellular A\u03b2 oligomers, both believed to contribute to AD pathology.", "doi": "10.1016/j.mcn.2017.10.009", "pmid": "29104140", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S1044-7431(16)30246-9"}], "notes": [], "created": "2020-01-23T16:33:43.558Z", "modified": "2021-06-21T14:57:52.544Z"}, {"entity": "publication", "iuid": "95ae32ed5cf940989a08d370d766bac4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95ae32ed5cf940989a08d370d766bac4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95ae32ed5cf940989a08d370d766bac4"}}, "title": "Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma", "authors": [{"family": "Sun", "given": "Yu", "initials": "Y"}, {"family": "Svedberg", "given": "Jesper", "initials": "J"}, {"family": "Hiltunen", "given": "Markus", "initials": "M"}, {"family": "Corcoran", "given": "P\u00e1draic", "initials": "P"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-01317-6", "pmid": "29074958", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:38:01.098Z", "modified": "2020-01-21T13:56:14.867Z"}, {"entity": "publication", "iuid": "847191bf36c749aebfb827e12d3cfe85", "links": {"self": {"href": "https://publications.scilifelab.se/publication/847191bf36c749aebfb827e12d3cfe85.json"}, "display": {"href": "https://publications.scilifelab.se/publication/847191bf36c749aebfb827e12d3cfe85"}}, "title": "Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors", "authors": [{"family": "Ric\u00e3o Canelhas", "given": "Monica", "initials": "M"}, {"family": "Andersson", "given": "Martin", "initials": "M"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "19", "issn": "1462-2912", "issue": "12", "pages": "5078-5087", "title": "Environ Microbiol", "issn-l": "1462-2912"}, "abstract": null, "doi": "10.1111/1462-2920.13979", "pmid": "29124844", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP075169"}], "notes": [], "created": "2018-01-09T20:54:59.136Z", "modified": "2020-01-21T13:56:12.023Z"}, {"entity": "publication", "iuid": "5dc932db5ed947d5912b3f59db7f4023", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5dc932db5ed947d5912b3f59db7f4023.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5dc932db5ed947d5912b3f59db7f4023"}}, "title": "Inflammatory infiltrates in parathyroid tumors.", "authors": [{"family": "Haglund", "given": "Felix", "initials": "F"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Nilsson", "given": "Inga-Lena", "initials": "IL"}, {"family": "H\u00f6\u00f6g", "given": "Anders", "initials": "A"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}], "type": "comparative study", "published": "2017-12-00", "journal": {"volume": "177", "issn": "1479-683X", "issue": "6", "pages": "445-453", "title": "Eur. J. Endocrinol.", "issn-l": "0804-4643"}, "abstract": "Inflammatory infiltrates are sometimes present in solid tumors and may be coupled to clinical behavior or etiology. Infectious viruses contribute to tumorigenesis in a significant fraction of human neoplasias.\n\nCharacterize inflammatory infiltrates and possible viral transcription in primary hyperparathyroidism.\n\nFrom the period 2007 to 2016, a total of 55 parathyroid tumors (51 adenomas and 4 hyperplasias) with prominent inflammatory infiltrates were identified from more than 2000 parathyroid tumors in the pathology archives, and investigated by immunohistochemistry for CD4, CD8, CD20 and CD45 and scored as +0, +1 or +2. Clinicopathological data were compared to 142 parathyroid adenomas without histological evidence of inflammation. Transcriptome sequencing was performed for 13 parathyroid tumors (four inflammatory, 9 non-inflammatory) to identify potential viral transcripts.\n\nTumors had prominent germinal center-like nodular (+2) lymphocytic infiltrates consisting of T and B lymphocytes (31%) and/or diffuse (+1-2) infiltrates of predominantly CD8+ T lymphocytes (84%). In the majority of cases with adjacent normal parathyroid tissue, the normal rim was unaffected by the inflammatory infiltrates (96%). Presence of inflammatory infiltrates was associated with higher levels of serum-PTH (P\u2005=\u20050.007) and oxyphilic differentiation (P\u2005=\u20050.002). Co-existent autoimmune disease was observed in 27% of patients with inflammatory infiltrates, which in turn was associated with oxyphilic differentiation (P\u2005=\u20050.041). Additionally, prescription of anti-inflammatory drugs was associated with lower serum ionized calcium (P\u2005=\u20050.037).\n\nNo evidence of virus-like sequences in the parathyroid tumors could be found by transcriptome sequencing, suggesting that other factors may contribute to attract the immune system to the parathyroid tumor tissue.", "doi": "10.1530/EJE-17-0277", "pmid": "28855268", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EJE-17-0277"}, {"db": "pmc", "key": "PMC5642267"}], "notes": [], "created": "2017-11-03T16:20:58.775Z", "modified": "2024-01-16T13:48:47.280Z"}, {"entity": "publication", "iuid": "a2b9445a65e8490793fea171bd20486e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b9445a65e8490793fea171bd20486e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b9445a65e8490793fea171bd20486e"}}, "title": "Increasing the permeability of Escherichia coli using MAC13243", "authors": [{"family": "Muheim", "given": "Claudio", "initials": "C"}, {"family": "G\u00f6tzke", "given": "Hansj\u00f6rg", "initials": "H"}, {"family": "Eriksson", "given": "Anna U", "initials": "AU"}, {"family": "Lindberg", "given": "Stina", "initials": "S"}, {"family": "Lauritsen", "given": "Ida", "initials": "I"}, {"family": "N\u00f8rholm", "given": "Morten H H", "initials": "MHH"}, {"family": "Daley", "given": "Daniel O", "initials": "DO"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-17772-6", "pmid": "29247166", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-02-12T12:53:39.343Z", "modified": "2025-10-17T13:04:29.085Z"}, {"entity": "publication", "iuid": "fccd51dc1ff549cd87f57650f7ecfb50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fccd51dc1ff549cd87f57650f7ecfb50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fccd51dc1ff549cd87f57650f7ecfb50"}}, "title": "Identification and description of three families with familial Alzheimer disease that segregate variants in the SORL1 gene", "authors": [{"family": "Thonberg", "given": "H\u00e5kan", "initials": "H"}, {"family": "Chiang", "given": "Huei Hsin", "initials": "HH"}, {"family": "Lilius", "given": "Lena", "initials": "L"}, {"family": "Forsell", "given": "Charlotte", "initials": "C"}, {"family": "Lindstr\u00f6m", "given": "Anna Karin", "initials": "AK"}, {"family": "Johansson", "given": "Charlotte", "initials": "C"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Jenny", "initials": "J"}, {"family": "Thordardottir", "given": "Steinunn", "initials": "S"}, {"family": "Sleegers", "given": "Kristel", "initials": "K"}, {"family": "Van Broeckhoven", "given": "Christine", "initials": "C"}, {"family": "R\u00f6nnb\u00e4ck", "given": "Annica", "initials": "A"}, {"family": "Graff", "given": "Caroline", "initials": "C"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "5", "issn": "2051-5960", "issue": "1", "pages": null, "title": "Acta Neuropathol Commun", "issn-l": "2051-5960"}, "abstract": null, "doi": "10.1186/s40478-017-0441-9", "pmid": "28595629", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-27T07:02:46.597Z", "modified": "2024-01-16T13:48:47.289Z"}, {"entity": "publication", "iuid": "25667b18e9cd4a24be39919d778fcecb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25667b18e9cd4a24be39919d778fcecb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25667b18e9cd4a24be39919d778fcecb"}}, "title": "Highly sensitive and specific protein detection via combined capillary isoelectric focusing and proximity ligation", "authors": [{"family": "Padhan", "given": "Narendra", "initials": "N"}, {"family": "Yan", "given": "Junhong", "initials": "J"}, {"family": "Boge", "given": "Annegret", "initials": "A"}, {"family": "Scrivener", "given": "Elaine", "initials": "E"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Gullberg", "given": "Mats", "initials": "M"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-01516-7", "pmid": "28473697", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T14:47:02.649Z", "modified": "2023-04-14T13:56:08.329Z"}, {"entity": "publication", "iuid": "179d461633984a84b5056070367e2884", "links": {"self": {"href": "https://publications.scilifelab.se/publication/179d461633984a84b5056070367e2884.json"}, "display": {"href": "https://publications.scilifelab.se/publication/179d461633984a84b5056070367e2884"}}, "title": "High levels of cerebrospinal fluid chemokines point to the presence of neuroinflammation in peripheral neuropathic pain: a cross-sectional study of 2 cohorts of patients compared with healthy controls.", "authors": [{"family": "B\u00e4ckryd", "given": "Emmanuel", "initials": "E"}, {"family": "Lind", "given": "Anne-Li", "initials": "AL"}, {"family": "Thulin", "given": "M\u00e5ns", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Gerdle", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gordh", "given": "Torsten", "initials": "T"}], "type": "comparative study", "published": "2017-12-00", "journal": {"title": "Pain", "issn": "1872-6623", "issn-l": "0304-3959", "volume": "158", "issue": "12", "pages": "2487-2495"}, "abstract": "Animal models suggest that chemokines are important mediators in the pathophysiology of neuropathic pain. Indeed, these substances have been called \"gliotransmitters,\" a term that illustrates the close interplay between glial cells and neurons in the context of neuroinflammation and pain. However, evidence in humans is scarce. The aim of the study was to determine a comprehensive cerebrospinal fluid (CSF) inflammatory profile of patients with neuropathic pain. Our hypothesis was that we would thereby find indications of a postulated on-going process of central neuroinflammation. Samples of CSF were collected from 2 cohorts of patients with neuropathic pain (n = 11 and n = 16, respectively) and healthy control subjects (n = 11). The samples were analyzed with a multiplex proximity extension assay in which 92 inflammation-related proteins were measured simultaneously (Proseek Multiplex Inflammation I; Olink Bioscience, Uppsala, Sweden). Univariate testing with control of false discovery rate, as well as orthogonal partial least squares discriminant analysis, were used for statistical analyses. Levels of chemokines CXCL6, CXCL10, CCL8, CCL11, CCL23 in CSF, as well as protein LAPTGF-beta-1, were significantly higher in both neuropathic pain cohorts compared with healthy controls, pointing to neuroinflammation in patients. These 6 proteins were also major results in a recent similar study in patients with fibromyalgia. The findings need to be confirmed in larger cohorts, and the question of causality remains to be settled. Because it has been suggested that prevalent comorbidities to chronic pain (eg, depression, anxiety, poor sleep, and tiredness) also are associated with neuroinflammation, it will be important to determine whether neuroinflammation is a common mediator.", "doi": "10.1097/j.pain.0000000000001061", "pmid": "28930774", "labels": {"Clinical Biomarkers": "Service", "Affinity Proteomics Stockholm": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5690569"}, {"db": "pii", "key": "00006396-201712000-00022"}], "notes": [], "created": "2020-01-23T15:08:27.848Z", "modified": "2023-04-14T13:56:08.522Z"}, {"entity": "publication", "iuid": "4c60c5b0a8564155ad92ca6e79e2a352", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c60c5b0a8564155ad92ca6e79e2a352.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c60c5b0a8564155ad92ca6e79e2a352"}}, "title": "Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens", "authors": [{"family": "Lillie", "given": "Mette", "initials": "M"}, {"family": "Sheng", "given": "Zheya", "initials": "Z"}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Dorshorst", "given": "Ben J", "initials": "BJ"}, {"family": "Ashwell", "given": "Christopher M", "initials": "CM"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-016-3414-7", "pmid": "28100171", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP094614"}, {"db": "SRA", "description": "High Antibody Relaxed", "key": "SRX2398013"}, {"db": "SRA", "description": "High Antibody Selected", "key": "SRX2398014"}, {"db": "SRA", "description": "Low Antibody Relaxed", "key": "SRX2398015"}, {"db": "SRA", "description": "Low Antibody Selected", "key": "SRX2398018"}], "notes": [], "created": "2017-10-19T20:19:08.913Z", "modified": "2020-01-21T13:56:11.293Z"}, {"entity": "publication", "iuid": "4b6adecc6108488ebb8d8a62a5fbd41a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b6adecc6108488ebb8d8a62a5fbd41a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b6adecc6108488ebb8d8a62a5fbd41a"}}, "title": "Genetic- and Lifestyle-dependent Dental Caries Defined by the Acidic Proline-rich Protein Genes  PRH1  and  PRH2", "authors": [{"family": "Str\u00f6mberg", "given": "Nicklas", "initials": "N"}, {"family": "Esberg", "given": "Anders", "initials": "A"}, {"family": "Sheng", "given": "Nongfei", "initials": "N"}, {"family": "M\u00e5rell", "given": "Lena", "initials": "L"}, {"family": "L\u00f6fgren-Burstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Karin", "initials": "K"}, {"family": "K\u00e4llest\u00e5l", "given": "Carina", "initials": "C"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "26", "issn": "2352-3964", "issue": null, "pages": "38-46", "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": null, "doi": "10.1016/j.ebiom.2017.11.019", "pmid": "29191562", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:52.544Z", "modified": "2020-01-21T13:56:12.007Z"}, {"entity": "publication", "iuid": "eae1806bb33f4b158e599d4c51c22371", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eae1806bb33f4b158e599d4c51c22371.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eae1806bb33f4b158e599d4c51c22371"}}, "title": "Filter Plate-Based Screening of MIP SPE Materials for Capture of the Biomarker Pro-Gastrin-Releasing Peptide.", "authors": [{"family": "Jagadeesan", "given": "Kishore Kumar", "initials": "KK"}, {"family": "Rossetti", "given": "Cecilia", "initials": "C"}, {"family": "Abdel Qader", "given": "Abed", "initials": "A"}, {"family": "Reubsaet", "given": "L\u00e9on", "initials": "L"}, {"family": "Sellergren", "given": "B\u00f6rje", "initials": "B"}, {"family": "Laurell", "given": "Thomas", "initials": "T"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "SLAS DISCOVERY: Advancing Life Sciences R&D", "issn": "2472-5560", "volume": "22", "issue": "10", "pages": "1253-1261", "issn-l": "2472-5552"}, "abstract": "Affinity-based solid-phase extraction (SPE) is an attractive low-cost sample preparation strategy for biomarker analysis. Molecularly imprinted polymers (MIPs) as affinity sorbents offer unique opportunities for affinity SPE, due to their low manufacturing cost and high robustness. A limitation is the prediction of their affinity; therefore, screening of analyte recovery and specificity within a large range of SPE conditions is important in order to ensure high-sensitivity detection and assay reproducibility. Here, a \u00b5-SPE method for screening of the MIP-SPE materials using a commercial 384-well filter plate is presented. The method allows for rapid and automated screening using 10-30 \u00b5L of packed SPE sorbent per well and sample volumes in the range of 10-70 \u00b5L. This enables screening of many different SPE sorbents while simultaneously identifying optimal SPE conditions. In addition, the 384-well format also facilitates detection with a multitude of analytical platforms. Performance of the \u00b5-MIP-SPE method was investigated using a series of MIPs designed to capture pro-gastrin-releasing peptide (ProGRP). Fractions coming from sample load, cartridge wash, and elution were collected and analyzed using mass spectrometry (MS). The top-performing MIPs were identified, together with proper SPE conditions.", "doi": "10.1177/2472555216689494", "pmid": "28346098", "labels": {"Structural Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-27T10:07:40.556Z", "modified": "2021-06-21T14:57:41.842Z"}, {"entity": "publication", "iuid": "813d95ce7f65416fadf79b46be3de884", "links": {"self": {"href": "https://publications.scilifelab.se/publication/813d95ce7f65416fadf79b46be3de884.json"}, "display": {"href": "https://publications.scilifelab.se/publication/813d95ce7f65416fadf79b46be3de884"}}, "title": "Elevated Markers of Death Receptor-Activated Apoptosis are Associated with Increased Risk for Development of Diabetes and Cardiovascular Disease.", "authors": [{"family": "Mattisson", "given": "Ingrid Yao", "initials": "IY"}, {"family": "Bj\u00f6rkbacka", "given": "Harry", "initials": "H"}, {"family": "Wigren", "given": "Maria", "initials": "M"}, {"family": "Edsfeldt", "given": "Andreas", "initials": "A"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Fredrikson", "given": "Gunilla Nordin", "initials": "GN"}, {"family": "Bengtsson", "given": "Eva", "initials": "E"}, {"family": "Gon\u00e7alves", "given": "Isabel", "initials": "I"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Nilsson", "given": "Jan", "initials": "J", "orcid": "0000-0002-9752-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8777140448bc47f0a7984db3c15c0e23.json"}}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "issn-l": "2352-3964", "volume": "26", "issue": null, "pages": "187-197"}, "abstract": null, "doi": "10.1016/j.ebiom.2017.11.023", "pmid": "29208468", "labels": {"Clinical Biomarkers": "Service", "Affinity Proteomics Stockholm": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(17)30466-8"}, {"db": "pmc", "key": "PMC5836474"}], "notes": [], "created": "2020-01-23T15:08:27.147Z", "modified": "2023-04-14T13:56:08.656Z"}, {"entity": "publication", "iuid": "79290fe0255d450fbbb5b0817adda42a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79290fe0255d450fbbb5b0817adda42a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79290fe0255d450fbbb5b0817adda42a"}}, "title": "Draft genome of the brown-rot fungus  Fomitopsis pinicola  GR9-4", "authors": [{"family": "Kancherla", "given": "Reddy Prakash", "initials": "RP"}, {"family": "Durling", "given": "Mikael Brandstr\u00f6m", "initials": "MB"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "H\u00f6gberg", "given": "Nils", "initials": "N"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "15", "issn": "2352-3409", "issue": null, "pages": "496-500", "title": "Data Brief", "issn-l": "2352-3409"}, "abstract": null, "doi": "10.1016/j.dib.2017.09.043", "pmid": "29062876", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Fomitopsis pinicola strain:GR9-4 Genome sequencing", "key": "PRJNA354689"}], "notes": [], "created": "2017-11-02T13:36:55.534Z", "modified": "2024-01-16T13:48:47.296Z"}, {"entity": "publication", "iuid": "1396a775cb7a4fc5a2fcc4011998a292", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1396a775cb7a4fc5a2fcc4011998a292.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1396a775cb7a4fc5a2fcc4011998a292"}}, "title": "Development of an efficient route for combined recycling of PET and cotton from mixed fabrics", "authors": [{"family": "Palme", "given": "Anna", "initials": "A", "orcid": "0000-0001-5276-2830", "researcher": {"href": "https://publications.scilifelab.se/researcher/23f84c15077e47439e2818bce78d0e24.json"}}, {"family": "Peterson", "given": "Anna", "initials": "A"}, {"family": "de la Motte", "given": "Hanna", "initials": "H"}, {"family": "Theliander", "given": "Hans", "initials": "H"}, {"family": "Brelid", "given": "Harald", "initials": "H"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "3", "issn": "2197-9936", "issue": "1", "pages": null, "title": "Text Cloth Sustain", "issn-l": "2197-9936"}, "abstract": null, "doi": "10.1186/s40689-017-0026-9", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:46:06.513Z", "modified": "2025-10-17T13:03:59.249Z"}, {"entity": "publication", "iuid": "93882542fa1d4c14ba3c35cdc360bd31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93882542fa1d4c14ba3c35cdc360bd31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93882542fa1d4c14ba3c35cdc360bd31"}}, "title": "Detection of QTL for greasy fleece weight in sheep using a 50\u00a0K single nucleotide polymorphism chip", "authors": [{"family": "Ebrahimi", "given": "Fatemeh", "initials": "F"}, {"family": "Gholizadeh", "given": "Mohsen", "initials": "M"}, {"family": "Rahimi-Mianji", "given": "Ghodrat", "initials": "G"}, {"family": "Farhadi", "given": "Ayoub", "initials": "A"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "49", "issn": "0049-4747", "issue": "8", "pages": "1657-1662", "title": "Trop Anim Health Prod", "issn-l": null}, "abstract": null, "doi": "10.1007/s11250-017-1373-x", "pmid": "28801813", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:54.961Z", "modified": "2020-01-21T13:56:12.030Z"}, {"entity": "publication", "iuid": "b16e57c3e23a42a7a678a2b216cebed3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b16e57c3e23a42a7a678a2b216cebed3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b16e57c3e23a42a7a678a2b216cebed3"}}, "title": "Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost", "authors": [{"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Seroussi", "given": "Eyal", "initials": "E"}, {"family": "Yosefi", "given": "Sara", "initials": "S"}, {"family": "Pendavis", "given": "Ken", "initials": "K"}, {"family": "Burgess", "given": "Shane C", "initials": "SC"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Friedman-Einat", "given": "Miriam", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "18", "issn": "1474-760X", "issue": "1", "pages": null, "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": null, "doi": "10.1186/s13059-017-1231-1", "pmid": "28615067", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T18:40:30.126Z", "modified": "2024-01-16T13:48:47.303Z"}, {"entity": "publication", "iuid": "160c3e46cac94203865242a34f55a770", "links": {"self": {"href": "https://publications.scilifelab.se/publication/160c3e46cac94203865242a34f55a770.json"}, "display": {"href": "https://publications.scilifelab.se/publication/160c3e46cac94203865242a34f55a770"}}, "title": "Comparison of laccase-catalyzed cross-linking of organosolv lignin and lignosulfonates", "authors": [{"family": "Gillgren", "given": "Thomas", "initials": "T"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "105", "issn": "0141-8130", "issue": null, "pages": "438-446", "title": "International Journal of Biological Macromolecules", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ijbiomac.2017.07.061", "pmid": "28711620", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-10-22T11:16:38.805Z", "modified": "2025-10-17T13:03:59.260Z"}, {"entity": "publication", "iuid": "685808b763124eb0af7fdba6c37bc156", "links": {"self": {"href": "https://publications.scilifelab.se/publication/685808b763124eb0af7fdba6c37bc156.json"}, "display": {"href": "https://publications.scilifelab.se/publication/685808b763124eb0af7fdba6c37bc156"}}, "title": "Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea", "authors": [{"family": "H\u00fcttner", "given": "Silvia", "initials": "S"}, {"family": "Nguyen", "given": "Thanh Thuy", "initials": "TT"}, {"family": "Granchi", "given": "Zoraide", "initials": "Z"}, {"family": "Chin-A-Woeng", "given": "Thomas", "initials": "T"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Larsbrink", "given": "Johan", "initials": "J"}, {"family": "Thanh", "given": "Vu Nguyen", "initials": "VN"}, {"family": "Olsson", "given": "Lisbeth", "initials": "L"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "10", "issn": "1754-6834", "issue": "1", "pages": null, "title": "Biotechnol Biofuels", "issn-l": "1754-6834"}, "abstract": null, "doi": "10.1186/s13068-017-0956-0", "pmid": "29158777", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-12-04T09:07:43.405Z", "modified": "2020-01-21T13:53:22.634Z"}, {"entity": "publication", "iuid": "42ab95d6b8f44dc38532ed2b323cc72e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42ab95d6b8f44dc38532ed2b323cc72e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42ab95d6b8f44dc38532ed2b323cc72e"}}, "title": "Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature", "authors": [{"family": "Martins", "given": "Sara", "initials": "S"}, {"family": "Montiel-Jorda", "given": "Alvaro", "initials": "A"}, {"family": "Cayrel", "given": "Anne", "initials": "A"}, {"family": "Huguet", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Roux", "given": "Christine Paysant Le", "initials": "CPL"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Vert", "given": "Gr\u00e9gory", "initials": "G"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-00355-4", "pmid": "28827608", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:33:46.381Z", "modified": "2025-10-17T13:03:18.458Z"}, {"entity": "publication", "iuid": "793737c7164b487eb6f97d8b1b3b984a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/793737c7164b487eb6f97d8b1b3b984a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/793737c7164b487eb6f97d8b1b3b984a"}}, "title": "Automated Training of Deep Convolutional Neural Networks for Cell Segmentation", "authors": [{"family": "Sadanandan", "given": "Sajith Kecheril", "initials": "SK"}, {"family": "Ranefall", "given": "Petter", "initials": "P"}, {"family": "Le Guyader", "given": "Sylvie", "initials": "S"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-017-07599-6", "pmid": "28798336", "labels": {"BioImage Informatics": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "cb.uu.se", "description": "Images and code", "key": "http://www.cb.uu.se/~carolina/timelapse_data/"}, {"db": "data.broadinstitute.org", "description": "Images", "key": "https://data.broadinstitute.org/bbbc/BBBC022/"}], "notes": [], "created": "2017-11-01T08:05:25.830Z", "modified": "2021-07-05T14:18:24.353Z"}, {"entity": "publication", "iuid": "89c700dbb2e04e4192b521bc3a2acc39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89c700dbb2e04e4192b521bc3a2acc39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89c700dbb2e04e4192b521bc3a2acc39"}}, "title": "Autoantibodies against aldehyde-modified collagen type IV are associated with risk of development of myocardial infarction.", "authors": [{"family": "Vallejo", "given": "J", "initials": "J", "orcid": "0000-0002-4836-8854", "researcher": {"href": "https://publications.scilifelab.se/researcher/329a21f429ea4e22853ed189f68b9fb5.json"}}, {"family": "Dun\u00e9r", "given": "P", "initials": "P"}, {"family": "Fredrikson", "given": "G N", "initials": "GN"}, {"family": "Nilsson", "given": "J", "initials": "J", "orcid": "0000-0002-9752-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8777140448bc47f0a7984db3c15c0e23.json"}}, {"family": "Bengtsson", "given": "E", "initials": "E"}], "type": "journal article", "published": "2017-12-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "issn-l": "0954-6820", "volume": "282", "issue": "6", "pages": "496-507"}, "abstract": "Oxidation of LDL particles entrapped in the extracellular matrix of the arterial wall is a key factor in the development of atherosclerosis. Lipid oxidation products, such as malondialdehyde (MDA), react with surrounding extracellular matrix proteins and cause modifications that are recognized by the immune system. MDA modification of collagen type IV is increased in carotid lesions from symptomatic patients and correlates with autoantibodies against MDA-modified collagen type IV in plasma.\n\nThe aim of this study was to determine whether autoantibodies against MDA-modified collagen type IV predict risk of development of myocardial infarction (MI).\n\nPlasma levels of MDA-modified collagen type IV IgM and IgG antibodies were analysed by enzyme-linked immunosorbent assay in 385 subjects with incident MI during 13 years of follow-up and 410 age- and sex-matched controls in the Malm\u00f6 Diet and Cancer study.\n\nMDA-modified collagen type IV IgG levels were higher in cases with incident MI than in controls. Subjects in the highest tertile of MDA-modified collagen type IV IgG had an increased risk of MI (hazard ratio 1.56, 95% confidence interval 1.22-2.00, P for trend 0.0004). This association remained significant after adjusting for factors included in the Framingham risk score and diabetes. High levels of MDA-collagen type IV IgG were associated with increased carotid intima-media thickness and elevated plasma levels of matrix metalloproteinase 10 and 12.\n\nImmune responses against MDA-modified collagen type IV are associated with more severe carotid disease and increased risk of MI. These immune responses may reflect LDL oxidation in the artery wall, but could also affect the atherosclerotic disease process.", "doi": "10.1111/joim.12659", "pmid": "28944562", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-23T15:08:28.793Z", "modified": "2023-04-14T13:56:08.826Z"}, {"entity": "publication", "iuid": "1cb0377941b44b6f906dd35e4b1d6eee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1cb0377941b44b6f906dd35e4b1d6eee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1cb0377941b44b6f906dd35e4b1d6eee"}}, "title": "An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus.", "authors": [{"family": "Schramm", "given": "Frederic D", "initials": "FD", "orcid": "0000-0003-1858-7770", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a56c58ad5de4950a837a7457e64a1e4.json"}}, {"family": "Heinrich", "given": "Kristina", "initials": "K"}, {"family": "Th\u00fcring", "given": "Marietta", "initials": "M"}, {"family": "Bernhardt", "given": "J\u00f6rg", "initials": "J"}, {"family": "Jonas", "given": "Kristina", "initials": "K", "orcid": "0000-0002-1469-4424", "researcher": {"href": "https://publications.scilifelab.se/researcher/3351b638c7904141b4ae20dd41929e26.json"}}], "type": "journal article", "published": "2017-12-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "12", "pages": "e1007148", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions. In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress. The molecular reasons underlying Hsp70 essentiality remain in most cases unclear. Here, we demonstrate that DnaK is essential in the \u03b1-proteobacterium Caulobacter crescentus due to its regulatory function in gene expression. Using a suppressor screen we identified mutations that allow growth in the absence of DnaK. All mutations reduced the activity of the heat shock sigma factor \u03c332, demonstrating that the DnaK-dependent inactivation of \u03c332 is a growth requirement. While most mutations occurred in the rpoH gene encoding \u03c332, we also identified mutations affecting \u03c332 activity or stability in trans, providing important new insight into the regulatory mechanisms controlling \u03c332 activity. Most notably, we describe a mutation in the ATP dependent protease HslUV that induces rapid degradation of \u03c332, and a mutation leading to increased levels of the house keeping \u03c370 that outcompete \u03c332 for binding to the RNA polymerase. We demonstrate that \u03c332 inhibits growth and that its unrestrained activity leads to an extensive reprogramming of global gene expression, resulting in upregulation of repair and maintenance functions and downregulation of the growth-promoting functions of protein translation, DNA replication and certain metabolic processes. While this re-allocation from proliferative to maintenance functions could provide an advantage during heat stress, it leads to growth defects under favorable conditions. We conclude that Caulobacter has co-opted the DnaK chaperone system as an essential regulator of gene expression under conditions when its folding activity is dispensable.", "doi": "10.1371/journal.pgen.1007148", "pmid": "29281627", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-01799"}, {"db": "pmc", "key": "PMC5760092"}], "notes": [], "created": "2019-01-07T11:23:22.013Z", "modified": "2021-06-21T14:57:09.516Z"}, {"entity": "publication", "iuid": "3ed56227ce694d0b8a4fbaabec439db8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ed56227ce694d0b8a4fbaabec439db8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ed56227ce694d0b8a4fbaabec439db8"}}, "title": "Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling", "authors": [{"family": "Petersen", "given": "Julian", "initials": "J"}, {"family": "Wright", "given": "Shane C", "initials": "SC"}, {"family": "Rodr\u00edguez", "given": "David", "initials": "D"}, {"family": "Matricon", "given": "Pierre", "initials": "P"}, {"family": "Lahav", "given": "Noa", "initials": "N"}, {"family": "Vromen", "given": "Aviv", "initials": "A"}, {"family": "Friedler", "given": "Assaf", "initials": "A"}, {"family": "Str\u00f6mqvist", "given": "Johan", "initials": "J"}, {"family": "Wennmalm", "given": "Stefan", "initials": "S"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Schulte", "given": "Gunnar", "initials": "G"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-00253-9", "pmid": "28790300", "labels": {"Fluorescence Correlation Spectroscopy": "Collaborative", "Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-26T08:07:07.658Z", "modified": "2021-05-24T15:33:38.128Z"}, {"entity": "publication", "iuid": "1b64378122df401ea8d44baa1f502671", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b64378122df401ea8d44baa1f502671.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b64378122df401ea8d44baa1f502671"}}, "title": "A female Viking warrior confirmed by genomics.", "authors": [{"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0001-8964-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3a47cc07e9d4b8592dba430785681b5.json"}}, {"family": "Zachrisson", "given": "Torun", "initials": "T"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Sobrado", "given": "Veronica", "initials": "V"}, {"family": "Price", "given": "Neil", "initials": "N"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}], "type": "historical article", "published": "2017-12-00", "journal": {"volume": "164", "issn": "1096-8644", "issue": "4", "title": "Am. J. Phys. Anthropol.", "pages": "853-860", "issn-l": "0002-9483"}, "abstract": "The objective of this study has been to confirm the sex and the affinity of an individual buried in a well-furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.\n\nGenome-wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern-day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.\n\nThe genomic results revealed the lack of a Y-chromosome and thus a female biological sex, and the mtDNA analyses support a single-individual origin of sampled elements. The genetic affinity is close to present-day North Europeans, and within Sweden to the southern and south-central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.\n\nThe identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time-period. The results call for caution against generalizations regarding social orders in past societies.", "doi": "10.1002/ajpa.23308", "pmid": "28884802", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5724682"}], "notes": [], "created": "2017-11-03T16:18:39.012Z", "modified": "2024-01-16T13:48:47.310Z"}, {"entity": "publication", "iuid": "80c5501a15564f2eb10243009cd39671", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c5501a15564f2eb10243009cd39671.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c5501a15564f2eb10243009cd39671"}}, "title": "A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family", "authors": [{"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Zitnik", "given": "Marinka", "initials": "M"}, {"family": "Jemth", "given": "Ann Sofie", "initials": "AS"}, {"family": "Carter", "given": "Megan", "initials": "M"}, {"family": "Unterlass", "given": "Judith E", "initials": "JE"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Karem", "given": "Zhir", "initials": "Z"}, {"family": "Calder\u00f3n-Monta\u00f1o", "given": "Jos\u00e9 Manuel", "initials": "JM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Edqvist", "given": "Per Henrik", "initials": "PH"}, {"family": "Matuszewski", "given": "Damian J", "initials": "DJ"}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Berntsson", "given": "Ronnie P A", "initials": "RPA"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Studham", "given": "Matthew", "initials": "M"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}, {"family": "Zupan", "given": "Blaz", "initials": "B"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-017-01642-w", "pmid": "29142246", "labels": {"Protein Science Facility (PSF)": "Service", "BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": "Biochemical and Cellular Screening", "created": "2017-11-16T10:37:23.396Z", "modified": "2025-10-17T13:05:08.653Z"}, {"entity": "publication", "iuid": "18346d9935a9491282d59dfb6b4cd277", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18346d9935a9491282d59dfb6b4cd277.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18346d9935a9491282d59dfb6b4cd277"}}, "title": "A short feature vector for image matching: The Log-Polar Magnitude feature descriptor.", "authors": [{"family": "Matuszewski", "given": "Damian J", "initials": "DJ", "orcid": "0000-0002-6148-5174", "researcher": {"href": "https://publications.scilifelab.se/researcher/0329e24125c3443e99e51435bea6af85.json"}}, {"family": "Hast", "given": "Anders", "initials": "A"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Sintorn", "given": "Ida-Maria", "initials": "IM", "orcid": "0000-0002-8307-7411", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ff79494ec3842ffaa7448d2e3277f6b.json"}}], "type": "journal article", "published": "2017-11-30", "journal": {"volume": "12", "issn": "1932-6203", "issue": "11", "pages": "e0188496", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The choice of an optimal feature detector-descriptor combination for image matching often depends on the application and the image type. In this paper, we propose the Log-Polar Magnitude feature descriptor-a rotation, scale, and illumination invariant descriptor that achieves comparable performance to SIFT on a large variety of image registration problems but with much shorter feature vectors. The descriptor is based on the Log-Polar Transform followed by a Fourier Transform and selection of the magnitude spectrum components. Selecting different frequency components allows optimizing for image patterns specific for a particular application. In addition, by relying only on coordinates of the found features and (optionally) feature sizes our descriptor is completely detector independent. We propose 48- or 56-long feature vectors that potentially can be shortened even further depending on the application. Shorter feature vectors result in better memory usage and faster matching. This combined with the fact that the descriptor does not require a time-consuming feature orientation estimation (the rotation invariance is achieved solely by using the magnitude spectrum of the Log-Polar Transform) makes it particularly attractive to applications with limited hardware capacity. Evaluation is performed on the standard Oxford dataset and two different microscopy datasets; one with fluorescence and one with transmission electron microscopy images. Our method performs better than SURF and comparable to SIFT on the Oxford dataset, and better than SIFT on both microscopy datasets indicating that it is particularly useful in applications with microscopy images.", "doi": "10.1371/journal.pone.0188496", "pmid": "29190737", "labels": {"BioImage Informatics": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-08232"}, {"db": "pmc", "key": "PMC5708636"}], "notes": [], "created": "2018-10-28T08:15:53.022Z", "modified": "2023-06-19T12:59:58.028Z"}, {"entity": "publication", "iuid": "dcdd0e77f81742ba8bd8593d8b5a6659", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcdd0e77f81742ba8bd8593d8b5a6659.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcdd0e77f81742ba8bd8593d8b5a6659"}}, "title": "Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.", "authors": [{"family": "Karthik", "given": "Govindasamy-Muralidharan", "initials": "GM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "St\u00e5lhammar", "given": "Gustav", "initials": "G"}, {"family": "L\u00f6vrot", "given": "John", "initials": "J"}, {"family": "Ullah", "given": "Ikram", "initials": "I"}, {"family": "Alkodsi", "given": "Amjad", "initials": "A"}, {"family": "Ma", "given": "Ran", "initials": "R"}, {"family": "Wedlund", "given": "Lena", "initials": "L"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Frisell", "given": "Jan", "initials": "J"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Hartman", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-11-29", "journal": {"volume": "17", "issn": "1471-2407", "issue": "1", "pages": "802", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Transcriptomic profiling of breast tumors provides opportunity for subtyping and molecular-based patient stratification. In diagnostic applications the specimen profiled should be representative of the expression profile of the whole tumor and ideally capture properties of the most aggressive part of the tumor. However, breast cancers commonly exhibit intra-tumor heterogeneity at molecular, genomic and in phenotypic level, which can arise during tumor evolution. Currently it is not established to what extent a random sampling approach may influence molecular breast cancer diagnostics.\n\nIn this study we applied RNA-sequencing to quantify gene expression in 43 pieces (2-5 pieces per tumor) from 12 breast tumors (Cohort 1). We determined molecular subtype and transcriptomic grade for all tumor pieces and analysed to what extent pieces originating from the same tumors are concordant or discordant with each other. Additionally, we validated our finding in an independent cohort consisting of 19 pieces (2-6 pieces per tumor) from 6 breast tumors (Cohort 2) profiled using microarray technique. Exome sequencing was also performed on this cohort, to investigate the extent of intra-tumor genomic heterogeneity versus the intra-tumor molecular subtype classifications.\n\nMolecular subtyping was consistent in 11 out of 12 tumors and transcriptomic grade assignments were consistent in 11 out of 12 tumors as well. Molecular subtype predictions revealed consistent subtypes in four out of six patients in this cohort 2. Interestingly, we observed extensive intra-tumor genomic heterogeneity in these tumor pieces but not in their molecular subtype classifications.\n\nOur results suggest that macroscopic intra-tumoral transcriptomic heterogeneity is limited and unlikely to have an impact on molecular diagnostics for most patients.", "doi": "10.1186/s12885-017-3815-2", "pmid": "29187174", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-017-3815-2"}, {"db": "pmc", "key": "PMC5708109"}], "notes": [], "created": "2018-01-10T09:45:04.700Z", "modified": "2020-01-21T13:56:11.065Z"}, {"entity": "publication", "iuid": "cc80f2d72073432f9e9ffc25bd0f21f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc80f2d72073432f9e9ffc25bd0f21f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc80f2d72073432f9e9ffc25bd0f21f9"}}, "title": "Evidence that circulating proteins are more promising than miRNAs for identification of patients with squamous cell carcinoma of the tongue.", "authors": [{"family": "Boldrup", "given": "Linda", "initials": "L"}, {"family": "Troiano", "given": "Giuseppe", "initials": "G"}, {"family": "Gu", "given": "Xiaolian", "initials": "X"}, {"family": "Coates", "given": "Philip", "initials": "P"}, {"family": "F\u00e5hraeus", "given": "Robin", "initials": "R"}, {"family": "Wilms", "given": "Torben", "initials": "T"}, {"family": "Norberg-Spaak", "given": "Lena", "initials": "L"}, {"family": "Wang", "given": "Lixiao", "initials": "L"}, {"family": "Nylander", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2017-11-28", "journal": {"title": "Oncotarget", "issn": "1949-2553", "issn-l": "1949-2553", "volume": "8", "issue": "61", "pages": "103437-103448"}, "abstract": "Despite intense research, squamous cell carcinoma of the tongue remains a devastating disease with a five-year survival of around 60%. Late detection and recurrence are the main causes for poor survival. The identification of circulating factors for early diagnosis and/or prognosis of cancer is a rapidly evolving field of interest, with the hope of finding stable and reliable markers of clinical significance. The aim of this study was to evaluate circulating miRNAs and proteins as potential factors for distinguishing patients with tongue squamous cell carcinoma from healthy controls. Array-based profiling of 372 miRNAs in plasma samples showed broad variations between different patients and did not show any evidence for their use in diagnosis of tongue cancer. Although one miRNA, miR-150, was significantly down-regulated in plasma from patients compared to controls. Surprisingly, the corresponding tumor tissue showed an up-regulation of miR-150. Among circulating proteins, 23 were identified as potential markers of squamous cell carcinoma of the tongue. These findings imply that circulating proteins are a more promising source of biomarkers for tongue squamous cell carcinomas than circulating miRNAs. The data also highlight that circulating markers are not always directly associated with tumor cell properties.", "doi": "10.18632/oncotarget.21402", "pmid": "29262574", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "21402"}, {"db": "pmc", "key": "PMC5732740"}], "notes": [], "created": "2020-01-23T15:08:27.505Z", "modified": "2023-04-14T13:56:09.027Z"}, {"entity": "publication", "iuid": "274665fc3b304c149ac41b8dc63b4994", "links": {"self": {"href": "https://publications.scilifelab.se/publication/274665fc3b304c149ac41b8dc63b4994.json"}, "display": {"href": "https://publications.scilifelab.se/publication/274665fc3b304c149ac41b8dc63b4994"}}, "title": "Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.", "authors": [{"family": "Kashif", "given": "Muhammad", "initials": "M"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Mansoori", "given": "Sharmineh", "initials": "S"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}], "type": "journal article", "published": "2017-11-28", "journal": {"title": "Oncotarget", "issn": "1949-2553", "volume": "8", "issue": "61", "pages": "103952-103967", "issn-l": "1949-2553"}, "abstract": "We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy\u2122 II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.", "doi": "10.18632/oncotarget.21895", "pmid": "29262612", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "21895"}, {"db": "pmc", "key": "PMC5732778"}], "notes": [], "created": "2020-12-10T12:22:28.979Z", "modified": "2025-10-17T13:05:08.682Z"}, {"entity": "publication", "iuid": "04e76f0947204c27a9f2e4e51b7d1713", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e76f0947204c27a9f2e4e51b7d1713.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e76f0947204c27a9f2e4e51b7d1713"}}, "title": "STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.", "authors": [{"family": "Hochgerner", "given": "Hannah", "initials": "H", "orcid": "0000-0002-7739-666X", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b8fc33efd44cfb2bb60a3f250a518.json"}}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Hodge", "given": "Rebecca", "initials": "R"}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Heskol", "given": "Abeer", "initials": "A"}, {"family": "Hubschle", "given": "Hermann", "initials": "H"}, {"family": "Lin", "given": "Philip", "initials": "P"}, {"family": "Picelli", "given": "Simone", "initials": "S"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Ratz", "given": "Michael", "initials": "M"}, {"family": "Dunne", "given": "Jude", "initials": "J"}, {"family": "Husain", "given": "Syed", "initials": "S"}, {"family": "Lein", "given": "Ed", "initials": "E", "orcid": "0000-0001-9012-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd450c764a4431aa798630053343cd6.json"}}, {"family": "Srinivasan", "given": "Maithreyan", "initials": "M"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}], "type": "journal article", "published": "2017-11-27", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "16327", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform while retaining a high degree of flexibility, potentially also for other high-throughput applications.", "doi": "10.1038/s41598-017-16546-4", "pmid": "29180631", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5703850"}, {"db": "pii", "key": "10.1038/s41598-017-16546-4"}], "notes": [], "created": "2018-01-10T09:45:09.064Z", "modified": "2024-01-21T18:00:22.804Z"}, {"entity": "publication", "iuid": "123bf2cc4a644ec4bb602d2feaa85eae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/123bf2cc4a644ec4bb602d2feaa85eae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/123bf2cc4a644ec4bb602d2feaa85eae"}}, "title": "Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control.", "authors": [{"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Franke", "given": "Kamila B", "initials": "KB"}, {"family": "Maurer", "given": "Michael", "initials": "M"}, {"family": "J\u00e4ger", "given": "Jasmin", "initials": "J"}, {"family": "Hantke", "given": "Ingo", "initials": "I"}, {"family": "Gloge", "given": "Felix", "initials": "F"}, {"family": "Linder", "given": "Daniela", "initials": "D"}, {"family": "Gremer", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-3421-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe66266bc6c94ec59e03a94d6e3fc997.json"}}, {"family": "Turgay", "given": "K\u00fcr\u015fad", "initials": "K", "orcid": "0000-0002-8959-492X", "researcher": {"href": "https://publications.scilifelab.se/researcher/55cd714404fb4112bd7b3ed1c4328a17.json"}}, {"family": "Bukau", "given": "Bernd", "initials": "B"}, {"family": "Mogk", "given": "Axel", "initials": "A", "orcid": "0000-0003-3674-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/56a1d7fc519743029c9ae615086d8093.json"}}], "type": "journal article", "published": "2017-11-22", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "Ring-forming AAA+ chaperones exert ATP-fueled substrate unfolding by threading through a central pore. This activity is potentially harmful requiring mechanisms for tight repression and substrate-specific activation. The AAA+ chaperone ClpC with the peptidase ClpP forms a bacterial protease essential to virulence and stress resistance. The adaptor MecA activates ClpC by targeting substrates and stimulating ClpC ATPase activity. We show how ClpC is repressed in its ground state by determining ClpC cryo-EM structures with and without MecA. ClpC forms large two-helical assemblies that associate via head-to-head contacts between coiled-coil middle domains (MDs). MecA converts this resting state to an active planar ring structure by binding to MD interaction sites. Loss of ClpC repression in MD mutants causes constitutive activation and severe cellular toxicity. These findings unravel an unexpected regulatory concept executed by coiled-coil MDs to tightly control AAA+ chaperone activity.", "doi": "10.7554/eLife.30120", "pmid": "29165246", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5699869"}], "notes": [], "created": "2017-11-24T14:39:40.774Z", "modified": "2021-07-05T17:22:27.628Z"}, {"entity": "publication", "iuid": "dd3127485e334ad7b4b073d0399d4d33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd3127485e334ad7b4b073d0399d4d33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd3127485e334ad7b4b073d0399d4d33"}}, "title": "Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Feuerborn", "given": "Tatiana", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "van der Plicht", "given": "Johannes", "initials": "J"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2017-11-20", "journal": {"volume": "27", "issn": "1879-0445", "issue": "22", "pages": "3505-3510.e3", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. We hypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.", "doi": "10.1016/j.cub.2017.09.064", "pmid": "29103934", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(17)31264-2"}], "notes": [], "created": "2017-11-03T13:20:53.917Z", "modified": "2021-07-07T20:31:10.935Z"}, {"entity": "publication", "iuid": "10063878eda648f79dc68fd0c818180e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10063878eda648f79dc68fd0c818180e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10063878eda648f79dc68fd0c818180e"}}, "title": "Dog ownership and the risk of cardiovascular disease and death - a nationwide cohort study.", "authors": [{"family": "Mubanga", "given": "Mwenya", "initials": "M"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Nowak", "given": "Christoph", "initials": "C"}, {"family": "Egenvall", "given": "Agneta", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}], "type": "journal article", "published": "2017-11-17", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15821", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Dogs may be beneficial in reducing cardiovascular risk in their owners by providing social support and motivation for physical activity. We aimed to investigate the association of dog ownership with incident cardiovascular disease (CVD) and death in a register-based prospective nation-wide cohort (n = 3,432,153) with up to 12 years of follow-up. Self-reported health and lifestyle habits were available for 34,202 participants in the Swedish Twin Register. Time-to-event analyses with time-updated covariates were used to calculate hazard ratios (HR) with 95% confidence intervals (CI). In single- and multiple-person households, dog ownership (13.1%) was associated with lower risk of death, HR 0.67 (95% CI, 0.65-0.69) and 0.89 (0.87-0.91), respectively; and CVD death, HR 0.64 (0.59-0.70), and 0.85 (0.81-0.90), respectively. In single-person households, dog ownership was inversely associated with cardiovascular outcomes (HR composite CVD 0.92, 95% CI, 0.89-0.94). Ownership of hunting breed dogs was associated with lowest risk of CVD. Further analysis in the Twin Register could not replicate the reduced risk of CVD or death but also gave no indication of confounding by disability, comorbidities or lifestyle factors. In conclusion, dog ownership appears to be associated with lower risk of CVD in single-person households and lower mortality in the general population.", "doi": "10.1038/s41598-017-16118-6", "pmid": "29150678", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-16118-6"}, {"db": "pmc", "key": "PMC5693989"}], "notes": [], "created": "2017-11-22T08:32:46.202Z", "modified": "2021-06-21T15:00:47.391Z"}, {"entity": "publication", "iuid": "02546012074748ecab75b03ca59eb1b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02546012074748ecab75b03ca59eb1b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02546012074748ecab75b03ca59eb1b9"}}, "title": "Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy", "authors": [{"family": "Bai", "given": "Bing", "initials": "B"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Hanson", "given": "Johannes", "initials": "J"}, {"family": "Bentsink", "given": "Le\u00f3nie", "initials": "L"}], "type": "journal-article", "published": "2017-11-15", "journal": {"volume": null, "issn": "0028-646X", "issue": null, "pages": null, "title": "New Phytol", "issn-l": "0028-646X"}, "abstract": "The importance of translational regulation during Arabidopsis seed germination has been shown previously. Here the role of transcriptional and translational regulation during seed imbibition of the very dormant DELAY OF GERMINATION 1 (DOG1) near-isogenic line was investigated. Polysome profiling was performed on dormant and after-ripened seeds imbibed for 6 and 24\u00a0h in water and in the transcription inhibitor cordycepin. Transcriptome and translatome changes were investigated. Ribosomal profiles of after-ripened seeds imbibed in cordycepin mimic those of dormant seeds. The polysome occupancy of mRNA species is not affected by germination inhibition, either as a result of seed dormancy or as a result of cordycepin treatment, indicating the importance of the regulation of transcript abundance. The expression of auxin metabolism genes is discriminative during the imbibition of after-ripened and dormant seeds, which is confirmed by altered concentrations of indole-3-acetic acid conjugates and precursors.", "doi": "10.1111/nph.14885", "pmid": "29139127", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:27:51.864Z", "modified": "2025-10-17T13:03:18.472Z"}, {"entity": "publication", "iuid": "86b4dfef19e14e50a0aa6009e61cb8e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86b4dfef19e14e50a0aa6009e61cb8e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86b4dfef19e14e50a0aa6009e61cb8e7"}}, "title": "Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.", "authors": [{"family": "Hammarsj\u00f6", "given": "A", "initials": "A"}, {"family": "Wang", "given": "Z", "initials": "Z"}, {"family": "Vaz", "given": "R", "initials": "R"}, {"family": "Taylan", "given": "F", "initials": "F"}, {"family": "Sedghi", "given": "M", "initials": "M"}, {"family": "Girisha", "given": "K M", "initials": "KM"}, {"family": "Chitayat", "given": "D", "initials": "D"}, {"family": "Neethukrishna", "given": "K", "initials": "K"}, {"family": "Shannon", "given": "P", "initials": "P"}, {"family": "Godoy", "given": "R", "initials": "R"}, {"family": "Gowrishankar", "given": "K", "initials": "K"}, {"family": "Lindstrand", "given": "A", "initials": "A"}, {"family": "Nasiri", "given": "J", "initials": "J"}, {"family": "Baktashian", "given": "M", "initials": "M"}, {"family": "Newton", "given": "P T", "initials": "PT"}, {"family": "Guo", "given": "L", "initials": "L"}, {"family": "Hofmeister", "given": "W", "initials": "W"}, {"family": "Pettersson", "given": "M", "initials": "M"}, {"family": "Chagin", "given": "A S", "initials": "AS"}, {"family": "Nishimura", "given": "G", "initials": "G"}, {"family": "Yan", "given": "L", "initials": "L"}, {"family": "Matsumoto", "given": "N", "initials": "N"}, {"family": "Nordgren", "given": "A", "initials": "A"}, {"family": "Miyake", "given": "N", "initials": "N"}, {"family": "Grigelioniene", "given": "G", "initials": "G"}, {"family": "Ikegawa", "given": "S", "initials": "S"}], "type": "journal article", "published": "2017-11-14", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15585", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The skeletal ciliopathies are a heterogeneous group of disorders with a significant clinical and genetic variability and the main clinical features are thoracic hypoplasia and short tubular bones. To date, 25 genes have been identified in association with skeletal ciliopathies. Mutations in the KIAA0753 gene have recently been associated with Joubert syndrome\u00a0(JBTS) and orofaciodigital (OFD) syndrome. We report biallelic pathogenic variants in KIAA0753 in four patients with short-rib type skeletal dysplasia. The manifestations in our patients are variable and ranging from fetal lethal to viable and moderate skeletal dysplasia with narrow thorax and abnormal metaphyses. We demonstrate that KIAA0753 is expressed in normal fetal human growth plate and show that the affected fetus, with a compound heterozygous frameshift and a nonsense mutation in KIAA0753, has an abnormal proliferative zone and a broad hypertrophic zone. The importance of KIAA0753 for normal skeletal development is further confirmed by our findings that zebrafish embryos homozygous for a nonsense mutation in kiaa0753 display altered cartilage patterning.", "doi": "10.1038/s41598-017-15442-1", "pmid": "29138412", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-15442-1"}, {"db": "pmc", "key": "PMC5686170"}], "notes": [], "created": "2018-01-10T09:44:15.685Z", "modified": "2020-01-21T13:56:11.126Z"}, {"entity": "publication", "iuid": "bab8d5625407431186a5d494ec9f43b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bab8d5625407431186a5d494ec9f43b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bab8d5625407431186a5d494ec9f43b3"}}, "title": "Diffusion in Ionic Liquid\u2013Cellulose Solutions during Coagulation in Water: Mass Transport and Coagulation Rate Measurements", "authors": [{"family": "Hedlund", "given": "Artur", "initials": "A", "orcid": "0000-0002-6498-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4d7f8b4fcc2420083d60c38b39e03fc.json"}}, {"family": "K\u00f6hnke", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1259-6414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3c2736c99494b3abe3373e03bfa8c62.json"}}, {"family": "Theliander", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-11-14", "journal": {"volume": "50", "issn": "0024-9297", "issue": "21", "pages": "8707-8719", "title": "Macromolecules", "issn-l": null}, "abstract": null, "doi": "10.1021/acs.macromol.7b01594", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:31:28.985Z", "modified": "2025-10-17T13:03:59.271Z"}, {"entity": "publication", "iuid": "322d19d8a8f24583bfce02ae7f8a2aa2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/322d19d8a8f24583bfce02ae7f8a2aa2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/322d19d8a8f24583bfce02ae7f8a2aa2"}}, "title": "Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema.", "authors": [{"family": "Ega\u00f1a", "given": "Isabel", "initials": "I"}, {"family": "Kaito", "given": "Hiroshi", "initials": "H"}, {"family": "Nitzsche", "given": "Anja", "initials": "A"}, {"family": "Becker", "given": "Lore", "initials": "L"}, {"family": "Ballester-Lopez", "given": "Carolina", "initials": "C"}, {"family": "Niaudet", "given": "Colin", "initials": "C"}, {"family": "Petkova", "given": "Milena", "initials": "M"}, {"family": "Liu", "given": "Wei", "initials": "W"}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M"}, {"family": "Vernaleken", "given": "Alexandra", "initials": "A"}, {"family": "Klopstock", "given": "Thomas", "initials": "T"}, {"family": "Fuchs", "given": "Helmut", "initials": "H"}, {"family": "Gailus-Durner", "given": "Valerie", "initials": "V"}, {"family": "Hrabe de Angelis", "given": "Martin", "initials": "M"}, {"family": "Rask-Andersen", "given": "Helge", "initials": "H"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Yildirim", "given": "Ali \u00d6", "initials": "A\u00d6"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "German Mouse Clinic Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-11-13", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15453", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Paladin (Pald1, mKIAA1274 or x99384) was identified in screens for vascular-specific genes and is a putative phosphatase. Paladin has also been proposed to be involved in various biological processes such as insulin signaling, innate immunity and neural crest migration. To determine the role of paladin we have now characterized the Pald1 knock-out mouse in a broad array of behavioral, physiological and biochemical tests. Here, we show that female, but not male, Pald1 heterozygous and homozygous knock-out mice display an emphysema-like histology with increased alveolar air spaces and impaired lung function with an obstructive phenotype. In contrast to many other tissues where Pald1 is restricted to the vascular compartment, Pald1 is expressed in both the epithelial and mesenchymal compartments of the postnatal lung. However, in Pald1 knock-out females, there is a specific increase in apoptosis and proliferation of endothelial cells, but not in non-endothelial cells. This results in a transient reduction of endothelial cells in the maturing lung. Our data suggests that Pald1 is required during lung vascular development and for normal function of the developing and adult lung in a sex-specific manner. To our knowledge, this is the first report of a sex-specific effect on endothelial cell apoptosis.", "doi": "10.1038/s41598-017-14894-9", "pmid": "29133847", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-14894-9"}, {"db": "pmc", "key": "PMC5684320"}], "notes": [], "created": "2017-12-05T16:14:22.822Z", "modified": "2021-07-08T11:36:15.159Z"}, {"entity": "publication", "iuid": "8a27a149914b497aba8916c5133fc80b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a27a149914b497aba8916c5133fc80b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a27a149914b497aba8916c5133fc80b"}}, "title": "Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal-article", "published": "2017-11-13", "journal": {"volume": "8", "issn": "1664-3224", "issue": null, "pages": null, "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "B cells produce antibodies, key effector molecules in health and disease. They mature their properties, including their affinity for antigen, through hypermutation events; processes that involve, e.g., base substitution, codon insertion and deletion, often in association with an isotype switch. Investigations of antibody evolution define modes whereby particular antibody responses are able to form, and such studies provide insight important for instance for development of efficient vaccines. Antibody evolution is also used \n            in vitro for the design of antibodies with improved properties. To better understand the basic concepts of antibody evolution, we analyzed the mutational paths, both in terms of amino acid substitution and insertions and deletions, taken by antibodies of the IgG isotype. The analysis focused on the evolution of the heavy chain variable domain of sets of antibodies, each with an origin in 1 of 11 different germline genes representing six human heavy chain germline gene subgroups. Investigated genes were isolated from cells of human bone marrow, a major site of antibody production, and characterized by next-generation sequencing and an in-house bioinformatics pipeline. Apart from substitutions within the complementarity determining regions, multiple framework residues including those in protein cores were targets of extensive diversification. Diversity, both in terms of substitutions, and insertions and deletions, in antibodies is focused to different positions in the sequence in a germline gene-unique manner. Altogether, our findings create a framework for understanding patterns of evolution of antibodies from defined germline genes.", "doi": "10.3389/fimmu.2017.01433", "pmid": "29180996", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-13T09:53:31.932Z", "modified": "2025-10-17T13:05:08.695Z"}, {"entity": "publication", "iuid": "37bd588cb5304fa29682016691c551fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37bd588cb5304fa29682016691c551fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37bd588cb5304fa29682016691c551fa"}}, "title": "Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.", "authors": [{"family": "Jabs", "given": "Verena", "initials": "V"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "K\u00f6nig", "given": "Helena", "initials": "H"}, {"family": "Grinberg", "given": "Marianna", "initials": "M"}, {"family": "Madjar", "given": "Katrin", "initials": "K"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Bergkvist", "given": "Michael", "initials": "M"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Ickstadt", "given": "Katja", "initials": "K"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Hengstler", "given": "Jan G", "initials": "JG"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2017-11-07", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "12", "issue": "11", "pages": "e0187246", "issn-l": "1932-6203"}, "abstract": "Non-small cell lung cancer (NSCLC) represents a genomically unstable cancer type with extensive copy number aberrations. The relationship of gene copy number alterations and subsequent mRNA levels has only fragmentarily been described. The aim of this study was to conduct a genome-wide analysis of gene copy number gains and corresponding gene expression levels in a clinically well annotated NSCLC patient cohort (n = 190) and their association with survival. While more than half of all analyzed gene copy number-gene expression pairs showed statistically significant correlations (10,296 of 18,756 genes), high correlations, with a correlation coefficient >0.7, were obtained only in a subset of 301 genes (1.6%), including KRAS, EGFR and MDM2. Higher correlation coefficients were associated with higher copy number and expression levels. Strong correlations were frequently based on few tumors with high copy number gains and correspondingly increased mRNA expression. Among the highly correlating genes, GO groups associated with posttranslational protein modifications were particularly frequent, including ubiquitination and neddylation. In a meta-analysis including 1,779 patients we found that survival associated genes were overrepresented among highly correlating genes (61 of the 301 highly correlating genes, FDR adjusted p<0.05). Among them are the chaperone CCT2, the core complex protein NUP107 and the ubiquitination and neddylation associated protein CAND1. In conclusion, in a comprehensive analysis we described a distinct set of highly correlating genes. These genes were found to be overrepresented among survival-associated genes based on gene expression in a large collection of publicly available datasets.", "doi": "10.1371/journal.pone.0187246", "pmid": "29112949", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-15601"}, {"db": "pmc", "key": "PMC5675410"}], "notes": [], "created": "2019-12-20T07:50:22.424Z", "modified": "2019-12-20T07:50:22.453Z"}, {"entity": "publication", "iuid": "7b3bd58219404f018bc4081bbecfde4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b3bd58219404f018bc4081bbecfde4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b3bd58219404f018bc4081bbecfde4f"}}, "title": "Adipocyte Expression of SLC19A1 Links DNA Hypermethylation to Adipose Tissue Inflammation and Insulin Resistance", "authors": [{"family": "Petrus", "given": "Paul", "initials": "P"}, {"family": "Bialesova", "given": "Lucia", "initials": "L"}, {"family": "Checa", "given": "Antonio", "initials": "A"}, {"family": "Kerr", "given": "Alastair", "initials": "A"}, {"family": "Naz", "given": "Shama", "initials": "S"}, {"family": "B\u00e4ckdahl", "given": "Jesper", "initials": "J"}, {"family": "Gracia", "given": "Ana", "initials": "A"}, {"family": "Toft", "given": "Sofia", "initials": "S"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Hed\u00e9n", "given": "Per", "initials": "P"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Mejhert", "given": "Niklas", "initials": "N"}, {"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}], "type": "journal-article", "published": "2017-11-07", "journal": {"volume": null, "issn": "0021-972X", "issue": null, "pages": null, "title": "", "issn-l": null}, "abstract": null, "doi": "10.1210/jc.2017-01382", "pmid": "29121255", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-20T15:14:16.662Z", "modified": "2017-11-21T11:52:12.393Z"}, {"entity": "publication", "iuid": "63a7fc722c47447b9dc981a289d38084", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63a7fc722c47447b9dc981a289d38084.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63a7fc722c47447b9dc981a289d38084"}}, "title": "Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Gillingwater", "given": "Thomas H", "initials": "TH"}, {"family": "MacCallum", "given": "Malcolm", "initials": "M"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Dobney", "given": "Keith", "initials": "K"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}], "type": "journal article", "published": "2017-11-06", "journal": {"volume": "27", "issn": "1879-0445", "issue": "21", "pages": "3396-3402.e5", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th-11th centuries CE) yielded sufficient autosomal genome coverage (0.21\u00d7 to 3.93\u00d7) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.", "doi": "10.1016/j.cub.2017.09.059", "pmid": "29107554", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(17)31257-5"}], "notes": [], "created": "2018-01-10T09:44:16.403Z", "modified": "2023-06-20T15:54:27.159Z"}, {"entity": "publication", "iuid": "61c4edd44f7c449aac10aa3423c4a688", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61c4edd44f7c449aac10aa3423c4a688.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61c4edd44f7c449aac10aa3423c4a688"}}, "title": "Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1756-9469", "researcher": {"href": "https://publications.scilifelab.se/researcher/1863fb821bdf444ba26e351f764e4a70.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3784-4285", "researcher": {"href": "https://publications.scilifelab.se/researcher/d56063f091264c0587c973a82335c578.json"}}, {"family": "Munters", "given": "Arielle R", "initials": "AR", "orcid": "0000-0003-1512-6565", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e089ee0008a4ea3a9603fa011f973de.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/603244b141da49dfa9ff3a8d17f42b70.json"}}, {"family": "Steyn", "given": "Maryna", "initials": "M", "orcid": "0000-0002-0215-9723", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d9921b3dba248eab7b85488dda530ad.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-11-03", "journal": {"volume": "358", "issn": "1095-9203", "issue": "6363", "pages": "652-655", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.", "doi": "10.1126/science.aao6266", "pmid": "28971970", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aao6266"}], "notes": [], "created": "2017-10-30T09:27:46.012Z", "modified": "2024-01-16T13:48:47.317Z"}, {"entity": "publication", "iuid": "ecc7551bf07d4ecf930ff13d013aeee3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecc7551bf07d4ecf930ff13d013aeee3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecc7551bf07d4ecf930ff13d013aeee3"}}, "title": "RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole", "authors": [{"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Tarbiat", "given": "Behdad", "initials": "B"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Jansson", "given": "D\u00e9sir\u00e9e S", "initials": "DS"}, {"family": "H\u00f6glund", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-11-03", "journal": {"volume": "12", "issn": "1932-6203", "issue": "11", "pages": "e0185182", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0185182", "pmid": "29099835", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "RNA-seq of the nematode Ascaridia galli exposed to flubendazole against untreated control", "key": "PRJEB20558"}], "notes": [], "created": "2017-11-06T13:08:22.384Z", "modified": "2020-01-21T13:56:17.125Z"}, {"entity": "publication", "iuid": "880eebdde88d41dc834023c786093f68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/880eebdde88d41dc834023c786093f68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/880eebdde88d41dc834023c786093f68"}}, "title": "Unique case of cerebrotendinous xanthomatosis revisited: All the mutations responsible for this disease are present in the CYP27A1 gene.", "authors": [{"family": "Jiao", "given": "H", "initials": "H"}, {"family": "Olin", "given": "M", "initials": "M"}, {"family": "Hansson", "given": "M", "initials": "M"}, {"family": "Eggertsen", "given": "G", "initials": "G"}, {"family": "Eriksson", "given": "M", "initials": "M"}, {"family": "Angelin", "given": "B", "initials": "B"}, {"family": "Bj\u00f6rkhem", "given": "I", "initials": "I"}], "type": "letter", "published": "2017-11-02", "journal": {"volume": null, "issn": "1365-2796", "issue": null, "title": "J. Intern. Med.", "issn-l": "0954-6820"}, "abstract": null, "doi": "10.1111/joim.12709", "pmid": "29095540", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-10T09:45:02.667Z", "modified": "2020-01-21T13:56:11.145Z"}, {"entity": "publication", "iuid": "f32d433317a047abadcdd972d785fce2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f32d433317a047abadcdd972d785fce2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f32d433317a047abadcdd972d785fce2"}}, "title": "Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.", "authors": [{"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Gaikwad", "given": "Swapnil S", "initials": "SS"}, {"family": "Jonsson", "given": "Viktor", "initials": "V"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2017-11-01", "journal": {"volume": "124", "issn": "1879-2448", "issue": null, "pages": "388-397", "title": "Water Res.", "issn-l": "0043-1354"}, "abstract": "Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India. Using shotgun metagenomics, we found a wide array (n\u00a0=\u00a0175) of horizontally transferable antibiotic resistance genes (ARGs) including carbapenemases such as NDM, VIM, KPC, OXA-48 and IMP types. The relative abundance of total ARGs was 30-fold higher in river sediments within the city compared to upstream sites. Forty four ARGs, including the tet(X) gene conferring resistance to tigecycline, OXA-58 and GES type carbapenemases, were significantly more abundant in city sediments, while two ARGs were more common at upstream sites. The recently identified mobile colistin resistance gene mcr-1 was detected only in one of the upstream samples, but not in city samples. In addition to ARGs, higher abundances of various mobile genetic elements were found in city samples, including integron-associated integrases and ISCR transposases, as well as some biocide/metal resistance genes. Virulence toxin genes as well as bacterial genera comprising many pathogens were more abundant here; the genus Acinetobacter, which is often associated with multidrug resistance and nosocomial infections, comprised up to 29% of the 16S rRNA reads, which to our best knowledge is unmatched in any other deeply sequenced metagenome. There was a strong correlation between the abundance of Acinetobacter and the OXA-58 carbapenemase gene. Our study shows that uncontrolled discharge of untreated urban waste can contribute to an overall increase of the abundance and diversity of ARGs in the environment, including those conferring resistance to last-resort antibiotics.", "doi": "10.1016/j.watres.2017.07.060", "pmid": "28780361", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(17)30633-4"}, {"db": "MG-RAST", "description": "raw metagenomic sequencing data", "key": "19878"}], "notes": [], "created": "2017-11-03T16:22:29.646Z", "modified": "2024-01-16T13:48:47.324Z"}, {"entity": "publication", "iuid": "a29d11d5638d409ebe3b76aee7ec77b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a29d11d5638d409ebe3b76aee7ec77b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a29d11d5638d409ebe3b76aee7ec77b3"}}, "title": "Highly HIV-exposed HIV uninfected Kenyan female sex workers display a thick ectocervical epithelium", "authors": [{"family": "R\u00f6hl", "given": "Maria", "initials": "M"}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/6538b950bbd440e3aa32435d23c98074.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Boily-Larouche", "given": "Genevieve", "initials": "G"}, {"family": "Cheruiyot", "given": "Julianna", "initials": "J"}, {"family": "Kimani", "given": "Makubo", "initials": "M"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Oyugi", "given": "Julius", "initials": "J"}, {"family": "Fowke", "given": "Keith R.", "initials": "KR"}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": null, "published": "2017-11-01", "journal": {"volume": null, "issn": null, "issue": null, "pages": null, "title": "HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29", "issn-l": null}, "abstract": "Background\r\nThe female genital tract is a critical site of HIV acquisition and a number of genetic and immunological correlates of relative resistance against infection have been described in the ectocervical mucosa. We hypothesize that a thick epithelium, a high concentration of epithelial junction proteins, together with a low concentration of HIV target cells (CCR5+CD4+T cells and dendritic cells) at a distant location is a beneficial combination that hinders sexual acquisition of HIV.\r\n\r\nMethods\r\nEctocervical biopsies were collected from female sex workers from Nairobi, Kenya, representing highly HIV-exposed but HIV seronegative who had been involved in sex work for 7 years or more (HESN) (n=29), HIV-infected (n=11), and uninfected individuals who were new to sex work (3 years or less) (n=39). Digital image analysis of immunofluorescent staining was used to identify genital mucosal factors affecting HIV susceptibility by characterizing the thickness and integrity as well as the spatial distribution of HIV target cells in the cervical epithelium.\r\n\r\nResults\r\nPreliminary results indicate that the HESN group display significantly thicker epithelium than the HIV+ group, and significantly lower numbers of potential HIV target cells than both the HIV+ group and those who were new to sex work.\r\n\r\nConclusion\r\nA deeper insight into what mucosal factors are affecting HIV susceptibility is of major importance to prevent sexual HIV transmission, and we hope to contribute to this needed knowledge.", "doi": null, "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T11:47:33.003Z", "modified": "2025-11-17T09:52:46.049Z"}, {"entity": "publication", "iuid": "8ce18e23922244cb80ddedc4e8cf83c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ce18e23922244cb80ddedc4e8cf83c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ce18e23922244cb80ddedc4e8cf83c2"}}, "title": "Cryo-EM reconstruction of the chlororibosome to 3.2 \u00c5 resolution within 24 h", "authors": [{"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5434ab128e04b2b951abbbea77221c8.json"}}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}}, {"family": "Paul", "given": "Bijoya", "initials": "B"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal-article", "published": "2017-11-01", "journal": {"volume": "4", "issn": "2052-2525", "issue": "6", "pages": "723-727", "title": "Int Union Crystallogr J IUCr J Int Union Cryst J IUCrJ", "issn-l": "2052-2525"}, "abstract": "The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 \u00c5 resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 \u00c5 resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.", "doi": "10.1107/s205225251701226x", "pmid": "29123673", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5668856"}, {"db": "pii", "key": "kf5004"}], "notes": [], "created": "2017-10-16T16:16:22.554Z", "modified": "2023-06-19T08:55:09.359Z"}, {"entity": "publication", "iuid": "3696fbf5832447b98e3ff70736927e22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3696fbf5832447b98e3ff70736927e22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3696fbf5832447b98e3ff70736927e22"}}, "title": "Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Lona Durazo", "given": "Frida", "initials": "F"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "17", "issn": "1755-0998", "issue": "6", "title": "Mol Ecol Resour", "pages": "e111-e121", "issn-l": "1755-098X"}, "abstract": "Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.", "doi": "10.1111/1755-0998.12699", "pmid": "28675688", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:21:38.460Z", "modified": "2024-01-16T13:48:47.331Z"}, {"entity": "publication", "iuid": "252391f3d98a43cdad8ff029b370ae4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/252391f3d98a43cdad8ff029b370ae4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/252391f3d98a43cdad8ff029b370ae4e"}}, "title": "Type B Response Regulators Act As Central Integrators in Transcriptional Control of the Auxin Biosynthesis Enzyme TAA1", "authors": [{"family": "Yan", "given": "Zhenwei", "initials": "Z"}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Li", "given": "Shuning", "initials": "S"}, {"family": "Zhao", "given": "Wanying", "initials": "W"}, {"family": "Yang", "given": "Fan", "initials": "F"}, {"family": "Wang", "given": "Meiling", "initials": "M"}, {"family": "Tao", "given": "Yi", "initials": "Y"}], "type": "journal-article", "published": "2017-11-00", "journal": {"volume": "175", "issn": "1532-2548", "issue": "3", "pages": "1438-1454", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": null, "doi": "10.1104/pp.17.00878", "pmid": "28931628", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:37:01.134Z", "modified": "2025-10-17T13:03:18.484Z"}, {"entity": "publication", "iuid": "f892ff63669141bc8f46e7fd8d8fde48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48"}}, "title": "SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Viklund", "given": "Johan", "initials": "J"}, {"family": "K\u00e4h\u00e4ri", "given": "Andreas Kusalananda", "initials": "AK"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Che", "given": "Huiwen", "initials": "H"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Dahlberg", "given": "Mats", "initials": "M"}, {"family": "Hagberg", "given": "Jonas", "initials": "J", "orcid": "0000-0003-2370-6025", "researcher": {"href": "https://publications.scilifelab.se/researcher/181649773b3e451981f5ffb2da4c60b9.json"}}, {"family": "Jareborg", "given": "Niclas", "initials": "N", "orcid": "0000-0002-4520-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09533c4bd4174ecab9ba866d22a1e585.json"}}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Jonasson", "given": "Inger", "initials": "I"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "25", "issn": "1476-5438", "issue": "11", "pages": "1253-1260", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.", "doi": "10.1038/ejhg.2017.130", "pmid": "28832569", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ejhg2017130"}, {"db": "pmc", "key": "PMC5765326"}], "notes": [], "created": "2017-08-24T14:18:14.989Z", "modified": "2024-01-16T13:48:47.338Z"}, {"entity": "publication", "iuid": "518a225ab46547e89068242a65fa52f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/518a225ab46547e89068242a65fa52f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/518a225ab46547e89068242a65fa52f2"}}, "title": "Registration free automatic identification of gold fiducial markers in MRI target delineation images for prostate radiotherapy.", "authors": [{"family": "Gustafsson", "given": "Christian", "initials": "C"}, {"family": "Korhonen", "given": "Juha", "initials": "J"}, {"family": "Persson", "given": "Emilia", "initials": "E"}, {"family": "Gunnlaugsson", "given": "Adalsteinn", "initials": "A"}, {"family": "Nyholm", "given": "Tufve", "initials": "T"}, {"family": "Olsson", "given": "Lars E", "initials": "LE"}], "type": "journal article", "published": "2017-11-00", "journal": {"title": "Med Phys", "issn": "2473-4209", "issn-l": null, "volume": "44", "issue": "11", "pages": "5563-5574"}, "abstract": "The superior soft tissue contrast of magnetic resonance imaging (MRI) compared to computed tomography (CT) has urged the integration of MRI and elimination of CT in radiotherapy treatment (RT) for prostate. An intraprostatic gold fiducial marker (GFM) appears hyperintense on CT. On T2-weighted (T2w) MRI target delineation images, the GFM appear as a small signal void similar to calcifications and post biopsy fibrosis. It can therefore be difficult to identify the markers without CT. Detectability of GFMs can be improved using additional MR images, which are manually registered to target delineation images. This task requires manual labor, and is associated with interoperator differences and image registration errors. The aim of this work was to develop and evaluate an automatic method for identification of GFMs directly in the target delineation images without the need for image registration.\r\n\r\nT2w images, intended for target delineation, and multiecho gradient echo (MEGRE) images intended for GFM identification, were acquired for prostate cancer patients. Signal voids in the target delineation images were identified as GFM candidates. The GFM appeared as round, symmetric, signal void with increasing area for increasing echo time in the MEGRE images. These image features were exploited for automatic identification of GFMs in a MATLAB model using a patient training dataset (n = 20). The model was validated on an independent patient dataset (n = 40). The distances between the identified GFM in the target delineation images and the GFM in CT images were measured. A human observatory study was conducted to validate the use of MEGRE images.\r\n\r\nThe sensitivity, specificity, and accuracy of the automatic method and the observatory study was 84%, 74%, 81% and 98%, 94%, 97%, respectively. The mean absolute difference in the GFM distances for the automatic method and observatory study was 1.28 \u00b1 1.25 mm and 1.14 \u00b1 1.06 mm, respectively.\r\n\r\nMultiecho gradient echo images were shown to be a feasible and reliable way to perform GFM identification. For clinical practice, visual inspection of the results from the automatic method is needed at the current stage.", "doi": "10.1002/mp.12516", "pmid": "28803447", "labels": {"AIDA Data Hub": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2021-11-10T17:00:08.197Z", "modified": "2021-11-26T10:54:57.619Z"}, {"entity": "publication", "iuid": "13b3499da98c4b919399fe6ad45b6104", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13b3499da98c4b919399fe6ad45b6104.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13b3499da98c4b919399fe6ad45b6104"}}, "title": "Rare X Chromosome Abnormalities in Systemic Lupus Erythematosus and Sj\u00f6gren's Syndrome.", "authors": [{"family": "Sharma", "given": "Rohan", "initials": "R"}, {"family": "Harris", "given": "Valerie M", "initials": "VM"}, {"family": "Cavett", "given": "Joshua", "initials": "J"}, {"family": "Kurien", "given": "Biji T", "initials": "BT"}, {"family": "Liu", "given": "Ke", "initials": "K"}, {"family": "Koelsch", "given": "Kristi A", "initials": "KA"}, {"family": "Fayaaz", "given": "Anum", "initials": "A"}, {"family": "Chaudhari", "given": "Kaustubh S", "initials": "KS"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Lewis", "given": "David", "initials": "D"}, {"family": "Stone", "given": "Donald U", "initials": "DU"}, {"family": "Kaufman", "given": "C Erick", "initials": "CE"}, {"family": "Li", "given": "Shibo", "initials": "S"}, {"family": "Segal", "given": "Barbara", "initials": "B"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Weisman", "given": "Michael H", "initials": "MH"}, {"family": "Venuturupalli", "given": "Swamy", "initials": "S"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Pons-Estel", "given": "Bernardo", "initials": "B"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Lu", "given": "Xianglan", "initials": "X"}, {"family": "Gottenberg", "given": "Jacques-Eric", "initials": "JE"}, {"family": "Anaya", "given": "Juan-Manuel", "initials": "JM"}, {"family": "Cunninghame-Graham", "given": "Deborah S", "initials": "DS"}, {"family": "Huang", "given": "Andrew J W", "initials": "AJW"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "Hughes", "given": "Pamela", "initials": "P"}, {"family": "Alevizos", "given": "Ilias", "initials": "I"}, {"family": "Miceli-Richard", "given": "Corinne", "initials": "C"}, {"family": "Keystone", "given": "Edward C", "initials": "EC"}, {"family": "Bykerk", "given": "Vivian P", "initials": "VP"}, {"family": "Hirschfield", "given": "Gideon", "initials": "G"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Rhodus", "given": "Nelson L", "initials": "NL"}, {"family": "Rischmueller", "given": "Maureen", "initials": "M"}, {"family": "Rohrer", "given": "Michael", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Witte", "given": "Torsten", "initials": "T"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta", "initials": "M"}, {"family": "Mariette", "given": "Xavier", "initials": "X"}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "69", "issn": "2326-5205", "issue": "11", "pages": "2187-2192", "title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn-l": "2326-5191"}, "abstract": "Sj\u00f6gren's syndrome (SS) and systemic lupus erythematosus (SLE) are related by clinical and serologic manifestations as well as genetic risks. Both diseases are more commonly found in women than in men, at a ratio of ~10 to 1. Common X chromosome aneuploidies, 47,XXY and 47,XXX, are enriched among men and women, respectively, in either disease, suggesting a dose effect on the X chromosome.\n\nWe examined cohorts of SS and SLE patients by constructing intensity plots of X chromosome single-nucleotide polymorphism alleles, along with determining the karyotype of selected patients.\n\nAmong ~2,500 women with SLE, we found 3 patients with a triple mosaic, consisting of 45,X/46,XX/47,XXX. Among ~2,100 women with SS, 1 patient had 45,X/46,XX/47,XXX, with a triplication of the distal p arm of the X chromosome in the 47,XXX cells. Neither the triple mosaic nor the partial triplication was found among the controls. In another SS cohort, we found a mother/daughter pair with partial triplication of this same region of the X chromosome. The triple mosaic occurs in ~1 in 25,000-50,000 live female births, while partial triplications are even rarer.\n\nVery rare X chromosome abnormalities are present among patients with either SS or SLE and may inform the location of a gene(s) that mediates an X dose effect, as well as critical cell types in which such an effect is operative.", "doi": "10.1002/art.40207", "pmid": "28692793", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:08.516Z", "modified": "2021-06-21T15:04:16.533Z"}, {"entity": "publication", "iuid": "d4ce1c0ed7c94ee7a6109cab0534cf0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4ce1c0ed7c94ee7a6109cab0534cf0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4ce1c0ed7c94ee7a6109cab0534cf0e"}}, "title": "Quantitative high-content/high-throughput microscopy analysis of lipid droplets in subject-specific adipogenesis models.", "authors": [{"family": "Bombrun", "given": "Maxime", "initials": "M"}, {"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Ranefall", "given": "Petter", "initials": "P"}, {"family": "Mejhert", "given": "Niklas", "initials": "N"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "91", "issn": "1552-4930", "issue": "11", "pages": "1068-1077", "title": "Cytometry A", "issn-l": "1552-4922"}, "abstract": "Neutral lipids packed in lipid droplets (LDs) are essential as a source of fuel for organisms, and specialized storing cells, the adipocytes, provide a buffer for energy variations. Many modern-society-disorders are connected with excess accumulation or deficiency of LDs in adipose tissue. Intracellular LD number and size distribution reflect the tissue conditions, while the associated mechanisms and genes rs are still poorly understood. Large-scale genetic screens using human in vitro differentiated primary adipocytes require cell samples donated from many patients. The heterogeneity appearing between donors highlighted the need for high-throughput methods robust to individual variations. Previous image analysis algorithms failed to handle individual LDs, but focused on averages, hiding population heterogeneity. We present a new high-content analysis (HCA) technique for analysis of fat cell metabolism using data from a large-scale RNAi screen including images of more than 500 k in vitro differentiated adipocytes from three donors. The RNAi-based suppression of Perilipin 1 (PLIN1), a protein involved in the adipocyte lipid metabolism, served as a positive control, while cells treated with randomized RNA served as negative controls. We validate our segmentation by comparing our results to those of previously published methods: We also evaluate the discriminative power of different morphological features describing LD size distribution. Classification of cells as containing few large or many small LDs followed by calculating the percentage of cells in each class proved to discriminate the positive PLIN1-suppressed phenotype from the untreated negative control with an area under the receiver operating characteristic curve of 0.98. The results suggest that this HCA method offers improved segmentation and classification accuracy, and can, thus, be utilized to quantify changes in LD metabolism in response to treatment in many cell models relevant to a variety of diseases. \u00a9 2017 International Society for Advancement of Cytometry.", "doi": "10.1002/cyto.a.23265", "pmid": "29031005", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T07:51:39.316Z", "modified": "2021-07-05T14:18:24.410Z"}, {"entity": "publication", "iuid": "b08d0d754d43447c84c8ec0f537e56ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b08d0d754d43447c84c8ec0f537e56ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b08d0d754d43447c84c8ec0f537e56ef"}}, "title": "Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity", "authors": [{"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Brus", "given": "Maja", "initials": "M"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Meijer", "given": "Harold J G", "initials": "HJG"}, {"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Govers", "given": "Francine", "initials": "F"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Grenville-Briggs", "given": "Laura", "initials": "L"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2017-11-00", "journal": {"volume": "16", "issn": "1535-9476", "issue": "11", "pages": "1958-1971", "title": "Mol Cell Proteomics", "issn-l": "1535-9476"}, "abstract": null, "doi": "10.1074/mcp.m116.065656", "pmid": "28935716", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T15:36:45.771Z", "modified": "2020-01-21T13:53:21.853Z"}, {"entity": "publication", "iuid": "b616130aa5e24ecab64baeba6c16c0a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b616130aa5e24ecab64baeba6c16c0a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b616130aa5e24ecab64baeba6c16c0a8"}}, "title": "Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.", "authors": [{"family": "Svartstr\u00f6m", "given": "Olov", "initials": "O"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Terrapon", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3693-6017", "researcher": {"href": "https://publications.scilifelab.se/researcher/08f47757224649faa4a6e81854b8578f.json"}}, {"family": "Lombard", "given": "Vincent", "initials": "V"}, {"family": "de Bruijn", "given": "Ino", "initials": "I"}, {"family": "Malmsten", "given": "Jonas", "initials": "J", "orcid": "0000-0003-1868-3746", "researcher": {"href": "https://publications.scilifelab.se/researcher/31afb191067641c9b2190aa36db6d225.json"}}, {"family": "Dalin", "given": "Ann-Marie", "initials": "AM"}, {"family": "El Muller", "given": "Emilie", "initials": "E"}, {"family": "Shah", "given": "Pranjul", "initials": "P"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}, {"family": "Henrissat", "given": "Bernard", "initials": "B"}, {"family": "Aspeborg", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8576-4370", "researcher": {"href": "https://publications.scilifelab.se/researcher/973b41980bd34391aa3be4e54b19ff2f.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "11", "pages": "2538-2551", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.", "doi": "10.1038/ismej.2017.108", "pmid": "28731473", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "EMS73237"}, {"db": "pmc", "key": "PMC5648042"}, {"db": "pii", "key": "ismej2017108"}], "notes": [], "created": "2017-11-03T16:11:39.460Z", "modified": "2024-01-16T13:48:47.346Z"}, {"entity": "publication", "iuid": "df165d9fceca44289765656792099a8b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df165d9fceca44289765656792099a8b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df165d9fceca44289765656792099a8b"}}, "title": "Integrative studies implicate matrix metalloproteinase-12 as a culprit gene for large-artery atherosclerotic stroke", "authors": [{"family": "Mahdessian", "given": "H", "initials": "H"}, {"family": "Perisic Matic", "given": "L", "initials": "L"}, {"family": "Lengquist", "given": "M", "initials": "M"}, {"family": "Gertow", "given": "K", "initials": "K"}, {"family": "Sennblad", "given": "B", "initials": "B"}, {"family": "Baldassarre", "given": "D", "initials": "D"}, {"family": "Veglia", "given": "F", "initials": "F"}, {"family": "Humphries", "given": "S E", "initials": "SE"}, {"family": "Rauramaa", "given": "R", "initials": "R"}, {"family": "de Faire", "given": "U", "initials": "U"}, {"family": "Smit", "given": "A J", "initials": "AJ"}, {"family": "Giral", "given": "P", "initials": "P"}, {"family": "Kurl", "given": "S", "initials": "S"}, {"family": "Mannarino", "given": "E", "initials": "E"}, {"family": "Tremoli", "given": "E", "initials": "E"}, {"family": "Hamsten", "given": "A", "initials": "A"}, {"family": "Eriksson", "given": "P", "initials": "P"}, {"family": "Hedin", "given": "U", "initials": "U"}, {"family": "M\u00e4larstig", "given": "A", "initials": "A"}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-11-00", "journal": {"volume": "282", "issn": "0954-6820", "issue": "5", "pages": "429-444", "title": "J Intern Med", "issn-l": "0954-6820"}, "abstract": null, "doi": "10.1111/joim.12655", "pmid": "28734077", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:56.405Z", "modified": "2020-01-21T13:56:11.992Z"}, {"entity": "publication", "iuid": "6fde580c283e4ad29b2f0f852b9d8da2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fde580c283e4ad29b2f0f852b9d8da2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fde580c283e4ad29b2f0f852b9d8da2"}}, "title": "High abundance and expression of transposases in bacteria from the Baltic Sea.", "authors": [{"family": "Vigil-Stenman", "given": "Theoden", "initials": "T"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Ekman", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "11", "pages": "2611-2623", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200\u2009\u03bcm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.", "doi": "10.1038/ismej.2017.114", "pmid": "28731472", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ismej2017114"}, {"db": "pmc", "key": "PMC5649170"}], "notes": [], "created": "2017-11-03T16:19:50.532Z", "modified": "2024-01-16T13:48:47.354Z"}, {"entity": "publication", "iuid": "84199c0fdcf3432a8f4e33a4246c420d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84199c0fdcf3432a8f4e33a4246c420d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84199c0fdcf3432a8f4e33a4246c420d"}}, "title": "Genotype-based recall to study metabolic effects of genetic variation: a pilot study of PPARG Pro12Ala carriers.", "authors": [{"family": "Kamble", "given": "Prasad G", "initials": "PG"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ"}, {"family": "Lundkvist", "given": "Per", "initials": "P"}, {"family": "Cook", "given": "Naomi", "initials": "N"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "122", "issn": "2000-1967", "issue": "4", "pages": "234-242", "title": "Ups. J. Med. Sci.", "issn-l": "0300-9734"}, "abstract": "To assess practical implications of genotype-based recall (GBR) studies, an increasingly popular approach for in-depth characterization of genotype-phenotype relationships.\n\nWe genotyped 2500 participants from the Swedish EpiHealth cohort and considered loss-of-function and missense variants in genes with relation to cardiometabolic traits as the basis for our GBR study. Therefore, we focused on carriers and non-carriers of the PPARG Pro12Ala (rs1801282) variant, as it is a relatively common variant with a minor allele frequency (MAF) of 0.14. It has also been shown to affect ligand binding and transcription, and carriage of the minor allele (Ala12) is associated with a reduced risk of type 2 diabetes. We re-invited 39 Pro12Pro, 34 Pro12Ala, and 30 Ala12Ala carriers and performed detailed anthropometric and serological assessments.\n\nThe participation rates in the GBR study were 31%, 44%, and 40%, and accordingly we included 12, 15, and 13 individuals with Pro12Pro, Pro12Ala, and Ala12Ala variants, respectively. There were no differences in anthropometric or metabolic variables among the different genotype groups.\n\nOur report highlights that from a practical perspective, GBR can be used to study genotype-phenotype relationships. This approach can prove to be a valuable tool for follow-up findings from large-scale genetic discovery studies by undertaking detailed phenotyping procedures that might not be feasible in large studies. However, our study also illustrates the need for a larger pool of genotyped or sequenced individuals to allow for selection of rare variants with larger effects that can be examined in a GBR study of the present size.", "doi": "10.1080/03009734.2017.1405127", "pmid": "29303622", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5810227"}], "notes": [], "created": "2018-05-25T13:31:05.888Z", "modified": "2020-01-21T13:56:10.921Z"}, {"entity": "publication", "iuid": "10631255696544f194076164c1ab4128", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10631255696544f194076164c1ab4128.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10631255696544f194076164c1ab4128"}}, "title": "Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age.", "authors": [{"family": "Pujolar", "given": "J M", "initials": "JM", "orcid": "0000-0001-6406-583X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6671dcfa12b94390807a1c2a175f451d.json"}}, {"family": "Dal\u00e9n", "given": "L", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Hansen", "given": "M M", "initials": "MM", "orcid": "0000-0001-5372-4828", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc21c1cf8e074f35a012494cdef48424.json"}}, {"family": "Madsen", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "26", "issn": "1365-294X", "issue": "22", "title": "Mol. Ecol.", "pages": "6270-6283", "issn-l": "0962-1083"}, "abstract": "We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, demographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the last glacial maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese, (2) the decline inferred during the Middle Ages is due to human persecution, and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.", "doi": "10.1111/mec.14374", "pmid": "28980346", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "BioProject", "description": "RAD-sequencing", "key": "PRJNA400851"}, {"db": "Dryad", "description": "Genotype data", "key": "https://doi.org/10.5061/dryad.c4r81"}], "notes": [], "created": "2017-11-03T16:21:37.140Z", "modified": "2021-07-07T20:31:10.703Z"}, {"entity": "publication", "iuid": "6919ea89c19846078b8eb8cd9e538de7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6919ea89c19846078b8eb8cd9e538de7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6919ea89c19846078b8eb8cd9e538de7"}}, "title": "An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans", "authors": [{"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Marullo", "given": "Letizia", "initials": "L"}, {"family": "Gaulton", "given": "Kyle J", "initials": "KJ"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Pervjakova", "given": "Natalia", "initials": "N"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Eicher", "given": "John D", "initials": "JD"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Lee", "given": "Yeji", "initials": "Y"}, {"family": "Ma", "given": "Clement", "initials": "C"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Van Zuydam", "given": "Natalie R", "initials": "NR"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Chen", "given": "Han", "initials": "H"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Voight", "given": "Ben F", "initials": "BF"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Ried", "given": "Janina S", "initials": "JS"}, {"family": "Rayner", "given": "Nigel W", "initials": "NW"}, {"family": "Robertson", "given": "Neil", "initials": "N"}, {"family": "Karssen", "given": "Lennart C", "initials": "LC"}, {"family": "van Leeuwen", "given": "Elisabeth M", "initials": "EM"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Kwan", "given": "Phoenix", "initials": "P"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Chanda", "given": "Pritam", "initials": "P"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "Thuillier", "given": "Dorothee", "initials": "D"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Jiang", "given": "Longda", "initials": "L"}, {"family": "Sparso", "given": "Thomas", "initials": "T"}, {"family": "Kestler", "given": "Hans A", "initials": "HA"}, {"family": "Chheda", "given": "Himanshu", "initials": "H"}, {"family": "Eisele", "given": "Lewin", "initials": "L"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Benediktsson", "given": "Rafn", "initials": "R"}, {"family": "Hreidarsson", "given": "Astradur B", "initials": "AB"}, {"family": "Kong", "given": "Augustine", "initials": "A"}, {"family": "Sigur\u00f0sson", "given": "Gunnar", "initials": "G"}, {"family": "Kerrison", "given": "Nicola D", "initials": "ND"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Roden", "given": "Michael", "initials": "M"}, {"family": "Thorand", "given": "Barbara", "initials": "B"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Fox", "given": "Caroline", "initials": "C"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Couper", "given": "David J", "initials": "DJ"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Have", "given": "Christian T", "initials": "CT"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Cornelis", "given": "Marilyn C", "initials": "MC"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Hunter", "given": "David J", "initials": "DJ"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Sun", "given": "Qi", "initials": "Q"}, {"family": "Edkins", "given": "Sarah", "initials": "S"}, {"family": "Owen", "given": "Katharine R", "initials": "KR"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Tajes-Fernandes", "given": "Juan", "initials": "J"}, {"family": "Abecasis", "given": "Goncalo R", "initials": "GR"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kinnunen", "given": "Leena", "initials": "L"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "M\u00fchleisen", "given": "Thomas W", "initials": "TW"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Pechlivanis", "given": "Sonali", "initials": "S"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Meyer", "given": "Julia", "initials": "J"}, {"family": "Steinbach", "given": "Gerald", "initials": "G"}, {"family": "Wennauer", "given": "Roman", "initials": "R"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "M\u04d3nnist\u00f6", "given": "Satu", "initials": "S"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Charpentier", "given": "Guillaume", "initials": "G"}, {"family": "Eury", "given": "Elodie", "initials": "E"}, {"family": "Lobbens", "given": "St\u00e9phane", "initials": "S"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "McLeod", "given": "Olga", "initials": "O"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Gottesman", "given": "Omri", "initials": "O"}, {"family": "Ruderfer", "given": "Douglas", "initials": "D"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Tonjes", "given": "Anke", "initials": "A"}, {"family": "Maruthur", "given": "Nisa M", "initials": "NM"}, {"family": "Scapoli", "given": "Chiara", "initials": "C"}, {"family": "Erbel", "given": "Raimund", "initials": "R"}, {"family": "J\u00f6ckel", "given": "Karl Heinz", "initials": "KH"}, {"family": "Moebus", "given": "Susanne", "initials": "S"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Deloukas", "given": "Panagiotis", "initials": "P"}, {"family": "Donnelly", "given": "Peter J", "initials": "PJ"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Hattersley", "given": "Andrew T", "initials": "AT"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Cauchi", "given": "Stephane", "initials": "S"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Boeing", "given": "Heiner", "initials": "H"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Barricarte Gurrea", "given": "Aurelio", "initials": "A"}, {"family": "Palli", "given": "Domenico", "initials": "D"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Groop", "given": "Leif C", "initials": "LC"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Sijbrands", "given": "Eric", "initials": "E"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}], "type": "journal-article", "published": "2017-11-00", "journal": {"volume": "66", "issn": "1939-327X", "issue": "11", "pages": "2888-2902", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": null, "doi": "10.2337/db16-1253", "pmid": "28566273", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:10.604Z", "modified": "2020-01-21T13:56:11.979Z"}, {"entity": "publication", "iuid": "8341db994d3947119c9378b946fbc80e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8341db994d3947119c9378b946fbc80e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8341db994d3947119c9378b946fbc80e"}}, "title": "A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders.", "authors": [{"family": "Wilbe", "given": "Maria", "initials": "M", "orcid": "0000-0003-3000-0696", "researcher": {"href": "https://publications.scilifelab.se/researcher/592ae099cb404e12bbc5109ceea99302.json"}}, {"family": "Gudmundsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-2332-074X", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb097c987504b2ca309e5f4e1cea5d2.json"}}, {"family": "Johansson", "given": "Josefin", "initials": "J"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Malmgren", "given": "Helena", "initials": "H"}, {"family": "Frykholm", "given": "Carina", "initials": "C"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}], "type": "case reports", "published": "2017-11-00", "journal": {"volume": "37", "issn": "1097-0223", "issue": "11", "pages": "1146-1154", "title": "Prenat. Diagn.", "issn-l": "0197-3851"}, "abstract": "De novo mutations contribute significantly to severe early-onset genetic disorders. Even if the mutation is apparently de novo, there is a recurrence risk due to parental germ line mosaicism, depending on in which gonadal generation the mutation occurred.\n\nWe demonstrate the power of using SMRT sequencing and ddPCR to determine parental origin and allele frequencies of de novo mutations in germ cells in two families whom had undergone assisted reproduction.\n\nIn the first family, a TCOF1 variant c.3156C>T was identified in the proband with Treacher Collins syndrome. The variant affects splicing and was determined to be of paternal origin. It was present in <1% of the paternal germ cells, suggesting a very low recurrence risk. In the second family, the couple had undergone several unsuccessful pregnancies where a de novo mutation PTPN11 c.923A>C causing Noonan syndrome was identified. The variant was present in 40% of the paternal germ cells suggesting a high recurrence risk.\n\nOur findings highlight a successful strategy to identify the parental origin of mutations and to investigate the recurrence risk in couples that have undergone assisted reproduction with an unknown donor or in couples with gonadal mosaicism that will undergo preimplantation genetic diagnosis.", "doi": "10.1002/pd.5156", "pmid": "28921562", "labels": {"National Genomics Infrastructure": "Technology development", "Clinical Genomics Uppsala": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5725701"}], "notes": [], "created": "2017-10-17T09:43:11.814Z", "modified": "2024-01-16T13:48:47.376Z"}, {"entity": "publication", "iuid": "e4168f55062149c1a8899883a4b45ce9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4168f55062149c1a8899883a4b45ce9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4168f55062149c1a8899883a4b45ce9"}}, "title": "A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.", "authors": [{"family": "Bondeson", "given": "M-L", "initials": "ML"}, {"family": "Ericson", "given": "K", "initials": "K"}, {"family": "Gudmundsson", "given": "S", "initials": "S"}, {"family": "Ameur", "given": "A", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Pont\u00e9n", "given": "F", "initials": "F"}, {"family": "Wesstr\u00f6m", "given": "J", "initials": "J"}, {"family": "Frykholm", "given": "C", "initials": "C"}, {"family": "Wilbe", "given": "M", "initials": "M", "orcid": "0000-0003-3000-0696", "researcher": {"href": "https://publications.scilifelab.se/researcher/592ae099cb404e12bbc5109ceea99302.json"}}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "92", "issn": "1399-0004", "issue": "5", "pages": "510-516", "title": "Clin. Genet.", "issn-l": "0009-9163"}, "abstract": "Mutations in genes involved in the cilium-centrosome complex are called ciliopathies. Meckel-Gruber syndrome (MKS) is a ciliopathic lethal autosomal recessive syndrome characterized by genetically and clinically heterogeneous manifestations, including renal cystic dysplasia, occipital encephalocele and polydactyly. Several genes have previously been associated with MKS and MKS-like phenotypes, but there are still genes remaining to be discovered. We have used whole-exome sequencing (WES) to uncover the genetics of a suspected autosomal recessive Meckel syndrome phenotype in a family with 2 affected fetuses. RNA studies and histopathological analysis was performed for further delineation. WES lead to identification of a homozygous nonsense mutation c.256C>T (p.Arg86*) in CEP55 (centrosomal protein of 55 kDa) in the affected fetus. The variant has previously been identified in carriers in low frequencies, and segregated in the family. CEP55 is an important centrosomal protein required for the mid-body formation at cytokinesis. Our results expand the list of centrosomal proteins implicated in human ciliopathies and provide evidence for an essential role of CEP55 during embryogenesis and development of disease.", "doi": "10.1111/cge.13012", "pmid": "28295209", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "Tissue Profiling": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T13:36:09.762Z", "modified": "2024-01-16T13:48:47.383Z"}, {"entity": "publication", "iuid": "0ea140596e2947cbba1cff3d94b7655c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ea140596e2947cbba1cff3d94b7655c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ea140596e2947cbba1cff3d94b7655c"}}, "title": "Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions", "authors": [{"family": "Hubalek", "given": "Valerie", "initials": "V"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Tan", "given": "BoonFei", "initials": "B"}, {"family": "Foght", "given": "Julia", "initials": "J"}, {"family": "Wendeberg", "given": "Annelie", "initials": "A"}, {"family": "Berry", "given": "David", "initials": "D"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal-article", "published": "2017-10-31", "journal": {"volume": "2", "issn": "2379-5077", "issue": "5", "pages": "e00038-17", "title": "mSystems", "issn-l": "2379-5077"}, "abstract": "Syntrophy among \n            Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.", "doi": "10.1128/msystems.00038-17", "pmid": "29104938", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:51:43.787Z", "modified": "2020-01-21T13:56:17.316Z"}, {"entity": "publication", "iuid": "11e771eaf5c34bec9f0f205c9dccdb33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11e771eaf5c34bec9f0f205c9dccdb33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11e771eaf5c34bec9f0f205c9dccdb33"}}, "title": "Orellanine specifically targets renal clear cell carcinoma.", "authors": [{"family": "Buvall", "given": "Lisa", "initials": "L"}, {"family": "Hedman", "given": "Heidi", "initials": "H"}, {"family": "Khramova", "given": "Alina", "initials": "A"}, {"family": "Najar", "given": "Deman", "initials": "D"}, {"family": "Bergwall", "given": "Lovisa", "initials": "L"}, {"family": "Ebefors", "given": "Kerstin", "initials": "K"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Lundstam", "given": "Sven", "initials": "S"}, {"family": "Herrmann", "given": "Anders", "initials": "A"}, {"family": "Wallentin", "given": "Hanna", "initials": "H"}, {"family": "Roos", "given": "Emelie", "initials": "E"}, {"family": "Nilsson", "given": "Ulf A", "initials": "UA"}, {"family": "Johansson", "given": "Martin", "initials": "M"}, {"family": "T\u00f6rnell", "given": "Jan", "initials": "J"}, {"family": "Haraldsson", "given": "B\u00f6rje", "initials": "B"}, {"family": "Nystr\u00f6m", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2017-10-31", "journal": {"volume": "8", "issn": "1949-2553", "issue": "53", "pages": "91085-91098", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Renal cell carcinoma (RCC), arising from the proximal tubule in the kidney, accounts for approximately 85% of kidney cancers and causes over 140,000 annual deaths worldwide. In the last decade, several new therapies have been identified for treatment of metastatic RCC. Although these therapies increase survival time compared to standard care, none of them has curative properties. The nephrotoxin orellanine specifically targets proximal tubular epithelial cells, leaving other organs unaffected. We therefore hypothesized that the selective toxicity of orellanine extends to clear cell RCC (ccRCC) cells since they emanate from proximal tubular cells. Orellanine would thus target both primary and metastatic ccRCC in vitro and in vivo. We found that orellanine induces dose-dependent cell death in proximal tubular cells and in all ccRCC cells tested, both primary and cell lines, with no toxicity detected in control cells. The toxic action of orellanine involve decreased protein synthesis, disrupted cell metabolism and induction of apoptosis. In nude rats carrying human ccRCC xenografts, brief orellanine treatment eliminated more than 90% of viable tumor mass compared to control rats. This identifies orellanine as a potential treatment concept for ccRCC patients on dialysis, due to its unique selective toxicity towards ccRCC.", "doi": "10.18632/oncotarget.19555", "pmid": "29207627", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "19555"}, {"db": "pmc", "key": "PMC5710908"}], "notes": [], "created": "2020-01-27T22:44:22.433Z", "modified": "2024-01-16T13:46:32.438Z"}, {"entity": "publication", "iuid": "3b92b628f3a047ae876c047ca9e89421", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b92b628f3a047ae876c047ca9e89421.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b92b628f3a047ae876c047ca9e89421"}}, "title": "Institutional profile: the national Swedish academic drug discovery & development platform at SciLifeLab.", "authors": [{"family": "Arvidsson", "given": "P I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}, {"family": "Sandberg", "given": "K", "initials": "K", "orcid": "0000-0002-6395-6590", "researcher": {"href": "https://publications.scilifelab.se/researcher/2747d3fe7810406fafc429d9e66225ef.json"}}, {"family": "Sakariassen", "given": "K S", "initials": "KS"}], "type": null, "published": "2017-10-30", "journal": {"volume": "3(2), FSO176", "issn": "2056-5623", "issue": "2", "pages": null, "title": "Future Sci. OA", "issn-l": "2056-5623"}, "abstract": "The Science for Life Laboratory Drug Discovery and Development Platform (SciLifeLab\r\nDDD) was established in Stockholm and Uppsala, Sweden, in 2014. It is one of ten\r\nplatforms of the Swedish national SciLifeLab which support projects run by Swedish\r\nacademic researchers with large-scale technologies for molecular biosciences with a\r\nfocus on health and environment. SciLifeLab was created by the coordinated effort\r\nof four universities in Stockholm and Uppsala: Stockholm University, Karolinska\r\nInstitutet, KTH Royal Institute of Technology and Uppsala University, and has recently\r\nexpanded to other Swedish university locations. The primary goal of the SciLifeLab\r\nDDD is to support selected academic discovery and development research projects\r\nwith tools and resources to discover novel lead therapeutics, either molecules or\r\nhuman antibodies. Intellectual property developed with the help of SciLifeLab DDD is\r\nwholly owned by the academic research group. The bulk of SciLifeLab DDD\u2019s research\r\nand service activities are funded from the Swedish state, with only consumables paid\r\nby the academic research group through individual grants.", "doi": "10.4155/fsoa-2017-0013", "pmid": "28670468", "labels": {"Drug Discovery and Development": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T15:14:01.061Z", "modified": "2025-10-17T13:05:08.734Z"}, {"entity": "publication", "iuid": "143b472121a44e75898dd001f521485f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/143b472121a44e75898dd001f521485f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/143b472121a44e75898dd001f521485f"}}, "title": "Exome-wide association study of plasma lipids in >300,000 individuals.", "authors": [{"family": "Liu", "given": "Dajiang J", "initials": "DJ"}, {"family": "Peloso", "given": "Gina M", "initials": "GM"}, {"family": "Yu", "given": "Haojie", "initials": "H"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Wang", "given": "Xiao", "initials": "X"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Emdin", "given": "Connor", "initials": "C"}, {"family": "Alam", "given": "Dewan", "initials": "D"}, {"family": "Alves", "given": "Alexessander Couto", "initials": "AC"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Di Angelantonio", "given": "Emanuele", "initials": "E"}, {"family": "Arveiler", "given": "Dominique", "initials": "D"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Auer", "given": "Paul L", "initials": "PL"}, {"family": "Baber", "given": "Usman", "initials": "U"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Bang", "given": "Lia E", "initials": "LE"}, {"family": "Benn", "given": "Marianne", "initials": "M"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Brandslund", "given": "Ivan", "initials": "I"}, {"family": "Brown", "given": "Morris", "initials": "M"}, {"family": "Busonero", "given": "Fabio", "initials": "F"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Y Eugene", "initials": "YE"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Chowdhury", "given": "Rajiv", "initials": "R"}, {"family": "Christensen", "given": "Cramer", "initials": "C"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Connell", "given": "John M", "initials": "JM"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Damrauer", "given": "Scott M", "initials": "SM"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Denny", "given": "Joshua C", "initials": "JC"}, {"family": "Dominiczak", "given": "Anna", "initials": "A"}, {"family": "Dub\u00e9", "given": "Marie-Pierre", "initials": "MP"}, {"family": "Ebeling", "given": "Tapani", "initials": "T"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Farmaki", "given": "Aliki-Eleni", "initials": "AE"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Ferrario", "given": "Marco", "initials": "M"}, {"family": "Ferrieres", "given": "Jean", "initials": "J"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Frikke-Schmidt", "given": "Ruth", "initials": "R"}, {"family": "Fritsche", "given": "Lars G", "initials": "LG"}, {"family": "Frossard", "given": "Philippe", "initials": "P"}, {"family": "Fuster", "given": "Valentin", "initials": "V"}, {"family": "Ganesh", "given": "Santhi K", "initials": "SK"}, {"family": "Gao", "given": "Wei", "initials": "W"}, {"family": "Garcia", "given": "Melissa E", "initials": "ME"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Holmen", "given": "Oddgeir L", "initials": "OL"}, {"family": "Huffman", "given": "Jennifer", "initials": "J"}, {"family": "Huo", "given": "Yong", "initials": "Y"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Jabeen", "given": "Sehrish", "initials": "S"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Jakobsdottir", "given": "Johanna", "initials": "J"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Jensen", "given": "Gorm B", "initials": "GB"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "Jukema", "given": "J 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"Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lauritzen", "given": "Torsten", "initials": "T"}, {"family": "Liewald", "given": "David C M", "initials": "DCM"}, {"family": "Lin", "given": "Li An", "initials": "LA"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Lu", "given": "Xiangfeng", "initials": "X"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Malarstig", "given": "Anders", "initials": "A"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "M\u00e4ntyselk\u00e4", "given": "Pekka", "initials": "P"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Masca", "given": "Nicholas G D", "initials": "NGD"}, {"family": "Maschio", "given": "Andrea", "initials": "A"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Mulas", "given": "Antonella", "initials": "A"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Neville", "given": "Matt J", "initials": "MJ"}, {"family": "Nielsen", "given": "Jonas B", "initials": "JB"}, {"family": "Nielsen", "given": "Sune F", "initials": "SF"}, {"family": "Nordestgaard", "given": "B\u00f8rge G", "initials": "BG"}, {"family": "Ordovas", "given": "Jose M", "initials": "JM"}, {"family": "Mehran", "given": "Roxana", "initials": "R"}, {"family": "O'Donnell", "given": "Christoper J", "initials": "CJ"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Molony", "given": "Cliona M", "initials": "CM"}, {"family": "Muntendam", "given": "Pieter", "initials": "P"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Pasko", "given": "Dorota", "initials": "D"}, {"family": "Patel", "given": "Aniruddh P", "initials": "AP"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Pisinger", "given": "Charlotta", "initials": "C"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Poulter", "given": "Neil", "initials": "N"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Rasheed", "given": "Asif", "initials": "A"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Reilly", "given": "Dermot F", "initials": "DF"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Roden", "given": "Dan M", "initials": "DM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Schmidt", "given": "Ellen M", "initials": "EM"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Sever", "given": "Peter", "initials": "P"}, {"family": 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"Surendran", "given": "Praveen", "initials": "P"}, {"family": "Tada", "given": "Hayato", "initials": "H"}, {"family": "Tall", "given": "Alan R", "initials": "AR"}, {"family": "Tang", "given": "Hua", "initials": "H"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Tsao", "given": "Philip S", "initials": "PS"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Tybjaerg-Hansen", "given": "Anne", "initials": "A"}, {"family": "van Zuydam", "given": "Natalie R", "initials": "NR"}, {"family": "Varbo", "given": "Anette", "initials": "A"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wang", "given": "Nan", "initials": "N"}, {"family": "Wareham", "given": "Nick J", "initials": "NJ"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Weinstock", "given": "Joshua", "initials": "J"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wilson", "given": "Peter W F", "initials": "PWF"}, {"family": "Xu", "given": "Ming", "initials": "M"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "Young", "given": "Robin", "initials": "R"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zhang", "given": "He", "initials": "H"}, {"family": "Zheng", "given": "Neil S", "initials": "NS"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhang", "given": "Yan", "initials": "Y"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Zoledziewska", "given": "Magdalena", "initials": "M"}, {"family": "Charge Diabetes Working Group", "given": "", "initials": ""}, {"family": "EPIC-InterAct Consortium", "given": "", "initials": ""}, {"family": "EPIC-CVD Consortium", "given": "", "initials": ""}, {"family": "GOLD Consortium", "given": "", "initials": ""}, {"family": "VA Million Veteran Program", "given": "", "initials": ""}, {"family": "Howson", "given": "Joanna M M", "initials": "JMM"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Cowan", "given": "Chad A", "initials": "CA"}, {"family": "Abecasis", "given": "Goncalo", "initials": "G"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Musunuru", "given": "Kiran", "initials": "K"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}], "type": "journal article", "published": "2017-10-30", "journal": {"volume": null, "issn": "1546-1718", "issue": null, "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "We screened variants on an exome-focused genotyping array in >300,000 participants (replication in >280,000 participants) and identified 444 independent variants in 250 loci significantly associated with total cholesterol (TC), high-density-lipoprotein cholesterol (HDL-C), low-density-lipoprotein cholesterol (LDL-C), and/or triglycerides (TG). At two loci (JAK2 and A1CF), experimental analysis in mice showed lipid changes consistent with the human data. We also found that: (i) beta-thalassemia trait carriers displayed lower TC and were protected from coronary artery disease (CAD); (ii) excluding the CETP locus, there was not a predictable relationship between plasma HDL-C and risk for age-related macular degeneration; (iii) only some mechanisms of lowering LDL-C appeared to increase risk for type 2 diabetes (T2D); and (iv) TG-lowering alleles involved in hepatic production of TG-rich lipoproteins (TM6SF2 and PNPLA3) tracked with higher liver fat, higher risk for T2D, and lower risk for CAD, whereas TG-lowering alleles involved in peripheral lipolysis (LPL and ANGPTL4) had no effect on liver fat but decreased risks for both T2D and CAD.", "doi": "10.1038/ng.3977", "pmid": "29083408", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3977"}], "notes": [], "created": "2017-11-09T16:02:23.213Z", "modified": "2020-01-21T13:56:10.219Z"}, {"entity": "publication", "iuid": "f6edb416401d4e0c8654c1e81fba413e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6edb416401d4e0c8654c1e81fba413e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6edb416401d4e0c8654c1e81fba413e"}}, "title": "Microbial mineralization of cellulose in frozen soils.", "authors": [{"family": "Segura", "given": "Javier H", "initials": "JH"}, {"family": "Nilsson", "given": "Mats B", "initials": "MB"}, {"family": "Haei", "given": "Mahsa", "initials": "M"}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Mikkola", "given": "Jyri-Pekka", "initials": "JP"}, {"family": "Gr\u00e4svik", "given": "John", "initials": "J"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}, {"family": "\u00d6quist", "given": "Mats G", "initials": "MG"}], "type": "journal article", "published": "2017-10-27", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "1154", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "High-latitude soils store ~40% of the global soil carbon and experience winters of up to 6 months or more. The winter soil CO2 efflux importantly contributes to the annual CO2 budget. Microorganisms can metabolize short chain carbon compounds in frozen soils. However, soil organic matter (SOM) is dominated by biopolymers, requiring exoenzymatic hydrolysis prior to mineralization. For winter SOM decomposition to have a substantial influence on soil carbon balances it is crucial whether or not biopolymers can be metabolized in frozen soils. We added 13C-labeled cellulose to frozen (-4 \u00b0C) mesocosms of boreal forest soil and followed its decomposition. Here we show that cellulose biopolymers are hydrolyzed under frozen conditions sustaining both CO2 production and microbial growth contributing to slow, but persistent, SOM mineralization. Given the long periods with frozen soils at high latitudes these findings are essential for understanding the contribution from winter to the global carbon balance.", "doi": "10.1038/s41467-017-01230-y", "pmid": "29074961", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-01230-y"}, {"db": "pmc", "key": "PMC5658388"}, {"db": "figshare", "key": "10.6084/m9.figshare.5318932"}], "notes": [], "created": "2017-10-31T12:11:16.407Z", "modified": "2025-10-17T13:03:59.540Z"}, {"entity": "publication", "iuid": "15afba9fe77f49b9a4b972893156fd87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15afba9fe77f49b9a4b972893156fd87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15afba9fe77f49b9a4b972893156fd87"}}, "title": "Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51.", "authors": [{"family": "Kumar", "given": "Rajnish", "initials": "R"}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Pavlov", "given": "Pavel F", "initials": "PF"}], "type": "journal article", "published": "2017-10-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "14288", "issn-l": "2045-2322"}, "abstract": "FK506 binding protein of 51\u2009kDa (FKBP51) is a heat shock protein 90 (Hsp90) co-chaperone involved in the regulation of steroid hormone receptors activity. It is known for its role in various regulatory pathways implicated in mood and stress-related disorders, cancer, obesity, Alzheimer's disease and corticosteroid resistant asthma. It consists of two FKBP12 like active peptidyl prolyl isomerase (PPIase) domains (an active FK1 and inactive FK2 domain) and one tetratricopeptide repeat (TPR) domain that mediates interaction with Hsp90 via its C-terminal MEEVD peptide. Here, we report a combined x-ray crystallography and molecular dynamics study to reveal the binding mechanism of Hsp90 MEEVD peptide to the TPR domain of FKBP51. The results demonstrated that the Hsp90 C-terminal peptide binds to the TPR domain of FKBP51 with the help of di-carboxylate clamp involving Lys272, Glu273, Lys352, Asn322, and Lys329 which are conserved throughout several di-carboxylate clamp TPR proteins. Interestingly, the results from molecular dynamics study are also in agreement to the complex structure where all the contacts between these two partners were consistent throughout the simulation period. In a nutshell, our findings provide new opportunity to engage this important protein-protein interaction target by small molecules designed by structure based drug design strategy.", "doi": "10.1038/s41598-017-14731-z", "pmid": "29079741", "labels": {"Protein Science Facility (PSF)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-14731-z"}], "notes": [], "created": "2017-10-30T11:35:55.545Z", "modified": "2017-10-30T11:35:55.556Z"}, {"entity": "publication", "iuid": "34f2371179704c95b05bc42435907de7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34f2371179704c95b05bc42435907de7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34f2371179704c95b05bc42435907de7"}}, "title": "Thiol-ene-epoxy thermoset for low-temperature bonding to biofunctionalized microarray surfaces.", "authors": [{"family": "Zhou", "given": "Xiamo C", "initials": "XC"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Druet", "given": "Amaury", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "van der Wijngaart", "given": "Wouter", "initials": "W"}, {"family": "Haraldsson", "given": "Tommy", "initials": "T"}, {"family": "Carlborg", "given": "Carl Fredrik", "initials": "CF"}], "type": "journal article", "published": "2017-10-25", "journal": {"volume": "17", "issn": "1473-0189", "issue": "21", "pages": "3672-3681", "title": "Lab Chip", "issn-l": null}, "abstract": "One way to improve the sensitivity and throughput of miniaturized biomolecular assays is to integrate microfluidics to enhance the transport efficiency of biomolecules to the reaction sites. Such microfluidic integration requires bonding of a prefabricated microfluidic gasket to an assay surface without destroying its biological activity. In this paper we address the largely unmet challenge to accomplish a proper seal between a microfluidic gasket and a protein surface, with maintained biological activity and without contaminating the surface or blocking the microfluidic channels. We introduce a novel dual cure polymer resin for the formation of microfluidic gaskets that can be room-temperature bonded to a range of substrates using only UVA light. This polymer is the first polymer that features over a month of shelf life between the structure formation and the bonding, moreover the fully cured polymer gaskets feature the following set of properties suitable for microfluidics: high stiffness, which prevents microfluidic channel collapse during handling; very limited absorption of biomolecules; and no significant leaching of uncured monomers. We describe the novel polymer resin and its characteristics, study through FT-IR, and demonstrate its use as microfluidic well-arrays bonded onto protein array slides at room temperature followed by multiplexed immunoassays. The results confirm maintained biological activity and show high repeatability between protein arrays. This new approach for integrating microfluidic gaskets to biofunctionalised surfaces has the potential to improve sample throughput and decrease manufacturing costs for miniaturized biomolecular systems.", "doi": "10.1039/c7lc00652g", "pmid": "28975170", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T12:13:55.170Z", "modified": "2021-07-08T12:07:34.033Z"}, {"entity": "publication", "iuid": "37e3547dbecb415db8dc52713feb0b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37e3547dbecb415db8dc52713feb0b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37e3547dbecb415db8dc52713feb0b69"}}, "title": "Efficient protein production by yeast requires global tuning of metabolism.", "authors": [{"family": "Huang", "given": "Mingtao", "initials": "M"}, {"family": "Bao", "given": "Jichen", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-10-25", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "1131", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion.", "doi": "10.1038/s41467-017-00999-2", "pmid": "29070809", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00999-2"}, {"db": "pmc", "key": "PMC5656615"}, {"db": "ENA", "description": "raw RNA-seq", "key": "ERP019558"}], "notes": [], "created": "2017-11-03T16:22:28.292Z", "modified": "2024-01-16T13:48:47.390Z"}, {"entity": "publication", "iuid": "07fa3c7a29984994a92f7ce91aba03a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07fa3c7a29984994a92f7ce91aba03a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07fa3c7a29984994a92f7ce91aba03a0"}}, "title": "Crystal structures of OrfX2 and P47 from a Botulinum neurotoxin OrfX type gene cluster.", "authors": [{"family": "Gustafsson", "given": "Robert", "initials": "R"}, {"family": "Berntsson", "given": "Ronnie P-A", "initials": "RP"}, {"family": "Mart\u00ednez-Carranza", "given": "Markel", "initials": "M"}, {"family": "El Tekle", "given": "Geniver", "initials": "G"}, {"family": "Odegrip", "given": "Richard", "initials": "R"}, {"family": "Johnson", "given": "Eric A", "initials": "EA"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}], "type": "letter", "published": "2017-10-25", "journal": {"title": "FEBS Lett.", "issn": "1873-3468", "volume": null, "issue": null, "issn-l": "0014-5793"}, "abstract": "Botulinum neurotoxins are highly toxic substances and are all encoded together with one of two alternative gene clusters, the HA or the OrfX gene cluster. Very little is known about the function and structure of the proteins encoded in the OrfX gene cluster, which in addition to the toxin contains 5 proteins (OrfX1, OrfX2, OrfX3, P47 and NTNH). We here present the structures of OrfX2 and P47, solved to 2.1\u00c5 and 1.8\u00c5 respectively. We show that they belong to the TULIP protein superfamily, which are often involved in lipid binding. OrfX1 and OrfX2 were both found to bind phosphatidyl-inositol lipids. This article is protected by copyright. All rights reserved.", "doi": "10.1002/1873-3468.12889", "pmid": "29067689", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T13:13:45.834Z", "modified": "2017-10-30T13:13:45.852Z"}, {"entity": "publication", "iuid": "293919f0d9c348b6b68db3fa0960d649", "links": {"self": {"href": "https://publications.scilifelab.se/publication/293919f0d9c348b6b68db3fa0960d649.json"}, "display": {"href": "https://publications.scilifelab.se/publication/293919f0d9c348b6b68db3fa0960d649"}}, "title": "Polysome-profiling in small tissue samples.", "authors": [{"family": "Liang", "given": "Shuo", "initials": "S"}, {"family": "Bellato", "given": "Hermano Martins", "initials": "HM"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Lupinacci", "given": "Fernanda C S", "initials": "FCS"}, {"family": "Oertlin", "given": "Christian", "initials": "C"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Andrade", "given": "Victor P", "initials": "VP"}, {"family": "Roff\u00e9", "given": "Mart\u00edn", "initials": "M"}, {"family": "Masvidal", "given": "Laia", "initials": "L"}, {"family": "Hajj", "given": "Glaucia N M", "initials": "GNM"}, {"family": "Larsson", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2017-10-23", "journal": {"volume": null, "issn": "1362-4962", "issue": null, "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Polysome-profiling is commonly used to study translatomes and applies laborious extraction of efficiently translated mRNA (associated with >3 ribosomes) from a large volume across many fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts. To address this, we optimized a non-linear sucrose gradient which reproducibly enriches for efficiently translated mRNA in only one or two fractions, thereby reducing sample handling 5-10-fold. The technique generates polysome-associated RNA with a quality reflecting the starting material and, when coupled with smart-seq2 single-cell RNA sequencing, translatomes in small tissues from biobanks can be obtained. Translatomes acquired using optimized non-linear gradients resemble those obtained with the standard approach employing linear gradients. Polysome-profiling using optimized non-linear gradients in serum starved HCT-116 cells with or without p53 showed that p53 status associates with changes in mRNA abundance and translational efficiency leading to changes in protein levels. Moreover, p53 status also induced translational buffering whereby changes in mRNA levels are buffered at the level of mRNA translation. Thus, here we present a polysome-profiling technique applicable to large study designs, primary cells and frozen tissue samples such as those collected in biobanks.", "doi": "10.1093/nar/gkx940", "pmid": "29069469", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4561642"}, {"db": "BioProject", "description": "raw RNA-seq", "key": "PRJNA390060"}], "notes": [], "created": "2017-11-03T16:22:26.268Z", "modified": "2024-01-16T13:48:47.401Z"}, {"entity": "publication", "iuid": "adde1bb6b8a84b5f8b2a912e531bec19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/adde1bb6b8a84b5f8b2a912e531bec19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/adde1bb6b8a84b5f8b2a912e531bec19"}}, "title": "Below-ground organic matter accumulation along a boreal forest fertility gradient relates to guild interaction within fungal communities", "authors": [{"family": "Kyaschenko", "given": "Julia", "initials": "J"}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE"}, {"family": "Karltun", "given": "Erik", "initials": "E"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}], "type": "journal-article", "published": "2017-10-22", "journal": {"volume": null, "issn": "1461-023X", "issue": null, "pages": null, "title": "Ecol Lett", "issn-l": "1461-023X"}, "abstract": null, "doi": "10.1111/ele.12862", "pmid": "29057614", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T16:07:33.213Z", "modified": "2024-01-16T13:48:47.409Z"}, {"entity": "publication", "iuid": "284397d670c047c6b81434e6154d6b8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/284397d670c047c6b81434e6154d6b8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/284397d670c047c6b81434e6154d6b8a"}}, "title": "Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS.", "authors": [{"family": "Ly", "given": "Tony", "initials": "T", "orcid": "0000-0002-8650-5215", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf0a17a252c14726a09986432c8a0022.json"}}, {"family": "Whigham", "given": "Arlene", "initials": "A"}, {"family": "Clarke", "given": "Rosemary", "initials": "R"}, {"family": "Brenes-Murillo", "given": "Alejandro J", "initials": "AJ"}, {"family": "Estes", "given": "Brett", "initials": "B"}, {"family": "Madhessian", "given": "Diana", "initials": "D"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Wadsworth", "given": "Patricia", "initials": "P"}, {"family": "Lamond", "given": "Angus I", "initials": "AI", "orcid": "0000-0001-6204-6045", "researcher": {"href": "https://publications.scilifelab.se/researcher/69bd35e565a34f01947b5673e793cc6c.json"}}], "type": "journal article", "published": "2017-10-20", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "The temporal regulation of protein abundance and post-translational modifications is a key feature of cell division. Recently, we analysed gene expression and protein abundance changes during interphase under minimally perturbed conditions (Ly et al., 2014, 2015). Here, we show that by using specific intracellular immunolabelling protocols, FACS separation of interphase and mitotic cells, including mitotic subphases, can be combined with proteomic analysis by mass spectrometry. Using this PRIMMUS (PRoteomic analysis of Intracellular iMMUnolabelled cell Subsets) approach, we now compare protein abundance and phosphorylation changes in interphase and mitotic fractions from asynchronously growing human cells. We identify a set of 115 phosphorylation sites increased during G2, termed 'early risers'. This set includes phosphorylation of S738 on TPX2, which we show is important for TPX2 function and mitotic progression. Further, we use PRIMMUS to provide the first a proteome-wide analysis of protein abundance remodeling between prophase, prometaphase and anaphase.", "doi": "10.7554/eLife.27574", "pmid": "29052541", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5650473"}], "notes": [], "created": "2017-10-31T15:29:44.055Z", "modified": "2021-07-05T16:23:51.099Z"}, {"entity": "publication", "iuid": "8325168daff7463fa7e0e4657bd6d96a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8325168daff7463fa7e0e4657bd6d96a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8325168daff7463fa7e0e4657bd6d96a"}}, "title": "Effects of long-term low oxygen tension in human chondrosarcoma cells", "authors": [{"family": "Piltti", "given": "Juha", "initials": "J"}, {"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Qu", "given": "Chengjuan", "initials": "C"}, {"family": "Lammi", "given": "Mikko J", "initials": "MJ"}], "type": "journal-article", "published": "2017-10-18", "journal": {"volume": null, "issn": "0730-2312", "issue": null, "pages": null, "title": "J. Cell. Biochem.", "issn-l": null}, "abstract": null, "doi": "10.1002/jcb.26394", "pmid": "28865129", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:35:57.392Z", "modified": "2020-01-21T13:53:21.710Z"}, {"entity": "publication", "iuid": "2e7c0c8184524ce4a068b4149d232819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e7c0c8184524ce4a068b4149d232819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e7c0c8184524ce4a068b4149d232819"}}, "title": "Zebrafish larvae as a model system for high-throughput, image-based screens in diabetes and insulin resistance", "authors": [{"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Ranefall", "given": "Petter", "initials": "P", "orcid": "0000-0002-6699-4015", "researcher": {"href": "https://publications.scilifelab.se/researcher/4332883c0058421f8dfb85406ec03524.json"}}, {"family": "Bandaru", "given": "Manoj", "initials": "M", "orcid": "0000-0002-5664-6711", "researcher": {"href": "https://publications.scilifelab.se/researcher/024e44747cdd4f5f85c1cf61d3320b09.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications.scilifelab.se/researcher/98fffa8e99254fb597bf07dea61d8e37.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}], "type": null, "published": "2017-10-17", "journal": {"volume": null, "issn": null, "issue": null, "pages": null, "title": "ASHG 2017 Annual Meeting - The American Society of Human Genetics", "issn-l": null}, "abstract": "Background\r\nGenome-wide association studies identified >100 loci that are robustly associated with the risk of insulin resistance and diabetes. The causal genes and mechanisms remain unidentified for most loci. We aim to examine if zebrafish larvae can serve as a model system for image-based genetic screens in insulin resistance and diabetes.\r\n\r\nMethods\r\nIn a dietary screen, ~500 larvae with transgenically expressed fluorescent labels on \u03b2-cells and/or hepatocytes were overfed on a normal or cholesterol-supplemented diet in the presence or absence of 3% glucose in the medium from 5 to 10 days post-fertilization. In a separate effort, ~800 larvae were metabolically challenged with or without concomitant treatment with rosiglitazone or metformin. At 10dpf, larvae were soaked in a lipid staining dye, followed by optical sectioning of the pancreatic islet, liver and subcutaneous lipid stores using an automated positioning system and fluorescence microscope. \u00df-cell volume and subcutaneous and liver fat accumulation were quantified objectively using custom-written scripts. Quantitative outcomes were inverse normally transformed and data were analyzed using linear (beta\u00b1SE) or logistic (OR [95% CI]) regression, adjusting for time of imaging and batch.\r\n\r\nResults\r\nContinuous exposure to 3% glucose showed a positive main effect (0.38\u00b10.17 SD) and a positive interaction with cholesterol supplementation (0.47\u00b10.23 SD) for \u03b2-cell volume. Glucose exposure also increased the odds of subcutaneous (2.24 [1.28-3.90]) and hepatic fat accumulation( 2.44 [1.20-4.96]). Dietary cholesterol supplementation increased the odds of hepatic fat accumulation (2.15 [1.10-4.22]) but reduced the odds of subcutaneous fat accumulation (0.40 [0.23-0.71]).\r\nTreatment with rosiglitazone reduced hepatic fat accumulation by -0.82\u00b10.10 SD and increased the odds of subcutaneous fat accumulation (2.16 [1.07-4.37]). Treatment with metformin had the opposite effect (0.33\u00b10.09 SD; 0.38 [0.16-0.92]). Neither rosiglitazone nor metformin affected \u00df-cell volume (P>0.3).\r\n\r\nConclusion\r\nChallenging zebrafish larvae metabolically for five days induces an insulin resistant state that can to some extent be prevented by treatment with rosiglitazone. Hence, zebrafish larvae are a promising model system for genetic screens in insulin resistance and diabetes. Multiplex CRISPR-Cas9 mutant models for proof-of-concept genes are currently being screened to further validate the model system.", "doi": null, "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-10T08:45:36.783Z", "modified": "2025-11-17T09:36:59.898Z"}, {"entity": "publication", "iuid": "483c2c8715ac4b629743df2a4398fb2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/483c2c8715ac4b629743df2a4398fb2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/483c2c8715ac4b629743df2a4398fb2e"}}, "title": "Zebrafish larvae as a model system for high-throughput, image-based genetic screens in cardiometabolic diseases", "authors": [{"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Bandaru", "given": "Manoj", "initials": "M", "orcid": "0000-0002-5664-6711", "researcher": {"href": "https://publications.scilifelab.se/researcher/024e44747cdd4f5f85c1cf61d3320b09.json"}}, {"family": "von der Heyde", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-9889-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/803c0e0639174a50b59ae597802e824f.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Ranefall", "given": "Petter", "initials": "P", "orcid": "0000-0002-6699-4015", "researcher": {"href": "https://publications.scilifelab.se/researcher/4332883c0058421f8dfb85406ec03524.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications.scilifelab.se/researcher/98fffa8e99254fb597bf07dea61d8e37.json"}}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": null, "published": "2017-10-17", "journal": {"volume": null, "issn": null, "issue": null, "pages": null, "title": "ASHG 2017 Annual Meeting - The American Society of Human Genetics", "issn-l": null}, "abstract": "Background: Genome-wide association, exome array and whole-exome sequencing efforts have identified hundreds of loci that are robustly associated with the risk of cardiometabolic diseases and risk factors. With few exceptions, the causal genes through which these loci influence the risk of disease remain uncharacterized. While in silico genomic annotation using results from e.g. the ENCODE and RoadMap Epigenomics projects provides valuable insights, novel model systems that enable systematic, in vivo characterization of candidate genes are desirable.\r\n\r\nMethods: My group has developed and validated zebrafish model systems that make optimal use of: 1) the zebrafish\u2019 well-annotated genome, with orthologues of \u226571.4% of human genes; 2) recent developments in multiplex CRISPR-Cas9-based mutagenesis; 3) advances in automated positioning of non-embedded zebrafish larvae; 4) fluorescent transgenes and dyes; and 5) custom-written image-quantification pipelines.\r\n\r\nResults: Five days of overfeeding, dietary cholesterol supplementation and/or exposure to glucose induce atherogenic and insulin resistant phenotypes (higher/more whole-body LDL cholesterol (LDLc) levels; vascular foam cell formation and inflammation; \u03b2-cell number and volume; subcutaneous and hepatic accumulation of fat) that can largely be prevented by concomitant treatment with lipid-lowering or diabetes medication (N>4000). Proof-of-principle studies show that each additional mutated allele in the zebrafish\u2019 orthologues of APOE (apoea, apoeb) results in higher LDLc levels and more vascular foam cell formation and inflammation (N~384). In line with recent results in humans, treatment with LDLc-lowering drugs (N~400) and mutations in pcsk9 (N~384) both result in higher whole-body glucose levels. Finally, characterization of candidate genes in loci identified in a recent GWAS for heart rate variability helped identify genes that influence early-stage cardiac development, cardiac rate, and/or cardiac rhythm.\r\n\r\nConclusions: Systematic, largely image-based characterization of candidate genes for cardiometabolic traits in zebrafish model systems will increase our understanding of human disease, and will likely identify novel targets that can be translated into efficient therapeutics. In addition, undesirable side effects can be quantified in vivo at an early stage, thereby preventing costly and time-consuming experiments for targets that would otherwise likely fail on the road towards clinical trials.", "doi": null, "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-10T14:47:25.028Z", "modified": "2025-11-17T09:52:37.258Z"}, {"entity": "publication", "iuid": "fbf2fa0eb8664f2399794717d866aeb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbf2fa0eb8664f2399794717d866aeb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbf2fa0eb8664f2399794717d866aeb7"}}, "title": "Large-scale validation of zebrafish larvae as a model system for genetic screens in dyslipidaemia, atherosclerosis and coronary artery disease", "authors": [{"family": "Bandaru", "given": "Manoj", "initials": "M", "orcid": "0000-0002-5664-6711", "researcher": {"href": "https://publications.scilifelab.se/researcher/024e44747cdd4f5f85c1cf61d3320b09.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Ranefall", "given": "Petter", "initials": "P", "orcid": "0000-0002-6699-4015", "researcher": {"href": "https://publications.scilifelab.se/researcher/4332883c0058421f8dfb85406ec03524.json"}}, {"family": "von der Heyde", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-9889-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/803c0e0639174a50b59ae597802e824f.json"}}, {"family": "Klingstr\u00f6m", "given": "Tiffany", "initials": "T"}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}], "type": null, "published": "2017-10-17", "journal": {"volume": null, "issn": null, "issue": null, "pages": null, "title": "ASHG 2017 Annual Meeting - The American Society of Human Genetics", "issn-l": null}, "abstract": "Background: Genome-wide association studies have identified 77 loci that are robustly associated with coronary artery disease (CAD). In all but a few of these loci the causal genes and mechanisms remain unknown. Results from small-scale studies suggest that zebrafish larvae represent a promising model system for genetic screens in dyslipidemia, early-stage atherosclerosis and CAD. We aim to confirm or refute these results in a large-scale study, expand the phenotypic pipeline, and increase the throughput.\r\n\r\nMethods: At the core of our setup is an automated positioning and imaging system that allows visualization and quantification of atherogenic traits in ~100 zebrafish larvae per day at 10 days post-fertilization, by making use of fluorescent transgenes and dyes. We used a three-tiered approach to validate the zebrafish model system: 1) a dietary intervention to examine the effect of overfeeding and cholesterol supplementation (N=2193); 2) a treatment regime with atorvastatin and ezetimibe (N=956); and 3) a genetic screen for zebrafish orthologues of LDLR, PCSK9, APOB and APOE using a multiplex CRISPR-Cas9 approach (N=2x384). After imaging, whole-body lipid and glucose levels were assessed using enzymatic assays, and CRISPR-Cas9 target sites were sequenced on a MiSeq.\r\n\r\nResults: Overfeeding and cholesterol supplementation have independent pro-atherogenic effects, including elevated total cholesterol and triglyceride levels, more vascular deposition of lipids and oxidized LDLc, and more co-localization of lipids with macrophages and neutrophils. Treatment with atorvastatin and ezetimibe results in lower whole-body total cholesterol, LDLc and triglyceride levels, as well as in less vascular lipid deposition and less co-localization of lipids and macrophages. Finally, mutations in APOE orthologues result in higher whole-body LDLc levels and more co-localization of lipids with macrophages or neutrophils compared with wildtypes. Mutations in APOB orthologues tend to result in higher LDLc levels, more vascular lipid deposition, and more co-localizing lipids and neutrophils. Treatment with lipid lowering drugs and mutations in pcsk9 both result in higher whole-body glucose levels. Data from all larvae combined show that atherosclerosis in 10-day-old zebrafish larvae is mainly driven by higher triglyceride but not LDLc levels.\r\n\r\nConclusion: Zebrafish larvae can be used to systematically identify and characterize causal genes for CAD.", "doi": null, "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-10T08:53:10.829Z", "modified": "2025-11-17T09:58:04.394Z"}, {"entity": "publication", "iuid": "9d3b2b76727e4b3ca3f069afd950242f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d3b2b76727e4b3ca3f069afd950242f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d3b2b76727e4b3ca3f069afd950242f"}}, "title": "Glycoforest 1.0.", "authors": [{"family": "Horlacher", "given": "Oliver", "initials": "O"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Alocci", "given": "Davide", "initials": "D"}, {"family": "Mariethoz", "given": "Julien", "initials": "J"}, {"family": "M\u00fcller", "given": "Markus", "initials": "M"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Lisacek", "given": "Frederique", "initials": "F"}], "type": "journal article", "published": "2017-10-17", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "89", "issue": "20", "pages": "10932-10940", "issn-l": "0003-2700"}, "abstract": "Tandem mass spectrometry, when combined with liquid chromatography and applied to complex mixtures, produces large amounts of raw data, which needs to be analyzed to identify molecular structures. This technique is widely used, particularly in glycomics. Due to a lack of high throughput glycan sequencing software, glycan spectra are predominantly sequenced manually. A challenge for writing glycan-sequencing software is that there is no direct template that can be used to infer structures detectable in an organism. To help alleviate this bottleneck, we present Glycoforest 1.0, a partial de novo algorithm for sequencing glycan structures based on MS/MS spectra. Glycoforest was tested on two data sets (human gastric and salmon mucosa O-linked glycomes) for which MS/MS spectra were annotated manually. Glycoforest generated the human validated structure for 92% of test cases. The correct structure was found as the best scoring match for 70% and among the top 3 matches for 83% of test cases. In addition, the Glycoforest algorithm detected glycan structures from MS/MS spectra missing a manual annotation. In total 1532 MS/MS previously unannotated spectra were annotated by Glycoforest. A portion containing 521 spectra was manually checked confirming that Glycoforest annotated an additional 50 MS/MS spectra overlooked during manual annotation.", "doi": "10.1021/acs.analchem.7b02754", "pmid": "28901741", "labels": {"Glycoproteomics and MS Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-30T16:24:14.863Z", "modified": "2024-01-16T13:46:32.448Z"}, {"entity": "publication", "iuid": "df2eb61058fa4f3083b44b82465c7e9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df2eb61058fa4f3083b44b82465c7e9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df2eb61058fa4f3083b44b82465c7e9f"}}, "title": "Glioblastoma and glioblastoma stem cells are dependent on functional MTH1.", "authors": [{"family": "Pudelko", "given": "Linda", "initials": "L"}, {"family": "Rouhi", "given": "Pegah", "initials": "P"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Gad", "given": "Helge", "initials": "H"}, {"family": "Kalder\u00e9n", "given": "Christina", "initials": "C"}, {"family": "H\u00f6glund", "given": "Andreas", "initials": "A"}, {"family": "Squatrito", "given": "Massimo", "initials": "M"}, {"family": "Schuhmacher", "given": "Alberto J", "initials": "AJ"}, {"family": "Edwards", "given": "Steven", "initials": "S"}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D"}, {"family": "Berglund", "given": "Ulrika Warpman", "initials": "UW"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2017-10-17", "journal": {"volume": "8", "issn": "1949-2553", "issue": "49", "pages": "84671-84684", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Glioblastoma multiforme (GBM) is an aggressive form of brain cancer with poor prognosis. Cancer cells are characterized by a specific redox environment that adjusts metabolism to its specific needs and allows the tumor to grow and metastasize. As a consequence, cancer cells and especially GBM cells suffer from elevated oxidative pressure which requires antioxidant-defense and other sanitation enzymes to be upregulated. MTH1, which degrades oxidized nucleotides, is one of these defense enzymes and represents a promising cancer target. We found MTH1 expression levels elevated and correlated with GBM aggressiveness and discovered that siRNA knock-down or inhibition of MTH1 with small molecules efficiently reduced viability of patient-derived GBM cultures. The effect of MTH1 loss on GBM viability was likely mediated through incorporation of oxidized nucleotides and subsequent DNA damage. We revealed that MTH1 inhibition targets GBM independent of aggressiveness as well as potently kills putative GBM stem cells in vitro. We used an orthotopic zebrafish model to confirm our results in vivo and light-sheet microscopy to follow the effect of MTH1 inhibition in GBM in real time. In conclusion, MTH1 represents a promising target for GBM therapy and MTH1 inhibitors may also be effective in patients that suffer from recurring disease.", "doi": "10.18632/oncotarget.19404", "pmid": "29156675", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "19404"}, {"db": "pmc", "key": "PMC5689565"}], "notes": "Steven Edwards collaboration (Light-sheet)", "created": "2018-10-29T15:25:36.224Z", "modified": "2021-07-08T13:01:30.944Z"}, {"entity": "publication", "iuid": "332dcd3609654bd8ae8d83a41b357d40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/332dcd3609654bd8ae8d83a41b357d40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/332dcd3609654bd8ae8d83a41b357d40"}}, "title": "Extracellular vesicles from human pancreatic islets suppress human islet amyloid polypeptide amyloid formation.", "authors": [{"family": "Ribeiro", "given": "Diana", "initials": "D"}, {"family": "Horvath", "given": "Istvan", "initials": "I"}, {"family": "Heath", "given": "Nikki", "initials": "N"}, {"family": "Hicks", "given": "Ryan", "initials": "R"}, {"family": "Forsl\u00f6w", "given": "Anna", "initials": "A"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2017-10-17", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "114", "issue": "42", "pages": "11127-11132", "issn-l": "0027-8424"}, "abstract": "Extracellular vesicles (EVs) are small vesicles released by cells to aid cell-cell communication and tissue homeostasis. Human islet amyloid polypeptide (IAPP) is the major component of amyloid deposits found in pancreatic islets of patients with type 2 diabetes (T2D). IAPP is secreted in conjunction with insulin from pancreatic \u03b2 cells to regulate glucose metabolism. Here, using a combination of analytical and biophysical methods in vitro, we tested whether EVs isolated from pancreatic islets of healthy patients and patients with T2D modulate IAPP amyloid formation. We discovered that pancreatic EVs from healthy patients reduce IAPP amyloid formation by peptide scavenging, but T2D pancreatic and human serum EVs have no effect. In accordance with these differential effects, the insulin:C-peptide ratio and lipid composition differ between EVs from healthy pancreas and EVs from T2D pancreas and serum. It appears that healthy pancreatic EVs limit IAPP amyloid formation via direct binding as a tissue-specific control mechanism.", "doi": "10.1073/pnas.1711389114", "pmid": "28973954", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "1711389114"}, {"db": "pmc", "key": "PMC5651775"}], "notes": [], "created": "2020-01-23T16:35:56.086Z", "modified": "2021-06-21T15:04:31.335Z"}, {"entity": "publication", "iuid": "5c6d158d23b64c578c3e49a06388e6b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c6d158d23b64c578c3e49a06388e6b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c6d158d23b64c578c3e49a06388e6b6"}}, "title": "RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer.", "authors": [{"family": "Rao", "given": "Shuan", "initials": "S"}, {"family": "Sigl", "given": "Verena", "initials": "V"}, {"family": "Wimmer", "given": "Reiner Alois", "initials": "RA"}, {"family": "Novatchkova", "given": "Maria", "initials": "M"}, {"family": "Jais", "given": "Alexander", "initials": "A"}, {"family": "Wagner", "given": "Gabriel", "initials": "G"}, {"family": "Handschuh", "given": "Stephan", "initials": "S"}, {"family": "Uribesalgo", "given": "Iris", "initials": "I"}, {"family": "Hagelkruys", "given": "Astrid", "initials": "A"}, {"family": "Kozieradzki", "given": "Ivona", "initials": "I"}, {"family": "Tortola", "given": "Luigi", "initials": "L"}, {"family": "Nitsch", "given": "Roberto", "initials": "R"}, {"family": "Cronin", "given": "Shane J", "initials": "SJ"}, {"family": "Orthofer", "given": "Michael", "initials": "M"}, {"family": "Branstetter", "given": "Daniel", "initials": "D"}, {"family": "Canon", "given": "Jude", "initials": "J"}, {"family": "Rossi", "given": "John", "initials": "J"}, {"family": "D'Arcangelo", "given": "Manolo", "initials": "M"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Fleur", "given": "Linnea La", "initials": "L"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Lendl", "given": "Thomas", "initials": "T"}, {"family": "Popper", "given": "Helmut", "initials": "H"}, {"family": "Takayanagi", "given": "Hiroshi", "initials": "H"}, {"family": "Kenner", "given": "Lukas", "initials": "L"}, {"family": "Hirsch", "given": "Fred R", "initials": "FR"}, {"family": "Dougall", "given": "William", "initials": "W"}, {"family": "Penninger", "given": "Josef M", "initials": "JM"}], "type": "journal article", "published": "2017-10-15", "journal": {"title": "Genes Dev.", "issn": "1549-5477", "volume": "31", "issue": "20", "pages": "2099-2112", "issn-l": "0890-9369"}, "abstract": "Lung cancer is the leading cause of cancer deaths. Besides smoking, epidemiological studies have linked female sex hormones to lung cancer in women; however, the underlying mechanisms remain unclear. Here we report that the receptor activator of nuclear factor-kB (RANK), the key regulator of osteoclastogenesis, is frequently expressed in primary lung tumors, an active RANK pathway correlates with decreased survival, and pharmacologic RANK inhibition reduces tumor growth in patient-derived lung cancer xenografts. Clonal genetic inactivation of KRas in mouse lung epithelial cells markedly impairs the progression of G12D KRas -driven lung cancer, resulting in a significant survival advantage. Mechanistically, RANK rewires energy homeostasis in human and murine lung cancer cells and promotes expansion of lung cancer stem-like cells, which is blocked by inhibiting mitochondrial respiration. Our data also indicate survival differences in G12D KRas -driven lung cancer between male and female mice, and we show that female sex hormones can promote lung cancer progression via the RANK pathway. These data uncover a direct role for RANK in lung cancer and may explain why female sex hormones accelerate lung cancer development. Inhibition of RANK using the approved drug denosumab may be a therapeutic drug candidate for primary lung cancer.G12D", "doi": "10.1101/gad.304162.117", "pmid": "29118048", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "gad.304162.117"}, {"db": "pmc", "key": "PMC5733500"}], "notes": [], "created": "2019-12-20T07:50:21.577Z", "modified": "2019-12-20T07:50:21.600Z"}, {"entity": "publication", "iuid": "ade35766ffb54a9d97b0dc19bdc77cd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ade35766ffb54a9d97b0dc19bdc77cd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ade35766ffb54a9d97b0dc19bdc77cd8"}}, "title": "Delivery of cyclodextrin polymers to bacterial biofilms - An exploratory study using rhodamine labelled cyclodextrins and multiphoton microscopy.", "authors": [{"family": "Thomsen", "given": "Hanna", "initials": "H"}, {"family": "Benkovics", "given": "G\u00e1bor", "initials": "G"}, {"family": "Fenyvesi", "given": "\u00c9va", "initials": "\u00c9"}, {"family": "Farewell", "given": "Anne", "initials": "A"}, {"family": "Malanga", "given": "Milo", "initials": "M"}, {"family": "Ericson", "given": "Marica B", "initials": "MB"}], "type": "journal article", "published": "2017-10-15", "journal": {"title": "Int J Pharm", "issn": "1873-3476", "volume": "531", "issue": "2", "pages": "650-657", "issn-l": "0378-5173"}, "abstract": "Cyclodextrin (CD) polymers are interesting nanoparticulate systems for pharmaceutical delivery; however, knowledge regarding their applications towards delivery into complex microbial biofilm structures is so far limited. The challenge is to demonstrate penetration and transport through the biofilm and its exopolysaccharide matrix. The ideal functionalization for penetration into mature biofilms is unexplored. In this paper, we present a novel set of rhodamine labelled \u03b2CD-polymers, with different charge moieties, i.e., neutral, anionic, and cationic, and explore their potential delivery into mature Staphylococcus epidermidis biofilms using multiphoton laser scanning microscopy (MPM). The S. epidermidis biofilms, being a medically relevant model organism, were stained with SYTO9. By using MPM, three-dimensional imaging and spectral investigation of the distribution of the \u03b2CD-polymers could be obtained. It was found that the cationic \u03b2CD-polymers showed significantly higher integration into the biofilms, compared to neutral and anionic functionalized \u03b2CDs. None of the carriers presented any inherent toxicity to the biofilms, meaning that the addition of rhodamine moiety does not affect the inertness of the delivery system. Taken together, this study demonstrates a novel approach by which delivery of fluorescently labelled CD nanoparticles to bacterial biofilms can be explored using MPM. Future studies should be undertaken investigating the potential in using cationic functionalization of CD based delivery systems for targeting anti-microbial effects in biofilms.", "doi": "10.1016/j.ijpharm.2017.06.011", "pmid": "28596141", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0378-5173(17)30519-7"}], "notes": [], "created": "2020-01-23T16:36:43.762Z", "modified": "2021-06-21T15:05:16.862Z"}, {"entity": "publication", "iuid": "7ca22d9ce1804e1091eafa311412cf2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ca22d9ce1804e1091eafa311412cf2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ca22d9ce1804e1091eafa311412cf2e"}}, "title": "Solid-phase extraction of the alcohol abuse biomarker phosphatidylethanol using newly synthesized polymeric sorbent materials containing quaternary heterocyclic groups.", "authors": [{"family": "Duarte", "given": "Mariana", "initials": "M"}, {"family": "Jagadeesan", "given": "Kishore Kumar", "initials": "KK"}, {"family": "Billing", "given": "Johan", "initials": "J"}, {"family": "Yilmaz", "given": "Ecevit", "initials": "E"}, {"family": "Laurell", "given": "Thomas", "initials": "T"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2017-10-13", "journal": {"title": "Journal of Chromatography A", "issn": "1873-3778", "volume": "1519", "issue": null, "pages": "1-8", "issn-l": "0021-9673"}, "abstract": "Phosphatidylethanol (PEth) is an interesting biomarker finding increased use for detecting long term alcohol abuse with high specificity and sensitivity. Prior to detection, sample preparation is an unavoidable step in the work-flow of PEth analysis and new protocols may facilitate it. Solid-phase extraction (SPE) is a versatile sample preparation method widely spread in biomedical laboratories due to its simplicity of use and the possibility of automation. In this work, SPE was used for the first time to directly extract PEth from spiked human plasma and spiked human blood. A library of polymeric SPE materials with different surface functionalities was screened for PEth extraction in order to identify the surface characteristics that control PEth retention and recovery. The plasma samples were diluted 1:10 (v/v) in water and spiked at different concentrations ranging from 0.3 to 5\u03bcM. The library of SPE materials was then evaluated using the proposed SPE method and detection was done by LC-MS/MS. One SPE material efficiently retained and recovered PEth from spiked human plasma. With this insight, four new SPE materials were formulated and synthesized based on the surface characteristics of the best SPE material found in the first screening. These new materials were tested with spiked human blood, to better mimic a real clinical sample. All the newly synthetized materials outperformed the pre-existing commercially available materials. Recovery values for the new SPE materials were found between 29.5% and 48.6% for the extraction of PEth in spiked blood. A material based on quaternized 1-vinylimidazole with a poly(trimethylolpropane trimethacrylate) backbone was found suitable for PEth extraction in spiked blood showing the highest analyte recovery in this experiment, 48.6%\u00b16.4%.", "doi": "10.1016/j.chroma.2017.08.051", "pmid": "28890270", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9673(17)31232-3"}], "notes": [], "created": "2020-01-27T10:07:24.181Z", "modified": "2021-06-21T15:05:29.496Z"}, {"entity": "publication", "iuid": "20350e23da2b43b187e363633928219f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20350e23da2b43b187e363633928219f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20350e23da2b43b187e363633928219f"}}, "title": "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo.", "authors": [{"family": "Saravanan", "given": "Rathi", "initials": "R"}, {"family": "Adav", "given": "Sunil S", "initials": "SS"}, {"family": "Choong", "given": "Yeu Khai", "initials": "YK"}, {"family": "van der Plas", "given": "Mariena J A", "initials": "MJA"}, {"family": "Petrlova", "given": "Jitka", "initials": "J"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Sze", "given": "Siu Kwan", "initials": "SK"}, {"family": "Schmidtchen", "given": "Artur", "initials": "A"}], "type": "journal article", "published": "2017-10-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "13136", "issn-l": "2045-2322"}, "abstract": "The disease burden of failing skin repair and non-healing ulcers is extensive. There is an unmet need for new diagnostic approaches to better predict healing activity and wound infection. Uncontrolled and excessive protease activity, of endogenous or bacterial origin, has been described as a major contributor to wound healing impairments. Proteolytic peptide patterns could therefore correlate and \"report\" healing activity and infection. This work describes a proof of principle delineating a strategy by which peptides from a selected protein, human thrombin, are detected and attributed to proteolytic actions. With a particular focus on thrombin-derived C-terminal peptides (TCP), we show that distinct peptide patterns are generated in vitro by the human S1 peptidases human neutrophil elastase and cathepsin G, and the bacterial M4 peptidases Pseudomonas aeruginosa elastase and Staphylococcus aureus aureolysin, respectively. Corresponding peptide sequences were identified in wound fluids from acute and non-healing ulcers, and notably, one peptide, FYT21 (FYTHVFRLKKWIQKVIDQFGE), was only present in wound fluid from non-healing ulcers colonized by P. aeruginosa and S. aureus. Our result is a proof of principle pointing at the possibility of defining peptide biomarkers reporting distinct proteolytic activities, of potential implication for improved diagnosis of wound healing and infection.", "doi": "10.1038/s41598-017-13197-3", "pmid": "29030565", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-13197-3"}, {"db": "pmc", "key": "PMC5640616"}], "notes": [], "created": "2020-01-27T10:03:54.414Z", "modified": "2021-05-24T15:39:50.141Z"}, {"entity": "publication", "iuid": "dccc5b57e965405481a268f2e6289c07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dccc5b57e965405481a268f2e6289c07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dccc5b57e965405481a268f2e6289c07"}}, "title": "Lubricin binds cartilage proteins, cartilage oligomeric matrix protein, fibronectin and collagen II at the cartilage surface.", "authors": [{"family": "Flowers", "given": "Sarah A", "initials": "SA"}, {"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "\u00d6rnros", "given": "Jessica", "initials": "J"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Rolfson", "given": "Ola", "initials": "O"}, {"family": "Bj\u00f6rkman", "given": "Lena I", "initials": "LI"}, {"family": "Eisler", "given": "Thomas", "initials": "T"}, {"family": "Kalamajski", "given": "Sebastian", "initials": "S"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2017-10-13", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "13149", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Lubricin, a heavily O-glycosylated protein, is essential for boundary lubrication of articular cartilage. Strong surface adherence of lubricin is required given the extreme force it must withstand. Disulfide bound complexes of lubricin and cartilage oligomeric matrix protein (COMP) have recently been identified in arthritic synovial fluid suggesting they may be lost from the cartilage surface in osteoarthritis and inflammatory arthritis. This investigation was undertaken to localise COMP-lubricin complexes within cartilage and investigate if other cartilage proteins are involved in anchoring lubricin to the joint. Immunohistochemical analysis of human cartilage biopsies showed lubricin and COMP co-localise to the cartilage surface. COMP knockout mice, however, presented with a lubricin layer on the articular cartilage leading to the further investigation of additional lubricin binding mechanisms. Proximity ligation assays (PLA) on human cartilage biopsies was used to localise additional lubricin binding partners and demonstrated that lubricin bound COMP, but also fibronectin and collagen II on the cartilage surface. Fibronectin and collagen II binding to lubricin was confirmed and characterised by solid phase binding assays with recombinant lubricin fragments. Overall, COMP, fibronectin and collagen II bind lubricin, exposed on the articular cartilage surface suggesting they may be involved in maintaining essential boundary lubrication.", "doi": "10.1038/s41598-017-13558-y", "pmid": "29030641", "labels": {"PLA and Single Cell Proteomics": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative", "Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-13558-y"}, {"db": "pmc", "key": "PMC5640667"}], "notes": [], "created": "2017-11-02T14:29:24.618Z", "modified": "2024-01-16T13:46:32.458Z"}, {"entity": "publication", "iuid": "96cef0508c7d4bbcb8073612e4e92080", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96cef0508c7d4bbcb8073612e4e92080.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96cef0508c7d4bbcb8073612e4e92080"}}, "title": "Entirely enzymatic nanofabrication of DNA\u2013protein conjugates", "authors": [{"family": "Bernardinelli", "given": "Giulio", "initials": "G"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal-article", "published": "2017-10-13", "journal": {"volume": "45", "issn": "0305-1048", "issue": "18", "pages": "e160-e160", "title": "Nucleic Acids Res", "issn-l": null}, "abstract": null, "doi": "10.1093/nar/gkx707", "pmid": "28977490", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-24T07:58:20.689Z", "modified": "2017-11-09T13:24:53.032Z"}, {"entity": "publication", "iuid": "f0cdf693f186495e8c270a4cb0d71915", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0cdf693f186495e8c270a4cb0d71915.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0cdf693f186495e8c270a4cb0d71915"}}, "title": "De novo design and synthesis of a 30-cistron translation-factor module", "authors": [{"family": "Shepherd", "given": "Tyson R", "initials": "TR"}, {"family": "Du", "given": "Liping", "initials": "L"}, {"family": "Liljeruhm", "given": "Josefine", "initials": "J"}, {"family": "Samudyata", "given": "", "initials": ""}, {"family": "Wang", "given": "Jinfan", "initials": "J"}, {"family": "Sj\u00f6din", "given": "Marcus O D", "initials": "MOD"}, {"family": "Wetterhall", "given": "Magnus", "initials": "M"}, {"family": "Yomo", "given": "Tetsuya", "initials": "T"}, {"family": "Forster", "given": "Anthony C", "initials": "AC"}], "type": "journal-article", "published": "2017-10-13", "journal": {"volume": "45", "issn": "0305-1048", "issue": "18", "pages": "10895-10905", "title": "Nucleic Acids Res", "issn-l": null}, "abstract": null, "doi": "10.1093/nar/gkx753", "pmid": "28977654", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:38:23.168Z", "modified": "2024-01-16T13:48:47.417Z"}, {"entity": "publication", "iuid": "0531312ee42d448cb3d9ac4c140ea664", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0531312ee42d448cb3d9ac4c140ea664.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0531312ee42d448cb3d9ac4c140ea664"}}, "title": "Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.", "authors": [{"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Felldin", "given": "Ulrika", "initials": "U"}, {"family": "L\u00f6fling", "given": "Marie", "initials": "M"}, {"family": "Fernandez Navarro", "given": "Jos\u00e9", "initials": "J"}, {"family": "Maaskola", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-9039-6023", "researcher": {"href": "https://publications.scilifelab.se/researcher/632b5a1e903240d5a0bf0ccbe13a1890.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2017-10-11", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "12941", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.", "doi": "10.1038/s41598-017-13462-5", "pmid": "29021611", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-13462-5"}, {"db": "pmc", "key": "PMC5636908"}], "notes": [], "created": "2017-11-03T16:20:56.701Z", "modified": "2024-01-16T13:48:47.424Z"}, {"entity": "publication", "iuid": "8407c40d77d04cb2bde84500f396cddc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8407c40d77d04cb2bde84500f396cddc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8407c40d77d04cb2bde84500f396cddc"}}, "title": "Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Sachpazidou", "given": "Varvara", "initials": "V"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}], "type": "journal article", "published": "2017-10-11", "journal": {"volume": "284", "issn": "1471-2954", "issue": "1864", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats.", "doi": "10.1098/rspb.2017.1617", "pmid": "28978732", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "rspb.2017.1617"}, {"db": "pmc", "key": "PMC5647304"}, {"db": "BioProject", "description": "Raw metatranscriptomic RNA data", "key": "PRJNA347538"}, {"db": "BioProject", "description": "Raw metagenome, 16S rRNA and metatranscriptome sequence data", "key": "PRJNA322450"}], "notes": [], "created": "2017-11-03T16:21:54.440Z", "modified": "2024-01-16T13:48:47.434Z"}, {"entity": "publication", "iuid": "54e7219a52504bec8636907c6fec869f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e7219a52504bec8636907c6fec869f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e7219a52504bec8636907c6fec869f"}}, "title": "Chemical Proteomics for Target Discovery of Head-to-Tail Cyclized Mini-Proteins", "authors": [{"family": "Hellinger", "given": "Roland", "initials": "R"}, {"family": "Thell", "given": "Kathrin", "initials": "K"}, {"family": "Vasileva", "given": "Mina", "initials": "M"}, {"family": "Muhammad", "given": "Taj", "initials": "T"}, {"family": "Gunasekera", "given": "Sunithi", "initials": "S"}, {"family": "K\u00fcmmel", "given": "Daniel", "initials": "D"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U"}, {"family": "Becker", "given": "Christian W", "initials": "CW"}, {"family": "Gruber", "given": "Christian W", "initials": "CW"}], "type": "journal-article", "published": "2017-10-11", "journal": {"volume": "5", "issn": "2296-2646", "issue": null, "pages": null, "title": "Front. Chem.", "issn-l": "2296-2646"}, "abstract": null, "doi": "10.3389/fchem.2017.00073", "pmid": "29075625", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:31:29.906Z", "modified": "2025-10-17T13:03:59.554Z"}, {"entity": "publication", "iuid": "2bd73789ab074bedbd1b4bdade0c4cab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bd73789ab074bedbd1b4bdade0c4cab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bd73789ab074bedbd1b4bdade0c4cab"}}, "title": "CRISPR/Cas9 screening using unique molecular identifiers.", "authors": [{"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Botla", "given": "Sandeep K", "initials": "SK", "orcid": "0000-0001-9937-0455", "researcher": {"href": "https://publications.scilifelab.se/researcher/b212bb391c24480bb02eb187a21bd7cc.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Kivioja", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7732-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c318f57c5ce4f4bb747e19514caa907.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2017-10-09", "journal": {"volume": "13", "issn": "1744-4292", "issue": "10", "pages": "945", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Loss-of-function screening by CRISPR/Cas9 gene knockout with pooled, lentiviral guide libraries is a widely applicable method for systematic identification of genes contributing to diverse cellular phenotypes. Here, Random Sequence Labels (RSLs) are incorporated into the guide library, which act as unique molecular identifiers (UMIs) to allow massively parallel lineage tracing and lineage dropout screening. RSLs greatly improve the reproducibility of results by increasing both the precision and the accuracy of screens. They reduce the number of cells needed to reach a set statistical power, or allow a more robust screen using the same number of cells.", "doi": "10.15252/msb.20177834", "pmid": "28993443", "labels": {"CRISPR Functional Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC5658704"}], "notes": [], "created": "2017-10-20T10:29:09.604Z", "modified": "2021-07-06T14:41:38.936Z"}, {"entity": "publication", "iuid": "0622ae34d9a6494b8e6514e89b1099e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0622ae34d9a6494b8e6514e89b1099e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0622ae34d9a6494b8e6514e89b1099e2"}}, "title": "Subphenotypes of inflammatory bowel disease are characterized by specific serum protein profiles.", "authors": [{"family": "Andersson", "given": "Erik", "initials": "E", "orcid": "0000-0002-6598-1984", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b4b839a52be43a3a71123736c4c01af.json"}}, {"family": "Bergemalm", "given": "Daniel", "initials": "D"}, {"family": "Kruse", "given": "Robert", "initials": "R"}, {"family": "Neumann", "given": "Gunter", "initials": "G"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2017-10-05", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "12", "issue": "10", "pages": "e0186142"}, "abstract": "Genetic and immunological data indicate that inflammatory bowel disease (IBD) are characterized by specific inflammatory protein profiles. However, the serum proteome of IBD is still to be defined. We aimed to characterize the inflammatory serum protein profiles of Crohn's disease (CD) and ulcerative colitis (UC), using the novel proximity extension assay.\n\nA panel of 91 inflammatory proteins were quantified in a discovery cohort of CD (n = 54), UC patients (n = 54), and healthy controls (HCs; n = 54). We performed univariate analyses by t-test, with false discovery rate correction. A sparse partial least-squares (sPLS) approach was used to identify additional discriminative proteins. The results were validated in a replication cohort.\n\nBy univariate analysis, 17 proteins were identified with significantly different abundances in CD and HCs, and 12 when comparing UC and HCs. Additionally, 64 and 45 discriminant candidate proteins, respectively, were identified with the multivariate approach. Correspondingly, significant cross-validation error rates of 0.12 and 0.19 were observed in the discovery cohort. Only FGF-19 was identified from univariate comparisons of CD and UC, but 37 additional discriminant candidates were identified using the multivariate approach. The observed cross-validation error rate for CD vs. UC remained significant when restricting the analyses to patients in clinical remission. Using univariate comparisons, 16 of 17 CD-associated proteins and 8 of 12 UC-associated proteins were validated in the replication cohort. The area under the curve for CD and UC was 0.96 and 0.92, respectively, when the sPLS model from the discovery cohort was applied to the replication cohort.\n\nBy using the novel PEA method and a panel of inflammatory proteins, we identified proteins with significantly different quantities in CD patients and UC patients compared to HCs. Our data highlight the potential of the serum IBD proteome as a source for identification of future diagnostic biomarkers.", "doi": "10.1371/journal.pone.0186142", "pmid": "28982144", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-13227"}, {"db": "pmc", "key": "PMC5628935"}], "notes": [], "created": "2020-01-23T15:08:28.310Z", "modified": "2023-04-14T13:56:09.416Z"}, {"entity": "publication", "iuid": "50e2dcce11a04e099509c3b4e9ae3bfe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50e2dcce11a04e099509c3b4e9ae3bfe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50e2dcce11a04e099509c3b4e9ae3bfe"}}, "title": "Late presenting atypical severe combined immunodeficiency (SCID) associated with a novel missense mutation in DCLRE1C.", "authors": [{"family": "Sundin", "given": "Mikael", "initials": "M"}, {"family": "Uhlin", "given": "Mikael", "initials": "M"}, {"family": "Gaballa", "given": "Ahmed", "initials": "A"}, {"family": "Ramme", "given": "Kim", "initials": "K"}, {"family": "Marits", "given": "Per", "initials": "P"}, {"family": "Nilsson", "given": "Jakob", "initials": "J"}], "type": "letter", "published": "2017-10-05", "journal": {"volume": null, "issn": "1399-3038", "issue": null, "title": "Pediatr Allergy Immunol", "issn-l": "0905-6157"}, "abstract": "Immunodeficiency associated with mutations in the DNA cross-link repair 1C gene (DCLRE1C) can have variable clinical presentations including severe combined immunodeficiency (SCID), Omenn syndrome, atypical SCID or common variable immunodeficiency (CVID) (1-3). DCLRE1C encodes the protein Artemis, a nuclease with intrinsic 5'-3' exonuclease activity on single-stranded DNA that is involved in non-homologous end joining (NHEJ). Artemis is essential for V(D)J recombination of the immunoglobulin and T-cell receptor genes that occur during B- and T-cell development.", "doi": "10.1111/pai.12812", "pmid": "28981982", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T12:53:37.439Z", "modified": "2017-11-03T12:55:15.399Z"}, {"entity": "publication", "iuid": "ef9cd281e9f048cdb7b6541b0876e08a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef9cd281e9f048cdb7b6541b0876e08a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef9cd281e9f048cdb7b6541b0876e08a"}}, "title": "Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.", "authors": [{"family": "Guo", "given": "Jingtao", "initials": "J"}, {"family": "Grow", "given": "Edward J", "initials": "EJ"}, {"family": "Yi", "given": "Chongil", "initials": "C"}, {"family": "Mlcochova", "given": "Hana", "initials": "H"}, {"family": "Maher", "given": "Geoffrey J", "initials": "GJ"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Murphy", "given": "Patrick J", "initials": "PJ"}, {"family": "Wike", "given": "Candice L", "initials": "CL"}, {"family": "Carrell", "given": "Douglas T", "initials": "DT"}, {"family": "Goriely", "given": "Anne", "initials": "A"}, {"family": "Hotaling", "given": "James M", "initials": "JM"}, {"family": "Cairns", "given": "Bradley R", "initials": "BR"}], "type": "journal article", "published": "2017-10-05", "journal": {"volume": "21", "issn": "1875-9777", "issue": "4", "pages": "533-546.e6", "title": "Cell Stem Cell", "issn-l": null}, "abstract": "Human adult spermatogonial stem cells (hSSCs) must balance self-renewal and differentiation. To understand how this is achieved, we profiled DNA methylation and open chromatin (ATAC-seq) in SSEA4(+) hSSCs, analyzed bulk and single-cell RNA transcriptomes (RNA-seq) in SSEA4(+) hSSCs and differentiating c-KIT(+) spermatogonia, and performed validation studies via immunofluorescence. First, DNA hypomethylation at embryonic developmental genes supports their epigenetic \"poising\" in hSSCs for future/embryonic expression, while core pluripotency genes (OCT4 and NANOG) were transcriptionally and epigenetically repressed. Interestingly, open chromatin in hSSCs was strikingly enriched in binding sites for pioneer factors (NFYA/B, DMRT1, and hormone receptors). Remarkably, single-cell RNA-seq clustering analysis identified four cellular/developmental states during hSSC differentiation, involving major transitions in cell-cycle and transcriptional regulators, splicing and signaling factors, and glucose/mitochondria regulators. Overall, our results outline the dynamic chromatin/transcription landscape operating in hSSCs and identify crucial molecular pathways that accompany the transition from quiescence to proliferation and differentiation.", "doi": "10.1016/j.stem.2017.09.003", "pmid": "28985528", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1934-5909(17)30370-3"}, {"db": "GEO", "description": "Genomic profiling of human spermatogonial stem cells", "key": "GSE92280"}, {"db": "GEO", "description": "scRNA-Seq", "key": "GSE92276"}, {"db": "GEO", "description": "BulkRNA-Seq", "key": "GSE92277"}, {"db": "GEO", "description": "Whole genome bisulfite sequencing", "key": "GSE92278"}], "notes": [], "created": "2017-11-05T13:07:00.197Z", "modified": "2018-11-14T11:32:27.610Z"}, {"entity": "publication", "iuid": "af5f27612c04438c89f6dd123393117f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af5f27612c04438c89f6dd123393117f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af5f27612c04438c89f6dd123393117f"}}, "title": "Motivating students with authentic science experiences: changes in motivation for school science", "authors": [{"family": "Hellgren", "given": "Jenny M", "initials": "JM"}, {"family": "Lindberg", "given": "Stina", "initials": "S"}], "type": "journal-article", "published": "2017-10-02", "journal": {"volume": "35", "issn": "0263-5143", "issue": "4", "pages": "409-426", "title": "Research in Science & Technological Education", "issn-l": null}, "abstract": null, "doi": "10.1080/02635143.2017.1322572", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T13:46:09.526Z", "modified": "2025-10-17T13:04:29.097Z"}, {"entity": "publication", "iuid": "52d76d09eecb42a7a4304b6c9869ef23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52d76d09eecb42a7a4304b6c9869ef23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52d76d09eecb42a7a4304b6c9869ef23"}}, "title": "Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).", "authors": [{"family": "von Mentzer", "given": "Astrid", "initials": "A"}, {"family": "Tobias", "given": "Joshua", "initials": "J"}, {"family": "Wiklund", "given": "Gudrun", "initials": "G"}, {"family": "Nordqvist", "given": "Stefan", "initials": "S"}, {"family": "Aslett", "given": "Martin", "initials": "M"}, {"family": "Dougan", "given": "Gordon", "initials": "G"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Svennerholm", "given": "Ann-Mari", "initials": "AM"}], "type": "journal article", "published": "2017-10-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "12514", "issn-l": "2045-2322"}, "abstract": "The ability to colonize the small intestine is essential for enterotoxigenic Escherichia coli (ETEC) to cause diarrhea. Although 22 antigenically different colonization factors (CFs) have been identified and characterized in ETEC at least 30% of clinical ETEC isolates lack known CFs. Ninety-four whole genome sequenced \"CF negative\" isolates were searched for novel CFs using a reverse genetics approach followed by phenotypic analyses. We identified a novel CF, CS30, encoded by a set of seven genes, csmA-G, related to the human CF operon CS18 and the porcine CF operon 987P (F6). CS30 was shown to be thermo-regulated, expressed at 37 \u00b0C, but not at 20 \u00b0C, by SDS-page and mass spectrometry analyses as well as electron microscopy imaging. Bacteria expressing CS30 were also shown to bind to differentiated human intestinal Caco-2 cells. The genes encoding CS30 were located on a plasmid (E873p3) together with the genes encoding LT and STp. PCR screening of ETEC isolates revealed that 8.6% (n = 13) of \"CF negative\" (n = 152) and 19.4% (n = 13) of \"CF negative\" LT + STp (n = 67) expressing isolates analyzed harbored CS30. Hence, we conclude that CS30 is common among \"CF negative\" LT + STp isolates and is associated with ETEC that cause diarrhea.", "doi": "10.1038/s41598-017-12743-3", "pmid": "28970563", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-12743-3"}, {"db": "pmc", "key": "PMC5624918"}], "notes": [], "created": "2020-01-30T16:00:46.181Z", "modified": "2024-01-16T13:46:32.470Z"}, {"entity": "publication", "iuid": "dbef244a97744185a5325c6bdeaf9b13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbef244a97744185a5325c6bdeaf9b13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbef244a97744185a5325c6bdeaf9b13"}}, "title": "The Evolution of Dark Matter in the Mitogenome of Seed Beetles", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Immonen", "given": "Elina", "initials": "E"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal-article", "published": "2017-10-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "10", "pages": "2697-2706", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evx205", "pmid": "29048527", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "GENBANK", "description": "Callosobruchus maculatus from India mitochondrion, complete genome", "key": "KY856743"}, {"db": "GENBANK", "description": "Callosobruchus chinensis mitochondrion, complete genome", "key": "KY856744"}, {"db": "GENBANK", "description": "Callosobruchus analis mitochondrion, complete genome", "key": "KY856745"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from Brazil mitochondrion, complete genome", "key": "KY942060"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from USA mitochondrion, complete genome", "key": "KY942061"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from Yemen mitochondrion, complete genome", "key": "KY942062"}, {"db": "GENBANK", "description": "Acanthoscelides obtectus mitochondrion, complete genome", "key": "MF925724"}], "notes": [], "created": "2017-10-13T08:02:37.993Z", "modified": "2024-01-16T13:48:47.441Z"}, {"entity": "publication", "iuid": "aafc7d3dacfa45c7a3ccc1f37b727ebf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aafc7d3dacfa45c7a3ccc1f37b727ebf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aafc7d3dacfa45c7a3ccc1f37b727ebf"}}, "title": "Shaping the Tumor Stroma and Sparking Immune Activation by CD40 and 4-1BB Signaling Induced by an Armed Oncolytic Virus", "authors": [{"family": "Eriksson", "given": "Emma", "initials": "E"}, {"family": "Milenova", "given": "Ioanna", "initials": "I"}, {"family": "Wenthe", "given": "Jessica", "initials": "J"}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Leja-Jarblad", "given": "Justyna", "initials": "J"}, {"family": "Ullenhag", "given": "Gustav", "initials": "G"}, {"family": "Dimberg", "given": "Anna", "initials": "A"}, {"family": "Moreno", "given": "Raphael", "initials": "R"}, {"family": "Alemany", "given": "Ramon", "initials": "R"}, {"family": "Loskog", "given": "Angelica", "initials": "A"}], "type": "journal-article", "published": "2017-10-01", "journal": {"volume": "23", "issn": "1078-0432", "issue": "19", "pages": "5846-5857", "title": "Clin. Cancer Res.", "issn-l": null}, "abstract": null, "doi": "10.1158/1078-0432.ccr-17-0285", "pmid": "28536305", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T08:06:06.350Z", "modified": "2024-01-16T13:48:47.449Z"}, {"entity": "publication", "iuid": "7288c350f11e45b4986bd6fa6331f24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d"}}, "title": "Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kalsoom", "given": "Faheema", "initials": "F"}, {"family": "Dinca", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "10", "pages": "2491-2505", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643\u2009Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72\u2009Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.", "doi": "10.1093/gbe/evx163", "pmid": "28981642", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4091610"}, {"db": "BioProject", "description": "Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (Leptidea) butterflies.", "key": "PRJEB21838"}, {"db": "GENBANK", "description": "Leptidea sinapis, whole genome shotgun sequencing project", "key": "FZQP00000000"}], "notes": [], "created": "2017-10-30T09:27:46.367Z", "modified": "2024-01-16T13:48:47.456Z"}, {"entity": "publication", "iuid": "f9b3f267ecd5422f97763146bba29f73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9b3f267ecd5422f97763146bba29f73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9b3f267ecd5422f97763146bba29f73"}}, "title": "Profiling of in vitro activities of urea-based inhibitors against cysteine synthases from Mycobacterium tuberculosis.", "authors": [{"family": "Brunner", "given": "Katharina", "initials": "K"}, {"family": "Steiner", "given": "Eva Maria", "initials": "EM"}, {"family": "Reshma", "given": "Rudraraju Srilakshmi", "initials": "RS"}, {"family": "Sriram", "given": "Dharmarajan", "initials": "D"}, {"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}], "type": "journal article", "published": "2017-10-01", "journal": {"title": "Bioorg. Med. Chem. Lett.", "issn": "1464-3405", "issn-l": "0960-894X", "volume": "27", "issue": "19", "pages": "4582-4587"}, "abstract": "CysK1 and CysK2 are two members of the cysteine/S-sulfocysteine synthase family in Mycobacterium tuberculosis, responsible for the de novo biosynthesis of l-cysteine, which is subsequently used as a building block for mycothiol. This metabolite is the first line defense of this pathogen against reactive oxygen and nitrogen species released by host macrophages after phagocytosis. In a previous medicinal chemistry campaign we had developed urea-based inhibitors of the cysteine synthase CysM with bactericidal activity against dormant M. tuberculosis. In this study we extended these efforts by examination of the in vitro activities of a library consisting of 71 urea compounds against CysK1 and CysK2. Binding was established by fluorescence spectroscopy and inhibition by enzyme assays. Several of the compounds inhibited these two cysteine synthases, with the most potent inhibitor displaying an IC50 value of 2.5\u00b5M for CysK1 and 6.6\u00b5M for CysK2, respectively. Four of the identified molecules targeting CysK1 and CysK2 were also among the top ten inhibitors of CysM, suggesting that potent compounds could be developed with activity against all three enzymes.", "doi": "10.1016/j.bmcl.2017.08.039", "pmid": "28882483", "labels": {"Protein Science Facility (PSF)": "Service", "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-894X(17)30840-5"}], "notes": [], "created": "2017-10-24T06:16:47.963Z", "modified": "2025-10-17T13:04:29.106Z"}, {"entity": "publication", "iuid": "23d5b7c33105443e802947adc403df94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23d5b7c33105443e802947adc403df94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23d5b7c33105443e802947adc403df94"}}, "title": "GlyTouCan: an accessible glycan structure repository.", "authors": [{"family": "Tiemeyer", "given": "Michael", "initials": "M"}, {"family": "Aoki", "given": "Kazuhiro", "initials": "K"}, {"family": "Paulson", "given": "James", "initials": "J"}, {"family": "Cummings", "given": "Richard D", "initials": "RD"}, {"family": "York", "given": "William S", "initials": "WS"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Lisacek", "given": "Frederique", "initials": "F"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "Campbell", "given": "Matthew P", "initials": "MP"}, {"family": "Aoki", "given": "Nobuyuki P", "initials": "NP"}, {"family": "Fujita", "given": "Akihiro", "initials": "A"}, {"family": "Matsubara", "given": "Masaaki", "initials": "M"}, {"family": "Shinmachi", "given": "Daisuke", "initials": "D"}, {"family": "Tsuchiya", "given": "Shinichiro", "initials": "S"}, {"family": "Yamada", "given": "Issaku", "initials": "I"}, {"family": "Pierce", "given": "Michael", "initials": "M"}, {"family": "Ranzinger", "given": "Ren\u00e9", "initials": "R"}, {"family": "Narimatsu", "given": "Hisashi", "initials": "H"}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "27", "issn": "1460-2423", "issue": "10", "pages": "915-919", "title": "Glycobiology", "issn-l": "0959-6658"}, "abstract": "Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.", "doi": "10.1093/glycob/cwx066", "pmid": "28922742", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4079955"}, {"db": "pmc", "key": "PMC5881658"}], "notes": [], "created": "2020-01-30T16:19:35.484Z", "modified": "2024-01-16T13:46:32.482Z"}, {"entity": "publication", "iuid": "9ede80c805924ab1bedf3741267a879d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ede80c805924ab1bedf3741267a879d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ede80c805924ab1bedf3741267a879d"}}, "title": "DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Brants\u00e6ter", "given": "Margrethe", "initials": "M"}, {"family": "Nordgreen", "given": "Janicke", "initials": "J"}, {"family": "Coutinho", "given": "Luiz Lehmann", "initials": "LL"}, {"family": "Janczak", "given": "Andrew M", "initials": "AM"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}], "type": "journal-article", "published": "2017-10-01", "journal": {"volume": "220", "issn": "0022-0949", "issue": "19", "pages": "3579-3587", "title": "J Exp Biol", "issn-l": null}, "abstract": null, "doi": "10.1242/jeb.157891", "pmid": "28784681", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T16:10:12.465Z", "modified": "2024-01-16T13:48:47.463Z"}, {"entity": "publication", "iuid": "fcf6935e1c56441cb92e0dbb3fde5b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcf6935e1c56441cb92e0dbb3fde5b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcf6935e1c56441cb92e0dbb3fde5b21"}}, "title": "A MIR4646 associated methylation locus is hypomethylated in adolescent depression.", "authors": [{"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Ciuculete", "given": "Diana-Maria", "initials": "DM"}, {"family": "Attwood", "given": "Misty", "initials": "M"}, {"family": "Krattinger", "given": "Regina", "initials": "R"}, {"family": "Nikontovic", "given": "Lamia", "initials": "L"}, {"family": "Titova", "given": "Olga E", "initials": "OE"}, {"family": "Kullak-Ublick", "given": "Gerd A", "initials": "GA"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "220", "issn": "1573-2517", "issue": null, "pages": "117-128", "title": "J Affect Disord", "issn-l": "0165-0327"}, "abstract": "Studies of epigenetics and transcriptional activity in adolescents may provide knowledge about possible preventive strategies of depression.\n\nWe present a methylome-wide association study (MWAS) and cohort validation analysis of depression in adolescents, in two separate cohorts: discovery (n=93) and validation data set 1 (n=78). The genome-wide methylation pattern was measured from whole blood using the Illumina 450K array. A second validation cohort, validation data set 2, consists of post-mortem brain biopsies from depressed adults (n=58). We performed a MWAS by robust multiple linear regressions of methylation to a modified risk-score assessment of depression. Methylation levels of candidate CpG sites were correlated with expression levels of the associated gene in an independent cohort of 11 healthy volunteers.\n\nThe methylation state of two CpG sites reliably predicted ratings of depression in adolescents (cg13227623 and cg04102384) (p<10E-06). Cohort validation analysis confirmed cg04102384 - located in the promoter region of microRNA 4646 (MIR4646) - to be hypomethylated in both validation data set 1 and validation data set 2 (p<0.05). Cg04102384 was inversely correlated to expression levels of MIR4646-3p in healthy controls (p<0.05).\n\nMIR4646 was not differentially expressed in a subset of samples with adolescent depression measured by qRT-PCR measurements.\n\nWe identify a specific MIR4646 associated epigenetic risk site to be associated with depression in adolescents. Cg04102384 putatively regulates gene expression of MIR4646-3p. Target gene prediction and gene set overrepresentation analysis revealed involvement of this miRNA in fatty acid elongation, a process related to omega-3 fatty acids, previously associated with depression.", "doi": "10.1016/j.jad.2017.05.017", "pmid": "28618313", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0165-0327(16)32420-X"}], "notes": [], "created": "2017-10-25T15:27:44.326Z", "modified": "2020-01-21T13:56:08.027Z"}, {"entity": "publication", "iuid": "350d74228bff46cebb1319f0ce47d46a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/350d74228bff46cebb1319f0ce47d46a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/350d74228bff46cebb1319f0ce47d46a"}}, "title": "Validation of risk stratification models in acute myeloid leukemia using sequencing-based molecular profiling.", "authors": [{"family": "Wang", "given": "M", "initials": "M"}, {"family": "Lindberg", "given": "J", "initials": "J"}, {"family": "Klevebring", "given": "D", "initials": "D"}, {"family": "Nilsson", "given": "C", "initials": "C"}, {"family": "Mer", "given": "A S", "initials": "AS"}, {"family": "Rantalainen", "given": "M", "initials": "M"}, {"family": "Lehmann", "given": "S", "initials": "S"}, {"family": "Gr\u00f6nberg", "given": "H", "initials": "H"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "31", "issn": "1476-5551", "issue": "10", "pages": "2029-2036", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "Risk stratification of acute myeloid leukemia (AML) patients needs improvement. Several AML risk classification models based on somatic mutations or gene-expression profiling have been proposed. However, systematic and independent validation of these models is required for future clinical implementation. We performed whole-transcriptome RNA-sequencing and panel-based deep DNA sequencing of 23 genes in 274 intensively treated AML patients (Clinseq-AML). We also utilized the The Cancer Genome Atlas (TCGA)-AML study (N=142) as a second validation cohort. We evaluated six previously proposed molecular-based models for AML risk stratification and two revised risk classification systems combining molecular- and clinical data. Risk groups stratified by five out of six models showed different overall survival in cytogenetic normal-AML patients in the Clinseq-AML cohort (P-value<0.05; concordance index >0.5). Risk classification systems integrating mutational or gene-expression data were found to add prognostic value to the current European Leukemia Net (ELN) risk classification. The prognostic value varied between models and across cohorts, highlighting the importance of independent validation to establish evidence of efficacy and general applicability. All but one model replicated in the Clinseq-AML cohort, indicating the potential for molecular-based AML risk models. Risk classification based on a combination of molecular and clinical data holds promise for improved AML patient stratification in the future.", "doi": "10.1038/leu.2017.48", "pmid": "28167833", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "leu201748"}, {"db": "pmc", "key": "PMC5629364"}], "notes": [], "created": "2017-11-03T12:53:33.081Z", "modified": "2017-11-04T13:31:17.521Z"}, {"entity": "publication", "iuid": "3b4e156dce6641fe8f7b0c50a6517fea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b4e156dce6641fe8f7b0c50a6517fea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b4e156dce6641fe8f7b0c50a6517fea"}}, "title": "Tumor SHB gene expression affects disease characteristics in human acute myeloid leukemia.", "authors": [{"family": "Jamalpour", "given": "Maria", "initials": "M"}, {"family": "Li", "given": "Xiujuan", "initials": "X"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Gustafsson", "given": "Karin", "initials": "K"}, {"family": "Mostoslavsky", "given": "Gustavo", "initials": "G"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Welsh", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2017-10-00", "journal": {"title": "Tumour Biol.", "issn": "1423-0380", "volume": "39", "issue": "10", "pages": "1010428317720643", "issn-l": "1010-4283"}, "abstract": "The mouse Shb gene coding for the Src Homology 2-domain containing adapter protein B has recently been placed in context of BCRABL1-induced myeloid leukemia in mice and the current study was performed in order to relate SHB to human acute myeloid leukemia (AML). Publicly available AML databases were mined for SHB gene expression and patient survival. SHB gene expression was determined in the Uppsala cohort of AML patients by qPCR. Cell proliferation was determined after SHB gene knockdown in leukemic cell lines. Despite a low frequency of SHB gene mutations, many tumors overexpressed SHB mRNA compared with normal myeloid blood cells. AML patients with tumors expressing low SHB mRNA displayed longer survival times. A subgroup of AML exhibiting a favorable prognosis, acute promyelocytic leukemia (APL) with a PMLRARA translocation, expressed less SHB mRNA than AML tumors in general. When examining genes co-expressed with SHB in AML tumors, four other genes ( PAX5, HDAC7, BCORL1, TET1) related to leukemia were identified. A network consisting of these genes plus SHB was identified that relates to certain phenotypic characteristics, such as immune cell, vascular and apoptotic features. SHB knockdown in the APL PMLRARA cell line NB4 and the monocyte/macrophage cell line MM6 adversely affected proliferation, linking SHB gene expression to tumor cell expansion and consequently to patient survival. It is concluded that tumor SHB gene expression relates to AML survival and its subgroup APL. Moreover, this gene is included in a network of genes that plays a role for an AML phenotype exhibiting certain immune cell, vascular and apoptotic characteristics.", "doi": "10.1177/1010428317720643", "pmid": "28982308", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-20T07:54:05.021Z", "modified": "2021-07-08T12:52:24.344Z"}, {"entity": "publication", "iuid": "bdd67e281a7b45e8ae66b45cc2a1eb36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdd67e281a7b45e8ae66b45cc2a1eb36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdd67e281a7b45e8ae66b45cc2a1eb36"}}, "title": "Tumor Necrosis Factor Receptor 1 and 2 Are Associated With Risk of Intracerebral Hemorrhage.", "authors": [{"family": "Svensson", "given": "Edith H", "initials": "EH"}, {"family": "S\u00f6derholm", "given": "Martin", "initials": "M"}, {"family": "Abul-Kasim", "given": "Kasim", "initials": "K"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2017-10-00", "journal": {"title": "Stroke", "issn": "1524-4628", "issn-l": "0039-2499", "volume": "48", "issue": "10", "pages": "2710-2715"}, "abstract": "Raised plasma concentrations of tumor necrosis factor receptors (TNFR) have been linked to arterial stiffness, cerebral microbleeds, and vascular events. The aim of this study was to investigate the association of circulating levels of TNFR1 and TNFR2 with risk for future intracerebral hemorrhage (ICH).\n\nThe population-based MDCS cohort (Malm\u00f6 Diet and Cancer Study; n=28 449) was conducted in 1991 to 1996. A nested case-control study was performed in the MDCS, including 220 cases who experienced ICH during the follow-up period (mean age at inclusion 62 years, 48% men) and 244 matched controls. Of the 220 ICH cases, 68 died within 28 days. Conditional logistic regression was used to study the association between plasma levels of TNFR1 and TNFR2 and incident ICH, adjusting for known ICH risk factors.\n\nConcentrations of both TNFR1 and TNFR2 were significantly higher in subjects who developed ICH during the follow-up. The associations remained after adjustment for ICH risk factors (TNFR1: odds ratio [OR], 2.28; 95% confidence interval [CI], 1.26-4.11; P=0.006; TNFR2: OR, 1.77; CI, 1.16-2.70; P=0.008). ORs were somewhat higher for nonlobar ICH (3.04; CI, 1.29-7.14 and 2.39; CI, 1.32-4.32, respectively) than for lobar ICH (2.03; CI, 0.93-4.41 and 1.35; CI, 0.78-2.37, respectively). TNFR1 and TNFR2 were also associated with increased risk of fatal ICH (TNFR1: OR, 4.42; CI, 1.67-11.6; TNFR2: OR, 2.90; CI, 1.50-5.58) and with poor functional outcome according to the modified Rankin Scale.\n\nHigh plasma levels of TNFR1 and TNFR2 were associated with incident ICH, most clearly with ICH of nonlobar location. The results suggest that tumor necrosis factor-mediated inflammation could be associated with vascular changes preceding ICH.", "doi": "10.1161/STROKEAHA.117.017849", "pmid": "28830973", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "STROKEAHA.117.017849"}], "notes": [], "created": "2017-10-30T12:26:09.138Z", "modified": "2023-04-14T13:56:09.608Z"}, {"entity": "publication", "iuid": "c1e7b793656f4cf59d29e696d55d5d38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1e7b793656f4cf59d29e696d55d5d38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1e7b793656f4cf59d29e696d55d5d38"}}, "title": "Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy.", "authors": [{"family": "Liu", "given": "Peidi", "initials": "P"}, {"family": "Lass\u00e9n", "given": "Emelie", "initials": "E"}, {"family": "Nair", "given": "Viji", "initials": "V"}, {"family": "Berthier", "given": "Celine C", "initials": "CC"}, {"family": "Suguro", "given": "Miyuki", "initials": "M"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Kretzler", "given": "Matthias", "initials": "M"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Haraldsson", "given": "B\u00f6rje", "initials": "B"}, {"family": "Ju", "given": "Wenjun", "initials": "W"}, {"family": "Ebefors", "given": "Kerstin", "initials": "K"}, {"family": "Nystr\u00f6m", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "28", "issn": "1533-3450", "issue": "10", "pages": "2961-2972", "title": "J. Am. Soc. Nephrol.", "issn-l": "1046-6673"}, "abstract": "IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN ( n=19) and controls (n=22). Using curated glomerular cell type-specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell-positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell-positive standard genes. Additionally, patient clinical parameters (serum creatinine values and eGFRs) significantly correlated with Z scores derived from the expression profile of mesangial cell-positive standard genes. Among patients grouped according to Oxford MEST score, patients with segmental glomerulosclerosis had a significantly higher mesangial cell-positive standard gene Z score than patients without segmental glomerulosclerosis. By investigating mesangial cell proteomics and glomerular transcriptomics, we identified 22 common pathways induced in mesangial cells by gd-IgA, most of which mediate inflammation. The genes, proteins, and corresponding pathways identified provide novel insights into the pathophysiologic mechanisms leading to IgAN.", "doi": "10.1681/ASN.2016101103", "pmid": "28646076", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ASN.2016101103"}, {"db": "pmc", "key": "PMC5619958"}], "notes": [], "created": "2020-01-27T22:45:07.519Z", "modified": "2024-01-16T13:46:32.504Z"}, {"entity": "publication", "iuid": "08d96437e2804f3f8139651b56ca60ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08d96437e2804f3f8139651b56ca60ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08d96437e2804f3f8139651b56ca60ce"}}, "title": "The evolutionary history of the DMRT3 \u2018Gait keeper\u2019 haplotype", "authors": [{"family": "Staiger", "given": "E A", "initials": "EA"}, {"family": "Alm\u00e9n", "given": "M S", "initials": "MS"}, {"family": "Promerov\u00e1", "given": "M", "initials": "M"}, {"family": "Brooks", "given": "S", "initials": "S"}, {"family": "Cothran", "given": "E G", "initials": "EG"}, {"family": "Imsland", "given": "F", "initials": "F"}, {"family": "J\u00e4derkvist Fegraeus", "given": "K", "initials": "K"}, {"family": "Lindgren", "given": "G", "initials": "G"}, {"family": "Mehrabani Yeganeh", "given": "H", "initials": "H"}, {"family": "Mikko", "given": "S", "initials": "S"}, {"family": "Vega-Pla", "given": "J L", "initials": "JL"}, {"family": "Tozaki", "given": "T", "initials": "T"}, {"family": "Rubin", "given": "C J", "initials": "CJ"}, {"family": "Andersson", "given": "L", "initials": "L"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "48", "issn": "0268-9146", "issue": "5", "pages": "551-559", "title": "Anim Genet", "issn-l": null}, "abstract": null, "doi": "10.1111/age.12580", "pmid": "28741731", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:54:59.924Z", "modified": "2020-01-21T13:56:14.875Z"}, {"entity": "publication", "iuid": "7eb6fc6150224e299c4f63c3842354ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7eb6fc6150224e299c4f63c3842354ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7eb6fc6150224e299c4f63c3842354ba"}}, "title": "The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains.", "authors": [{"family": "Johansson", "given": "A", "initials": "A"}, {"family": "Claesson", "given": "R", "initials": "R"}, {"family": "H\u00f6glund \u00c5berg", "given": "C", "initials": "C"}, {"family": "Haubek", "given": "D", "initials": "D"}, {"family": "Oscarsson", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "52", "issn": "1600-0765", "issue": "5", "pages": "903-912", "title": "J. Periodont. Res.", "issn-l": "0022-3484"}, "abstract": "Aggregatibacter actinomycetemcomitans is involved in oral and systemic infections, and is associated with, eg aggressive forms of periodontitis and with endocarditis. The cagE gene encodes a \u224839\u00a0kDa putative exotoxin expressed by A.\u00a0actinomycetemcomitans. The level of conservation of cagE, and its possible significance in periodontal disease, has not yet been thoroughly investigated. In the present study, the role of the cagE gene as a diagnostic marker has been investigated.\n\nWe have used conventional polymerase chain reaction (PCR), quantitative PCR and whole genome sequencing data to determine the prevalence of cagE in A.\u00a0actinomycetemcomitans based on analysis of: (i) 249 isolates, collected and cultivated in a Ghanaian longitudinal cohort study; (ii) a serotype b collection of 19 strains; and (iii) the 36 A.\u00a0actinomycetemcomitans genomes available in the NCBI database.\n\nWhereas cagE was absent in the other serotypes, our data support that this gene sequence is linked to a virulent and highly leukotoxic group of serotype b strains, including both JP2 and non-JP2 genotypes of A.\u00a0actinomycetemcomitans.\n\nWe propose that cagE has the potential to be used as a PCR-based gene marker for the identification of a virulent and highly leukotoxic group of serotype b strains, including both JP2 and non-JP2 genotypes. This finding might be of importance in the risk assessment of the development of periodontal attachment loss in young individuals and hence suggested to be a relevant discovery in future development of new diagnostic tools and/or treatment strategies.", "doi": "10.1111/jre.12462", "pmid": "28397250", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "GENBANK", "key": "LT601546"}, {"db": "GENBANK", "key": "LT601547"}, {"db": "GENBANK", "key": "LT601548"}, {"db": "GENBANK", "key": "AAM68959"}, {"db": "GENBANK", "key": "AHN72937"}], "notes": [], "created": "2019-01-15T11:43:22.448Z", "modified": "2020-01-21T13:53:22.548Z"}, {"entity": "publication", "iuid": "2169891b741d469abe009aa481604680", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2169891b741d469abe009aa481604680.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2169891b741d469abe009aa481604680"}}, "title": "Structures of the human mitochondrial ribosome in native states of assembly", "authors": [{"family": "Brown", "given": "Alan", "initials": "A", "orcid": "0000-0002-0021-0476", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bb38a7f086247fdb2e2b3bfb80dae1e.json"}}, {"family": "Rathore", "given": "Sorbhi", "initials": "S", "orcid": "0000-0001-9178-1006", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2293f9f60f44cfa47f1e3691c1309d.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Bai", "given": "Xiao chen", "initials": "Xc"}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Ramakrishnan", "given": "V", "initials": "V", "orcid": "0000-0002-4699-2194", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c59648b4e90409da2fcd0c4ae0355c6.json"}}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "24", "issn": "1545-9993", "issue": "10", "pages": "866-869", "title": "Nat Struct Mol Biol", "issn-l": "1545-9985"}, "abstract": "Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to \u223c3-\u00c5 resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.", "doi": "10.1038/nsmb.3464", "pmid": "28892042", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "mid", "key": "EMS73849"}, {"db": "pmc", "key": "PMC5633077"}, {"db": "pii", "key": "nsmb.3464"}], "notes": [], "created": "2017-10-16T16:18:18.520Z", "modified": "2023-12-04T10:11:28.653Z"}, {"entity": "publication", "iuid": "fe676690ff9d483394c2d54033ee1aac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe676690ff9d483394c2d54033ee1aac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe676690ff9d483394c2d54033ee1aac"}}, "title": "Spheroid Segmentation Using Multiscale Deep Adversarial Networks", "authors": [{"family": "Sadanandan", "given": "Sajith Kecheril", "initials": "SK"}, {"family": "Karlsson", "given": "Johan", "initials": "J"}, {"family": "Wahlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "proceedings-article", "published": "2017-10-00", "journal": {"title": "The IEEE International Conference on Computer Vision (ICCV), 2017", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": "36-41"}, "abstract": "In this work, we segment spheroids with different sizes, shapes, and illumination conditions from bright-field microscopy images. To segment the spheroids we create a novel multiscale deep adversarial network with different deep feature extraction layers at different scales. We show that linearly increasing the adversarial loss contribution results in a stable segmentation algorithm for our dataset. We qualitatively and quantitatively compare the performance of our deep adversarial network with two other networks without adversarial losses. We show that our deep adversarial network performs better than the other two networks at segmenting the spheroids from our 2D bright-field microscopy images.", "doi": "10.1109/iccvw.2017.11", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T08:33:16.067Z", "modified": "2023-06-02T10:28:50.765Z"}, {"entity": "publication", "iuid": "14eb5706d8aa4e83800ec409e0517584", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14eb5706d8aa4e83800ec409e0517584.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14eb5706d8aa4e83800ec409e0517584"}}, "title": "Reduced cell surface levels of GPI-linked markers in a new case with PIGG loss of function.", "authors": [{"family": "Zhao", "given": "Jin James", "initials": "JJ", "orcid": "0000-0001-8367-8391", "researcher": {"href": "https://publications.scilifelab.se/researcher/fad3b22c21064a85a351f549bedfc36e.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Knaus", "given": "Alexej", "initials": "A"}, {"family": "Georgii-Hemming", "given": "Patrik", "initials": "P"}, {"family": "Baeck", "given": "Peter", "initials": "P"}, {"family": "Krawitz", "given": "Peter M", "initials": "PM"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "38", "issn": "1098-1004", "issue": "10", "pages": "1394-1401", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Glycosylphosphatidylinositol (GPI) is a glycolipid that tethers more than 150 different proteins to the cell surface. Aberrations in biosynthesis of GPI anchors cause congenital disorders of glycosylation with clinical features including intellectual disability (ID), seizures, and facial dysmorphism. Here, we present two siblings with ID, cerebellar hypoplasia, cerebellar ataxia, early-onset seizures, and minor facial dysmorphology. Using exome sequencing, we identified a homozygous nonsense variant (NM_001127178.1:c.1640G>A, p.Trp547*) in the gene Phosphatidylinositol Glycan Anchor Biosynthesis, Class G (PIGG) in both the patients. Variants in several other GPI anchor synthesis genes lead to a reduced expression of GPI-anchored proteins (GPI-APs) that can be measured by flow cytometry. No significant differences in GPI-APs could be detected in patient granulocytes, consistent with recent findings. However, fibroblasts showed a reduced global level of GPI anchors and of specific GPI-linked markers. These findings suggest that fibroblasts might be more sensitive to pathogenic variants in GPI synthesis pathway and are well suited to screen for GPI-anchor deficiencies. Based on genetic and functional evidence, we confirm that pathogenic variants in PIGG cause an ID syndrome, and we find that loss of function of PIGG is associated with GPI deficiency.", "doi": "10.1002/humu.23268", "pmid": "28581210", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6180480"}], "notes": [], "created": "2017-10-17T09:44:01.955Z", "modified": "2024-01-16T13:48:47.470Z"}, {"entity": "publication", "iuid": "17879f3c58aa4207abc4e240fa2b1fc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17879f3c58aa4207abc4e240fa2b1fc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17879f3c58aa4207abc4e240fa2b1fc8"}}, "title": "Quantitative interactions between the biocontrol fungus Phlebiopsis gigantea, the forest pathogen Heterobasidion annosum and the fungal community inhabiting Norway spruce stumps", "authors": [{"family": "Oliva", "given": "Jon\u00e0s", "initials": "J"}, {"family": "Messal", "given": "Mandy", "initials": "M", "orcid": "0000-0002-2473-2009", "researcher": {"href": "https://publications.scilifelab.se/researcher/e76c488f2d9540f78cba410ecd67ee86.json"}}, {"family": "Wendt", "given": "Lucile", "initials": "L"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "402", "issn": "0378-1127", "issue": null, "pages": "253-264", "title": "Forest Ecology and Management", "issn-l": null}, "abstract": null, "doi": "10.1016/j.foreco.2017.07.046", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:34:16.785Z", "modified": "2024-01-16T13:48:47.477Z"}, {"entity": "publication", "iuid": "be3bbe044c8f4442af1d1d01ac5f4aa8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be3bbe044c8f4442af1d1d01ac5f4aa8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be3bbe044c8f4442af1d1d01ac5f4aa8"}}, "title": "Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia.", "authors": [{"family": "Moisseiev", "given": "Elad", "initials": "E"}, {"family": "Anderson", "given": "Johnathon D", "initials": "JD"}, {"family": "Oltjen", "given": "Sharon", "initials": "S"}, {"family": "Goswami", "given": "Mayank", "initials": "M"}, {"family": "Zawadzki", "given": "Robert J", "initials": "RJ"}, {"family": "Nolta", "given": "Jan A", "initials": "JA"}, {"family": "Park", "given": "Susanna S", "initials": "SS"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "42", "issn": "1460-2202", "issue": "10", "pages": "1358-1367", "title": "Current Eye Research", "issn-l": "0271-3683"}, "abstract": "Exosomes derived from human mesenchymal stem cells (hMSCs) cultured under hypoxic conditions contain proteins and growth factors that promote angiogenesis. This study investigated the effect of intravitreal administration of these exosomes on retinal ischemia using a murine model.\n\nOxygen-induced retinopathy (OIR) was induced by exposing one-week-old male C57BL/6J mice to 5 days of 75% hyperoxic conditioning, and returning to room air. After hyperoxic conditioning, the right eye of each mouse was injected intravitreally with 1 \u00b5l saline or exosomes derived from hMSCs and compared to control mice of the same age raised in room air without OIR injected intravitreally with saline. Two weeks post-injection, fluorescein angiography (FA) and phase-variance optical coherence tomography angiography (pvOCTA) were used to assess retinal perfusion. Retinal thickness was determined by OCT. The extent of retinal neovascularization was quantitated histologically by counting vascular nuclei on the retinal surface.\n\nAmong eyes with OIR, intravitreal exosome treatment partially preserved retinal vascular flow in vivo and reduced associated retinal thinning; retinal thickness on OCT was 111.1 \u00b1 7.4\u00b5m with saline versus 132.1 \u00b1 11.6\u00b5m with exosome, p < 0.001. Retinal neovascularization among OIR eyes was reduced with exosome treatment when compared to saline-treated eyes (7.75 \u00b1 3.68 versus 2.68 \u00b1 1.35 neovascular nuclei per section, p < 0.0001). No immunogenicity or ocular/systemic adverse effect was associated with intravitreal exosome treatment.\n\nIntravitreal administration of exosomes derived from hMSCs was well tolerated without immunosuppression and decreased the severity of retinal ischemia in this murine model. This appealing novel non-cellular therapeutic approach warrants further exploration.", "doi": "10.1080/02713683.2017.1319491", "pmid": "28636406", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7008268"}, {"db": "mid", "key": "NIHMS1023062"}], "notes": [], "created": "2019-01-07T11:23:22.866Z", "modified": "2021-06-21T15:04:53.013Z"}, {"entity": "publication", "iuid": "16781fb9aaae414bb5b27ea73128ba92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16781fb9aaae414bb5b27ea73128ba92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16781fb9aaae414bb5b27ea73128ba92"}}, "title": "Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis", "authors": [{"family": "Varade", "given": "Jezabel", "initials": "J"}, {"family": "Wang", "given": "Ning", "initials": "N"}, {"family": "Lim", "given": "Che Kang", "initials": "CK"}, {"family": "Zhang", "given": "Tao", "initials": "T"}, {"family": "Zhang", "given": "Yuanwei", "initials": "Y"}, {"family": "Liu", "given": "Xiaomin", "initials": "X"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Matell", "given": "Ritva", "initials": "R"}, {"family": "Cao", "given": "Hongzhi", "initials": "H"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": null, "issn": "0896-8411", "issue": null, "pages": null, "title": "Journal of Autoimmunity", "issn-l": "0896-8411"}, "abstract": null, "doi": "10.1016/j.jaut.2017.10.002", "pmid": "29037440", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:53.289Z", "modified": "2020-01-21T13:56:11.955Z"}, {"entity": "publication", "iuid": "3f6086e7614a4402bcc94904e166a97e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f6086e7614a4402bcc94904e166a97e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f6086e7614a4402bcc94904e166a97e"}}, "title": "NorWood: a gene expression resource for evo-devo studies of conifer wood development.", "authors": [{"family": "Jokipii-Lukkari", "given": "Soile", "initials": "S"}, {"family": "Sundell", "given": "David", "initials": "D"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "216", "issn": "1469-8137", "issue": "2", "pages": "482-494", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P.\u00a0abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A.\u00a0thaliana and P.\u00a0tremula, but not in P.\u00a0abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P.\u00a0abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P.\u00a0abies.", "doi": "10.1111/nph.14458", "pmid": "28186632", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "ENA", "description": "raw RNA-seq", "key": "ERP017340"}], "notes": [], "created": "2017-11-03T16:21:20.692Z", "modified": "2024-01-16T13:48:47.485Z"}, {"entity": "publication", "iuid": "66d129fdaa424216a637ee29b4d4255b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66d129fdaa424216a637ee29b4d4255b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66d129fdaa424216a637ee29b4d4255b"}}, "title": "N-Acylated Derivatives of Sulfamethoxazole Block Chlamydia Fatty Acid Synthesis and Interact with FabF.", "authors": [{"family": "Mojica", "given": "Sergio A", "initials": "SA"}, {"family": "Salin", "given": "Olli", "initials": "O"}, {"family": "Bastidas", "given": "Robert J", "initials": "RJ"}, {"family": "Sunduru", "given": "Naresh", "initials": "N"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "N\u00fa\u00f1ez-Otero", "given": "Carlos", "initials": "C"}, {"family": "Engstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Valdivia", "given": "Raphael H", "initials": "RH"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Gylfe", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "61", "issn": "1098-6596", "issue": "10", "pages": "e00716-17", "title": "Antimicrob. Agents Chemother.", "issn-l": "0066-4804"}, "abstract": "The type II fatty acid synthesis (FASII) pathway is essential for bacterial lipid biosynthesis and continues to be a promising target for novel antibacterial compounds. Recently, it has been demonstrated that Chlamydia is capable of FASII and this pathway is indispensable for Chlamydia growth. Previously, a high-content screen with Chlamydia trachomatis-infected cells was performed, and acylated sulfonamides were identified to be potent growth inhibitors of the bacteria. C. trachomatis strains resistant to acylated sulfonamides were isolated by serial passage of a wild-type strain in the presence of low compound concentrations. Results from whole-genome sequencing of 10 isolates from two independent drug-resistant populations revealed that mutations that accumulated in fabF were predominant. Studies of the interaction between the FabF protein and small molecules showed that acylated sulfonamides directly bind to recombinant FabF in vitro and treatment of C. trachomatis-infected HeLa cells with the compounds leads to a decrease in the synthesis of Chlamydia fatty acids. This work demonstrates the importance of FASII for Chlamydia development and may lead to the development of new antimicrobials.", "doi": "10.1128/AAC.00716-17", "pmid": "28784680", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "AAC.00716-17"}, {"db": "pmc", "key": "PMC5610512"}], "notes": [], "created": "2017-10-31T12:05:28.123Z", "modified": "2025-10-17T13:03:59.574Z"}, {"entity": "publication", "iuid": "3a20cca7788948b9842e3782ab5b9269", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a20cca7788948b9842e3782ab5b9269.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a20cca7788948b9842e3782ab5b9269"}}, "title": "Multivariate strategy for the sample selection and integration of multi-batch data in metabolomics", "authors": [{"family": "Surowiec", "given": "Izabella", "initials": "I"}, {"family": "Johansson", "given": "Erik", "initials": "E"}, {"family": "Torell", "given": "Frida", "initials": "F"}, {"family": "Idborg", "given": "Helena", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Jakobsson", "given": "Per Johan", "initials": "PJ"}, {"family": "Trygg", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "13", "issn": "1573-3882", "issue": "10", "pages": null, "title": "Metabolomics", "issn-l": null}, "abstract": null, "doi": "10.1007/s11306-017-1248-1", "pmid": "28890672", "labels": {"Swedish Metabolomics Centre": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:35:56.526Z", "modified": "2025-10-17T13:03:18.495Z"}, {"entity": "publication", "iuid": "3b3f11eeb832485ba926a24d253d1a6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b3f11eeb832485ba926a24d253d1a6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b3f11eeb832485ba926a24d253d1a6d"}}, "title": "Hormonal contraceptive use affects HIV susceptibility: mechanisms revealed by image analysis", "authors": [{"family": "Edfeldt G", "given": "", "initials": ""}, {"family": "Lajoie J", "given": "", "initials": ""}, {"family": "R\u00f6hl M", "given": "", "initials": ""}, {"family": "Tjernlund A", "given": "", "initials": ""}], "type": "journal-article", "published": "2017-10-00", "journal": {"title": "Scand J Immunol", "issn": "0300-9475", "issn-l": "0300-9475", "volume": "86", "issue": "4", "pages": "249-350"}, "abstract": null, "doi": null, "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T11:56:35.341Z", "modified": "2022-07-05T09:33:11.674Z"}, {"entity": "publication", "iuid": "552a527eb843406ebc131479949c6fda", "links": {"self": {"href": "https://publications.scilifelab.se/publication/552a527eb843406ebc131479949c6fda.json"}, "display": {"href": "https://publications.scilifelab.se/publication/552a527eb843406ebc131479949c6fda"}}, "title": "GDF-15 and TRAIL-R2 are powerful predictors of long-term mortality in patients with acute myocardial infarction.", "authors": [{"family": "Skau", "given": "Emma", "initials": "E"}, {"family": "Henriksen", "given": "Egil", "initials": "E"}, {"family": "Wagner", "given": "Philippe", "initials": "P"}, {"family": "Hedberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Leppert", "given": "Jerzy", "initials": "J"}], "type": "journal article", "published": "2017-10-00", "journal": {"title": "Eur J Prev Cardiol", "issn": "2047-4881", "issn-l": "2047-4873", "volume": "24", "issue": "15", "pages": "1576-1583"}, "abstract": "Background The Proximity Extension Assay proteomics chip provides a large-scale analysis of 92 biomarkers linked to cardiovascular disease or inflammation. We aimed to identify the biomarkers that best predicted long-term all-cause mortality in patients with acute myocardial infarction. Methods In this prospective cohort study, 92 biomarkers were analysed in 847 consecutive patients from the V\u00e4stmanland Myocardial Infarction Study with a median follow-up of 6.9 years. Results The mean (\u00b1 standard deviation) age of the patients was 70 (11.8) years and 32.7% were female. Two hundred and seven patients had died after follow-up. The biomarkers most strongly linked to all-cause mortality were growth differentiation factor 15 (GDF-15) and tumour necrosis factor-related apoptosis-inducing ligand receptor 2 (TRAIL-R2). Cox regression analysis showed that GDF-15 (hazard ratio 1.25 per unit change, 95% confidence interval, 1.02-1.53, p = 0.031) and TRAIL-R2 (hazard ratio 1.37 per unit change, 95% confidence interval 1.12-1.67, p = 0.002) were independent predictors of long-term all-cause mortality after adjusting for age, gender, diabetes, previous myocardial infarction, stroke, heart failure, hypertension, smoking, hypercholesterolaemia, body mass index, ST-elevation myocardial infarction, left ventricular ejection fraction, troponin I, estimated glomerular filtration rate, N-terminal pro-brain natriuretic peptide and C-reactive protein. The combination of GDF-15 and TRAIL-R2 with established risk factors and biomarkers showed a discriminating accuracy of separating survivors from non-survivors with a cross-validated area under the receiving operating characteristics curve of 0.88 within five years. Conclusion GDF-15 and TRAIL-R2 were the most powerful Proximity Extension Assay chip biomarkers in predicting long-term all-cause mortality in patients with acute myocardial infarction.", "doi": "10.1177/2047487317725017", "pmid": "28762762", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-31T09:48:39.714Z", "modified": "2023-04-14T13:56:09.808Z"}, {"entity": "publication", "iuid": "38a5ead2934448f3b398604d0efdec2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38a5ead2934448f3b398604d0efdec2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38a5ead2934448f3b398604d0efdec2e"}}, "title": "Eosinophil Cationic Protein, Carotid Plaque, and Incidence of Stroke.", "authors": [{"family": "Sundstr\u00f6m", "given": "Johannes", "initials": "J"}, {"family": "S\u00f6derholm", "given": "Martin", "initials": "M"}, {"family": "Born\u00e9", "given": "Yan", "initials": "Y"}, {"family": "Nilsson", "given": "Jan", "initials": "J"}, {"family": "Persson", "given": "Margaretha", "initials": "M"}, {"family": "\u00d6stling", "given": "Gerd", "initials": "G"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2017-10-00", "journal": {"title": "Stroke", "issn": "1524-4628", "issn-l": "0039-2499", "volume": "48", "issue": "10", "pages": "2686-2692"}, "abstract": "ECP (eosinophil cationic protein) is a marker of eosinophil activity and degranulation, which has been linked to atherosclerosis and cardiovascular disease. We examined the relationship between ECP, carotid plaque, and incidence of stroke in a prospective population-based cohort.\n\nThe subjects participated in the Malm\u00f6 Diet and Cancer Study between 1991 and 1994. A total of 4706 subjects with no history of stroke were included (40% men; mean age, 57.5 years). Carotid plaque was determined by B-mode ultrasound of the right carotid artery. Incidence of stroke was followed up during a mean period of 16.5 years in relation to plasma ECP levels.\n\nSubjects in the third tertile (versus first tertile) of ECP tended to have higher prevalence of carotid plaque (odds ratio: 1.18; 95% confidence interval: 1.003-1.39; P=0.044 after multivariate adjustments). A total of 258 subjects were diagnosed with ischemic stroke (IS) during follow-up. ECP was associated with increased incidence of IS after risk factor adjustment (hazard ratio, 1.57; 95% confidence interval: 1.13-2.18; for third versus first tertile; P=0.007). High ECP was associated with increased risk of IS in subjects with carotid plaque. The risk factor-adjusted hazard ratio for IS was 1.86 (95% confidence interval: 1.32-2.63) in subjects with carotid plaque and ECP in the top tertile, compared with those without plaque and ECP in the first or second tertiles.\n\nHigh ECP is associated with increased incidence of IS. The association between ECP and IS was also present in the subgroup with carotid plaque.", "doi": "10.1161/STROKEAHA.117.018450", "pmid": "28904229", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "STROKEAHA.117.018450"}], "notes": [], "created": "2017-10-30T12:15:08.330Z", "modified": "2023-04-14T13:56:10.043Z"}, {"entity": "publication", "iuid": "0cd49b807b98485fb62dcca6a680aa25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cd49b807b98485fb62dcca6a680aa25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cd49b807b98485fb62dcca6a680aa25"}}, "title": "Deep Convolutional Neural Networks for Detecting Cellular Changes Due to Malignancy", "authors": [{"family": "Forslid", "given": "Gustav", "initials": "G"}, {"family": "Wieslander", "given": "Hakan", "initials": "H"}, {"family": "Bengtsson", "given": "Ewert", "initials": "E"}, {"family": "Wahlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Hirsch", "given": "Jan Michael", "initials": "JM"}, {"family": "Stark", "given": "Christina Runow", "initials": "CR"}, {"family": "Sadanandan", "given": "Sajith Kecheril", "initials": "SK"}], "type": "proceedings-article", "published": "2017-10-00", "journal": {"title": "The IEEE International Conference on Computer Vision (ICCV), 2017", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Discovering cancer at an early stage is an effective way to increase the chance of survival. However, since most screening processes are done manually it is time inef\ufb01cient and thus a costly process. One way of automizing the screening process could be to classify cells using Convolutional Neural Networks. Convolutional Neural Networks have been proven to be accurate for image classi\ufb01cation tasks. Two datasets containing oral cells and two datasets containing cervical cells were used. For the cervical cancer dataset the cells were classi\ufb01ed by medical experts as normal or abnormal. For the oral cell dataset we only used the diagnosis of the patient. All cells obtained from a patient with malignancy were thus considered malignant even though most of them looked normal. The performance was evaluated for two different network architectures, ResNet and VGG. For the oral datasets the accuracy varied between 78-82% correctly classi\ufb01ed cells depending on the dataset and network. For the cervical datasets the accuracy varied between 84-86% correctly classi\ufb01ed cells depending on the dataset and network. The results indicate a high potential for detecting abnormalities in oral cavity and in uterine cervix. ResNet was shown to be the preferable network, with a higher accuracy and a smaller standard deviation.", "doi": "10.1109/iccvw.2017.18", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T08:42:44.190Z", "modified": "2023-06-02T10:28:56.445Z"}, {"entity": "publication", "iuid": "cd261cbdf4ce4347baaaf237956dccdd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd261cbdf4ce4347baaaf237956dccdd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd261cbdf4ce4347baaaf237956dccdd"}}, "title": "Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny", "authors": [{"family": "Rydin", "given": "Catarina", "initials": "C"}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Bremer", "given": "Birgitta", "initials": "B"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "104", "issn": "0002-9122", "issue": "10", "pages": "1522-1532", "title": "Am. J. Bot.", "issn-l": null}, "abstract": null, "doi": "10.3732/ajb.1700255", "pmid": "29885222", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:38.978Z", "modified": "2024-01-16T13:48:47.493Z"}, {"entity": "publication", "iuid": "2fa8678337844af495bbed186ee7611d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fa8678337844af495bbed186ee7611d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fa8678337844af495bbed186ee7611d"}}, "title": "Comprehensive analysis of NMR data using advanced line shape fitting", "authors": [{"family": "Niklasson", "given": "Markus", "initials": "M"}, {"family": "Otten", "given": "Renee", "initials": "R"}, {"family": "Ahlner", "given": "Alexandra", "initials": "A"}, {"family": "Andresen", "given": "Cecilia", "initials": "C"}, {"family": "Schlagnitweit", "given": "Judith", "initials": "J"}, {"family": "Petzold", "given": "Katja", "initials": "K"}, {"family": "Lundstr\u00f6m", "given": "Patrik", "initials": "P"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "69", "issn": "0925-2738", "issue": "2", "pages": "93-99", "title": "J Biomol NMR", "issn-l": "0925-2738"}, "abstract": null, "doi": "10.1007/s10858-017-0141-6", "pmid": "29043470", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:31:27.306Z", "modified": "2025-10-17T13:03:59.584Z"}, {"entity": "publication", "iuid": "2eaa9e4176c54896b9e05102c6299463", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2eaa9e4176c54896b9e05102c6299463.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2eaa9e4176c54896b9e05102c6299463"}}, "title": "Cetuximab sensitivity of head and neck squamous cell carcinoma xenografts is associated with treatment-induced reduction in EGFR, pEGFR, and pSrc.", "authors": [{"family": "Jedlinski", "given": "Adam", "initials": "A"}, {"family": "Garvin", "given": "Stina", "initials": "S"}, {"family": "Johansson", "given": "Ann-Charlotte", "initials": "A"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "P"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Roberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "46", "issn": "1600-0714", "issue": "9", "pages": "717-724", "title": "J. Oral Pathol. Med.", "issn-l": "0904-2512"}, "abstract": "The aims of this study were to validate in vitro drug sensitivity testing of head and neck squamous cell carcinoma (HNSCC) cell lines in an in vivo xenograft model and to identify treatment-induced changes in the epidermal growth factor receptor (EGFR) signaling pathway that could be used as markers for cetuximab treatment response.\r\n\r\nThe in vitro and in vivo cetuximab sensitivity of two HNSCC cell lines, UT-SCC-14 and UT-SCC-45, was assessed using a crystal violet assay and xenografts in nude mice, respectively. The expression of EGFR, phosphorylated EGFR (pEGFR), phosphorylated Src (pSrc), and Ki-67 was investigated by immunohistochemistry. To verify these results, the in vitro expression of EGFR and pEGFR was analyzed with ELISA in a panel of 10 HNSCC cell lines.\r\n\r\nA close correlation was found between in vitro and in vivo cetuximab sensitivity data in the two investigated HNSCC cell lines. In treatment sensitive UT-SCC-14 xenografts, there was a decrease in EGFR, pEGFR, and pSrc upon cetuximab treatment. Interestingly, in insensitive UT-SCC-45 xenografts, an increased expression of these three proteins was found. The change in EGFR and pEGFR expression in vivo was confirmed in cetuximab-sensitive and cetuximab-insensitive HNSCC cell lines using ELISA.\r\n\r\nHigh sensitivity to cetuximab was strongly associated with a treatment-induced reduction in pEGFR both in vivo and in vitro in a panel of HNSCC cell lines, suggesting that EGFR and pEGFR dynamics could be used as a predictive biomarker for cetuximab treatment response.", "doi": "10.1111/jop.12545", "pmid": "28036101", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:55:59.236Z", "modified": "2017-11-05T12:39:35.466Z"}, {"entity": "publication", "iuid": "59ec533b78ce498da5e03aa6d32178da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59ec533b78ce498da5e03aa6d32178da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59ec533b78ce498da5e03aa6d32178da"}}, "title": "Breast cancer in young women and prognosis: How important are proliferation markers?", "authors": [{"family": "Fredholm", "given": "Hanna", "initials": "H"}, {"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Linda S", "initials": "LS"}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP"}, {"family": "Lindman", "given": "Henrik", "initials": "H"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Frisell", "given": "Jan", "initials": "J"}, {"family": "Fredriksson", "given": "Irma", "initials": "I"}], "type": "comparative study", "published": "2017-10-00", "journal": {"title": "Eur. J. Cancer", "issn": "1879-0852", "volume": "84", "issue": null, "pages": "278-289", "issn-l": "0959-8049"}, "abstract": "Compared to middle-aged women, young women with breast cancer have a higher risk of systemic disease. We studied expression of proliferation markers in relation to age and subtype and their association with long-term prognosis.\n\nDistant disease-free survival (DDFS) was studied in 504 women aged <40 years and 383 women aged \u226540 years from a population-based cohort. Information on patient characteristics, treatment and follow-up was collected from medical records. Tissue microarrays were produced for analysis of oestrogen receptor, progesterone receptor (PR), Her2, Ki-67\u00a0and cyclins.\n\nYoung women with luminal tumours had significantly higher expression of Ki-67 and cyclins. Proliferation markers were prognostic only within this subtype. Ki-67 was a prognostic indicator only in young women with luminal PR+ tumours. The optimal cut-off for Ki-67 varied by age. High expression of cyclin E1 conferred a better DDFS in women aged <40 years with luminal PR- tumours (hazard ratio [HR] 0.47 [0.24-0.92]). Age <40 years was an independent risk factor of DDFS exclusively in women with luminal B PR+ tumours (HR 2.35 [1.22-4.50]). Young women with luminal B PR- tumours expressing low cyclin E1 had a six-fold risk of distant disease compared with luminal A (HR 6.21 [2.17-17.6]).\n\nThe higher expression of proliferation markers in young women does not have a strong impact on prognosis. Ki-67 is only prognostic in the subgroup of young women with luminal PR+\u00a0tumours. The only cyclin adding prognostic value beyond subtype is cyclin E1. Age is an independent prognostic factor only in women with luminal B PR+ tumours.", "doi": "10.1016/j.ejca.2017.07.044", "pmid": "28844016", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0959-8049(17)31177-2"}], "notes": [], "created": "2017-11-05T12:43:28.113Z", "modified": "2017-11-05T12:43:28.149Z"}, {"entity": "publication", "iuid": "6b579fa6a62344afa63ce461a7ce0be5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b579fa6a62344afa63ce461a7ce0be5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b579fa6a62344afa63ce461a7ce0be5"}}, "title": "Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer.", "authors": [{"family": "Malgerud", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-1691-0880", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c4ba0afe85a4328b373dc0ebd862c1a.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Gustafsson-Liljefors", "given": "Maria", "initials": "M"}, {"family": "Karimi", "given": "Masoud", "initials": "M"}, {"family": "Moro", "given": "Carlos Fern\u00e1ndez", "initials": "CF"}, {"family": "Stecker", "given": "Katrin", "initials": "K"}, {"family": "Picker", "given": "Alexander", "initials": "A"}, {"family": "Huelsewig", "given": "Carolin", "initials": "C"}, {"family": "Stein", "given": "Martin", "initials": "M"}, {"family": "Bohnert", "given": "Regina", "initials": "R"}, {"family": "Del Chiaro", "given": "Marco", "initials": "M"}, {"family": "Haas", "given": "Stephan L", "initials": "SL"}, {"family": "Heuchel", "given": "Rainer L", "initials": "RL"}, {"family": "Permert", "given": "Johan", "initials": "J"}, {"family": "Maeurer", "given": "Markus J", "initials": "MJ"}, {"family": "Brock", "given": "Stephan", "initials": "S"}, {"family": "Verbeke", "given": "Caroline S", "initials": "CS"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Jackson", "given": "David B", "initials": "DB"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "L\u00f6hr", "given": "Johannes Matthias", "initials": "JM"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "11", "issn": "1878-0261", "issue": "10", "pages": "1413-1429", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is a tumor with an extremely poor prognosis, predominantly as a result of chemotherapy resistance and numerous somatic mutations. Consequently, PDAC is a prime candidate for the use of sequencing to identify causative mutations, facilitating subsequent administration of targeted therapy. In a feasibility study, we retrospectively assessed the therapeutic recommendations of a novel, evidence-based software that analyzes next-generation sequencing (NGS) data using a large panel of pharmacogenomic biomarkers for efficacy and toxicity. Tissue from 14 patients with PDAC was sequenced using NGS with a 620 gene panel. FASTQ files were fed into treatmentmap. The results were compared with chemotherapy in the patients, including all side effects. No changes in therapy were made. Known driver mutations for PDAC were confirmed (e.g. KRAS, TP53). Software analysis revealed positive biomarkers for predicted effective and ineffective treatments in all patients. At least one biomarker associated with increased toxicity could be detected in all patients. Patients had been receiving one of the currently approved chemotherapy agents. In two patients, toxicity could have been correctly predicted by the software analysis. The results suggest that NGS, in combination with an evidence-based software, could be conducted within a 2-week period, thus being feasible for clinical routine. Therapy recommendations were principally off-label use. Based on the predominant KRAS mutations, other drugs were predicted to be ineffective. The pharmacogenomic biomarkers indicative of increased toxicity could be retrospectively linked to reported negative side effects in the respective patients. Finally, the occurrence of somatic and germline mutations in cancer syndrome-associated genes is noteworthy, despite a high frequency of these particular variants in the background population. These results suggest software-analysis of NGS data provides evidence-based information on effective, ineffective and toxic drugs, potentially forming the basis for precision cancer medicine in PDAC.", "doi": "10.1002/1878-0261.12108", "pmid": "28675654", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5623817"}, {"db": "figshare", "key": "10.6084/m9.figshare.5311114"}], "notes": [], "created": "2017-11-03T12:53:31.739Z", "modified": "2023-06-19T07:51:37.793Z"}, {"entity": "publication", "iuid": "bb30b72c6f4547829967dbcf17c35eb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb30b72c6f4547829967dbcf17c35eb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb30b72c6f4547829967dbcf17c35eb7"}}, "title": "Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture", "authors": [{"family": "Zan", "given": "Yanjun", "initials": "Y"}, {"family": "Sheng", "given": "Zheya", "initials": "Z"}, {"family": "Lillie", "given": "Mette", "initials": "M"}, {"family": "R\u00f6nneg\u00e5rd", "given": "Lars", "initials": "L"}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "34", "issn": "0737-4038", "issue": "10", "pages": "2678-2689", "title": "", "issn-l": null}, "abstract": null, "doi": "10.1093/molbev/msx194", "pmid": "28957504", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-12-05T12:58:21.130Z", "modified": "2020-01-21T13:56:11.962Z"}, {"entity": "publication", "iuid": "a6910e07accd4f5495ef7e4d0c9c35cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6910e07accd4f5495ef7e4d0c9c35cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6910e07accd4f5495ef7e4d0c9c35cc"}}, "title": "Antibody Affinity Against 2009 A/H1N1 Influenza and Pandemrix Vaccine Nucleoproteins Differs Between Childhood Narcolepsy Patients and Controls.", "authors": [{"family": "Lind", "given": "Alexander", "initials": "A"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Ramelius", "given": "Anita", "initials": "A"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Arnheim-Dahlstr\u00f6m", "given": "Lisen", "initials": "L"}, {"family": "Lamb", "given": "Favelle", "initials": "F"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Ambati", "given": "Aditya", "initials": "A"}, {"family": "Maeurer", "given": "Markus", "initials": "M"}, {"family": "Lima Bomfim", "given": "Izaura", "initials": "I"}, {"family": "Fink", "given": "Katharina", "initials": "K"}, {"family": "Fex", "given": "Malin", "initials": "M"}, {"family": "T\u00f6rn", "given": "Carina", "initials": "C"}, {"family": "Elding Larsson", "given": "Helena", "initials": "H"}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "30", "issn": "1557-8976", "issue": "8", "pages": "590-600", "title": "Viral Immunol.", "issn-l": "0882-8245"}, "abstract": "Increased narcolepsy incidence was observed in Sweden following the 2009 influenza vaccination with Pandemrix\u00ae. A substitution of the 2009 nucleoprotein for the 1934 variant has been implicated in narcolepsy development. The aims were to determine (a) antibody levels toward wild-type A/H1N1-2009[A/California/04/2009(H1N1)] (NP-CA2009) and Pandemrix-[A/Puerto Rico/8/1934(H1N1)] (NP-PR1934) nucleoproteins in 43 patients and 64 age-matched controls; (b) antibody affinity in reciprocal competitive assays in 11 childhood narcolepsy patients compared with 21 age-matched controls; and (c) antibody levels toward wild-type A/H1N1-2009[A/California/04/2009(H1N1)] (H1N1 NS1), not a component of the Pandemrix vaccine. In vitro transcribed and translated 35S-methionine-labeled H1N1 influenza A virus proteins were used in radiobinding reciprocal competition assays to estimate antibody levels and affinity (Kd). Childhood patients had higher NP-CA2009 (p\u2009=\u20090.0339) and NP-PR1934 (p\u2009=\u20090.0246) antibody levels compared with age-matched controls. These childhood controls had lower NP-CA2009 (p\u2009=\u20090.0221) and NP-PR1934 (p\u2009=\u20090.00619) antibodies compared with controls 13 years or older. In contrast, in patients 13 years or older, the levels of NP-PR1934 (p\u2009=\u20090.279) and NP-CA2009 (p\u2009=\u20090.0644) antibodies did not differ from the older controls. Childhood antibody affinity (Kd) against NP-CA2009 was comparable between controls (68\u2009ng/mL) and patients (74\u2009ng/mL; p\u2009=\u20090.21) with NP-CA2009 and NP-PR1934 displacement (controls: 165\u2009ng/mL; patients: 199\u2009ng/mL; p\u2009=\u20090.48). In contrast, antibody affinity against NP-PR1934 was higher in controls with either NP-PR1934 (controls: 9\u2009ng/mL; patients: 20\u2009ng/mL; p\u2009=\u20090.0031) or NP-CA2009 (controls: 14\u2009ng/mL; patients: 23\u2009ng/mL; p\u2009=\u20090.0048). A/H1N1-NS1 antibodies were detected in 0/43 of the narcolepsy patients compared with 3/64 (4.7%) controls (p\u2009=\u20090.272). Similarly, none (0/11) of the childhood patients and 1/21 (4.8%) of the childhood controls had A/H1N1-NS1 antibodies. The higher antibody affinities against NP-PR1934 in controls suggest better protection against wild-type virus. In contrast, the reduced NP-PR1934 antibody affinities among childhood narcolepsy patients suggest poor protection from the wild-type A/H1N1 virus and possibly increased risk for viral damage.", "doi": "10.1089/vim.2017.0066", "pmid": "28796576", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-12-06T13:19:22.836Z", "modified": "2020-01-21T13:53:21.900Z"}, {"entity": "publication", "iuid": "81fd04ba3bf84bc4834ed150228a7f58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81fd04ba3bf84bc4834ed150228a7f58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81fd04ba3bf84bc4834ed150228a7f58"}}, "title": "Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli.", "authors": [{"family": "Cimdins", "given": "Annika", "initials": "A"}, {"family": "Simm", "given": "Roger", "initials": "R"}, {"family": "Li", "given": "Fengyang", "initials": "F"}, {"family": "L\u00fcthje", "given": "Petra", "initials": "P"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Brauner", "given": "Annelie", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "6", "issn": "2045-8827", "issue": "5", "title": "Microbiologyopen", "issn-l": "2045-8827"}, "abstract": "Agar plate-based biofilm of enterobacteria like Escherichia coli is characterized by expression of the extracellular matrix components amyloid curli and cellulose exopolysaccharide, which can be visually enhanced upon addition of the dye Congo Red, resulting in a red, dry, and rough (rdar) colony morphology. Expression of the rdar morphotype depends on the transcriptional regulator CsgD and occurs predominantly at ambient temperature in model strains. In contrast, commensal and pathogenic isolates frequently express the csgD-dependent rdar morphotype semi-constitutively, also at human host body temperature. To unravel the molecular basis of temperature-independent rdar morphotype expression, biofilm components and c-di-GMP turnover proteins of seven commensal and uropathogenic E. coli isolates were analyzed. A diversity within the c-di-GMP signaling network was uncovered which suggests alteration of activity of the trigger phosphodiesterase YciR to contribute to (up)regulation of csgD expression and consequently semi-constitutive rdar morphotype development.", "doi": "10.1002/mbo3.508", "pmid": "28913868", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5635171"}], "notes": [], "created": "2019-01-15T08:21:16.720Z", "modified": "2020-01-21T13:53:22.475Z"}, {"entity": "publication", "iuid": "60b0d98d513c4af988e4c92ae49decbd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60b0d98d513c4af988e4c92ae49decbd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60b0d98d513c4af988e4c92ae49decbd"}}, "title": "Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization.", "authors": [{"family": "Zhao", "given": "Miao", "initials": "M"}, {"family": "Spiess", "given": "Matthias", "initials": "M"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Olofsson", "given": "Helene", "initials": "H"}, {"family": "Hu", "given": "Jianjiang", "initials": "J"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Str\u00f6mblad", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2017-09-29", "journal": {"volume": "8", "issn": "1949-2553", "issue": "44", "pages": "77061-77074", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "p21-activated kinase 4 (PAK4) regulates cell proliferation, apoptosis, cell motility and F-actin remodeling, but the PAK4 interactome has not been systematically analyzed. Here, we comprehensively characterized the human PAK4 interactome by iTRAQ quantitative mass spectrometry of PAK4-immunoprecipitations. Consistent with its multiple reported functions, the PAK4 interactome was enriched in diverse protein networks, including the 14-3-3, proteasome, replication fork, CCT and Arp2/3 complexes. Because PAK4 co-immunoprecipitated most subunits of the Arp2/3 complex, we hypothesized that PAK4 may play a role in Arp2/3 dependent actin regulation. Indeed, we found that PAK4 interacts with and phosphorylates the nucleation promoting factor N-WASP at Ser484/Ser485 and promotes Arp2/3-dependent actin polymerization in vitro. Also, PAK4 ablation in vivo reduced N-WASP Ser484/Ser485 phosphorylation and altered the cellular balance between G- and F-actin as well as the actin organization. By presenting the PAK4 interactome, we here provide a powerful resource for further investigations and as proof of principle, we also indicate a novel mechanism by which PAK4 regulates actin cytoskeleton remodeling.", "doi": "10.18632/oncotarget.20352", "pmid": "29100370", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "20352"}, {"db": "pmc", "key": "PMC5652764"}], "notes": [], "created": "2017-12-05T16:14:23.542Z", "modified": "2021-07-08T11:36:15.220Z"}, {"entity": "publication", "iuid": "83a7f53f82784bc18e60e7b0bf1ea3f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83a7f53f82784bc18e60e7b0bf1ea3f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83a7f53f82784bc18e60e7b0bf1ea3f9"}}, "title": "A Drosophila female pheromone elicits species-specific long-range attraction via an olfactory channel with dual specificity for sex and food.", "authors": [{"family": "Lebreton", "given": "Sebastien", "initials": "S"}, {"family": "Borrero-Echeverry", "given": "Felipe", "initials": "F"}, {"family": "Gonzalez", "given": "Francisco", "initials": "F"}, {"family": "Solum", "given": "Marit", "initials": "M"}, {"family": "Wallin", "given": "Erika A", "initials": "EA"}, {"family": "Hedenstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Hansson", "given": "Bill S", "initials": "BS"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Bengtsson", "given": "Marie", "initials": "M"}, {"family": "Birgersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Walker", "given": "William B", "initials": "WB"}, {"family": "Dweck", "given": "Hany K M", "initials": "HKM"}, {"family": "Becher", "given": "Paul G", "initials": "PG"}, {"family": "Witzgall", "given": "Peter", "initials": "P", "orcid": "0000-0002-4697-3380", "researcher": {"href": "https://publications.scilifelab.se/researcher/548d4ff93a3f488e8133e5f7b1f79097.json"}}], "type": "journal article", "published": "2017-09-29", "journal": {"volume": "15", "issn": "1741-7007", "issue": "1", "pages": "88", "title": "BMC Biol.", "issn-l": "1741-7007"}, "abstract": "Mate finding and recognition in animals evolves during niche adaptation and involves social signals and habitat cues. Drosophila melanogaster and related species are known to be attracted to fermenting fruit for feeding and egg-laying, which poses the question of whether species-specific fly odours contribute to long-range premating communication.\n\nWe have discovered an olfactory channel in D. melanogaster with a dual affinity to sex and food odorants. Female flies release a pheromone, (Z)-4-undecenal (Z4-11Al), that elicits flight attraction in both sexes. Its biosynthetic precursor is the cuticular hydrocarbon (Z,Z)-7,11-heptacosadiene (7,11-HD), which is known to afford reproductive isolation between the sibling species D. melanogaster and D. simulans during courtship. Twin olfactory receptors, Or69aB and Or69aA, are tuned to Z4-11Al and food odorants, respectively. They are co-expressed in the same olfactory sensory neurons, and feed into a neural circuit mediating species-specific, long-range communication; however, the close relative D. simulans, which shares food resources with D. melanogaster, does not respond to Z4-11Al.\n\nThe Or69aA and Or69aB isoforms have adopted dual olfactory traits. The underlying gene yields a collaboration between natural and sexual selection, which has the potential to drive speciation.", "doi": "10.1186/s12915-017-0427-x", "pmid": "28962619", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-017-0427-x"}, {"db": "pmc", "key": "PMC5622430"}, {"db": "Dryad", "key": "10.5061/dryad.v54v8"}], "notes": [], "created": "2017-10-31T13:35:54.413Z", "modified": "2025-10-17T13:04:29.117Z"}, {"entity": "publication", "iuid": "badabce6ebc648ef88ba8754e445e30f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/badabce6ebc648ef88ba8754e445e30f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/badabce6ebc648ef88ba8754e445e30f"}}, "title": "The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus", "authors": [{"family": "Matzov", "given": "Donna", "initials": "D"}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Basu", "given": "Arnab", "initials": "A"}, {"family": "Zimmerman", "given": "Ella", "initials": "E"}, {"family": "Bashan", "given": "Anat", "initials": "A"}, {"family": "Yap", "given": "Mee Ngan F", "initials": "MNF", "orcid": "0000-0003-4213-4050", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2d55604c3f742569d9bf7cb2ad50cdf.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Yonath", "given": "Ada E", "initials": "AE"}], "type": "journal-article", "published": "2017-09-28", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "723", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.", "doi": "10.1038/s41467-017-00753-8", "pmid": "28959035", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5620080"}, {"db": "pii", "key": "10.1038/s41467-017-00753-8"}], "notes": [], "created": "2017-10-16T16:17:43.190Z", "modified": "2023-06-19T08:55:09.375Z"}, {"entity": "publication", "iuid": "38ade6881a5c4c4aa4aeabe2fe7eb85d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38ade6881a5c4c4aa4aeabe2fe7eb85d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38ade6881a5c4c4aa4aeabe2fe7eb85d"}}, "title": "Identification of a novel proinsulin-associated SNP and demonstration that proinsulin is unlikely to be a causal factor in subclinical vascular remodelling using Mendelian randomisation.", "authors": [{"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Hoed", "given": "Marcel den", "initials": "MD"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Haljas", "given": "Kadri", "initials": "K"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "B\u00e4cklund", "given": "Alexandra", "initials": "A"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Giral", "given": "Phillipe", "initials": "P"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Lannfelt", "given": "Lars L", "initials": "LL"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia C M", "initials": "CCM"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Saliba-Gustafsson", "given": "Peter", "initials": "P"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Zethelius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "IMPROVE study group", "given": "", "initials": ""}], "type": "journal article", "published": "2017-09-28", "journal": {"volume": "266", "issn": "1879-1484", "issue": null, "pages": "196-204", "title": "Atherosclerosis", "issn-l": "0021-9150"}, "abstract": "Increased proinsulin relative to insulin levels have been associated with subclinical atherosclerosis (measured by carotid intima-media thickness (cIMT)) and are predictive of future cardiovascular disease (CVD), independently of established risk factors. The mechanisms linking proinsulin to atherosclerosis and CVD are unclear. A genome-wide meta-analysis has identified nine loci associated with circulating proinsulin levels. Using proinsulin-associated SNPs, we set out to use a Mendelian randomisation approach to test the hypothesis that proinsulin plays a causal role in subclinical vascular remodelling.\n\nWe studied the high CVD-risk IMPROVE cohort (n\u00a0=\u00a03345), which has detailed biochemical phenotyping and repeated, state-of-the-art, high-resolution carotid ultrasound examinations. Genotyping was performed using Illumina Cardio-Metabo and Immuno arrays, which include reported proinsulin-associated loci. Participants with type 2 diabetes (n\u00a0=\u00a0904) were omitted from the analysis. Linear regression was used to identify proinsulin-associated genetic variants.\n\nWe identified a proinsulin locus on chromosome 15 (rs8029765) and replicated it in data from 20,003 additional individuals. An 11-SNP score, including the previously identified and the chromosome 15 proinsulin-associated loci, was significantly and negatively associated with baseline IMTmean and IMTmax (the primary cIMT phenotypes) but not with progression measures. However, MR-Eggers refuted any significant effect of the proinsulin-associated 11-SNP score, and a non-pleiotropic SNP score of three variants (including rs8029765) demonstrated no effect on baseline or progression cIMT measures.\n\nWe identified a novel proinsulin-associated locus and demonstrated that whilst proinsulin levels are associated with cIMT measures, proinsulin per se is unlikely to have a causative effect on cIMT.", "doi": "10.1016/j.atherosclerosis.2017.09.031", "pmid": "29040868", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9150(17)31317-5"}], "notes": [], "created": "2017-10-25T15:41:50.212Z", "modified": "2024-01-16T13:48:47.500Z"}, {"entity": "publication", "iuid": "da31c112341047c5a5ca23114213fd81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da31c112341047c5a5ca23114213fd81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da31c112341047c5a5ca23114213fd81"}}, "title": "Epidemiological characterization of a nosocomial outbreak of extended spectrum \u03b2-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing", "authors": [{"family": "Woksepp", "given": "Hanna", "initials": "H"}, {"family": "Ryberg", "given": "Anna", "initials": "A"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Sch\u00f6n", "given": "Thomas", "initials": "T"}, {"family": "S\u00f6derman", "given": "Jan", "initials": "J"}], "type": "journal-article", "published": "2017-09-28", "journal": {"volume": null, "issn": "0903-4641", "issue": null, "pages": null, "title": "APMIS", "issn-l": null}, "abstract": null, "doi": "10.1111/apm.12753", "pmid": "28960453", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genome sequencing and assembly", "key": "PRJEB15588"}], "notes": [], "created": "2017-10-30T09:30:03.674Z", "modified": "2020-01-21T13:56:14.881Z"}, {"entity": "publication", "iuid": "5bf6ada8a181454a9e92e6f8553fa50b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bf6ada8a181454a9e92e6f8553fa50b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bf6ada8a181454a9e92e6f8553fa50b"}}, "title": "Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods.", "authors": [{"family": "Carapito", "given": "Christine", "initials": "C"}, {"family": "Duek", "given": "Paula", "initials": "P"}, {"family": "Macron", "given": "Charlotte", "initials": "C"}, {"family": "Seffals", "given": "Marine", "initials": "M"}, {"family": "Rondel", "given": "Karine", "initials": "K"}, {"family": "Delalande", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Fr\u00e9our", "given": "Thomas", "initials": "T"}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y"}, {"family": "Lane", "given": "Lydie", "initials": "L"}, {"family": "Pineau", "given": "Charles", "initials": "C"}], "type": "journal article", "published": "2017-09-26", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": null, "issue": null, "issn-l": "1535-3893"}, "abstract": "The present study is a contribution to the \"neXt50 challenge\", a coordinated effort across C-HPP teams to identify the 50 most tractable missing proteins (MPs) on each chromosome. We report the targeted search of 38 theoretically detectable MPs from chromosomes 2 and 14 in Triton X-100 soluble and insoluble sperm fractions from a total of 15 healthy donors. A targeted mass-spectrometry-based strategy consisting of the development of LC-PRM assays (with heavy labeled synthetic peptides) targeting 92 proteotypic peptides of the 38 selected MPs was used. Out of the 38 selected MPs, 12 were identified with two or more peptides and 3 with one peptide after extensive SDS-PAGE fractionation of the two samples and with overall low-intensity signals. The PRM data are available via ProteomeXchange in PASSEL (PASS01013). Further validation by immunohistochemistry on human testes sections and cytochemistry on sperm smears was performed for eight MPs with antibodies available from the Human Protein Atlas. Deep analysis of human sperm still allows the validation of MPs and therefore contributes to the C-HPP worldwide effort. We anticipate that our results will be of interest to the reproductive biology community because an in-depth analysis of these MPs may identify potential new candidates in the context of human idiopathic infertilities.", "doi": "10.1021/acs.jproteome.7b00374", "pmid": "28891297", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-05T13:06:27.707Z", "modified": "2017-11-05T13:06:27.724Z"}, {"entity": "publication", "iuid": "96eafa28ec7c4b058885ebcf5b82c2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96eafa28ec7c4b058885ebcf5b82c2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96eafa28ec7c4b058885ebcf5b82c2d1"}}, "title": "Novel spirocyclic systems via multicomponent aza-Diels-Alder reaction.", "authors": [{"family": "Llona-Minguez", "given": "Sabin", "initials": "S"}, {"family": "Throup", "given": "Adam", "initials": "A"}, {"family": "Steiner", "given": "Emilie", "initials": "E"}, {"family": "Lightowler", "given": "Molly", "initials": "M"}, {"family": "Van der Haegen", "given": "Sandra", "initials": "S"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Eriksson", "given": "Lars", "initials": "L"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Jenmalm-Jensen", "given": "Annika", "initials": "A"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-09-26", "journal": {"volume": "15", "issn": "1477-0539", "issue": "37", "pages": "7758-7764", "title": "Org. Biomol. Chem.", "issn-l": "1477-0520"}, "abstract": "Here we present a two-step diastereoselective methodology building on a multicomponent aza-Diels-Alder reaction. Using previously unexplored cyclic ketones, heterocyclic amines and cyclopentadiene derivatives, we obtained novel spiro-heterocyclic frameworks at the interphase between \"drug-like\" molecules and natural products.", "doi": "10.1039/c7ob02069d", "pmid": "28891572", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-01-13T12:56:59.001Z", "modified": "2025-10-17T13:04:29.155Z"}, {"entity": "publication", "iuid": "1e2ade93efce4c0f8d791467a61493cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb"}}, "title": "Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.", "authors": [{"family": "Verma", "given": "Deepti", "initials": "D"}, {"family": "Parasa", "given": "Venkata Ramanarao", "initials": "VR"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J"}, {"family": "Martis", "given": "Mihaela", "initials": "M"}, {"family": "Mehta", "given": "Ratnesh B", "initials": "RB"}, {"family": "Netea", "given": "Mihai", "initials": "M"}, {"family": "Lerm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2017-09-26", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "12305", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The reason for the largely variable protective effect against TB of the vaccine Bacille Calmette-Guerin (BCG) is not understood. In this study, we investigated whether epigenetic mechanisms are involved in the response of immune cells to the BCG vaccine. We isolated peripheral blood mononuclear cells (PBMCs) from BCG-vaccinated subjects and performed global DNA methylation analysis in combination with functional assays representative of innate immunity against Mycobacterium tuberculosis infection. Enhanced containment of replication was observed in monocyte-derived macrophages from a sub-group of BCG-vaccinated individuals (identified as 'responders'). A stable and robust differential DNA methylation pattern in response to BCG could be observed in PBMCs isolated from the responders but not from the non-responders. Gene ontology analysis revealed that promoters with altered DNA methylation pattern were strongly enriched among genes belonging to immune pathways in responders, however no enrichments could be observed in the non-responders. Our findings suggest that BCG-induced epigenetic reprogramming of immune cell function can enhance anti-mycobacterial immunity in macrophages. Understanding why BCG induces this response in responders but not in non-responders could provide clues to improvement of TB vaccine efficacy.", "doi": "10.1038/s41598-017-12110-2", "pmid": "28951586", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-12110-2"}, {"db": "pmc", "key": "PMC5615063"}], "notes": [], "created": "2017-10-25T15:27:48.394Z", "modified": "2024-01-16T13:48:47.507Z"}, {"entity": "publication", "iuid": "923f95c531b44fe183b15bd21bee0a6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/923f95c531b44fe183b15bd21bee0a6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/923f95c531b44fe183b15bd21bee0a6f"}}, "title": "Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.", "authors": [{"family": "Lu", "given": "Y", "initials": "Y"}, {"family": "Pouget", "given": "J G", "initials": "JG"}, {"family": "Andreassen", "given": "O A", "initials": "OA"}, {"family": "Djurovic", "given": "S", "initials": "S"}, {"family": "Esko", "given": "T", "initials": "T"}, {"family": "Hultman", "given": "C M", "initials": "CM"}, {"family": "Metspalu", "given": "A", "initials": "A"}, {"family": "Milani", "given": "L", "initials": "L"}, {"family": "Werge", "given": "T", "initials": "T"}, {"family": "Sullivan", "given": "P F", "initials": "PF"}], "type": "journal article", "published": "2017-09-25", "journal": {"volume": null, "issn": "1469-8978", "issue": null, "pages": "1-9", "title": "Psychol Med", "issn-l": "0033-2917"}, "abstract": "Family history is a long-standing and readily obtainable risk factor for schizophrenia (SCZ). Low-cost genotyping technologies have enabled large genetic studies of SCZ, and the results suggest the utility of genetic risk scores (GRS, direct assessments of inherited common variant risk). Few studies have evaluated family history and GRS simultaneously to ask whether one can explain away the other.\n\nWe studied 5959 SCZ cases and 8717 controls from four Nordic countries. All subjects had family history data from national registers and genome-wide genotypes that were processed through the quality control procedures used by the Psychiatric Genomics Consortium. Using external training data, GRS were estimated for SCZ, bipolar disorder (BIP), major depression, autism, educational attainment, and body mass index. Multivariable modeling was used to estimate effect sizes.\n\nUsing harmonized genomic and national register data from Denmark, Estonia, Norway, and Sweden, we confirmed that family history of SCZ and GRS for SCZ and BIP were risk factors for SCZ. In a joint model, the effects of GRS for SCZ and BIP were essentially unchanged, and the effect of family history was attenuated but remained significant. The predictive capacity of a model including GRS and family history neared the minimum for clinical utility.\n\nCombining national register data with measured genetic risk factors represents an important investigative approach for psychotic disorders. Our findings suggest the potential clinical utility of combining GRS and family history for early prediction and diagnostic improvements.", "doi": "10.1017/S0033291717002665", "pmid": "28942743", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0033291717002665"}], "notes": [], "created": "2017-10-25T15:27:49.142Z", "modified": "2024-01-16T13:48:47.514Z"}, {"entity": "publication", "iuid": "04ded7be42f34b5ba55d710ff6d8662a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04ded7be42f34b5ba55d710ff6d8662a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04ded7be42f34b5ba55d710ff6d8662a"}}, "title": "The human protein atlas: A spatial map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2017-09-23", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": null, "issue": null, "issn-l": "0961-8368"}, "abstract": "The correct spatial distribution of proteins is vital for their function and often mis-localization or ectopic expression leads to diseases. For more than a decade, the Human Protein Atlas (HPA) has constituted a valuable tool for researchers studying protein localization and expression in human tissues and cells. The centerpiece of the HPA is its unique antibody collection for mapping the entire human proteome by immunohistochemistry and immunocytochemistry. By these approaches, more than 10 million images showing protein expression patterns at a single-cell level were generated and are publicly available at www.proteinatlas.org. The antibody-based approach is combined with transcriptomics data for an overview of global expression profiles. The present article comprehensively describes the HPA database functions and how users can utilize it for their own research as well as discusses the future path of spatial proteomics.", "doi": "10.1002/pro.3307", "pmid": "28940711", "labels": {"Tissue Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-05T13:06:43.719Z", "modified": "2017-11-05T13:06:43.736Z"}, {"entity": "publication", "iuid": "e9e8da47ca5147caace04385ea2be779", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9e8da47ca5147caace04385ea2be779.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9e8da47ca5147caace04385ea2be779"}}, "title": "The regulation of hydroxysteroid 17\u03b2-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.", "authors": [{"family": "Hilborn", "given": "Erik", "initials": "E"}, {"family": "St\u00e5l", "given": "Olle", "initials": "O"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Jansson", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2017-09-22", "journal": {"volume": "8", "issn": "1949-2553", "issue": "37", "pages": "62183-62194", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "To investigate the influence of estrogen, androgen, microRNAs, and genes implicated in breast cancer on the expression of HSD17B1 and HSD17B2.\n\nBreast cancer cell lines ZR-75-1, MCF7, T47D, SK-BR-3, and the immortalized epithelial cell line MCF10A were used. Cells were treated either with estradiol or dihydrotestosterone for 6, 24, 48 hours, or 7 days or treated with miRNAs or siRNAs predicted to influence HSD17B expression Results and discussion. Estradiol treatment decreased\n\nWe show that", "doi": "10.18632/oncotarget.19136", "pmid": "28977936", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "19136"}, {"db": "pmc", "key": "PMC5617496"}], "notes": [], "created": "2018-03-29T07:15:32.386Z", "modified": "2020-01-21T13:53:21.925Z"}, {"entity": "publication", "iuid": "10bec96369d048eb94fe40d1762af16b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10bec96369d048eb94fe40d1762af16b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10bec96369d048eb94fe40d1762af16b"}}, "title": "New oncogenic subtypes in pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}], "type": "journal article", "published": "2017-09-21", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "130", "issue": "12", "pages": "1395-1401", "issn-l": "0006-4971"}, "abstract": "Until recently, 20% to 30% of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) could not be classified into any of the established molecular subtypes. Recent molecular studies of such cases have, however, further clarified their mutational spectrum and identified new oncogenic subtypes consisting of cases with DUX4 rearrangements, ETV6-RUNX1-like gene expression, MEF2D rearrangements, and ZNF384 rearrangements. In this review, we describe these new subtypes, which account for up to 50% of previously unclassified pediatric BCP-ALL cases.", "doi": "10.1182/blood-2017-05-742643", "pmid": "28778863", "labels": {"Clinical Genomics Lund": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)32845-7"}], "notes": [], "created": "2017-12-22T12:36:43.783Z", "modified": "2021-07-06T15:38:38.650Z"}, {"entity": "publication", "iuid": "8022a99f3bf947d5b23922574afb9d5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8022a99f3bf947d5b23922574afb9d5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8022a99f3bf947d5b23922574afb9d5d"}}, "title": "Cu/Zn Superoxide Dismutase Forms Amyloid Fibrils under Near-Physiological Quiescent Conditions: The Roles of Disulfide Bonds and Effects of Denaturant.", "authors": [{"family": "Khan", "given": "M Ashhar I", "initials": "MAI"}, {"family": "Respondek", "given": "Michal", "initials": "M"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Deep", "given": "Shashank", "initials": "S"}, {"family": "Linse", "given": "Sara", "initials": "S"}, {"family": "Akke", "given": "Mikael", "initials": "M", "orcid": "0000-0002-2395-825X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e36b418e03154b90a8722670bed9e81a.json"}}], "type": "journal article", "published": "2017-09-20", "journal": {"title": "ACS Chem Neurosci", "issn": "1948-7193", "volume": "8", "issue": "9", "pages": "2019-2026", "issn-l": "1948-7193"}, "abstract": "Cu/Zn superoxide dismutase (SOD1) forms intracellular aggregates that are pathological indicators of amyotrophic lateral sclerosis. A large body of research indicates that the entry point to aggregate formation is a monomeric, metal-ion free (apo), and disulfide-reduced species. Fibril formation by SOD1 in vitro has typically been reported only for harsh solvent conditions or mechanical agitation. Here we show that monomeric apo-SOD1 in the disulfide-reduced state forms fibrillar aggregates under near-physiological quiescent conditions. Monomeric apo-SOD1 with an intact intramolecular disulfide bond is highly resistant to aggregation under the same conditions. A cysteine-free variant of SOD1 exhibits fibrillization behavior and fibril morphology identical to those of disulfide-reduced SOD1, firmly establishing that intermolecular disulfide bonds or intramolecular disulfide shuffling are not required for aggregation and fibril formation. The decreased lag time for fibril formation resulting from reduction of the intramolecular disulfide bond thus primarily reflects the decreased stability of the folded state relative to partially unfolded states, rather than an active role of free sulfhydryl groups in mediating aggregation. Addition of urea to increase the amount of fully unfolded SOD1 increases the lag time for fibril formation, indicating that the population of this species does not dominate over other factors in determining the onset of aggregation. Our results contrast with previous results obtained for agitated samples, in which case amyloid formation was accelerated by denaturant. We reconcile these observations by suggesting that denaturants destabilize monomeric and aggregated species to different extents and thus affect nucleation and growth.", "doi": "10.1021/acschemneuro.7b00162", "pmid": "28585802", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1021/acschemneuro.7b00162"}], "notes": [], "created": "2020-01-27T10:04:14.767Z", "modified": "2021-06-16T10:21:21.392Z"}, {"entity": "publication", "iuid": "d23e11e266a14e9d9e84db92232867a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d23e11e266a14e9d9e84db92232867a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d23e11e266a14e9d9e84db92232867a5"}}, "title": "Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria.", "authors": [{"family": "Quin", "given": "Jaclyn E", "initials": "JE"}, {"family": "Bujila", "given": "Ioana", "initials": "I"}, {"family": "Ch\u00e9rif", "given": "Mariama", "initials": "M"}, {"family": "Sanou", "given": "Guillaume S", "initials": "GS"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Vafa Homann", "given": "Manijeh", "initials": "M"}, {"family": "Rolicka", "given": "Anna", "initials": "A"}, {"family": "Sirima", "given": "Sodiomon B", "initials": "SB"}, {"family": "O'Connell", "given": "Mary A", "initials": "MA"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Troye-Blomberg", "given": "Marita", "initials": "M"}, {"family": "Nebie", "given": "Issa", "initials": "I"}, {"family": "\u00d6stlund Farrants", "given": "Ann-Kristin", "initials": "AK"}], "type": "journal article", "published": "2017-09-19", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "The Fulani ethnic group has relatively better protection from Plasmodium falciparum malaria, as reflected by fewer symptomatic cases of malaria, lower infection rates, and lower parasite densities compared to sympatric ethnic groups. However, the basis for this lower susceptibility to malaria by the Fulani is unknown. The incidence of classic malaria resistance genes are lower in the Fulani than in other sympatric ethnic populations, and targeted SNP analyses of other candidate genes involved in the immune response to malaria have not been able to account for the observed difference in the Fulani susceptibility to P.falciparum. Therefore, we have performed a pilot study to examine global transcription and DNA methylation patterns in specific immune cell populations in the Fulani to elucidate the mechanisms that confer the lower susceptibility to P.falciparum malaria. When we compared uninfected and infected Fulani individuals, in contrast to uninfected and infected individuals from the sympatric ethnic group Mossi, we observed a key difference: a strong transcriptional response was only detected in the monocyte fraction of the Fulani, where over 1000 genes were significantly differentially expressed upon P.falciparum infection.", "doi": "10.7554/eLife.29156", "pmid": "28923166", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5629023"}, {"db": "GEO", "description": "Sequence data", "key": "GSE100563"}], "notes": [], "created": "2017-11-03T16:19:28.128Z", "modified": "2020-01-21T13:56:11.453Z"}, {"entity": "publication", "iuid": "14aefb7c1c5149a0907cf18d42a50b44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14aefb7c1c5149a0907cf18d42a50b44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14aefb7c1c5149a0907cf18d42a50b44"}}, "title": "The complete genome sequence of human adenovirus 84, a highly recombinant new Human mastadenovirus D type with a unique fiber gene.", "authors": [{"family": "Kaj\u00e1n", "given": "Gy\u0151z\u0151 L", "initials": "GL"}, {"family": "Kajon", "given": "Adriana E", "initials": "AE"}, {"family": "Pinto", "given": "Alexis Castillo", "initials": "AC"}, {"family": "Bartha", "given": "D\u00e1niel", "initials": "D"}, {"family": "Arnberg", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2017-09-18", "journal": {"volume": "242", "issn": "1872-7492", "issue": null, "pages": "79-84", "title": "Virus Res.", "issn-l": "0168-1702"}, "abstract": "A novel human adenovirus was isolated from a pediatric case of acute respiratory disease in Panama City, Panama in 2011. The clinical isolate was initially identified as an intertypic recombinant based on hexon and fiber gene sequencing. Based on the analysis of its complete genome sequence, the novel complex recombinant Human mastadenovirus D (HAdV-D) strain was classified into a new HAdV type: HAdV-84, and it was designated Adenovirus D human/PAN/P309886/2011/84[P43H17F84]. HAdV-D types possess usually an ocular or gastrointestinal tropism, and respiratory association is scarcely reported. The virus has a novel fiber type, most closely related to, but still clearly distant from that of HAdV-36. The predicted fiber is hypothesised to bind sialic acid with lower affinity compared to HAdV-37. Bioinformatic analysis of the complete genomic sequence of HAdV-84 revealed multiple homologous recombination events and provided deeper insight into HAdV evolution.", "doi": "10.1016/j.virusres.2017.09.012", "pmid": "28923509", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0168-1702(17)30628-7"}], "notes": [], "created": "2017-10-17T09:27:58.155Z", "modified": "2024-01-16T13:48:47.522Z"}, {"entity": "publication", "iuid": "d1e74ad1e3134682be2aa625c2c3d42f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1e74ad1e3134682be2aa625c2c3d42f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1e74ad1e3134682be2aa625c2c3d42f"}}, "title": "Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGF\u03b22/T\u03b2R and CD44 in MDA-MB-231 breast cancer cells.", "authors": [{"family": "Reithmeier", "given": "Anja", "initials": "A"}, {"family": "Panizza", "given": "Elena", "initials": "E"}, {"family": "Krumpel", "given": "Michael", "initials": "M"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Branca", "given": "Rui M M", "initials": "RMM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Ek-Rylander", "given": "Barbro", "initials": "B"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2017-09-15", "journal": {"volume": "17", "issn": "1471-2407", "issue": "1", "pages": "650", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Tartrate-resistant acid phosphatase (TRAP/ACP5), a metalloenzyme that is characteristic for its expression in activated osteoclasts and in macrophages, has recently gained considerable focus as a driver of metastasis and was associated with clinically relevant parameters of cancer progression and cancer aggressiveness.\n\nMDA-MB-231 breast cancer cells with different TRAP expression levels (overexpression and knockdown) were generated and characterized for protein expression and activity levels. Functional cell experiments, such as proliferation, migration and invasion assays were performed as well as global phosphoproteomic and proteomic analysis was conducted to connect molecular perturbations to the phenotypic changes.\n\nWe identified an association between metastasis-related properties of TRAP-overexpressing MDA-MB-231 breast cancer cells and a TRAP-dependent regulation of Transforming growth factor (TGF\u03b2) pathway proteins and Cluster of differentiation 44 (CD44). Overexpression of TRAP increased anchorage-independent and anchorage-dependent cell growth and proliferation, induced a more elongated cellular morphology and promoted cell migration and invasion. Migration was increased in the presence of the extracellular matrix (ECM) proteins osteopontin and fibronectin and the basement membrane proteins collagen IV and laminin I. TRAP-induced properties were reverted upon shRNA-mediated knockdown of TRAP or treatment with the small molecule TRAP inhibitor 5-PNA. Global phosphoproteomics and proteomics analyses identified possible substrates of TRAP phosphatase activity or signaling intermediates and outlined a TRAP-dependent regulation of proteins involved in cell adhesion and ECM organization. Upregulation of TGF\u03b2 isoform 2 (TGF\u03b22), TGF\u03b2 receptor type 1 (T\u03b2R1) and Mothers against decapentaplegic homolog 2 (SMAD2), as well as increased intracellular phosphorylation of CD44 were identified upon TRAP perturbation. Functional antibody-mediated blocking and chemical inhibition demonstrated that TRAP-dependent migration and proliferation is regulated via TGF\u03b22/T\u03b2R, whereas proliferation beyond basal levels is regulated through CD44.\n\nAltogether, TRAP promotes metastasis-related cell properties in MDA-MB-231 breast cancer cells via TGF\u03b22/T\u03b2R and CD44, thereby identifying a potential signaling mechanism associated to TRAP action in breast cancer cells.", "doi": "10.1186/s12885-017-3616-7", "pmid": "28915803", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-017-3616-7"}, {"db": "pmc", "key": "PMC5602878"}], "notes": [], "created": "2017-12-05T16:14:25.657Z", "modified": "2021-07-08T11:36:15.281Z"}, {"entity": "publication", "iuid": "483f894a78344929b828147d37312dcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/483f894a78344929b828147d37312dcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/483f894a78344929b828147d37312dcd"}}, "title": "Metabolic profiles from two different breakfast meals characterized by 1H NMR-based metabolomics.", "authors": [{"family": "R\u00e5djurs\u00f6ga", "given": "Millie", "initials": "M"}, {"family": "Karlsson", "given": "G\u00f6ran B", "initials": "GB", "orcid": "0000-0002-1821-4715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6463abd05b415696c52be577ca2be6.json"}}, {"family": "Lindqvist", "given": "Helen M", "initials": "HM"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}, {"family": "Persson", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-6663-6536", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fb6fe3555374aec90b2a8b9dfd8016b.json"}}, {"family": "Pinto", "given": "Rui Climaco", "initials": "RC"}, {"family": "Elleg\u00e5rd", "given": "Lars", "initials": "L"}, {"family": "Winkvist", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-09-15", "journal": {"volume": "231", "issn": "1873-7072", "issue": null, "pages": "267-274", "title": "Food Chem", "issn-l": "0308-8146"}, "abstract": "It is challenging to measure dietary exposure with techniques that are both accurate and applicable to free-living individuals. We performed a cross-over intervention, with 24 healthy individuals, to capture the acute metabolic response of a cereal breakfast (CB) and an egg and ham breakfast (EHB). Fasting and postprandial urine samples were analyzed using 1H nuclear magnetic resonance (NMR) spectroscopy and multivariate data analysis. Metabolic profiles were distinguished in relation to ingestion of either CB or EHB. Phosphocreatine/creatine and citrate were identified at higher concentrations after consumption of EHB. Beverage consumption (i.e., tea or coffee) could clearly be seen in the data. 2-furoylglycine and 5-hydroxymethyl-2-furoic acid - potential biomarkers for coffee consumption were identified at higher concentrations in coffee drinkers. Thus 1H NMR urine metabolomics is applicable in the characterization of acute metabolic fingerprints from meal consumption and in the identification of metabolites that may serve as potential biomarkers.", "doi": "10.1016/j.foodchem.2017.03.142", "pmid": "28450006", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0308-8146(17)30539-3"}], "notes": [], "created": "2017-11-03T10:46:28.345Z", "modified": "2025-10-17T13:03:59.595Z"}, {"entity": "publication", "iuid": "dcb0e08b9cc14e2ea73e5730f308e0a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcb0e08b9cc14e2ea73e5730f308e0a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcb0e08b9cc14e2ea73e5730f308e0a2"}}, "title": "Effects of tumour necrosis factor \u03b1 upon the metabolism of the endocannabinoid anandamide in prostate cancer cells.", "authors": [{"family": "Karlsson", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8572-5841", "researcher": {"href": "https://publications.scilifelab.se/researcher/3598df69dd754edc85babf7931914b88.json"}}, {"family": "Gouveia-Figueira", "given": "Sandra", "initials": "S"}, {"family": "Alhouayek", "given": "Mireille", "initials": "M"}, {"family": "Fowler", "given": "Christopher J", "initials": "CJ"}], "type": "journal article", "published": "2017-09-14", "journal": {"volume": "12", "issn": "1932-6203", "issue": "9", "pages": "e0185011", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Tumour necrosis factor \u03b1 (TNF\u03b1) is involved in the pathogenesis of prostate cancer, a disease where disturbances in the endocannabinoid system are seen. In the present study we have investigated whether treatment of DU145 human prostate cancer cells affects anandamide (AEA) catabolic pathways. Additionally, we have investigated whether cyclooxygenase-2 (COX-2) can regulate the uptake of AEA into cells. Levels of AEA synthetic and catabolic enzymes were determined by qPCR. AEA uptake and hydrolysis in DU145 and RAW264.7 macrophage cells were assayed using AEA labeled in the arachidonic and ethanolamine portions of the molecule, respectively. Levels of AEA, related N-acylethanolamines (NAEs), prostaglandins (PG) and PG-ethanolamines (PG-EA) in DU145 cells and medium were quantitated by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis. TNF\u03b1 treatment of DU145 cells increased mRNA levels of PTSG2 (gene of COX-2) and decreased the mRNA of the AEA synthetic enzyme N-acyl-phosphatidylethanolamine selective phospholipase D. mRNA levels of the AEA hydrolytic enzymes fatty acid amide hydrolase (FAAH) and N-acylethanolamine-hydrolyzing acid amidase were not changed. AEA uptake in both DU145 and RAW264.7 cells was inhibited by FAAH inhibition, but not by COX-2 inhibition, even in RAW264.7 cells where the expression of this enzyme had greatly been induced by lipopolysaccharide + interferon \u03b3 treatment. AEA and related NAEs were detected in DU145 cells, but PGs and PGE2-EA were only detected when the cells had been preincubated with 100 nM AEA. The data demonstrate that in DU145 cells, TNF\u03b1 treatment changes the relative expression of the enzymes involved in the hydrolytic and oxygenation catabolic pathways for AEA. In RAW264.7 cells, COX-2, in contrast to FAAH, does not regulate the cellular accumulation of AEA. Further studies are necessary to determine the extent to which inflammatory mediators are involved in the abnormal endocannabinoid signalling system in prostate cancer.", "doi": "10.1371/journal.pone.0185011", "pmid": "28910408", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-21764"}, {"db": "pmc", "key": "PMC5599064"}], "notes": [], "created": "2018-01-09T12:32:32.848Z", "modified": "2025-10-17T13:03:18.517Z"}, {"entity": "publication", "iuid": "e89a879922894049b66ca40f1e485cf3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e89a879922894049b66ca40f1e485cf3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e89a879922894049b66ca40f1e485cf3"}}, "title": "Correction to Piperazin-1-ylpyridazine Derivatives Are a Novel Class of Human dCTP Pyrophosphatase 1 Inhibitors.", "authors": [{"family": "Llona-Minguez", "given": "Sabin", "initials": "S", "orcid": "0000-0003-3187-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/437b1f98ad21471f884226ed89a3da12.json"}}, {"family": "H\u00f6glund", "given": "Andreas", "initials": "A"}, {"family": "Ghassemian", "given": "Artin", "initials": "A"}, {"family": "Desroses", "given": "Matthieu", "initials": "M"}, {"family": "Calder\u00f3n-Monta\u00f1o", "given": "Jos\u00e9 Manuel", "initials": "JM"}, {"family": "Burgos Mor\u00f3n", "given": "Estefan\u00eda", "initials": "E"}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}, {"family": "Wiita", "given": "Elisee", "initials": "E"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Cazares-K\u00f6rner", "given": "Cindy", "initials": "C"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Darabi", "given": "Masoud", "initials": "M"}, {"family": "Mehdizadeh", "given": "Amir", "initials": "A"}, {"family": "Fayezi", "given": "Shabnam", "initials": "S"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Sigmundsson", "given": "Kristmundur", "initials": "K"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Jenmalm Jensen", "given": "Annika", "initials": "A"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2017-09-14", "journal": {"title": "J. Med. Chem.", "issn": "1520-4804", "volume": "60", "issue": "17", "pages": "7614", "issn-l": "0022-2623"}, "abstract": null, "doi": "10.1021/acs.jmedchem.7b01137", "pmid": "28862438", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2024-04-03T14:50:41.036Z", "modified": "2024-04-03T14:50:41.094Z"}, {"entity": "publication", "iuid": "05b4dacde1b34c7db34d7a6b147d1346", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05b4dacde1b34c7db34d7a6b147d1346.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05b4dacde1b34c7db34d7a6b147d1346"}}, "title": "Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.", "authors": [{"family": "Yu", "given": "Nancy Y", "initials": "NY"}, {"family": "Bieder", "given": "Andrea", "initials": "A"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Mileti", "given": "Enrichetta", "initials": "E"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Fredholm", "given": "Bertil B", "initials": "BB"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Tapia-P\u00e1ez", "given": "Isabel", "initials": "I"}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2017-09-13", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "11458", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Caffeine is a widely consumed psychoactive substance, but little is known about the effects of caffeine stimulation on global gene expression changes in neurons. Here, we conducted gene expression profiling of human neuroepithelial stem cell-derived neurons, stimulated with normal consumption levels of caffeine (3\u2009\u03bcM and 10\u2009\u03bcM), over a period of 9\u2009h. We found dosage-dependent activation of immediate early genes after 1\u2009h. Neuronal projection development processes were up-regulated and negative regulation of axon extension processes were down-regulated at 3\u2009h. In addition, genes involved in extracellular matrix organization, response for wound healing, and regulation of immune system processes were down-regulated by caffeine at 3\u2009h. This study identified novel genes within the neuronal projection guidance pathways that respond to acute caffeine stimulation and suggests potential mechanisms for the effects of caffeine on neuronal cells.", "doi": "10.1038/s41598-017-11574-6", "pmid": "28904364", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-11574-6"}, {"db": "pmc", "key": "PMC5597620"}, {"db": "BioProject", "description": "raw RNA-seq", "key": "PRJEB20092"}], "notes": [], "created": "2017-11-03T16:18:37.631Z", "modified": "2024-01-16T13:48:47.529Z"}, {"entity": "publication", "iuid": "fc55a99f7e8b438a84619b9622d75fca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc55a99f7e8b438a84619b9622d75fca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc55a99f7e8b438a84619b9622d75fca"}}, "title": "Mass Cytometry Identifies Distinct Lung CD4+ T Cell Patterns in L\u00f6fgren's Syndrome and Non-L\u00f6fgren's Syndrome Sarcoidosis.", "authors": [{"family": "Kaiser", "given": "Ylva", "initials": "Y"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Eklund", "given": "Anders", "initials": "A"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Grunewald", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-09-12", "journal": {"volume": "8", "issn": "1664-3224", "issue": null, "pages": "1130", "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "Sarcoidosis is a granulomatous disorder of unknown etiology, characterized by accumulation of activated CD4+ T cells in the lungs. Disease phenotypes L\u00f6fgren's syndrome (LS) and \"non-LS\" differ in terms of clinical manifestations, genetic background, HLA association, and prognosis, but the underlying inflammatory mechanisms largely remain unknown. Bronchoalveolar lavage fluid cells from four HLA-DRB1*03+ LS and four HLA-DRB1*03- non-LS patients were analyzed by mass cytometry, using a panel of 33 unique markers. Differentially regulated CD4+ T cell populations were identified using the Citrus algorithm, and t-stochastic neighborhood embedding was applied for dimensionality reduction and single-cell data visualization. We identified 19 individual CD4+ T cell clusters differing significantly in abundance between LS and non-LS patients. Seven clusters more frequent in LS patients were characterized by significantly higher expression of regulatory receptors CTLA-4, PD-1, and ICOS, along with low expression of adhesion marker CD44. In contrast, 12 clusters primarily found in non-LS displayed elevated expression of activation and effector markers HLA-DR, CD127, CD39, as well as CD44. Hierarchical clustering further indicated functional heterogeneity and diverse origins of T cell receptor V\u03b12.3/V\u03b222-restricted cells in LS. Finally, a near-complete overlap of CD8 and Ki-67 expression suggested larger influence of CD8+ T cell activity on sarcoid inflammation than previously appreciated. In this study, we provide detailed characterization of pulmonary T cells and immunological parameters that define separate disease pathways in LS and non-LS. With direct association to clinical parameters, such as granuloma persistence, resolution, or chronic inflammation, these results provide a valuable foundation for further exploration and potential clinical application.", "doi": "10.3389/fimmu.2017.01130", "pmid": "28955342", "labels": {"Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5601005"}], "notes": [], "created": "2017-10-04T13:39:42.230Z", "modified": "2021-07-08T09:26:23.184Z"}, {"entity": "publication", "iuid": "ba5631775a314411b73ca7a1569aae73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba5631775a314411b73ca7a1569aae73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba5631775a314411b73ca7a1569aae73"}}, "title": "Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis", "authors": [{"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Leong", "given": "Aaron", "initials": "A"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Hivert", "given": "Marie France", "initials": "MF"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Podmore", "given": "Clara", "initials": "C"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Hong", "given": "Jaeyoung", "initials": "J"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Wang", "given": "Xu", "initials": "X"}, {"family": "Chen", "given": "Peng", "initials": "P"}, {"family": "Maruthur", "given": "Nisa M", "initials": "NM"}, {"family": "Porneala", "given": "Bianca C", "initials": "BC"}, {"family": "Sharp", "given": "Stephen J", "initials": "SJ"}, {"family": "Jia", "given": "Yucheng", "initials": "Y"}, {"family": "Kabagambe", "given": "Edmond K", "initials": "EK"}, {"family": "Chang", "given": "Li Ching", "initials": "LC"}, {"family": "Chen", "given": "Wei Min", "initials": "WM"}, {"family": "Elks", "given": "Cathy E", "initials": "CE"}, {"family": "Evans", "given": "Daniel S", "initials": "DS"}, {"family": "Fan", "given": "Qiao", "initials": "Q"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Go", "given": "Min Jin", "initials": "MJ"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Hu", "given": "Yao", "initials": "Y"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Kim", "given": "Young Jin", "initials": "YJ"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C"}, {"family": "Lim", "given": "Sing Hui", "initials": "SH"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Marzi", "given": "Carola", "initials": "C"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Rybin", "given": "Denis V", "initials": "DV"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Shi", "given": "Yuan", "initials": "Y"}, {"family": "Stram", "given": "Daniel O", "initials": "DO"}, {"family": "Takeuchi", "given": "Fumihiko", "initials": "F"}, {"family": "Tan", "given": "Shu Pei", "initials": "SP"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Zhao", "given": "Wanting", "initials": "W"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Martinez Larrad", "given": "Maria Teresa", "initials": "MT"}, {"family": "Radke", "given": "D\u00f6rte", "initials": "D"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "van Iperen", "given": "Erik P A", "initials": "EPA"}, {"family": "Abecasis", "given": "Goncalo", "initials": "G"}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Bertoni", "given": "Alain G", "initials": "AG"}, {"family": "Bonnefond", "given": "Amelie", "initials": "A"}, {"family": "B\u00f6ttcher", "given": "Yvonne", "initials": "Y"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Carlson", "given": "Olga D", "initials": "OD"}, {"family": "Chen", "given": "Chien Hsiun", "initials": "CH"}, {"family": "Cho", "given": "Yoon Shin", "initials": "YS"}, {"family": "Garvey", "given": "W Timothy", "initials": "WT"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Herder", "given": "Christian", "initials": "C"}, {"family": "Hsiung", "given": "Chao Agnes", "initials": "CA"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Igase", "given": "Michiya", "initials": "M"}, {"family": "Isono", "given": "Masato", "initials": "M"}, {"family": "Katsuya", "given": "Tomohiro", "initials": "T"}, {"family": "Khor", "given": "Chiea Chuen", "initials": "CC"}, {"family": "Kiess", "given": "Wieland", "initials": "W"}, {"family": "Kohara", "given": "Katsuhiko", "initials": "K"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Lee", "given": "Juyoung", "initials": "J"}, {"family": "Lee", "given": "Wen Jane", "initials": "WJ"}, {"family": "Lehne", "given": "Benjamin", "initials": "B"}, {"family": "Li", "given": "Huaixing", "initials": "H"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Lobbens", "given": "Stephane", "initials": "S"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Miki", "given": "Tetsuro", "initials": "T"}, {"family": "Miljkovic", "given": "Iva", "initials": "I"}, {"family": "Moon", "given": "Sanghoon", "initials": "S"}, {"family": "Mulas", "given": "Antonella", "initials": "A"}, {"family": "M\u00fcller", "given": "Gabriele", "initials": "G"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Nagaraja", "given": "Ramaiah", "initials": "R"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Ramos", "given": "Paula S", "initials": "PS"}, {"family": "Rasmussen-Torvik", "given": "Laura", "initials": "L"}, {"family": "Rathmann", "given": "Wolfgang", "initials": "W"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Roden", "given": "Michael", "initials": "M"}, {"family": "Roussel", "given": "Ronan", "initials": "R"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Scott", "given": "William R", "initials": "WR"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Sun", "given": "Liang", "initials": "L"}, {"family": "Swertz", "given": "Morris", "initials": "M"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teo", "given": "Yik Ying", "initials": "YY"}, {"family": "Tham", "given": "Yih Chung", "initials": "YC"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilsgaard", "given": "Tom", "initials": "T"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Egan", "given": "Josephine", "initials": "J"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Nj\u00f8lstad", "given": "Inger", "initials": "I"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Serrano R\u00edos", "given": "Manuel", "initials": "M"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Aung", "given": "Tin", "initials": "T"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Yii Der Ida", "initials": "YDI"}, {"family": "Chen", "given": "Yduan Tsong", "initials": "YT"}, {"family": "Cheng", "given": "Ching Yu", "initials": "CY"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Friedlander", "given": "Yechiel", "initials": "Y"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Gross", "given": "Myron D", "initials": "MD"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heng", "given": "Chew Kiat", "initials": "CK"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kato", "given": "Norihiro", "initials": "N"}, {"family": "Kim", "given": "Bong Jo", "initials": "BJ"}, {"family": "Koh", "given": "Woon Puay", "initials": "WP"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lin", "given": "Xu", "initials": "X"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pereira", "given": "Mark A", "initials": "MA"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C"}, {"family": "Sale", "given": "Michele", "initials": "M"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Saltevo", "given": "Juha", "initials": "J"}, {"family": "Schwarz", "given": "Peter EH", "initials": "PE"}, {"family": "Sheu", "given": "Wayne H H", "initials": "WHH"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Tabara", "given": "Yasuharu", "initials": "Y"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Wu", "given": "Jer Yuarn", "initials": "JY"}, {"family": "Yuan", "given": "Jian Min", "initials": "JM"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Roberts", "given": "David J", "initials": "DJ"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Sladek", "given": "Robert", "initials": "R"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Selvin", "given": "Elizabeth", "initials": "E"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": null, "given": "", "initials": ""}, {"family": null, "given": "", "initials": ""}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-09-12", "journal": {"volume": "14", "issn": "1549-1676", "issue": "9", "pages": "e1002383", "title": "PLoS Med.", "issn-l": "1549-1277"}, "abstract": null, "doi": "10.1371/journal.pmed.1002383", "pmid": "28898252", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "MAGIC", "description": "spreadsheets (tsv)", "key": "https://www.magicinvestigators.org/downloads/"}], "notes": [], "created": "2018-01-09T13:55:53.834Z", "modified": "2020-01-21T13:56:11.937Z"}, {"entity": "publication", "iuid": "3de90d2d26634b8d88e9baaba3bf166b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3de90d2d26634b8d88e9baaba3bf166b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3de90d2d26634b8d88e9baaba3bf166b"}}, "title": "Deficiency in Calcium-Binding Protein S100A4 Impairs the Adjuvant Action of Cholera Toxin.", "authors": [{"family": "Sun", "given": "Jia-Bin", "initials": "JB"}, {"family": "Holmgren", "given": "Jan", "initials": "J"}, {"family": "Larena", "given": "Maximilian", "initials": "M"}, {"family": "Terrinoni", "given": "Manuela", "initials": "M"}, {"family": "Fang", "given": "Yu", "initials": "Y"}, {"family": "Bresnick", "given": "Anne R", "initials": "AR"}, {"family": "Xiang", "given": "Zou", "initials": "Z"}], "type": "journal article", "published": "2017-09-11", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "8", "issue": null, "pages": "1119", "issn-l": "1664-3224"}, "abstract": "The calcium-binding protein S100A4 has been described to promote pathological inflammation in experimental autoimmune and inflammatory disorders and in allergy and to contribute to antigen presentation and antibody response after parenteral immunization with an alum-adjuvanted antigen. In this study, we extend these findings by demonstrating that mice lacking S100A4 have a defective humoral and cellular immune response to mucosal (sublingual) immunization with a model protein antigen [ovalbumin (OVA)] given together with the strong mucosal adjuvant cholera toxin (CT), and that this impairment is due to defective adjuvant-stimulated antigen presentation by antigen-presenting cells. In comparison to wild-type (WT) mice, mice genetically lacking S100A4 had reduced humoral and cellular immune responses after immunization with OVA plus CT, including a complete lack of detectable germinal center reaction. Further, when stimulated in vitro with OVA plus CT, S100A4-/- dendritic cells (DCs) showed impaired responses in several CT-stimulated immune regulatory molecules including the co-stimulatory molecule CD86, inflammasome-associated caspase-1 and IL-1\u03b2. Coculture of OVA-specific OT-II T cells with S100A4-/- DCs that had been pulse incubated with OVA plus CT resulted in impaired OT-II T cell proliferation and reduced production of Th1, Th2, and Th17 cytokines compared to similar cocultures with WT DCs. In accordance with these findings, transfection of WT DCs with S100A4-targeting small interfering RNA (siRNA) but not mock-siRNA resulted in significant reductions in the expression of caspase-1 and IL-1\u03b2 as well as CD86 in response to CT. Importantly, also engraftment of WT DCs into S100A4-/- mice effectively restored the immune response to immunization in the recipients. In conclusion, our results demonstrate that deficiency in S100A4 has a strong impact on the development of both humoral and cellular immunity after mucosal immunization using CT as adjuvant.", "doi": "10.3389/fimmu.2017.01119", "pmid": "28951732", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5600718"}], "notes": [], "created": "2020-01-23T16:36:26.452Z", "modified": "2021-06-21T15:29:05.152Z"}, {"entity": "publication", "iuid": "118d534f4a2f4cc6a9430bdc114ee50b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/118d534f4a2f4cc6a9430bdc114ee50b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/118d534f4a2f4cc6a9430bdc114ee50b"}}, "title": "Copper chaperone ATOX1 regulates pluripotency factor OCT4 in preimplantation mouse embryos.", "authors": [{"family": "Celauro", "given": "Emanuele", "initials": "E"}, {"family": "Mukaj", "given": "Amisa", "initials": "A"}, {"family": "Fierro-Gonz\u00e1lez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2017-09-09", "journal": {"volume": "491", "issn": "1090-2104", "issue": "1", "pages": "147-153", "title": "Biochem. Biophys. Res. Commun.", "issn-l": "0006-291X"}, "abstract": "Despite of the importance of copper (Cu) during pregnancy, the roles of Cu-binding proteins during early embryonic development are unknown. The Cu chaperone ATOX1 was recently suggested to have additional functions related to transcription and cancer. When we analyzed single-cell RNA transcript data from early mouse embryos, Atox1 transcript levels increased dramatically at the 8-cell stage and, at 16- and 32-cell embryo stages, matched those of Oct4 which expresses a transcription factor essential for pluripotency in the inner cell mass. To explore this, we probed Atox1 expression during the first week of development of mouse embryos. ATOX1 appeared ubiquitously expressed throughout the cells until compaction; in subsequent embryo stages, ATOX1 relocalized to cytoplasmic perinuclear domains in the inner cell mass. Silencing of Oct4 did not affect Atox1 expression, but silencing of Atox1 at the 2-cell stage strongly diminished Oct4 expression in 16-cell embryos.", "doi": "10.1016/j.bbrc.2017.07.064", "pmid": "28711491", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-291X(17)31406-7"}], "notes": [], "created": "2017-11-02T12:15:40.115Z", "modified": "2021-06-16T16:16:13.321Z"}, {"entity": "publication", "iuid": "fb6cd985b2214826bf1603929fdb4a76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb6cd985b2214826bf1603929fdb4a76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb6cd985b2214826bf1603929fdb4a76"}}, "title": "Impact of N-methylation of the substance P 1-7 amide on anti-allodynic effect in mice after peripheral administration.", "authors": [{"family": "Skogh", "given": "Anna", "initials": "A"}, {"family": "Lesniak", "given": "Anna", "initials": "A"}, {"family": "Gaugaz", "given": "Fabienne Z", "initials": "FZ"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Lindeberg", "given": "Gunnar", "initials": "G"}, {"family": "Fransson", "given": "Rebecca", "initials": "R"}, {"family": "Nyberg", "given": "Fred", "initials": "F"}, {"family": "Hallberg", "given": "Mathias", "initials": "M"}, {"family": "Sandstr\u00f6m", "given": "Anja", "initials": "A"}], "type": "journal article", "published": "2017-09-05", "journal": {"volume": "109", "issn": "1879-0720", "issue": null, "pages": "533-540", "title": "Eur J Pharm Sci", "issn-l": "0928-0987"}, "abstract": "Substance P 1-7 (SP1-7, Arg(1)-Pro(2)-Lys(3)-Pro(4)-Gln(5)-Gln(6)-Phe(7)) is the major bioactive metabolite formed after proteolytic degradation of the tachykinin substance P (SP). This heptapeptide often opposes the effects of the mother peptide. Hence, SP1-7 is having anti-inflammatory, anti-nociceptive and anti-hyperalgesic effects in experimental models. Despite all encouraging properties of SP1-7 its exact mode of action has not yet been elucidated which has hampered further development of this heptapeptide in drug discovery. Contrary to SP that mediates its biological activity via the NK-1 receptor, the N-terminal fragment SP1-7 acts through an unknown target that is distinct from all known opioid and tachykinin receptors. The SP1-7 amide 1 (Arg(1)-Pro(2)-Lys(3)-Pro(4)-Gln(5)-Gln(6)-Phe(7)-NH2) was previously shown to be superior to the endogenous SP1-7 in all experimental pain models where the two compounds were compared. Herein, we report that N-methylation scan of the backbone of the SP1-7 amide (1) results in peptides that are significantly less prone to undergo proteolysis in plasma from both mouse and human. However, with the two exceptions of the [MeLys(3)]SP1-7 amide (3) and the [MeGln(5)]SP1-7 amide (4), the peptides with a methyl group attached to the backbone are devoid of significant anti-allodynic effects after peripheral administration in the spared nerve injury (SNI) mouse model of neuropathic pain. It is suggested that the N-methylation does not allow these peptides to form the accurate bioactive conformations or interactions required for efficient binding to the macromolecular target. The importance of intact N-terminal Arg(1) and C-terminal Phe(7), anticipated to serve as address and message residues, respectively, for achieving the anti-allodynic effect is emphasized. Notably, the three heptapeptides: the SP1-7 amide (1), the [MeLys(3)]SP1-7 amide (3) amide and the [MeGln(5)]SP1-7 amide (4) are all considerably more effective in the SNI mouse model than gabapentin that is widely used in the clinic for treatment of neuropathic pain.", "doi": "10.1016/j.ejps.2017.09.007", "pmid": "28887235", "labels": {"Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "S0928-0987(17)30497-9"}], "notes": [], "created": "2017-10-24T12:16:43.310Z", "modified": "2025-10-17T13:05:08.746Z"}, {"entity": "publication", "iuid": "d18f096274994cefa586627ca0599ec4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d18f096274994cefa586627ca0599ec4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d18f096274994cefa586627ca0599ec4"}}, "title": "Capturing LTA 4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis.", "authors": [{"family": "Stsiapanava", "given": "Alena", "initials": "A"}, {"family": "Samuelsson", "given": "Bengt", "initials": "B"}, {"family": "Haeggstr\u00f6m", "given": "Jesper Z", "initials": "JZ", "orcid": "0000-0002-1823-5153", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee1e25240017456f80599973397b4bd6.json"}}], "type": "journal article", "published": "2017-09-05", "journal": {"volume": "114", "issn": "1091-6490", "issue": "36", "pages": "9689-9694", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Human leukotriene (LT) A 4 hydrolase/aminopeptidase (LTA4H) is a bifunctional enzyme that converts the highly unstable epoxide intermediate LTA4 into LTB4, a potent leukocyte activating agent, while the aminopeptidase activity cleaves and inactivates the chemotactic tripeptide Pro-Gly-Pro. Here, we describe high-resolution crystal structures of LTA4H complexed with LTA4, providing the structural underpinnings of the enzyme's unique epoxide hydrolase (EH) activity, involving Zn2+, Y383, E271, D375, and two catalytic waters. The structures reveal that a single catalytic water is involved in both catalytic activities of LTA4H, alternating between epoxide ring opening and peptide bond hydrolysis, assisted by E271 and E296, respectively. Moreover, we have found two conformations of LTA4H, uncovering significant domain movements. The resulting structural alterations indicate that LTA4 entrance into the active site is a dynamic process that includes rearrangement of three moving domains to provide fast and efficient alignment and processing of the substrate. Thus, the movement of one dynamic domain widens the active site entrance, while another domain acts like a lid, opening and closing access to the hydrophobic tunnel, which accommodates the aliphatic tale of LTA4 during EH reaction. The enzyme-LTA4 complex structures and dynamic domain movements provide critical insights for development of drugs targeting LTA4H.", "doi": "10.1073/pnas.1710850114", "pmid": "28827365", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "1710850114"}, {"db": "pmc", "key": "PMC5594697"}, {"db": "PDB", "key": "5NI2"}, {"db": "PDB", "key": "5NI4"}, {"db": "PDB", "key": "5NI6"}, {"db": "PDB", "key": "5NIA"}, {"db": "PDB", "key": "5NID"}, {"db": "PDB", "key": "5NIE"}], "notes": [], "created": "2017-10-05T06:48:37.617Z", "modified": "2021-06-21T15:29:43.563Z"}, {"entity": "publication", "iuid": "4f6a27020d4e4cc8a66101b05df1d17e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f6a27020d4e4cc8a66101b05df1d17e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f6a27020d4e4cc8a66101b05df1d17e"}}, "title": "Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root.", "authors": [{"family": "Di Mambro", "given": "Riccardo", "initials": "R", "orcid": "0000-0002-1243-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/e06682ddf24e45648d08dc1db5a272d5.json"}}, {"family": "De Ruvo", "given": "Micol", "initials": "M"}, {"family": "Pacifici", "given": "Elena", "initials": "E"}, {"family": "Salvi", "given": "Elena", "initials": "E"}, {"family": "Sozzani", "given": "Rosangela", "initials": "R"}, {"family": "Benfey", "given": "Philip N", "initials": "PN"}, {"family": "Busch", "given": "Wolfgang", "initials": "W", "orcid": "0000-0003-2042-7290", "researcher": {"href": "https://publications.scilifelab.se/researcher/690f19002a5e49aea937eb9025827fae.json"}}, {"family": "Novak", "given": "Ondrej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Di Paola", "given": "Luisa", "initials": "L"}, {"family": "Mar\u00e9e", "given": "Athanasius F M", "initials": "AFM"}, {"family": "Costantino", "given": "Paolo", "initials": "P"}, {"family": "Grieneisen", "given": "Ver\u00f4nica A", "initials": "VA"}, {"family": "Sabatini", "given": "Sabrina", "initials": "S"}], "type": "journal article", "published": "2017-09-05", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "114", "issue": "36", "pages": "E7641-E7649", "issn-l": "0027-8424"}, "abstract": "In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin's control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.", "doi": "10.1073/pnas.1705833114", "pmid": "28831001", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "1705833114"}, {"db": "pmc", "key": "PMC5594665"}], "notes": [], "created": "2018-01-09T12:29:37.442Z", "modified": "2025-10-17T13:03:18.557Z"}, {"entity": "publication", "iuid": "dd70e362cb6943229c091af5a0fe1185", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd70e362cb6943229c091af5a0fe1185.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd70e362cb6943229c091af5a0fe1185"}}, "title": "Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.", "authors": [{"family": "Amlinger", "given": "Lina", "initials": "L"}, {"family": "Hoekzema", "given": "Mirthe", "initials": "M"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "Lundgren", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1122-3352", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e56842987ca489ba79c0606d9ce6849.json"}}], "type": "journal article", "published": "2017-09-04", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10392", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.", "doi": "10.1038/s41598-017-10876-z", "pmid": "28871175", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10876-z"}, {"db": "pmc", "key": "PMC5583386"}], "notes": [], "created": "2017-10-17T09:52:30.751Z", "modified": "2024-01-16T13:48:47.536Z"}, {"entity": "publication", "iuid": "4a316c8916a44647a751f72482d76147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a316c8916a44647a751f72482d76147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a316c8916a44647a751f72482d76147"}}, "title": "Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2017-09-04", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": "1561", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.", "doi": "10.3389/fmicb.2017.01561", "pmid": "28928718", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5591341"}], "notes": [], "created": "2017-11-03T16:11:38.776Z", "modified": "2024-01-16T13:48:47.543Z"}, {"entity": "publication", "iuid": "ff12426bd7b6452a9ad5149f09bf4d57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff12426bd7b6452a9ad5149f09bf4d57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff12426bd7b6452a9ad5149f09bf4d57"}}, "title": "The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes.", "authors": [{"family": "Yip", "given": "Bon Ham", "initials": "BH"}, {"family": "Steeples", "given": "Violetta", "initials": "V"}, {"family": "Repapi", "given": "Emmanouela", "initials": "E"}, {"family": "Armstrong", "given": "Richard N", "initials": "RN"}, {"family": "Llorian", "given": "Miriam", "initials": "M"}, {"family": "Roy", "given": "Swagata", "initials": "S"}, {"family": "Shaw", "given": "Jacqueline", "initials": "J"}, {"family": "Dolatshad", "given": "Hamid", "initials": "H"}, {"family": "Taylor", "given": "Stephen", "initials": "S"}, {"family": "Verma", "given": "Amit", "initials": "A"}, {"family": "Bartenstein", "given": "Matthias", "initials": "M"}, {"family": "Vyas", "given": "Paresh", "initials": "P"}, {"family": "Cross", "given": "Nicholas Cp", "initials": "NC"}, {"family": "Malcovati", "given": "Luca", "initials": "L"}, {"family": "Cazzola", "given": "Mario", "initials": "M"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Ogawa", "given": "Seishi", "initials": "S"}, {"family": "Smith", "given": "Christopher Wj", "initials": "CW"}, {"family": "Pellagatti", "given": "Andrea", "initials": "A"}, {"family": "Boultwood", "given": "Jacqueline", "initials": "J"}], "type": "journal article", "published": "2017-09-01", "journal": {"title": "J. Clin. Invest.", "issn": "1558-8238", "volume": "127", "issue": "9", "pages": "3557", "issn-l": "0021-9738"}, "abstract": null, "doi": "10.1172/JCI96202", "pmid": "28862641", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "96202"}, {"db": "pmc", "key": "PMC5669537"}], "notes": [], "created": "2018-10-31T13:10:33.407Z", "modified": "2021-06-21T15:30:18.144Z"}, {"entity": "publication", "iuid": "b46fa2b578db4907b0a04e5f54b935bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b46fa2b578db4907b0a04e5f54b935bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b46fa2b578db4907b0a04e5f54b935bc"}}, "title": "The TLR2 Antagonist Staphylococcal Superantigen-Like Protein 3 Acts as a Virulence Factor to Promote Bacterial Pathogenicity in vivo.", "authors": [{"family": "Koymans", "given": "Kirsten J", "initials": "KJ"}, {"family": "Goldmann", "given": "Oliver", "initials": "O"}, {"family": "Karlsson", "given": "Christofer A Q", "initials": "CAQ"}, {"family": "Sital", "given": "Wiedjai", "initials": "W"}, {"family": "Th\u00e4nert", "given": "Robert", "initials": "R"}, {"family": "Bisschop", "given": "Adinda", "initials": "A"}, {"family": "Vrieling", "given": "Manouk", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "van Kessel", "given": "Kok P M", "initials": "KPM"}, {"family": "de Haas", "given": "Carla J C", "initials": "CJC"}, {"family": "van Strijp", "given": "Jos A G", "initials": "JAG"}, {"family": "Medina", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2017-09-01", "journal": {"title": "J Innate Immun", "issn": "1662-8128", "volume": "9", "issue": "6", "pages": "561-573", "issn-l": "1662-811X"}, "abstract": "Toll-like receptor (TLR) signaling is important in the initiation of immune responses and subsequent instigation of adaptive immunity. TLR2 recognizes bacterial lipoproteins and plays a central role in the host defense against bacterial infections, including those caused by Staphylococcus aureus. Many studies have demonstrated the importance of TLR2 in murine S. aureus infection. S. aureus evades TLR2 activation by secreting two proteins, staphylococcal superantigen-like protein 3 (SSL3) and 4 (SSL4). In this study, we demonstrate that antibodies against SSL3 and SSL4 are found in healthy individuals, indicating that humans are exposed to these proteins during S. aureus colonization or infection. To investigate the TLR2-antagonistic properties of SSL3 and SSL4, we compared the infection with wild-type and SSL3/4 knockout S. aureus strains in an intravenous murine infection model. Direct evaluation of the contribution of SSL3/4 to infection pathogenesis was hindered by the fact that the SSLs were not expressed in the murine system. To circumvent this limitation, an SSL3-overproducing strain (pLukM-SSL3) was generated, resulting in constitutive expression of SSL3. pLukM-SSL3 exhibited increased virulence compared to the parental strain in a murine model that was found to be TLR2 dependent. Altogether, these data indicate that SSL3 contributes to S. aureus virulence in vivo.", "doi": "10.1159/000479100", "pmid": "28858870", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "000479100"}], "notes": [], "created": "2020-01-27T10:14:29.324Z", "modified": "2021-05-24T15:39:50.377Z"}, {"entity": "publication", "iuid": "f57321685c0b4169a4414640c3787e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f"}}, "title": "The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.", "authors": [{"family": "Evkaikina", "given": "Anastasiia I", "initials": "AI"}, {"family": "Berke", "given": "Lidija", "initials": "L"}, {"family": "Romanova", "given": "Marina A", "initials": "MA"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Ivanova", "given": "Alexandra N", "initials": "AN"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}, {"family": "Voitsekhovskaja", "given": "Olga V", "initials": "OV"}], "type": "journal article", "published": "2017-09-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "9", "pages": "2444-2460", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls-that is, leaves with a single, unbranched vein, emerging from the protostele without a leaf gap-not megaphylls. All leaves represent determinate organs originating on the flanks of indeterminate SAMs. Thus, leaf formation requires the suppression of indeterminacy, that is, of KNOX transcription factors. In seed plants, this is mediated by different groups of transcription factors including ARP and YABBY.We generated a shoot tip transcriptome of Huperzia selago (Lycopodiales) to examine the genes involved in leaf formation. Our H. selago transcriptome does not contain any ARP homolog, although transcriptomes of Selaginella spp. do. Surprisingly, we discovered a YABBY homolog, although these transcription factors were assumed to have evolved only in seed plants.The existence of a YABBY homolog in H. selago suggests that YABBY evolved already in the common ancestor of the vascular plants, and subsequently was lost in some lineages like Selaginellales, whereas ARP may have been lost in Lycopodiales. The presence of YABBY in the common ancestor of vascular plants would also support the hypothesis that this common ancestor had a simplex SAM. Furthermore, a comparison of the expression patterns of ARP in shoot tips of Selaginella kraussiana (Harrison CJ, etal. 2005. Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434(7032):509-514.) and YABBY in shoot tips of H. selago implies that the development of microphylls, unlike megaphylls, does not seem to depend on the combined activities of ARP and YABBY. Altogether, our data show that Lycopodiophyta are a diverse group; so, in order to understand the role of Lycopodiophyta in evolution, representatives of Lycopodiales, Selaginellales, as well as of Isoetales, have to be examined.", "doi": "10.1093/gbe/evx169", "pmid": "28957460", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4097580"}, {"db": "pmc", "key": "PMC5622374"}, {"db": "BioProject", "description": "DNA sequencing data", "key": "PRJNA281995"}], "notes": [], "created": "2017-11-03T16:20:59.430Z", "modified": "2024-01-16T13:48:47.550Z"}, {"entity": "publication", "iuid": "9f0b79f79d544180a69aae67b033683b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f0b79f79d544180a69aae67b033683b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f0b79f79d544180a69aae67b033683b"}}, "title": "Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests.", "authors": [{"family": "Varenius", "given": "Kerstin", "initials": "K"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}, {"family": "Dahlberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-09-01", "journal": {"volume": "93", "issn": "1574-6941", "issue": "9", "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": "Fennoscandian forestry has in the past decades changed from natural regeneration of forests towards replantation of clear-cuts, which negatively impacts ectomycorrhizal fungal (EMF) diversity. Retention of trees during harvesting enables EMF survival, and we therefore expected EMF communities to be more similar to those in old natural stands after forest regeneration using seed trees compared to full clear-cutting and replanting. We sequenced fungal internal transcribed spacer 2 (ITS2) amplicons to assess EMF communities in 10- to 60-year-old Scots pine stands regenerated either using seed trees or through replanting of clear-cuts with old natural stands as reference. We also investigated local EMF communities around retained old trees. We found that retention of seed trees failed to mitigate the impact of harvesting on EMF community composition and diversity. With increasing stand age, EMF communities became increasingly similar to those in old natural stands and permanently retained trees maintained EMF locally. From our observations, we conclude that EMF communities, at least common species, post-harvest are more influenced by environmental filtering, resulting from environmental changes induced by harvest, than by the continuity of trees. These results suggest that retention of intact forest patches is a more efficient way to conserve EMF diversity than retaining dispersed single trees.", "doi": "10.1093/femsec/fix105", "pmid": "28957584", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4094915"}], "notes": [], "created": "2017-10-17T09:39:31.791Z", "modified": "2024-01-16T13:48:47.557Z"}, {"entity": "publication", "iuid": "e5e8cb279e504c34b1cfa3fd00bf4c12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5e8cb279e504c34b1cfa3fd00bf4c12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5e8cb279e504c34b1cfa3fd00bf4c12"}}, "title": "Multifocus structured illumination microscopy for fast volumetric super-resolution imaging", "authors": [{"family": "Abrahamsson", "given": "Sara", "initials": "S"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Agostinho", "given": "Ana", "initials": "A"}, {"family": "Jans", "given": "Daniel C", "initials": "DC"}, {"family": "Jost", "given": "Aurelie", "initials": "A"}, {"family": "M\u00fcller", "given": "Marcel", "initials": "M"}, {"family": "Nilsson", "given": "Linnea", "initials": "L"}, {"family": "Bernhem", "given": "Kristoffer", "initials": "K"}, {"family": "Lambert", "given": "Talley J", "initials": "TJ"}, {"family": "Heintzmann", "given": "Rainer", "initials": "R"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}], "type": "journal-article", "published": "2017-09-01", "journal": {"volume": "8", "issn": "2156-7085", "issue": "9", "pages": "4135", "title": "Biomed. Opt. Express", "issn-l": "2156-7085"}, "abstract": "We here report for the first time the synergistic implementation of structured illumination microscopy (SIM) and multifocus microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in super-resolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.", "doi": "10.1364/boe.8.004135", "pmid": "28966852", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-05T09:08:40.370Z", "modified": "2021-07-05T13:48:51.637Z"}, {"entity": "publication", "iuid": "fcfaeb8733fc4821bcb008f42c9c5c34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcfaeb8733fc4821bcb008f42c9c5c34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcfaeb8733fc4821bcb008f42c9c5c34"}}, "title": "Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production.", "authors": [{"family": "Thammarongtham", "given": "Chinae", "initials": "C"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Vorapreeda", "given": "Tayvich", "initials": "T"}, {"family": "Srisuk", "given": "Tanawut", "initials": "T"}, {"family": "Land", "given": "Miriam L", "initials": "ML"}, {"family": "Jeennor", "given": "Sukanya", "initials": "S"}, {"family": "Laoteng", "given": "Kobkul", "initials": "K"}], "type": "journal article", "published": "2017-09-01", "journal": {"volume": null, "issn": "1432-0991", "issue": null, "title": "Curr. Microbiol.", "issn-l": "0343-8651"}, "abstract": "The selected robust fungus, Aspergillus oryzae strain BCC7051 is of interest for biotechnological production of lipid-derived products due to its capability to accumulate high amount of intracellular lipids using various sugars and agro-industrial substrates. Here, we report the genome sequence of the oleaginous A. oryzae BCC7051. The obtained reads were de novo assembled into 25 scaffolds spanning of 38,550,958\u00a0bps with predicted 11,456 protein-coding genes. By synteny mapping, a large rearrangement was found in two scaffolds of A. oryzae BCC7051 as compared to the reference RIB40 strain. The genetic relationship between BCC7051 and other strains of A. oryzae in terms of aflatoxin production was investigated, indicating that the A. oryzae BCC7051 was categorized into group 2 nonaflatoxin-producing strain. Moreover, a comparative analysis of the structural genes focusing on the involvement in lipid metabolism among oleaginous yeast and fungi revealed the presence of multiple isoforms of metabolic enzymes responsible for fatty acid synthesis in BCC7051. The alternative routes of acetyl-CoA generation as oleaginous features and malate/citrate/pyruvate shuttle were also identified in this A. oryzae strain. The genome sequence generated in this work is a dedicated resource for expanding genome-wide study of microbial lipids at systems level, and developing the fungal-based platform for production of diversified lipids with commercial relevance.", "doi": "10.1007/s00284-017-1350-7", "pmid": "28865010", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00284-017-1350-7"}], "notes": [], "created": "2017-10-17T09:39:09.724Z", "modified": "2020-01-21T13:56:06.561Z"}, {"entity": "publication", "iuid": "186d9c669252431592bb26afb3bcb39d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/186d9c669252431592bb26afb3bcb39d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/186d9c669252431592bb26afb3bcb39d"}}, "title": "A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog", "authors": [{"family": "Montero-Mendieta", "given": "Santiago", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "De la Riva", "given": "Ignacio", "initials": "I"}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal-article", "published": "2017-09-01", "journal": {"volume": "5", "issn": "2167-8359", "issue": null, "pages": "e3702", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled \n            de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.", "doi": "10.7717/peerj.3702", "pmid": "28879061", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP106442"}, {"db": "GENBANK", "description": "TSA: Oreobates cruralis, transcriptome shotgun assembly", "key": "GFNJ00000000"}, {"db": "BioProject", "description": "Oreobates cruralis isolate:MNCN/ADN:65263 Transcriptome or Gene expression", "key": "PRJNA384528"}], "notes": [], "created": "2017-10-30T09:27:45.542Z", "modified": "2024-01-16T13:48:47.564Z"}, {"entity": "publication", "iuid": "e3ed08c8a4f04017b148c7c3bd163285", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3ed08c8a4f04017b148c7c3bd163285.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3ed08c8a4f04017b148c7c3bd163285"}}, "title": "The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases.", "authors": [{"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Lind-Thomsen", "given": "Allan", "initials": "A"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-09-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "9", "pages": "e1007005", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Associations between epigenetic alterations and disease status have been identified for many diseases. However, there is no strong evidence that epigenetic alterations are directly causal for disease pathogenesis. In this study, we combined SNP and DNA methylation data with measurements of protein biomarkers for cancer, inflammation or cardiovascular disease, to investigate the relative contribution of genetic and epigenetic variation on biomarker levels. A total of 121 protein biomarkers were measured and analyzed in relation to DNA methylation at 470,000 genomic positions and to over 10 million SNPs. We performed epigenome-wide association study (EWAS) and genome-wide association study (GWAS) analyses, and integrated biomarker, DNA methylation and SNP data using between 698 and 1033 samples depending on data availability for the different analyses. We identified 124 and 45 loci (Bonferroni adjusted P < 0.05) with effect sizes up to 0.22 standard units' change per 1% change in DNA methylation levels and up to four standard units' change per copy of the effective allele in the EWAS and GWAS respectively. Most GWAS loci were cis-regulatory whereas most EWAS loci were located in trans. Eleven EWAS loci were associated with multiple biomarkers, including one in NLRC5 associated with CXCL11, CXCL9, IL-12, and IL-18 levels. All EWAS signals that overlapped with a GWAS locus were driven by underlying genetic variants and three EWAS signals were confounded by smoking. While some cis-regulatory SNPs for biomarkers appeared to have an effect also on DNA methylation levels, cis-regulatory SNPs for DNA methylation were not observed to affect biomarker levels. We present associations between protein biomarker and DNA methylation levels at numerous loci in the genome. The associations are likely to reflect the underlying pattern of genetic variants, specific environmental exposures, or represent secondary effects to the pathogenesis of disease.", "doi": "10.1371/journal.pgen.1007005", "pmid": "28915241", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00622"}, {"db": "pmc", "key": "PMC5617224"}, {"db": "GEO", "description": "sequences", "key": "GSE87571"}], "notes": [], "created": "2017-10-25T15:27:49.784Z", "modified": "2024-01-16T13:48:47.571Z"}, {"entity": "publication", "iuid": "9cbb19e653c646618c1f02621a306881", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cbb19e653c646618c1f02621a306881.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cbb19e653c646618c1f02621a306881"}}, "title": "The adiponectin receptor AdipoR2 and its Caenorhabditis elegans homolog PAQR-2 prevent membrane rigidification by exogenous saturated fatty acids.", "authors": [{"family": "Devkota", "given": "Ranjan", "initials": "R"}, {"family": "Svensk", "given": "Emma", "initials": "E"}, {"family": "Ruiz", "given": "Mario", "initials": "M"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Pilon", "given": "Marc", "initials": "M", "orcid": "0000-0003-3919-2882", "researcher": {"href": "https://publications.scilifelab.se/researcher/d45c4ecf9afe463c971af2de53a770a8.json"}}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "13", "issue": "9", "pages": "e1007004", "issn-l": "1553-7390"}, "abstract": "Dietary fatty acids can be incorporated directly into phospholipids. This poses a specific challenge to cellular membranes since their composition, hence properties, could greatly vary with different diets. That vast variations in diets are tolerated therefore implies the existence of regulatory mechanisms that monitor and regulate membrane compositions. Here we show that the adiponectin receptor AdipoR2, and its C. elegans homolog PAQR-2, are essential to counter the membrane rigidifying effects of exogenously provided saturated fatty acids. In particular, we use dietary supplements or mutated E. coli as food, together with direct measurements of membrane fluidity and composition, to show that diets containing a high ratio of saturated to monounsaturated fatty acids cause membrane rigidity and lethality in the paqr-2 mutant. We also show that mammalian cells in which AdipoR2 has been knocked-down by siRNA are unable to prevent the membrane-rigidifying effects of palmitic acid. We conclude that the PAQR-2 and AdipoR2 proteins share an evolutionarily conserved function that maintains membrane fluidity in the presence of exogenous saturated fatty acids.", "doi": "10.1371/journal.pgen.1007004", "pmid": "28886012", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-01342"}, {"db": "pmc", "key": "PMC5607217"}], "notes": [], "created": "2020-01-23T16:34:44.458Z", "modified": "2021-06-21T15:29:30.012Z"}, {"entity": "publication", "iuid": "d156d94896ef42ec85ebfcebe517ee2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d156d94896ef42ec85ebfcebe517ee2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d156d94896ef42ec85ebfcebe517ee2d"}}, "title": "The Abl-1 Kinase is Dispensable for NK Cell Inhibitory Signalling and is not Involved in Murine NK Cell Education.", "authors": [{"family": "Ganesan", "given": "S", "initials": "S"}, {"family": "Luu", "given": "T T", "initials": "TT"}, {"family": "Chambers", "given": "B J", "initials": "BJ", "orcid": "0000-0003-0437-8441", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bdd56cf648f4411945163135f9a7140.json"}}, {"family": "Meinke", "given": "S", "initials": "S"}, {"family": "Brodin", "given": "P", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Vivier", "given": "E", "initials": "E"}, {"family": "Wetzel", "given": "D M", "initials": "DM"}, {"family": "Koleske", "given": "A J", "initials": "AJ"}, {"family": "Kadri", "given": "N", "initials": "N"}, {"family": "H\u00f6glund", "given": "P", "initials": "P", "orcid": "0000-0002-9233-626X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7c852c7cc0043b88fa096adf6af92dd.json"}}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "issn-l": "0300-9475", "volume": "86", "issue": "3", "pages": "135-142"}, "abstract": "Natural killer (NK) cell responsiveness in the mouse is determined in an education process guided by inhibitory Ly49 and NKG2A receptors binding to MHC class I molecules. It has been proposed that inhibitory signalling in human NK cells involves Abl-1 (c-Abl)-mediated phosphorylation of Crk, lowering NK cell function via disruption of a signalling complex including C3G and c-Cbl, suggesting that NK cell education might involve c-Abl. Mice deficient in c-Abl expression specifically in murine NK cells displayed normal inhibitory and activating receptor repertoires. Furthermore, c-Abl-deficient NK cells fluxed Ca2+ normally after triggering of ITAM receptors, killed YAC-1 tumour cells efficiently and showed normal, or even slightly elevated, capacity to produce IFN-\u03b3 after activating receptor stimulation. Consistent with these results, c-Abl deficiency in NK cells did not affect NK cell inhibition via the receptors Ly49G2, Ly49A and NKG2A. We conclude that signalling downstream of murine inhibitory receptors does not involve c-Abl and that c-Abl plays no major role in NK cell education in the mouse.", "doi": "10.1111/sji.12574", "pmid": "28605050", "labels": {"Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5568956"}, {"db": "mid", "key": "NIHMS883530"}], "notes": [], "created": "2019-03-25T19:56:43.705Z", "modified": "2023-11-28T12:55:14.127Z"}, {"entity": "publication", "iuid": "66d24b7109db42189f2a13e21a5d38fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66d24b7109db42189f2a13e21a5d38fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66d24b7109db42189f2a13e21a5d38fe"}}, "title": "Serotonin, ATRX, and DAXX Expression in Pituitary Adenomas: Markers in the Differential Diagnosis of Neuroendocrine Tumors of the Sellar Region.", "authors": [{"family": "Casar-Borota", "given": "Olivera", "initials": "O"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Granberg", "given": "Dan", "initials": "D"}, {"family": "Stigare", "given": "Jerker", "initials": "J"}, {"family": "Wikstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Boldt", "given": "Henning B\u00fcnsow", "initials": "HB"}, {"family": "Kristensen", "given": "Bjarne Winther", "initials": "BW"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Trouillas", "given": "Jacqueline", "initials": "J"}], "type": "case reports", "published": "2017-09-00", "journal": {"title": "Am. J. Surg. Pathol.", "issn": "1532-0979", "volume": "41", "issue": "9", "pages": "1238-1246", "issn-l": "0147-5185"}, "abstract": "Differential diagnosis based on morphology and immunohistochemistry between a clinically nonfunctioning pituitary neuroendocrine tumor (NET)/pituitary adenoma and a primary or secondary NET of nonpituitary origin in the sellar region may be difficult. Serotonin, a frequently expressed marker in the NETs, has not been systematically evaluated in pituitary NETs. Although mutations in ATRX or DAXX have been reported in a significant proportion of pancreatic NETs, the mutational status of ATRX and DAXX and their possible pathogenetic role in pituitary NETs are unknown. Facing a difficult diagnostic case of an invasive serotonin and adrenocorticotroph hormone immunoreactive NET in the sellar region, we explored the immunohistochemical expression of serotonin, ATRX, and DAXX in a large series of pituitary endocrine tumors of different types from 246 patients and in 2 corticotroph carcinomas. None of the pituitary tumors expressed serotonin, suggesting that serotonin immunoreactive sellar tumors represent primary or secondary NETs of nonpituitary origin. Normal expression of ATRX and DAXX in pituitary tumors suggests that ATRX and DAXX do not play a role in the pathogenesis of pituitary endocrine tumors that remain localized to the sellar and perisellar region. A lack of ATRX or DAXX in a sellar NET suggests a nonpituitary NET, probably of pancreatic origin. One of the 2 examined corticotroph carcinomas, however, demonstrated negative ATRX immunolabeling due to an ATRX gene mutation. Further studies on a larger cohort of pituitary carcinomas are needed to clarify whether ATRX mutations may contribute to the metastatic potential in a subset of pituitary NETs.", "doi": "10.1097/PAS.0000000000000908", "pmid": "28719461", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-05T12:42:14.469Z", "modified": "2017-11-05T12:42:14.485Z"}, {"entity": "publication", "iuid": "d07e00d31a13460682d9cb1e01855da0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07e00d31a13460682d9cb1e01855da0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07e00d31a13460682d9cb1e01855da0"}}, "title": "Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water", "authors": [{"family": "Bailey", "given": "Allison", "initials": "A"}, {"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Thor", "given": "Peter", "initials": "P"}, {"family": "Browman", "given": "Howard I", "initials": "HI"}, {"family": "Bjelland", "given": "Reidun", "initials": "R"}, {"family": "Shema", "given": "Steven", "initials": "S"}, {"family": "Fields", "given": "David M", "initials": "DM"}, {"family": "Runge", "given": "Jeffrey A", "initials": "JA"}, {"family": "Thompson", "given": "Cameron", "initials": "C"}, {"family": "Hop", "given": "Haakon", "initials": "H"}], "type": "journal-article", "published": "2017-09-00", "journal": {"volume": "7", "issn": "2045-7758", "issue": "18", "pages": "7145-7160", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": null, "doi": "10.1002/ece3.3063", "pmid": "28944006", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Calanus glacialis Transcriptome or Gene expression", "key": "PRJNA352656"}, {"db": "SRA", "description": null, "key": "SRP092884"}], "notes": [], "created": "2018-01-09T20:49:54.365Z", "modified": "2020-01-21T13:56:14.887Z"}, {"entity": "publication", "iuid": "f05f5c82f01046389ee7a1357add1a10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f05f5c82f01046389ee7a1357add1a10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f05f5c82f01046389ee7a1357add1a10"}}, "title": "Proteomics in Hypothermia as Adjunctive Therapy in Patients with ST-Segment Elevation Myocardial Infarction: A CHILL-MI Substudy.", "authors": [{"family": "Mohammad", "given": "Moman A", "initials": "MA"}, {"family": "Noc", "given": "Marco", "initials": "M"}, {"family": "Lang", "given": "Irene", "initials": "I"}, {"family": "Holzer", "given": "Michael", "initials": "M"}, {"family": "Clemmensen", "given": "Peter", "initials": "P"}, {"family": "Jensen", "given": "Ulf", "initials": "U"}, {"family": "Metzler", "given": "Bernhard", "initials": "B"}, {"family": "Erlinge", "given": "David", "initials": "D"}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Ther Hypothermia Temp Manag", "issn": "2153-7933", "issn-l": "2153-7658", "volume": "7", "issue": "3", "pages": "152-161"}, "abstract": "Cardiovascular and inflammatory biomarkers in therapeutic hypothermia have been studied in cardiac arrest, but data on patients with ST-segment elevation myocardial infarction (STEMI) treated with therapeutic hypothermia are currently unavailable. A multiplex proximity extension assay allowed us to measure 157 cardiovascular disease (CVD) and inflammatory disease-related biomarkers in patients from the international, multicenter, and randomized trial; CHILL-myocardial infarction (MI) and to explore the associations of cardiovascular and inflammatory biomarkers. Blood samples were obtained from 119 patients with STEMI, randomized to hypothermia as adjunctive therapy to percutaneous coronary intervention (PCI) or standard care with PCI only. Blood samples were obtained at baseline (0 hour), 6, 24, and 96 hours post PCI, and stored at -80\u00b0C until they were analyzed by PROSEEK Multiplex CVD and PROSEEK Multiplex INF (Olink Bioscience, Uppsala, Sweden). Peak values from 6, 24, and 96 hours postrandomization were compared between treatment groups. One hundred fifty-seven cardiovascular and inflammatory biomarkers were evaluated. Peak values of four biomarkers (BDNF, DNER, CCL20, MMP3) were reduced in the hypothermia group as compared with the control group. In addition, seven markers were slightly elevated in the hypothermia group (OPG, FGF21, FS, IL12B, PRL, TIM, IL6). In a prespecified subgroup analysis of anterior infarctions, two additional markers were reduced (PTX3 and SELE). In this explorative proteomic study from the randomized trial CHILL-MI, four biomarkers were identified as having reduced peak plasma values in patients with STEMI treated with therapeutic hypothermia as adjunctive therapy to PCI as compared with patients treated with standard care of PCI. In addition, seven biomarkers were elevated in the group treated with hypothermia therapy. The effect of hypothermia on biomarker peak values was modest, possibly due to a low reduction in mean body temperature. Whether a faster and deeper cooling results in more pronounced effects is yet to be established.", "doi": "10.1089/ther.2016.0041", "pmid": "28437237", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1089/ther.2016.0041"}], "notes": [], "created": "2017-10-31T07:39:27.606Z", "modified": "2023-04-14T13:56:10.527Z"}, {"entity": "publication", "iuid": "d191900a13564a93919851f2d6c7594d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d191900a13564a93919851f2d6c7594d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d191900a13564a93919851f2d6c7594d"}}, "title": "Measurement of protein backbone 13CO and 15N relaxation dispersion at high resolution", "authors": [{"family": "Mayzel", "given": "Maxim", "initials": "M"}, {"family": "Ahlner", "given": "Alexandra", "initials": "A"}, {"family": "Lundstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Orekhov", "given": "Vladislav Y", "initials": "VY"}], "type": "journal-article", "published": "2017-09-00", "journal": {"volume": "69", "issn": "0925-2738", "issue": "1", "pages": "1-12", "title": "J Biomol NMR", "issn-l": "0925-2738"}, "abstract": null, "doi": "10.1007/s10858-017-0127-4", "pmid": "28864905", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T10:36:16.579Z", "modified": "2025-10-17T13:03:59.606Z"}, {"entity": "publication", "iuid": "636d576384944722819703a146cf1555", "links": {"self": {"href": "https://publications.scilifelab.se/publication/636d576384944722819703a146cf1555.json"}, "display": {"href": "https://publications.scilifelab.se/publication/636d576384944722819703a146cf1555"}}, "title": "Genome scale metabolic modeling of cancer.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-09-00", "journal": {"volume": "43", "issn": "1096-7184", "issue": "Pt B", "pages": "103-112", "title": "Metab. Eng.", "issn-l": "1096-7176"}, "abstract": "Cancer cells reprogram metabolism to support rapid proliferation and survival. Energy metabolism is particularly important for growth and genes encoding enzymes involved in energy metabolism are frequently altered in cancer cells. A genome scale metabolic model (GEM) is a mathematical formalization of metabolism which allows simulation and hypotheses testing of metabolic strategies. It has successfully been applied to many microorganisms and is now used to study cancer metabolism. Generic models of human metabolism have been reconstructed based on the existence of metabolic genes in the human genome. Cancer specific models of metabolism have also been generated by reducing the number of reactions in the generic model based on high throughput expression data, e.g. transcriptomics and proteomics. Targets for drugs and bio markers for diagnostics have been identified using these models. They have also been used as scaffolds for analysis of high throughput data to allow mechanistic interpretation of changes in expression. Finally, GEMs allow quantitative flux predictions using flux balance analysis (FBA). Here we critically review the requirements for successful FBA simulations of cancer cells and discuss the symmetry between the methods used for modeling of microbial and cancer metabolism. GEMs have great potential for translational research on cancer and will therefore become of increasing importance in the future.", "doi": "10.1016/j.ymben.2016.10.022", "pmid": "27825806", "labels": {"Systems Biology": "Technology development", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1096-7176(16)30212-9"}], "notes": [], "created": "2017-12-01T10:32:36.883Z", "modified": "2021-07-05T13:05:37.658Z"}, {"entity": "publication", "iuid": "e32054b9cbfd42f392e10ffcbc8443f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e32054b9cbfd42f392e10ffcbc8443f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e32054b9cbfd42f392e10ffcbc8443f5"}}, "title": "Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal Medicago truncatula", "authors": [{"family": "Adolfsson", "given": "Lisa", "initials": "L"}, {"family": "Nziengui", "given": "Hugues", "initials": "H"}, {"family": "Abreu", "given": "Ilka N", "initials": "IN"}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Beebo", "given": "Azeez", "initials": "A"}, {"family": "Herdean", "given": "Andrei", "initials": "A"}, {"family": "Aboalizadeh", "given": "Jila", "initials": "J"}, {"family": "\u0160irok\u00e1", "given": "Jitka", "initials": "J"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Schoefs", "given": "Beno\u00eet", "initials": "B"}, {"family": "Spetea", "given": "Cornelia", "initials": "C"}], "type": "journal-article", "published": "2017-09-00", "journal": {"volume": "175", "issn": "1532-2548", "issue": "1", "pages": "392-411", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": null, "doi": "10.1104/pp.16.01509", "pmid": "28698354", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:26:59.757Z", "modified": "2025-10-17T13:03:18.565Z"}, {"entity": "publication", "iuid": "586e74b3539548239e73d43d6f3d0175", "links": {"self": {"href": "https://publications.scilifelab.se/publication/586e74b3539548239e73d43d6f3d0175.json"}, "display": {"href": "https://publications.scilifelab.se/publication/586e74b3539548239e73d43d6f3d0175"}}, "title": "Effect of food intake on 92 neurological biomarkers in plasma.", "authors": [{"family": "Dencker", "given": "Magnus", "initials": "M", "orcid": "0000-0001-9991-3712", "researcher": {"href": "https://publications.scilifelab.se/researcher/606b9b3272824d92a66dfd715c5e4842.json"}}, {"family": "Bj\u00f6rgell", "given": "Ola", "initials": "O"}, {"family": "Hlebowicz", "given": "Joanna", "initials": "J"}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Brain Behav", "issn": "2162-3279", "issn-l": "2162-3279", "volume": "7", "issue": "9", "pages": "e00747"}, "abstract": "This study evaluates the effect of food intake on 92 neurological biomarkers in plasma. Moreover, it investigated if any of the biomarkers were correlated with body mass index.\n\nTwenty-two healthy subjects (11 male and 11 female aged 25.9 \u00b1 4.2 years) were investigated. A total of 92 biomarkers were measured before a standardized meal as well as 30 and 120 min afterward with the Proseek Multiplex Neurology I kit.\n\nThe levels for 13 biomarkers decreased significantly (p < .001) 30 min after food intake. The levels for four biomarkers remained significantly decreased (p < .001) 120 min after food intake. One biomarker increased significantly (p < .001) 30 min after food intake. The changes were between 1% and 12%, with an average difference of about 5%. Only one biomarker showed a difference over 10% due to food intake. The biggest difference was observed for Plexin-B3 120 min after food intake (12%). Of all the 92 neurological biomarkers, only one was correlated with BMI, Kynureninase r = .46, p < .05.\n\nThis study shows that food intake has a very modest effect on 92 different neurological biomarkers. Timing of blood sampling in relation to food intake, therefore, appears not to be a major concern. Only Kynureninase was correlated with BMI. Further studies are warranted in older healthy subjects and in patients with various neurological diseases to determine whether the findings are reproducible in such populations.", "doi": "10.1002/brb3.747", "pmid": "28948068", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "BRB3747"}, {"db": "pmc", "key": "PMC5607537"}], "notes": [], "created": "2020-01-23T15:08:29.124Z", "modified": "2023-04-14T13:56:10.734Z"}, {"entity": "publication", "iuid": "98d3aef7c1154236ac3e331a2b2b70ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98d3aef7c1154236ac3e331a2b2b70ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98d3aef7c1154236ac3e331a2b2b70ab"}}, "title": "Cartilage oligomeric matrix protein neoepitope in the synovial fluid of horses with acute lameness: A new biomarker for the early stages of osteoarthritis.", "authors": [{"family": "Ski\u00f6ldebrand", "given": "E", "initials": "E"}, {"family": "Ekman", "given": "S", "initials": "S"}, {"family": "Mattsson Hult\u00e9n", "given": "L", "initials": "L"}, {"family": "Svala", "given": "E", "initials": "E"}, {"family": "Bj\u00f6rkman", "given": "K", "initials": "K"}, {"family": "Lindahl", "given": "A", "initials": "A"}, {"family": "Lundqvist", "given": "A", "initials": "A"}, {"family": "\u00d6nnerfjord", "given": "P", "initials": "P"}, {"family": "Sihlbom", "given": "C", "initials": "C"}, {"family": "R\u00fcetschi", "given": "U", "initials": "U"}], "type": "journal article", "published": "2017-09-00", "journal": {"volume": "49", "issn": "2042-3306", "issue": "5", "pages": "662-667", "title": "Equine Vet. J.", "issn-l": "0425-1644"}, "abstract": "Clinical tools to diagnose the early changes of osteoarthritis (OA) that occur in the articular cartilage are lacking.\n\nWe sought to identify and quantify a novel cartilage oligomeric matrix protein (COMP) neoepitope in the synovial fluid from the joints of healthy horses and those with different stages of OA.\n\nIn vitro quantitative proteomics and assay development with application in synovial fluids samples obtained from biobanks of well-characterised horses.\n\nArticular cartilage explants were incubated with or without interleukin-1\u03b2 for 25 days. Media were analysed via quantitative proteomics. Synovial fluid was obtained from either normal joints (n = 15) or joints causing lameness (n = 17) or with structural OA lesions (n = 7) and analysed for concentrations of the COMP neoepitope using a custom-developed inhibition enzyme-linked immunosorbent assay (ELISA). Explants were immunostained with polyclonal antibodies against COMP and the COMP neoepitopes.\n\nSemitryptic COMP peptides were identified and quantified in cell culture media from cartilage explants. A rabbit polyclonal antibody was raised against the neoepitope of the N-terminal portion of one COMP fragment (sequence SGPTHEGVC). An inhibition ELISA was developed to quantify the COMP neoepitope in synovial fluid. The mean concentration of the COMP neoepitope significantly increased in the synovial fluid from the joints responsible for acute lameness compared with normal joints and the joints of chronically lame horses and in joints with chronic structural OA. Immunolabelling for the COMP neoepitope revealed a pericellular staining in the interleukin-1\u03b2-stimulated explants.\n\nThe ELISA is based on polyclonal antisera rather than a monoclonal antibody.\n\nThe increase in the COMP neoepitope in the synovial fluid from horses with acute lameness suggests that this neoepitope has the potential to be a unique candidate biomarker for the early molecular changes in articular cartilage associated with OA.", "doi": "10.1111/evj.12666", "pmid": "28097685", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5573946"}, {"db": "GENBANK", "key": "PXD004993"}], "notes": [], "created": "2020-01-27T22:45:39.391Z", "modified": "2024-01-16T13:46:32.540Z"}, {"entity": "publication", "iuid": "af2a5618f69c44d599789f5f20298f78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af2a5618f69c44d599789f5f20298f78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af2a5618f69c44d599789f5f20298f78"}}, "title": "Cartilage oligomeric matrix protein forms protein complexes with synovial lubricin via non-covalent and covalent interactions.", "authors": [{"family": "Flowers", "given": "S A", "initials": "SA"}, {"family": "Kalamajski", "given": "S", "initials": "S"}, {"family": "Ali", "given": "L", "initials": "L"}, {"family": "Bj\u00f6rkman", "given": "L I", "initials": "LI"}, {"family": "Raj", "given": "J R", "initials": "JR"}, {"family": "Aspberg", "given": "A", "initials": "A"}, {"family": "Karlsson", "given": "N G", "initials": "NG"}, {"family": "Jin", "given": "C", "initials": "C"}], "type": "journal article", "published": "2017-09-00", "journal": {"volume": "25", "issn": "1522-9653", "issue": "9", "pages": "1496-1504", "title": "Osteoarthr. Cartil.", "issn-l": "1063-4584"}, "abstract": "Understanding the cartilage surface structure, lost in arthritic disease, is essential for developing strategies to effectively restore it. Given that adherence of the lubricating protein, lubricin, to the cartilage surface is critical for boundary lubrication, an interaction with cartilage oligomeric matrix protein (COMP) was investigated. COMP, an abundant cartilage protein, is known to be important for matrix formation.\n\nSynovial fluid (SF) from arthritic patients was used to detect possible COMP-lubricin complexes by immunological methods. Recombinant (RC) COMP and lubricin fragments were expressed to characterize this bonding and mass spectrometry employed to specifically identify the cysteines involved in inter-protein disulfide bonds.\n\nCOMP-lubricin complexes were identified in the SF of arthritic patients by Western blot, co-immunoprecipitation and sandwich ELISA. RC fragment solid-phase binding assays showed that the C-terminal (amino acids (AA) 518-757) of COMP bound non-covalently to the N-terminal of lubricin (AA 105-202). Mass spectrometry determined that although cysteines throughout COMP were involved in binding with lubricin, the cysteines in lubricin were primarily focused to an N-terminal region (AA 64-86). The close proximity of the non-covalent and disulfide binding domains on lubricin suggest a two-step mechanism to strongly bind lubricin to COMP.\n\nThese data demonstrate that lubricin forms a complex network with COMP involving both non-covalent and covalent bonds. This complex between lubricin and the cartilage protein COMP can be identified in the SF of patients with arthritis conditions including osteoarthritis (OA) and rheumatoid arthritis (RA).", "doi": "10.1016/j.joca.2017.03.016", "pmid": "28373131", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1063-4584(17)30937-8"}], "notes": [], "created": "2020-01-30T16:19:33.479Z", "modified": "2024-01-16T13:46:32.553Z"}, {"entity": "publication", "iuid": "63b39bb1eaf04c36872718d4820a746d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63b39bb1eaf04c36872718d4820a746d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63b39bb1eaf04c36872718d4820a746d"}}, "title": "Analytically Sensitive Protein Detection in Microtiter Plates by Proximity Ligation with Rolling Circle Amplification", "authors": [{"family": "Ebai", "given": "Tonge", "initials": "T"}, {"family": "Souza de Oliveira", "given": "Felipe Marques", "initials": "FM"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Schweiger", "given": "Caroline", "initials": "C"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Keilholtz", "given": "Ulrich", "initials": "U"}, {"family": "Haybaeck", "given": "Johannes", "initials": "J"}, {"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": "2017-09-00", "journal": {"volume": "63", "issn": "0009-9147", "issue": "9", "pages": "1497-1505", "title": "Clinical Chemistry", "issn-l": "0009-9147"}, "abstract": null, "doi": "10.1373/clinchem.2017.271833", "pmid": "28667186", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T14:42:38.120Z", "modified": "2023-04-14T13:56:10.979Z"}, {"entity": "publication", "iuid": "2f59f8580bdd4dd1a18e63bb9cde2f07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f59f8580bdd4dd1a18e63bb9cde2f07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f59f8580bdd4dd1a18e63bb9cde2f07"}}, "title": "A CRISPR-Cas9 Generated MDCK Cell Line Expressing Human MDR1 Without Endogenous Canine MDR1 (cABCB1): An Improved Tool for Drug Efflux Studies.", "authors": [{"family": "Karlgren", "given": "Maria", "initials": "M"}, {"family": "Simoff", "given": "Ivailo", "initials": "I"}, {"family": "Backlund", "given": "Maria", "initials": "M"}, {"family": "Wegler", "given": "Christine", "initials": "C"}, {"family": "Keiser", "given": "Markus", "initials": "M"}, {"family": "Handin", "given": "Niklas", "initials": "N"}, {"family": "M\u00fcller", "given": "Janett", "initials": "J"}, {"family": "Lundquist", "given": "Patrik", "initials": "P"}, {"family": "Jareborg", "given": "Anne-Christine", "initials": "AC"}, {"family": "Oswald", "given": "Stefan", "initials": "S"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2017-09-00", "journal": {"volume": "106", "issn": "1520-6017", "issue": "9", "pages": "2909-2913", "title": "J Pharm Sci", "issn-l": "0022-3549"}, "abstract": "Madin-Darby canine kidney (MDCK) II cells stably transfected with transport proteins are commonly used models for drug transport studies. However, endogenous expression of especially canine MDR1 (cMDR1) confounds the interpretation of such studies. Here we have established an MDCK cell line stably overexpressing the human MDR1 transporter (hMDR1; P-glycoprotein), and used CRISPR-Cas9 gene editing to knockout the endogenous cMDR1. Genomic screening revealed the generation of a clonal cell line homozygous for a 4-nucleotide deletion in the canine ABCB1 gene leading to a frameshift and a premature stop codon. Knockout of cMDR1 expression was verified by quantitative protein analysis and functional studies showing retained activity of the human MDR1 transporter. Application of this cell line allowed unbiased reclassification of drugs previously defined as both substrates and non-substrates in different studies using commonly used MDCK-MDR1 clones. Our new MDCK-hMDR1 cell line, together with a previously developed control cell line, both with identical deletions in the canine ABCB1 gene and lack of cMDR1 expression represent excellent in\u00a0vitro tools for use in drug discovery.", "doi": "10.1016/j.xphs.2017.04.018", "pmid": "28450237", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Technology development", "Drug Discovery and Development": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0022-3549(17)30251-4"}], "notes": [], "created": "2017-10-17T09:29:45.458Z", "modified": "2025-10-17T13:05:08.756Z"}, {"entity": "publication", "iuid": "481f7584fddd4db2a5d9f3833a7ed7e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/481f7584fddd4db2a5d9f3833a7ed7e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/481f7584fddd4db2a5d9f3833a7ed7e8"}}, "title": "Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.", "authors": [{"family": "Azimi", "given": "Alireza", "initials": "A"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Costa Svedman", "given": "Fernanda", "initials": "F"}, {"family": "Caramuta", "given": "Stefano", "initials": "S"}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Frostvik Stolt", "given": "Marianne", "initials": "M"}, {"family": "Kanter", "given": "Lena", "initials": "L"}, {"family": "Kharaziha", "given": "Pedram", "initials": "P"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Hertzman Johansson", "given": "Carolina", "initials": "C"}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Egyhazi Brage", "given": "Suzanne", "initials": "S", "orcid": "0000-0002-0524-2346", "researcher": {"href": "https://publications.scilifelab.se/researcher/40eddeacb66f490089dbf72978d20721.json"}}], "type": "journal article", "published": "2017-08-31", "journal": {"volume": "8", "issn": "2041-4889", "issue": "8", "pages": "e3029", "title": "Cell Death Dis", "issn-l": "2041-4889"}, "abstract": "A majority of patients with BRAF-mutated metastatic melanoma respond to therapy with BRAF inhibitors (BRAFi), but relapses are common owing to acquired resistance. To unravel BRAFi resistance mechanisms we have performed gene expression and mass spectrometry based proteome profiling of the sensitive parental A375 BRAF V600E-mutated human melanoma cell line and of daughter cell lines with induced BRAFi resistance. Increased expression of two novel resistance candidates, aminopeptidase-N (CD13/ANPEP) and ETS transcription factor FLI1 was observed in the BRAFi-resistant daughter cell lines. In addition, increased levels of the previously reported resistance mediators, receptor tyrosine kinase ephrine receptor A2 (EPHA2) and the hepatocyte growth factor receptor MET were also identified. The expression of these proteins was assessed in matched tumor samples from melanoma patients obtained before BRAFi and after disease progression. MET was overexpressed in all progression samples while the expression of the other candidates varied between the individual patients. Targeting CD13/ANPEP by a blocking antibody induced apoptosis in both parental A375- and BRAFi-resistant daughter cells as well as in melanoma cells with intrinsic BRAFi resistance and led to dephosphorylation of EPHA2 on S897, previously demonstrated to cause inhibition of the migratory capacity. AKT and RSK, both reported to induce EPHA2 S897 phosphorylation, were also dephosphorylated after inhibition of CD13/ANPEP. FLI1 silencing also caused decreases in EPHA2 S897 phosphorylation and in total MET protein expression. In addition, silencing of FLI1 sensitized the resistant cells to BRAFi. Furthermore, we show that BRAFi in combination with the multi kinase inhibitor dasatinib can abrogate BRAFi resistance and decrease both EPHA2 S897 phosphorylation and total FLI1 protein expression. This is the first report presenting CD13/ANPEP and FLI1 as important mediators of resistance to BRAF inhibition with potential as drug targets in BRAFi refractory melanoma.", "doi": "10.1038/cddis.2017.406", "pmid": "29048432", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "Clinical Proteomics Mass spectrometry": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "cddis2017406"}, {"db": "pmc", "key": "PMC5596587"}], "notes": [], "created": "2017-10-17T07:53:20.719Z", "modified": "2021-07-08T11:36:54.639Z"}, {"entity": "publication", "iuid": "7168010a658143b6885ba6d7ded87f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7168010a658143b6885ba6d7ded87f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7168010a658143b6885ba6d7ded87f69"}}, "title": "Neuroblastoma patient-derived xenograft cells cultured in stem-cell promoting medium retain tumorigenic and metastatic capacities but differentiate in serum.", "authors": [{"family": "Persson", "given": "Camilla U", "initials": "CU"}, {"family": "von Stedingk", "given": "Kristoffer", "initials": "K"}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Merselius", "given": "My", "initials": "M"}, {"family": "Braekeveldt", "given": "No\u00e9mie", "initials": "N"}, {"family": "Gisselsson", "given": "David", "initials": "D"}, {"family": "Arsenian-Henriksson", "given": "Marie", "initials": "M"}, {"family": "P\u00e5hlman", "given": "Sven", "initials": "S"}, {"family": "Wigerup", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2017-08-31", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10274", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cultured cancer cells serve as important models for preclinical testing of anti-cancer compounds. However, the optimal conditions for retaining original tumor features during in vitro culturing of cancer cells have not been investigated in detail. Here we show that serum-free conditions are critical for maintaining an immature phenotype of neuroblastoma cells isolated from orthotopic patient-derived xenografts (PDXs). PDX cells could be grown either as spheres or adherent on laminin in serum-free conditions with retained patient-specific genomic aberrations as well as tumorigenic and metastatic capabilities. However, addition of serum led to morphological changes, neuronal differentiation and reduced cell proliferation. The epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) were central for PDX cell proliferation and MYCN expression, and also hindered the serum-induced differentiation. Although serum induced a robust expression of neurotrophin receptors, stimulation with their cognate ligands did not induce further sympathetic differentiation, which likely reflects a block in PDX cell differentiation capacity coupled to their tumor genotype. Finally, PDX cells cultured as spheres or adherent on laminin responded similarly to various cytotoxic drugs, suggesting that both conditions are suitable in vitro screening models for neuroblastoma-targeting compounds.", "doi": "10.1038/s41598-017-09662-8", "pmid": "28860499", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09662-8"}, {"db": "pmc", "key": "PMC5579187"}], "notes": [], "created": "2017-10-17T09:34:44.876Z", "modified": "2020-01-21T13:56:06.568Z"}, {"entity": "publication", "iuid": "fd24c7f3c9d14b86bcabb5a7734c46a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd24c7f3c9d14b86bcabb5a7734c46a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd24c7f3c9d14b86bcabb5a7734c46a5"}}, "title": "A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors.", "authors": [{"family": "Br\u00e6nne", "given": "Ingrid", "initials": "I"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Reiz", "given": "Benedikt", "initials": "B"}, {"family": "Kleinecke", "given": "Mariana", "initials": "M"}, {"family": "von Ameln", "given": "Simon", "initials": "S"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}], "type": "journal article", "published": "2017-08-31", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10252", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cyclooxygenase-2 inhibitors (coxibs) are characterized by multiple molecular off-target effects and increased coronary artery disease (CAD) risk. Here, we systematically explored common variants of genes representing molecular targets of coxibs for association with CAD. Given a broad spectrum of pleiotropic effects of coxibs, our intention was to narrow potential mechanisms affecting CAD risk as we hypothesized that the affected genes may also display genomic signals of coronary disease risk. A Drug Gene Interaction Database search identified 47 gene products to be affected by coxibs. We traced association signals in 200-kb regions surrounding these genes in 84,813 CAD cases and 202,543 controls. Based on a threshold of 1\u2009\u00d7\u200910(-5) (Bonferroni correction for 3131 haplotype blocks), four gene loci yielded significant associations. The lead SNPs were rs7270354 (MMP9), rs4888383 (BCAR1), rs6905288 (VEGFA1), and rs556321 (CACNA1E). By additional genotyping, rs7270354 at MMP9 and rs4888383 at BCAR1 also reached the established GWAS threshold for genome-wide significance. The findings demonstrate overlap of genes affected by coxibs and those mediating CAD risk and points to further mechanisms, which are potentially responsible for coxib-associated CAD risk. The novel approach furthermore suggests that genetic studies may be useful to explore the clinical relevance of off-target drug effects.", "doi": "10.1038/s41598-017-10928-4", "pmid": "28860667", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10928-4"}, {"db": "pmc", "key": "PMC5579257"}], "notes": [], "created": "2017-10-25T15:27:50.730Z", "modified": "2024-01-16T13:48:47.586Z"}, {"entity": "publication", "iuid": "07677b1e93c84aba875182cf118ebb28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07677b1e93c84aba875182cf118ebb28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07677b1e93c84aba875182cf118ebb28"}}, "title": "Importance of N- and C-terminal residues of substance P 1-7 for alleviating allodynia in mice after peripheral administration.", "authors": [{"family": "Skogh", "given": "Anna", "initials": "A"}, {"family": "Lesniak", "given": "Anna", "initials": "A"}, {"family": "Gaugaz", "given": "Fabienne Z", "initials": "FZ"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Lindeberg", "given": "Gunnar", "initials": "G"}, {"family": "Fransson", "given": "Rebecca", "initials": "R"}, {"family": "Nyberg", "given": "Fred", "initials": "F"}, {"family": "Hallberg", "given": "Mathias", "initials": "M"}, {"family": "Sandstr\u00f6m", "given": "Anja", "initials": "A"}], "type": "journal article", "published": "2017-08-30", "journal": {"volume": "106", "issn": "1879-0720", "issue": null, "pages": "345-351", "title": "Eur J Pharm Sci", "issn-l": "0928-0987"}, "abstract": "The heptapeptide SP1-7 (1, Arg(1)-Pro(2)-Lys(3)-Pro(4)-Gln(5)-Gln(6)-Phe(7)) is the major bioactive metabolite formed after proteolytic processing of the neuropeptide substance P (SP, Arg(1)-Pro(2)-Lys(3)-Pro(4)-Gln(5)-Gln(6)-Phe(7)-Phe(8)-Gly(9)-Leu(10)-Met(11)-NH2). The heptapeptide 1 frequently exhibits opposite effects to those induced by SP, such as exerting antinociception, or attenuating thermal hyperalgesia and mechanical allodynia. The heptapeptide SP1-7 amide (2, Arg(1)-Pro(2)-Lys(3)-Pro(4)-Gln(5)-Gln(6)-Phe(7)-NH2) is often more efficacious than 1 in experimental pain models. We have now assessed the anti-allodynic outcome after systemic administration of 2 and a series of Ala-substituted and truncated analogues of 2, in the spared nerve injury (SNI) mice model and the results obtained were correlated with in vitro plasma stability and permeability measurements. It is herein demonstrated that an intact Arg(1) in SP1-7 amide analogues is fundamental for retaining a potent in vivo effect, while Lys(3) of 2 is less important. A displacement with Ala(1) or truncation rendered the peptide analogues either inactive or with a significantly attenuated in vivo activity. Thus, the pentapeptide SP3-7 amide (7, t1/2=11.1 min) proven to be the major metabolite of 2, demonstrated an in vivo effect itself although considerably less significant than 2 in the SNI model. Intraperitoneal administration of 2 in a low dose furnished the most powerful anti-allodynic effect in the SNI model of all the analogous evaluated, despite a fast proteolysis of 2 in plasma (t1/2=6.4 min). It is concluded that not only the C-terminal residue, that we previously demonstrated, but also the N-terminal with its basic side chain, are important for achieving effective pain relief. This information is of value for the further design process aimed at identifying more drug-like SP1-7 amide related peptidomimetics with pronounced anti-allodynic effects.", "doi": "10.1016/j.ejps.2017.06.004", "pmid": "28587787", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0928-0987(17)30336-6"}], "notes": [], "created": "2017-10-24T12:41:03.996Z", "modified": "2025-10-17T13:05:08.767Z"}, {"entity": "publication", "iuid": "8fbff4cafbc24d9294ca916bcd0620e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fbff4cafbc24d9294ca916bcd0620e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fbff4cafbc24d9294ca916bcd0620e2"}}, "title": "Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer.", "authors": [{"family": "Asim", "given": "Mohammad", "initials": "M", "orcid": "0000-0002-2074-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/493226a4e3fd47a88deb79a1a0e82674.json"}}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Zecchini", "given": "Heather I", "initials": "HI"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Massie", "given": "Charles E", "initials": "CE", "orcid": "0000-0003-2314-4843", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5d5818846044987b78e434586c54357.json"}}, {"family": "Baridi", "given": "Ajoeb", "initials": "A"}, {"family": "Warren", "given": "Anne Y", "initials": "AY"}, {"family": "Zhao", "given": "Wanfeng", "initials": "W"}, {"family": "Ogris", "given": "Christoph", "initials": "C"}, {"family": "McDuffus", "given": "Leigh-Anne", "initials": "LA"}, {"family": "Mascalchi", "given": "Patrice", "initials": "P"}, {"family": "Shaw", "given": "Greg", "initials": "G"}, {"family": "Dev", "given": "Harveer", "initials": "H"}, {"family": "Wadhwa", "given": "Karan", "initials": "K"}, {"family": "Wijnhoven", "given": "Paul", "initials": "P"}, {"family": "Forment", "given": "Josep V", "initials": "JV"}, {"family": "Lyons", "given": "Scott R", "initials": "SR"}, {"family": "Lynch", "given": "Andy G", "initials": "AG"}, {"family": "O'Neill", "given": "Cormac", "initials": "C"}, {"family": "Zecchini", "given": "Vincent R", "initials": "VR"}, {"family": "Rennie", "given": "Paul S", "initials": "PS"}, {"family": "Baniahmad", "given": "Aria", "initials": "A"}, {"family": "Tavar\u00e9", "given": "Simon", "initials": "S"}, {"family": "Mills", "given": "Ian G", "initials": "IG"}, {"family": "Galanty", "given": "Yaron", "initials": "Y"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Neal", "given": "David", "initials": "D", "orcid": "0000-0002-6033-5086", "researcher": {"href": "https://publications.scilifelab.se/researcher/a32f7c812c7e40a78ee61a43bfa6c9fc.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-08-29", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "374", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Emerging data demonstrate homologous recombination (HR) defects in castration-resistant prostate cancers, rendering these tumours sensitive to PARP inhibition. Here we demonstrate a direct requirement for the androgen receptor (AR) to maintain HR gene expression and HR activity in prostate cancer. We show that PARP-mediated repair pathways are upregulated in prostate cancer following androgen-deprivation therapy (ADT). Furthermore, upregulation of PARP activity is essential for the survival of prostate cancer cells and we demonstrate a synthetic lethality between ADT and PARP inhibition in vivo. Our data suggest that ADT can functionally impair HR prior to the development of castration resistance and that, this potentially could be exploited therapeutically using PARP inhibitors in combination with androgen-deprivation therapy upfront in advanced or high-risk prostate cancer.Tumours with homologous recombination (HR) defects become sensitive to PARPi. Here, the authors show that androgen receptor (AR) regulates HR and AR inhibition activates the PARP pathway in vivo, thus inhibition of both AR and PARP is required for effective treatment of high risk prostate cancer.", "doi": "10.1038/s41467-017-00393-y", "pmid": "28851861", "labels": {"Advanced FISH Technologies": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00393-y"}, {"db": "pmc", "key": "PMC5575038"}], "notes": [], "created": "2020-01-21T12:35:14.244Z", "modified": "2021-07-08T13:01:30.859Z"}, {"entity": "publication", "iuid": "be2151aaed4f49dfbc9c4a4edbf69dfb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be2151aaed4f49dfbc9c4a4edbf69dfb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be2151aaed4f49dfbc9c4a4edbf69dfb"}}, "title": "Mass Cytometry and Topological Data Analysis Reveal Immune Parameters Associated with Complications after Allogeneic Stem Cell Transplantation.", "authors": [{"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Olin", "given": "Axel", "initials": "A"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Remberger", "given": "Mats", "initials": "M"}, {"family": "Omazic", "given": "Brigitta", "initials": "B"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2017-08-29", "journal": {"volume": "20", "issn": "2211-1247", "issue": "9", "pages": "2238-2250", "title": "Cell Rep", "issn-l": null}, "abstract": "Human immune systems are variable, and immune responses are often unpredictable. Systems-level analyses offer increased power to sort patients on the basis of coordinated changes across immune cells and proteins. Allogeneic stem cell transplantation is a well-established form of immunotherapy whereby a donor immune system induces a graft-versus-leukemia response. This fails when the donor immune system regenerates improperly, leaving the patient susceptible to infections and leukemia relapse. We present a systems-level analysis by mass cytometry and serum profiling in 26 patients sampled 1, 2, 3, 6, and 12 months after transplantation. Using a combination of machine learning and topological data analyses, we show that global immune signatures associated with clinical outcome can be revealed, even when patients are few and heterogeneous. This high-resolution systems immune monitoring approach holds the potential for improving the development and evaluation of immunotherapies in the future.", "doi": "10.1016/j.celrep.2017.08.021", "pmid": "28854371", "labels": {"Cellular Immunomonitoring": "Technology development"}, "xrefs": [{"db": "pii", "key": "S2211-1247(17)31113-0"}], "notes": "Brodin Lab", "created": "2017-10-04T13:40:44.701Z", "modified": "2021-07-08T09:26:23.171Z"}, {"entity": "publication", "iuid": "964b8cd9b8d4479290d16cee188d3b8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/964b8cd9b8d4479290d16cee188d3b8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/964b8cd9b8d4479290d16cee188d3b8c"}}, "title": "Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry.", "authors": [{"family": "Rolandsson Enes", "given": "Sara", "initials": "S"}, {"family": "\u00c5hrman", "given": "Emma", "initials": "E"}, {"family": "Palani", "given": "Anitha", "initials": "A"}, {"family": "Hallgren", "given": "Oskar", "initials": "O"}, {"family": "Bjermer", "given": "Leif", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Scheding", "given": "Stefan", "initials": "S"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G"}], "type": "comparative study", "published": "2017-08-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "9316", "issn-l": "2045-2322"}, "abstract": "Mesenchymal stromal cells (MSC) are ideal candidates for cell therapies, due to their immune-regulatory and regenerative properties. We have previously reported that lung-derived MSC are tissue-resident cells with lung-specific properties compared to bone marrow-derived MSC. Assessing relevant molecular differences between lung-MSC and bone marrow-MSC is important, given that such differences may impact their behavior and potential therapeutic use. Here, we present an in-depth mass spectrometry (MS) based strategy to investigate the proteomes of lung-MSC and bone marrow-MSC. The MS-strategy relies on label free quantitative data-independent acquisition (DIA) analysis and targeted data analysis using a MSC specific spectral library. We identified several significantly differentially expressed proteins between lung-MSC and bone marrow-MSC within the cell layer (352 proteins) and in the conditioned medium (49 proteins). Bioinformatics analysis revealed differences in regulation of cell proliferation, which was functionally confirmed by decreasing proliferation rate through Cytochrome P450 stimulation. Our study reveals important differences within proteome and matrisome profiles between lung- and bone marrow-derived MSC that may influence their behavior and affect the clinical outcome when used for cell-therapy.", "doi": "10.1038/s41598-017-09127-y", "pmid": "28839187", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09127-y"}, {"db": "pmc", "key": "PMC5570998"}], "notes": [], "created": "2020-01-27T10:14:39.128Z", "modified": "2021-05-24T15:39:50.294Z"}, {"entity": "publication", "iuid": "ed1a31c6a9714b3b8295461e629c0af9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed1a31c6a9714b3b8295461e629c0af9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed1a31c6a9714b3b8295461e629c0af9"}}, "title": "Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce-Investigating the specific role of glutamine.", "authors": [{"family": "Carlsson", "given": "Johanna", "initials": "J"}, {"family": "Svennerstam", "given": "Henrik", "initials": "H"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Egertsdotter", "given": "Ulrika", "initials": "U"}, {"family": "Ganeteg", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-0616-3041", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3db575b2a844ecfbb8ff4ab9393860a.json"}}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "12", "issn": "1932-6203", "issue": "8", "pages": "e0181785", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Somatic embryogenesis is an in vitro system employed for plant propagation and the study of embryo development. Nitrogen is essential for plant growth and development and, hence, the production of healthy embryos during somatic embryogenesis. Glutamine has been shown to increase plant biomass in many in vitro applications, including somatic embryogenesis. However, several aspects of nitrogen nutrition during somatic embryogenesis remain unclear. Therefore, we investigated the uptake and assimilation of nitrogen in Norway spruce pro-embryogenic masses to elucidate some of these aspects. In our study, addition of glutamine had a more positive effect on growth than inorganic nitrogen. The nitrogen uptake appeared to be regulated, with a strong preference for glutamine; 67% of the assimilated nitrogen in the free amino acid pool originated from glutamine-nitrogen. Glutamine addition also relieved the apparently limited metabolism (as evidenced by the low concentration of free amino acids) of pro-embryogenic masses grown on inorganic nitrogen only. The unusually high alanine concentration in the presence of glutamine, suggests that alanine biosynthesis was involved in alleviating these constraints. These findings inspire further studies of nitrogen nutrition during the somatic embryogenesis process; identifying the mechanism(s) that govern glutamine enhancement of pro-embryogenic masses growth is especially important in this regard.", "doi": "10.1371/journal.pone.0181785", "pmid": "28837647", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-15940"}, {"db": "pmc", "key": "PMC5570297"}], "notes": [], "created": "2018-01-09T12:28:28.098Z", "modified": "2025-10-17T13:03:18.582Z"}, {"entity": "publication", "iuid": "c000b2d71662419d80ada5c60423b8dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c000b2d71662419d80ada5c60423b8dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c000b2d71662419d80ada5c60423b8dd"}}, "title": "Identification of NCAN as a candidate gene for developmental dyslexia.", "authors": [{"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Peyrard-Janvid", "given": "Myriam", "initials": "M"}, {"family": "Darki", "given": "Fahimeh", "initials": "F"}, {"family": "Tuulari", "given": "Jetro J", "initials": "JJ"}, {"family": "Merisaari", "given": "Harri", "initials": "H", "orcid": "0000-0002-8515-5399", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca8ef9e0084e48db88fd47fd51dd23a4.json"}}, {"family": "Karlsson", "given": "Linnea", "initials": "L"}, {"family": "Scheinin", "given": "Noora M", "initials": "NM"}, {"family": "Saunavaara", "given": "Jani", "initials": "J"}, {"family": "Parkkola", "given": "Riitta", "initials": "R"}, {"family": "Kantoj\u00e4rvi", "given": "Katri", "initials": "K"}, {"family": "\u00c4mm\u00e4l\u00e4", "given": "Antti-Jussi", "initials": "AJ"}, {"family": "Yiu-Lin Yu", "given": "Nancy", "initials": "N", "orcid": "0000-0001-8321-8141", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff7b0ebe0de64edca6546aff2292c376.json"}}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Nopola-Hemmi", "given": "Jaana", "initials": "J"}, {"family": "Karlsson", "given": "Hasse", "initials": "H"}, {"family": "Paunio", "given": "Tiina", "initials": "T"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}, {"family": "Leinonen", "given": "Eira", "initials": "E"}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "9294", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A whole-genome linkage analysis in a Finnish pedigree of eight cases with developmental dyslexia (DD) revealed several regions shared by the affected individuals. Analysis of coding variants from two affected individuals identified rs146011974G > A (Ala1039Thr), a rare variant within the NCAN gene co-segregating with DD in the pedigree. This variant prompted us to consider this gene as a putative candidate for DD. The RNA expression pattern of the NCAN gene in human tissues was highly correlated (R > 0.8) with that of the previously suggested DD susceptibility genes KIAA0319, CTNND2, CNTNAP2 and GRIN2B. We investigated the association of common variation in NCAN to brain structures in two data sets: young adults (Brainchild study, Sweden) and infants (FinnBrain study, Finland). In young adults, we found associations between a common genetic variant in NCAN, rs1064395, and white matter volume in the left and right temporoparietal as well as the left inferior frontal brain regions. In infants, this same variant was found to be associated with cingulate and prefrontal grey matter volumes. Our results suggest NCAN as a new candidate gene for DD and indicate that NCAN variants affect brain structure.", "doi": "10.1038/s41598-017-10175-7", "pmid": "28839234", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10175-7"}, {"db": "pmc", "key": "PMC5570950"}], "notes": [], "created": "2017-10-17T09:24:33.409Z", "modified": "2024-01-16T13:48:47.593Z"}, {"entity": "publication", "iuid": "5b8b687aecf24e9eba5daa40a6545bc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b8b687aecf24e9eba5daa40a6545bc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b8b687aecf24e9eba5daa40a6545bc9"}}, "title": "Clonal Evolution of Autoreactive Germinal Centers.", "authors": [{"family": "Degn", "given": "S\u00f8ren E", "initials": "SE"}, {"family": "van der Poel", "given": "Cees E", "initials": "CE"}, {"family": "Firl", "given": "Daniel J", "initials": "DJ"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Al Qureshah", "given": "Fahd A", "initials": "FA"}, {"family": "Bajic", "given": "Goran", "initials": "G"}, {"family": "Mesin", "given": "Luka", "initials": "L"}, {"family": "Reynaud", "given": "Claude-Agn\u00e8s", "initials": "CA"}, {"family": "Weill", "given": "Jean-Claude", "initials": "JC"}, {"family": "Utz", "given": "Paul J", "initials": "PJ"}, {"family": "Victora", "given": "Gabriel D", "initials": "GD"}, {"family": "Carroll", "given": "Michael C", "initials": "MC"}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "170", "issn": "1097-4172", "issue": "5", "pages": "913-926.e19", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "Germinal centers (GCs) are the primary sites of clonal B cell expansion and affinity maturation, directing the production of high-affinity antibodies. This response is a central driver of pathogenesis in autoimmune diseases, such as systemic lupus erythematosus (SLE), but the natural history of autoreactive GCs remains unclear. Here, we present a novel mouse model where the presence of a single autoreactive B cell clone drives the TLR7-dependent activation, expansion, and differentiation of other autoreactive B\u00a0cells in spontaneous GCs. Once tolerance was broken for one self-antigen, autoreactive GCs generated B cells targeting other self-antigens. GCs became independent of the initial clone and evolved toward dominance of individual clonal lineages, indicating affinity maturation. This process produced serum autoantibodies to a breadth of self-antigens, leading to antibody deposition in the kidneys. Our data provide insight into the maturation of the self-reactive B cell response, contextualizing the epitope spreading observed in autoimmune disease.", "doi": "10.1016/j.cell.2017.07.026", "pmid": "28841417", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(17)30833-4"}], "notes": [], "created": "2017-12-19T15:31:50.567Z", "modified": "2021-03-05T08:22:49.621Z"}, {"entity": "publication", "iuid": "5521219aa1794ec98838a8591df79469", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469"}}, "title": "Cerium oxide nanoparticles inhibit differentiation of neural stem cells.", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Edoff", "given": "Karin", "initials": "K"}, {"family": "Caputo", "given": "Fanny", "initials": "F"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}, {"family": "Ghibelli", "given": "Lina", "initials": "L"}, {"family": "Traversa", "given": "Enrico", "initials": "E"}, {"family": "Ceccatelli", "given": "Sandra", "initials": "S"}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "9284", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cerium oxide nanoparticles (nanoceria) display antioxidant properties and have shown cytoprotective effects both in vitro and in vivo. Here, we explored the effects of nanoceria on neural progenitor cells using the C17.2 murine cell line as a model. First, we assessed the effects of nanoceria versus samarium (Sm) doped nanoceria on cell viability in the presence of the prooxidant, DMNQ. Both particles were taken up by cells and nanoceria, but not Sm-doped nanoceria, elicited a temporary cytoprotective effect upon exposure to DMNQ. Next, we employed RNA sequencing to explore the transcriptional responses induced by nanoceria or Sm-doped nanoceria during neuronal differentiation. Detailed computational analyses showed that nanoceria altered pathways and networks relevant for neuronal development, leading us to hypothesize that nanoceria inhibits neuronal differentiation, and that nanoceria and Sm-doped nanoceria both interfere with cytoskeletal organization. We confirmed that nanoceria reduced neuron specific \u03b23-tubulin expression, a marker of neuronal differentiation, and GFAP, a neuroglial marker. Furthermore, using super-resolution microscopy approaches, we could show that both particles interfered with cytoskeletal organization and altered the structure of neural growth cones. Taken together, these results reveal that nanoceria may impact on neuronal differentiation, suggesting that nanoceria could pose a developmental neurotoxicity hazard.", "doi": "10.1038/s41598-017-09430-8", "pmid": "28839176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Integrated Microscopy Technologies Stockholm": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09430-8"}, {"db": "pmc", "key": "PMC5570910"}, {"db": "ArrayExpress", "description": "raw RNA-seq", "key": "E-MTAB-4398"}], "notes": [], "created": "2017-10-05T09:22:50.002Z", "modified": "2021-07-05T13:48:51.542Z"}, {"entity": "publication", "iuid": "04d609a90c47487388785c1d3bb89419", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04d609a90c47487388785c1d3bb89419.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04d609a90c47487388785c1d3bb89419"}}, "title": "Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae).", "authors": [{"family": "Haddad", "given": "Nizar", "initials": "N", "orcid": "0000-0003-0250-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ff610b5673c4050a4e4377c48b2a372.json"}}, {"family": "Adjlane", "given": "Noureddine", "initials": "N"}, {"family": "Loucif-Ayad", "given": "Wahida", "initials": "W"}, {"family": "Dash", "given": "Abhinandita", "initials": "A"}, {"family": "S", "given": "Naganeeswaran", "initials": "N"}, {"family": "Rajashekar", "given": "Balaji", "initials": "B"}, {"family": "Al-Nakeeb", "given": "Kosai", "initials": "K", "orcid": "0000-0003-3432-3628", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d87f93200b4f0ba3480a0f975e9cd9.json"}}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}], "type": "journal article", "published": "2017-08-22", "journal": {"volume": "2", "issn": "2380-2359", "issue": "2", "pages": "548-549", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "We present the complete mitochondrial genome of honey bee subspecies, Apis mellifera sahariensis (Apidae) belonging to the African lineage. The assembled circular genome has a length of 16,569 bp which comprises 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and AT rich region.", "doi": "10.1080/23802359.2017.1365647", "pmid": "33473895", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1365647"}, {"db": "pmc", "key": "PMC7800622"}], "notes": [], "created": "2017-11-03T15:53:39.359Z", "modified": "2021-06-21T15:45:29.250Z"}, {"entity": "publication", "iuid": "f29099c2af6a4d45a91f29c169b87c86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f29099c2af6a4d45a91f29c169b87c86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f29099c2af6a4d45a91f29c169b87c86"}}, "title": "Genomic correlates of glatiramer acetate adverse cardiovascular effects lead to a novel locus mediating coronary risk", "authors": [{"family": "Br\u00e6nne", "given": "Ingrid", "initials": "I"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": null, "given": "", "initials": ""}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-08-22", "journal": {"volume": "12", "issn": "1932-6203", "issue": "8", "pages": "e0182999", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0182999", "pmid": "28829817", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:54.435Z", "modified": "2020-01-21T13:56:11.919Z"}, {"entity": "publication", "iuid": "31acc210a2d6415399b70ab963602fd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31acc210a2d6415399b70ab963602fd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31acc210a2d6415399b70ab963602fd1"}}, "title": "A specific antibody to detect transcription factor T-Pit: a reliable marker of corticotroph cell differentiation and a tool to improve the classification of pituitary neuroendocrine tumours.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Bollerslev", "given": "Jens", "initials": "J"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Casar-Borota", "given": "Olivera", "initials": "O"}], "type": "letter", "published": "2017-08-19", "journal": {"title": "Acta Neuropathol.", "issn": "1432-0533", "volume": null, "issue": null, "issn-l": "0001-6322"}, "abstract": null, "doi": "10.1007/s00401-017-1768-9", "pmid": "28823042", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00401-017-1768-9"}], "notes": [], "created": "2017-11-05T12:44:02.422Z", "modified": "2017-11-05T12:44:02.435Z"}, {"entity": "publication", "iuid": "b41ba5e6c6044499b5c69eb35fec418c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b41ba5e6c6044499b5c69eb35fec418c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b41ba5e6c6044499b5c69eb35fec418c"}}, "title": "Identification of bacterial biofilm and the Staphylococcus aureus derived protease, staphopain, on the skin surface of patients with atopic dermatitis.", "authors": [{"family": "Sonesson", "given": "Andreas", "initials": "A"}, {"family": "Przybyszewska", "given": "Kornelia", "initials": "K"}, {"family": "Eriksson", "given": "Sigrid", "initials": "S"}, {"family": "M\u00f6rgelin", "given": "Matthias", "initials": "M"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Davies", "given": "Julia", "initials": "J"}, {"family": "Potempa", "given": "Jan", "initials": "J"}, {"family": "Schmidtchen", "given": "Artur", "initials": "A"}], "type": "journal article", "published": "2017-08-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "8689", "issn-l": "2045-2322"}, "abstract": "Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by an impaired epidermal barrier, dysregulation of innate and adaptive immunity, and a high susceptibility to bacterial colonization and infection. In the present study, bacterial biofilm was visualized by electron microscopy at the surface of AD skin. Correspondingly, Staphylococcus aureus (S. aureus) isolates from lesional skin of patients with AD, produced a substantial amount of biofilm in vitro. S. aureus biofilms showed less susceptibility to killing by the antimicrobial peptide LL-37 when compared with results obtained using planktonic cells. Confocal microscopy analysis showed that LL-37 binds to the S. aureus biofilms. Immuno-gold staining of S. aureus biofilm of AD skin detected the S. aureus derived protease staphopain adjacent to the bacteria. In vitro, staphopain B degraded LL-37 into shorter peptide fragments. Further, LL-37 significantly inhibited S. aureus biofilm formation, but no such effects were observed for the degradation products. The data presented here provide novel information on staphopains present in S. aureus biofilms in vivo, and illustrate the complex interplay between biofilm and LL-37 in skin of AD patients, possibly leading to a disturbed host defense, which facilitates bacterial persistence.", "doi": "10.1038/s41598-017-08046-2", "pmid": "28821865", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-08046-2"}, {"db": "pmc", "key": "PMC5562790"}], "notes": [], "created": "2020-01-27T10:04:35.026Z", "modified": "2021-05-24T15:39:50.372Z"}, {"entity": "publication", "iuid": "9a66e1ee51af4d9dacf0840a88138663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c76df55999a74ebfaada13e0cc775de8.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a62a58b12f4f4c87ebe4135826c91a.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/17058abc202c4da794e35722c1f234df.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6352", "title": "Science", "pages": "eaan2507", "issn-l": "0036-8075"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2017-11-03T16:19:27.334Z", "modified": "2024-01-16T13:48:47.600Z"}, {"entity": "publication", "iuid": "abce13eb4ef24e25889d09c9d701907f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abce13eb4ef24e25889d09c9d701907f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abce13eb4ef24e25889d09c9d701907f"}}, "title": "SF3B1-initiating mutations in MDS-RSs target lymphomyeloid hematopoietic stem cells", "authors": [{"family": "Mortera-Blanco", "given": "Teresa", "initials": "T"}, {"family": "Dimitriou", "given": "Marios", "initials": "M"}, {"family": "Woll", "given": "Petter S", "initials": "PS"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Elvarsdottir", "given": "Edda", "initials": "E"}, {"family": "Conte", "given": "Simona", "initials": "S"}, {"family": "Tobiasson", "given": "Magnus", "initials": "M"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Douagi", "given": "Iyadh", "initials": "I"}, {"family": "Moarii", "given": "Matahi", "initials": "M"}, {"family": "Saft", "given": "Leonie", "initials": "L"}, {"family": "Papaemmanuil", "given": "Elli", "initials": "E"}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}], "type": "journal-article", "published": "2017-08-17", "journal": {"volume": "130", "issn": "1528-0020", "issue": "7", "pages": "881-890", "title": "Blood", "issn-l": "0006-4971"}, "abstract": null, "doi": "10.1182/blood-2017-03-776070", "pmid": "28634182", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T13:12:22.860Z", "modified": "2018-12-10T12:31:58.858Z"}, {"entity": "publication", "iuid": "142739defdfa4835934e427e05a7af39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/142739defdfa4835934e427e05a7af39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/142739defdfa4835934e427e05a7af39"}}, "title": "Tea and coffee consumption in relation to DNA methylation in four European cohorts.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Tobi", "given": "Elmar W", "initials": "EW"}, {"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Lampa", "given": "Erik", "initials": "E"}, {"family": "Ponzi", "given": "Erica", "initials": "E"}, {"family": "Kyrtopoulos", "given": "Soterios A", "initials": "SA"}, {"family": "Georgiadis", "given": "Panagiotis", "initials": "P"}, {"family": "Lumey", "given": "L H", "initials": "LH"}, {"family": "Heijmans", "given": "Bastiaan T", "initials": "BT"}, {"family": "Botsivali", "given": "Maria", "initials": "M"}, {"family": "Bergdahl", "given": "Ingvar A", "initials": "IA"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Palli", "given": "Domenico", "initials": "D"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Nilsson", "given": "Lena M", "initials": "LM"}, {"family": "Vineis", "given": "Paolo", "initials": "P"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Flanagan", "given": "James M", "initials": "JM"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Epigenome-Wide Association Study Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-08-15", "journal": {"volume": "26", "issn": "1460-2083", "issue": "16", "pages": "3221-3231", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea have been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation. To investigate if DNA methylation in blood is associated with coffee and tea consumption, we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N\u2009=\u20093,096). DNA methylation was measured from whole blood at 421,695 CpG sites distributed throughout the genome and analysed in men and women both separately and together in each cohort. Meta-analyses of the results and additional regional-level analyses were performed. After adjusting for multiple testing, the meta-analysis revealed that two individual CpG-sites, mapping to DNAJC16 and TTC17, were differentially methylated in relation to tea consumption in women. No individual sites were associated with men or with the sex-combined analysis for tea or coffee. The regional analysis revealed that 28 regions were differentially methylated in relation to tea consumption in women. These regions contained genes known to interact with estradiol metabolism and cancer. No significant regions were found in the sex-combined and male-only analysis for either tea or coffee consumption.", "doi": "10.1093/hmg/ddx194", "pmid": "28535255", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3848993"}], "notes": [], "created": "2017-10-25T15:18:22.652Z", "modified": "2024-01-16T13:48:47.609Z"}, {"entity": "publication", "iuid": "e4ff20b402654d2cb68b4793d8c80728", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4ff20b402654d2cb68b4793d8c80728.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4ff20b402654d2cb68b4793d8c80728"}}, "title": "SubCons: a new ensemble method for improved human subcellular localization predictions.", "authors": [{"family": "Salvatore", "given": "M", "initials": "M"}, {"family": "Warholm", "given": "P", "initials": "P"}, {"family": "Shu", "given": "N", "initials": "N"}, {"family": "Basile", "given": "W", "initials": "W"}, {"family": "Elofsson", "given": "A", "initials": "A"}], "type": "journal article", "published": "2017-08-15", "journal": {"volume": "33", "issn": "1367-4811", "issue": "16", "pages": "2464-2470", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Knowledge of the correct protein subcellular localization is necessary for understanding the function of a protein. Unfortunately large-scale experimental studies are limited in their accuracy. Therefore, the development of prediction methods has been limited by the amount of accurate experimental data. However, recently large-scale experimental studies have provided new data that can be used to evaluate the accuracy of subcellular predictions in human cells. Using this data we examined the performance of state of the art methods and developed SubCons, an ensemble method that combines four predictors using a Random Forest classifier.\r\n\r\nSubCons outperforms earlier methods in a dataset of proteins where two independent methods confirm the subcellular localization. Given nine subcellular localizations, SubCons achieves an F1-Score of 0.79 compared to 0.70 of the second best method. Furthermore, at a FPR of 1% the true positive rate (TPR) is over 58% for SubCons compared to less than 50% for the best individual predictor.\r\n\r\nSubCons is freely available as a webserver (http://subcons.bioinfo.se) and source code from https://bitbucket.org/salvatore_marco/subcons-web-server. The golden dataset as well is available from http://subcons.bioinfo.se/pred/download.\r\n\r\narne@bioinfo.se.\r\n\r\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btx219", "pmid": "28407043", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "3603546"}], "notes": [], "created": "2017-11-10T13:08:59.009Z", "modified": "2020-01-21T13:53:21.906Z"}, {"entity": "publication", "iuid": "67cef94833744aff8d5931288cde32a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67cef94833744aff8d5931288cde32a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67cef94833744aff8d5931288cde32a1"}}, "title": "Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 1: Triazoles, triazolopyrimidines, triazinoindoles, quinoline hydrazones and arylpiperazines.", "authors": [{"family": "Llona-Minguez", "given": "Sabin", "initials": "S"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Throup", "given": "Adam", "initials": "A"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-08-15", "journal": {"volume": "27", "issn": "1464-3405", "issue": "16", "pages": "3897-3904", "title": "Bioorg. Med. Chem. Lett.", "issn-l": "0960-894X"}, "abstract": "A high-throughput screening campaign using a commercial compound library (ChemBridge DiverSET) revealed diverse chemotypes as inhibitors of the human dCTP pyrophosphatase 1 (dCTPase). Triazole, triazolopyrimidine, triazinoindole, quinoline hydrazone and arylpiperazine hits were clustered, confirmed by IC50 determinations, and their preliminary structure-activity-relationships (SAR) and ligand efficiency scores are discussed in this letter.", "doi": "10.1016/j.bmcl.2017.06.038", "pmid": "28687206", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-894X(17)30640-6"}], "notes": "Biochemical and Cellular Screening", "created": "2017-11-01T09:58:40.357Z", "modified": "2025-10-17T13:05:08.785Z"}, {"entity": "publication", "iuid": "afa24fc1819e436d80de149201a9f101", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afa24fc1819e436d80de149201a9f101.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afa24fc1819e436d80de149201a9f101"}}, "title": "Circulating GDF-15 levels predict future secondary manifestations of cardiovascular disease explicitly in women but not men with atherosclerosis.", "authors": [{"family": "Gohar", "given": "Aisha", "initials": "A"}, {"family": "Gon\u00e7alves", "given": "Isabel", "initials": "I"}, {"family": "Vrijenhoek", "given": "Joyce", "initials": "J"}, {"family": "Haitjema", "given": "Saskia", "initials": "S"}, {"family": "van Koeverden", "given": "Ian", "initials": "I", "orcid": "0000-0003-4220-8611", "researcher": {"href": "https://publications.scilifelab.se/researcher/656193ceae264ce7bc3a066715663435.json"}}, {"family": "Nilsson", "given": "Jan", "initials": "J"}, {"family": "de Borst", "given": "Gert J", "initials": "GJ"}, {"family": "de Vries", "given": "Jean-Paul", "initials": "JP"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "den Ruijter", "given": "Hester M", "initials": "HM"}, {"family": "Bj\u00f6rkbacka", "given": "Harry", "initials": "H", "orcid": "0000-0003-3918-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f4c07bc840f491d843f67a9932d5f3a.json"}}, {"family": "de Jager", "given": "Saskia C A", "initials": "SCA"}], "type": "journal article", "published": "2017-08-15", "journal": {"title": "Int. J. Cardiol.", "issn": "1874-1754", "issn-l": "0167-5273", "volume": "241", "issue": null, "pages": "430-436"}, "abstract": "Elevated serum levels of growth differentiation factor-15 (GDF-15), is an established risk factor for a range of cardiovascular diseases. We aimed to evaluate the predictive value of plasma GDF-15 as a biomarker for secondary cardiovascular events (CVE) in patients with atherosclerosis undergoing carotid endarterectomy (CEA). Secondly, we determined whether plasma GDF-15 was associated with carotid plaque characteristics.\n\nCirculating GDF-15 levels were determined by Luminex assay in a cohort of 1056 patients from the Athero-Express biobank. Composite endpoint was defined as major CVE, death and peripheral vascular interventions. Findings were validated in 473 patients from the independent Carotid Plaque Imaging Project biobank.\n\nGDF-15 levels did not associate with secondary CVE in the total cohort. However, following a significant interaction with sex, it was found to be strongly, independently predictive of secondary CVE in women but not men (quartile 4 vs. quartile 1: HR 3.04 [95% CI 1.35-6.86], p=0.007 in women vs. HR 0.96 [95% CI 0.66-1.40], p=0.845 in men). This was also observed in the validation cohort (women: HR 2.28 [95% CI 1.04-5.05], p=0.041), albeit dependent upon renal function. In addition, GDF-15 was associated with the presence of plaque smooth muscle cells and calcification.\n\nHigh circulating GDF-15 levels are predictive of secondary CVE in women but not in men with carotid atherosclerotic disease undergoing CEA, suggesting a potential use for GDF-15 as a biomarker for secondary prevention in women. Sex differences in the role of GDF-15 in atherosclerotic disease deserve further interest.", "doi": "10.1016/j.ijcard.2017.03.101", "pmid": "28389123", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S0167-5273(16)33754-8"}], "notes": [], "created": "2020-01-23T15:08:29.914Z", "modified": "2023-04-14T13:56:11.454Z"}, {"entity": "publication", "iuid": "29256f43a3fd4115a18d255f5802b221", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29256f43a3fd4115a18d255f5802b221.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29256f43a3fd4115a18d255f5802b221"}}, "title": "Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles.", "authors": [{"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Sara", "initials": "S"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Nystedt", "given": "Sara", "initials": "S"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2017-08-14", "journal": {"volume": "10", "issn": "1756-8722", "issue": "1", "pages": "148", "title": "J Hematol Oncol", "issn-l": "1756-8722"}, "abstract": "Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts.\n\nWe combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes.\n\nWe identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations.\n\nOur study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.", "doi": "10.1186/s13045-017-0515-y", "pmid": "28806978", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s13045-017-0515-y"}, {"db": "pmc", "key": "PMC5557398"}], "notes": [], "created": "2017-10-30T09:26:29.124Z", "modified": "2024-01-16T13:48:47.617Z"}, {"entity": "publication", "iuid": "c6865940a64846deae8bff24a02f2424", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6865940a64846deae8bff24a02f2424.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6865940a64846deae8bff24a02f2424"}}, "title": "The Sydney Heart Bank: improving translational research while eliminating or reducing the use of animal models of human heart disease.", "authors": [{"family": "Dos Remedios", "given": "C G", "initials": "CG"}, {"family": "Lal", "given": "S P", "initials": "SP"}, {"family": "Li", "given": "A", "initials": "A"}, {"family": "McNamara", "given": "J", "initials": "J"}, {"family": "Keogh", "given": "A", "initials": "A"}, {"family": "Macdonald", "given": "P S", "initials": "PS"}, {"family": "Cooke", "given": "R", "initials": "R"}, {"family": "Ehler", "given": "E", "initials": "E"}, {"family": "Kn\u00f6ll", "given": "R", "initials": "R"}, {"family": "Marston", "given": "S B", "initials": "SB"}, {"family": "Stelzer", "given": "J", "initials": "J"}, {"family": "Granzier", "given": "H", "initials": "H"}, {"family": "Bezzina", "given": "C", "initials": "C"}, {"family": "van Dijk", "given": "S", "initials": "S"}, {"family": "De Man", "given": "F", "initials": "F"}, {"family": "Stienen", "given": "G J M", "initials": "GJM"}, {"family": "Odeberg", "given": "J", "initials": "J"}, {"family": "Pont\u00e9n", "given": "F", "initials": "F"}, {"family": "Linke", "given": "W", "initials": "W"}, {"family": "van der Velden", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-08-14", "journal": {"title": "Biophys Rev", "issn": "1867-2450", "volume": null, "issue": null, "issn-l": null}, "abstract": "The Sydney Heart Bank (SHB) is one of the largest human heart tissue banks in existence. Its mission is to provide high-quality human heart tissue for research into the molecular basis of human heart failure by working collaboratively with experts in this field. We argue that, by comparing tissues from failing human hearts with age-matched non-failing healthy donor hearts, the results will be more relevant than research using animal models, particularly if their physiology is very different from humans. Tissue from heart surgery must generally be used soon after collection or it significantly deteriorates. Freezing is an option but it raises concerns that freezing causes substantial damage at the cellular and molecular level. The SHB contains failing samples from heart transplant patients and others who provided informed consent for the use of their tissue for research. All samples are cryopreserved in liquid nitrogen within 40\u00a0min of their removal from the patient, and in less than 5-10\u00a0min in the case of coronary arteries and left ventricle samples. To date, the SHB has collected tissue from about 450 failing hearts (>15,000 samples) from patients with a wide range of etiologies as well as increasing numbers of cardiomyectomy samples from patients with hypertrophic cardiomyopathy. The Bank also has hearts from over 120 healthy organ donors whose hearts, for a variety of reasons (mainly tissue-type incompatibility with waiting heart transplant recipients), could not be used for transplantation. Donor hearts were collected by the St Vincent's Hospital Heart and Lung transplantation team from local hospitals or within a 4-h jet flight from Sydney. They were flushed with chilled cardioplegic solution and transported to Sydney where they were quickly cryopreserved in small samples. Failing and/or donor samples have been used by more than 60 research teams around the world, and have resulted in more than 100 research papers. The tissues most commonly requested are from donor left ventricles, but right ventricles, atria, interventricular system, and coronary arteries vessels have also been reported. All tissues are stored for long-term use in liquid N or vapor (170-180\u00a0\u00b0C), and are shipped under nitrogen vapor to avoid degradation of sensitive molecules such as RNAs and giant proteins. We present evidence that the availability of these human heart samples has contributed to a reduction in the use of animal models of human heart failure.", "doi": "10.1007/s12551-017-0305-3", "pmid": "28808947", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s12551-017-0305-3"}, {"db": "pmc", "key": "PMC5578936"}], "notes": [], "created": "2017-11-05T12:43:03.839Z", "modified": "2017-11-05T12:43:03.869Z"}, {"entity": "publication", "iuid": "bb346b64fe4d4505b502eae46d2fe04e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb346b64fe4d4505b502eae46d2fe04e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb346b64fe4d4505b502eae46d2fe04e"}}, "title": "Mucin-Inspired Lubrication on Hydrophobic Surfaces", "authors": [{"family": "K\u00e4sdorf", "given": "Benjamin T", "initials": "BT"}, {"family": "Weber", "given": "Florian", "initials": "F"}, {"family": "Petrou", "given": "Georgia", "initials": "G"}, {"family": "Srivastava", "given": "Vaibhav", "initials": "V"}, {"family": "Crouzier", "given": "Thomas", "initials": "T"}, {"family": "Lieleg", "given": "Oliver", "initials": "O"}], "type": "journal-article", "published": "2017-08-14", "journal": {"volume": "18", "issn": "1526-4602", "issue": "8", "pages": "2454-2462", "title": "Biomacromolecules", "issn-l": "1525-7797"}, "abstract": null, "doi": "10.1021/acs.biomac.7b00605", "pmid": "28635258", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T08:50:58.510Z", "modified": "2017-11-09T13:19:33.884Z"}, {"entity": "publication", "iuid": "8b7c4d75fc1a4d75ab4c9519a85a6c35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b7c4d75fc1a4d75ab4c9519a85a6c35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b7c4d75fc1a4d75ab4c9519a85a6c35"}}, "title": "Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.", "authors": [{"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Lattenkamp", "given": "Ella Z", "initials": "EZ"}, {"family": "Meyer-Lucht", "given": "Yvonne", "initials": "Y"}, {"family": "Luquet", "given": "Emilien", "initials": "E"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2017-08-14", "journal": {"volume": "17", "issn": "1471-2148", "issue": "1", "pages": "189", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites.\n\nUsing outlier analyses, we identified the MHC II exon 2 (corresponding to the \u03b2-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations.\n\nOur results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.", "doi": "10.1186/s12862-017-1022-z", "pmid": "28806900", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-017-1022-z"}, {"db": "pmc", "key": "PMC5557520"}], "notes": [], "created": "2018-01-09T20:49:55.495Z", "modified": "2021-06-21T14:58:37.712Z"}, {"entity": "publication", "iuid": "d52da91e6ca846bf92b3a0ef6e53b0ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d52da91e6ca846bf92b3a0ef6e53b0ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d52da91e6ca846bf92b3a0ef6e53b0ef"}}, "title": "High RBM3 expression is associated with an improved survival and oxaliplatin response in patients with metastatic colorectal cancer.", "authors": [{"family": "Siesing", "given": "Christina", "initials": "C"}, {"family": "Sorbye", "given": "Halfdan", "initials": "H"}, {"family": "Dragomir", "given": "Anca", "initials": "A"}, {"family": "Pfeiffer", "given": "Per", "initials": "P"}, {"family": "Qvortrup", "given": "Camilla", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}], "type": "journal article", "published": "2017-08-11", "journal": {"volume": "12", "issn": "1932-6203", "issue": "8", "pages": "e0182512", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "High expression of the RNA-binding motif protein 3 (RBM3) has been shown to correlate, with prolonged survival in several malignant diseases and with the benefit of platinum-based chemotherapy in ovarian cancer. The aim of this study was to evaluate RBM3 in metastatic colorectal cancer (mCRC) as a prognostic factor for overall survival and in relation to benefit of first-line chemotherapy.\n\nImmunohistochemical staining was conducted and evaluated in tumours from 455 mCRC patients. Kaplan-Meier analysis and Cox regression proportional hazards models were used to access the impact of RBM3 expression on overall survival (OS) and progression-free survival (PFS).\n\nHigh RBM3 expression, both nuclear and cytoplasmic, was an independent prognostic factor for prolonged OS (hazard ratio [HR] 0.67, 95% confidence interval [CI] 0.50-0.90 and HR 0.66, 95% CI 0.48-0.91, respectively). PFS was significantly longer in patients with high RBM3 expression who had received first-line oxaliplatin based treatment, compared to those who had received irinotecan based treatment, both regarding nuclear and cytoplasmic expression (p-value 0.020 and 0.022 respectively).\n\nHigh RBM3 expression is an independent predictor of prolonged survival in mCRC patients, in particular in patients treated with first-line oxaliplatin based chemotherapy.", "doi": "10.1371/journal.pone.0182512", "pmid": "28800641", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-04916"}, {"db": "pmc", "key": "PMC5553773"}], "notes": [], "created": "2017-11-05T12:42:39.758Z", "modified": "2018-11-14T11:00:01.697Z"}, {"entity": "publication", "iuid": "61acb9a9d7df4876a2dfbd51ace9511a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61acb9a9d7df4876a2dfbd51ace9511a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61acb9a9d7df4876a2dfbd51ace9511a"}}, "title": "Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life", "authors": [{"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Caceres", "given": "Eva F", "initials": "EF"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal-article", "published": "2017-08-11", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6351", "pages": "eaaf3883", "title": "Science", "issn-l": "0036-8075"}, "abstract": null, "doi": "10.1126/science.aaf3883", "pmid": "28798101", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:44.609Z", "modified": "2024-01-16T13:48:47.624Z"}, {"entity": "publication", "iuid": "b85241f44e074517a87e335217e446e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b85241f44e074517a87e335217e446e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b85241f44e074517a87e335217e446e7"}}, "title": "Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-08-09", "journal": {"volume": "5", "issn": "2049-2618", "issue": "1", "pages": "96", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.\n\nCompared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.\n\nThese novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.", "doi": "10.1186/s40168-017-0311-5", "pmid": "28793929", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0311-5"}, {"db": "pmc", "key": "PMC5549381"}], "notes": [], "created": "2017-11-03T16:21:35.164Z", "modified": "2024-01-16T13:48:47.631Z"}, {"entity": "publication", "iuid": "b95838961321464bbddc6e42c65bc466", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b95838961321464bbddc6e42c65bc466.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b95838961321464bbddc6e42c65bc466"}}, "title": "Rho-associated kinase is a therapeutic target in neuroblastoma.", "authors": [{"family": "Dyberg", "given": "Cecilia", "initials": "C"}, {"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "Andonova", "given": "Teodora", "initials": "T"}, {"family": "Sveinbj\u00f6rnsson", "given": "Baldur", "initials": "B"}, {"family": "L\u00e4nnerholm-Palm", "given": "Jessika", "initials": "J"}, {"family": "Olsen", "given": "Thale K", "initials": "TK"}, {"family": "Forsberg", "given": "David", "initials": "D"}, {"family": "Herlenius", "given": "Eric", "initials": "E"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}, {"family": "Brodin", "given": "Bertha", "initials": "B"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Johnsen", "given": "John Inge", "initials": "JI"}, {"family": "Wickstr\u00f6m", "given": "Malin", "initials": "M"}], "type": "journal article", "published": "2017-08-08", "journal": {"volume": "114", "issn": "1091-6490", "issue": "32", "pages": "E6603-E6612", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Neuroblastoma is a peripheral neural system tumor that originates from the neural crest and is the most common and deadly tumor of infancy. Here we show that neuroblastoma harbors frequent mutations of genes controlling the Rac/Rho signaling cascade important for proper migration and differentiation of neural crest cells during neuritogenesis. RhoA is activated in tumors from neuroblastoma patients, and elevated expression of Rho-associated kinase (ROCK)2 is associated with poor patient survival. Pharmacological or genetic inhibition of ROCK1 and 2, key molecules in Rho signaling, resulted in neuroblastoma cell differentiation and inhibition of neuroblastoma cell growth, migration, and invasion. Molecularly, ROCK inhibition induced glycogen synthase kinase 3\u03b2-dependent phosphorylation and degradation of MYCN protein. Small-molecule inhibition of ROCK suppressed MYCN-driven neuroblastoma growth in TH-MYCN homozygous transgenic mice and MYCN gene-amplified neuroblastoma xenograft growth in nude mice. Interference with Rho/Rac signaling might offer therapeutic perspectives for high-risk neuroblastoma.", "doi": "10.1073/pnas.1706011114", "pmid": "28739902", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "1706011114"}, {"db": "pmc", "key": "PMC5559038"}], "notes": [], "created": "2017-11-03T16:22:26.931Z", "modified": "2024-01-16T13:48:47.638Z"}, {"entity": "publication", "iuid": "8beff3e9198b4083aa18de81baf79e2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8beff3e9198b4083aa18de81baf79e2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8beff3e9198b4083aa18de81baf79e2b"}}, "title": "Use of Proteomics To Investigate Kidney Function Decline over 5 Years.", "authors": [{"family": "Carlsson", "given": "Axel C", "initials": "AC"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Carrero", "given": "Juan Jesus", "initials": "JJ"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Feldreich", "given": "Tobias", "initials": "T"}, {"family": "Stenemo", "given": "Markus", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-08-07", "journal": {"title": "Clin J Am Soc Nephrol", "issn": "1555-905X", "issn-l": "1555-9041", "volume": "12", "issue": "8", "pages": "1226-1235"}, "abstract": "Using a discovery/replication approach, we investigated associations between a multiplex panel of 80 circulating proteins associated with cardiovascular pathology or inflammation, and eGFR decline per year and CKD incidence.\n\nWe used two cohorts, the Prospective Investigation of the Vasculature in Uppsala Seniors Study (PIVUS; n=687, mean age of 70 years, 51% women) and the Uppsala Longitudinal Study of Adult Men (ULSAM; n=360 men, mean age of 78 years), with 5-year follow-up data on eGFR. There were 231 and 206 incident cases of CKD during follow-up in the PIVUS and ULSAM studies, respectively. Proteomic profiling of 80 proteins was assessed by a multiplex assay (proximity extension assay). The assay uses two antibodies for each protein and a PCR step to achieve a high-specific binding and the possibility to measure multiple proteins in parallel, but gives no absolute concentrations.\n\nIn the discovery cohort from the PIVUS Study, 28 plasma proteins were significantly associated with eGFR decline per year, taking into account the multiple testing. Twenty of these proteins were significantly associated with eGFR decline per year in the replication cohort from the ULSAM Study after adjustment for age, sex, cardiovascular risk factors, medications, and urinary albumin-to-creatinine ratio (in order of significance: TNF-related apoptosis-inducing ligand receptor 2*, CD40L receptor, TNF receptor 1*, placenta growth factor*, thrombomodulin*, urokinase plasminogen activator surface receptor*, growth/differentiation factor 15*, macrophage colony-stimulating factor 1, fatty acid-binding protein*, cathepsin D, resistin, kallikrein 11*, C-C motif chemokine 3, proteinase-activated receptor 1*, cathepsin L, chitinase 3-like protein 1, TNF receptor 2*, fibroblast growth factor 23*, monocyte chemotactic protein 1, and kallikrein 6). Moreover, 11 of the proteins predicted CKD incidence (marked with * above). No protein consistently predicted eGFR decline per year independently of baseline eGFR in both cohorts.\n\nSeveral circulating proteins involved in phosphate homeostasis, inflammation, apoptosis, extracellular matrix remodeling, angiogenesis, and endothelial dysfunction were associated with worsening kidney function. Multiplex proteomics appears to be a promising way of discovering novel aspects of kidney disease pathology.", "doi": "10.2215/CJN.08780816", "pmid": "28784837", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "CJN.08780816"}, {"db": "pmc", "key": "PMC5544512"}], "notes": [], "created": "2017-10-30T11:54:26.168Z", "modified": "2023-04-14T13:56:11.680Z"}, {"entity": "publication", "iuid": "d24174e71c854ddfb3f607e66dfac13e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d24174e71c854ddfb3f607e66dfac13e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d24174e71c854ddfb3f607e66dfac13e"}}, "title": "PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization.", "authors": [{"family": "K\u00e4mpe", "given": "Anders J", "initials": "AJ"}, {"family": "Costantini", "given": "Alice", "initials": "A"}, {"family": "Levy-Shraga", "given": "Yael", "initials": "Y"}, {"family": "Zeitlin", "given": "Leonid", "initials": "L"}, {"family": "Roschger", "given": "Paul", "initials": "P"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Paschalis", "given": "Eleftherios P", "initials": "EP"}, {"family": "Gamsjaeger", "given": "Sonja", "initials": "S"}, {"family": "Raas-Rothschild", "given": "Annick", "initials": "A"}, {"family": "H\u00f6vel", "given": "Matthias", "initials": "M"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Klaushofer", "given": "Klaus", "initials": "K"}, {"family": "Grasemann", "given": "Corinna", "initials": "C"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}], "type": "journal article", "published": "2017-08-04", "journal": {"volume": null, "issn": "1523-4681", "issue": null, "title": "J. Bone Miner. Res.", "issn-l": "0884-0431"}, "abstract": "Mutations in the PLS3 gene, encoding Plastin 3, were described in 2013 as a cause for X-linked primary bone fragility in children. The specific role of PLS3 in bone metabolism remains inadequately understood. Here we describe for the first time PLS3 deletions as the underlying cause for childhood-onset primary osteoporosis in 3 boys from 2 families. We carried out thorough clinical, radiological, and bone tissue analyses to explore the consequences of these deletions and to further elucidate the role of PLS3 in bone homeostasis. In family 1, the 2 affected brothers had a deletion of exons 4-16 (NM_005032) in PLS3, inherited from their healthy mother. In family 2, the index patient had a deletion involving the entire PLS3 gene (exons 1-16), inherited from his mother who had osteoporosis. The 3 patients presented in early childhood with severe spinal compression fractures involving all vertebral bodies. The 2 brothers in family 1 also displayed subtle dysmorphic facial features and both had developed a myopathic gait. Extensive analyses of a transiliac bone biopsy from 1 patient showed a prominent increase in osteoid volume, osteoid thickness, and in mineralizing lag time. Results from quantitative backscattered electron imaging and Raman microspectroscopy showed a significant hypomineralization of the bone. Together our results indicate that PLS3 deletions lead to severe childhood-onset osteoporosis resulting from defective bone matrix mineralization, suggesting a specific role for PLS3 in the mineralization process. \u00a9 2017 American Society for Bone and Mineral Research.", "doi": "10.1002/jbmr.3233", "pmid": "28777485", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:19:23.777Z", "modified": "2024-01-16T13:48:47.646Z"}, {"entity": "publication", "iuid": "3b69e05e11fc40e5ba4d2a38f8e60dda", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b69e05e11fc40e5ba4d2a38f8e60dda.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b69e05e11fc40e5ba4d2a38f8e60dda"}}, "title": "Membrane trafficking under the microscope, what new imaging technologies have brought to light", "authors": [{"family": "Fernandez-Rodriguez", "given": "J", "initials": "J", "orcid": "0000-0003-4522-0966", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bd9c743e99d479cb752aeec947acab3.json"}}, {"family": "Nilsson", "given": "T", "initials": "T"}], "type": null, "published": "2017-08-01", "journal": {"volume": "1st Edition", "issn": null, "issue": null, "pages": null, "title": "CRC Press", "issn-l": null}, "abstract": null, "doi": null, "pmid": null, "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-23T16:38:57.196Z", "modified": "2025-11-17T09:36:50.246Z"}, {"entity": "publication", "iuid": "8b7c4d6802d344fb9c124aae688ece80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b7c4d6802d344fb9c124aae688ece80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b7c4d6802d344fb9c124aae688ece80"}}, "title": "Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 2: Pyridone- and pyrimidinone-derived systems.", "authors": [{"family": "Llona-Minguez", "given": "Sabin", "initials": "S"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Sigmundsson", "given": "Kristmundur", "initials": "K"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Jensen", "given": "Annika Jenmalm", "initials": "AJ"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-08-01", "journal": {"volume": "27", "issn": "1464-3405", "issue": "15", "pages": "3219-3225", "title": "Bioorg. Med. Chem. Lett.", "issn-l": "0960-894X"}, "abstract": "Two screening campaigns using commercial (Chembridge DiverSET) and proprietary (Chemical Biology Consortium Sweden, CBCS) compound libraries, revealed a number of pyridone- and pyrimidinone-derived systems as inhibitors of the human dCTP pyrophosphatase 1 (dCTPase). In this letter, we present their preliminary structure-activity-relationships (SAR) and ligand efficiency scores (LE and LLE).", "doi": "10.1016/j.bmcl.2017.06.039", "pmid": "28655422", "labels": {"Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-894X(17)30641-8"}], "notes": "Biochemical and Cellular Screening", "created": "2017-10-31T13:29:22.883Z", "modified": "2025-10-17T13:05:08.796Z"}, {"entity": "publication", "iuid": "9b3c47e1ea0843e3a015238ec949a229", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b3c47e1ea0843e3a015238ec949a229.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b3c47e1ea0843e3a015238ec949a229"}}, "title": "Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing", "authors": [{"family": "Corcoll", "given": "Nat\u00e0lia", "initials": "N"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Sinclair", "given": "Lucas", "initials": "L"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Backhaus", "given": "Thomas", "initials": "T"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}], "type": "journal-article", "published": "2017-08-01", "journal": {"volume": "364", "issn": "1574-6968", "issue": "14", "pages": null, "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": null, "doi": "10.1093/femsle/fnx139", "pmid": "28673033", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": null, "key": "PRJNA378915"}], "notes": [], "created": "2017-10-30T09:27:43.376Z", "modified": "2024-01-16T13:48:47.653Z"}, {"entity": "publication", "iuid": "d7cca67c91f44fdeb9f673db8956d17b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7cca67c91f44fdeb9f673db8956d17b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7cca67c91f44fdeb9f673db8956d17b"}}, "title": "Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds", "authors": [{"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "26", "issn": "0962-1083", "issue": "16", "pages": "4158-4172", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": null, "doi": "10.1111/mec.14197", "pmid": "28597534", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genetic variation in Ficedula flycatchers", "key": "PRJEB7359"}, {"db": "Dryad", "description": null, "key": "https://doi.org/10.5061/dryad.hp5h2"}], "notes": [], "created": "2018-01-09T20:51:44.961Z", "modified": "2020-01-21T13:56:11.900Z"}, {"entity": "publication", "iuid": "9203b36c328341a68a31f5b7742b332b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9203b36c328341a68a31f5b7742b332b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9203b36c328341a68a31f5b7742b332b"}}, "title": "The structure of the tetanus toxin reveals pH-mediated domain dynamics.", "authors": [{"family": "Masuyer", "given": "Geoffrey", "initials": "G", "orcid": "0000-0002-9527-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/41dcc0806dba4a56bb04725812f3a000.json"}}, {"family": "Conrad", "given": "Julian", "initials": "J", "orcid": "0000-0003-2475-0431", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3eff719b8fa41a9a1e1e3876c0b66d2.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "18", "issn": "1469-3178", "issue": "8", "pages": "1306-1317", "title": "EMBO Rep.", "issn-l": "1469-221X"}, "abstract": "The tetanus neurotoxin (TeNT) is a highly potent toxin produced by Clostridium tetani that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. TeNT differs from the other clostridial neurotoxins by its unique ability to target the central nervous system by retrograde axonal transport. The crystal structure of the tetanus toxin reveals a \"closed\" domain arrangement stabilised by two disulphide bridges, and the molecular details of the toxin's interaction with its polysaccharide receptor. An integrative analysis combining X-ray crystallography, solution scattering and single particle electron cryo-microscopy reveals pH-mediated domain rearrangements that may give TeNT the ability to adapt to the multiple environments encountered during intoxication, and facilitate binding to distinct receptors.", "doi": "10.15252/embr.201744198", "pmid": "28645943", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "embr.201744198"}, {"db": "pmc", "key": "PMC5538627"}], "notes": [], "created": "2017-10-16T16:21:49.646Z", "modified": "2021-06-21T15:33:47.706Z"}, {"entity": "publication", "iuid": "f3751b92f0cc4d8481d00a5096b36f9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3751b92f0cc4d8481d00a5096b36f9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3751b92f0cc4d8481d00a5096b36f9d"}}, "title": "The anticancer effect of mebendazole may be due to M1 monocyte/macrophage activation via ERK1/2 and TLR8-dependent inflammasome activation.", "authors": [{"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Senkowski", "given": "Wojciech", "initials": "W"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Berglund", "given": "Malin", "initials": "M"}, {"family": "Rubin", "given": "Jenny", "initials": "J"}, {"family": "Lenhammar", "given": "Lena", "initials": "L"}, {"family": "Parrow", "given": "Vendela", "initials": "V"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Loskog", "given": "Angelica", "initials": "A"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2017-08-00", "journal": {"title": "Immunopharmacol Immunotoxicol", "issn": "1532-2513", "volume": "39", "issue": "4", "pages": "199-210", "issn-l": null}, "abstract": "Mebendazole (MBZ), a drug commonly used for helminitic infections, has recently gained substantial attention as a repositioning candidate for cancer treatment. However, the mechanism of action behind its anticancer activity remains unclear. To address this problem, we took advantage of the curated MBZ-induced gene expression signatures in the LINCS Connectivity Map (CMap) database. The analysis revealed strong negative correlation with MEK/ERK1/2 inhibitors. Moreover, several of the most upregulated genes in response to MBZ exposure were related to monocyte/macrophage activation. The MBZ-induced gene expression signature in the promyeloblastic HL-60 cell line was strongly enriched in genes involved in monocyte/macrophage pro-inflammatory (M1) activation. This was subsequently validated using MBZ-treated THP-1 monocytoid cells that demonstrated gene expression, surface markers and cytokine release characteristic of the M1 phenotype. At high concentrations MBZ substantially induced the release of IL-1\u03b2 and this was further potentiated by lipopolysaccharide (LPS). At low MBZ concentrations, cotreatment with LPS was required for MBZ-stimulated IL-1\u03b2 secretion to occur. Furthermore, we show that the activation of protein kinase C, ERK1/2 and NF-kappaB were required for MBZ-induced IL-1\u03b2 release. MBZ-induced IL-1\u03b2 release was found to be dependent on NLRP3 inflammasome activation and to involve TLR8 stimulation. Finally, MBZ induced tumor-suppressive effects in a coculture model with differentiated THP-1 macrophages and HT29 colon cancer cells. In summary, we report that MBZ induced a pro-inflammatory (M1) phenotype of monocytoid cells, which may, at least partly, explain MBZ's anticancer activity observed in animal tumor models and in the clinic.", "doi": "10.1080/08923973.2017.1320671", "pmid": "28472897", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-10T12:20:35.589Z", "modified": "2025-10-17T13:05:08.806Z"}, {"entity": "publication", "iuid": "e4fc28f2c5c74d039c4451ab145fb784", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4fc28f2c5c74d039c4451ab145fb784.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4fc28f2c5c74d039c4451ab145fb784"}}, "title": "Switchable ionic liquids enable efficient nanofibrillation of wood pulp", "authors": [{"family": "Berglund", "given": "Linn", "initials": "L"}, {"family": "Anugwom", "given": "Ikenna", "initials": "I"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Aitom\u00e4ki", "given": "Yvonne", "initials": "Y"}, {"family": "Mikkola", "given": "Jyri Pekka", "initials": "JP"}, {"family": "Oksman", "given": "Kristiina", "initials": "K", "orcid": "0000-0003-4762-2854", "researcher": {"href": "https://publications.scilifelab.se/researcher/e82a38d99dd749079c031353ac2f4182.json"}}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "24", "issn": "0969-0239", "issue": "8", "pages": "3265-3279", "title": "Cellulose", "issn-l": null}, "abstract": null, "doi": "10.1007/s10570-017-1354-2", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:05:28.949Z", "modified": "2025-10-17T13:03:59.617Z"}, {"entity": "publication", "iuid": "daf09ae6d7c44e24bf34efb14d8edacb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/daf09ae6d7c44e24bf34efb14d8edacb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/daf09ae6d7c44e24bf34efb14d8edacb"}}, "title": "Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.", "authors": [{"family": "Deville", "given": "C\u00e9lia", "initials": "C", "orcid": "0000-0002-0235-6735", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c716cbe85a047c595efdb2a55a7dcb6.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Franke", "given": "Kamila B", "initials": "KB"}, {"family": "Topf", "given": "Maya", "initials": "M", "orcid": "0000-0002-8185-1215", "researcher": {"href": "https://publications.scilifelab.se/researcher/de031511a9374c3f97b14433944dee8c.json"}}, {"family": "Bukau", "given": "Bernd", "initials": "B"}, {"family": "Mogk", "given": "Axel", "initials": "A", "orcid": "0000-0003-3674-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/56a1d7fc519743029c9ae615086d8093.json"}}, {"family": "Saibil", "given": "Helen R", "initials": "HR", "orcid": "0000-0002-2266-8891", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d53e27939a416893b968a87fedd92e.json"}}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "3", "issn": "2375-2548", "issue": "8", "pages": "e1701726", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'-O-(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.", "doi": "10.1126/sciadv.1701726", "pmid": "28798962", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "1701726"}, {"db": "pmc", "key": "PMC5544394"}], "notes": [], "created": "2017-10-16T16:20:48.109Z", "modified": "2021-07-05T17:22:20.822Z"}, {"entity": "publication", "iuid": "aac1e4e2d8574eaa8cd182dc2b887297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aac1e4e2d8574eaa8cd182dc2b887297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aac1e4e2d8574eaa8cd182dc2b887297"}}, "title": "Site-specific gene expression analysis of implant-near cells in a soft tissue infection model - Application of laser microdissection to study biomaterial-associated infection.", "authors": [{"family": "Svensson", "given": "Sara", "initials": "S"}, {"family": "Trobos", "given": "Margarita", "initials": "M"}, {"family": "Omar", "given": "Omar", "initials": "O"}, {"family": "Thomsen", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2017-08-00", "journal": {"title": "J. Biomed. Mater. Res.", "issn": "1552-4965", "volume": "105", "issue": "8", "pages": "2210-2217", "issn-l": "1549-3296"}, "abstract": "Analysis of the implant-tissue interface is important for an understanding of the cellular response to biomaterials with different surface characteristics. However, inaccessibility to the site has restricted the detailed evaluation of the tissue surrounding the implant. Laser microdissection enables the isolation of specific cells and tissues for subsequent DNA, RNA, or protein analysis. The present experimental study employed laser microdissection to analyze tissue-specific differences in gene expression in cells around infected or control titanium implants 72 h after subcutaneous implantation in a rat model. Three different tissue zones located 0-800 \u03bcm away from the implant-tissue interface were analyzed. Implant sites challenged with a dose of 10 6 CFU Staphylococcus epidermidis demonstrated higher gene expression of selected markers for inflammation (TNF-\u03b1, IL-6), cell recruitment (MCP-1, IL-8, IL-8 R), infection (TLR2), and tissue remodeling (MMP-9) compared with control implants. Furthermore, the gene expression analysis of the three extracted tissue zones revealed marked spatial differences, depending on the distance to the implant. Control implants continuously induced higher cell gene expression in the implant-tissue interface compared with cells 200-800 \u03bcm away from the implant, whereas the sites inoculated with S. epidermidis resulted in high gene expression further away from the implant as well. In conclusion, this study demonstrates that laser microdissection is an interesting tool, revealing both gene- and site-specific gene expression patterns in the implant-tissue interface. The technique provides an opportunity for detailed molecular dissection of the biological events related to the implant but occurring at different distances from the implant. \u00a9 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2210-2217, 2017.", "doi": "10.1002/jbm.a.36088", "pmid": "28395127", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-23T16:36:33.854Z", "modified": "2021-06-21T15:33:17.885Z"}, {"entity": "publication", "iuid": "371f92da9ec140d28854d341b99ef5e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/371f92da9ec140d28854d341b99ef5e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/371f92da9ec140d28854d341b99ef5e9"}}, "title": "Regional genetic differentiation in the blue mussel from the Baltic Sea area", "authors": [{"family": "Larsson", "given": "J", "initials": "J"}, {"family": "Lind", "given": "E E", "initials": "EE"}, {"family": "Corell", "given": "H", "initials": "H"}, {"family": "Grahn", "given": "M", "initials": "M"}, {"family": "Smolarz", "given": "K", "initials": "K"}, {"family": "L\u00f6nn", "given": "M", "initials": "M"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "195", "issn": "0272-7714", "issue": null, "pages": "98-109", "title": "Estuarine, Coastal and Shelf Science", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ecss.2016.06.016", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:57:14.428Z", "modified": "2024-01-16T13:48:47.660Z"}, {"entity": "publication", "iuid": "3976107b7f9a4fee91d089e1cbdc071e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3976107b7f9a4fee91d089e1cbdc071e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3976107b7f9a4fee91d089e1cbdc071e"}}, "title": "Rates of gene flow in a freshwater snail and the evolution of phenotypic plasticity", "authors": [{"family": "Hollander", "given": "Johan", "initials": "J"}, {"family": "Ahlgren", "given": "Johan", "initials": "J"}, {"family": "Br\u00f6nmark", "given": "Christer", "initials": "C"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "121", "issn": "0024-4066", "issue": "4", "pages": "764-770", "title": "Biol J Linn Soc Lond", "issn-l": null}, "abstract": null, "doi": "10.1093/biolinnean/blx028", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:26:42.053Z", "modified": "2021-06-21T15:33:58.347Z"}, {"entity": "publication", "iuid": "afb5a02c1c6643a6b4c048017818af1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afb5a02c1c6643a6b4c048017818af1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afb5a02c1c6643a6b4c048017818af1b"}}, "title": "Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds", "authors": [{"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Rautio", "given": "Milla", "initials": "M"}, {"family": "Peura", "given": "Sari", "initials": "S"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "8", "pages": "1938-1941", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": null, "doi": "10.1038/ismej.2017.54", "pmid": "28430187", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds", "key": "PRJEB18117"}], "notes": [], "created": "2018-01-09T20:57:48.038Z", "modified": "2020-01-21T13:56:11.889Z"}, {"entity": "publication", "iuid": "d66cd6742ac545c7a7c30d4f264ec1b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d66cd6742ac545c7a7c30d4f264ec1b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d66cd6742ac545c7a7c30d4f264ec1b2"}}, "title": "Objective automated quantification of fluorescence signal in histological sections of rat lens", "authors": [{"family": "Talebizadeh", "given": "Nooshin", "initials": "N"}, {"family": "Hagstr\u00f6m", "given": "Nanna Zhou", "initials": "NZ"}, {"family": "Yu", "given": "Zhaohua", "initials": "Z"}, {"family": "Kronschl\u00e4ger", "given": "Martin", "initials": "M"}, {"family": "S\u00f6derberg", "given": "Per", "initials": "P"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "91", "issn": "1552-4922", "issue": "8", "pages": "815-821", "title": "Cytometry", "issn-l": "1552-4922"}, "abstract": null, "doi": "10.1002/cyto.a.23131", "pmid": "28494118", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T08:23:18.937Z", "modified": "2021-07-05T14:18:24.417Z"}, {"entity": "publication", "iuid": "7119a4bbab9f46d2a03b17b778804251", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7119a4bbab9f46d2a03b17b778804251.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7119a4bbab9f46d2a03b17b778804251"}}, "title": "Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations.", "authors": [{"family": "Hollfelder", "given": "Nina", "initials": "N"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Babiker", "given": "Hiba", "initials": "H"}, {"family": "Hassan", "given": "Hisham Y", "initials": "HY", "orcid": "0000-0003-0026-5781", "researcher": {"href": "https://publications.scilifelab.se/researcher/df40ecb572c5470e9bd4368095fdb308.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "8", "pages": "e1006976", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.", "doi": "10.1371/journal.pgen.1006976", "pmid": "28837655", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00483"}, {"db": "pmc", "key": "PMC5587336"}], "notes": [], "created": "2017-10-25T15:27:45.744Z", "modified": "2024-01-16T13:48:47.667Z"}, {"entity": "publication", "iuid": "33aa392964354a89af4f54cfac4626c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33aa392964354a89af4f54cfac4626c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33aa392964354a89af4f54cfac4626c2"}}, "title": "Molecular composition and distribution of gap junctions in the sensory epithelium of the human cochlea-a super-resolution structured illumination microscopy (SR-SIM) study.", "authors": [{"family": "Liu", "given": "Wei", "initials": "W"}, {"family": "Li", "given": "Hao", "initials": "H"}, {"family": "Edin", "given": "Fredrik", "initials": "F"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Glueckert", "given": "Rudolf", "initials": "R"}, {"family": "Schrott-Fischer", "given": "Annelies", "initials": "A"}, {"family": "Molnar", "given": "Matyas", "initials": "M"}, {"family": "Pacholsky", "given": "Dirk", "initials": "D"}, {"family": "Pfaller", "given": "Kristian", "initials": "K"}, {"family": "Rask-Andersen", "given": "Helge", "initials": "H"}], "type": "journal article", "published": "2017-08-00", "journal": {"title": "Ups. J. Med. Sci.", "issn": "2000-1967", "volume": "122", "issue": "3", "pages": "160-170", "issn-l": "0300-9734"}, "abstract": "Mutations in the GJB2 gene, which encodes the Connexin26 (Cx26) protein, are the most common cause of childhood hearing loss in American and European populations. The cochlea contains a gap junction (GJ) network in the sensory epithelium and two connective tissue networks in the lateral wall and spiral limbus. The syncytia contain the GJ proteins beta 2 (GJB2/Cx26) and beta 6 (GJB6/Cx30). Our knowledge of their expression in humans is insufficient due to the limited availability of tissue. Here, we sought to establish the molecular arrangement of GJs in the epithelial network of the human cochlea using surgically obtained samples.\n\nWe analyzed Cx26 and Cx30 expression in GJ networks in well-preserved adult human auditory sensory epithelium using confocal, electron, and super-resolution structured illumination microscopy (SR-SIM).\n\nCx30 plaques (<5 \u03bcm) dominated, while Cx26 plaques were subtle and appeared as 'mini-junctions' (2-300 nm). 3-D volume rendering of Z-stacks and orthogonal projections from single optical sections suggested that the GJs are homomeric/homotypic and consist of assemblies of identical GJs composed of either Cx26 or Cx30. Occasionally, the two protein types were co-expressed, suggesting functional cooperation.\n\nEstablishing the molecular composition and distribution of the GJ networks in the human cochlea may increase our understanding of the pathophysiology of Cx-related hearing loss. This information may also assist in developing future strategies to treat genetic hearing loss.", "doi": "10.1080/03009734.2017.1322645", "pmid": "28513246", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5649321"}], "notes": [], "created": "2021-09-27T07:22:04.410Z", "modified": "2021-11-10T11:51:53.769Z"}, {"entity": "publication", "iuid": "11a0e20f7a4b4d8fb8049f4e5f2d5e70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11a0e20f7a4b4d8fb8049f4e5f2d5e70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11a0e20f7a4b4d8fb8049f4e5f2d5e70"}}, "title": "Low-Frequency Synonymous Coding Variation in  CYP2R1  Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis", "authors": [{"family": "Manousaki", "given": "Despoina", "initials": "D"}, {"family": "Dudding", "given": "Tom", "initials": "T"}, {"family": "Haworth", "given": "Simon", "initials": "S"}, {"family": "Hsu", "given": "Yi Hsiang", "initials": "YH"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Medina-G\u00f3mez", "given": "Carolina", "initials": "C"}, {"family": "Voortman", "given": "Trudy", "initials": "T"}, {"family": "van der Velde", "given": "Nathalie", "initials": "N"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Robinson-Cohen", "given": "Cassianne", "initials": "C"}, {"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Nethander", "given": "Maria", "initials": "M"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Forgetta", "given": "Vincenzo", "initials": "V"}, {"family": "Greenwood", "given": "Celia M T", "initials": "CMT"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Zemel", "given": "Babette S", "initials": "BS"}, {"family": "Mitchell", "given": "Jonathan A", "initials": "JA"}, {"family": "Taylor", "given": "Bruce", "initials": "B"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Jaddoe", "given": "Vincent V W", "initials": "VVW"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Campos-Obando", "given": "Natalia", "initials": "N"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Utterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "Ham", "given": "Annelies C", "initials": "AC"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Rosendaal", "given": "Frits R", "initials": "FR"}, {"family": "den Heijer", "given": "Martin", "initials": "M"}, {"family": "Wang", "given": "Thomas J", "initials": "TJ"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Orwoll", "given": "Eric S", "initials": "ES"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Kestenbaum", "given": "Bryan", "initials": "B"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Mellstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "de Groot", "given": "Lisette C P G M", "initials": "LCPGM"}, {"family": "Grant", "given": "Struan F A", "initials": "SFA"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Sawcer", "given": "Stephen", "initials": "S"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Richards", "given": "J Brent", "initials": "JB"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "101", "issn": "0002-9297", "issue": "2", "pages": "227-238", "title": "The American Journal of Human Genetics", "issn-l": "0002-9297"}, "abstract": null, "doi": "10.1016/j.ajhg.2017.06.014", "pmid": "28757204", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:55.321Z", "modified": "2020-01-21T13:56:11.861Z"}, {"entity": "publication", "iuid": "b8df50988dd14ad9808582b7400559b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8df50988dd14ad9808582b7400559b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8df50988dd14ad9808582b7400559b1"}}, "title": "Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Jawad", "given": "Abbtesaim", "initials": "A"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Ni", "given": "Gaofeng", "initials": "G"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Sundkvist", "given": "Jan-Eric", "initials": "JE"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "28", "issn": "1572-9729", "issue": "4", "pages": "287-301", "title": "Biodegradation", "issn-l": "0923-9820"}, "abstract": "Wastewaters generated during mining and processing of metal sulfide ores are often acidic (pH\u00a0<\u00a03) and can contain significant concentrations of nitrate, nitrite, and ammonium from nitrogen based explosives. In addition, wastewaters from sulfide ore treatment plants and tailings ponds typically contain large amounts of inorganic sulfur compounds, such as thiosulfate and tetrathionate. Release of these wastewaters can lead to environmental acidification as well as an increase in nutrients (eutrophication) and compounds that are potentially toxic to humans and animals. Waters from cyanidation plants for gold extraction will often conjointly include toxic, sulfur containing thiocyanate. More stringent regulatory limits on the release of mining wastes containing compounds such as inorganic sulfur compounds, nitrate, and thiocyanate, along the need to increase production from sulfide mineral mining calls for low cost techniques to remove these pollutants under ambient temperatures (approximately 8\u00a0\u00b0C). In this study, we used both aerobic and anaerobic continuous cultures to successfully couple inorganic sulfur compound (i.e. thiosulfate and thiocyanate) oxidation for the removal of nitrogenous compounds under neutral to acidic pH at the low temperatures typical for boreal climates. Furthermore, the development of the respective microbial communities was identified over time by DNA sequencing, and found to contain a consortium including populations aligning within Flavobacterium, Thiobacillus, and Comamonadaceae lineages. This is the first study to remediate mining waste waters by coupling autotrophic thiocyanate oxidation to nitrate reduction at low temperatures and acidic pH by means of an identified microbial community.", "doi": "10.1007/s10532-017-9796-7", "pmid": "28577026", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s10532-017-9796-7"}, {"db": "pmc", "key": "PMC5500686"}], "notes": [], "created": "2017-11-03T16:21:55.117Z", "modified": "2024-01-16T13:48:47.674Z"}, {"entity": "publication", "iuid": "482e4ddecdcd4d2aaae1ac0d32206932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/482e4ddecdcd4d2aaae1ac0d32206932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/482e4ddecdcd4d2aaae1ac0d32206932"}}, "title": "Investigation of calcium-dependent activity and conformational dynamics of zebra fish 12-lipoxygenase", "authors": [{"family": "Mittal", "given": "Monica", "initials": "M"}, {"family": "Hasan", "given": "Mahmudul", "initials": "M"}, {"family": "Balagunaseelan", "given": "Navisraj", "initials": "N"}, {"family": "Fauland", "given": "Alexander", "initials": "A"}, {"family": "Wheelock", "given": "Craig", "initials": "C"}, {"family": "R\u00e5dmark", "given": "Olof", "initials": "O"}, {"family": "Haeggstr\u00f6m", "given": "Jesper Z", "initials": "JZ"}, {"family": "Rinaldo-Matthis", "given": "Agnes", "initials": "A"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "1861", "issn": "0304-4165", "issue": "8", "pages": "2099-2111", "title": "Biochimica et Biophysica Acta (BBA) - General Subjects", "issn-l": null}, "abstract": null, "doi": "10.1016/j.bbagen.2017.05.015", "pmid": "28528958", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:48:37.275Z", "modified": "2017-11-09T13:19:06.961Z"}, {"entity": "publication", "iuid": "74c53c67def3412e8e38204982fc1ee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74c53c67def3412e8e38204982fc1ee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74c53c67def3412e8e38204982fc1ee8"}}, "title": "Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa", "authors": [{"family": "Vijay", "given": "Nagarjun", "initials": "N"}, {"family": "Weissensteiner", "given": "Matthias", "initials": "M"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "26", "issn": "0962-1083", "issue": "16", "pages": "4284-4295", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": null, "doi": "10.1111/mec.14195", "pmid": "28570015", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:57:47.611Z", "modified": "2020-01-21T13:56:11.870Z"}, {"entity": "publication", "iuid": "2839bc783f824749afb3c002b0292fe2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2839bc783f824749afb3c002b0292fe2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2839bc783f824749afb3c002b0292fe2"}}, "title": "Genome-Wide Association Study of Angioedema Induced by Ace Inhibitors or Arbs in Sweden", "authors": [{"family": "Wadelius", "given": "M", "initials": "M"}, {"family": "Eriksson", "given": "N", "initials": "N"}, {"family": "Johansson", "given": "C", "initials": "C"}, {"family": "Persson", "given": "M", "initials": "M"}, {"family": "Karawajczyk", "given": "M", "initials": "M"}, {"family": "Nordang", "given": "L", "initials": "L"}, {"family": "Islander", "given": "G", "initials": "G"}, {"family": "Hugosson", "given": "S", "initials": "S"}, {"family": "Axelsson", "given": "T", "initials": "T"}, {"family": "Yue", "given": "Q Y", "initials": "QY"}, {"family": "Magnusson", "given": "P K E", "initials": "PKE"}, {"family": "Hallberg", "given": "P", "initials": "P"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "39", "issn": "0149-2918", "issue": "8", "pages": "e76", "title": "Clinical Therapeutics", "issn-l": null}, "abstract": null, "doi": "10.1016/j.clinthera.2017.05.235", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-02T15:37:52.480Z", "modified": "2021-06-21T15:34:22.418Z"}, {"entity": "publication", "iuid": "e1513cc970f64beb9b07fcd904d17c04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1513cc970f64beb9b07fcd904d17c04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1513cc970f64beb9b07fcd904d17c04"}}, "title": "Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks", "authors": [{"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Liedvogel", "given": "Miriam", "initials": "M"}, {"family": "Larson", "given": "Keith", "initials": "K"}, {"family": "Sigeman", "given": "Hanna", "initials": "H"}, {"family": "Grahn", "given": "Mats", "initials": "M"}, {"family": "Wright", "given": "Anthony", "initials": "A"}, {"family": "\u00c5kesson", "given": "Susanne", "initials": "S"}, {"family": "Bensch", "given": "Staffan", "initials": "S"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "1", "issn": "2056-3744", "issue": "3", "pages": "155-168", "title": "Evolution Letters", "issn-l": "2056-3744"}, "abstract": null, "doi": "10.1002/evl3.15", "pmid": "30283646", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:41.042Z", "modified": "2024-01-16T13:48:47.681Z"}, {"entity": "publication", "iuid": "120f84a1df5044b78876873a8b8f46e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/120f84a1df5044b78876873a8b8f46e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/120f84a1df5044b78876873a8b8f46e7"}}, "title": "Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification", "authors": [{"family": "Karlsson", "given": "Anna", "initials": "A"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Veerla", "given": "Srinivas", "initials": "S"}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "La Fleur", "given": "Linnea", "initials": "L"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "J\u00f6nsson", "given": "Mats", "initials": "M"}, {"family": "Reutersw\u00e4rd", "given": "Christel", "initials": "C"}, {"family": "Planck", "given": "Maria", "initials": "M"}, {"family": "Staaf", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "12", "issn": "1556-0864", "issue": "8", "pages": "1257-1267", "title": "Journal of Thoracic Oncology", "issn-l": "1556-0864"}, "abstract": "Large cell lung cancer (LCLC) and large cell neuroendocrine carcinoma (LCNEC) constitute a small proportion of NSCLC. The WHO 2015 classification guidelines changed the definition of the debated histological subtype LCLC to be based on immunomarkers for adenocarcinoma and squamous cancer. We sought to determine whether these new guidelines also translate into the transcriptional landscape of lung cancer, and LCLC specifically.\n\nGene expression profiling was performed by using Illumina V4 HT12 microarrays (Illumina, San Diego, CA) on samples from 159 cases (comprising all histological subtypes, including 10 classified as LCLC WHO 2015 and 14 classified as LCNEC according to the WHO 2015 guidelines), with complimentary mutational and immunohistochemical data. Derived transcriptional phenotypes were validated in 199 independent tumors, including six WHO 2015 LCLCs and five LCNECs.\n\nUnsupervised analysis of gene expression data identified a phenotype comprising 90% of WHO 2015 LCLC tumors, with characteristics of poorly differentiated proliferative cancer, a 90% tumor protein p53 gene (TP53) mutation rate, and lack of well-known NSCLC oncogene driver alterations. Validation in independent data confirmed aggregation of WHO 2015 LCLCs in the specific phenotype. For LCNEC tumors, the unsupervised gene expression analysis suggested two different transcriptional patterns corresponding to a proposed genetic division of LCNEC tumors into SCLC-like and NSCLC-like cancer on the basis of TP53 and retinoblastoma 1 gene (RB1) alteration patterns.\n\nRefined classification of LCLC has implications for diagnosis, prognostics, and therapy decisions. Our molecular analyses support the WHO 2015 classification of LCLC and LCNEC tumors, which herein follow different tumorigenic paths and can accordingly be stratified into different transcriptional subgroups, thus linking diagnostic immunohistochemical staining-driven classification with the transcriptional landscape of lung cancer.", "doi": "10.1016/j.jtho.2017.05.008", "pmid": "28535939", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-17T12:52:48.443Z", "modified": "2019-12-20T07:50:23.143Z"}, {"entity": "publication", "iuid": "154ec29d9d7b4cefad3d468bf743f6ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/154ec29d9d7b4cefad3d468bf743f6ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/154ec29d9d7b4cefad3d468bf743f6ee"}}, "title": "Dual herbivore attack and herbivore density affect metabolic profiles of Brassica nigra leaves", "authors": [{"family": "Ponzio", "given": "Camille", "initials": "C"}, {"family": "Papazian", "given": "Stefano", "initials": "S"}, {"family": "Albrectsen", "given": "Benedicte R", "initials": "BR"}, {"family": "Dicke", "given": "Marcel", "initials": "M"}, {"family": "Gols", "given": "Rieta", "initials": "R"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "40", "issn": "0140-7791", "issue": "8", "pages": "1356-1367", "title": "Plant, Cell & Environment", "issn-l": "0140-7791"}, "abstract": null, "doi": "10.1111/pce.12926", "pmid": "28155236", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:34:31.812Z", "modified": "2025-10-17T13:03:18.620Z"}, {"entity": "publication", "iuid": "a71bda38666649719500918c81c066aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a71bda38666649719500918c81c066aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a71bda38666649719500918c81c066aa"}}, "title": "Differences in genetic and environmental variation in adult BMI by sex, age, time period, and region: an individual-based pooled analysis of 40 twin cohorts", "authors": [{"family": "Silventoinen", "given": "Karri", "initials": "K"}, {"family": "Jelenkovic", "given": "Aline", "initials": "A"}, {"family": "Sund", "given": "Reijo", "initials": "R"}, {"family": "Yokoyama", "given": "Yoshie", "initials": "Y"}, {"family": "Hur", "given": "Yoon Mi", "initials": "YM"}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Hwang", "given": "Amie E", "initials": "AE"}, {"family": "Mack", "given": "Thomas M", "initials": "TM"}, {"family": "Honda", "given": "Chika", "initials": "C"}, {"family": "Inui", "given": "Fujio", "initials": "F"}, {"family": "Iwatani", "given": "Yoshinori", "initials": "Y"}, {"family": "Watanabe", "given": "Mikio", "initials": "M"}, {"family": "Tomizawa", "given": "Rie", "initials": "R"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Rissanen", "given": "Aila", "initials": "A"}, {"family": "Siribaddana", "given": "Sisira H", "initials": "SH"}, {"family": "Hotopf", "given": "Matthew", "initials": "M"}, {"family": "Sumathipala", "given": "Athula", "initials": "A"}, {"family": "Rijsdijk", "given": "Fruhling", "initials": "F"}, {"family": "Tan", "given": "Qihua", "initials": "Q"}, {"family": "Zhang", "given": "Dongfeng", "initials": "D"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Piirtola", "given": "Maarit", "initials": "M"}, {"family": "Aaltonen", "given": "Sari", "initials": "S"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Hjelmborg", "given": "Jacob B", "initials": "JB"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Skytthe", "given": "Axel", "initials": "A"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Eaves", "given": "Lindon J", "initials": "LJ"}, {"family": "Cutler", "given": "Tessa L", "initials": "TL"}, {"family": "Ordo\u00f1ana", "given": "Juan R", "initials": "JR"}, {"family": "S\u00e1nchez-Romera", "given": "Juan F", "initials": "JF"}, {"family": "Colodro-Conde", "given": "Lucia", "initials": "L"}, {"family": "Song", "given": "Yun Mi", "initials": "YM"}, {"family": "Yang", "given": "Sarah", "initials": "S"}, {"family": "Lee", "given": "Kayoung", "initials": "K"}, {"family": "Franz", "given": "Carol E", "initials": "CE"}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Lyons", "given": "Michael J", "initials": "MJ"}, {"family": "Busjahn", "given": "Andreas", "initials": "A"}, {"family": "Nelson", "given": "Tracy L", "initials": "TL"}, {"family": "Whitfield", "given": "Keith E", "initials": "KE"}, {"family": "Kandler", "given": "Christian", "initials": "C"}, {"family": "Jang", "given": "Kerry L", "initials": "KL"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Butler", "given": "David A", "initials": "DA"}, {"family": "Stazi", "given": "Maria A", "initials": "MA"}, {"family": "Fagnani", "given": "Corrado", "initials": "C"}, {"family": "D\u2019Ippolito", "given": "Cristina", "initials": "C"}, {"family": "Duncan", "given": "Glen E", "initials": "GE"}, {"family": "Buchwald", "given": "Dedra", "initials": "D"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Jeong", "given": "Hoe Uk", "initials": "HU"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "Krasnow", "given": "Ruth", "initials": "R"}, {"family": "Magnusson", "given": "Patrik KE", "initials": "PK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Dahl Aslan", "given": "Anna K", "initials": "AK"}, {"family": "McAdams", "given": "Tom A", "initials": "TA"}, {"family": "Eley", "given": "Thalia C", "initials": "TC"}, {"family": "Gregory", "given": "Alice M", "initials": "AM"}, {"family": "Tynelius", "given": "Per", "initials": "P"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Bayasgalan", "given": "Gombojav", "initials": "G"}, {"family": "Narandalai", "given": "Danshiitsoodol", "initials": "D"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Lachance", "given": "Genevieve", "initials": "G"}, {"family": "Burt", "given": "S Alexandra", "initials": "SA"}, {"family": "Klump", "given": "Kelly L", "initials": "KL"}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Brandt", "given": "Ingunn", "initials": "I"}, {"family": "Nilsen", "given": "Thomas S", "initials": "TS"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "van Beijsterveldt", "given": "Catharina EM", "initials": "CE"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Goldberg", "given": "Jack H", "initials": "JH"}, {"family": "Rasmussen", "given": "Finn", "initials": "F"}, {"family": "Tarnoki", "given": "Adam D", "initials": "AD"}, {"family": "Tarnoki", "given": "David L", "initials": "DL"}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Loos", "given": "Ruth JF", "initials": "RJ"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Sung", "given": "Joohon", "initials": "J"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Turkheimer", "given": "Eric", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "S\u00f8rensen", "given": "Thorkild IA", "initials": "TI"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "106", "issn": "0002-9165", "issue": "2", "pages": "457-466", "title": "Am J Clin Nutr", "issn-l": "0002-9165"}, "abstract": null, "doi": "10.3945/ajcn.117.153643", "pmid": "28679550", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:09.302Z", "modified": "2020-01-21T13:56:11.877Z"}, {"entity": "publication", "iuid": "5ef10a01a35845139e73fd3393b8b2a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ef10a01a35845139e73fd3393b8b2a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ef10a01a35845139e73fd3393b8b2a7"}}, "title": "Data on haplotype-supported immunoglobulin germline gene inference.", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "13", "issn": "2352-3409", "issue": null, "pages": "620-640", "title": "Data Brief", "issn-l": "2352-3409"}, "abstract": "Data that defines IGHV (immunoglobulin heavy chain variable) germline gene inference using sequences of IgM-encoding transcriptomes obtained by Illumina MiSeq sequencing technology are described. Such inference is used to establish personalized germline gene sets for in-depth antibody repertoire studies and to detect new antibody germline genes from widely available immunoglobulin-encoding transcriptome data sets. Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery (DOI: 10.1016/j.molimm.2017.03.012) (Kirik et al., 2017) [1]) the inference process. This was accomplished based on analysis of the inferred germline genes' association to the donors' different haplotypes as defined by their different, expressed IGHJ alleles and/or IGHD genes/alleles. The data is important for development of validated germline gene databases containing entries inferred from immunoglobulin-encoding transcriptome sequencing data sets, and for generation of valid, personalized antibody germline gene repertoires.", "doi": "10.1016/j.dib.2017.06.031", "pmid": "28725665", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3409(17)30275-5"}, {"db": "pmc", "key": "PMC5502703"}], "notes": [], "created": "2017-11-03T16:22:11.988Z", "modified": "2024-01-16T13:48:47.688Z"}, {"entity": "publication", "iuid": "d6314ad2f0b440b2a2c489ca5019859b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6314ad2f0b440b2a2c489ca5019859b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6314ad2f0b440b2a2c489ca5019859b"}}, "title": "Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns.", "authors": [{"family": "De Laere", "given": "Bram", "initials": "B"}, {"family": "van Dam", "given": "Pieter-Jan", "initials": "PJ"}, {"family": "Whitington", "given": "Tom", "initials": "T"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Diaz", "given": "Emanuela Henao", "initials": "EH"}, {"family": "Van den Eynden", "given": "Gert", "initials": "G"}, {"family": "Vandebroek", "given": "Jean", "initials": "J"}, {"family": "Del-Favero", "given": "Jurgen", "initials": "J"}, {"family": "Van Laere", "given": "Steven", "initials": "S"}, {"family": "Dirix", "given": "Luc", "initials": "L"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "72", "issn": "1873-7560", "issue": "2", "pages": "192-200", "title": "Eur. Urol.", "issn-l": "0302-2838"}, "abstract": "Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative.\n\nTo investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy.\n\nPeripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy. We performed profiling of circulating tumour DNA via low-pass whole-genome sequencing and targeted sequencing of the entire AR gene, including introns. Targeted RNA sequencing was performed on enriched circulating tumour cell fractions to assess the expression levels of seven AR splice variants (ARVs).\n\nSomatic AR variations, including copy-number alterations, structural variations, and point mutations, were combined with ARV expression patterns and correlated to clinicopathologic parameters.\n\nCollectively, any AR perturbation, including ARV, was detected in 25/30 patients. Surprisingly, intra-AR structural variation was present in 15/30 patients, of whom 14 expressed ARVs. The majority of ARV-positive patients expressed multiple ARVs, with AR-V3 the most abundantly expressed. The presence of any ARV was associated with progression-free survival after second-line endocrine treatment (hazard ratio 4.53, 95% confidence interval 1.424-14.41; p=0.0105). Six out of 17 poor responders were AR-V7-negative, but four carried other AR perturbations.\n\nComprehensive AR profiling, which is feasible using liquid biopsies, is necessary to increase our understanding of the mechanisms underpinning resistance to endocrine treatment.\n\nAlterations in the androgen receptor are associated with endocrine treatment outcomes. This study demonstrates that it is possible to identify different types of alterations via simple blood draws. Follow-up studies are needed to determine the effect of such alterations on hormonal therapy.", "doi": "10.1016/j.eururo.2017.01.011", "pmid": "28104311", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0302-2838(17)30018-0"}], "notes": [], "created": "2017-11-03T12:53:33.758Z", "modified": "2017-11-04T13:31:16.799Z"}, {"entity": "publication", "iuid": "132b02e3f2a04a58a7a4909db3048757", "links": {"self": {"href": "https://publications.scilifelab.se/publication/132b02e3f2a04a58a7a4909db3048757.json"}, "display": {"href": "https://publications.scilifelab.se/publication/132b02e3f2a04a58a7a4909db3048757"}}, "title": "CKM Glu83Gly Is Associated With Blunted Creatine Kinase Variation, but Not With Myalgia.", "authors": [{"family": "Siddiqui", "given": "Moneeza Kalhan", "initials": "MK"}, {"family": "Veluchamy", "given": "Abirami", "initials": "A"}, {"family": "Maroteau", "given": "Cyrielle", "initials": "C"}, {"family": "Tavendale", "given": "Roger", "initials": "R"}, {"family": "Carr", "given": "Fiona", "initials": "F"}, {"family": "Pearson", "given": "Ewan", "initials": "E"}, {"family": "Colhoun", "given": "Helen", "initials": "H"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "George", "given": "Jacob", "initials": "J"}, {"family": "Doney", "given": "Alexander", "initials": "A"}, {"family": "Pirmohamed", "given": "Munir", "initials": "M"}, {"family": "Alfirevic", "given": "Ana", "initials": "A"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Maitland van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "PREDICTION-ADR Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "10", "issn": "1942-3268", "issue": "4", "pages": "e001737", "title": "Circ Cardiovasc Genet", "issn-l": null}, "abstract": "To test the association of a recently reported variant in the creatine kinase (CK) muscle gene, CKM Glu83Gly (rs11559024) with constitutive creatine phosphokinase (CK) levels, CK variation, and inducibility. Given the diagnostic importance of CK in determining muscle damage, we tested the association of the variant with myalgia.\n\nMeta-analysis between longitudinal cohort GoDARTS (Genetics of Diabetes Audit and Research, Tayside Scotland), minor allele frequency (=0.02), and randomized clinical trial (JUPITER [Justification for the Use of Statins in Primary Prevention: An Intervention Trial Evaluating Rosuvastatin], minor allele frequency=0.018) was used to replicate the association with baseline CK measures. GoDARTS was used to study the relationship with CK variability. Myalgia was studied in JUPITER trial participants. Baseline and SDs of CK were on average 18% ( P value=6\u00d710-63) and 24% (P value=2\u00d710-5) lower for carriers of the variant, respectively. The variant was not associated with myalgia (odds ratio, 0.84; 95% confidence interval, 0.52-1.38).\n\nThis study highlights that a genetic factor known to be associated with constitutive CK levels is also associated with CK variability and inducibility. This is discussed in the context of evidence to suggest that the variant has an impact on inducibility of CK by trauma through a previously reported case of a homozygous carrier. However, the lack of association between the variant and myalgia suggests that it cannot reliably be used as a biomarker for muscle symptoms.", "doi": "10.1161/CIRCGENETICS.117.001737", "pmid": "28790154", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "CIRCGENETICS.117.001737"}], "notes": [], "created": "2018-01-09T20:54:59.536Z", "modified": "2021-06-21T15:34:34.341Z"}, {"entity": "publication", "iuid": "9b17776095cb4586a4ed84d38eaa61f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b17776095cb4586a4ed84d38eaa61f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b17776095cb4586a4ed84d38eaa61f7"}}, "title": "Bioinformatic processing of RAD\u2010seq data dramatically impacts downstream population genetic inference", "authors": [{"family": "Shafer", "given": "Aaron B A", "initials": "ABA"}, {"family": "Peart", "given": "Claire R", "initials": "CR"}, {"family": "Tusso", "given": "Sergio", "initials": "S"}, {"family": "Maayan", "given": "Inbar", "initials": "I"}, {"family": "Brelsford", "given": "Alan", "initials": "A"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "8", "issn": "2041-210X", "issue": "8", "pages": "907-917", "title": "Methods Ecol Evol", "issn-l": "2041-210X"}, "abstract": null, "doi": "10.1111/2041-210x.12700", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Galapagos sea lion resequencing", "key": "PRJNA349123"}, {"db": "Dryad", "description": "Data from: Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference", "key": "https://doi.org/10.5061/dryad.q14c1"}, {"db": "Dryad", "description": "Data from: A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them", "key": "https://doi.org/10.5061/dryad.8kn8c.2"}, {"db": "Assembly", "description": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000349705.1/", "key": "GCF_000349705.1"}, {"db": "Assembly", "description": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000321225.1/", "key": "GCF_000321225.1"}], "notes": [], "created": "2017-10-19T20:42:24.110Z", "modified": "2024-01-16T13:48:47.696Z"}, {"entity": "publication", "iuid": "6218fac1cf6840859cb5418044d20eb1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6218fac1cf6840859cb5418044d20eb1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6218fac1cf6840859cb5418044d20eb1"}}, "title": "Aeromonas salmonicida Growth in Response to Atlantic Salmon Mucins Differs between Epithelial Sites, Is Governed by Sialylated and N-Acetylhexosamine-Containing O-Glycans, and Is Affected by Ca2.", "authors": [{"family": "Padra", "given": "J\u00e1nos Tam\u00e1s", "initials": "JT"}, {"family": "Sundh", "given": "Henrik", "initials": "H"}, {"family": "Sundell", "given": "Kristina", "initials": "K"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Samuelsson", "given": "Tore", "initials": "T"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Lind\u00e9n", "given": "Sara K", "initials": "SK"}], "type": "journal article", "published": "2017-08-00", "journal": {"title": "Infect. Immun.", "issn": "1098-5522", "volume": "85", "issue": "8", "issn-l": "0019-9567"}, "abstract": "Aeromonas salmonicida causes furunculosis in salmonids and is a threat to Atlantic salmon aquaculture. The epithelial surfaces that the pathogen colonizes are covered by a mucus layer predominantly comprised of secreted mucins. By using mass spectrometry to identify mucin glycan structures with and without enzymatic removal of glycan residues, coupled to measurements of bacterial growth, we show here that the complex Atlantic salmon intestinal mucin glycans enhance A. salmonicida growth, whereas the more simple skin mucin glycans do not. Of the glycan residues present terminally on the salmon mucins, only N-acetylglucosamine (GlcNAc) enhances growth. Sialic acids, which have an abundance of 75% among terminal glycans from skin and of <50% among intestinal glycans, cannot be removed or used by A. salmonicida for growth-enhancing purposes, and they shield internal GlcNAc from utilization. A Ca2+ concentration above 0.1 mM is needed for A. salmonicida to be able to utilize mucins for growth-promoting purposes, and 10 mM further enhances both A. salmonicida growth in response to mucins and binding of the bacterium to mucins. In conclusion, GlcNAc and sialic acids are important determinants of the A. salmonicida interaction with its host at the mucosal surface. Furthermore, since the mucin glycan repertoire affects pathogen growth, the glycan repertoire may be a factor to take into account during breeding and selection of strains for aquaculture.", "doi": "10.1128/IAI.00189-17", "pmid": "28533470", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "IAI.00189-17"}, {"db": "pmc", "key": "PMC5520437"}], "notes": [], "created": "2020-01-30T16:24:41.005Z", "modified": "2024-01-16T13:46:32.626Z"}, {"entity": "publication", "iuid": "00efcc10c8fe4acdb9bdc477e661536f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00efcc10c8fe4acdb9bdc477e661536f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00efcc10c8fe4acdb9bdc477e661536f"}}, "title": "A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.", "authors": [{"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Rasi", "given": "Chiara", "initials": "C"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Ali", "given": "Abir S", "initials": "AS"}, {"family": "Gr\u00f6nberg", "given": "Malin", "initials": "M"}, {"family": "Welin", "given": "Staffan", "initials": "S"}, {"family": "Sorbye", "given": "Halfdan", "initials": "H"}, {"family": "Gr\u00f8nb\u00e6k", "given": "Henning", "initials": "H"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Tiensuu Janson", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "24", "issn": "1479-6821", "issue": "8", "pages": "427-443", "title": "Endocr. Relat. Cancer", "issn-l": "1351-0088"}, "abstract": "The genetics behind predisposition to small intestinal neuroendocrine tumors (SI-NETs) is largely unknown, but there is growing awareness of a familial form of the disease. We aimed to identify germline mutations involved in the carcinogenesis of SI-NETs. The strategy included next-generation sequencing of exome- and/or whole-genome of blood DNA, and in selected cases, tumor DNA, from 24 patients from 15 families with the history of SI-NETs. We identified seven candidate mutations in six genes that were further studied using 215 sporadic SI-NET patients. The result was compared with the frequency of the candidate mutations in three control cohorts with a total of 35,688 subjects. A heterozygous variant causing an amino acid substitution p.(Gly396Asp) in the MutY DNA glycosylase gene (MUTYH) was significantly enriched in SI-NET patients (minor allele frequencies 0.013 and 0.003 for patients and controls respectively) and resulted in odds ratio of 5.09 (95% confidence interval 1.56-14.74; P value\u2009=\u20090.0038). We also found a statistically significant difference in age at diagnosis between familial and sporadic SI-NETs. MUTYH is involved in the protection of DNA from mutations caused by oxidative stress. The inactivation of this gene leads to specific increase of G:C-\u2009>\u2009T:A transversions in DNA sequence and has been shown to cause various cancers in humans and experimental animals. Our results suggest that p.(Gly396Asp) in MUTYH, and potentially other mutations in additional members of the same DNA excision-repair pathway (such as the OGG1 gene) might be involved in driving the tumorigenesis leading to familial and sporadic SI-NETs.", "doi": "10.1530/ERC-17-0196", "pmid": "28634180", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ERC-17-0196"}, {"db": "pmc", "key": "PMC5527373"}], "notes": [], "created": "2017-10-17T09:23:36.141Z", "modified": "2024-01-16T13:48:47.705Z"}, {"entity": "publication", "iuid": "878c25b1d7b24483baabfa5b17fc27db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/878c25b1d7b24483baabfa5b17fc27db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/878c25b1d7b24483baabfa5b17fc27db"}}, "title": "Dual action of bacteriocin PLNC8 \u03b1\u03b2 through inhibition of Porphyromonas gingivalis infection and promotion of cell proliferation.", "authors": [{"family": "Bengtsson", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Zhang", "given": "Boxi", "initials": "B"}, {"family": "Seleg\u00e5rd", "given": "Robert", "initials": "R"}, {"family": "Wiman", "given": "Emanuel", "initials": "E"}, {"family": "Aili", "given": "Daniel", "initials": "D"}, {"family": "Khalaf", "given": "Hazem", "initials": "H"}], "type": "journal article", "published": "2017-07-31", "journal": {"title": "Pathog Dis", "issn": "2049-632X", "volume": "75", "issue": "5", "issn-l": "2049-632X"}, "abstract": "Periodontitis is a chronic inflammatory disease that is characterised by accumulation of pathogenic bacteria, including Porphyromonas gingivalis, in periodontal pockets. The lack of effective treatments has emphasised in an intense search for alternative methods to prevent bacterial colonisation and disease progression. Bacteriocins are bacterially produced antimicrobial peptides gaining increased consideration as alternatives to traditional antibiotics. We show rapid permeabilisation and aggregation of P. gingivalis by the two-peptide bacteriocin PLNC8 \u03b1\u03b2. In a cell culture model, P. gingivalis was cytotoxic against gingival fibroblasts. The proteome profile of fibroblasts is severely affected by P. gingivalis, including induction of the ubiquitin-proteasome pathway. PLNC8 \u03b1\u03b2 enhanced the expression of growth factors and promoted cell proliferation, and suppressed proteins associated with apoptosis. PLNC8 \u03b1\u03b2 efficiently counteracted P. gingivalis-mediated cytotoxicity, increased expression of a large number of proteins and restored the levels of inflammatory mediators. In conclusion, we show that bacteriocin PLNC8 \u03b1\u03b2 displays dual effects by acting as a potent antimicrobial agent killing P. gingivalis and as a stimulatory factor promoting cell proliferation. We suggest preventive and therapeutical applications of PLNC8 \u03b1\u03b2 in periodontitis to supplement the host immune defence against P. gingivalis infection and support wound healing processes.", "doi": "10.1093/femspd/ftx064", "pmid": "28605543", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "3866614"}, {"db": "pmc", "key": "PMC5808647"}], "notes": [], "created": "2020-01-30T16:00:43.537Z", "modified": "2024-01-16T13:46:32.636Z"}, {"entity": "publication", "iuid": "ea1597d1311c489880b8fff89b458a5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea1597d1311c489880b8fff89b458a5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea1597d1311c489880b8fff89b458a5f"}}, "title": "Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain", "authors": [{"family": "Wallenhammar", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Anandapadamanaban", "given": "Madhanagopal", "initials": "M"}, {"family": "Lemak", "given": "Alexander", "initials": "A"}, {"family": "Mirabello", "given": "Claudio", "initials": "C"}, {"family": "Lundstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}], "type": "journal-article", "published": "2017-07-28", "journal": {"volume": "12", "issn": "1932-6203", "issue": "7", "pages": "e0181551", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0181551", "pmid": "28753623", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "PDB", "description": "NMR protein structure", "key": "5JPX"}, {"db": "Biological Magnetic Resonance Data Bank", "description": "1H, 15N and 13C resonance assignment", "key": "30075"}], "notes": [], "created": "2017-11-03T16:46:07.337Z", "modified": "2025-10-17T13:03:59.654Z"}, {"entity": "publication", "iuid": "7744ce583f08458c9b5c9c8dea19b02d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7744ce583f08458c9b5c9c8dea19b02d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7744ce583f08458c9b5c9c8dea19b02d"}}, "title": "Isoflavones and Rotenoids from the Leaves of Millettia oblata ssp. teitensis", "authors": [{"family": "Deyou", "given": "Tsegaye", "initials": "T"}, {"family": "Marco", "given": "Makungu", "initials": "M"}, {"family": "Heydenreich", "given": "Matthias", "initials": "M"}, {"family": "Pan", "given": "Fangfang", "initials": "F"}, {"family": "Gruhonjic", "given": "Amra", "initials": "A"}, {"family": "Fitzpatrick", "given": "Paul A", "initials": "PA"}, {"family": "Koch", "given": "Andreas", "initials": "A"}, {"family": "Derese", "given": "Solomon", "initials": "S"}, {"family": "Pelletier", "given": "Jerry", "initials": "J"}, {"family": "Rissanen", "given": "Kari", "initials": "K"}, {"family": "Yenesew", "given": "Abiy", "initials": "A"}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M"}], "type": "journal-article", "published": "2017-07-28", "journal": {"volume": "80", "issn": "1520-6025", "issue": "7", "pages": "2060-2066", "title": "J. Nat. Prod.", "issn-l": "0163-3864"}, "abstract": null, "doi": "10.1021/acs.jnatprod.7b00255", "pmid": "28665590", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T11:01:03.744Z", "modified": "2025-10-17T13:03:59.666Z"}, {"entity": "publication", "iuid": "4bce9e4e56a24b87b1fc941557a2ade8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bce9e4e56a24b87b1fc941557a2ade8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bce9e4e56a24b87b1fc941557a2ade8"}}, "title": "Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.", "authors": [{"family": "Redin", "given": "David", "initials": "D"}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "He", "given": "Mengxiao", "initials": "M"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2017-07-27", "journal": {"volume": "45", "issn": "1362-4962", "issue": "13", "pages": "e125", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable exploration of other forms of genetic variation; beyond studies of just nucleotide polymorphisms, such as compound heterozygosity and structural variations. Here we describe Droplet Barcode Sequencing, a novel approach for creating linked-read sequencing libraries by uniquely barcoding the information within single DNA molecules in emulsion droplets, without the aid of specialty reagents or microfluidic devices. Barcode generation and template amplification is performed simultaneously in a single enzymatic reaction, greatly simplifying the workflow and minimizing assay costs compared to alternative approaches. The method has been applied to phase multiple loci targeting all exons of the highly variable Human Leukocyte Antigen A (HLA-A) gene, with DNA from eight individuals present in the same assay. Barcode-based clustering of sequencing reads confirmed analysis of over 2000 independently assayed template molecules, with an average of 753 reads in support of called polymorphisms. Our results show unequivocal characterization of all alleles present, validated by correspondence against confirmed HLA database entries and haplotyping results from previous studies.", "doi": "10.1093/nar/gkx436", "pmid": "28525570", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3835310"}, {"db": "pmc", "key": "PMC5569991"}], "notes": [], "created": "2017-11-03T16:11:37.322Z", "modified": "2024-01-16T13:48:47.712Z"}, {"entity": "publication", "iuid": "fd87172e6f1e446c876e6805eeb45307", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd87172e6f1e446c876e6805eeb45307.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd87172e6f1e446c876e6805eeb45307"}}, "title": "PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.", "authors": [{"family": "K\u00e4mpe", "given": "A J", "initials": "AJ"}, {"family": "Costantini", "given": "A", "initials": "A"}, {"family": "M\u00e4kitie", "given": "R E", "initials": "RE"}, {"family": "J\u00e4ntti", "given": "N", "initials": "N"}, {"family": "Valta", "given": "H", "initials": "H"}, {"family": "M\u00e4yr\u00e4np\u00e4\u00e4", "given": "M", "initials": "M"}, {"family": "Kr\u00f6ger", "given": "H", "initials": "H"}, {"family": "Pekkinen", "given": "M", "initials": "M"}, {"family": "Taylan", "given": "F", "initials": "F"}, {"family": "Jiao", "given": "H", "initials": "H"}, {"family": "M\u00e4kitie", "given": "O", "initials": "O"}], "type": "journal article", "published": "2017-07-26", "journal": {"volume": null, "issn": "1433-2965", "issue": null, "title": "Osteoporos Int", "issn-l": "0937-941X"}, "abstract": "Altogether 95 children with primary bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Two children with multiple peripheral and spinal fractures and low BMD had novel disease-causing PLS3 variants. Children with milder phenotypes had no pathogenic variants. PLS3 screening is indicated in childhood-onset primary osteoporosis.\n\nThe study aimed to determine the role of pathogenic PLS3 variants in children's bone fragility and to elucidate the associated phenotypic features.\n\nTwo cohorts of children with bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Cohort I comprised 31 patients with childhood-onset primary osteoporosis of unknown etiology. Cohort II comprised 64 children who had sustained multiple fractures but were otherwise healthy. Clinical and radiological data were reviewed. Peripheral blood DNA was Sanger sequenced for coding exons and flanking intronic regions of PLS3.\n\nIn two patients of cohort I, where other common genetic causes had been excluded, we identified two novel disease-causing PLS3 variants. Patient 1 was a male with bilateral femoral fractures at 10\u00a0years, low BMD (Z-score -4.1; 18\u00a0years), and multiple vertebral compression fractures. He had a novel nonsense variant in PLS3. Patient 2 was a girl with multiple long bone and vertebral fractures and low BMD (Z-score -6.6 at 6\u00a0years). She had a de novo missense variant in PLS3; whole exome sequencing and array-CGH identified no other genetic causes. Iliac crest bone biopsies confirmed low-turnover osteoporosis in both patients. In cohort II, no pathogenic PLS3 variants were identified in any of the subjects.\n\nTwo novel disease-causing variants in PLS3 were identified in a boy and a girl with multiple peripheral and spinal fractures and very low BMD while no pathogenic variants were identified in children with less severe skeletal fragility. PLS3 screening is warranted in male and female patients with childhood-onset primary osteoporosis.", "doi": "10.1007/s00198-017-4150-9", "pmid": "28748388", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00198-017-4150-9"}, {"db": "pmc", "key": "PMC5624974"}], "notes": [], "created": "2017-11-03T16:21:20.042Z", "modified": "2024-01-16T13:48:47.719Z"}, {"entity": "publication", "iuid": "9a4725f904ef40cc9b59e855208cec4d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a4725f904ef40cc9b59e855208cec4d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a4725f904ef40cc9b59e855208cec4d"}}, "title": "Biophysical characterization of the calmodulin-like domain of Plasmodium falciparum calcium dependent protein kinase 3", "authors": [{"family": "Andresen", "given": "Cecilia", "initials": "C"}, {"family": "Niklasson", "given": "Markus", "initials": "M"}, {"family": "Cassman Ekl\u00f6f", "given": "Sofie", "initials": "S"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lundstr\u00f6m", "given": "Patrik", "initials": "P"}], "type": "journal-article", "published": "2017-07-26", "journal": {"volume": "12", "issn": "1932-6203", "issue": "7", "pages": "e0181721", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0181721", "pmid": "28746405", "labels": {"Protein Science Facility (PSF)": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-23T06:36:29.890Z", "modified": "2025-10-17T13:03:59.677Z"}, {"entity": "publication", "iuid": "fab4dc02905244e1b74ac43991c94aef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fab4dc02905244e1b74ac43991c94aef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fab4dc02905244e1b74ac43991c94aef"}}, "title": "About structural changes of lignin during kraft cooking and the kinetics of delignification", "authors": [{"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Hasani", "given": "Merima", "initials": "M"}, {"family": "Dang", "given": "Binh", "initials": "B"}, {"family": "Mayzel", "given": "Maxim", "initials": "M"}, {"family": "Theliander", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-07-26", "journal": {"volume": "71", "issn": "1437-434X", "issue": "7-8", "pages": "545-553", "title": "Holzforschung", "issn-l": null}, "abstract": null, "doi": "10.1515/hf-2016-0190", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T10:46:27.639Z", "modified": "2025-10-17T13:03:59.688Z"}, {"entity": "publication", "iuid": "216ae64b6c9f43328ad351f4c4320330", "links": {"self": {"href": "https://publications.scilifelab.se/publication/216ae64b6c9f43328ad351f4c4320330.json"}, "display": {"href": "https://publications.scilifelab.se/publication/216ae64b6c9f43328ad351f4c4320330"}}, "title": "Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis.", "authors": [{"family": "Zandian", "given": "A", "initials": "A"}, {"family": "Wing\u00e5rd", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "H", "initials": "H"}, {"family": "Sj\u00f6stedt", "given": "E", "initials": "E"}, {"family": "Johansson", "given": "D X", "initials": "DX"}, {"family": "Just", "given": "D", "initials": "D"}, {"family": "Hellstr\u00f6m", "given": "C", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "M", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "J M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "A", "initials": "A"}, {"family": "Norbeck", "given": "O", "initials": "O"}, {"family": "Owe-Larsson", "given": "B", "initials": "B"}, {"family": "Nilsson", "given": "P", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Persson", "given": "M A A", "initials": "MAA"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "7", "issn": "2158-3188", "issue": "7", "pages": "e1177", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "Immunological and inflammatory reactions have been suggested to have a role in the development of schizophrenia, a hypothesis that has recently been supported by genetic data. The aim of our study was to perform an unbiased search for autoantibodies in patients with a first psychotic episode, and to explore the association between any seroreactivity and the development of a Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV) disorder characterized by chronic or relapsing psychotic symptoms. We collected plasma samples from 53 patients when they were treated for their first-episode psychosis, and 41 non-psychotic controls, after which the patients were followed for a mean duration of 7 years. Thirty patients were diagnosed with schizophrenia, delusional disorder, schizoaffective disorder, bipolar disorder or a long-term unspecified nonorganic psychosis during follow-up, whereas 23 patients achieved complete remission. At the end of follow-up, plasma samples were analyzed for IgG reactivity to 2304 fragments of human proteins using a multiplexed affinity proteomic technique. Eight patient samples showed autoreactivity to the N-terminal fragment of the PAGE (P antigen) protein family (PAGE2B/PAGE2/PAGE5), whereas no such autoreactivity was seen among the controls. PAGE autoreactivity was associated with a significantly increased risk of being diagnosed with schizophrenia during follow-up (odds ratio 6.7, relative risk 4.6). An immunohistochemistry analysis using antisera raised against the N-terminal fragment stained an unknown extracellular target in human cortical brain tissue. Our findings suggest that autoreactivity to the N-terminal portion of the PAGE protein family is associated with schizophrenia in a subset of patients with first-episode psychosis.", "doi": "10.1038/tp.2017.160", "pmid": "28742074", "labels": {"Tissue Profiling": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "tp2017160"}, {"db": "pmc", "key": "PMC5538130"}], "notes": [], "created": "2017-11-02T11:35:53.436Z", "modified": "2021-07-08T13:44:33.083Z"}, {"entity": "publication", "iuid": "3da58343c0134a8797edd61438e049be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3da58343c0134a8797edd61438e049be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3da58343c0134a8797edd61438e049be"}}, "title": "Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.", "authors": [{"family": "Neogi", "given": "Ujjwal", "initials": "U"}, {"family": "Siddik", "given": "Abu Bakar", "initials": "AB"}, {"family": "Kalaghatgi", "given": "Prabhav", "initials": "P"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Bratt", "given": "G\u00f6ran", "initials": "G"}, {"family": "Marrone", "given": "Gaetano", "initials": "G"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "6371", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A temporal increase in non-B subtypes has earlier been described in Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex and unique recombinant forms (URFs) if the epidemics converge. In the present study, we performed subtyping using four automated tools and phylogenetic analysis by RAxML of pol gene sequences (n\u2009=\u20095246) and HIV-1 near full-length genome (HIV-NFLG) sequences (n\u2009=\u2009104). A CD4+ T-cell decline trajectory algorithm was used to estimate time of HIV infection. Transmission clusters were identified using the family-joining method. The analysis of HIV-NFLG and pol gene described 10.6% (11/104) and 2.6% (137/5246) of the strains as URFs, respectively. An increasing trend of URFs was observed in recent years by both approaches (p\u2009=\u20090\u00b70082; p\u2009<\u20090\u00b70001). Transmission cluster analysis using the pol gene of all URFs identified 14 clusters with two to eight sequences. Larger transmission clusters of URFs (BF1 and 01B) were observed among MSM who mostly were sero-diagnosed in recent time. Understanding the increased appearance and transmission of URFs in recent years could have importance for public health interventions and the use of HIV-NFLG would provide better statistical support for such assessments.", "doi": "10.1038/s41598-017-06860-2", "pmid": "28744024", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-06860-2"}, {"db": "pmc", "key": "PMC5527090"}], "notes": [], "created": "2018-01-10T09:44:11.655Z", "modified": "2020-01-21T13:56:10.864Z"}, {"entity": "publication", "iuid": "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": "214fed5eee6944f5813ceee80a079e90", "links": {"self": {"href": "https://publications.scilifelab.se/publication/214fed5eee6944f5813ceee80a079e90.json"}, "display": {"href": "https://publications.scilifelab.se/publication/214fed5eee6944f5813ceee80a079e90"}}, "title": "Mass Spectrometry Imaging proves differential absorption profiles of well-characterised permeability markers along the crypt-villus axis.", "authors": [{"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Peric", "given": "Alexandra", "initials": "A"}, {"family": "Strimfors", "given": "Marie", "initials": "M"}, {"family": "Goodwin", "given": "Richard J A", "initials": "RJA"}, {"family": "Hayes", "given": "Martin A", "initials": "MA"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "Hilgendorf", "given": "Constanze", "initials": "C"}], "type": "journal article", "published": "2017-07-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "6352", "issn-l": "2045-2322"}, "abstract": "Knowledge about the region-specific absorption profiles from the gastrointestinal tract of orally administered drugs is a critical factor guiding dosage form selection in drug development. We have used a novel approach to study three well-characterized permeability and absorption marker drugs in the intestine. Propranolol and metoprolol (highly permeable compounds) and atenolol (low-moderate permeability compound) were orally co-administered to rats. The site of drug absorption was revealed by high spatial resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and complemented by quantitative measurement of drug concentration in tissue homogenates. MALDI-MSI identified endogenous molecular markers that illustrated the villi structures and confirmed the different absorption sites assigned to histological landmarks for the three drugs. Propranolol and metoprolol showed a rapid absorption and shorter transit distance in contrast to atenolol, which was absorbed more slowly from more distal sites. This study provides novel insights into site specific absorption for each of the compounds along the crypt-villus axis, as well as confirming a proximal-distal absorption gradient along the intestine. The combined analytical approach allowed the quantification and spatial resolution of drug distribution in the intestine and provided experimental evidence for the suggested absorption behaviour of low and highly permeable compounds.", "doi": "10.1038/s41598-017-06583-4", "pmid": "28743866", "labels": {"Spatial Mass Spectrometry": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-06583-4"}, {"db": "pmc", "key": "PMC5526999"}], "notes": [], "created": "2020-01-24T08:59:38.975Z", "modified": "2021-05-17T08:47:18.642Z"}, {"entity": "publication", "iuid": "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": "887eb366a308433fb9a6011acbce974c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/887eb366a308433fb9a6011acbce974c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/887eb366a308433fb9a6011acbce974c"}}, "title": "Continuous immunotypes describe human immune variation and predict diverse responses.", "authors": [{"family": "Kaczorowski", "given": "Kevin J", "initials": "KJ"}, {"family": "Shekhar", "given": "Karthik", "initials": "K"}, {"family": "Nkulikiyimfura", "given": "Dieudonn\u00e9", "initials": "D", "orcid": "0000-0002-6981-2053", "researcher": {"href": "https://publications.scilifelab.se/researcher/6af6961b78de4d0b96b011009cccc14c.json"}}, {"family": "Dekker", "given": "Cornelia L", "initials": "CL"}, {"family": "Maecker", "given": "Holden", "initials": "H", "orcid": "0000-0003-0795-9946", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3bcc923a42f4137a30d6ba7cb850d7f.json"}}, {"family": "Davis", "given": "Mark M", "initials": "MM"}, {"family": "Chakraborty", "given": "Arup K", "initials": "AK"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2017-07-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "114", "issue": "30", "pages": "E6097-E6106"}, "abstract": "The immune system consists of many specialized cell populations that communicate with each other to achieve systemic immune responses. Our analyses of various measured immune cell population frequencies in healthy humans and their responses to diverse stimuli show that human immune variation is continuous in nature, rather than characterized by discrete groups of similar individuals. We show that the same three key combinations of immune cell population frequencies can define an individual's immunotype and predict a diverse set of functional responses to cytokine stimulation. We find that, even though interindividual variations in specific cell population frequencies can be large, unrelated individuals of younger age have more homogeneous immunotypes than older individuals. Across age groups, cytomegalovirus seropositive individuals displayed immunotypes characteristic of older individuals. The conceptual framework for defining immunotypes suggested by our results could guide the development of better therapies that appropriately modulate collective immunotypes, rather than individual immune components.", "doi": "10.1073/pnas.1705065114", "pmid": "28696306", "labels": {"Cellular Immunomonitoring": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC5544312"}, {"db": "pii", "key": "1705065114"}], "notes": "Brodin Lab", "created": "2017-10-04T13:41:22.408Z", "modified": "2023-11-28T12:54:43.512Z"}, {"entity": "publication", "iuid": "4d52df4d173f48a3bb793b23674dbb2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d52df4d173f48a3bb793b23674dbb2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d52df4d173f48a3bb793b23674dbb2a"}}, "title": "Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2\u03b1 to tumor suppression.", "authors": [{"family": "Westerlund", "given": "Isabelle", "initials": "I"}, {"family": "Shi", "given": "Yao", "initials": "Y"}, {"family": "Toskas", "given": "Konstantinos", "initials": "K"}, {"family": "Fell", "given": "Stuart M", "initials": "SM"}, {"family": "Li", "given": "Shuijie", "initials": "S"}, {"family": "Surova", "given": "Olga", "initials": "O"}, {"family": "S\u00f6dersten", "given": "Erik", "initials": "E"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Nyman", "given": "Ulrika", "initials": "U"}, {"family": "Schlisio", "given": "Susanne", "initials": "S"}, {"family": "Holmberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "114", "issn": "1091-6490", "issue": "30", "pages": "E6137-E6146", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Neuroblastoma is a pediatric cancer characterized by variable outcomes ranging from spontaneous regression to life-threatening progression. High-risk neuroblastoma patients receive myeloablative chemotherapy with hematopoietic stem-cell transplant followed by adjuvant retinoid differentiation treatment. However, the overall survival remains low; hence, there is an urgent need for alternative therapeutic approaches. One feature of high-risk neuroblastoma is the high level of DNA methylation of putative tumor suppressors. Combining the reversibility of DNA methylation with the differentiation-promoting activity of retinoic acid (RA) could provide an alternative strategy to treat high-risk neuroblastoma. Here we show that treatment with the DNA-demethylating drug 5-Aza-deoxycytidine (AZA) restores high-risk neuroblastoma sensitivity to RA. Combined systemic distribution of AZA and RA impedes tumor growth and prolongs survival. Genome-wide analysis of treated tumors reveals that this combined treatment rapidly induces a HIF2\u03b1-associated hypoxia-like transcriptional response followed by an increase in neuronal gene expression and a decrease in cell-cycle gene expression. A small-molecule inhibitor of HIF2\u03b1 activity diminishes the tumor response to AZA+RA treatment, indicating that the increase in HIF2\u03b1 levels is a key component in tumor response to AZA+RA. The link between increased HIF2\u03b1 levels and inhibited tumor growth is reflected in large neuroblastoma patient datasets. Therein, high levels of HIF2\u03b1, but not HIF1\u03b1, significantly correlate with expression of neuronal differentiation genes and better prognosis but negatively correlate with key features of high-risk tumors, such as MYCN amplification. Thus, contrary to previous studies, our findings indicate an unanticipated tumor-suppressive role for HIF2\u03b1 in neuroblastoma.", "doi": "10.1073/pnas.1700655114", "pmid": "28696319", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1700655114"}, {"db": "pmc", "key": "PMC5544284"}], "notes": [], "created": "2018-01-10T09:44:13.665Z", "modified": "2020-01-21T13:56:10.878Z"}, {"entity": "publication", "iuid": "9fde1a0d154342d4827703089345f6f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fde1a0d154342d4827703089345f6f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fde1a0d154342d4827703089345f6f9"}}, "title": "Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney.", "authors": [{"family": "Wain", "given": "Louise V", "initials": "LV"}, {"family": "Vaez", "given": "Ahmad", "initials": "A"}, {"family": "Jansen", "given": "Rick", "initials": "R"}, {"family": "Joehanes", "given": "Roby", "initials": "R"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Erzurumluoglu", "given": "A Mesut", "initials": "AM"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Cabrera", "given": "Claudia P", "initials": "CP"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Verwoert", "given": "Germaine C", "initials": "GC"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Esko", "given": "Tonu", "initials": "T"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Kutalik", "given": "Zoltan", "initials": "Z"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Shrine", "given": "Nick", "initials": "N"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Ried", "given": "Janina S", "initials": "JS"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Traglia", "given": "Michela", "initials": "M"}, {"family": "Havulinna", "given": "Aki S", "initials": "AS"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "S\u00f5ber", "given": "Siim", "initials": "S"}, {"family": "Vuckovic", "given": "Dragana", "initials": "D"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Del Greco M", "given": "Fabiola", "initials": "F"}, {"family": "Ayers", "given": "Kristin L", "initials": "KL"}, {"family": "Marrugat", "given": "Jaume", "initials": "J"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "Niiranen", "given": "Teemu", "initials": "T"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Gandin", "given": "Ilaria", "initials": "I"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Shah", "given": "Nabi", "initials": "N"}, {"family": "de Borst", "given": "Martin H", "initials": "MH"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Prins", "given": "Bram P", "initials": "BP"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Oldmeadow", "given": "Christopher", "initials": "C"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Abedi", "given": "Maryam", "initials": "M"}, {"family": "Barbieri", "given": "Caterina M", "initials": "CM"}, {"family": "Barnes", "given": "Michael R", "initials": "MR"}, {"family": "Batini", "given": "Chiara", "initials": "C"}, {"family": "Beilby", "given": "John", "initials": "J"}, {"family": "Blake", "given": "Tineka", "initials": "T"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Brown", "given": "Morris", "initials": "M"}, {"family": "Brumat", "given": "Marco", "initials": "M"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M"}, {"family": "Collins", "given": "Francis", "initials": "F"}, {"family": "Connell", "given": "John", "initials": "J"}, {"family": "Cordell", "given": "Heather J", "initials": "HJ"}, {"family": "Damman", "given": "Jeffrey J", "initials": "JJ"}, {"family": "Davies", "given": "Gail", 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"JH"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "James", "given": "Alan", "initials": "A"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Palmas", "given": "Walter", "initials": "W"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chakravarti", "given": "Aravinda", "initials": "A"}, {"family": "Knight", "given": "Joanne", "initials": "J"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Ehret", "given": "Georg B", "initials": "GB"}], "type": "journal article", "published": "2017-07-24", "journal": {"volume": "70", "issn": "1524-4563", "issue": "3", "pages": "e4-e19", "title": "Hypertension", "issn-l": "0194-911X"}, "abstract": "Elevated blood pressure is a major risk factor for cardiovascular disease and has a substantial genetic contribution. Genetic variation influencing blood pressure has the potential to identify new pharmacological targets for the treatment of hypertension. To discover additional novel blood pressure loci, we used 1000 Genomes Project-based imputation in 150 134 European ancestry individuals and sought significant evidence for independent replication in a further 228 245 individuals. We report 6 new signals of association in or near HSPB7, TNXB, LRP12, LOC283335, SEPT9, and AKT2, and provide new replication evidence for a further 2 signals in EBF2 and NFKBIA Combining large whole-blood gene expression resources totaling 12 607 individuals, we investigated all novel and previously reported signals and identified 48 genes with evidence for involvement in blood pressure regulation that are significant in multiple resources. Three novel kidney-specific signals were also detected. These robustly implicated genes may provide new leads for therapeutic innovation.", "doi": "10.1161/HYPERTENSIONAHA.117.09438", "pmid": "28739976", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "HYPERTENSIONAHA.117.09438"}, {"db": "pmc", "key": "PMC5783787"}, {"db": "mid", "key": "NIHMS902240"}], "notes": [], "created": "2018-01-09T13:55:55.847Z", "modified": "2021-06-21T15:30:31.426Z"}, {"entity": "publication", "iuid": "2fc4e31b250e495ca1b009d046c37ce5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fc4e31b250e495ca1b009d046c37ce5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fc4e31b250e495ca1b009d046c37ce5"}}, "title": "Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.", "authors": [{"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Demissie", "given": 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"initials": "ST"}, {"family": "Tarnopolsky", "given": "Mark A", "initials": "MA"}, {"family": "Thompson", "given": "Patricia", "initials": "P"}, {"family": "Thomson", "given": "Cynthia A", "initials": "CA"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Tranah", "given": "Gregory J", "initials": "GJ"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "Verma", "given": "Arjun", "initials": "A"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wactawski-Wende", "given": "Jean", "initials": "J"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Welch", "given": "Ryan", "initials": "R"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Williams", "given": "Frances M K", "initials": "FMK"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wright", "given": "Nicole C", "initials": "NC"}, {"family": "Xie", "given": "Weijia", "initials": "W"}, {"family": "Yu", "given": "Lei", "initials": "L"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Econs", "given": "Michael J", "initials": "MJ"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Ossowski", "given": "Vicky", "initials": "V"}, {"family": "Waterworth", "given": "Dawn", "initials": "D"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}], "type": "journal article", "published": "2017-07-19", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "80", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 \u00d7 10 -8) or suggestively genome wide (p < 2.3 \u00d7 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.Lean body mass is a highly heritable trait and is associated with various health conditions. Here, Kiel and colleagues perform a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.", "doi": "10.1038/s41467-017-00031-7", "pmid": "28724990", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00031-7"}, {"db": "pmc", "key": "PMC5517526"}], "notes": [], "created": "2018-01-09T13:55:56.946Z", "modified": "2021-06-21T14:59:44.927Z"}, {"entity": "publication", "iuid": "a782b516dd7b4b838b69f46f09a13e7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a782b516dd7b4b838b69f46f09a13e7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a782b516dd7b4b838b69f46f09a13e7d"}}, "title": "Tuning Metabolome Coverage in Reversed Phase LC-MS Metabolomics of MeOH Extracted Samples Using the Reconstitution Solvent Composition.", "authors": [{"family": "Lindahl", "given": "Anna", "initials": "A"}, {"family": "S\u00e4\u00e4f", "given": "Siv", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Nordstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0003-3676-817X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b1803a3f7624f0d82abd552448bdaed.json"}}], "type": "journal article", "published": "2017-07-18", "journal": {"volume": "89", "issn": "1520-6882", "issue": "14", "pages": "7356-7364", "title": "Anal. Chem.", "issn-l": "0003-2700"}, "abstract": "Considering the physicochemical diversity of the metabolome, untargeted metabolomics will inevitably discriminate against certain compound classes. Efforts are nevertheless made to maximize the metabolome coverage. Contrary to the main steps of a typical liquid chromatography-mass spectrometry (LC-MS) metabolomics workflow, such as metabolite extraction, the sample reconstitution step has not been optimized for maximal metabolome coverage. This sample concentration step typically occurs after metabolite extraction, when dried samples are reconstituted in a solvent for injection on column. The aim of this study was to evaluate the impact of the sample reconstitution solvent composition on metabolome coverage in untargeted LC-MS metabolomics. Lysogeny Broth medium samples reconstituted in MeOH/H 2O ratios ranging from 0 to 100% MeOH and analyzed with untargeted reversed phase LC-MS showed that the highest number of metabolite features (n = 1500) was detected in samples reconstituted in 100% H2O. As compared to a commonly used reconstitution solvent mixture of 50/50 MeOH/H2O, our results indicate that the small fraction of compounds increasing in peak area response by the addition of MeOH to H2O, 5%, is outweighed by the fraction of compounds with decreased response, 57%. We evaluated our results on human serum samples from lymphoma patients and healthy control subjects. Reconstitution in 100% H2O resulted in a higher number of significant metabolites discriminating between these two groups than both 50% and 100% MeOH. These findings show that the sample reconstitution step has a clear impact on the metabolome coverage of MeOH extracted biological samples, highlighting the importance of the reconstitution solvent composition for untargeted discovery metabolomics.", "doi": "10.1021/acs.analchem.7b00475", "pmid": "28613827", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Service", "Swedish Metabolomics Centre": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-12-05T16:14:27.211Z", "modified": "2025-10-17T13:03:18.634Z"}, {"entity": "publication", "iuid": "762da9d75b1c48ae9ed377c0491cee2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/762da9d75b1c48ae9ed377c0491cee2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/762da9d75b1c48ae9ed377c0491cee2a"}}, "title": "Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3", "authors": [{"family": "Bersani", "given": "Cinzia", "initials": "C"}, {"family": "Sivars", "given": "Lars", "initials": "L"}, {"family": "Haeggblom", "given": "Linnea", "initials": "L"}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Mints", "given": "Michael", "initials": "M"}, {"family": "\u00c4hrlund-Richter", "given": "Andreas", "initials": "A"}, {"family": "Tertipis", "given": "Nikolaos", "initials": "N"}, {"family": "Munck-Wikland", "given": "Eva", "initials": "E"}, {"family": "N\u00e4sman", "given": "Anders", "initials": "A"}, {"family": "Ramqvist", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Dalianis", "given": "Tina", "initials": "T"}], "type": "journal-article", "published": "2017-07-18", "journal": {"volume": null, "issn": "1949-2553", "issue": null, "pages": null, "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": null, "doi": "10.18632/oncotarget.15240", "pmid": "28525363", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T15:01:37.369Z", "modified": "2020-01-21T13:53:22.273Z"}, {"entity": "publication", "iuid": "7783b21966b7491599b406ca7b2ba22a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7783b21966b7491599b406ca7b2ba22a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7783b21966b7491599b406ca7b2ba22a"}}, "title": "Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.", "authors": [{"family": "Morud", "given": "Julia", "initials": "J"}, {"family": "Ashouri", "given": "Arghavan", "initials": "A"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Ericson", "given": "Mia", "initials": "M"}, {"family": "S\u00f6derpalm", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "12", "issn": "1932-6203", "issue": "7", "pages": "e0181084", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Alcohol use disorder is a chronic relapsing brain disorder and a global health issue. Prolonged high alcohol consumption increases the risk for dependence development, a complex state that includes progressive alterations in brain function. The molecular mechanisms behind these changes remain to be fully disclosed, but several genes show altered expression in various regions of the rat brain even after modest alcohol exposure. The present study utilizes whole-transcriptome sequencing (RNA-seq) to investigate expression changes in the brain nucleus accumbens (NAc), an area of particular interest in addictive disorders, of alcohol consuming rats. The impact on gene expression after eight weeks of moderate voluntary alcohol consumption or voluntary consumption combined with forced excessive exposure was explored in two separate experiments. The results point to a lack of strong and consistent expression alterations in the NAc after alcohol exposure, suggesting that transcriptional effects of alcohol are weak or transient, or occur primarily in brain regions other than NAc.", "doi": "10.1371/journal.pone.0181084", "pmid": "28715440", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-11371"}, {"db": "pmc", "key": "PMC5513432"}, {"db": "GEO", "description": "Genome-wide analysis of nucleus accumbens gene expression after ethanol consumption in rat", "key": "GSE73627"}], "notes": [], "created": "2017-11-03T16:20:57.403Z", "modified": "2024-01-16T13:48:47.727Z"}, {"entity": "publication", "iuid": "c3577bba83a74b17857adfd5789c0771", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3577bba83a74b17857adfd5789c0771.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3577bba83a74b17857adfd5789c0771"}}, "title": "Transancestral mapping and genetic load in systemic lupus erythematosus.", "authors": [{"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Ainsworth", "given": "Hannah C", "initials": "HC"}, {"family": "Cunninghame Graham", "given": "Deborah S", "initials": "DS"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Comeau", "given": "Mary E", "initials": "ME"}, {"family": "Marion", "given": "Miranda C", "initials": "MC"}, {"family": "Howard", "given": "Timothy D", "initials": "TD"}, {"family": "Ramos", "given": "Paula S", "initials": "PS"}, {"family": "Croker", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0002-6292-4132", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdd33d806494a78901e9f697d49bfe1.json"}}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC"}, {"family": "Acevedo-V\u00e1squez", "given": "Eduardo M", "initials": "EM"}, {"family": "Alarc\u00f3n", "given": "Graciela S", "initials": "GS"}, {"family": "Babini", "given": "Alejandra M", "initials": "AM"}, {"family": "Baca", "given": "Vicente", "initials": "V"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Berbotto", "given": "Guillermo A", "initials": "GA"}, {"family": "Bijl", "given": "Marc", "initials": "M"}, {"family": "Brown", "given": "Elizabeth E", "initials": "EE"}, {"family": "Brunner", "given": "Hermine I", "initials": "HI"}, {"family": "Cardiel", "given": "Mario H", "initials": "MH"}, {"family": "Catoggio", "given": "Luis", "initials": "L", "orcid": "0000-0002-4047-4863", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbd0233f695c411cb64194cd0900d4bb.json"}}, {"family": "Cervera", "given": "Ricard", "initials": "R"}, {"family": "Cucho-Venegas", "given": "Jorge M", "initials": "JM"}, {"family": "Dahlqvist", "given": "Solbritt Rantap\u00e4\u00e4", "initials": "SR"}, {"family": "D'Alfonso", "given": "Sandra", "initials": "S"}, {"family": "Da Silva", "given": "Berta Martins", "initials": "BM"}, {"family": "de la R\u00faa Figueroa", "given": "I\u00f1igo", "initials": "I"}, {"family": "Doria", "given": "Andrea", "initials": "A"}, {"family": "Edberg", "given": "Jeffrey C", "initials": "JC"}, {"family": "Endreffy", "given": "Em\u0151ke", "initials": "E"}, {"family": "Esquivel-Valerio", "given": "Jorge A", "initials": "JA"}, {"family": "Fortin", "given": "Paul R", "initials": "PR"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Frosteg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Garc\u00eda", "given": "Mercedes A", "initials": "MA"}, {"family": "de la Torre", "given": "Ignacio Garc\u00eda", "initials": "IG"}, {"family": "Gilkeson", "given": "Gary S", "initials": "GS"}, {"family": "Gladman", "given": "Dafna D", "initials": "DD"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Guthridge", "given": "Joel M", "initials": "JM"}, {"family": "Huggins", "given": "Jennifer L", "initials": "JL"}, {"family": "James", "given": "Judith A", "initials": "JA"}, {"family": "Kallenberg", "given": "Cees G M", "initials": "CGM"}, {"family": "Kamen", "given": "Diane L", "initials": "DL"}, {"family": "Karp", "given": "David R", "initials": "DR"}, {"family": "Kaufman", "given": "Kenneth M", "initials": "KM"}, {"family": "Kottyan", "given": "Leah C", "initials": "LC", "orcid": "0000-0003-3979-2220", "researcher": {"href": "https://publications.scilifelab.se/researcher/661ee875ca2445cb96d30e95bb8a7728.json"}}, {"family": "Kov\u00e1cs", "given": "L\u00e1szl\u00f3", "initials": "L"}, {"family": "Laustrup", "given": "Helle", "initials": "H"}, {"family": "Lauwerys", "given": "Bernard R", "initials": "BR"}, {"family": "Li", "given": "Quan-Zhen", "initials": "QZ"}, {"family": "Maradiaga-Cece\u00f1a", "given": "Marco A", "initials": "MA"}, {"family": "Mart\u00edn", "given": "Javier", "initials": "J"}, {"family": "McCune", "given": "Joseph M", "initials": "JM"}, {"family": "McWilliams", "given": "David R", "initials": "DR"}, {"family": "Merrill", "given": "Joan T", "initials": "JT"}, {"family": "Miranda", "given": "Pedro", "initials": "P"}, {"family": "Moctezuma", "given": "Jos\u00e9 F", "initials": "JF"}, {"family": "Nath", "given": "Swapan K", "initials": "SK"}, {"family": "Niewold", "given": "Timothy B", "initials": "TB"}, {"family": "Orozco", "given": "Lorena", "initials": "L"}, {"family": "Ortego-Centeno", "given": "Norberto", "initials": "N"}, {"family": "Petri", "given": "Michelle", "initials": "M"}, {"family": "Pineau", "given": "Christian A", "initials": "CA"}, {"family": "Pons-Estel", "given": "Bernardo A", "initials": "BA"}, {"family": "Pope", "given": "Janet", "initials": "J"}, {"family": "Raj", "given": "Prithvi", "initials": "P"}, {"family": "Ramsey-Goldman", "given": "Rosalind", "initials": "R"}, {"family": "Reveille", "given": "John D", "initials": "JD"}, {"family": "Russell", "given": "Laurie P", "initials": "LP"}, {"family": "Sabio", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Aguilar-Salinas", "given": "Carlos A", "initials": "CA"}, {"family": "Scherbarth", "given": "Hugo R", "initials": "HR"}, {"family": "Scorza", "given": "Raffaella", "initials": "R"}, {"family": "Seldin", "given": "Michael F", "initials": "MF"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Thompson", "given": "Susan D", "initials": "SD"}, {"family": "Toloza", "given": "Sergio M A", "initials": "SMA"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "Tusi\u00e9-Luna", "given": "Teresa", "initials": "T"}, {"family": "Vasconcelos", "given": "Carlos", "initials": "C"}, {"family": "Vil\u00e1", "given": "Luis M", "initials": "LM"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Weisman", "given": "Michael H", "initials": "MH"}, {"family": "Wither", "given": "Joan E", "initials": "JE"}, {"family": "Bhangale", "given": "Tushar", "initials": "T"}, {"family": "Oksenberg", "given": "Jorge R", "initials": "JR"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Gregersen", "given": "Peter K", "initials": "PK"}, {"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": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Jacob", "given": "Chaim O", "initials": "CO"}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Tsao", "given": "Betty P", "initials": "BP"}, {"family": "Schanberg", "given": "Laura E", "initials": "LE"}, {"family": "Behrens", "given": "Timothy W", "initials": "TW"}, {"family": "Silverman", "given": "Earl D", "initials": "ED"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}, {"family": "Kimberly", "given": "Robert P", "initials": "RP"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Wakeland", "given": "Edward K", "initials": "EK"}, {"family": "Graham", "given": "Robert R", "initials": "RR"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "16021", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (\u223c50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 \u00d7 10-8), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.", "doi": "10.1038/ncomms16021", "pmid": "28714469", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms16021"}, {"db": "pmc", "key": "PMC5520018"}], "notes": [], "created": "2017-10-25T15:18:21.921Z", "modified": "2024-01-16T13:48:47.734Z"}, {"entity": "publication", "iuid": "486b9a2053714ec0b814295e77d2e76d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/486b9a2053714ec0b814295e77d2e76d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/486b9a2053714ec0b814295e77d2e76d"}}, "title": "Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.", "authors": [{"family": "Larsson", "given": "Chatarina", "initials": "C"}, {"family": "Ali", "given": "Muhammad Akhtar", "initials": "MA"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Lindroth", "given": "Anders M", "initials": "AM"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "17", "issn": "1471-2407", "issue": "1", "pages": "487", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in human cancer cells.\n\nWe engineered human DIP2C knockout cells by genome editing in cancer cells. The growth properties of the engineered cells were characterised and transcriptome and methylation analyses were carried out to identify pathways deregulated by inactivation of DIP2C. Effects on cell death pathways and epithelial-mesenchymal transition traits were studied based on the results from expression profiling.\n\nKnockout of DIP2C in RKO cells resulted in cell enlargement and growth retardation. Expression profiling revealed 780 genes for which the expression level was affected by the loss of DIP2C, including the tumour-suppressor encoding CDKN2A gene, the epithelial-mesenchymal transition (EMT) regulator-encoding ZEB1, and CD44 and CD24 that encode breast cancer stem cell markers. Analysis of DNA methylation showed more than 30,000 sites affected by differential methylation, the majority of which were hypomethylated following loss of DIP2C. Changes in DNA methylation at promoter regions were strongly correlated to changes in gene expression, and genes involved with EMT and cell death were enriched among the differentially regulated genes. The DIP2C knockout cells had higher wound closing capacity and showed an increase in the proportion of cells positive for cellular senescence markers.\n\nLoss of DIP2C triggers substantial DNA methylation and gene expression changes, cellular senescence and epithelial-mesenchymal transition in cancer cells.", "doi": "10.1186/s12885-017-3472-5", "pmid": "28716088", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-017-3472-5"}, {"db": "pmc", "key": "PMC5513093"}], "notes": [], "created": "2017-10-17T09:31:57.476Z", "modified": "2024-01-16T13:48:47.742Z"}, {"entity": "publication", "iuid": "1c679203ec3d46318d64bb6dce8e0b08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c679203ec3d46318d64bb6dce8e0b08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c679203ec3d46318d64bb6dce8e0b08"}}, "title": "Association analyses based on false discovery rate implicate new loci for coronary artery disease", "authors": [{"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Webb", "given": "Tom R", "initials": "TR"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Lai", "given": "Florence Y", "initials": "FY"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Giannakopoulou", "given": "Olga", "initials": "O"}, {"family": "Jiang", "given": "Tao", "initials": "T"}, {"family": "Hamby", "given": "Stephen E", "initials": "SE"}, {"family": "Di Angelantonio", "given": "Emanuele", "initials": "E"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Cubbon", "given": "Richard M", "initials": "RM"}, {"family": "Ellinor", "given": "Patrick", "initials": "P"}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Grace", "given": "Christopher", "initials": "C"}, {"family": "Gu", "given": "Dongfeng", "initials": "D"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Howson", "given": "Joanna M M", "initials": "JMM"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kastrati", "given": "Adnan", "initials": "A"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Kyriakou", "given": "Theodosios", "initials": "T"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lu", "given": "Xiangfeng", "initials": "X"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Pujades-Rodriguez", "given": "Mar", "initials": "M"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "Sweeting", "given": "Michael J", "initials": "MJ"}, {"family": "Zalloua", "given": "Pierre A", "initials": "PA"}, {"family": "AlGhalayini", "given": "Kamal", "initials": "K"}, {"family": "Keavney", "given": "Bernard D", "initials": "BD"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Patel", "given": "Riyaz S", "initials": "RS"}, {"family": "Rutter", "given": "Martin K", "initials": "MK"}, {"family": "Tomaszewski", "given": "Maciej", "initials": "M"}, {"family": "Tzoulaki", "given": "Ioanna", "initials": "I"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}], "type": "journal-article", "published": "2017-07-17", "journal": {"volume": "49", "issn": "1061-4036", "issue": "9", "pages": "1385-1391", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/ng.3913", "pmid": "28714975", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:07.831Z", "modified": "2020-01-21T13:56:11.833Z"}, {"entity": "publication", "iuid": "a3a741c3582e433b9c7ff312acb3c831", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3a741c3582e433b9c7ff312acb3c831.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3a741c3582e433b9c7ff312acb3c831"}}, "title": "Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.", "authors": [{"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "J\u00e4rv\u00e5", "given": "Michael", "initials": "M"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Pingitore", "given": "Piero", "initials": "P"}, {"family": "Karlsson", "given": "Emil", "initials": "E"}, {"family": "Wrange", "given": "Anna-Lisa", "initials": "AL"}, {"family": "Kamdal", "given": "Emelie", "initials": "E"}, {"family": "Sundell", "given": "Kristina", "initials": "K"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Havenhand", "given": "Jon", "initials": "J"}, {"family": "Eriksson", "given": "Leif A", "initials": "LA"}, {"family": "Hedfalk", "given": "Kristina", "initials": "K"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "12", "issn": "1932-6203", "issue": "7", "pages": "e0181192", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms. The knowledge of the function of aquaporins in crustaceans is, however, limited and nothing is known about them in barnacles. We here present the repertoire of aquaporins from a thecostracan crustacean, the barnacle B. improvisus, based on genome and transcriptome sequencing. Our analyses reveal that B. improvisus contains eight genes for aquaporins. Phylogenetic analysis showed that they represented members of the classical water aquaporins (Aqp1, Aqp2), the aquaglyceroporins (Glp1, Glp2), the unorthodox aquaporin (Aqp12) and the arthropod-specific big brain aquaporin (Bib). Interestingly, we also found two big brain-like proteins (BibL1 and BibL2) constituting a new group of aquaporins not yet described in arthropods. In addition, we found that the two water-specific aquaporins were expressed as C-terminal splice variants. Heterologous expression of some of the aquaporins followed by functional characterization showed that Aqp1 transported water and Glp2 water and glycerol, agreeing with the predictions of substrate specificity based on 3D modeling and phylogeny. To investigate a possible role for the B. improvisus aquaporins in osmoregulation, mRNA expression changes in adult barnacles were analysed after long-term acclimation to different salinities. The most pronounced expression difference was seen for AQP1 with a substantial (>100-fold) decrease in the mantle tissue in low salinity (3 PSU) compared to high salinity (33 PSU). Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation.", "doi": "10.1371/journal.pone.0181192", "pmid": "28715506", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-05123"}, {"db": "pmc", "key": "PMC5513457"}, {"db": "GENBANK", "description": "sequence", "key": "KY508284"}, {"db": "GENBANK", "description": "sequence", "key": "KY508285"}, {"db": "GENBANK", "description": "sequence", "key": "KY508286"}, {"db": "GENBANK", "description": "sequence", "key": "KY508287"}, {"db": "GENBANK", "description": "sequence", "key": "KY508289"}, {"db": "GENBANK", "description": "sequence", "key": "KY508290"}, {"db": "GENBANK", "description": "sequence", "key": "KY508291"}, {"db": "GENBANK", "description": "sequence", "key": "KY508292"}, {"db": "GENBANK", "description": "sequence", "key": "KY508288"}, {"db": "GENBANK", "description": "sequence", "key": "KY508293"}, {"db": "GENBANK", "description": "sequence", "key": "KY508294"}, {"db": "GENBANK", "description": "sequence", "key": "KY508295"}, {"db": "GENBANK", "description": "sequence", "key": "KY508296"}, {"db": "GENBANK", "description": "sequence", "key": "KY508297"}, {"db": "GENBANK", "description": "sequence", "key": "KY508298"}], "notes": [], "created": "2017-10-17T09:32:54.872Z", "modified": "2024-01-16T13:48:47.750Z"}, {"entity": "publication", "iuid": "f3a2d64e36bb42668a6ae25c44c3b53e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a2d64e36bb42668a6ae25c44c3b53e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a2d64e36bb42668a6ae25c44c3b53e"}}, "title": "Moderate Expression of SEC16 Increases Protein Secretion by Saccharomyces cerevisiae.", "authors": [{"family": "Bao", "given": "Jichen", "initials": "J"}, {"family": "Huang", "given": "Mingtao", "initials": "M"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-07-15", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "volume": "83", "issue": "14", "pages": null, "issn-l": "0099-2240"}, "abstract": "The yeast Saccharomyces cerevisiae is widely used to produce biopharmaceutical proteins. However, the limited capacity of the secretory pathway may reduce its productivity. Here, we increased the secretion of a heterologous \u03b1-amylase, a model protein used for studying the protein secretory pathway in yeast, by moderately overexpressing SEC16, which is involved in protein translocation from the endoplasmic reticulum to the Golgi apparatus. The moderate overexpression of SEC16 increased \u03b1-amylase secretion by generating more endoplasmic reticulum exit sites. The production of reactive oxygen species resulting from the heterologous \u03b1-amylase production was reduced. A genome-wide expression analysis indicated decreased endoplasmic reticulum stress in the strain that moderately overexpressed SEC16, which was consistent with a decreased volume of the endoplasmic reticulum. Additionally, fewer mitochondria were observed. Finally, the moderate overexpression of SEC16 was shown to improve the secretion of two other recombinant proteins, Trichoderma reesei endoglucanase I and Rhizopus oryzae glucan-1,4-\u03b1-glucosidase, indicating that this mechanism is of general relevance.IMPORTANCE There is an increasing demand for recombinant proteins to be used as enzymes and pharmaceuticals. The yeast Saccharomyces cerevisiae is a cell factory that is widely used to produce recombinant proteins. Our study revealed that moderate overexpression of SEC16 increased recombinant protein secretion in S. cerevisiae This new strategy can be combined with other targets to engineer cell factories to efficiently produce protein in the future.", "doi": "10.1128/AEM.03400-16", "pmid": "28476767", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "AEM.03400-16"}, {"db": "pmc", "key": "PMC5494634"}], "notes": [], "created": "2020-01-23T16:33:54.617Z", "modified": "2021-07-05T13:05:37.790Z"}, {"entity": "publication", "iuid": "358a7e145b1147069d52e3cd9b925630", "links": {"self": {"href": "https://publications.scilifelab.se/publication/358a7e145b1147069d52e3cd9b925630.json"}, "display": {"href": "https://publications.scilifelab.se/publication/358a7e145b1147069d52e3cd9b925630"}}, "title": "Does antifouling paint select for antibiotic resistance?", "authors": [{"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Svensson", "given": "Carl Johan", "initials": "CJ"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "\u00d6stman", "given": "Marcus", "initials": "M"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2017-07-15", "journal": {"volume": "590-591", "issn": "1879-1026", "issue": null, "pages": "461-468", "title": "Sci. Total Environ.", "issn-l": "0048-9697"}, "abstract": "There is concern that heavy metals and biocides contribute to the development of antibiotic resistance via co-selection. Most antifouling paints contain high amounts of such substances, which risks turning painted ship hulls into highly mobile refuges and breeding grounds for antibiotic-resistant bacteria. The objectives of this study were to start investigate if heavy-metal based antifouling paints can pose a risk for co-selection of antibiotic-resistant bacteria and, if so, identify the underlying genetic basis. Plastic panels with one side painted with copper and zinc-containing antifouling paint were submerged in a Swedish marina and biofilms from both sides of the panels were harvested after 2.5-4weeks. DNA was isolated from the biofilms and subjected to metagenomic sequencing. Biofilm bacteria were cultured on marine agar supplemented with tetracycline, gentamicin, copper sulfate or zinc sulfate. Biofilm communities from painted surfaces displayed lower taxonomic diversity and enrichment of Gammaproteobacteria. Bacteria from these communities showed increased resistance to both heavy metals and tetracycline but not to gentamicin. Significantly higher abundance of metal and biocide resistance genes was observed, whereas mobile antibiotic resistance genes were not enriched in these communities. In contrast, we found an enrichment of chromosomal RND efflux system genes, including such with documented ability to confer decreased susceptibility to both antibiotics and biocides/heavy metals. This was paralleled by increased abundances of integron-associated integrase and ISCR transposase genes. The results show that the heavy metal-based antifouling paint exerts a strong selection pressure on marine bacterial communities and can co-select for certain antibiotic-resistant bacteria, likely by favoring species and strains carrying genes that provide cross-resistance. Although this does not indicate an immediate risk for promotion of mobile antibiotic resistance, the clear increase of genes involved in mobilizing DNA provides a foundation for increased opportunities for gene transfer in such communities, which might also involve yet unknown resistance mechanisms.", "doi": "10.1016/j.scitotenv.2017.01.213", "pmid": "28284638", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(17)30230-9"}], "notes": [], "created": "2017-11-03T16:21:00.820Z", "modified": "2024-01-16T13:48:47.758Z"}, {"entity": "publication", "iuid": "3b1e943157da4156b2c0640f2a2c3e1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b1e943157da4156b2c0640f2a2c3e1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b1e943157da4156b2c0640f2a2c3e1a"}}, "title": "Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data", "authors": [{"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}, {"family": "Malmodin", "given": "Daniel", "initials": "D"}, {"family": "Karlsson", "given": "B G\u00f6ran", "initials": "BG"}, {"family": "Andersson", "given": "Lars I", "initials": "LI"}, {"family": "Tybring", "given": "Gunnel", "initials": "G"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}], "type": "journal-article", "published": "2017-07-14", "journal": {"volume": null, "issn": "1367-4811", "issue": null, "pages": null, "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": null, "doi": "10.1093/bioinformatics/btx442", "pmid": "29036400", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-03T20:42:49.944Z", "modified": "2025-10-17T13:03:59.697Z"}, {"entity": "publication", "iuid": "d02a556562e44a34b6ef847d62486f9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d02a556562e44a34b6ef847d62486f9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d02a556562e44a34b6ef847d62486f9a"}}, "title": "Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered.", "authors": [{"family": "Koukalov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Amaro", "given": "Mariana", "initials": "M", "orcid": "0000-0002-4868-227X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b32679d78144a5b89cee7fecc2f0271.json"}}, {"family": "Aydogan", "given": "Gokcan", "initials": "G"}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-7380-8797", "researcher": {"href": "https://publications.scilifelab.se/researcher/85bd86ebc85d4653bc880bc9be25bc80.json"}}, {"family": "Williamson", "given": "Philip T F", "initials": "PTF", "orcid": "0000-0002-0231-8640", "researcher": {"href": "https://publications.scilifelab.se/researcher/034a75ccf4884c4ba4b2f9962734d693.json"}}, {"family": "Mikhalyov", "given": "Ilya", "initials": "I"}, {"family": "Hof", "given": "Martin", "initials": "M", "orcid": "0000-0003-2884-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ee7e14809ee4a579220428faa1cb058.json"}}, {"family": "\u0160achl", "given": "Radek", "initials": "R"}], "type": "journal article", "published": "2017-07-14", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "5460", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "It is a fundamental question in cell biology and biophysics whether sphingomyelin (SM)- and cholesterol (Chol)- driven nanodomains exist in living cells and in model membranes. Biophysical studies on model membranes revealed SM and Chol driven micrometer-sized liquid-ordered domains. Although the existence of such microdomains has not been proven for the plasma membrane, such lipid mixtures have been often used as a model system for 'rafts'. On the other hand, recent super resolution and single molecule results indicate that the plasma membrane might organize into nanocompartments. However, due to the limited resolution of those techniques their unambiguous characterization is still missing. In this work, a novel combination of F\u00f6rster resonance energy transfer and Monte Carlo simulations (MC-FRET) identifies directly 10 nm large nanodomains in liquid-disordered model membranes composed of lipid mixtures containing SM and Chol. Combining MC-FRET with solid-state wide-line and high resolution magic angle spinning NMR as well as with fluorescence correlation spectroscopy we demonstrate that these nanodomains containing hundreds of lipid molecules are fluid and disordered. In terms of their size, fluidity, order and lifetime these nanodomains may represent a relevant model system for cellular membranes and are closely related to nanocompartments suggested to exist in cellular membranes.", "doi": "10.1038/s41598-017-05539-y", "pmid": "28710349", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-05539-y"}, {"db": "pmc", "key": "PMC5511215"}], "notes": [], "created": "2017-11-02T17:26:50.120Z", "modified": "2025-10-17T13:03:59.712Z"}, {"entity": "publication", "iuid": "ae326cc43f784533bbcec9e0dfdf1173", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae326cc43f784533bbcec9e0dfdf1173.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae326cc43f784533bbcec9e0dfdf1173"}}, "title": "A TRPV1-to-secretagogin regulatory axis controls pancreatic \u03b2-cell survival by modulating protein turnover.", "authors": [{"family": "Malenczyk", "given": "Katarzyna", "initials": "K"}, {"family": "Girach", "given": "Fatima", "initials": "F"}, {"family": "Szodorai", "given": "Edit", "initials": "E"}, {"family": "Storm", "given": "Petter", "initials": "P"}, {"family": "Segerstolpe", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Tortoriello", "given": "Giuseppe", "initials": "G"}, {"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Romanov", "given": "Roman A", "initials": "RA"}, {"family": "Bor\u00f3k", "given": "Erzs\u00e9bet", "initials": "E"}, {"family": "Piscitelli", "given": "Fabiana", "initials": "F"}, {"family": "Di Marzo", "given": "Vincenzo", "initials": "V"}, {"family": "Szab\u00f3", "given": "G\u00e1bor", "initials": "G"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Kubicek", "given": "Stefan", "initials": "S"}, {"family": "Lubec", "given": "Gert", "initials": "G"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Wagner", "given": "Ludwig", "initials": "L"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Harkany", "given": "Tibor", "initials": "T", "orcid": "0000-0002-6637-5900", "researcher": {"href": "https://publications.scilifelab.se/researcher/09d3d0d2a30f4bb39b23901be4d25793.json"}}], "type": "journal article", "published": "2017-07-14", "journal": {"volume": "36", "issn": "1460-2075", "issue": "14", "pages": "2107-2125", "title": "EMBO J.", "issn-l": "0261-4189"}, "abstract": "Ca2+-sensor proteins are generally implicated in insulin release through SNARE interactions. Here, secretagogin, whose expression in human pancreatic islets correlates with their insulin content and the incidence of type 2 diabetes, is shown to orchestrate an unexpectedly distinct mechanism. Single-cell RNA-seq reveals retained expression of the TRP family members in \u03b2-cells from diabetic donors. Amongst these, pharmacological probing identifies Ca2+-permeable transient receptor potential vanilloid type 1 channels (TRPV1) as potent inducers of secretagogin expression through recruitment of Sp1 transcription factors. Accordingly, agonist stimulation of TRPV1s fails to rescue insulin release from pancreatic islets of glucose intolerant secretagogin knock-out(-/-) mice. However, instead of merely impinging on the SNARE machinery, reduced insulin availability in secretagogin-/- mice is due to \u03b2-cell loss, which is underpinned by the collapse of protein folding and deregulation of secretagogin-dependent USP9X deubiquitinase activity. Therefore, and considering the desensitization of TRPV1s in diabetic pancreata, a TRPV1-to-secretagogin regulatory axis seems critical to maintain the structural integrity and signal competence of \u03b2-cells.", "doi": "10.15252/embj.201695347", "pmid": "28637794", "labels": {"Fluorescence Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "embj.201695347"}, {"db": "pmc", "key": "PMC5510001"}], "notes": [], "created": "2017-10-30T14:57:00.389Z", "modified": "2021-07-07T11:46:33.613Z"}, {"entity": "publication", "iuid": "9d1149cec7524719adbeb5945a9f03b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d1149cec7524719adbeb5945a9f03b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d1149cec7524719adbeb5945a9f03b2"}}, "title": "Lansoprazole-sulfide, pharmacokinetics of this promising anti-tuberculous agent", "authors": [{"family": "Mdanda", "given": "Sipho", "initials": "S"}, {"family": "Baijnath", "given": "Sooraj", "initials": "S"}, {"family": "Shobo", "given": "Adeola", "initials": "A"}, {"family": "Singh", "given": "Sanil D", "initials": "SD"}, {"family": "Maguire", "given": "Glenn E M", "initials": "GEM"}, {"family": "Kruger", "given": "Hendrik G", "initials": "HG"}, {"family": "Arvidsson", "given": "Per I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}, {"family": "Naicker", "given": "Tricia", "initials": "T"}, {"family": "Govender", "given": "Thavendran", "initials": "T"}], "type": "journal-article", "published": "2017-07-13", "journal": {"volume": null, "issn": "0269-3879", "issue": null, "pages": "e4035", "title": "Biomedical Chromatography", "issn-l": null}, "abstract": null, "doi": "10.1002/bmc.4035", "pmid": "28623874", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T08:32:56.829Z", "modified": "2025-10-17T13:05:08.825Z"}, {"entity": "publication", "iuid": "fbc51120b36048ecaa8ce43eb420a46b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbc51120b36048ecaa8ce43eb420a46b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbc51120b36048ecaa8ce43eb420a46b"}}, "title": "Genotype\u2013covariate interaction effects and the heritability of adult body mass index", "authors": [{"family": "Robinson", "given": "Matthew R", "initials": "MR"}, {"family": "English", "given": "Geoffrey", "initials": "G"}, {"family": "Moser", "given": "Gerhard", "initials": "G"}, {"family": "Lloyd-Jones", "given": "Luke R", "initials": "LR"}, {"family": "Triplett", "given": "Marcus A", "initials": "MA"}, {"family": "Zhu", "given": "Zhihong", "initials": "Z"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Esko", "given": "Tonu", "initials": "T"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}], "type": "journal-article", "published": "2017-07-10", "journal": {"volume": "49", "issn": "1061-4036", "issue": "8", "pages": "1174-1181", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/ng.3912", "pmid": "28692066", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:08.920Z", "modified": "2020-01-21T13:56:11.819Z"}, {"entity": "publication", "iuid": "acb58d7aee874712bfe513222e3e8926", "links": {"self": {"href": "https://publications.scilifelab.se/publication/acb58d7aee874712bfe513222e3e8926.json"}, "display": {"href": "https://publications.scilifelab.se/publication/acb58d7aee874712bfe513222e3e8926"}}, "title": "Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla.", "authors": [{"family": "Furlan", "given": "Alessandro", "initials": "A"}, {"family": "Dyachuk", "given": "Vyacheslav", "initials": "V"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME"}, {"family": "Calvo-Enrique", "given": "Laura", "initials": "L"}, {"family": "Abdo", "given": "Hind", "initials": "H"}, {"family": "Hadjab", "given": "Saida", "initials": "S"}, {"family": "Chontorotzea", "given": "Tatiana", "initials": "T"}, {"family": "Akkuratova", "given": "Natalia", "initials": "N"}, {"family": "Usoskin", "given": "Dmitry", "initials": "D"}, {"family": "Kamenev", "given": "Dmitry", "initials": "D"}, {"family": "Petersen", "given": "Julian", "initials": "J"}, {"family": "Sunadome", "given": "Kazunori", "initials": "K"}, {"family": "Memic", "given": "Fatima", "initials": "F"}, {"family": "Marklund", "given": "Ulrika", "initials": "U"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Topilko", "given": "Piotr", "initials": "P"}, {"family": "Lallemend", "given": "Francois", "initials": "F"}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}], "type": "journal article", "published": "2017-07-07", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6346", "pages": null, "title": "Science", "issn-l": "0036-8075"}, "abstract": "Adrenaline is a fundamental circulating hormone for bodily responses to internal and external stressors. Chromaffin cells of the adrenal medulla (AM) represent the main neuroendocrine adrenergic component and are believed to differentiate from neural crest cells. We demonstrate that large numbers of chromaffin cells arise from peripheral glial stem cells, termed Schwann cell precursors (SCPs). SCPs migrate along the visceral motor nerve to the vicinity of the forming adrenal gland, where they detach from the nerve and form postsynaptic neuroendocrine chromaffin cells. An intricate molecular logic drives two sequential phases of gene expression, one unique for a distinct transient cellular state and another for cell type specification. Subsequently, these programs down-regulate SCP-gene and up-regulate chromaffin cell-gene networks. The AM forms through limited cell expansion and requires the recruitment of numerous SCPs. Thus, peripheral nerves serve as a stem cell niche for neuroendocrine system development.", "doi": "10.1126/science.aal3753", "pmid": "28684471", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service"}, "xrefs": [{"db": "pii", "key": "357/6346/eaal3753"}], "notes": [], "created": "2017-10-05T08:31:04.367Z", "modified": "2017-11-03T20:34:58.979Z"}, {"entity": "publication", "iuid": "abdbca126350420e9b7f8ebdea2f3541", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abdbca126350420e9b7f8ebdea2f3541.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abdbca126350420e9b7f8ebdea2f3541"}}, "title": "Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.", "authors": [{"family": "Ge", "given": "Changrong", "initials": "C"}, {"family": "Tong", "given": "Dongmei", "initials": "D"}, {"family": "Liang", "given": "Bibo", "initials": "B"}, {"family": "L\u00f6nnblom", "given": "Erik", "initials": "E"}, {"family": "Schneider", "given": "Nadine", "initials": "N"}, {"family": "Hagert", "given": "Cecilia", "initials": "C"}, {"family": "Viljanen", "given": "Johan", "initials": "J"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Stawikowska", "given": "Roma", "initials": "R"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Fields", "given": "Gregg B", "initials": "GB"}, {"family": "Skogh", "given": "Thomas", "initials": "T"}, {"family": "Kastbom", "given": "Alf", "initials": "A"}, {"family": "Kihlberg", "given": "Jan", "initials": "J"}, {"family": "Burkhardt", "given": "Harald", "initials": "H"}, {"family": "Dobritzsch", "given": "Doreen", "initials": "D"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2017-07-06", "journal": {"volume": "2", "issn": "2379-3708", "issue": "13", "pages": null, "title": "JCI Insight", "issn-l": "2379-3708"}, "abstract": "Today, it is known that autoimmune diseases start a long time before clinical symptoms appear. Anti-citrullinated protein antibodies (ACPAs) appear many years before the clinical onset of rheumatoid arthritis (RA). However, it is still unclear if and how ACPAs are arthritogenic. To better understand the molecular basis of pathogenicity of ACPAs, we investigated autoantibodies reactive against the C1 epitope of collagen type II (CII) and its citrullinated variants. We found that these antibodies are commonly occurring in RA. A mAb (ACC1) against citrullinated C1 was found to cross-react with several noncitrullinated epitopes on native CII, causing proteoglycan depletion of cartilage and severe arthritis in mice. Structural studies by X-ray crystallography showed that such recognition is governed by a shared structural motif \"RG-TG\" within all the epitopes, including electrostatic potential-controlled citrulline specificity. Overall, we have demonstrated a molecular mechanism that explains how ACPAs trigger arthritis.", "doi": "10.1172/jci.insight.93688", "pmid": "28679953", "labels": {"Protein Science Facility (PSF)": "Service", "Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "93688"}, {"db": "pmc", "key": "PMC5499374"}], "notes": [], "created": "2017-10-05T06:44:19.600Z", "modified": "2021-07-07T15:50:03.269Z"}, {"entity": "publication", "iuid": "1fbfeb18c3aa4a91b322f65e6504dbe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fbfeb18c3aa4a91b322f65e6504dbe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fbfeb18c3aa4a91b322f65e6504dbe5"}}, "title": "High-Density Serum/Plasma Reverse Phase Protein Arrays.", "authors": [{"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}], "type": "journal article", "published": "2017-07-05", "journal": {"volume": "1619", "issn": "1940-6029", "issue": null, "pages": "229-238", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay.", "doi": "10.1007/978-1-4939-7057-5_18", "pmid": "28674890", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:36:59.288Z", "modified": "2021-07-08T12:07:33.995Z"}, {"entity": "publication", "iuid": "c9b9363dc7944969871a7b73e3161be9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9b9363dc7944969871a7b73e3161be9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9b9363dc7944969871a7b73e3161be9"}}, "title": "Detection of Extracellular Vesicles Using Proximity Ligation Assay with Flow Cytometry Readout-ExoPLA.", "authors": [{"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Ebai", "given": "Tonge", "initials": "T"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2017-07-05", "journal": {"volume": "81", "issn": "1934-9300", "issue": null, "pages": "4.8.1-4.8.10", "title": "Curr Protoc Cytom", "issn-l": "1934-9297"}, "abstract": "Extracellular vesicles (EVs) are continuously released by most cells, and they carry surface markers of their cells of origin. Found in all body fluids, EVs function as conveyers of cellular information, and evidence implicates them as markers of disease. These characteristics make EVs attractive diagnostic targets. However, detection and characterization of EVs is challenging due to their small size. We've established a method, called ExoPLA, that allows individual EVs to be detected and characterized at high specificity and sensitivity. Based on the in situ proximity ligation assay (in situ PLA), proximal oligonucleotide-conjugated antibodies bound to their targets on the surfaces of the EVs allow formation of circular products that can be fluorescently labeled by rolling circle amplification. The intense fluorescent signals produced in this assay allow detection and enumeration of individual EVs by flow cytometry. We describe the procedures for ExoPLA, along with expected results and troubleshooting. \u00a9 2017 by John Wiley & Sons, Inc.", "doi": "10.1002/cpcy.22", "pmid": "28678418", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T10:10:33.398Z", "modified": "2023-04-14T13:56:12.030Z"}, {"entity": "publication", "iuid": "491a561955fc44909ca8782a3b02cbdd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/491a561955fc44909ca8782a3b02cbdd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/491a561955fc44909ca8782a3b02cbdd"}}, "title": "Bead-Based and Multiplexed Immunoassays for Protein Profiling via Sequential Affinity Capture.", "authors": [{"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}], "type": "journal article", "published": "2017-07-05", "journal": {"volume": "1619", "issn": "1940-6029", "issue": null, "pages": "45-54", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Antibody microarrays offer high-throughput immunoassays for multiplexed analyses of clinical samples. For such approaches, samples are either labeled in solution to enable a direct readout on the single binder assay format or detected by matched pairs of capture and detection antibodies in dual binder assay format, also known as sandwich assays. Aiming to benefit from the flexibility and capacity offered by single binder assay readout and the specificity and sensitivity of dual binder assays, we developed a multiplexed dual binder procedure that is based on a sequential, rather than combined, antigen binding. The method, entitled dual capture assay (DCA), is composed of an initial antigen capture by antibodies on beads, followed by labeling of captured protein targets on beads, combinatorial elution steps at high and low pH, and a readout using a secondary bead array. Compared to classical single binder assays, the described method demonstrated several advantages such as reduced contribution of off-target binding, lower noise levels, and improved correlation when comparing with clinical reference values. This procedure describes a novel and versatile immunoassay strategy for proteome profiling in body fluids.", "doi": "10.1007/978-1-4939-7057-5_4", "pmid": "28674876", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:17:20.403Z", "modified": "2021-07-08T12:07:34.090Z"}, {"entity": "publication", "iuid": "f4dc3cf02d2449a18177221e5fc4126e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4dc3cf02d2449a18177221e5fc4126e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4dc3cf02d2449a18177221e5fc4126e"}}, "title": "Paternal personality and social status influence offspring activity in zebrafish.", "authors": [{"family": "Zajitschek", "given": "Susanne", "initials": "S"}, {"family": "Herbert-Read", "given": "James E", "initials": "JE"}, {"family": "Abbasi", "given": "Nasir M", "initials": "NM"}, {"family": "Zajitschek", "given": "Felix", "initials": "F"}, {"family": "Immler", "given": "Simone", "initials": "S"}], "type": "journal article", "published": "2017-07-03", "journal": {"title": "BMC Evol. Biol.", "issn": "1471-2148", "volume": "17", "issue": "1", "pages": "157", "issn-l": "1471-2148"}, "abstract": "Evidence for the transmission of non-genetic information from father to offspring is rapidly accumulating. While the impact of chemical and physical factors such as toxins or diet on the fitness of the parents and their offspring have been studied extensively, the importance of behavioural and social circumstances has only recently been recognised. Behavioural traits such as personality characteristics can be relatively stable, and partly comprise a genetic component but we know little about the non-genetic transmission of plastic behavioural traits from parents to offspring. We investigated the relative effect of personality and of social dominance as indicators at the opposite ends of the plasticity range on offspring behaviour in the zebrafish (Danio rerio). We assessed male boldness, a behavioural trait that has previously been shown previously to possess genetic underpinnings, and experimentally manipulated male social status to assess the association between the two types of behaviour and their correlation with offspring activity.\n\nWe found a clear interaction between the relatively stable and putative genetic effects based on inherited differences in personality and the experimentally induced epigenetic effects from changes in the social status of the father on offspring activity.\n\nOur study shows that offspring behaviour is determined by a combination of paternal personality traits and on-genetic effects derived from the social status of the father.", "doi": "10.1186/s12862-017-1005-0", "pmid": "28673261", "labels": {"Genome Engineering Zebrafish": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-017-1005-0"}, {"db": "pmc", "key": "PMC5496241"}], "notes": [], "created": "2017-10-26T09:24:43.057Z", "modified": "2017-10-26T09:24:43.060Z"}, {"entity": "publication", "iuid": "c39c34f5c43d412487543502873a6519", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c39c34f5c43d412487543502873a6519.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c39c34f5c43d412487543502873a6519"}}, "title": "Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation.", "authors": [{"family": "Mead", "given": "Adam J", "initials": "AJ"}, {"family": "Neo", "given": "Wen Hao", "initials": "WH"}, {"family": "Barkas", "given": "Nikolaos", "initials": "N"}, {"family": "Matsuoka", "given": "Sahoko", "initials": "S"}, {"family": "Giustacchini", "given": "Alice", "initials": "A"}, {"family": "Facchini", "given": "Raffaella", "initials": "R"}, {"family": "Thongjuea", "given": "Supat", "initials": "S"}, {"family": "Jamieson", "given": "Lauren", "initials": "L"}, {"family": "Booth", "given": "Christopher A G", "initials": "CAG"}, {"family": "Fordham", "given": "Nicholas", "initials": "N"}, {"family": "Di Genua", "given": "Cristina", "initials": "C"}, {"family": "Atkinson", "given": "Deborah", "initials": "D"}, {"family": "Chowdhury", "given": "Onima", "initials": "O"}, {"family": "Repapi", "given": "Emmanouela", "initials": "E"}, {"family": "Gray", "given": "Nicki", "initials": "N"}, {"family": "Kharazi", "given": "Shabnam", "initials": "S"}, {"family": "Clark", "given": "Sally-Ann", "initials": "SA"}, {"family": "Bouriez", "given": "Tiphaine", "initials": "T"}, {"family": "Woll", "given": "Petter", "initials": "P"}, {"family": "Suda", "given": "Toshio", "initials": "T"}, {"family": "Nerlov", "given": "Claus", "initials": "C"}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW"}], "type": "journal article", "published": "2017-07-03", "journal": {"volume": "214", "issn": "1540-9538", "issue": "7", "pages": "2005-2021", "title": "J. Exp. Med.", "issn-l": "0022-1007"}, "abstract": "Although previous studies suggested that the expression of FMS-like tyrosine kinase 3 (Flt3) initiates downstream of mouse hematopoietic stem cells (HSCs), FLT3 internal tandem duplications (FLT3 ITDs) have recently been suggested to intrinsically suppress HSCs. Herein, single-cell interrogation found Flt3 mRNA expression to be absent in the large majority of phenotypic HSCs, with a strong negative correlation between Flt3 and HSC-associated gene expression. Flt3-ITD knock-in mice showed reduced numbers of phenotypic HSCs, with an even more severe loss of long-term repopulating HSCs, likely reflecting the presence of non-HSCs within the phenotypic HSC compartment. Competitive transplantation experiments established that Flt3-ITD compromises HSCs through an extrinsically mediated mechanism of disrupting HSC-supporting bone marrow stromal cells, with reduced numbers of endothelial and mesenchymal stromal cells showing increased inflammation-associated gene expression. Tumor necrosis factor (TNF), a cell-extrinsic potent negative regulator of HSCs, was overexpressed in bone marrow niche cells from FLT3-ITD mice, and anti-TNF treatment partially rescued the HSC phenotype. These findings, which establish that Flt3-ITD-driven myeloproliferation results in cell-extrinsic suppression of the normal HSC reservoir, are of relevance for several aspects of acute myeloid leukemia biology.", "doi": "10.1084/jem.20161418", "pmid": "28637883", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "jem.20161418"}, {"db": "pmc", "key": "PMC5502426"}], "notes": [], "created": "2018-01-10T09:44:12.302Z", "modified": "2020-01-21T13:56:10.871Z"}, {"entity": "publication", "iuid": "1fe52c77fec94407939714b233d44d7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fe52c77fec94407939714b233d44d7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fe52c77fec94407939714b233d44d7b"}}, "title": "Mineral Type Structures Soil Microbial Communities", "authors": [{"family": "Ahmed", "given": "Engy", "initials": "E"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Logue", "given": "J\u00fcrg B", "initials": "JB"}, {"family": "Br\u00fcchert", "given": "Volker", "initials": "V"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Holmstr\u00f6m", "given": "Sara J M", "initials": "SJM"}], "type": "journal-article", "published": "2017-07-03", "journal": {"volume": "34", "issn": "0149-0451", "issue": "6", "pages": "538-545", "title": "Geomicrobiology Journal", "issn-l": null}, "abstract": null, "doi": "10.1080/01490451.2016.1225868", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:57:48.638Z", "modified": "2024-01-16T13:48:47.765Z"}, {"entity": "publication", "iuid": "44e0dcce999c41adb598ab8a38a2cc4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44e0dcce999c41adb598ab8a38a2cc4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44e0dcce999c41adb598ab8a38a2cc4c"}}, "title": "Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.", "authors": [{"family": "Panizza", "given": "Elena", "initials": "E"}, {"family": "Branca", "given": "Rui M M", "initials": "RMM"}, {"family": "Oliviusson", "given": "Peter", "initials": "P"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2017-07-03", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "4513", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Protein phosphorylation is involved in the regulation of most eukaryotic cells functions and mass spectrometry-based analysis has made major contributions to our understanding of this regulation. However, low abundance of phosphorylated species presents a major challenge in achieving comprehensive phosphoproteome coverage and robust quantification. In this study, we developed a workflow employing titanium dioxide phospho-enrichment coupled with isobaric labeling by Tandem Mass Tags (TMT) and high-resolution isoelectric focusing (HiRIEF) fractionation to perform in-depth quantitative phosphoproteomics starting with a low sample quantity. To benchmark the workflow, we analyzed HeLa cells upon pervanadate treatment or cell cycle arrest in mitosis. Analyzing 300 \u00b5g of peptides per sample, we identified 22,712 phosphorylation sites, of which 19,075 were localized with high confidence and 1,203 are phosphorylated tyrosine residues, representing 6.3% of all detected phospho-sites. HiRIEF fractions with the most acidic isoelectric points are enriched in multiply phosphorylated peptides, which represent 18% of all the phospho-peptides detected in the pH range 2.5-3.7. Cross-referencing with the PhosphoSitePlus database reveals 1,264 phosphorylation sites that have not been previously reported and kinase association analysis suggests that a subset of these may be functional during the mitotic phase.", "doi": "10.1038/s41598-017-04798-z", "pmid": "28674419", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-04798-z"}, {"db": "pmc", "key": "PMC5495806"}], "notes": [], "created": "2017-12-05T16:14:26.493Z", "modified": "2021-07-08T11:36:15.117Z"}, {"entity": "publication", "iuid": "0dc9a5e9c187433aa563f22ad6abdaf1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dc9a5e9c187433aa563f22ad6abdaf1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dc9a5e9c187433aa563f22ad6abdaf1"}}, "title": "Structure-metabolism-relationships in the microsomal clearance of piperazin-1-ylpyridazines.", "authors": [{"family": "Llona-Minguez", "given": "Sabin", "initials": "S", "orcid": "0000-0003-3187-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/437b1f98ad21471f884226ed89a3da12.json"}}, {"family": "Ghassemian", "given": "Artin", "initials": "A"}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Desroses", "given": "Matthieu", "initials": "M", "orcid": "0000-0003-4152-3855", "researcher": {"href": "https://publications.scilifelab.se/researcher/b232b70751004e9ea6b547533f901376.json"}}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-07-01", "journal": {"volume": "8", "issn": "2040-2503", "issue": "7", "pages": "1553-1560", "title": "Med. Chem. Commun.", "issn-l": null}, "abstract": "In this study, we provide insight into the metabolic profile of a series of piperazin-1-ylpyridazines suffering from rapid in vitro intrinsic clearance in a metabolic stability assay using liver microsomes (e.g. compound 1 MLM/HLM t1/2 = 2/3 min). Aided by empirical metabolite identification and computational predictive models, we designed the structural modifications required to improve in vitro intrinsic clearance by more than 50-fold (e.g. compound 29 MLM/HLM t1/2 = 113/105 min).", "doi": "10.1039/c7md00230k", "pmid": "30108867", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "c7md00230k"}, {"db": "pmc", "key": "PMC6072423"}], "notes": [], "created": "2017-10-25T12:50:13.984Z", "modified": "2025-10-17T13:05:08.838Z"}, {"entity": "publication", "iuid": "e81cd30a07184c74adb303274bd88923", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e81cd30a07184c74adb303274bd88923.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e81cd30a07184c74adb303274bd88923"}}, "title": "Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).", "authors": [{"family": "Sullivan", "given": "Alexis R", "initials": "AR"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Thompson", "given": "Stacey Lee", "initials": "SL"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Wang", "given": "Xiao-Ru", "initials": "XR"}], "type": "journal article", "published": "2017-07-01", "journal": {"volume": "34", "issn": "1537-1719", "issue": "7", "pages": "1689-1701", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of \u223c35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.", "doi": "10.1093/molbev/msx111", "pmid": "28383641", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3104592"}, {"db": "pmc", "key": "PMC5455968"}], "notes": [], "created": "2017-11-03T16:22:17.119Z", "modified": "2024-01-16T13:48:47.773Z"}, {"entity": "publication", "iuid": "7531a3c092394bef971ba96e83bd5466", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7531a3c092394bef971ba96e83bd5466.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7531a3c092394bef971ba96e83bd5466"}}, "title": "Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years", "authors": [{"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Hallingb\u00e4ck", "given": "Henrik R", "initials": "HR"}, {"family": "Beyer", "given": "Friderike", "initials": "F"}, {"family": "Nordh", "given": "Nils Erik", "initials": "NE"}, {"family": "Weih", "given": "Martin", "initials": "M"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann Christin", "initials": "AC"}], "type": "journal-article", "published": "2017-07-01", "journal": {"volume": "120", "issn": "0305-7364", "issue": "1", "pages": "87-100", "title": "", "issn-l": null}, "abstract": null, "doi": "10.1093/aob/mcx029", "pmid": "28449073", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:32.552Z", "modified": "2020-01-21T13:56:11.809Z"}, {"entity": "publication", "iuid": "07bf66914419434180e929e4cb7416c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07bf66914419434180e929e4cb7416c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07bf66914419434180e929e4cb7416c0"}}, "title": "Epitope mapping of a new anti-Tn antibody detecting gastric cancer cells.", "authors": [{"family": "Persson", "given": "Nina", "initials": "N"}, {"family": "Stuhr-Hansen", "given": "Nicolai", "initials": "N"}, {"family": "Risinger", "given": "Christian", "initials": "C"}, {"family": "Mereiter", "given": "Stefan", "initials": "S"}, {"family": "Pol\u00f3nia", "given": "Ant\u00f3nio", "initials": "A"}, {"family": "Polom", "given": "Karol", "initials": "K"}, {"family": "Kov\u00e1cs", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Roviello", "given": "Franco", "initials": "F"}, {"family": "Reis", "given": "Celso A", "initials": "CA"}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Danielsson", "given": "Lena", "initials": "L"}, {"family": "Jansson", "given": "Bo", "initials": "B"}, {"family": "Blixt", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2017-07-01", "journal": {"title": "Glycobiology", "issn": "1460-2423", "volume": "27", "issue": "7", "pages": "635-645", "issn-l": "0959-6658"}, "abstract": "Here, we introduce a novel scFv antibody, G2-D11, specific for two adjacent Tn-antigens (GalNAc-Ser/Thr) binding equally to three dimeric forms of the epitope, Ser-Thr, Thr-Thr and Thr-Ser. Compared to other anti-Tn reagents, the binding of G2-D11 is minimally influenced by the peptide structure, which indicates a high degree of carbohydrate epitope dominance and a low influence from the protein backbone. With a high affinity (KDapp = 1.3 \u00d7 10-8 M) and no cross-reactivity to either sialyl-Tn epitope or blood group A antigens, scFv G2-D11 is an excellent candidate for a well-defined anti-Tn-antigen reagent. Detailed immunohistochemical evaluation of tissue sections from a cohort of 80 patients with gastric carcinoma showed in all cases positive tumor cells. The observed staining was localized to the cytoplasm and in some cases to the membrane, whereas the surrounding tissue was completely negative demonstrating the usefulness of the novel Tn-antigen binding antibody.", "doi": "10.1093/glycob/cwx033", "pmid": "28419225", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "3611453"}], "notes": [], "created": "2020-01-27T10:10:40.886Z", "modified": "2021-05-24T15:39:50.116Z"}, {"entity": "publication", "iuid": "6eaf552089d04408868b0adaa7a16350", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6eaf552089d04408868b0adaa7a16350.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6eaf552089d04408868b0adaa7a16350"}}, "title": "Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.", "authors": [{"family": "Andersson", "given": "Kristina E", "initials": "KE"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Thuresson", "given": "Narda", "initials": "N"}, {"family": "Rascon", "given": "Ana", "initials": "A"}, {"family": "\u00d6ste", "given": "Rickard", "initials": "R"}, {"family": "Sterner", "given": "Olov", "initials": "O"}, {"family": "Olsson", "given": "Olof", "initials": "O"}, {"family": "Hellstrand", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "61", "issn": "1613-4133", "issue": "7", "title": "Mol Nutr Food Res", "issn-l": "1613-4125"}, "abstract": "The molecular mechanisms underlying the cholesterol-lowering properties of oats are only partly known. To study possible pathways involved, we investigated gene expressions in the liver and small intestine of mice fed oats.\n\nCholesterol and bile acids were analyzed in plasma and feces from LDL-receptor deficient (LDLr(-/-) ) mice fed Western diet with wholegrain oats. A transcriptome analysis of mRNA from liver and jejunum was performed together with quantitative RT-PCR. Oat-fed mice had lower levels of plasma lipids and increased levels of bile acids and cholesterol in feces compared with controls. Two hundred thirty nine genes in jejunum and 25 genes in liver were differentially expressed (FDR corrected p < 0.05). The most affected biological process in jejunum was lipid biosynthesis and regulation. The apical sodium-dependent bile acid transporter (ASBT, Slc10a) and the intracellular bile acid binding protein (Fabp6) were both upregulated, whereas small heterodimer partner-1 (Shp-1) and apolipoprotein CII (Apoc2) were downregulated.\n\nWhole oats attenuated responses typically induced by high-fat diet. Increased expression of genes for intestinal bile acid uptake following oat consumption suggests retention in the gut lumen rather than decreased uptake capacity as cause for the increased bile acid excretion and the concomitant reduction of plasma cholesterol.", "doi": "10.1002/mnfr.201600874", "pmid": "28205325", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:18:36.937Z", "modified": "2024-01-16T13:48:47.781Z"}, {"entity": "publication", "iuid": "a6bf9afecb2a4ea69f910f4d85ef780f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6bf9afecb2a4ea69f910f4d85ef780f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6bf9afecb2a4ea69f910f4d85ef780f"}}, "title": "Three-dimensional structures and functional studies of two GH43 arabinofuranosidases from Weissella sp. strain 142 and Lactobacillus brevis.", "authors": [{"family": "Linares-Past\u00e9n", "given": "Javier A", "initials": "JA"}, {"family": "Falck", "given": "Peter", "initials": "P"}, {"family": "Albasri", "given": "Khalil", "initials": "K"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Adlercreutz", "given": "Patrick", "initials": "P"}, {"family": "Logan", "given": "Derek T", "initials": "DT"}, {"family": "Karlsson", "given": "Eva Nordberg", "initials": "EN"}], "type": "journal article", "published": "2017-07-00", "journal": {"title": "FEBS J.", "issn": "1742-4658", "volume": "284", "issue": "13", "pages": "2019-2036", "issn-l": "1742-464X"}, "abstract": "Arabinofuranosidases degrade arabinose-containing oligo and polysaccharides, releasing l-arabinose, which is a potentially useful sugar, shown to reduce glycemic response under certain conditions. Arabinofuranosidases (Arafs) are frequently found in GH43, one of the most common GH-families encoded in genomes in gut microbiota, and hence it is of interest to increase understanding of the function of these enzymes in species occurring in the gut. Here we have produced, characterized and solved the three-dimensional structures, at 1.9 and 2.0 \u00c5 resolution respectively, of two homologous GH43 enzymes, classified under subfamily 26, from Lactobacillus brevis DSM1269 (LbAraf43) and Weissella strain 142 (WAraf43), respectively. The enzymes, with 74% sequence identity to each other, are composed of a single catalytic module with a \u03b2-propeller structure typical of GH43, and an active-site pocket with three identifiable subsites (-1, +1, and +2). According to size exclusion chromatography, native WAraf43 is a dimer, while LbAraf43 is a tetramer in solution. Both of them show activity with similar catalytic efficiency on 1,5-\u03b1-l-arabinooligosaccharides with a degree of polymerization (DP) of 2-3. Activity is restricted to substrates of low DP, and the reason for this is believed to be an extended loop at the entrance to the active site, creating interactions in the +2 subsite.\n\nStructural data are available in the PDB under the accession numbers 5M8B (LbAraf43) and 5M8E (WAraf43).", "doi": "10.1111/febs.14101", "pmid": "28485897", "labels": {"Structural Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-27T10:05:14.527Z", "modified": "2021-05-24T15:39:50.346Z"}, {"entity": "publication", "iuid": "0636dfbb9c2945ca93ada365e8d8299d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0636dfbb9c2945ca93ada365e8d8299d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0636dfbb9c2945ca93ada365e8d8299d"}}, "title": "Stability of Proteins in Dried Blood Spot Biobanks", "authors": [{"family": "Bj\u00f6rkesten", "given": "Johan", "initials": "J"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Shen", "given": "Qiujin", "initials": "Q"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Hougaard", "given": "David M", "initials": "DM"}, {"family": "Cohen", "given": "Arieh S", "initials": "AS"}, {"family": "S\u00f6rensen", "given": "Lene", "initials": "L"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "16", "issn": "1535-9476", "issue": "7", "pages": "1286-1296", "title": "Mol Cell Proteomics", "issn-l": "1535-9476"}, "abstract": null, "doi": "10.1074/mcp.ra117.000015", "pmid": "28501802", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T14:43:01.618Z", "modified": "2023-04-14T13:56:12.310Z"}, {"entity": "publication", "iuid": "685e135330d64bf8b825df7e44a76180", "links": {"self": {"href": "https://publications.scilifelab.se/publication/685e135330d64bf8b825df7e44a76180.json"}, "display": {"href": "https://publications.scilifelab.se/publication/685e135330d64bf8b825df7e44a76180"}}, "title": "Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease: a molecular and genetic association study", "authors": [{"family": "Zewinger", "given": "Stephen", "initials": "S"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "McCubrey", "given": "Raymond O", "initials": "RO"}, {"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "Direk", "given": "Kenan", "initials": "K"}, {"family": "Laufs", "given": "Ulrich", "initials": "U"}, {"family": "Werner", "given": "Christian", "initials": "C"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Rothenbacher", "given": "Dietrich", "initials": "D"}, {"family": "Mons", "given": "Ute", "initials": "U"}, {"family": "Breitling", "given": "Lutz P", "initials": "LP"}, {"family": "Brenner", "given": "Herrmann", "initials": "H"}, {"family": "Jennings", "given": "Richard T", "initials": "RT"}, {"family": "Petrakis", "given": "Ioannis", "initials": "I"}, {"family": "Triem", "given": "Sarah", "initials": "S"}, {"family": "Klug", "given": "Mira", "initials": "M"}, {"family": "Filips", "given": "Alexandra", "initials": "A"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Waldeyer", "given": "Christoph", "initials": "C"}, {"family": "Sinning", "given": "Christoph", "initials": "C"}, {"family": "Schnabel", "given": "Renate B", "initials": "RB"}, {"family": "Lackner", "given": "Karl J", "initials": "KJ"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Nyg\u00e5rd", "given": "Ottar", "initials": "O"}, {"family": "Svingen", "given": "Gard Frodahl Tveitev\u00e5g", "initials": "GFT"}, {"family": "Pedersen", "given": "Eva Ringdal", "initials": "ER"}, {"family": "Tell", "given": "Grethe S", "initials": "GS"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Laaksonen", "given": "Reijo", "initials": "R"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Smit", "given": "Roelof A J", "initials": "RAJ"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Groesdonk", "given": "Heinrich V", "initials": "HV"}, {"family": "Delgado", "given": "Graciela", "initials": "G"}, {"family": "Stojakovic", "given": "Tatjana", "initials": "T"}, {"family": "Pilbrow", "given": "Anna P", "initials": "AP"}, {"family": "Cameron", "given": "Vicky A", "initials": "VA"}, {"family": "Richards", "given": "A Mark", "initials": "AM"}, {"family": "Doughty", "given": "Robert N", "initials": "RN"}, {"family": "Gong", "given": "Yan", "initials": "Y"}, {"family": "Cooper-DeHoff", "given": "Rhonda", "initials": "R"}, {"family": "Johnson", "given": "Julie", "initials": "J"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Beutner", "given": "Frank", "initials": "F"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Vilmundarson", "given": "Ragnar O", "initials": "RO"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AFR"}, {"family": "Cresci", "given": "Sharon", "initials": "S"}, {"family": "Lenzini", "given": "Petra A", "initials": "PA"}, {"family": "Spertus", "given": "John A", "initials": "JA"}, {"family": "Olivieri", "given": "Oliviero", "initials": "O"}, {"family": "Girelli", "given": "Domenico", "initials": "D"}, {"family": "Martinelli", "given": "Nicola I", "initials": "NI"}, {"family": "Leiherer", "given": "Andreas", "initials": "A"}, {"family": "Saely", "given": "Christoph H", "initials": "CH"}, {"family": "Drexel", "given": "Heinz", "initials": "H"}, {"family": "M\u00fcndlein", "given": "Axel", "initials": "A"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Kofink", "given": "Daniel", "initials": "D"}, {"family": "Hoefer", "given": "Imo E", "initials": "IE"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "Quyyumi", "given": "Arshed A", "initials": "AA"}, {"family": "Ko", "given": "Yi An", "initials": "YA"}, {"family": "Hartiala", "given": "Jaana A", "initials": "JA"}, {"family": "Allayee", "given": "Hooman", "initials": "H"}, {"family": "Tang", "given": "W H Wilson", "initials": "WHW"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Held", "given": "Claes", "initials": "C"}, {"family": "Hagstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "\u00c5kerblom", "given": "Axel", "initials": "A"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Karp", "given": "Igor", "initials": "I"}, {"family": "Labos", "given": "Christopher", "initials": "C"}, {"family": "Pilote", "given": "Louise", "initials": "L"}, {"family": "Engert", "given": "James C", "initials": "JC"}, {"family": "Brophy", "given": "James M", "initials": "JM"}, {"family": "Thanassoulis", "given": "George", "initials": "G"}, {"family": "Bogaty", "given": "Peter", "initials": "P"}, {"family": "Szczeklik", "given": "Wojciech", "initials": "W"}, {"family": "Kaczor", "given": "Marcin", "initials": "M"}, {"family": "Sanak", "given": "Marek", "initials": "M"}, {"family": "Virani", "given": "Salim S", "initials": "SS"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Lee", "given": "Vei Vei", "initials": "VV"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Horne", "given": "Benjamin D", "initials": "BD"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Patel", "given": "Riyaz S", "initials": "RS"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Scharnagl", "given": "Hubert", "initials": "H"}, {"family": "Fliser", "given": "Danilo", "initials": "D"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Speer", "given": "Thimoteus", "initials": "T"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "5", "issn": "2213-8587", "issue": "7", "pages": "534-543", "title": "The Lancet Diabetes & Endocrinology", "issn-l": "2213-8587"}, "abstract": "Lipoprotein(a) concentrations in plasma are associated with cardiovascular risk in the general population. Whether lipoprotein(a) concentrations or LPA genetic variants predict long-term mortality in patients with established coronary heart disease remains less clear.\n\nWe obtained data from 3313 patients with established coronary heart disease in the Ludwigshafen Risk and Cardiovascular Health (LURIC) study. We tested associations of tertiles of lipoprotein(a) concentration in plasma and two LPA single-nucleotide polymorphisms ([SNPs] rs10455872 and rs3798220) with all-cause mortality and cardiovascular mortality by Cox regression analysis and with severity of disease by generalised linear modelling, with and without adjustment for age, sex, diabetes diagnosis, systolic blood pressure, BMI, smoking status, estimated glomerular filtration rate, LDL-cholesterol concentration, and use of lipid-lowering therapy. Results for plasma lipoprotein(a) concentrations were validated in five independent studies involving 10 195 patients with established coronary heart disease. Results for genetic associations were replicated through large-scale collaborative analysis in the GENIUS-CHD consortium, comprising 106 353 patients with established coronary heart disease and 19 332 deaths in 22 studies or cohorts.\n\nThe median follow-up was 9\u00b79 years. Increased severity of coronary heart disease was associated with lipoprotein(a) concentrations in plasma in the highest tertile (adjusted hazard radio [HR] 1\u00b744, 95% CI 1\u00b714-1\u00b783) and the presence of either LPA SNP (1\u00b788, 1\u00b740-2\u00b753). No associations were found in LURIC with all-cause mortality (highest tertile of lipoprotein(a) concentration in plasma 0\u00b795, 0\u00b781-1\u00b711 and either LPA SNP 1\u00b710, 0\u00b792-1\u00b731) or cardiovascular mortality (0\u00b799, 0\u00b781-1\u00b72 and 1\u00b713, 0\u00b790-1\u00b740, respectively) or in the validation studies.\n\nIn patients with prevalent coronary heart disease, lipoprotein(a) concentrations and genetic variants showed no associations with mortality. We conclude that these variables are not useful risk factors to measure to predict progression to death after coronary heart disease is established.\n\nSeventh Framework Programme for Research and Technical Development (AtheroRemo and RiskyCAD), INTERREG IV Oberrhein Programme, Deutsche Nierenstiftung, Else-Kroener Fresenius Foundation, Deutsche Stiftung f\u00fcr Herzforschung, Deutsche Forschungsgemeinschaft, Saarland University, German Federal Ministry of Education and Research, Willy Robert Pitzer Foundation, and Waldburg-Zeil Clinics Isny.", "doi": "10.1016/s2213-8587(17)30096-7", "pmid": "28566218", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS909985"}, {"db": "pmc", "key": "PMC5651679"}, {"db": "pii", "key": "S2213-8587(17)30096-7"}], "notes": [], "created": "2018-01-09T13:58:11.019Z", "modified": "2023-06-19T11:44:07.841Z"}, {"entity": "publication", "iuid": "cdd9add0db12422690baa0c8bf58021d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cdd9add0db12422690baa0c8bf58021d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cdd9add0db12422690baa0c8bf58021d"}}, "title": "Reaching the limits of prognostication in non-small cell lung cancer: an optimized biomarker panel fails to outperform clinical parameters.", "authors": [{"family": "Grinberg", "given": "Marianna", "initials": "M"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Brunnstr\u00f6m", "given": "Hans Rr", "initials": "HR"}, {"family": "Mattsson", "given": "Johanna Sm", "initials": "JS"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Hengstler", "given": "Jan G", "initials": "JG"}, {"family": "La Fleur", "given": "Linnea", "initials": "L"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Branden", "given": "Eva", "initials": "E"}, {"family": "St\u00e5hle", "given": "Elisabeth", "initials": "E"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Tracy", "given": "Derek K", "initials": "DK"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "30", "issn": "1530-0285", "issue": "7", "pages": "964-977", "title": "Mod. Pathol.", "issn-l": "0893-3952"}, "abstract": "Numerous protein biomarkers have been analyzed to improve prognostication in non-small cell lung cancer, but have not yet demonstrated sufficient value to be introduced into clinical practice. Here, we aimed to develop and validate a prognostic model for surgically resected non-small cell lung cancer. A biomarker panel was selected based on (1) prognostic association in published literature, (2) prognostic association in gene expression data sets, (3) availability of reliable antibodies, and (4) representation of diverse biological processes. The five selected proteins (MKI67, EZH2, SLC2A1, CADM1, and NKX2-1 alias TTF1) were analyzed by immunohistochemistry on tissue microarrays including tissue from 326 non-small cell lung cancer patients. One score was obtained for each tumor and each protein. The scores were combined, with or without the inclusion of clinical parameters, and the best prognostic model was defined according to the corresponding concordance index (C-index). The best-performing model was subsequently validated in an independent cohort consisting of tissue from 345 non-small cell lung cancer patients. The model based only on protein expression did not perform better compared to clinicopathological parameters, whereas combining protein expression with clinicopathological data resulted in a slightly better prognostic performance (C-index: all non-small cell lung cancer 0.63 vs 0.64; adenocarcinoma: 0.66 vs 0.70, squamous cell carcinoma: 0.57 vs 0.56). However, this modest effect did not translate into a significantly improved accuracy of survival prediction. The combination of a prognostic biomarker panel with clinicopathological parameters did not improve survival prediction in non-small cell lung cancer, questioning the potential of immunohistochemistry-based assessment of protein biomarkers for prognostication in clinical practice.", "doi": "10.1038/modpathol.2017.14", "pmid": "28281552", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Tissue Profiling": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "modpathol201714"}], "notes": [], "created": "2017-11-05T12:40:54.465Z", "modified": "2019-12-20T07:50:23.881Z"}, {"entity": "publication", "iuid": "fed9a0e44bda4fa89406ae38f21e2413", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fed9a0e44bda4fa89406ae38f21e2413.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fed9a0e44bda4fa89406ae38f21e2413"}}, "title": "Primary familial brain calcification linked to deletion of 5' noncoding region of SLC20A2.", "authors": [{"family": "Pasanen", "given": "P", "initials": "P"}, {"family": "M\u00e4kinen", "given": "J", "initials": "J"}, {"family": "Myllykangas", "given": "L", "initials": "L"}, {"family": "Guerreiro", "given": "R", "initials": "R"}, {"family": "Bras", "given": "J", "initials": "J"}, {"family": "Valori", "given": "M", "initials": "M"}, {"family": "Viitanen", "given": "M", "initials": "M"}, {"family": "Baumann", "given": "M", "initials": "M"}, {"family": "Tienari", "given": "P J", "initials": "PJ"}, {"family": "P\u00f6yh\u00f6nen", "given": "M", "initials": "M"}, {"family": "Baumann", "given": "P", "initials": "P"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "136", "issn": "1600-0404", "issue": "1", "pages": "59-63", "title": "Acta Neurol. Scand.", "issn-l": "0001-6314"}, "abstract": "Primary familial brain calcification (PFBC) is a rare neurological disease often inherited as a dominant trait. Mutations in four genes (SLC20A2, PDGFB, PDGFRB, and XPR1) have been reported in patients with PFBC. Of these, point mutations or small deletions in SLC20A2 are most common. Thus far, only one large deletion covering entire SLC20A2 and several smaller, exonic deletions of SLC20A2 have been reported. The aim of this study was to identify the causative gene defect in a Finnish PFBC family with three affected patients.\n\nA Finnish family with three PFBC patients and five unaffected subjects was studied. Sanger sequencing was used to exclude mutations in the coding and splice site regions of SLC20A2, PDGFRB, and PDGFB. Whole-exome (WES) and whole-genome sequencing (WGS) were performed to identify the causative mutation. A SNP array was used in segregation analysis.\n\nCopy number analysis of the WGS data revealed a heterozygous deletion of ~578\u00a0kb on chromosome 8. The deletion removes the 5' UTR region, the noncoding exon 1 and the putative promoter region of SLC20A2 as well as the coding regions of six other genes.\n\nOur results support haploinsufficiency of SLC20A2 as a pathogenetic mechanism in PFBC. Analysis of copy number variations (CNVs) is emerging as a crucial step in the molecular genetic diagnostics of PFBC, and it should not be limited to coding regions, as causative variants may reside in the noncoding parts of known disease-associated genes.", "doi": "10.1111/ane.12697", "pmid": "27726124", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:01:04.288Z", "modified": "2020-01-21T13:56:09.131Z"}, {"entity": "publication", "iuid": "c821e88dea2e412b8fe53454a68c5fb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c821e88dea2e412b8fe53454a68c5fb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c821e88dea2e412b8fe53454a68c5fb0"}}, "title": "Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "87", "issn": "1872-9142", "issue": null, "pages": "12-22", "title": "Mol. Immunol.", "issn-l": "0161-5890"}, "abstract": "Analysis of antibody repertoire development and specific antibody responses important for e.g. autoimmune conditions, allergy, and protection against disease is supported by high throughput sequencing and associated bioinformatics pipelines that describe the diversity of the encoded antibody variable domains. Proper assignment of sequences to germline genes are important for many such processes, for instance in the analysis of somatic hypermutation. Germline gene inference from antibody-encoding transcriptomes, by using tools such as TIgGER or IgDiscover, has a potential to enhance the quality of such analyses. These tools may also be used to identify germline genes not previously known. In this study, we exploited such software for germline gene inference and define aspects of analysis settings and pre-existing knowledge of germline genes that affect the outcome of gene inference. Furthermore, we demonstrate the capacity of IGHJ and IGHD haplotype inference, whenever subjects are heterozygous with respect to such genes, to lend support to IGHV gene inference in general, and to the identification of novel alleles presently not recognized by germline gene reference directories. We propose that such haplotype analysis shall, whenever possible, be used in future best practice to support the outcome of germline gene inference. IGHJ-directed haplotype inference was also used to identify haplotypes not expressing some IGHV germline genes. In particular, we identified a haplotype that did not express several major germline genes such as IGHV1-8, IGHV3-9, IGHV3-15, IGHV1-18, IGHV3-21, and IGHV3-23. We envisage that haplotype analysis will provide an efficient approach to identify subjects for further studies of the link between the available immunoglobulin repertoire and outcomes of immune responses.", "doi": "10.1016/j.molimm.2017.03.012", "pmid": "28388445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0161-5890(17)30081-0"}], "notes": [], "created": "2017-11-03T16:22:12.638Z", "modified": "2024-01-16T13:48:47.788Z"}, {"entity": "publication", "iuid": "088bba2accd9465f9b4514b515296a99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/088bba2accd9465f9b4514b515296a99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/088bba2accd9465f9b4514b515296a99"}}, "title": "Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes", "authors": [{"family": "Unnikrishnan", "given": "Ashwin", "initials": "A"}, {"family": "Papaemmanuil", "given": "Elli", "initials": "E"}, {"family": "Beck", "given": "Dominik", "initials": "D"}, {"family": "Deshpande", "given": "Nandan P", "initials": "NP"}, {"family": "Verma", "given": "Arjun", "initials": "A"}, {"family": "Kumari", "given": "Ashu", "initials": "A"}, {"family": "Woll", "given": "Petter S", "initials": "PS"}, {"family": "Richards", "given": "Laura A", "initials": "LA"}, {"family": "Knezevic", "given": "Kathy", "initials": "K"}, {"family": "Chandrakanthan", "given": "Vashe", "initials": "V"}, {"family": "Thoms", "given": "Julie A I", "initials": "JAI"}, {"family": "Tursky", "given": "Melinda L", "initials": "ML"}, {"family": "Huang", "given": "Yizhou", "initials": "Y"}, {"family": "Ali", "given": "Zara", "initials": "Z"}, {"family": "Olivier", "given": "Jake", "initials": "J"}, {"family": "Galbraith", "given": "Sally", "initials": "S"}, {"family": "Kulasekararaj", "given": "Austin G", "initials": "AG"}, {"family": "Tobiasson", "given": "Magnus", "initials": "M"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Pellagatti", "given": "Andrea", "initials": "A"}, {"family": "Wilson", "given": "Susan R", "initials": "SR"}, {"family": "Lindeman", "given": "Robert", "initials": "R"}, {"family": "Young", "given": "Boris", "initials": "B"}, {"family": "Ramakrishna", "given": "Raj", "initials": "R"}, {"family": "Arthur", "given": "Christopher", "initials": "C"}, {"family": "Stark", "given": "Richard", "initials": "R"}, {"family": "Crispin", "given": "Philip", "initials": "P"}, {"family": "Curnow", "given": "Jennifer", "initials": "J"}, {"family": "Warburton", "given": "Pauline", "initials": "P"}, {"family": "Roncolato", "given": "Fernando", "initials": "F"}, {"family": "Boultwood", "given": "Jacqueline", "initials": "J"}, {"family": "Lynch", "given": "Kevin", "initials": "K"}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW"}, {"family": "Mufti", "given": "Ghulam J", "initials": "GJ"}, {"family": "Hellstrom-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Wilkins", "given": "Marc R", "initials": "MR"}, {"family": "MacKenzie", "given": "Karen L", "initials": "KL"}, {"family": "Wong", "given": "Jason W H", "initials": "JWH"}, {"family": "Campbell", "given": "Peter J", "initials": "PJ"}, {"family": "Pimanda", "given": "John E", "initials": "JE"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "20", "issn": "2211-1247", "issue": "3", "pages": "572-585", "title": "Cell Rep", "issn-l": null}, "abstract": null, "doi": "10.1016/j.celrep.2017.06.067", "pmid": "28723562", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T13:11:25.608Z", "modified": "2018-12-10T12:30:55.664Z"}, {"entity": "publication", "iuid": "e1ee87b50807452bbdaa71bc517f10ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1ee87b50807452bbdaa71bc517f10ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1ee87b50807452bbdaa71bc517f10ca"}}, "title": "Genomewide analysis of admixture and adaptation in the Africanized honeybee.", "authors": [{"family": "Nelson", "given": "Ronald M", "initials": "RM"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Sim\u00f5es", "given": "Zil\u00e1 Luz Paulino", "initials": "ZLP"}, {"family": "Lawson", "given": "Daniel J", "initials": "DJ"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "26", "issn": "1365-294X", "issue": "14", "pages": "3603-3617", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60\u00a0years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here, we analyse whole-genome sequences of 32 Africanized honeybees sampled from throughout Brazil to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene-rich 1.4-Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0\u00a0years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments.", "doi": "10.1111/mec.14122", "pmid": "28378497", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Population-scale sequencing of Apis mellifera and Apis cerana", "key": "PRJNA236426"}, {"db": "BioProject", "description": "Africanized honeybee (Apis mellifera) sequencing", "key": "PRJNA350769"}], "notes": [], "created": "2017-11-02T13:51:52.946Z", "modified": "2024-01-16T13:48:47.796Z"}, {"entity": "publication", "iuid": "5cf4730cf1b146878c93fd28bd5b83ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cf4730cf1b146878c93fd28bd5b83ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cf4730cf1b146878c93fd28bd5b83ec"}}, "title": "Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence.", "authors": [{"family": "Sniekers", "given": "Suzanne", "initials": "S"}, {"family": "Stringer", "given": "Sven", "initials": "S", "orcid": "0000-0003-3115-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7e6ae56d0474688b3722f58d33f385d.json"}}, {"family": "Watanabe", "given": "Kyoko", "initials": "K"}, {"family": "Jansen", "given": "Philip R", "initials": "PR"}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI"}, {"family": "Krapohl", "given": "Eva", "initials": "E"}, {"family": "Taskesen", "given": "Erdogan", "initials": "E"}, {"family": "Hammerschlag", "given": "Anke R", "initials": "AR", "orcid": "0000-0003-4847-4814", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf251c46945046c79447bcdb7d3f28da.json"}}, {"family": "Okbay", "given": "Aysu", "initials": "A"}, {"family": "Zabaneh", "given": "Delilah", "initials": "D"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Chabris", "given": "Christopher F", "initials": "CF"}, {"family": "Iacono", "given": "William G", "initials": "WG"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}, {"family": "Johannesson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8759-6393", "researcher": {"href": "https://publications.scilifelab.se/researcher/164991d6c183431d8245e08bd876f400.json"}}, {"family": "Koellinger", "given": "Philipp", "initials": "P"}, {"family": "Lee", "given": "James J", "initials": "JJ", "orcid": "0000-0001-6547-5128", "researcher": {"href": "https://publications.scilifelab.se/researcher/a62c02dc148145f78d711190c246a59e.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Miller", "given": "Mike B", "initials": "MB"}, {"family": "Ollier", "given": "William E R", "initials": "WER"}, {"family": "Payton", "given": "Antony", "initials": "A"}, {"family": "Pendleton", "given": "Neil", "initials": "N"}, {"family": "Plomin", "given": "Robert", "initials": "R"}, {"family": "Rietveld", "given": "Cornelius A", "initials": "CA"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Posthuma", "given": "Danielle", "initials": "D", "orcid": "0000-0001-7582-2365", "researcher": {"href": "https://publications.scilifelab.se/researcher/406e98180d174e8ca087f50074c025c9.json"}}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "7", "pages": "1107-1112", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Intelligence is associated with important economic and health-related life outcomes. Despite intelligence having substantial heritability (0.54) and a confirmed polygenic nature, initial genetic studies were mostly underpowered. Here we report a meta-analysis for intelligence of 78,308 individuals. We identify 336 associated SNPs (METAL P < 5 \u00d7 10 -8) in 18 genomic loci, of which 15 are new. Around half of the SNPs are located inside a gene, implicating 22 genes, of which 11 are new findings. Gene-based analyses identified an additional 30 genes (MAGMA P < 2.73 \u00d7 10-6), of which all but one had not been implicated previously. We show that the identified genes are predominantly expressed in brain tissue, and pathway analysis indicates the involvement of genes regulating cell development (MAGMA competitive P = 3.5 \u00d7 10-6). Despite the well-known difference in twin-based heritability for intelligence in childhood (0.45) and adulthood (0.80), we show substantial genetic correlation (rg = 0.89, LD score regression P = 5.4 \u00d7 10-29). These findings provide new insight into the genetic architecture of intelligence.", "doi": "10.1038/ng.3869", "pmid": "28530673", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3869"}, {"db": "pmc", "key": "PMC5665562"}, {"db": "mid", "key": "NIHMS871043"}], "notes": [], "created": "2018-01-09T14:01:32.174Z", "modified": "2021-06-21T15:38:03.122Z"}, {"entity": "publication", "iuid": "50bf4910f1e345aeb3712d65fa4662dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50bf4910f1e345aeb3712d65fa4662dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50bf4910f1e345aeb3712d65fa4662dd"}}, "title": "EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia", "authors": [{"family": "Young", "given": "E", "initials": "E"}, {"family": "Noerenberg", "given": "D", "initials": "D"}, {"family": "Mansouri", "given": "L", "initials": "L"}, {"family": "Ljungstr\u00f6m", "given": "V", "initials": "V"}, {"family": "Frick", "given": "M", "initials": "M"}, {"family": "Sutton", "given": "L A", "initials": "LA"}, {"family": "Blakemore", "given": "S J", "initials": "SJ"}, {"family": "Galan-Sousa", "given": "J", "initials": "J"}, {"family": "Plevova", "given": "K", "initials": "K"}, {"family": "Baliakas", "given": "P", "initials": "P"}, {"family": "Rossi", "given": "D", "initials": "D"}, {"family": "Clifford", "given": "R", "initials": "R"}, {"family": "Roos-Weil", "given": "D", "initials": "D"}, {"family": "Navrkalova", "given": "V", "initials": "V"}, {"family": "D\u00f6rken", "given": "B", "initials": "B"}, {"family": "Schmitt", "given": "C A", "initials": "CA"}, {"family": "Smedby", "given": "K E", "initials": "KE"}, {"family": "Juliusson", "given": "G", "initials": "G"}, {"family": "Giacopelli", "given": "B", "initials": "B"}, {"family": "Blachly", "given": "J S", "initials": "JS"}, {"family": "Belessi", "given": "C", "initials": "C"}, {"family": "Panagiotidis", "given": "P", "initials": "P"}, {"family": "Chiorazzi", "given": "N", "initials": "N"}, {"family": "Davi", "given": "F", "initials": "F"}, {"family": "Langerak", "given": "A W", "initials": "AW"}, {"family": "Oscier", "given": "D", "initials": "D"}, {"family": "Schuh", "given": "A", "initials": "A"}, {"family": "Gaidano", "given": "G", "initials": "G"}, {"family": "Ghia", "given": "P", "initials": "P"}, {"family": "Xu", "given": "W", "initials": "W"}, {"family": "Fan", "given": "L", "initials": "L"}, {"family": "Bernard", "given": "O A", "initials": "OA"}, {"family": "Nguyen-Khac", "given": "F", "initials": "F"}, {"family": "Rassenti", "given": "L", "initials": "L"}, {"family": "Li", "given": "J", "initials": "J"}, {"family": "Kipps", "given": "T J", "initials": "TJ"}, {"family": "Stamatopoulos", "given": "K", "initials": "K"}, {"family": "Pospisilova", "given": "S", "initials": "S"}, {"family": "Zenz", "given": "T", "initials": "T"}, {"family": "Oakes", "given": "C C", "initials": "CC"}, {"family": "Strefford", "given": "J C", "initials": "JC"}, {"family": "Rosenquist", "given": "R", "initials": "R"}, {"family": "Damm", "given": "F", "initials": "F"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "31", "issn": "1476-5551", "issue": "7", "pages": "1547-1554", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": null, "doi": "10.1038/leu.2016.359", "pmid": "27890934", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:30:04.162Z", "modified": "2024-01-16T13:48:47.805Z"}, {"entity": "publication", "iuid": "d80d46210e60415ab9346a07ca5f1198", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d80d46210e60415ab9346a07ca5f1198.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d80d46210e60415ab9346a07ca5f1198"}}, "title": "Design and synthesis of potent inhibitors of the mono(ADP-ribosyl)transferase, PARP14", "authors": [{"family": "Upton", "given": "Kristen", "initials": "K"}, {"family": "Meyers", "given": "Matthew", "initials": "M"}, {"family": "Thorsell", "given": "Ann Gerd", "initials": "AG"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Holechek", "given": "Jacob", "initials": "J"}, {"family": "Lease", "given": "Robert", "initials": "R"}, {"family": "Schey", "given": "Garrett", "initials": "G"}, {"family": "Wolf", "given": "Emily", "initials": "E"}, {"family": "Lucente", "given": "Adrianna", "initials": "A"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}, {"family": "Ferraris", "given": "Dana", "initials": "D"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "27", "issn": "0960-894X", "issue": "13", "pages": "2907-2911", "title": "Bioorganic & Medicinal Chemistry Letters", "issn-l": "0960-894X"}, "abstract": null, "doi": "10.1016/j.bmcl.2017.04.089", "pmid": "28495083", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:19.224Z", "modified": "2017-11-09T13:18:39.439Z"}, {"entity": "publication", "iuid": "c6255372cfff4cc8a74c45529a41fa9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6255372cfff4cc8a74c45529a41fa9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6255372cfff4cc8a74c45529a41fa9d"}}, "title": "D-methionine interferes with non-typeable Haemophilus influenzae peptidoglycan synthesis during growth and biofilm formation.", "authors": [{"family": "Dawe", "given": "Harriet", "initials": "H"}, {"family": "Berger", "given": "Evelin", "initials": "E"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Angus", "given": "Elizabeth M", "initials": "EM"}, {"family": "Howlin", "given": "Robert P", "initials": "RP"}, {"family": "Laver", "given": "Jay R", "initials": "JR"}, {"family": "Tebruegge", "given": "Marc", "initials": "M"}, {"family": "Hall-Stoodley", "given": "Luanne", "initials": "L"}, {"family": "Stoodley", "given": "Paul", "initials": "P"}, {"family": "Faust", "given": "Saul N", "initials": "SN"}, {"family": "Allan", "given": "Raymond N", "initials": "RN"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "163", "issn": "1465-2080", "issue": "7", "pages": "1093-1104", "title": "Microbiology (Reading, Engl.)", "issn-l": "1350-0872"}, "abstract": "Non-typeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that plays a major role in a number of respiratory tract infections, including otitis media, cystic fibrosis and chronic obstructive pulmonary disease. Biofilm formation has been implicated in both NTHi colonization and disease, and is responsible for the increased tolerance of this pathogen towards antibiotic treatment. Targeting metabolic pathways that are important in NTHi biofilm formation represents a potential strategy to combat this antibiotic recalcitrance. A previous investigation demonstrated increased expression of a putative d-methionine uptake protein following exposure of NTHi biofilms to the ubiquitous signalling molecule, nitric oxide. We therefore hypothesized that treatment with exogenous d-methionine would impact on NTHi biofilm formation and increase antibiotic sensitivity. Treatment of NTHi during the process of biofilm formation resulted in a reduction in biofilm viability, increased biomass, changes in the overall biofilm architecture and the adoption of an amorphous cellular morphology. Quantitative proteomic analyses identified 124 proteins that were differentially expressed following d-methionine treatment, of which 51 (41 %) were involved in metabolic and transport processes. Nine proteins involved in peptidoglycan synthesis and cell division showed significantly increased expression. Furthermore, d-methionine treatment augmented the efficacy of azithromycin treatment and highlighted the potential of d-methionine as an adjunctive therapeutic approach for NTHi biofilm-associated infections.", "doi": "10.1099/mic.0.000491", "pmid": "28699879", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-27T22:44:34.196Z", "modified": "2024-01-16T13:46:32.646Z"}, {"entity": "publication", "iuid": "e3ed6bf1225e4c6cb261acd854b6c874", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3ed6bf1225e4c6cb261acd854b6c874.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3ed6bf1225e4c6cb261acd854b6c874"}}, "title": "Close Encounters \u2013 Probing Proximal Proteins in Live or Fixed Cells", "authors": [{"family": "L\u00f6nn", "given": "Peter", "initials": "P"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "42", "issn": "0968-0004", "issue": "7", "pages": "504-515", "title": "Trends in Biochemical Sciences", "issn-l": null}, "abstract": null, "doi": "10.1016/j.tibs.2017.05.003", "pmid": "28566215", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T07:32:49.202Z", "modified": "2023-04-14T13:56:12.506Z"}, {"entity": "publication", "iuid": "74bdc77a2a8a4d918aeb02299ccac60b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74bdc77a2a8a4d918aeb02299ccac60b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74bdc77a2a8a4d918aeb02299ccac60b"}}, "title": "Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)", "authors": [{"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Wang", "given": "Biao", "initials": "B"}, {"family": "Saether", "given": "Stein Are", "initials": "SA"}, {"family": "Blom", "given": "Mozes Pil Kyu", "initials": "MPK"}, {"family": "Fiske", "given": "Peder", "initials": "P"}, {"family": "Halvarsson", "given": "Peter", "initials": "P"}, {"family": "Horsburgh", "given": "Gavin J", "initials": "GJ"}, {"family": "Burke", "given": "Terry", "initials": "T"}, {"family": "K\u00e5l\u00e5s", "given": "John Atle", "initials": "JA"}, {"family": "Ekblom", "given": "Robert", "initials": "R"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "26", "issn": "0962-1083", "issue": "13", "pages": "3458-3471", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": "We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin \u03b1-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.", "doi": "10.1111/mec.14118", "pmid": "28345264", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:48:44.020Z", "modified": "2020-01-21T13:56:11.928Z"}, {"entity": "publication", "iuid": "11cec8cacdd44603bc2ae2054cc21468", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11cec8cacdd44603bc2ae2054cc21468.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11cec8cacdd44603bc2ae2054cc21468"}}, "title": "A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.", "authors": [{"family": "Manning", "given": "Alisa", "initials": "A"}, {"family": "Highland", "given": "Heather M", "initials": "HM"}, {"family": "Gasser", "given": "Jessica", 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"initials": "M"}, {"family": "Taylor", "given": "Herman A", "initials": "HA"}, {"family": "Wilson", "given": "Gregory", "initials": "G"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Oksa", "given": "Heikki", "initials": "H"}, {"family": "Scott", "given": "William R", "initials": "WR"}, {"family": "Afzal", "given": "Uzma", "initials": "U"}, {"family": "Tan", "given": "Sian-Tsung", "initials": "ST"}, {"family": "Loh", "given": "Marie", "initials": "M"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Sehmi", "given": "Jobanpreet", "initials": "J"}, {"family": "Kooner", "given": "Jaspal Singh", "initials": "JS"}, {"family": "Lehne", "given": "Benjamin", "initials": "B"}, {"family": "Cho", "given": "Yoon Shin", "initials": "YS"}, {"family": "Lee", "given": "Jong-Young", "initials": "JY"}, {"family": "Han", "given": "Bok-Ghee", "initials": "BG"}, {"family": "K\u00e4r\u00e4j\u00e4m\u00e4ki", "given": "Annemari", "initials": "A"}, {"family": 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"Allan", "initials": "A"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Hakaste", "given": "Liisa", "initials": "L"}, {"family": "Kravic", "given": "Jasmina", "initials": "J"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "Lauritzen", "given": "Torsten", "initials": "T"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Stirrups", "given": "Kathleen E", "initials": "KE"}, {"family": "Owen", "given": "Katharine R", "initials": "KR"}, {"family": "Farmer", "given": "Andrew J", "initials": "AJ"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "O'Rahilly", "given": "Stephen P", "initials": "SP"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Levy", "given": "Jonathan C", "initials": "JC"}, {"family": "Hodgkiss", "given": "Dylan", "initials": 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"CNA"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Bell", "given": "Graeme I", "initials": "GI"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "Cox", "given": "Nancy J", "initials": "NJ"}, {"family": "Duggirala", "given": "Ravindranath", "initials": "R"}, {"family": "Seielstad", "given": "Mark", "initials": "M"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Dupuis", "given": "Josee", "initials": "J"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Hanis", "given": "Craig L", "initials": "CL"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "66", "issn": "1939-327X", "issue": "7", "pages": "2019-2032", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.", "doi": "10.2337/db16-1329", "pmid": "28341696", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "db16-1329"}, {"db": "pmc", "key": "PMC5482074"}, {"db": "mid", "key": "EMS72347"}], "notes": [], "created": "2017-10-25T15:18:19.643Z", "modified": "2024-01-16T13:48:47.816Z"}, {"entity": "publication", "iuid": "b81d4cdfd4e04cea8794379691537941", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b81d4cdfd4e04cea8794379691537941.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b81d4cdfd4e04cea8794379691537941"}}, "title": "2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.", "authors": [{"family": "Hernandez-Castro", "given": "Luis E", "initials": "LE"}, {"family": "Paterno", "given": "Marta", "initials": "M"}, {"family": "Villac\u00eds", "given": "Anita G", "initials": "AG"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Costales", "given": "Jaime A", "initials": "JA"}, {"family": "De Noia", "given": "Michele", "initials": "M"}, {"family": "Oca\u00f1a-Mayorga", "given": "Sof\u00eda", "initials": "S"}, {"family": "Yumiseva", "given": "Cesar A", "initials": "CA"}, {"family": "Grijalva", "given": "Mario J", "initials": "MJ"}, {"family": "Llewellyn", "given": "Martin S", "initials": "MS"}], "type": "evaluation studies", "published": "2017-07-00", "journal": {"volume": "11", "issn": "1935-2735", "issue": "7", "pages": "e0005710", "title": "PLoS Negl Trop Dis", "issn-l": "1935-2727"}, "abstract": "Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses.\n\nThe 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area.\n\nOur findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment.", "doi": "10.1371/journal.pntd.0005710", "pmid": "28723901", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PNTD-D-16-01890"}, {"db": "pmc", "key": "PMC5536387"}], "notes": [], "created": "2017-11-03T16:19:49.882Z", "modified": "2024-01-16T13:48:47.833Z"}, {"entity": "publication", "iuid": "64f09ccd0fe64bf093e9d17de685ef9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64f09ccd0fe64bf093e9d17de685ef9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64f09ccd0fe64bf093e9d17de685ef9c"}}, "title": "Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate", "authors": [{"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Rubin", "given": "Carl Johan", "initials": "CJ"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Folkvord", "given": "Arild", "initials": "A"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal-article", "published": "2017-06-30", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": null, "doi": "10.7554/elife.23907", "pmid": "28665273", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Clupea harengus Raw sequence reads", "key": "PRJNA356817"}], "notes": [], "created": "2017-10-30T09:27:43.834Z", "modified": "2024-01-16T13:48:47.843Z"}, {"entity": "publication", "iuid": "7c8cc7a768524b84be600507b658f4b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9"}}, "title": "The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.", "authors": [{"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Samaniego Castruita", "given": "Jose A", "initials": "JA"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Kuderna", "given": "Lukas F K", "initials": "LFK"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Jannikke", "initials": "J"}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}, {"family": "Larson", "given": "Greger", "initials": "G"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Hansen", "given": "Anders J", "initials": "AJ"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2017-06-29", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "495", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference.\n\nReassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples.\n\nIn conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome.", "doi": "10.1186/s12864-017-3883-3", "pmid": "28662691", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3883-3"}, {"db": "pmc", "key": "PMC5492679"}], "notes": [], "created": "2017-11-03T16:21:39.181Z", "modified": "2021-07-07T20:31:10.838Z"}, {"entity": "publication", "iuid": "aee194257ec94bb3bae080f4e5720c88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aee194257ec94bb3bae080f4e5720c88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aee194257ec94bb3bae080f4e5720c88"}}, "title": "New Promises of Chemical Proteomics for Drug Development", "authors": [{"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": null, "published": "2017-06-27", "journal": {"title": "Novel Approaches in Drug Designing & Development", "issn": "2575-8942", "issn-l": null, "volume": "2", "issue": "1", "pages": "555579"}, "abstract": null, "doi": "10.19080/NAPDD.2017.02.555579", "pmid": null, "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-08T13:39:38.348Z", "modified": "2024-01-18T23:43:48.969Z"}, {"entity": "publication", "iuid": "e2b8720b84934d35b88c22094e92af4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2b8720b84934d35b88c22094e92af4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2b8720b84934d35b88c22094e92af4f"}}, "title": "Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation", "authors": [{"family": "Danelius", "given": "Emma", "initials": "E"}, {"family": "Andersson", "given": "Hanna", "initials": "H"}, {"family": "Jarvoll", "given": "Patrik", "initials": "P"}, {"family": "Lood", "given": "Kajsa", "initials": "K"}, {"family": "Gr\u00e4fenstein", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M"}], "type": "journal-article", "published": "2017-06-27", "journal": {"volume": "56", "issn": "1520-4995", "issue": "25", "pages": "3265-3272", "title": "Biochemistry", "issn-l": "0006-2960"}, "abstract": null, "doi": "10.1021/acs.biochem.7b00429", "pmid": "28581720", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T11:01:04.100Z", "modified": "2025-10-17T13:03:59.743Z"}, {"entity": "publication", "iuid": "b44a0f0daee34fa6824e98bb3e46ce93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b44a0f0daee34fa6824e98bb3e46ce93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b44a0f0daee34fa6824e98bb3e46ce93"}}, "title": "Identification of a Sj\u00f6gren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons", "authors": [{"family": "Li", "given": "He", "initials": "H"}, {"family": "Reksten", "given": "Tove Ragna", "initials": "TR"}, {"family": "Ice", "given": "John A", "initials": "JA"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Adrianto", "given": "Indra", "initials": "I"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Wang", "given": "Shaofeng", "initials": "S"}, {"family": "He", "given": "Bo", "initials": "B"}, {"family": "Grundahl", "given": "Kiely M", "initials": "KM"}, {"family": "Glenn", "given": "Stuart B", "initials": "SB"}, {"family": "Miceli-Richard", "given": "Corinne", "initials": "C"}, {"family": "Bowman", "given": "Simon", "initials": "S"}, {"family": "Lester", "given": "Sue", "initials": "S"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Eloranta", "given": "Maija Leena", "initials": "ML"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "G\u00f8ransson", "given": "Lasse G", "initials": "LG"}, {"family": "Harboe", "given": "Erna", "initials": "E"}, {"family": "Guthridge", "given": "Joel M", "initials": "JM"}, {"family": "Kaufman", "given": "Kenneth M", "initials": "KM"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Cunninghame Graham", "given": "Deborah S", "initials": "DS"}, {"family": "Patel", "given": "Ketan", "initials": "K"}, {"family": "Adler", "given": "Adam J", "initials": "AJ"}, {"family": "Farris", "given": "A Darise", "initials": "AD"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "Chodosh", "given": "James", "initials": "J"}, {"family": "Gopalakrishnan", "given": "Rajaram", "initials": "R"}, {"family": "Weisman", "given": "Michael H", "initials": "MH"}, {"family": "Venuturupalli", "given": "Swamy", "initials": "S"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Hefner", "given": "Kimberly S", "initials": "KS"}, {"family": "Houston", "given": "Glen D", "initials": "GD"}, {"family": "Huang", "given": "Andrew J W", "initials": "AJW"}, {"family": "Hughes", "given": "Pamela J", "initials": "PJ"}, {"family": "Lewis", "given": "David M", "initials": "DM"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Vista", "given": "Evan S", "initials": "ES"}, {"family": "Edgar", "given": "Contessa E", "initials": "CE"}, {"family": "Rohrer", "given": "Michael D", "initials": "MD"}, {"family": "Stone", "given": "Donald U", "initials": "DU"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "James", "given": "Judith A", "initials": "JA"}, {"family": "Turner", "given": "Sean", "initials": "S"}, {"family": "Alevizos", "given": "Ilias", "initials": "I"}, {"family": "Anaya", "given": "Juan Manuel", "initials": "JM"}, {"family": "Rhodus", "given": "Nelson L", "initials": "NL"}, {"family": "Segal", "given": "Barbara M", "initials": "BM"}, {"family": "Montgomery", "given": "Courtney G", "initials": "CG"}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}, {"family": "Kovats", "given": "Susan", "initials": "S"}, {"family": "Mariette", "given": "Xavier", "initials": "X"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Witte", "given": "Torsten", "initials": "T"}, {"family": "Rischmueller", "given": "Maureen", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Ng", "given": "Wan Fai", "initials": "WF"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ"}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-06-22", "journal": {"volume": "13", "issn": "1553-7404", "issue": "6", "pages": "e1006820", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": null, "doi": "10.1371/journal.pgen.1006820", "pmid": "28640813", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T15:58:57.273Z", "modified": "2020-01-21T13:56:11.789Z"}, {"entity": "publication", "iuid": "42bb648065a04077b503ed68fe0d859d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42bb648065a04077b503ed68fe0d859d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42bb648065a04077b503ed68fe0d859d"}}, "title": "Functional metabolomics as a tool to analyze Mediator function and structure in plants.", "authors": [{"family": "Davoine", "given": "Celine", "initials": "C"}, {"family": "Abreu", "given": "Ilka N", "initials": "IN"}, {"family": "Khajeh", "given": "Khalil", "initials": "K"}, {"family": "Blomberg", "given": "Jeanette", "initials": "J"}, {"family": "Kidd", "given": "Brendan N", "initials": "BN"}, {"family": "Kazan", "given": "Kemal", "initials": "K"}, {"family": "Schenk", "given": "Peer M", "initials": "PM"}, {"family": "Gerber", "given": "Lorenz", "initials": "L"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1181-0415", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae5cb7a54364e74b4f0261ab8d8e0ce.json"}}], "type": "journal article", "published": "2017-06-22", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "12", "issue": "6", "pages": "e0179640", "issn-l": "1932-6203"}, "abstract": "Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast. Based on these results, we suggest localization of previously unassigned plant Mediator subunits to specific modules. We also describe novel roles for individual subunits in development, and demonstrate changes in gene expression patterns and specific metabolite levels in med18 and med25, which can explain their phenotypes. We find that med18 displays levels of phytoalexins normally found in wild type plants only after exposure to pathogens. Our results indicate that different Mediator subunits are involved in specific signaling pathways that control developmental processes and tolerance to pathogen infections.", "doi": "10.1371/journal.pone.0179640", "pmid": "28640868", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5480960"}, {"db": "pii", "key": "PONE-D-16-45854"}], "notes": [], "created": "2023-04-12T14:19:27.306Z", "modified": "2025-10-17T13:03:18.678Z"}, {"entity": "publication", "iuid": "68e6f0f7bb304127afa33736575f35d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68e6f0f7bb304127afa33736575f35d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68e6f0f7bb304127afa33736575f35d0"}}, "title": "Identifying Bird Remains Using Ancient DNA Barcoding.", "authors": [{"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Barton", "given": "Nick", "initials": "N"}, {"family": "Bochenski", "given": "Zbigniew M", "initials": "ZM"}, {"family": "Tomek", "given": "Teresa", "initials": "T"}, {"family": "Rudling", "given": "David", "initials": "D"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Stewart", "given": "John R", "initials": "JR"}], "type": "journal article", "published": "2017-06-21", "journal": {"volume": "8", "issn": "2073-4425", "issue": "6", "pages": "169", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.", "doi": "10.3390/genes8060169", "pmid": "28635635", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "genes8060169"}, {"db": "pmc", "key": "PMC5485533"}], "notes": [], "created": "2017-11-03T13:16:04.796Z", "modified": "2021-07-07T20:31:10.826Z"}, {"entity": "publication", "iuid": "4aca1a288471461c987de11a37210caf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4aca1a288471461c987de11a37210caf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4aca1a288471461c987de11a37210caf"}}, "title": "Identification of novel small molecules that inhibit STAT3-dependent transcription and function.", "authors": [{"family": "Kolosenko", "given": "Iryna", "initials": "I", "orcid": "0000-0003-3988-1784", "researcher": {"href": "https://publications.scilifelab.se/researcher/83553ab04ddb43b38934b61ddacb8e9a.json"}}, {"family": "Yu", "given": "Yasmin", "initials": "Y"}, {"family": "Busker", "given": "Sander", "initials": "S"}, {"family": "Dyczynski", "given": "Matheus", "initials": "M"}, {"family": "Liu", "given": "Jianping", "initials": "J"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Palm Apergi", "given": "Caroline", "initials": "C"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP"}, {"family": "Page", "given": "Brent D G", "initials": "BDG"}, {"family": "Grander", "given": "Dan", "initials": "D"}], "type": "journal article", "published": "2017-06-21", "journal": {"volume": "12", "issn": "1932-6203", "issue": "6", "pages": "e0178844", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Activation of Signal Transducer and Activator of Transcription 3 (STAT3) has been linked to several processes that are critical for oncogenic transformation, cancer progression, cancer cell proliferation, survival, drug resistance and metastasis. Inhibition of STAT3 signaling has shown a striking ability to inhibit cancer cell growth and therefore, STAT3 has become a promising target for anti-cancer drug development. The aim of this study was to identify novel inhibitors of STAT-dependent gene transcription. A cellular reporter-based system for monitoring STAT3 transcriptional activity was developed which was suitable for high-throughput screening (Z' = 0,8). This system was used to screen a library of 28,000 compounds (the ENAMINE Drug-Like Diversity Set). Following counter-screenings and toxicity studies, we identified four hit compounds that were subjected to detailed biological characterization. Of the four hits, KI16 stood out as the most promising compound, inhibiting STAT3 phosphorylation and transcriptional activity in response to IL6 stimulation. In silico docking studies showed that KI16 had favorable interactions with the STAT3 SH2 domain, however, no inhibitory activity could be observed in the STAT3 fluorescence polarization assay. KI16 inhibited cell viability preferentially in STAT3-dependent cell lines. Taken together, using a targeted, cell-based approach, novel inhibitors of STAT-driven transcriptional activity were discovered which are interesting leads to pursue further for the development of anti-cancer therapeutic agents.", "doi": "10.1371/journal.pone.0178844", "pmid": "28636670", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-09843"}, {"db": "pmc", "key": "PMC5479526"}], "notes": [], "created": "2017-10-31T13:34:40.881Z", "modified": "2025-10-17T13:04:29.218Z"}, {"entity": "publication", "iuid": "dbf3020544ba44c1b2aa92b11685c804", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbf3020544ba44c1b2aa92b11685c804.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbf3020544ba44c1b2aa92b11685c804"}}, "title": "Systems Biology of Metabolism.", "authors": [{"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-06-20", "journal": {"volume": "86", "issn": "1545-4509", "issue": "1", "pages": "245-275", "title": "Annu. Rev. Biochem.", "issn-l": "0066-4154"}, "abstract": "Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.", "doi": "10.1146/annurev-biochem-061516-044757", "pmid": "28301739", "labels": {"Systems Biology": "Technology development", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-12-01T10:32:36.485Z", "modified": "2021-06-21T15:35:36.840Z"}, {"entity": "publication", "iuid": "5f80f81f0f7c4ae7ab8b10c643e0c47c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f80f81f0f7c4ae7ab8b10c643e0c47c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f80f81f0f7c4ae7ab8b10c643e0c47c"}}, "title": "Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.", "authors": [{"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ"}, {"family": "Kim", "given": "Young-Mo", "initials": "YM"}, {"family": "Wei", "given": "Siwei", "initials": "S"}, {"family": "Nicora", "given": "Carrie D", "initials": "CD"}, {"family": "Fillmore", "given": "Thomas L", "initials": "TL"}, {"family": "Purvine", "given": "Samuel O", "initials": "SO"}, {"family": "Webb-Robertson", "given": "Bobbie-Jo", "initials": "BJ"}, {"family": "Smith", "given": "Richard D", "initials": "RD"}, {"family": "Baker", "given": "Scott E", "initials": "SE"}, {"family": "Metz", "given": "Thomas O", "initials": "TO"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-06-20", "journal": {"volume": "8", "issn": "2150-7511", "issue": "3", "title": "MBio", "issn-l": null}, "abstract": "The yeast Yarrowia lipolytica is a potent accumulator of lipids, and lipogenesis in this organism can be influenced by a variety of factors, such as genetics and environmental conditions. Using a multifactorial study, we elucidated the effects of both genetic and environmental factors on regulation of lipogenesis in Y.\u00a0lipolytica and identified how two opposite regulatory states both result in lipid accumulation. This study involved comparison of a strain overexpressing diacylglycerol acyltransferase (DGA1) with a control strain grown under either nitrogen or carbon limitation conditions. A strong correlation was observed between the responses on the transcript and protein levels. Combination of DGA1 overexpression with nitrogen limitation resulted in a high level of lipid accumulation accompanied by downregulation of several amino acid biosynthetic pathways, including that of leucine in particular, and these changes were further correlated with a decrease in metabolic fluxes. This downregulation was supported by the measured decrease in the level of 2-isopropylmalate, an intermediate of leucine biosynthesis. Combining the multi-omics data with putative transcription factor binding motifs uncovered a contradictory role for TORC1 in controlling lipid accumulation, likely mediated through 2-isopropylmalate and a Leu3-like transcription factor.IMPORTANCE The ubiquitous metabolism of lipids involves refined regulation, and an enriched understanding of this regulation would have wide implications. Various factors can influence lipid metabolism, including the environment and genetics. We demonstrated, using a multi-omics and multifactorial experimental setup, that multiple factors affect lipid accumulation in the yeast Yarrowia lipolytica Using integrative analysis, we identified novel interactions between nutrient restriction and genetic factors involving regulators that are highly conserved among eukaryotes. Given that lipid metabolism is involved in many diseases but is also vital to the development of microbial cell factories that can provide us with sustainable fuels and oleochemicals, we envision that our report introduces foundational work to further unravel the regulation of lipid accumulation in eukaryal cells.", "doi": "10.1128/mBio.00857-17", "pmid": "28634240", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mBio.00857-17"}, {"db": "pmc", "key": "PMC5478895"}], "notes": [], "created": "2017-11-03T16:22:28.954Z", "modified": "2024-01-16T13:48:47.862Z"}, {"entity": "publication", "iuid": "9486574ac8694aadb050ec7121208a0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9486574ac8694aadb050ec7121208a0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9486574ac8694aadb050ec7121208a0b"}}, "title": "Global Kinetic Mechanism of Microsomal Glutathione Transferase 1 and Insights into Dynamic Enzyme Activation.", "authors": [{"family": "Spahiu", "given": "Linda", "initials": "L"}, {"family": "\u00c5lander", "given": "Johan", "initials": "J"}, {"family": "Ottosson-Wadlund", "given": "Astrid", "initials": "A"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Lehmer", "given": "Carina", "initials": "C"}, {"family": "Armstrong", "given": "Richard N", "initials": "RN"}, {"family": "Morgenstern", "given": "Ralf", "initials": "R"}], "type": "journal article", "published": "2017-06-20", "journal": {"volume": "56", "issn": "1520-4995", "issue": "24", "pages": "3089-3098", "title": "Biochemistry", "issn-l": "0006-2960"}, "abstract": "Microsomal glutathione transferase 1 (MGST1) has a unique ability to be activated, \u226430-fold, by modification with sulfhydryl reagents. MGST1 exhibits one-third-of-the-sites reactivity toward glutathione and hence heterogeneous binding to different active sites in the homotrimer. Limited turnover stopped-flow kinetic measurements of the activated enzyme allowed us to more accurately determine the KD for the \"third\" low-affinity GSH binding site (1.4 \u00b1 0.3 mM). The rate of thiolate formation, k2 (0.77 \u00b1 0.06 s(-1)), relevant to turnover, could also be determined. By deriving the steady-state rate equation for a random sequential mechanism for MGST1, we can predict KM, kcat, and kcat/KM values from these and previously determined pre-steady-state rate constants (all determined at 5 \u00b0C). To assess whether the pre-steady-state behavior can account for the steady-state kinetic behavior, we have determined experimental values for kinetic parameters at 5 \u00b0C. For reactive substrates and the activated enzyme, data for the microscopic steps account for the global mechanism of MGST1. For the unactivated enzyme and more reactive electrophilic substrates, pre-steady-state and steady-state data can be reconciled only if a more active subpopulation of MGST1 is assumed. We suggest that unactivated MGST1 can be partially activated in its unmodified form. The existence of an activated subpopulation (approximately 10%) could be demonstrated in limited turnover experiments. We therefore suggest that MSGT1 displays a preexisting dynamic equilibrium between high- and low-activity forms.", "doi": "10.1021/acs.biochem.7b00285", "pmid": "28558199", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-24T12:50:45.776Z", "modified": "2025-10-17T13:05:08.857Z"}, {"entity": "publication", "iuid": "7756f797074341b993192bb115457cdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7756f797074341b993192bb115457cdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7756f797074341b993192bb115457cdf"}}, "title": "Combining Flow and Mass Cytometry in the Search for Biomarkers in Chronic Graft-versus-Host Disease.", "authors": [{"family": "Stikvoort", "given": "Arwen", "initials": "A"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "R\u00e5destad", "given": "Emelie", "initials": "E"}, {"family": "T\u00f6rl\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Bj\u00f6rklund", "given": "Andreas", "initials": "A"}, {"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Gertow", "given": "Jens", "initials": "J"}, {"family": "Sundberg", "given": "Berit", "initials": "B"}, {"family": "Remberger", "given": "Mats", "initials": "M"}, {"family": "Sundin", "given": "Mikael", "initials": "M"}, {"family": "Mattsson", "given": "Jonas", "initials": "J"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Uhlin", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2017-06-19", "journal": {"volume": "8", "issn": "1664-3224", "issue": null, "pages": "717", "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "Chronic graft-versus-host disease (cGVHD) is a debilitating complication arising in around half of all patients treated with an allogeneic hematopoietic stem cell transplantation. Even though treatment of severe cGVHD has improved during recent years, it remains one of the main causes of morbidity and mortality in affected patients. Biomarkers in blood that could aid in the diagnosis and classification of cGVHD severity are needed for the development of novel treatment strategies that can alleviate symptoms and reduce the need for painful and sometimes complicated tissue biopsies. Methods that comprehensively profile complex biological systems such as the immune system can reveal unanticipated markers when used with the appropriate methods of data analysis. Here, we used mass cytometry, flow cytometry, enzyme-linked immunosorbent assay, and multiplex assays to systematically profile immune cell populations in 68 patients with varying grades of cGVHD. We identified multiple subpopulations across T, B, and NK-cell lineages that distinguished patients with cGVHD from those without cGVHD and which were associated in varying ways with severity of cGVHD. Specifically, initial flow cytometry demonstrated that patients with more severe cGVHD had lower mucosal-associated T cell frequencies, with a concomitant higher level of CD38 expression on T cells. Mass cytometry could identify unique subpopulations specific for cGVHD severity albeit with some seemingly conflicting results. For instance, patients with severe cGVHD had an increased frequency of activated B cells compared to patients with moderate cGVHD while activated B cells were found at a reduced frequency in patients with mild cGVHD compared to patients without cGVHD. Moreover, results indicate it may be possible to validate mass cytometry results with clinically viable, smaller flow cytometry panels. Finally, no differences in levels of blood soluble markers could be identified, with the exception for the semi-soluble combined marker B-cell activating factor/B cell ratio, which was increased in patients with mild cGVHD compared to patients without cGVHD. These findings suggest that interdependencies between such perturbed subpopulations of cells play a role in cGVHD pathogenesis and can serve as future diagnostic and therapeutic targets.", "doi": "10.3389/fimmu.2017.00717", "pmid": "28674539", "labels": {"Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5474470"}], "notes": [], "created": "2017-10-04T13:41:42.065Z", "modified": "2021-07-08T09:26:23.132Z"}, {"entity": "publication", "iuid": "82ad34b83108423895e507826359e13b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82ad34b83108423895e507826359e13b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82ad34b83108423895e507826359e13b"}}, "title": "Establishment of photosynthesis is controlled by two distinct regulatory phases", "authors": [{"family": "Dubreuil", "given": "Carole", "initials": "C"}, {"family": "Jin", "given": "Xu", "initials": "X"}, {"family": "Barajas-L\u00f3pez", "given": "Juan de Dios", "initials": "JdD"}, {"family": "Hewitt", "given": "Timothy Hewitt", "initials": "TH"}, {"family": "Tanz", "given": "Sandra", "initials": "S"}, {"family": "Dobrenel", "given": "Thomas", "initials": "T"}, {"family": "Schr\u00f6der", "given": "Wolfgang", "initials": "W"}, {"family": "Hanson", "given": "Johannes", "initials": "J"}, {"family": "Pesquet", "given": "Edouard", "initials": "E"}, {"family": "Gr\u00f6nlund", "given": "Andreas", "initials": "A"}, {"family": "Small", "given": "Ian D", "initials": "ID"}, {"family": "Strand", "given": "Asa", "initials": "A"}], "type": "journal-article", "published": "2017-06-16", "journal": {"volume": null, "issn": "1532-2548", "issue": null, "pages": "pp.00435.2017", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": null, "doi": "10.1104/pp.17.00435", "pmid": "28626007", "labels": {"Cryo-EM": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:30:24.233Z", "modified": "2025-10-17T13:03:18.719Z"}, {"entity": "publication", "iuid": "1a7366ba8d23449d91515036583cef23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a7366ba8d23449d91515036583cef23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a7366ba8d23449d91515036583cef23"}}, "title": "Protein expression in tension wood formation monitored at high tissue resolution in Populus", "authors": [{"family": "Bygdell", "given": "Joakim", "initials": "J"}, {"family": "Srivastava", "given": "Vaibhav", "initials": "V"}, {"family": "Obudulu", "given": "Ogonna", "initials": "O"}, {"family": "Srivastava", "given": "Manoj K", "initials": "MK"}, {"family": "Nilsson", "given": "Robert", "initials": "R"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ"}, {"family": "Wingsle", "given": "Gunnar", "initials": "G"}], "type": "journal-article", "published": "2017-06-15", "journal": {"volume": "68", "issn": "0022-0957", "issue": "13", "pages": "3405-3417", "title": null, "issn-l": null}, "abstract": null, "doi": "10.1093/jxb/erx186", "pmid": "28633298", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T13:05:31.386Z", "modified": "2020-01-21T13:53:21.847Z"}, {"entity": "publication", "iuid": "420b235c51914d58af7a8184175a8059", "links": {"self": {"href": "https://publications.scilifelab.se/publication/420b235c51914d58af7a8184175a8059.json"}, "display": {"href": "https://publications.scilifelab.se/publication/420b235c51914d58af7a8184175a8059"}}, "title": "Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey.", "authors": [{"family": "Neubeck", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Ivarsson", "given": "Magnus", "initials": "M"}, {"family": "Hosg\u00f6rmez", "given": "Hakan", "initials": "H"}, {"family": "\u00d6zcan", "given": "Dogacan", "initials": "D"}, {"family": "Broman", "given": "Curt", "initials": "C"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-06-15", "journal": {"volume": "83", "issn": "1098-5336", "issue": "12", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "The surface waters at the ultramafic ophiolitic outcrop in Chimaera, Turkey, are characterized by high pH values and high metal levels due to the percolation of fluids through areas of active serpentinization. We describe the influence of the liquid chemistry, mineralogy, and H2 and CH4 levels on the bacterial community structure in a semidry, exposed, ultramafic environment. The bacterial and archaeal community structures were monitored using Illumina sequencing targeting the 16S rRNA gene. At all sampling points, four phyla, Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria, accounted for the majority of taxa. Members of the Chloroflexi phylum dominated low-diversity sites, whereas Proteobacteria dominated high-diversity sites. Methane, nitrogen, iron, and hydrogen oxidizers were detected as well as archaea and metal-resistant bacteria.IMPORTANCE Our study is a comprehensive microbial investigation of the Chimaera ophiolite. DNA has been extracted from 16 sites in the area and has been studied from microbial and geochemical points of view. We describe a microbial community structure that is dependent on terrestrial, serpentinization-driven abiotic H2, which is poorly studied due to the rarity of these environments on Earth.", "doi": "10.1128/AEM.03430-16", "pmid": "28389534", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "AEM.03430-16"}, {"db": "pmc", "key": "PMC5452829"}], "notes": [], "created": "2017-11-03T16:19:53.338Z", "modified": "2020-01-21T13:56:09.096Z"}, {"entity": "publication", "iuid": "d21fdb60a89943a9ad8a18a57abebba8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d21fdb60a89943a9ad8a18a57abebba8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d21fdb60a89943a9ad8a18a57abebba8"}}, "title": "Stimulated Emission Depletion Microscopy.", "authors": [{"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Widengren", "given": "Jerker", "initials": "J", "orcid": "0000-0003-3200-0374", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5db653aece8408bb5aff6531edff22c.json"}}], "type": "journal article", "published": "2017-06-14", "journal": {"volume": "117", "issn": "1520-6890", "issue": "11", "pages": "7377-7427", "title": "Chem. Rev.", "issn-l": "0009-2665"}, "abstract": "Despite its short history, diffraction-unlimited fluorescence microscopy techniques have already made a substantial imprint in the biological sciences. In this review, we describe how stimulated emission depletion (STED) imaging originally evolved, how it compares to other optical super-resolution imaging techniques, and what advantages it provides compared to previous golden-standards for biological microscopy, such as diffraction-limited optical microscopy and electron microscopy. We outline the prerequisites for successful STED imaging experiments, emphasizing the equally critical roles of instrumentation, sample preparation, and photophysics, and describe major evolving strategies for how to push the borders of STED imaging even further in life science. Finally, we provide examples of how STED nanoscopy can be applied, within three different fields with particular potential for STED imaging experiments: neuroscience, plasma membrane biophysics, and subcellular clinical diagnostics. In these areas, and in many more, STED imaging can be expected to play an increasingly important role in the future.", "doi": "10.1021/acs.chemrev.6b00653", "pmid": "28262022", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-05T09:07:25.091Z", "modified": "2021-06-21T15:35:57.559Z"}, {"entity": "publication", "iuid": "47a95096d95246f5af1345d226433fb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47a95096d95246f5af1345d226433fb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47a95096d95246f5af1345d226433fb0"}}, "title": "Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions", "authors": [{"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Deng", "given": "Wei Q", "initials": "WQ"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-06-14", "journal": {"volume": "13", "issn": "1553-7404", "issue": "6", "pages": "e1006812", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": null, "doi": "10.1371/journal.pgen.1006812", "pmid": "28614350", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:09.716Z", "modified": "2020-01-21T13:56:11.781Z"}, {"entity": "publication", "iuid": "88adbd607a954e539fe5a35a01aba19a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88adbd607a954e539fe5a35a01aba19a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88adbd607a954e539fe5a35a01aba19a"}}, "title": "Genetic loci associated with heart rate variability and their effects on cardiac disease risk.", "authors": [{"family": "Nolte", "given": "Ilja M", "initials": "IM", "orcid": "0000-0001-5047-4077", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd76becaa8a4df284103c3e20261f10.json"}}, {"family": "Munoz", "given": "M Loretto", "initials": "ML"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Amare", "given": "Azmeraw T", "initials": "AT", "orcid": "0000-0002-7940-0335", "researcher": {"href": "https://publications.scilifelab.se/researcher/028fd1a615ef4dc1a71067d82f094c9c.json"}}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Vaez", "given": "Ahmad", "initials": "A", "orcid": "0000-0001-9048-3795", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a09aa88bc74e1285ddd71655dbddc3.json"}}, {"family": "von der Heyde", "given": "Benedikt", "initials": "B"}, {"family": "Avery", "given": "Christy L", "initials": "CL"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Dierckx", "given": "Bram", "initials": "B"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Gogarten", "given": "Stephanie M", "initials": "SM"}, {"family": "Goyette", "given": "Philippe", "initials": "P"}, {"family": "Hernesniemi", "given": "Jussi", "initials": "J"}, {"family": "Huikari", "given": "Ville", "initials": "V"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Jaju", "given": "Deepali", "initials": "D"}, {"family": "Kerr", "given": "Kathleen F", "initials": "KF"}, {"family": "Kluttig", "given": "Alexander", "initials": "A"}, {"family": "Krijthe", "given": "Bouwe P", "initials": "BP"}, {"family": "Kumar", "given": "Jitender", "initials": "J"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW", "orcid": "0000-0001-6888-1404", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bd54ab413974b9096ff3d924f8b8eb6.json"}}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Maihofer", "given": "Adam X", "initials": "AX"}, {"family": "Minassian", "given": "Arpi", "initials": "A"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ", "orcid": "0000-0001-8450-3518", "researcher": {"href": 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{"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Hemerich", "given": "Daiane", "initials": "D"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Huikuri", "given": "Heikki", "initials": "H"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Jouven", "given": "Xavier", "initials": "X"}, {"family": "Junttila", "given": "Juhani", "initials": "J"}, {"family": "Juonala", "given": "Markus", "initials": "M"}, {"family": "Kiviniemi", "given": "Antti M", "initials": "AM", "orcid": "0000-0002-1160-493X", "researcher": {"href": "https://publications.scilifelab.se/researcher/583df0b19f724b0395d90fd9f8785e50.json"}}, {"family": "Kors", "given": "Jan A", "initials": "JA"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kuznetsova", "given": "Tatiana", "initials": "T"}, {"family": "Laurie", "given": "Cathy C", "initials": "CC"}, 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"initials": "M"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "O'Connor", "given": "Daniel T", "initials": "DT"}, {"family": "Ormel", "given": "Johan", "initials": "J"}, {"family": "Perz", "given": "Siegfried", "initials": "S"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Risbrough", "given": "Victoria B", "initials": "VB"}, {"family": "Sinner", "given": "Moritz F", "initials": "MF"}, {"family": "Siscovick", "given": "David", "initials": "D"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Soliman", "given": "Elsayed Z", "initials": "EZ", "orcid": "0000-0001-5632-8150", "researcher": {"href": 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"0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Thornton", "given": "Timothy A", "initials": "TA"}, {"family": "Tinker", "given": "Lesley E", "initials": "LE"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Setten", "given": "Jessica", "initials": "J", "orcid": "0000-0002-4934-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/4be6dce84e8a4f46bf15f4de178f70ba.json"}}, {"family": "Voss", "given": "Andreas", "initials": "A"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wilhelmsen", "given": "Kirk C", "initials": "KC"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wong", "given": "Quenna", "initials": "Q"}, {"family": "Zhang", "given": "Zhu-Ming", "initials": "ZM"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Greiser", "given": "Halina K", "initials": "HK"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Hassan", "given": "Mohammad", "initials": "M"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "K\u00e4\u00e4b", "given": "Stefan", "initials": "S"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kivimaki", "given": "Mika", "initials": "M", "orcid": "0000-0002-4699-5627", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f81f2fb70b14197829de8cd819ceaa6.json"}}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Nievergelt", "given": "Caroline M", "initials": "CM"}, {"family": "O'Donnell", "given": "Chris J", "initials": "CJ"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Penninx", "given": "Brenda", "initials": "B"}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Riese", "given": "Harri\u00ebtte", "initials": "H"}, {"family": "van Roon", "given": "Arie M", "initials": "AM"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Sofer", "given": "Tamar", "initials": "T"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Tiemeier", "given": "Henning", "initials": "H", "orcid": "0000-0002-4395-1397", "researcher": {"href": "https://publications.scilifelab.se/researcher/73e05bd74af344ba8d963463f49bb242.json"}}, {"family": "Vrijkotte", "given": "Tanja G M", "initials": "TGM"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/7037429ef1304bdaabd837d242b1e6f5.json"}}, {"family": "Brundel", "given": "Bianca J J M", "initials": "BJJM"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}], "type": "journal article", "published": "2017-06-14", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "15805", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4). Genetic risk scores account for 0.9 to 2.6% of the HRV variance. Significant genetic correlation is found for HRV with heart rate (-0.74<rg<-0.55) and blood pressure (-0.35<rg<-0.20). These findings provide clinically relevant biological insight into heritable variation in vagal heart rhythm regulation, with a key role for genetic variants (GNG11, RGS6) that influence G-protein heterotrimer action in GIRK-channel induced pacemaker membrane hyperpolarization.", "doi": "10.1038/ncomms15805", "pmid": "28613276", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms15805"}, {"db": "pmc", "key": "PMC5474732"}], "notes": [], "created": "2017-10-25T15:27:47.158Z", "modified": "2024-01-16T13:48:47.870Z"}, {"entity": "publication", "iuid": "ca1109f2f30146e3a210e2f88f61853d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca1109f2f30146e3a210e2f88f61853d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca1109f2f30146e3a210e2f88f61853d"}}, "title": "Structural basis for ligand binding to an enzyme by a conformational selection pathway.", "authors": [{"family": "Kovermann", "given": "Michael", "initials": "M"}, {"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": "Magnus", "initials": "M"}], "type": "journal article", "published": "2017-06-13", "journal": {"volume": "114", "issn": "1091-6490", "issue": "24", "pages": "6298-6303", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Proteins can bind target molecules through either induced fit or conformational selection pathways. In the conformational selection model, a protein samples a scarcely populated high-energy state that resembles a target-bound conformation. In enzymatic catalysis, such high-energy states have been identified as crucial entities for activity and the dynamic interconversion between ground states and high-energy states can constitute the rate-limiting step for catalytic turnover. The transient nature of these states has precluded direct observation of their properties. Here, we present a molecular description of a high-energy enzyme state in a conformational selection pathway by an experimental strategy centered on NMR spectroscopy, protein engineering, and X-ray crystallography. Through the introduction of a disulfide bond, we succeeded in arresting the enzyme adenylate kinase in a closed high-energy conformation that is on-pathway for catalysis. A 1.9-\u00c5 X-ray structure of the arrested enzyme in complex with a transition state analog shows that catalytic sidechains are properly aligned for catalysis. We discovered that the structural sampling of the substrate free enzyme corresponds to the complete amplitude that is associated with formation of the closed and catalytically active state. In addition, we found that the trapped high-energy state displayed improved ligand binding affinity, compared with the wild-type enzyme, demonstrating that substrate binding to the high-energy state is not occluded by steric hindrance. Finally, we show that quenching of fast time scale motions observed upon ligand binding to adenylate kinase is dominated by enzyme-substrate interactions and not by intramolecular interactions resulting from the conformational change.", "doi": "10.1073/pnas.1700919114", "pmid": "28559350", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "1700919114"}, {"db": "pmc", "key": "PMC5474765"}], "notes": [], "created": "2017-11-02T17:26:49.640Z", "modified": "2025-10-17T13:03:59.759Z"}, {"entity": "publication", "iuid": "41693810bf914d9095a1db79a7f44a49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41693810bf914d9095a1db79a7f44a49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41693810bf914d9095a1db79a7f44a49"}}, "title": "Four simple recommendations to encourage best practices in research software", "authors": [{"family": "Jim\u00e9nez", "given": "Rafael C", "initials": "RC"}, {"family": "Kuzak", "given": "Mateusz", "initials": "M"}, {"family": "Alhamdoosh", "given": "Monther", "initials": "M"}, {"family": "Barker", "given": "Michelle", "initials": "M"}, {"family": "Batut", "given": "B\u00e9r\u00e9nice", "initials": "B"}, {"family": "Borg", "given": "Mikael", "initials": "M"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S"}, {"family": "Chue Hong", "given": "Neil", "initials": "N"}, {"family": "Cook", "given": "Martin", "initials": "M"}, {"family": "Corpas", "given": "Manuel", "initials": "M"}, {"family": "Flannery", "given": "Madison", "initials": "M"}, {"family": "Garcia", "given": "Leyla", "initials": "L"}, {"family": "Gelp\u00ed", "given": "Josep Ll", "initials": "JL"}, {"family": "Gladman", "given": "Simon", "initials": "S"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Gonz\u00e1lez Ferreiro", "given": "Montserrat", "initials": "M"}, {"family": "Gonzalez-Beltran", "given": "Alejandra", "initials": "A"}, {"family": "Griffin", "given": "Philippa C", "initials": "PC"}, {"family": "Gr\u00fcning", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hagberg", "given": "Jonas", "initials": "J"}, {"family": "Holub", "given": "Petr", "initials": "P"}, {"family": "Hooft", "given": "Rob", "initials": "R"}, {"family": "Ison", "given": "Jon", "initials": "J"}, {"family": "Katz", "given": "Daniel S", "initials": "DS"}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "L\u00f3pez G\u00f3mez", "given": "Federico", "initials": "F"}, {"family": "Oliveira", "given": "Luis J", "initials": "LJ"}, {"family": "Mellor", "given": "David", "initials": "D"}, {"family": "Mosbergen", "given": "Rowland", "initials": "R"}, {"family": "Mulder", "given": "Nicola", "initials": "N"}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y"}, {"family": "Pergl", "given": "Robert", "initials": "R"}, {"family": "Pichler", "given": "Horst", "initials": "H"}, {"family": "Pope", "given": "Bernard", "initials": "B"}, {"family": "Sanz", "given": "Ferran", "initials": "F"}, {"family": "Schneider", "given": "Maria V", "initials": "MV"}, {"family": "Stodden", "given": "Victoria", "initials": "V"}, {"family": "Suchecki", "given": "Rados\u0142aw", "initials": "R"}, {"family": "Svobodov\u00e1 Va\u0159ekov\u00e1", "given": "Radka", "initials": "R"}, {"family": "Talvik", "given": "Harry Anton", "initials": "HA"}, {"family": "Todorov", "given": "Ilian", "initials": "I"}, {"family": "Treloar", "given": "Andrew", "initials": "A"}, {"family": "Tyagi", "given": "Sonika", "initials": "S"}, {"family": "van Gompel", "given": "Maarten", "initials": "M"}, {"family": "Vaughan", "given": "Daniel", "initials": "D"}, {"family": "Via", "given": "Allegra", "initials": "A"}, {"family": "Wang", "given": "Xiaochuan", "initials": "X"}, {"family": "Watson-Haigh", "given": "Nathan S", "initials": "NS"}, {"family": "Crouch", "given": "Steve", "initials": "S"}], "type": "journal-article", "published": "2017-06-13", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "876", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.11407.1", "pmid": "28751965", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:15.160Z", "modified": "2020-01-21T13:53:21.698Z"}, {"entity": "publication", "iuid": "fefb54b862b242c7a4164b64ca3b488b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fefb54b862b242c7a4164b64ca3b488b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fefb54b862b242c7a4164b64ca3b488b"}}, "title": "A community proposal to integrate proteomics activities in ELIXIR", "authors": [{"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA"}, {"family": "Walzer", "given": "Mathias", "initials": "M"}, {"family": "Jim\u00e9nez", "given": "Rafael C", "initials": "RC"}, {"family": "Bittremieux", "given": "Wout", "initials": "W"}, {"family": "Bouyssi\u00e9", "given": "David", "initials": "D"}, {"family": "Carapito", "given": "Christine", "initials": "C"}, {"family": "Corrales", "given": "Fernando", "initials": "F"}, {"family": "Ferro", "given": "Myriam", "initials": "M"}, {"family": "Heck", "given": "Albert J R", "initials": "AJR"}, {"family": "Horvatovich", "given": "Peter", "initials": "P"}, {"family": "Hubalek", "given": "Martin", "initials": "M"}, {"family": "Lane", "given": "Lydie", "initials": "L"}, {"family": "Laukens", "given": "Kris", "initials": "K"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Lisacek", "given": "Frederique", "initials": "F"}, {"family": "Novak", "given": "Petr", "initials": "P"}, {"family": "Palmblad", "given": "Magnus", "initials": "M"}, {"family": "Piovesan", "given": "Damiano", "initials": "D"}, {"family": "P\u00fchler", "given": "Alfred", "initials": "A"}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V"}, {"family": "Valkenborg", "given": "Dirk", "initials": "D"}, {"family": "van Rijswijk", "given": "Merlijn", "initials": "M"}, {"family": "Vondrasek", "given": "Jiri", "initials": "J"}, {"family": "Eisenacher", "given": "Martin", "initials": "M"}, {"family": "Martens", "given": "Lennart", "initials": "L"}, {"family": "Kohlbacher", "given": "Oliver", "initials": "O"}], "type": "journal-article", "published": "2017-06-13", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "875", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.11751.1", "pmid": "28713550", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:14.669Z", "modified": "2020-01-21T13:53:21.691Z"}, {"entity": "publication", "iuid": "2db12a99ec304f50af096d7ae0467df3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2db12a99ec304f50af096d7ae0467df3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2db12a99ec304f50af096d7ae0467df3"}}, "title": "Alterations of anti-inflammatory lipids in plasma from women with chronic widespread pain - a case control study.", "authors": [{"family": "Stensson", "given": "Niclas", "initials": "N"}, {"family": "Ghafouri", "given": "Bijar", "initials": "B"}, {"family": "Gerdle", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ghafouri", "given": "Nazdar", "initials": "N"}], "type": "journal article", "published": "2017-06-12", "journal": {"title": "Lipids Health Dis", "issn": "1476-511X", "issn-l": "1476-511X", "volume": "16", "issue": "1", "pages": "112"}, "abstract": "Chronic widespread pain conditions (CWP) such as the pain associated with fibromyalgia syndrome (FMS) are significant health problems with unclear aetiology. Although CWP and FMS can alter both central and peripheral pain mechanisms, there are no validated markers for such alterations. Pro- and anti-inflammatory components of the immune system such as cytokines and endogenous lipid mediators could serve as systemic markers of alterations in chronic pain. Lipid mediators associated with anti-inflammatory qualities - e.g., oleoylethanolamide (OEA), palmitoylethanolamide (PEA), and stearoylethanolamide (SEA) - belong to N-acylethanolamines (NAEs). Previous studies have concluded that these lipid mediators may modulate pain and inflammation via the activation of peroxisome proliferator activating receptors (PPARs) and the activation of PPARs may regulate gene transcriptional factors that control the expression of distinct cytokines.\n\nThis study investigates NAEs and cytokines in 17 women with CWP and 21 healthy controls. Plasma levels of the anti-inflammatory lipids OEA, PEA, and SEA, the pro-inflammatory cytokines TNF-\u03b1, IL-1\u03b2, IL-6, and IL-8, and the anti-inflammatory cytokine IL-10 were investigated. T-test of independent samples was used for group comparisons. Bivariate correlation analyses, and multivariate regression analysis were performed between lipids, cytokines, and pain intensity of the participants.\n\nSignificantly higher levels of OEA and PEA in plasma were found in CWP. No alterations in the levels of cytokines existed and no correlations between levels of lipids and cytokines were found.\n\nWe conclude that altered levels of OEA and PEA might indicate the presence of systemic inflammation in CWP. In addition, we believe our findings contribute to the understanding of the biochemical mechanisms involved in chronic musculoskeletal pain.", "doi": "10.1186/s12944-017-0505-7", "pmid": "28606089", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12944-017-0505-7"}, {"db": "pmc", "key": "PMC5469054"}], "notes": [], "created": "2020-01-23T15:08:29.585Z", "modified": "2023-04-14T13:56:12.770Z"}, {"entity": "publication", "iuid": "11b11d52ef8f47d8b685c7a4eccadc9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11b11d52ef8f47d8b685c7a4eccadc9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11b11d52ef8f47d8b685c7a4eccadc9a"}}, "title": "Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes", "authors": [{"family": "Berga", "given": "Merc\u00e8", "initials": "M"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}], "type": "journal-article", "published": "2017-06-08", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": null, "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": null, "doi": "10.3389/fmicb.2017.00948", "pmid": "28642735", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:49:54.874Z", "modified": "2020-01-21T13:56:11.774Z"}, {"entity": "publication", "iuid": "8debe2b674394b34846e436ba217e239", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8debe2b674394b34846e436ba217e239.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8debe2b674394b34846e436ba217e239"}}, "title": "SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.", "authors": [{"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Henning", "given": "Petra", "initials": "P"}, {"family": "Klar", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4185-7409", "researcher": {"href": "https://publications.scilifelab.se/researcher/3310cb2ab70f43d78cc7cd7e36ac8f83.json"}}, {"family": "McDermott", "given": "Emma", "initials": "E"}, {"family": "Stecksen-Blicks", "given": "Christina", "initials": "C"}, {"family": "Sandstr\u00f6m", "given": "Per-Erik", "initials": "PE"}, {"family": "Kellgren", "given": "Therese G", "initials": "TG"}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "L\u00f6nnerholm", "given": "Torsten", "initials": "T"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Helfrich", "given": "Miep H", "initials": "MH"}, {"family": "Coxon", "given": "Fraser P", "initials": "FP"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Wikstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Lerner", "given": "Ulf H", "initials": "UH"}], "type": "journal article", "published": "2017-06-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "3012", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Autosomal recessive osteopetrosis (ARO) is a heterogeneous disorder, characterized by defective osteoclastic resorption of bone that results in increased bone density. We have studied nine individuals with an intermediate form of ARO, from the county of V\u00e4sterbotten in Northern Sweden. All afflicted individuals had an onset in early infancy with optic atrophy, and in four patients anemia was present at diagnosis. Tonsillar herniation, foramen magnum stenosis, and severe osteomyelitis of the jaw were common clinical features. Whole exome sequencing, verified by Sanger sequencing, identified a splice site mutation c.212 + 1 G > T in the SNX10 gene encoding sorting nexin 10. Sequence analysis of the SNX10 transcript in patients revealed activation of a cryptic splice site in intron 4 resulting in a frame shift and a premature stop (p.S66Nfs * 15). Haplotype analysis showed that all cases originated from a single mutational event, and the age of the mutation was estimated to be approximately 950 years. Functional analysis of osteoclast progenitors isolated from peripheral blood of patients revealed that stimulation with receptor activator of nuclear factor kappa-B ligand (RANKL) resulted in a robust formation of large, multinucleated osteoclasts which generated sealing zones; however these osteoclasts exhibited defective ruffled borders and were unable to resorb bone in vitro.", "doi": "10.1038/s41598-017-02533-2", "pmid": "28592808", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-02533-2"}, {"db": "pmc", "key": "PMC5462793"}], "notes": [], "created": "2017-10-30T13:36:01.438Z", "modified": "2024-01-16T13:48:47.879Z"}, {"entity": "publication", "iuid": "b95add923913483c89ea2e12850ab207", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b95add923913483c89ea2e12850ab207.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b95add923913483c89ea2e12850ab207"}}, "title": "Fast and general tests of genetic interaction for genome-wide association studies", "authors": [{"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-06-06", "journal": {"volume": "13", "issn": "1553-7358", "issue": "6", "pages": "e1005556", "title": "PLoS Comput. Biol.", "issn-l": "1553-734X"}, "abstract": null, "doi": "10.1371/journal.pcbi.1005556", "pmid": "28586362", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:10.227Z", "modified": "2020-01-21T13:56:11.767Z"}, {"entity": "publication", "iuid": "902562561e624de6ba03ba60d53d59f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/902562561e624de6ba03ba60d53d59f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/902562561e624de6ba03ba60d53d59f5"}}, "title": "Effect of food intake on 92 biomarkers for cardiovascular disease.", "authors": [{"family": "Dencker", "given": "Magnus", "initials": "M", "orcid": "0000-0001-9991-3712", "researcher": {"href": "https://publications.scilifelab.se/researcher/606b9b3272824d92a66dfd715c5e4842.json"}}, {"family": "G\u00e5rdinger", "given": "Ylva", "initials": "Y"}, {"family": "Bj\u00f6rgell", "given": "Ola", "initials": "O"}, {"family": "Hlebowicz", "given": "Joanna", "initials": "J"}], "type": "journal article", "published": "2017-06-06", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "12", "issue": "6", "pages": "e0178656"}, "abstract": "The present study evaluates the effect of food intake on 92 biomarkers for cardiovascular disease (CVD).\n\nTwenty two healthy subjects (11 male and 11 female aged 25.9\u00b14.2 years) were investigated. A total of 92 biomarkers were measured before a standardized meal as well as 30 and 120 minutes afterwards with the Proseek Multiplex CVD III kit.\n\nThe levels for eight biomarkers decreased significantly (P<0.05) 30 minutes after food intake. The levels for seven biomarkers remained significantly decreased 120 minutes after food intake. Nine biomarker decreased significantly at 120 minutes after food intake. The changes were between 4-30%, most commonly around 5%. Only six biomarkers showed a difference of 10% or more due to food intake. The biggest differences were observed for Insulin-like growth factor-binding protein 1 (30%); Azurocidin, Cystatin-B, and Myeloperoxidase (13%); Monocyte chemotactic protein 1 (11%); and Myeloblastin (10%), all 120 minutes after food intake.\n\nThis study shows that food intake affects several different CVD biomarkers, but the effect is predominantly modest. Timing of blood sampling in relation to food intake, therefore, appears not to be a major concern. Further studies are warranted in older healthy subjects and in patients with various cardiac diseases to determine whether the findings are reproducible.", "doi": "10.1371/journal.pone.0178656", "pmid": "28586402", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-02534"}, {"db": "pmc", "key": "PMC5460853"}], "notes": [], "created": "2020-01-23T15:08:30.269Z", "modified": "2023-04-14T13:56:13.096Z"}, {"entity": "publication", "iuid": "986e55f889574733b2df4e85fba55ee5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/986e55f889574733b2df4e85fba55ee5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/986e55f889574733b2df4e85fba55ee5"}}, "title": "Mass spectrometry imaging identifies palmitoylcarnitine as an immunological mediator during Salmonella Typhimurium infection.", "authors": [{"family": "Hulme", "given": "Heather E", "initials": "HE"}, {"family": "Meikle", "given": "Lynsey M", "initials": "LM"}, {"family": "Wessel", "given": "Hannah", "initials": "H"}, {"family": "Strittmatter", "given": "Nicole", "initials": "N"}, {"family": "Swales", "given": "John", "initials": "J"}, {"family": "Thomson", "given": "Carolyn", "initials": "C"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Nibbs", "given": "Robert J B", "initials": "RJB"}, {"family": "Milling", "given": "Simon", "initials": "S"}, {"family": "Andren", "given": "Per E", "initials": "PE"}, {"family": "Mackay", "given": "C Logan", "initials": "CL"}, {"family": "Dexter", "given": "Alex", "initials": "A"}, {"family": "Bunch", "given": "Josephine", "initials": "J"}, {"family": "Goodwin", "given": "Richard J A", "initials": "RJA"}, {"family": "Burchmore", "given": "Richard", "initials": "R"}, {"family": "Wall", "given": "Daniel M", "initials": "DM"}], "type": "journal article", "published": "2017-06-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "2786", "issn-l": "2045-2322"}, "abstract": "Salmonella Typhimurium causes a self-limiting gastroenteritis that may lead to systemic disease. Bacteria invade the small intestine, crossing the intestinal epithelium from where they are transported to the mesenteric lymph nodes (MLNs) within migrating immune cells. MLNs are an important site at which the innate and adaptive immune responses converge but their architecture and function is severely disrupted during S. Typhimurium infection. To further understand host-pathogen interactions at this site, we used mass spectrometry imaging (MSI) to analyse MLN tissue from a murine model of S. Typhimurium infection. A molecule, identified as palmitoylcarnitine (PalC), was of particular interest due to its high abundance at loci of S. Typhimurium infection and MLN disruption. High levels of PalC localised to sites within the MLNs where B and T cells were absent and where the perimeter of CD169 + sub capsular sinus macrophages was disrupted. MLN cells cultured ex vivo and treated with PalC had reduced CD4+CD25+ T cells and an increased number of B220+CD19+ B cells. The reduction in CD4+CD25+ T cells was likely due to apoptosis driven by increased caspase-3/7 activity. These data indicate that PalC significantly alters the host response in the MLNs, acting as a decisive factor in infection outcome.", "doi": "10.1038/s41598-017-03100-5", "pmid": "28584281", "labels": {"Spatial Mass Spectrometry": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-03100-5"}, {"db": "pmc", "key": "PMC5459799"}], "notes": [], "created": "2020-01-24T08:59:38.206Z", "modified": "2021-05-17T08:47:18.753Z"}, {"entity": "publication", "iuid": "1aef5d2c4709404bb4b18ad91957495f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1aef5d2c4709404bb4b18ad91957495f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1aef5d2c4709404bb4b18ad91957495f"}}, "title": "Mast Cell Infiltration in Human Brain Metastases Modulates the Microenvironment and Contributes to the Metastatic Potential.", "authors": [{"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Libard", "given": "Sylwia", "initials": "S"}, {"family": "Weishaupt", "given": "Holger", "initials": "H"}, {"family": "Gustavsson", "given": "Ida", "initials": "I"}, {"family": "Uhrbom", "given": "Lene", "initials": "L"}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I"}, {"family": "Tchougounova", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2017-06-02", "journal": {"title": "Front Oncol", "issn": "2234-943X", "volume": "7", "issue": null, "pages": "115", "issn-l": "2234-943X"}, "abstract": "Metastatic brain tumors continue to be a clinical problem, despite new therapeutic advances in cancer treatment. Brain metastases (BMs) are among the most common mass lesions in the brain that are resistant to chemotherapies, have a very poor prognosis, and currently lack any efficient diagnostic tests. Predictions estimate that about 40% of lung and breast cancer patients will develop BM. Despite this, very little is known about the immunological and genetic aberrations that drive tumorigenesis in BM. In this study, we demonstrate the infiltration of mast cells (MCs) in a large cohort of human BM samples with different tissues of origin for primary cancer. We applied patient-derived BM cell models to the study of BM cell-MC interactions. BM cells when cocultured with MCs demonstrate enhanced growth and self-renewal capacity. Gene set enrichment analyses indicate increased expression of signal transduction and transmembrane proteins related genes in the cocultured BM cells. MCs exert their effect by release of mediators such as IL-8, IL-10, matrix metalloprotease 2, and vascular endothelial growth factor, thereby permitting metastasis. In conclusion, we provide evidence for a role of MCs in BM. Our findings indicate MCs' capability of modulating gene expression in BM cells and suggest that MCs can serve as a new target for drug development against metastases in the brain.", "doi": "10.3389/fonc.2017.00115", "pmid": "28626727", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5454042"}], "notes": [], "created": "2017-11-05T12:41:52.997Z", "modified": "2017-11-05T12:41:53.014Z"}, {"entity": "publication", "iuid": "8d30f96d3ed34e76b303cfeab798e8e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d30f96d3ed34e76b303cfeab798e8e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d30f96d3ed34e76b303cfeab798e8e9"}}, "title": "Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression.", "authors": [{"family": "Hauberg", "given": "Mads Engel", "initials": "ME"}, {"family": "Zhang", "given": "Wen", "initials": "W"}, {"family": "Giambartolomei", "given": "Claudia", "initials": "C"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "CommonMind Consortium", "given": "", "initials": ""}, {"family": "Sklar", "given": "Pamela", "initials": "P"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Roussos", "given": "Panos", "initials": "P"}], "type": "journal article", "published": "2017-06-01", "journal": {"volume": "100", "issn": "1537-6605", "issue": "6", "pages": "885-894", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Genome-wide association studies (GWASs) have identified a multitude of genetic loci involved with traits and diseases. However, it is often unclear which genes are affected in such loci and whether the associated genetic variants lead to increased or decreased gene function. To mitigate this, we integrated associations of common genetic variants in 57 GWASs with 24 studies of expression quantitative trait loci (eQTLs) from a broad range of tissues by using a Mendelian randomization approach. We discovered a total of 3,484 instances of gene-trait-associated changes in expression at a false-discovery rate < 0.05. These genes were often not closest to the genetic variant and were primarily identified in eQTLs derived from pathophysiologically relevant tissues. For instance, genes with expression changes associated with lipid traits were mostly identified in the liver, and those associated with cardiovascular disease were identified in arterial tissue. The affected genes additionally point to biological processes implicated in the interrogated traits, such as the interleukin-27 pathway in rheumatoid arthritis. Further, comparing trait-associated gene expression changes across traits suggests that pleiotropy is a widespread phenomenon and points to specific instances of both agonistic and antagonistic pleiotropy. For instance, expression of SNX19 and ABCB9 is positively correlated with both the risk of schizophrenia and educational attainment. To facilitate interpretation, we provide this lexicon of how common trait-associated genetic variants alter gene expression in various tissues as the online database GWAS2Genes.", "doi": "10.1016/j.ajhg.2017.04.016", "pmid": "28552197", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(17)30161-1"}, {"db": "pmc", "key": "PMC5474225"}], "notes": [], "created": "2017-10-27T06:59:34.187Z", "modified": "2021-06-21T15:36:46.748Z"}, {"entity": "publication", "iuid": "58ac3a28707245c785c96dd26ae5d18c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58ac3a28707245c785c96dd26ae5d18c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58ac3a28707245c785c96dd26ae5d18c"}}, "title": "Injury Leads to the Appearance of Cells with Characteristics of Both Microglia and Astrocytes in Mouse and Human Brain.", "authors": [{"family": "Wilhelmsson", "given": "Ulrika", "initials": "U"}, {"family": "Andersson", "given": "Daniel", "initials": "D"}, {"family": "de Pablo", "given": "Yolanda", "initials": "Y"}, {"family": "Pekny", "given": "Roy", "initials": "R"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Hortob\u00e1gyi", "given": "Tibor", "initials": "T"}, {"family": "Pekny", "given": "Milos", "initials": "M"}, {"family": "Pekna", "given": "Marcela", "initials": "M"}], "type": "journal article", "published": "2017-06-01", "journal": {"volume": "27", "issn": "1460-2199", "issue": "6", "pages": "3360-3377", "title": "Cereb. Cortex", "issn-l": "1047-3211"}, "abstract": "Microglia and astrocytes have been considered until now as cells with very distinct identities. Here, we assessed the heterogeneity within microglia/monocyte cell population in mouse hippocampus and determined their response to injury, by using single-cell gene expression profiling of cells isolated from uninjured and deafferented hippocampus. We found that in individual cells, microglial markers Cx3cr1, Aif1, Itgam, and Cd68 were co-expressed. Interestingly, injury led to the co-expression of the astrocyte marker Gfap in a subpopulation of Cx3cr1-expressing cells from both the injured and contralesional hippocampus. Cells co-expressing astrocyte and microglia markers were also detected in the in vitro LPS activation/injury model and in sections from human brain affected by stroke, Alzheimer's disease, and Lewy body dementia. Our findings indicate that injury and chronic neurodegeneration lead to the appearance of cells that share molecular characteristics of both microglia and astrocytes, 2 cell types with distinct embryologic origin and function.", "doi": "10.1093/cercor/bhx069", "pmid": "28398520", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "3111278"}], "notes": [], "created": "2017-10-30T14:57:53.920Z", "modified": "2021-05-24T15:37:29.389Z"}, {"entity": "publication", "iuid": "3a3c6631eadb4decbde40c86edda9348", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a3c6631eadb4decbde40c86edda9348.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a3c6631eadb4decbde40c86edda9348"}}, "title": "Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.", "authors": [{"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Pinder", "given": "Matthew I M", "initials": "MIM"}, {"family": "Johansson", "given": "Oskar N", "initials": "ON"}, {"family": "Kourtchenko", "given": "Olga", "initials": "O"}, {"family": "Godhe", "given": "Anna", "initials": "A"}, {"family": "Clarke", "given": "Adrian K", "initials": "AK"}], "type": "journal article", "published": "2017-06-01", "journal": {"volume": "5", "issn": "2169-8287", "issue": "22", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "We present the genome of Roseovarius mucosus strain SMR3, a marine bacterium isolated from the diatom Skeletonema marinoi strain RO5AC sampled from top layer sediments at 14\u00a0m depth. Its 4,381,426\u00a0bp genome consists of a circular chromosome and two circular plasmids and contains 4,178 coding sequences (CDSs).", "doi": "10.1128/genomeA.00394-17", "pmid": "28572309", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5/22/e00394-17"}, {"db": "pmc", "key": "PMC5454192"}], "notes": [], "created": "2017-10-30T13:56:28.143Z", "modified": "2024-01-16T13:48:47.888Z"}, {"entity": "publication", "iuid": "18125175c6fe42a69999f7984962cb47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18125175c6fe42a69999f7984962cb47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18125175c6fe42a69999f7984962cb47"}}, "title": "Coordinated nitrogen and carbon remobilization for nitrate assimilation in leaf, sheath and root and associated cytokinin signals during early regrowth of Lolium perenne.", "authors": [{"family": "Roche", "given": "Jessica", "initials": "J"}, {"family": "Turnbull", "given": "Matthew H", "initials": "MH"}, {"family": "Guo", "given": "Qianqian", "initials": "Q"}, {"family": "Nov\u00e1k", "given": "Ondrej", "initials": "O"}, {"family": "Sp\u00e4th", "given": "Jana", "initials": "J"}, {"family": "Gieseg", "given": "Steven P", "initials": "SP"}, {"family": "Jameson", "given": "Paula E", "initials": "PE"}, {"family": "Love", "given": "Jonathan", "initials": "J"}], "type": "journal article", "published": "2017-06-01", "journal": {"title": "Ann. Bot.", "issn": "1095-8290", "volume": "119", "issue": "8", "pages": "1353-1364", "issn-l": "0305-7364"}, "abstract": "The efficiency of N assimilation in response to defoliation is a critical component of plant regrowth and forage production. The aim of this research was to test the effect of the internal C/N balance on NO3- assimilation and to estimate the associated cytokinin signals following defoliation of perennial ryegrass ( Lolium perenne L. 'Grasslands Nui') plants.\n\nPlants, manipulated to have contrasting internal N content and contrasting availability of water soluble carbohydrates (WSCs), were obtained by exposure to either continuous light or short days (8:16 h light-dark), and watered with modified N-free Hoagland medium containing either high (5 m m ) or low (50 \u03bc m ) NO3- as sole N source. Half of the plants were defoliated and the root, sheath and leaf tissue were harvested at 8, 24 and 168 h after cutting. The spatiotemporal changes in WSCs, synthesis of amino acids and associated cytokinin content were recorded after cutting.\n\nLeaf regrowth following defoliation involved changes in the low- and high-molecular weight WSCs. The extent of the changes and the partitioning of the WSC following defoliation were dependant on the initial WSC levels and the C and N availability. Cytokinin levels varied in the sheath and root as early as 8 h following defoliation and preceded an overall increase in amino acids at 24 h. Subsequently, negative feedback brought the amino acid response back towards pre-defoliation levels within 168 h after cutting, a response that was under control of the C/N ratio.\n\nWSC remobilization in the leaf is coordinated with N availability to the root, potentially via a systemic cytokinin signal, leading to efficient N assimilation in the leaf and the sheath tissues and to early leaf regrowth following defoliation.", "doi": "10.1093/aob/mcx014", "pmid": "28334245", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5604574"}, {"db": "pii", "key": "3071429"}], "notes": [], "created": "2023-04-12T14:19:33.110Z", "modified": "2025-10-17T13:03:18.729Z"}, {"entity": "publication", "iuid": "0cc74488286b407d8f3342222eb757eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cc74488286b407d8f3342222eb757eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cc74488286b407d8f3342222eb757eb"}}, "title": "Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics.", "authors": [{"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Karami", "given": "Nahid", "initials": "N"}, {"family": "Al-Bayati", "given": "Omar", "initials": "O"}, {"family": "\u00c5hr\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2017-06-00", "journal": {"title": "Mol. Cell Proteomics", "issn": "1535-9484", "volume": "16", "issue": "6", "pages": "1052-1063", "issn-l": "1535-9476"}, "abstract": "Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. However, the generated data are highly fragmented, making downstream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS. TCUP compares the generated protein sequence data to reference databases and automatically finds peptides suitable for characterization of taxonomic composition and identification of expressed antimicrobial resistance genes. TCUP was evaluated using several clinically relevant bacterial species ( Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae), using both simulated data generated by in silico peptide digestion and experimental proteomics data generated by liquid chromatography-tandem mass spectrometry (MS/MS). The results showed that TCUP performs correct peptide classifications at rates between 90.3 and 98.5% at the species level. The method was also able to estimate the relative abundances of individual species in mixed cultures. Furthermore, TCUP could identify expressed \u03b2-lactamases in an extended spectrum \u03b2-lactamase-producing (ESBL) E. coli strain, even when the strain was cultivated in the absence of antibiotics. Finally, TCUP is computationally efficient, easy to integrate in existing bioinformatics workflows, and freely available under an open source license for both Windows and Linux environments.", "doi": "10.1074/mcp.M116.061721", "pmid": "28420677", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "M116.061721"}, {"db": "pmc", "key": "PMC5461537"}], "notes": [], "created": "2020-01-30T16:00:21.160Z", "modified": "2024-01-16T13:46:32.657Z"}, {"entity": "publication", "iuid": "d4773ae4a45046d682911d0f085c4ac3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4773ae4a45046d682911d0f085c4ac3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4773ae4a45046d682911d0f085c4ac3"}}, "title": "Tumoral cubilin is a predictive marker for treatment of renal cancer patients with sunitinib and sorafenib.", "authors": [{"family": "Niinivirta", "given": "Marjut", "initials": "M"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Dragomir", "given": "Anca", "initials": "A"}, {"family": "Ullenhag", "given": "Gustav J", "initials": "GJ"}], "type": "journal article", "published": "2017-06-00", "journal": {"title": "J. Cancer Res. Clin. Oncol.", "issn": "1432-1335", "volume": "143", "issue": "6", "pages": "961-970", "issn-l": "0171-5216"}, "abstract": "Tyrosine kinase inhibitors like sunitinib and sorafenib are commonly used to treat metastatic renal cell cancer patients. Cubilin is a membrane protein expressed in the proximal renal tubule. Cubilin and megalin function together as endocytic receptors mediating uptake of many proteins. There is no established predictive marker for metastatic renal cell cancer patients and the purpose of the present study was to assess if cubilin can predict response to treatment with tyrosine kinase inhibitors.\n\nCubilin protein expression was analyzsed in tumor tissue from a cohort of patients with metastatic renal cell cancer (n\u2009=\u2009139) using immunohistochemistry. One hundred and thirty six of the patients were treated with sunitinib or sorafenib in the first- or second-line setting. Thirty of these were censored because of toxicity leading to the termination of treatment and the remaining (n\u2009=\u2009106) were selected for the current study.\n\nFifty-three (50%) of the tumors expressed cubilin in the membrane. The median progression-free survival was 8\u00a0months in patients with cubilin expressing tumors and 4\u00a0months in the cubilin negative group. In addition, the overall survival was better for patients with cubilin positive tumors. We also found that the fraction of cubilin negative patients was significantly higher in the non-responding group (PFS \u22643\u00a0months) compared to responding patients (PFS >3\u00a0months).\n\nWe show for the first time that tumoral expression of cubilin is a positive predictive marker for treatment of metastatic renal cell cancer patients with sunitinib and sorafenib.", "doi": "10.1007/s00432-017-2365-y", "pmid": "28260162", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00432-017-2365-y"}, {"db": "pmc", "key": "PMC5427164"}], "notes": [], "created": "2017-11-05T12:39:07.015Z", "modified": "2017-11-05T12:39:07.044Z"}, {"entity": "publication", "iuid": "dc532e7f651d4cc39a2271712494c35c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc532e7f651d4cc39a2271712494c35c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc532e7f651d4cc39a2271712494c35c"}}, "title": "The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.", "authors": [{"family": "Videvall", "given": "Elin", "initials": "E"}, {"family": "Cornwallis", "given": "Charlie K", "initials": "CK"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Palinauskas", "given": "Vaidas", "initials": "V"}, {"family": "Valki\u016bnas", "given": "Gediminas", "initials": "G"}, {"family": "Hellgren", "given": "Olof", "initials": "O"}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "26", "issn": "1365-294X", "issue": "11", "pages": "2939-2958", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Malaria parasites (Plasmodium spp.) include some of the world's most widespread and virulent pathogens. Our knowledge of the molecular mechanisms these parasites use to invade and exploit their hosts other than in mice and primates is, however, extremely limited. It is therefore imperative to characterize transcriptome-wide gene expression from nonmodel malaria parasites and how this varies across individual hosts. Here, we used high-throughput Illumina RNA sequencing on blood from wild-caught Eurasian siskins experimentally infected with a clonal strain of the avian malaria parasite Plasmodium ashfordi (lineage GRW2). Using a bioinformatic multistep approach to filter out host transcripts, we successfully assembled the blood-stage transcriptome of P.\u00a0ashfordi. A total of 11\u00a0954 expressed transcripts were identified, and 7860 were annotated with protein information. We quantified gene expression levels of all parasite transcripts across three hosts during two infection stages - peak and decreasing parasitemia. Interestingly, parasites from the same host displayed remarkably similar expression profiles during different infection stages, but showed large differences across hosts, indicating that P.\u00a0ashfordi may adjust its gene expression to specific host individuals. We further show that the majority of transcripts are most similar to the human parasite Plasmodium falciparum, and a large number of red blood cell invasion genes were discovered, suggesting evolutionary conserved invasion strategies between mammalian and avian Plasmodium. The transcriptome of P.\u00a0ashfordi and its host-specific gene expression advances our understanding of Plasmodium plasticity and is a valuable resource as it allows for further studies analysing gene evolution and comparisons of parasite gene expression.", "doi": "10.1111/mec.14085", "pmid": "28267239", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-15T07:44:42.594Z", "modified": "2020-01-21T13:53:22.294Z"}, {"entity": "publication", "iuid": "4e2f894adeeb4c3ba0f9407e74526985", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e2f894adeeb4c3ba0f9407e74526985.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e2f894adeeb4c3ba0f9407e74526985"}}, "title": "The effects of thawing on the plasma metabolome: evaluating differences between thawed plasma and multi-organ samples", "authors": [{"family": "Torell", "given": "Frida", "initials": "F"}, {"family": "Bennett", "given": "Kate", "initials": "K"}, {"family": "R\u00e4nnar", "given": "Stefan", "initials": "S"}, {"family": "Lundstedt-Enkel", "given": "Katrin", "initials": "K"}, {"family": "Lundstedt", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Trygg", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "13", "issn": "1573-3882", "issue": "6", "pages": null, "title": "Metabolomics", "issn-l": null}, "abstract": null, "doi": "10.1007/s11306-017-1196-9", "pmid": "28473743", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:36:25.810Z", "modified": "2025-10-17T13:03:18.756Z"}, {"entity": "publication", "iuid": "c29f83a0dc514f559fe377084b7d53ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c29f83a0dc514f559fe377084b7d53ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c29f83a0dc514f559fe377084b7d53ac"}}, "title": "Synthetic approaches to radiochemical probes for imaging of bacterial infections", "authors": [{"family": "Dutta", "given": "Jyotibon", "initials": "J"}, {"family": "Naicker", "given": "Tricia", "initials": "T"}, {"family": "Ebenhan", "given": "Thomas", "initials": "T"}, {"family": "Kruger", "given": "Hendrik G", "initials": "HG"}, {"family": "Arvidsson", "given": "Per I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}, {"family": "Govender", "given": "Thavendran", "initials": "T"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "133", "issn": "0223-5234", "issue": null, "pages": "287-308", "title": "European Journal of Medicinal Chemistry", "issn-l": "0223-5234"}, "abstract": null, "doi": "10.1016/j.ejmech.2017.03.060", "pmid": 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Following 2 years at the ETH Zurich (Switzerland) as a postdoctoral fellow, he went on to establish an independent research group at the Department of Biochemistry and Organic Chemistry at Uppsala University (Sweden). In 2006, he joined AstraZeneca R&D S\u00f6dert\u00e4lje (Sweden). After 1-year in-house training for future leaders in drug discovery and development, he became team leader in Medicinal Chemistry in 2007. In 2008, he was appointed Candidate Drug Delivery team leader with responsibility for preclinical drug discoveries in several CNS and pain projects. In 2010, he became Project Director at the innovative medicine unit for CNS & Pain research in S\u00f6dert\u00e4lje with responsibility from lead optimization to end of Phase II for projects in the neurodegeneration area. After joining AstraZeneca, he continued to pursue academic research as Adjunct Professor in bioorganic chemistry at the Department of Biochemistry and Organic Chemistry, Uppsala University (2007-2010), and the Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University (2010-2013). In 2010, he was appointed honorary professor in Pharmacy and Pharmacology at the University of KwaZulu Natal (South Africa). In 2013, he was recruited to the Karolinska Institute in Stockholm as Director of Drug Discovery & Development, to build up the National Swedish infrastructure for Drug Discovery & Development at the Science for Life Laboratory (SciLifeLab). Since 2013, he has been a part-time research professor at the College of Health Science at the University of KwaZulu Natal. 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"https://publications.scilifelab.se/researcher/ed343544e1324911931517689ad9ba6b.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Scott", "given": "Stuart A", "initials": "SA", "orcid": "0000-0001-5720-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cb1efe5da074b6885f59ba4d80cbcd5.json"}}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Bottinger", "given": "Erwin B", "initials": "EB"}, {"family": "Hernesniemi", "given": "Jussi", "initials": "J"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Wong", "given": "Jorge A", "initials": "JA"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Eskola", "given": "Markku", "initials": "M"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Delgado", "given": "Graciela", "initials": "G"}, {"family": "Chen", "given": "Lin Y", "initials": "LY"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Sandhu", "given": "Roopinder K", "initials": "RK"}, {"family": "Li", "given": "Man", "initials": "M", "orcid": "0000-0002-3839-0281", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c39506589c43b783f9e00c32882045.json"}}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Eisele", "given": "Lewin", "initials": "L"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Rost", "given": "Natalia", "initials": "N"}, {"family": "Anderson", "given": "Christopher D", "initials": "CD"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Campbell", "given": "Archie", "initials": "A", "orcid": "0000-0003-0198-5078", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d6b9cb975246e5aa97c60035e2fdcc.json"}}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Porteous", "given": "David", "initials": "D"}, {"family": "Hocking", "given": "Lynne J", "initials": "LJ"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Heeringa", "given": "Jan", "initials": "J"}, {"family": "Denny", "given": "Joshua C", "initials": "JC"}, {"family": "Kriebel", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4270-018X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a5728278da946db8197313a6d301d77.json"}}, {"family": "Darbar", "given": "Dawood", "initials": "D"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Shaffer", "given": "Christian", "initials": "C"}, {"family": "Macfarlane", "given": "Peter W", "initials": "PW"}, {"family": "Heilmann-Heimbach", "given": "Stefanie", "initials": "S"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Huang", "given": "Paul L", "initials": "PL"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Soliman", "given": "Elsayed Z", "initials": "EZ", "orcid": "0000-0001-5632-8150", "researcher": {"href": "https://publications.scilifelab.se/researcher/96e79156ff664c509217e8834a728c79.json"}}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "J\u00f6ckel", "given": "Karl-Heinz", "initials": "KH"}, {"family": "Sinner", "given": "Moritz F", "initials": "MF"}, {"family": "Lin", "given": "Henry J", "initials": "HJ"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "METASTROKE Consortium of the ISGC", "given": "", "initials": ""}, {"family": "Neurology Working Group of the CHARGE Consortium", "given": "", "initials": ""}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Laurikka", "given": "Jari", "initials": "J"}, {"family": "Conen", "given": "David", "initials": "D"}, {"family": "Rosand", "given": "Jonathan", "initials": "J"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "ML"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Pereira", "given": "Alexandre", "initials": "A"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW", "orcid": "0000-0002-3246-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Chung", "given": "Mina K", "initials": "MK"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Alonso", "given": "Alvaro", "initials": "A"}, {"family": "Roden", "given": "Dan M", "initials": "DM"}, {"family": "K\u00e4\u00e4b", "given": "Stefan", "initials": "S"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ", "orcid": "0000-0003-4076-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/31c69bdf118d4b36ad65a6c4f780bab2.json"}}, {"family": "Tanaka", "given": "Toshihiro", "initials": "T", "orcid": "0000-0001-6201-9784", "researcher": {"href": "https://publications.scilifelab.se/researcher/021685ef890444bbb2870298ca2399d1.json"}}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}, {"family": "AFGen Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "6", "pages": "946-952", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death. Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups. To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery.", "doi": "10.1038/ng.3843", "pmid": "28416818", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3843"}, {"db": "pmc", "key": "PMC5585859"}, {"db": "mid", "key": "NIHMS901319"}], "notes": [], "created": "2018-01-09T14:01:34.761Z", "modified": "2021-06-21T15:40:01.019Z"}, {"entity": "publication", "iuid": "172827be8ae144cdabd6065140ce0c9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/172827be8ae144cdabd6065140ce0c9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/172827be8ae144cdabd6065140ce0c9b"}}, "title": "Identification and characterization of inhibitors of UDP-glucose and UDP-sugar pyrophosphorylases for in vivo studies.", "authors": [{"family": "Decker", "given": "Daniel", "initials": "D"}, {"family": "\u00d6berg", "given": "Christopher", "initials": "C"}, {"family": "Kleczkowski", "given": "Leszek A", "initials": "LA", "orcid": "0000-0001-8685-9665", "researcher": {"href": "https://publications.scilifelab.se/researcher/81510028dd76431082d79f3df7fb3252.json"}}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "90", "issn": "1365-313X", "issue": "6", "pages": "1093-1107", "title": "Plant J.", "issn-l": "0960-7412"}, "abstract": "UDP-sugars serve as ultimate precursors in hundreds of glycosylation reactions (e.g. for protein and lipid glycosylation, synthesis of sucrose, cell wall polysaccharides, etc.), underlying an important role of UDP-sugar-producing enzymes in cellular metabolism. However, genetic studies on mechanisms of UDP-sugar formation were frequently hampered by reproductive impairment of the resulting mutants, making it difficult to assess an in vivo role of a given enzyme. Here, a chemical library containing 17 500 compounds was separately screened against purified UDP-glucose pyrophosphorylase (UGPase) and UDP-sugar pyrophosphorylase (USPase), both enzymes representing the primary mechanisms of UDP-sugar formation. Several compounds have been identified which, at 50 \u03bcm, exerted at least 50% inhibition of the pyrophosphorylase activity. In all cases, both UGPase and USPase activities were inhibited, probably reflecting common structural features of active sites of these enzymes. One of these compounds (cmp #6), a salicylamide derivative, was found as effective inhibitor of Arabidopsis pollen germination and Arabidopsis cell culture growth. Hit optimization on cmp #6 yielded two analogs (cmp #6D and cmp #6D2), which acted as uncompetitive inhibitors against both UGPase and USPase, and were strong inhibitors in the pollen test, with apparent inhibition constants of less than 1 \u03bcm. Their effects on pollen germination were relieved by addition of UDP-glucose and UDP-galactose, suggesting that the inhibitors targeted UDP-sugar formation. The results suggest that cmp #6 and its analogs may represent useful tools to study in vivo roles of the pyrophosphorylases, helping to overcome the limitations of genetic approaches.", "doi": "10.1111/tpj.13531", "pmid": "28273406", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-01-10T09:44:34.132Z", "modified": "2025-10-17T13:04:29.232Z"}, {"entity": "publication", "iuid": "8bd2429d596e4fb8bac36780cb81deed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bd2429d596e4fb8bac36780cb81deed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bd2429d596e4fb8bac36780cb81deed"}}, "title": "Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches", "authors": [{"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "27", "issn": "1549-5469", "issue": "6", "pages": "1004-1015", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": null, "doi": "10.1101/gr.212522.116", "pmid": "28442558", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:25:53.822Z", "modified": "2024-01-16T13:48:47.908Z"}, {"entity": "publication", "iuid": "31715c08ce5546469fc28a95c4489f27", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31715c08ce5546469fc28a95c4489f27.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31715c08ce5546469fc28a95c4489f27"}}, "title": "Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).", "authors": [{"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Cleary", "given": "Michelle R", "initials": "MR"}, {"family": "Witzell", "given": "Johanna", "initials": "J"}, {"family": "Savenkov", "given": "Eugene I", "initials": "EI"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "12", "issn": "2213-5960", "issue": null, "pages": "155-156", "title": "Genom Data", "issn-l": "2213-5960"}, "abstract": "Phytophthora cactorum is a broad host range phytopathogenic oomycete. P. cactorum strain LV007 was isolated from a diseased European Beech (Fagus sylvatica) in Malm\u00f6, Sweden in 2016. The draft genome of P. cactorum strain LV007 is 67.81\u00a0Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmic effector proteins including RxLR and CRN families were identified. The genome sequence has been deposited at DDBJ/ENA/GenBank under the accession NBIJ00000000. The version described in this paper is version NBIJ01000000.", "doi": "10.1016/j.gdata.2017.05.010", "pmid": "28560165", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2213-5960(17)30097-1"}, {"db": "pmc", "key": "PMC5435576"}], "notes": [], "created": "2019-01-15T08:06:17.294Z", "modified": "2020-01-21T13:53:22.640Z"}, {"entity": "publication", "iuid": "9e60bfe9960242a8bcacdab4c55450c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e60bfe9960242a8bcacdab4c55450c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e60bfe9960242a8bcacdab4c55450c6"}}, "title": "Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification.", "authors": [{"family": "Pawar", "given": "Prashant Mohan-Anupama", "initials": "PM"}, {"family": "Ratke", "given": "Christine", "initials": "C"}, {"family": "Balasubramanian", "given": "Vimal K", "initials": "VK"}, {"family": "Chong", "given": "Sun-Li", "initials": "SL"}, {"family": "Gandla", "given": "Madhavi Latha", "initials": "ML"}, {"family": "Adriasola", "given": "Mathilda", "initials": "M"}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Szwaj", "given": "Klaudia", "initials": "K"}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M"}, {"family": "Gaertner", "given": "Cyril", "initials": "C"}, {"family": "Mouille", "given": "Gregory", "initials": "G"}, {"family": "Ezcurra", "given": "Ines", "initials": "I"}, {"family": "Tenkanen", "given": "Maija", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "214", "issn": "1469-8137", "issue": "4", "pages": "1491-1505", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter::GUS lines in hybrid aspen (Populus tremula \u00d7 tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.", "doi": "10.1111/nph.14489", "pmid": "28257170", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:00:51.700Z", "modified": "2025-10-17T13:03:59.803Z"}, {"entity": "publication", "iuid": "fefb85a3d39a4972a4f6d33401fe4909", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fefb85a3d39a4972a4f6d33401fe4909.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fefb85a3d39a4972a4f6d33401fe4909"}}, "title": "Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons", "authors": [{"family": "Comte", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Berga", "given": "Merc\u00e8", "initials": "M"}, {"family": "Severin", "given": "Ina", "initials": "I"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "19", "issn": "1462-2912", "issue": "6", "pages": "2391-2404", "title": "Environ Microbiol", "issn-l": "1462-2912"}, "abstract": null, "doi": "10.1111/1462-2920.13749", "pmid": "28401636", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:16:45.696Z", "modified": "2020-01-21T13:56:10.121Z"}, {"entity": "publication", "iuid": "89512b7b68e84197bca3b4ea0e9ddfae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89512b7b68e84197bca3b4ea0e9ddfae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89512b7b68e84197bca3b4ea0e9ddfae"}}, "title": "Chemisorption of air CO2 on cellulose: an overlooked feature of the cellulose/NaOH(aq) dissolution system", "authors": [{"family": "Gunnarsson", "given": "Maria", "initials": "M"}, {"family": "Theliander", "given": "Hans", "initials": "H"}, {"family": "Hasani", "given": "Merima", "initials": "M"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "24", "issn": "0969-0239", "issue": "6", "pages": "2427-2436", "title": "Cellulose", "issn-l": null}, "abstract": null, "doi": "10.1007/s10570-017-1288-8", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T11:01:06.000Z", "modified": "2025-10-17T13:03:59.834Z"}, {"entity": "publication", "iuid": "224613e7ab0048afa546c615a18f079b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/224613e7ab0048afa546c615a18f079b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/224613e7ab0048afa546c615a18f079b"}}, "title": "An automated method measures variability in P-glycoprotein and ABCG2 densities across brain regions and brain matter.", "authors": [{"family": "Kannan", "given": "Pavitra", "initials": "P"}, {"family": "Schain", "given": "Martin", "initials": "M"}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW"}, {"family": "Weidner", "given": "Lora", "initials": "L"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Guly\u00e1s", "given": "Bal\u00e1zs", "initials": "B"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Gottesman", "given": "Michael M", "initials": "MM"}, {"family": "Innis", "given": "Robert B", "initials": "RB"}, {"family": "Hall", "given": "Matthew D", "initials": "MD"}, {"family": "Mulder", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": null, "issn": "1559-7016", "issue": null, "pages": "271678X16660984", "title": "J. Cereb. Blood Flow Metab.", "issn-l": "0271-678X"}, "abstract": "Changes in P-glycoprotein and ABCG2 densities may play a role in amyloid-beta accumulation in Alzheimer's disease. However, previous studies report conflicting results from different brain regions, without correcting for changes in vessel density. We developed an automated method to measure transporter density exclusively within the vascular space, thereby correcting for vessel density. We then examined variability in transporter density across brain regions, matter, and disease using two cohorts of post-mortem brains from Alzheimer's disease patients and age-matched controls. Changes in transporter density were also investigated in capillaries near plaques and on the mRNA level. P-glycoprotein density varied with brain region and matter, whereas ABCG2 density varied with brain matter. In temporal cortex, P-glycoprotein density was 53% lower in Alzheimer's disease samples than in controls, and was reduced by 35% in capillaries near plaque deposits within Alzheimer's disease samples. ABCG2 density was unaffected in Alzheimer's disease. No differences were detected at the transcript level. Our study indicates that region-specific changes in transporter densities can occur globally and locally near amyloid-beta deposits in Alzheimer's disease, providing an explanation for conflicting results in the literature. When differences in region and matter are accounted for, changes in density can be reproducibly measured using our automated method.", "doi": "10.1177/0271678X16660984", "pmid": "27488911", "labels": {"Fluorescence Tissue Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "0271678X16660984"}], "notes": [], "created": "2017-05-03T12:58:51.602Z", "modified": "2021-07-05T13:48:51.522Z"}, {"entity": "publication", "iuid": "feb578c0af8f44d999e4cdc360c28358", "links": {"self": {"href": "https://publications.scilifelab.se/publication/feb578c0af8f44d999e4cdc360c28358.json"}, "display": {"href": "https://publications.scilifelab.se/publication/feb578c0af8f44d999e4cdc360c28358"}}, "title": "Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence.", "authors": [{"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Nyaiesh", "given": "Etienne-Nicholas", "initials": "EN"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"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": "2017-06-00", "journal": {"volume": "10", "issn": "1936-5233", "issue": "3", "pages": "385-395", "title": "Transl Oncol", "issn-l": null}, "abstract": "Blood-based proteomic profiling may aid and expand our understanding of diseases and their different phenotypes. The aim of the presented study was to profile serum samples from patients with malignant melanoma using affinity proteomic assays to describe proteins in the blood stream that are associated to stage or recurrence of melanoma.\n\nMultiplexed protein analysis was conducted using antibody suspension bead arrays. A total of 232 antibodies against 132 proteins were selected from (i) a screening with 4595 antibodies and 32 serum samples from melanoma patients and controls, (ii) antibodies used for immunohistochemistry, (iii) protein targets previously related with melanoma. The analysis was performed with 149 serum samples from patients with malignant melanoma. Antibody selectivity was then assessed by Western blot, immunocapture mass spectrometry, and epitope mapping. Lastly, indicative antibodies were applied for IHC analysis of melanoma tissues.\n\nSerum levels of regucalcin (RGN) and syntaxin 7 (STX7) were found to be lower in patients with both recurring tumors and a high Breslow's thickness (T-stage 3/4) compared to low thickness (T-stage 1/2) without disease recurrence. Serum levels of methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L) were instead elevated in sera of T3/4 patients with recurrence. The analysis of tissue sections with S100A6 and MTHFD1L showed positive staining in a majority of patients with melanoma, and S100A6 was significantly associated to T-stage.\n\nOur findings provide a starting point to further study RGN, STX7, MTHFD1L and S100A6 in serum to elucidate their involvement in melanoma progression and to assess a possible contribution to support clinical indications.", "doi": "10.1016/j.tranon.2017.03.002", "pmid": "28433799", "labels": {"Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1936-5233(17)30031-1"}, {"db": "pmc", "key": "PMC5403766"}], "notes": [], "created": "2017-08-30T14:34:48.682Z", "modified": "2021-07-08T13:44:33.779Z"}, {"entity": "publication", "iuid": "8ab76bb5c3c34939abfe74effe61f98a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ab76bb5c3c34939abfe74effe61f98a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ab76bb5c3c34939abfe74effe61f98a"}}, "title": "A missense variant in ITPR1 provides evidence for autosomal recessive SCA29 with asymptomatic cerebellar hypoplasia in carriers", "authors": [{"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Ali", "given": "Zafar", "initials": "Z"}, {"family": "Farooq", "given": "Muhammad", "initials": "M"}, {"family": "Khan", "given": "Kamal", "initials": "K"}, {"family": "Wikstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Iqbal", "given": "Maria", "initials": "M"}, {"family": "Zulfiqar", "given": "Shumaila", "initials": "S"}, {"family": "Faryal", "given": "Sanam", "initials": "S"}, {"family": "Baig", "given": "Shahid Mahmood", "initials": "SM"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "25", "issn": "1018-4813", "issue": "7", "pages": "848-853", "title": "Eur J Hum Genet", "issn-l": "1018-4813"}, "abstract": null, "doi": "10.1038/ejhg.2017.54", "pmid": "28488678", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T13:29:57.964Z", "modified": "2024-01-16T13:48:47.917Z"}, {"entity": "publication", "iuid": "6993e12273c44e0ea535c85e7bfc107d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6993e12273c44e0ea535c85e7bfc107d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6993e12273c44e0ea535c85e7bfc107d"}}, "title": "A DNA methylation site within the KLF13 gene is associated with orexigenic processes based on neural responses and ghrelin levels.", "authors": [{"family": "Wiemerslage", "given": "L", "initials": "L"}, {"family": "Islam", "given": "R", "initials": "R"}, {"family": "van der Kamp", "given": "C", "initials": "C"}, {"family": "Cao", "given": "H", "initials": "H"}, {"family": "Olivo", "given": "G", "initials": "G"}, {"family": "Ence-Eriksson", "given": "F", "initials": "F"}, {"family": "Castillo", "given": "S", "initials": "S"}, {"family": "Larsen", "given": "A L", "initials": "AL"}, {"family": "Bandstein", "given": "M", "initials": "M"}, {"family": "Dahlberg", "given": "L S", "initials": "LS"}, {"family": "Perland", "given": "E", "initials": "E"}, {"family": "Gustavsson", "given": "V", "initials": "V"}, {"family": "Nilsson", "given": "J", "initials": "J"}, {"family": "Vogel", "given": "H", "initials": "H"}, {"family": "Sch\u00fcrmann", "given": "A", "initials": "A"}, {"family": "Larsson", "given": "E-M", "initials": "EM"}, {"family": "Rask-Andersen", "given": "M", "initials": "M"}, {"family": "Benedict", "given": "C", "initials": "C"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "41", "issn": "1476-5497", "issue": "6", "pages": "990-994", "title": "Int J Obes (Lond)", "issn-l": "0307-0565"}, "abstract": "We investigated five methylation markers recently linked to body mass index, for their role in the neuropathology of obesity. In neuroimaging experiments, our analysis involving 23 participants showed that methylation levels for the cg07814318 site, which lies within the KLF13 gene, correlated with brain activity in the claustrum, putamen, cingulate gyrus and frontal gyri, some of which have been previously associated to food signaling, obesity or reward. Methylation levels at cg07814318 also positively correlated with ghrelin levels. Moreover, expression of KLF13 was augmented in the brains of obese and starved mice. Our results suggest the cg07814318 site could be involved in orexigenic processes, and also implicate KLF13 in obesity. Our findings are the first to associate methylation levels in blood with brain activity in obesity-related regions, and further support previous findings between ghrelin, brain activity and genetic differences.", "doi": "10.1038/ijo.2017.43", "pmid": "28194012", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ijo201743"}], "notes": [], "created": "2017-10-25T15:27:46.412Z", "modified": "2024-01-16T13:48:47.929Z"}, {"entity": "publication", "iuid": "64b356ba093a4bf180f042a619c896a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64b356ba093a4bf180f042a619c896a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64b356ba093a4bf180f042a619c896a0"}}, "title": "High-affinity recognition of the human C-reactive protein independent of phosphocholine.", "authors": [{"family": "Yang", "given": "Jie", "initials": "J"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1821-4715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6463abd05b415696c52be577ca2be6.json"}}, {"family": "Norberg", "given": "Thomas", "initials": "T", "orcid": "0000-0002-0675-7675", "researcher": {"href": "https://publications.scilifelab.se/researcher/a85dcf5837e641a4a844401b54dae2d9.json"}}, {"family": "Baltzer", "given": "Lars", "initials": "L", "orcid": "0000-0001-5807-2726", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca711c9ac6fd43e4baf6e95886c85774.json"}}], "type": "journal article", "published": "2017-05-31", "journal": {"volume": "15", "issn": "1477-0539", "issue": "21", "pages": "4644-4654", "title": "Org. Biomol. Chem.", "issn-l": "1477-0520"}, "abstract": "A high-affinity polypeptide conjugate 4-C25L22-DQ, has been developed for the molecular recognition of the human C-reactive protein, CRP, a well-known inflammation biomarker. CRP is one of the most frequently quantified targets in diagnostic applications and a target in drug development. With the exception of antibodies, most molecular constructs take advantage of the known affinity for CRP of phosphocholine that depends on Ca2+ for its ability to bind. 4-C25L22-DQ which is unrelated to phosphocholine binds in the absence of Ca2+ with a dissociation constant of 760 nM, an order of magnitude lower than that of phosphocholine, the KD of which is 5 \u03bcM. The small organic molecule 2-oxo-1,2-dihydroquinoline-8-carboxylic acid (DQ) was designed based on the structural similarities between three hits from a set of compounds selected from a building block collection and evaluated with regards to affinity for CRP by NMR spectroscopy. 4-C25L22-DQ was shown in a competition experiment to bind CRP three orders of magnitude more strongly than DQ itself, and in a pull-down experiment 4-C25L22-DQ was shown to extract CRP from human serum. The development of a robust and phosphocholine-independent recognition element provides unprecedented opportunities in bioanalytical applications in vivo and in vitro under conditions where the concentration of Ca2+ ions is low, or where Ca2+ binding agents such as EDTA or heparin are needed to prevent blood coagulation. The identification from a compound library of a small organic molecule and its conjugation to a small set of polypeptides, none of which were previously known to bind CRP, illustrates a convenient and general route to selective high-affinity binders for proteins with dissociation constants in the \u03bcM to nM range for which no small molecule ligands are known.", "doi": "10.1039/c7ob00684e", "pmid": "28513744", "labels": {"Swedish NMR Centre": "Service", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-20T15:12:12.567Z", "modified": "2025-10-17T13:04:29.262Z"}, {"entity": "publication", "iuid": "dfc6452e87c54ae4a5a175da905f3a44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfc6452e87c54ae4a5a175da905f3a44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfc6452e87c54ae4a5a175da905f3a44"}}, "title": "Expression of CD226 is associated to but not required for NK cell education.", "authors": [{"family": "Wagner", "given": "Arnika K", "initials": "AK"}, {"family": "Kadri", "given": "Nadir", "initials": "N"}, {"family": "Sn\u00e4ll", "given": "Johanna", "initials": "J"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Gilfillan", "given": "Susan", "initials": "S"}, {"family": "Colonna", "given": "Marco", "initials": "M"}, {"family": "Bernhardt", "given": "G\u00fcnter", "initials": "G"}, {"family": "H\u00f6glund", "given": "Petter", "initials": "P"}, {"family": "K\u00e4rre", "given": "Klas", "initials": "K"}, {"family": "Chambers", "given": "Benedict J", "initials": "BJ"}], "type": "journal article", "published": "2017-05-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "8", "issue": null, "pages": "15627"}, "abstract": "DNAX accessory molecule-1 (DNAM-1, also known as CD226) is an activating receptor expressed on subsets of natural killer (NK) and T cells, interacts with its ligands CD155 or CD112, and has co-varied expression with inhibitory receptors. Since inhibitory receptors control NK-cell activation and are necessary for MHC-I-dependent education, we investigated whether DNAM-1 expression is also involved in NK-cell education. Here we show an MHC-I-dependent correlation between DNAM-1 expression and NK-cell education, and an association between DNAM-1 and NKG2A that occurs even in MHC class I deficient mice. DNAM-1 is expressed early during NK-cell development, precedes the expression of MHC-I-specific inhibitory receptors, and is modulated in an education-dependent fashion. Cd226-/- mice have missing self-responses and NK cells with a normal receptor repertoire. We propose a model in which NK-cell education prevents or delays downregulation of DNAM-1. This molecule endows educated NK cells with enhanced effector functions but is dispensable for education.", "doi": "10.1038/ncomms15627", "pmid": "28561023", "labels": {"Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms15627"}, {"db": "pmc", "key": "PMC5460037"}], "notes": [], "created": "2019-03-25T19:57:01.145Z", "modified": "2023-11-28T12:54:23.964Z"}, {"entity": "publication", "iuid": "1d8f9559700447cb85c24a82a88e4d3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d8f9559700447cb85c24a82a88e4d3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d8f9559700447cb85c24a82a88e4d3d"}}, "title": "Genetic susceptibility to cardiovascular disease and risk of dementia.", "authors": [{"family": "Karlsson", "given": "I K", "initials": "IK"}, {"family": "Ploner", "given": "A", "initials": "A"}, {"family": "Song", "given": "C", "initials": "C"}, {"family": "Gatz", "given": "M", "initials": "M"}, {"family": "Pedersen", "given": "N L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "S", "initials": "S"}], "type": "journal article", "published": "2017-05-30", "journal": {"volume": "7", "issn": "2158-3188", "issue": "5", "pages": "e1142", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "Several studies have shown cardiovascular disease (CVD) to be associated with dementia, but it is not clear whether CVD per se increases the risk of dementia or whether the association is due to shared risk factors. We tested how a genetic risk score (GRS) for coronary artery disease (CAD) affects dementia risk after CVD in 13 231 Swedish twins. We also utilized summarized genome-wide association data to study genetic overlap between CAD and Alzheimer\u00b4s disease (AD), and additionally between shared risk factors and each disease. There was no direct effect of a CAD GRS on dementia (hazard ratio 0.99, 95% confidence interval (CI): 0.98-1.01). However, the GRS for CAD modified the association between CVD and dementia within 3 years of CVD diagnosis, ranging from a hazard ratio of 1.59 (95% CI: 1.05-2.41) in the first GRS quartile to 1.91 (95% CI: 1.28-2.86) in the fourth GRS quartile. Using summary statistics, we found no genetic overlap between CAD and AD. We did, however, find that both AD and CAD share a significant genetic overlap with lipids, but that the overlap arose from clearly distinct gene clusters. In conclusion, genetic susceptibility to CAD was found to modify the association between CVD and dementia, most likely through associations with shared risk factors.", "doi": "10.1038/tp.2017.110", "pmid": "28556832", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "tp2017110"}, {"db": "pmc", "key": "PMC5534941"}], "notes": [], "created": "2018-01-09T13:58:11.467Z", "modified": "2021-06-21T15:37:39.117Z"}, {"entity": "publication", "iuid": "9ffdf7a669174f9b940bb01c93fab8a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9"}}, "title": "A subcellular map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1441c2fca5d4946987ec975986fcfa2.json"}}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b0ca6c2a8f64be89222a6029885b08c.json"}}, {"family": "Wiking", "given": "Mikaela", "initials": "M", "orcid": "0000-0002-6368-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/b69baef540a14859a7b4fd966c3b9245.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc22f13eb21a4c75a6e7cad7686bcc8a.json"}}, {"family": "Geladaki", "given": "Aikaterini", "initials": "A", "orcid": "0000-0002-0530-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/28081295132343c5bfc4b1e9bcfb8201.json"}}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Alm", "given": "Tove", "initials": "T", "orcid": "0000-0002-2643-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0b5ee89148475581faf42ea53d61bd.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L", "orcid": "0000-0002-8116-882X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1092280955d44d1f99258f4f812fb6c7.json"}}, {"family": "Breckels", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-8918-7171", "researcher": {"href": "https://publications.scilifelab.se/researcher/3efbca65f39d4f7aa8df049a39e0c8a9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Fall", "given": "Jenny", "initials": "J"}, {"family": "Gatto", "given": "Laurent", "initials": "L", "orcid": "0000-0002-1520-2268", "researcher": {"href": "https://publications.scilifelab.se/researcher/242f5219a40547439c0cc4b07e26e71d.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications.scilifelab.se/researcher/80019f26676347d5b6c4124d63eeaf86.json"}}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Mulvey", "given": "Claire M", "initials": "CM", "orcid": "0000-0002-2989-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc08b919bd8a423f8a6df8b880979045.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/83314cf7a93543bf9cd6f68f9657e99e.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a96138841741f9acff4a50100c2a25.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Winsnes", "given": "Casper", "initials": "C", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a64c707c8b54b6bbd31dae6485a1392.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS"}, {"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": "2017-05-26", "journal": {"volume": "356", "issn": "1095-9203", "issue": "6340", "pages": null, "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.", "doi": "10.1126/science.aal3321", "pmid": "28495876", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Spatial Proteomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aal3321"}], "notes": [], "created": "2017-10-31T15:27:28.787Z", "modified": "2024-01-16T13:48:47.941Z"}, {"entity": "publication", "iuid": "914e667e695641e7827adaf9b0dcf69b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/914e667e695641e7827adaf9b0dcf69b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/914e667e695641e7827adaf9b0dcf69b"}}, "title": "Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.", "authors": [{"family": "V\u00e4remo", "given": "Leif", "initials": "L"}, {"family": "Henriksen", "given": "Tora Ida", "initials": "TI"}, {"family": "Scheele", "given": "Camilla", "initials": "C"}, {"family": "Broholm", "given": "Christa", "initials": "C"}, {"family": "Pedersen", "given": "Maria", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pedersen", "given": "Bente Klarlund", "initials": "BK"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-05-25", "journal": {"volume": "9", "issn": "1756-994X", "issue": "1", "pages": "47", "title": "Genome Med", "issn-l": "1756-994X"}, "abstract": "Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity.\n\nWe generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription. This setup enabled us to identify intrinsic properties, originating from muscle precursor cells and retained in the corresponding myocytes. Bioinformatic and statistical methods, including differential expression analysis, gene-set analysis, and metabolic network analysis, were used to characterize the different myocytes.\n\nWe found that the transcriptional program associated with obesity alone was strikingly similar to that induced specifically by T2D. We identified a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating these transcriptional signatures. T2D and obesity were independently associated with dysregulated myogenesis, down-regulated muscle function, and up-regulation of inflammation and extracellular matrix components. Metabolic network analysis identified that in T2D but not obesity a specific metabolite subnetwork involved in sphingolipid metabolism was transcriptionally regulated.\n\nOur findings identify inherent characteristics in myocytes, as a memory of the in vivo phenotype, without the influence from a diabetic or obese extracellular environment, highlighting their importance in the development of T2D.", "doi": "10.1186/s13073-017-0432-2", "pmid": "28545587", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13073-017-0432-2"}, {"db": "pmc", "key": "PMC5444103"}], "notes": [], "created": "2017-11-03T15:53:40.517Z", "modified": "2024-01-16T13:48:47.954Z"}, {"entity": "publication", "iuid": "8c77e3f7b1d74d738582830376424535", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c77e3f7b1d74d738582830376424535.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c77e3f7b1d74d738582830376424535"}}, "title": "Piperazin-1-ylpyridazine Derivatives Are a Novel Class of Human dCTP Pyrophosphatase 1 Inhibitors.", "authors": [{"family": "Llona-Minguez", "given": "Sabin", "initials": "S", "orcid": "0000-0003-3187-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/437b1f98ad21471f884226ed89a3da12.json"}}, {"family": "H\u00f6glund", "given": "Andreas", "initials": "A"}, {"family": "Ghassemian", "given": "Artin", "initials": "A"}, {"family": "Desroses", "given": "Matthieu", "initials": "M"}, {"family": "Calder\u00f3n-Monta\u00f1o", "given": "Jos\u00e9 Manuel", "initials": "JM"}, {"family": "Burgos Mor\u00f3n", "given": "Estefan\u00eda", "initials": "E"}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NCK", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}, {"family": "Wiita", "given": "Elisee", "initials": "E"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Cazares-K\u00f6rner", "given": "Cindy", "initials": "C"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Darabi", "given": "Masoud", "initials": "M"}, {"family": "Mehdizadeh", "given": "Amir", "initials": "A"}, {"family": "Fayezi", "given": "Shabnam", "initials": "S"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Sigmundsson", "given": "Kristmundur", "initials": "K"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Jenmalm Jensen", "given": "Annika", "initials": "A"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-05-25", "journal": {"volume": "60", "issn": "1520-4804", "issue": "10", "pages": "4279-4292", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "The dCTP pyrophosphatase 1 (dCTPase) is a nucleotide pool \"housekeeping\" enzyme responsible for the catabolism of canonical and noncanonical nucleoside triphosphates (dNTPs) and has been associated with cancer progression and cancer cell stemness. We have identified a series of piperazin-1-ylpyridazines as a new class of potent dCTPase inhibitors. Lead compounds increase dCTPase thermal and protease stability, display outstanding selectivity over related enzymes and synergize with a cytidine analogue against leukemic cells. This new class of dCTPase inhibitors lays the first stone toward the development of drug-like probes for the dCTPase enzyme.", "doi": "10.1021/acs.jmedchem.7b00182", "pmid": "28508636", "labels": {"Protein Science Facility (PSF)": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-25T12:40:01.845Z", "modified": "2025-10-17T13:05:08.916Z"}, {"entity": "publication", "iuid": "1b262db9b2e649d3b068b24a164ca06f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b262db9b2e649d3b068b24a164ca06f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b262db9b2e649d3b068b24a164ca06f"}}, "title": "Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.", "authors": [{"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2017-05-25", "journal": {"volume": "5", "issn": "2169-8287", "issue": "21", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "The oomycete Pythium oligandrum is a mycoparasite and licenced biological control agent. Here, we report the draft genome sequence of P.\u00a0oligandrum strain CBS 530.74, which is 36.80\u00a0Mb. It contains 341 scaffolds and 11,647 predicted protein-coding genes. As reported for plant-pathogenic Pythium species, RXLR-type effector sequences are absent.", "doi": "10.1128/genomeA.00346-17", "pmid": "28546478", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5/21/e00346-17"}, {"db": "pmc", "key": "PMC5477391"}], "notes": [], "created": "2017-11-03T16:21:52.480Z", "modified": "2020-01-21T13:56:17.422Z"}, {"entity": "publication", "iuid": "13dd6b3f7ca945c8a989fb4ceacb6b35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13dd6b3f7ca945c8a989fb4ceacb6b35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13dd6b3f7ca945c8a989fb4ceacb6b35"}}, "title": "Apoptotic Bax at Oxidatively Stressed Mitochondrial Membranes: Lipid Dynamics and Permeabilization.", "authors": [{"family": "Dingeldein", "given": "Artur Peter G\u00fcnther", "initials": "APG"}, {"family": "Pokorn\u00e1", "given": "\u0160\u00e1rka", "initials": "\u0160"}, {"family": "Lidman", "given": "Martin", "initials": "M"}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "\u0160achl", "given": "Radek", "initials": "R"}, {"family": "Hof", "given": "Martin", "initials": "M"}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-7380-8797", "researcher": {"href": "https://publications.scilifelab.se/researcher/85bd86ebc85d4653bc880bc9be25bc80.json"}}], "type": "journal article", "published": "2017-05-23", "journal": {"volume": "112", "issn": "1542-0086", "issue": "10", "pages": "2147-2158", "title": "Biophysical Journal", "issn-l": "0006-3495"}, "abstract": "Mitochondria are crucial compartments of eukaryotic cells because they function as the cellular power plant and play a central role in the early stages of programmed cell death (apoptosis). To avoid undesired cell death, this apoptotic pathway is tightly regulated by members of the Bcl-2 protein family, which interact on the external surface of the mitochondria, i.e., the mitochondrial outer membrane (MOM), and modulate its permeability to apoptotic factors, controlling their release into the cytosol. A growing body of evidence suggests that the MOM lipids play active roles in this permeabilization process. In particular, oxidized phospholipids (OxPls) formed under intracellular stress seem to directly induce apoptotic activity at the MOM. Here we show that the process of MOM pore formation is sensitive to the type of OxPls species that are generated. We created MOM-mimicking liposome systems, which resemble the cellular situation before apoptosis and upon triggering of oxidative stress conditions. These vesicles were studied using 31P solid-state magic-angle-spinning nuclear magnetic resonance spectroscopy and differential scanning calorimetry, together with dye leakage assays. Direct polarization and cross-polarization nuclear magnetic resonance experiments enabled us to probe the heterogeneity of these membranes and their associated molecular dynamics. The addition of apoptotic Bax protein to OxPls-containing vesicles drastically changed the membranes' dynamic behavior, almost completely negating the previously observed effect of temperature on the lipids' molecular dynamics and inducing an ordering effect that led to more cooperative membrane melting. Our results support the hypothesis that the mitochondrion-specific lipid cardiolipin functions as a first contact site for Bax during its translocation to the MOM in the onset of apoptosis. In addition, dye leakage assays revealed that different OxPls species in the MOM-mimicking vesicles can have opposing effects on Bax pore formation.", "doi": "10.1016/j.bpj.2017.04.019", "pmid": "28538152", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0006-3495(17)30435-6"}, {"db": "pmc", "key": "PMC5444002"}], "notes": [], "created": "2017-10-31T12:11:16.758Z", "modified": "2025-10-17T13:03:59.857Z"}, {"entity": "publication", "iuid": "38aaed196e084a14b7adad22ab9523a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38aaed196e084a14b7adad22ab9523a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38aaed196e084a14b7adad22ab9523a9"}}, "title": "Neuroproteomic Profiling of Cerebrospinal Fluid (CSF) by Multiplexed Affinity Arrays.", "authors": [{"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2017-05-17", "journal": {"volume": "1598", "issn": "1940-6029", "issue": null, "pages": "247-254", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Protein profiling through affinity proteomic approaches represents a powerful strategy for the analysis of human body fluids. Cerebrospinal fluid (CSF), being the fluid proximal to the central nervous system, is commonly analyzed in the context of neurological diseases, and can offer novel insights into the physiological state of the brain. Ultimately, and by analyzing the presence of brain-derived proteins in larger sets of samples that represent different phenotypes, profiling of CSF may serve as an important source to discover and verify disease-associated markers. Here, we describe a multiplexed and flexible protein profiling approach using antibody-based assays on suspension bead arrays. Through streamlined sample processing, protein biotinylation, and single-binder assay readout, this method enables high-throughput neuroproteomic analysis of up to 384 proteins in 384 samples.", "doi": "10.1007/978-1-4939-6952-4_11", "pmid": "28508365", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:18:02.763Z", "modified": "2021-07-08T12:07:34.045Z"}, {"entity": "publication", "iuid": "0013c1ea0aa54c31903307c143eca156", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0013c1ea0aa54c31903307c143eca156.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0013c1ea0aa54c31903307c143eca156"}}, "title": "ProQ3D: improved model quality assessments using deep learning.", "authors": [{"family": "Uziela", "given": "Karolis", "initials": "K"}, {"family": "Men\u00e9ndez Hurtado", "given": "David", "initials": "D"}, {"family": "Shu", "given": "Nanjiang", "initials": "N"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2017-05-15", "journal": {"volume": "33", "issn": "1367-4811", "issue": "10", "pages": "1578-1580", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased from 0.60 in ProQ to 0.81 in ProQ2 and 0.85 in ProQ3 mainly by adding a large set of carefully tuned descriptions of a protein. Here, we show that a substantial improvement can be obtained using exactly the same inputs as in ProQ2 or ProQ3 but replacing the support vector machine by a deep neural network. This improves the Pearson correlation to 0.90 (0.85 using ProQ2 input features).\r\n\r\nProQ3D is freely available both as a webserver and a stand-alone program at http://proq3.bioinfo.se/.\r\n\r\narne@bioinfo.se.\r\n\r\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btw819", "pmid": "28052925", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "btw819"}], "notes": [], "created": "2017-11-01T12:35:54.198Z", "modified": "2020-01-21T13:53:21.650Z"}, {"entity": "publication", "iuid": "6b96a366c06542319f176c1ff67cf59a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b96a366c06542319f176c1ff67cf59a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b96a366c06542319f176c1ff67cf59a"}}, "title": "Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.", "authors": [{"family": "Nguyen", "given": "Chinh Bkrong", "initials": "CB"}, {"family": "Als\u00f8e", "given": "Lene", "initials": "L"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Sulheim", "given": "Dag", "initials": "D"}, {"family": "Fagermoen", "given": "Even", "initials": "E"}, {"family": "Winger", "given": "Anette", "initials": "A"}, {"family": "Kaarb\u00f8", "given": "Mari", "initials": "M"}, {"family": "Nilsen", "given": "Hilde", "initials": "H"}, {"family": "Wyller", "given": "Vegard Bruun", "initials": "VB"}], "type": "journal article", "published": "2017-05-11", "journal": {"volume": "15", "issn": "1479-5876", "issue": "1", "pages": "102", "title": "J Transl Med", "issn-l": "1479-5876"}, "abstract": "Chronic fatigue syndrome (CFS) is a prevalent and disabling condition affecting adolescents. The pathophysiology is poorly understood, but immune alterations might be an important component. This study compared whole blood gene expression in adolescent CFS patients and healthy controls, and explored associations between gene expression and neuroendocrine markers, immune markers and clinical markers within the CFS group.\n\nCFS patients (12-18\u00a0years old) were recruited nation-wide to a single referral center as part of the NorCAPITAL project. A broad case definition of CFS was applied, requiring 3\u00a0months of unexplained, disabling chronic/relapsing fatigue of new onset, whereas no accompanying symptoms were necessary. Healthy controls having comparable distribution of gender and age were recruited from local schools. Whole blood samples were subjected to RNA sequencing. Immune markers were blood leukocyte counts, plasma cytokines, serum C-reactive protein and immunoglobulins. Neuroendocrine markers encompassed plasma and urine levels of catecholamines and cortisol, as well as heart rate variability indices. Clinical markers consisted of questionnaire scores for symptoms of post-exertional malaise, inflammation, fatigue, depression and trait anxiety, as well as activity recordings.\n\nA total of 29 CFS patients and 18 healthy controls were included. We identified 176 genes as differentially expressed in patients compared to controls, adjusting for age and gender factors. Gene set enrichment analyses suggested impairment of B cell differentiation and survival, as well as enhancement of innate antiviral responses and inflammation in the CFS group. A pattern of co-expression could be identified, and this pattern, as well as single gene transcripts, was significantly associated with indices of autonomic nervous activity, plasma cortisol, and blood monocyte and eosinophil counts. Also, an association with symptoms of post-exertional malaise was demonstrated.\n\nAdolescent CFS is characterized by differential gene expression pattern in whole blood suggestive of impaired B cell differentiation and survival, and enhanced innate antiviral responses and inflammation. This expression pattern is associated with neuroendocrine markers of altered HPA axis and autonomic nervous activity, and with symptoms of post-exertional malaise. Trial registration Clinical Trials NCT01040429.", "doi": "10.1186/s12967-017-1201-0", "pmid": "28494812", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12967-017-1201-0"}, {"db": "pmc", "key": "PMC5426002"}, {"db": "ClinicalTrials.gov", "key": "NCT01040429"}, {"db": "ClinicalTrials.gov", "key": "NCT01040429"}], "notes": [], "created": "2019-01-15T07:56:54.940Z", "modified": "2021-07-05T12:48:15.991Z"}, {"entity": "publication", "iuid": "02b1d36f7ef04089bd0f08e4bd278f47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02b1d36f7ef04089bd0f08e4bd278f47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02b1d36f7ef04089bd0f08e4bd278f47"}}, "title": "Genome Sequence of a Bovine Rhinitis B Virus Identified in Cattle in Sweden", "authors": [{"family": "Blomstr\u00f6m", "given": "Anne Lie", "initials": "AL"}, {"family": "Oma", "given": "Veslem\u00f8y", "initials": "V"}, {"family": "Khatri", "given": "Mamata", "initials": "M"}, {"family": "Hansen", "given": "Hanne H", "initials": "HH"}, {"family": "Stokstad", "given": "Maria", "initials": "M"}, {"family": "Berg", "given": "Mikael", "initials": "M"}, {"family": "Myrmel", "given": "Mette", "initials": "M"}], "type": "journal-article", "published": "2017-05-11", "journal": {"volume": "5", "issn": "2169-8287", "issue": "19", "pages": "e00172-17", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": null, "doi": "10.1128/genomea.00172-17", "pmid": "28495761", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T07:54:31.662Z", "modified": "2024-01-16T13:48:47.967Z"}, {"entity": "publication", "iuid": "cb72c2b5a1184d3591fc1e7dc95f3813", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb72c2b5a1184d3591fc1e7dc95f3813.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb72c2b5a1184d3591fc1e7dc95f3813"}}, "title": "TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-05-10", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "664", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.", "doi": "10.12688/f1000research.11168.2", "pmid": "28781756", "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", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5521161"}], "notes": [], "created": "2017-10-04T15:14:48.609Z", "modified": "2024-01-16T13:48:47.976Z"}, {"entity": "publication", "iuid": "4240e65983424a2bb62b383b13885f5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4240e65983424a2bb62b383b13885f5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4240e65983424a2bb62b383b13885f5c"}}, "title": "Reproducible diagnostic metabolites in plasma from typhoid fever patients in Asia and Africa", "authors": [{"family": "N\u00e4sstr\u00f6m", "given": "Elin", "initials": "E"}, {"family": "Parry", "given": "Christopher M", "initials": "CM"}, {"family": "Vu Thieu", "given": "Nga Tran", "initials": "NT"}, {"family": "Maude", "given": "Rapeephan R", "initials": "RR"}, {"family": "de Jong", "given": "Hanna K", "initials": "HK"}, {"family": "Fukushima", "given": "Masako", "initials": "M"}, {"family": "Rzhepishevska", "given": "Olena", "initials": "O"}, {"family": "Marks", "given": "Florian", "initials": "F"}, {"family": "Panzner", "given": "Ursula", "initials": "U"}, {"family": "Im", "given": "Justin", "initials": "J"}, {"family": "Jeon", "given": "Hyonjin", "initials": "H"}, {"family": "Park", "given": "Seeun", "initials": "S"}, {"family": "Chaudhury", "given": "Zabeen", "initials": "Z"}, {"family": "Ghose", "given": "Aniruddha", "initials": "A"}, {"family": "Samad", "given": "Rasheda", "initials": "R"}, {"family": "Van", "given": "Tan Trinh", "initials": "TT"}, {"family": "Johansson", "given": "Anders", "initials": "A"}, {"family": "Dondorp", "given": "Arjen M", "initials": "AM"}, {"family": "Thwaites", "given": "Guy E", "initials": "GE"}, {"family": "Faiz", "given": "Abul", "initials": "A"}, {"family": "Antti", "given": "Henrik", "initials": "H"}, {"family": "Baker", "given": "Stephen", "initials": "S"}], "type": "journal-article", "published": "2017-05-09", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": null, "doi": "10.7554/elife.15651", "pmid": "28483042", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:34:03.253Z", "modified": "2025-10-17T13:03:18.815Z"}, {"entity": "publication", "iuid": "bb6d4614c26347a3bd247c38cd10c6a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb6d4614c26347a3bd247c38cd10c6a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb6d4614c26347a3bd247c38cd10c6a2"}}, "title": "Influence of Glycosylation on Interfacial Properties of Recombinant Mucins: Adsorption, Surface Forces, and Friction.", "authors": [{"family": "An", "given": "Junxue", "initials": "J"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "D\u0117dinait\u0117", "given": "Andra", "initials": "A"}, {"family": "Holgersson", "given": "Jan", "initials": "J"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Claesson", "given": "Per M", "initials": "PM"}], "type": "journal article", "published": "2017-05-09", "journal": {"volume": "33", "issn": "1520-5827", "issue": "18", "pages": "4386-4395", "title": "Langmuir", "issn-l": "0743-7463"}, "abstract": "Interfacial properties of two brush-with-anchor mucins, C-P55 and C-PSLex, have been investigated at the aqueous solution/poly(methyl methacrylate) (PMMA) interface. Both are recombinant mucin-type fusion proteins, produced by fusing the glycosylated mucin part of P-selectin glycoprotein ligand-1 (PSLG-1) to the Fc part of a mouse immunoglobulin in two different cells. They are mainly expressed as dimers upon production. Analysis of the O-glycans shows that the C-PSLex mucin has the longer and more branched side chains, but C-P55 has slightly higher sialic acid content. The adsorption of the mucins to PMMA surfaces was studied by quartz crystal microbalance with dissipation. The sensed mass, including the adsorbed mucin and water trapped in the layer, was found to be similar for these two mucin layers. Atomic force microscopy with colloidal probe was employed to study surface and friction forces between mucin-coated PMMA surfaces. Purely repulsive forces of steric origin were observed between mucin layers on compression, whereas a small adhesion was detected between both mucin layers on decompression. This was attributed to chain entanglement. The friction force between C-PSLex-coated PMMA is lower than that between C-P55-coated PMMA at low loads, but vice versa at high loads. We discuss our results in terms of the differences in the glycosylation composition of these two mucins.", "doi": "10.1021/acs.langmuir.7b00030", "pmid": "28431467", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-01-30T16:19:34.217Z", "modified": "2024-01-16T13:46:32.669Z"}, {"entity": "publication", "iuid": "788bcedf458c46bca3f4b731190d6c65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65"}}, "title": "Spatially resolved transcriptome profiling in model plant species.", "authors": [{"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Navarro", "given": "Jos\u00e9 Fernandez", "initials": "JF"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "McKee", "given": "Lauren S", "initials": "LS"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Bulone", "given": "Vincent", "initials": "V"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2017-05-08", "journal": {"volume": "3", "issn": "2055-0278", "issue": null, "pages": "17061", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.", "doi": "10.1038/nplants.2017.61", "pmid": "28481330", "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": "pii", "key": "nplants201761"}], "notes": [], "created": "2017-08-23T14:09:59.506Z", "modified": "2024-01-16T13:48:47.983Z"}, {"entity": "publication", "iuid": "8447b66fc57d40adb9dc7b36a4840536", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8447b66fc57d40adb9dc7b36a4840536.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8447b66fc57d40adb9dc7b36a4840536"}}, "title": "Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.", "authors": [{"family": "Chan", "given": "Sherwin", "initials": "S"}, {"family": "Frasch", "given": "Alejandra", "initials": "A"}, {"family": "Mandava", "given": "Chandra Sekhar", "initials": "CS"}, {"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Quintana", "given": "Maria Del Pilar", "initials": "MDP"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}, {"family": "Ghorbal", "given": "Mehdi", "initials": "M"}, {"family": "Joannin", "given": "Nicolas", "initials": "N"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Lopez-Rubio", "given": "Jose-Juan", "initials": "JJ"}, {"family": "Barbieri", "given": "Sonia", "initials": "S"}, {"family": "Lanzavecchia", "given": "Antonio", "initials": "A"}, {"family": "Sanyal", "given": "Suparna", "initials": "S"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-05-08", "journal": {"volume": "2", "issn": "2058-5276", "issue": null, "pages": "17068", "title": "Nat Microbiol", "issn-l": "2058-5276"}, "abstract": "Pregnancy-associated malaria commonly involves the binding of Plasmodium falciparum-infected erythrocytes to placental chondroitin sulfate A (CSA) through the PfEMP1-VAR2CSA protein. VAR2CSA is translationally repressed by an upstream open reading frame. In this study, we report that the P. falciparum translation enhancing factor (PTEF) relieves upstream open reading frame repression and thereby facilitates VAR2CSA translation. VAR2CSA protein levels in var2csa-transcribing parasites are dependent on the expression level of PTEF, and the alleviation of upstream open reading frame repression requires the proteolytic processing of PTEF by PfCalpain. Cleavage generates a C-terminal domain that contains a sterile-alpha-motif-like domain. The C-terminal domain is permissive to cytoplasmic shuttling and interacts with ribosomes to facilitate translational derepression of the var2csa coding sequence. It also enhances translation in a heterologous translation system and thus represents the first non-canonical translation enhancing factor to be found in a protozoan. Our results implicate PTEF in regulating placental CSA binding of infected erythrocytes.", "doi": "10.1038/nmicrobiol.2017.68", "pmid": "28481333", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Global Proteomics and Proteogenomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nmicrobiol201768"}], "notes": [], "created": "2017-11-03T16:22:14.766Z", "modified": "2024-01-16T13:48:47.993Z"}, {"entity": "publication", "iuid": "60f106fef94544f29aab7a81662a8624", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60f106fef94544f29aab7a81662a8624.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60f106fef94544f29aab7a81662a8624"}}, "title": "Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies.", "authors": [{"family": "Sierra-S\u00e1nchez", "given": "\u00c1lvaro", "initials": "\u00c1"}, {"family": "Garrido-Mart\u00edn", "given": "Diego", "initials": "D"}, {"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Gonz\u00e1lez-Gonz\u00e1lez", "given": "Mar\u00eda", "initials": "M"}, {"family": "D\u00edez", "given": "Paula", "initials": "P"}, {"family": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"family": "Sj\u00f6ber", "given": "Ronald", "initials": "R"}, {"family": "Droste", "given": "Conrad", "initials": "C"}, {"family": "De Las Rivas", "given": "Javier", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Blanco", "given": "Francisco", "initials": "F"}, {"family": "Fuentes", "given": "Manuel", "initials": "M"}], "type": "journal article", "published": "2017-05-05", "journal": {"volume": "16", "issn": "1535-3907", "issue": "5", "pages": "1890-1899", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Osteoarthritis (OA) is one of the most prevalent articular diseases. The identification of proteins closely associated with the diagnosis, progression, prognosis, and treatment response is dramatically required for this pathology. In this work, differential serum protein profiles have been identified in OA and rheumatoid arthritis (RA) by antibody arrays containing 151 antibodies against 121 antigens in a cohort of 36 samples. Then the identified differential serum protein profiles have been validated in a larger cohort of 282 samples. The overall immunoreactivity is higher in the pathological situations in comparison with the controls. Several proteins have been identified as biomarker candidates for OA and RA. Most of these biomarker candidates are proteins related to inflammatory response, lipid metabolism, or bone and extracellular matrix formation, degradation, or remodeling.", "doi": "10.1021/acs.jproteome.6b00980", "pmid": "28379711", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:37:51.039Z", "modified": "2021-07-07T15:50:03.155Z"}, {"entity": "publication", "iuid": "a2e1d3ebe2ba437f93cd653482788ae5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2e1d3ebe2ba437f93cd653482788ae5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2e1d3ebe2ba437f93cd653482788ae5"}}, "title": "QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl.", "authors": [{"family": "Fallahsharoudi", "given": "Amir", "initials": "A", "orcid": "0000-0001-8820-0098", "researcher": {"href": "https://publications.scilifelab.se/researcher/3254f702d33342ed8e40e90dd9e72823.json"}}, {"family": "de Kock", "given": "Neil", "initials": "N", "orcid": "0000-0002-7167-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/81ad05a2eb494c5eb3a7a1f7d0a66b9c.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Bektic", "given": "Lejla", "initials": "L", "orcid": "0000-0003-1590-0653", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebc866f430e34e5a9af55ecc227047e6.json"}}, {"family": "Ubhayasekera", "given": "S J Kumari A", "initials": "SJ"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Jensen", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2017-05-05", "journal": {"volume": "446", "issn": "1872-8057", "issue": null, "pages": "52-58", "title": "Mol. Cell. Endocrinol.", "issn-l": "0303-7207"}, "abstract": "Domestication of animals is associated with numerous alterations in physiology, morphology, and behavior. Lower reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and reduced fearfulness is seen in most studied domesticates, including chickens. Previously we have shown that the physiological stress response as well as expression levels of hundreds of genes in the hypothalamus and adrenal glands are different between domesticated White Leghorn and the progenitor of modern chickens, the Red Junglefowl. To map genetic loci associated with the transcription levels of genes involved in the physiological stress response, we conducted an eQTL analysis in the F 12 generation of an inter-cross between White Leghorn and Red Junglefowl. We selected genes for further studies based on their known function in the regulation of the HPA axis or sympathoadrenal (SA) system, and measured their expression levels in the hypothalamus and the adrenal glands after a brief stress exposure (physical restraint). The expression values were treated as quantitative traits for the eQTL mapping. The plasma levels of corticosterone were also assessed. We analyzed the correlation between gene expression and corticosterone levels and mapped eQTL and their potential effects on corticosterone levels. The effects on gene transcription of a previously found QTL for corticosterone response were also investigated. The expression levels of the glucocorticoid receptor (GR) in the hypothalamus and several genes in the adrenal glands were correlated with the post-stress levels of corticosterone in plasma. We found several cis- and trans-acting eQTL for stress-related genes in both hypothalamus and adrenal. In the hypothalamus, one eQTL for c-FOS and one QTL for expression of GR were found. In the adrenal tissue, we identified eQTL for the genes NR0B1, RGS4, DBH, MAOA, GRIN1, GABRB2, GABRB3, and HSF1. None of the found eQTL were significant predictors of corticosterone levels. The previously found QTL for corticosterone was associated with GR expression in hypothalamus. Our data suggests that domestication related modification in the stress response is driven by changes in the transcription levels of several modulators of the HPA and SA systems in hypothalamus and adrenal glands and not by changes in the expression of the steroidogenic genes. The presence of eQTL for GR in hypothalamus combined with the negative correlation between GR expression and corticosterone response suggests GR as a candidate for further functional studies regarding modification of stress response during chicken domestication.", "doi": "10.1016/j.mce.2017.02.010", "pmid": "28189567", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0303-7207(17)30090-4"}], "notes": [], "created": "2018-01-09T14:03:02.813Z", "modified": "2021-06-21T15:38:58.284Z"}, {"entity": "publication", "iuid": "db1125cf848046238492e0393b3cd22a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db1125cf848046238492e0393b3cd22a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db1125cf848046238492e0393b3cd22a"}}, "title": "Impact of cytosine methylation on DNA binding specificities of human transcription factors", "authors": [{"family": "Yin", "given": "Yimeng", "initials": "Y"}, {"family": "Morgunova", "given": "Ekaterina", "initials": "E"}, {"family": "Jolma", "given": "Arttu", "initials": "A"}, {"family": "Kaasinen", "given": "Eevi", "initials": "E"}, {"family": "Sahu", "given": "Biswajyoti", "initials": "B"}, {"family": "Khund-Sayeed", "given": "Syed", "initials": "S"}, {"family": "Das", "given": "Pratyush K", "initials": "PK"}, {"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "Dave", "given": "Kashyap", "initials": "K"}, {"family": "Zhong", "given": "Fan", "initials": "F"}, {"family": "Nitta", "given": "Kazuhiro R", "initials": "KR"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Popov", "given": "Alexander", "initials": "A"}, {"family": "Ginno", "given": "Paul A", "initials": "PA"}, {"family": "Domcke", "given": "Silvia", "initials": "S"}, {"family": "Yan", "given": "Jian", "initials": "J"}, {"family": "Sch\u00fcbeler", "given": "Dirk", "initials": "D"}, {"family": "Vinson", "given": "Charles", "initials": "C"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal-article", "published": "2017-05-05", "journal": {"volume": "356", "issn": "1095-9203", "issue": "6337", "pages": "eaaj2239", "title": "Science", "issn-l": "0036-8075"}, "abstract": null, "doi": "10.1126/science.aaj2239", "pmid": "28473536", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:18.850Z", "modified": "2017-11-09T13:17:36.819Z"}, {"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": "40f9f3fc1b444b0e93af1e0487695f12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/40f9f3fc1b444b0e93af1e0487695f12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/40f9f3fc1b444b0e93af1e0487695f12"}}, "title": "PDE2A2 regulates mitochondria morphology and apoptotic cell death via local modulation of cAMP/PKA signalling.", "authors": [{"family": "Monterisi", "given": "Stefania", "initials": "S", "orcid": "0000-0002-8802-9742", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b139738d17449fc9a91465d3e5ad9cc.json"}}, {"family": "Lobo", "given": "Miguel J", "initials": "MJ"}, {"family": "Livie", "given": "Craig", "initials": "C"}, {"family": "Castle", "given": "John C", "initials": "JC", "orcid": "0000-0002-6017-7794", "researcher": {"href": "https://publications.scilifelab.se/researcher/8da2f3d0e8e448b1ad6b2c090db980c6.json"}}, {"family": "Weinberger", "given": "Michael", "initials": "M"}, {"family": "Baillie", "given": "George", "initials": "G"}, {"family": "Surdo", "given": "Nicoletta C", "initials": "NC"}, {"family": "Musheshe", "given": "Nshunge", "initials": "N"}, {"family": "Stangherlin", "given": "Alessandra", "initials": "A", "orcid": "0000-0001-7296-1183", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6b0df4758a140ccad8bf23cd15f85ea.json"}}, {"family": "Gottlieb", "given": "Eyal", "initials": "E"}, {"family": "Maizels", "given": "Rory", "initials": "R"}, {"family": "Bortolozzi", "given": "Mario", "initials": "M", "orcid": "0000-0001-7198-9838", "researcher": {"href": "https://publications.scilifelab.se/researcher/35b1c39a3d1d43608e14d7eba3107ca2.json"}}, {"family": "Micaroni", "given": "Massimo", "initials": "M"}, {"family": "Zaccolo", "given": "Manuela", "initials": "M", "orcid": "0000-0002-0934-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/959c5abbe3ec4af4adb37d5549ba2d5c.json"}}], "type": "journal article", "published": "2017-05-02", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "6", "issue": null, "pages": null, "issn-l": "2050-084X"}, "abstract": "cAMP/PKA signalling is compartmentalised with tight spatial and temporal control of signal propagation underpinning specificity of response. The cAMP-degrading enzymes, phosphodiesterases (PDEs), localise to specific subcellular domains within which they control local cAMP levels and are key regulators of signal compartmentalisation. Several components of the cAMP/PKA cascade are located to different mitochondrial sub-compartments, suggesting the presence of multiple cAMP/PKA signalling domains within the organelle. The function and regulation of these domains remain largely unknown. Here, we describe a novel cAMP/PKA signalling domain localised at mitochondrial membranes and regulated by PDE2A2. Using pharmacological and genetic approaches combined with real-time FRET imaging and high resolution microscopy, we demonstrate that in rat cardiac myocytes and other cell types mitochondrial PDE2A2 regulates local cAMP levels and PKA-dependent phosphorylation of Drp1. We further demonstrate that inhibition of PDE2A, by enhancing the hormone-dependent cAMP response locally, affects mitochondria dynamics and protects from apoptotic cell death.", "doi": "10.7554/eLife.21374", "pmid": "28463107", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5423767"}], "notes": [], "created": "2020-01-23T16:35:40.005Z", "modified": "2021-06-21T15:38:15.280Z"}, {"entity": "publication", "iuid": "5ce336d8ab0f4bef991c0fecc88cabdd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ce336d8ab0f4bef991c0fecc88cabdd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ce336d8ab0f4bef991c0fecc88cabdd"}}, "title": "Mechanistic characterization of a copper containing thiosemicarbazone with potent antitumor activity.", "authors": [{"family": "Karlsson", "given": "Henning", "initials": "H"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Strese", "given": "Sara", "initials": "S"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Westman", "given": "Gunnar", "initials": "G"}, {"family": "Bremberg", "given": "Ulf", "initials": "U"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Nygren", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2017-05-02", "journal": {"title": "Oncotarget", "issn": "1949-2553", "volume": "8", "issue": "18", "pages": "30217-30234", "issn-l": "1949-2553"}, "abstract": "The thiosemicarbazone CD 02750 (VLX50) was recently reported as a hit compound in a phenotype-based drug screen in primary cultures of patient tumor cells. We synthesized a copper complex of VLX50, denoted VLX60, and characterized its antitumor and mechanistic properties.\n\nThe cytotoxic effects and mechanistic properties of VLX60 were investigated in monolayer cultures of multiple human cell lines, in tumor cells from patients, in a 3-D spheroid cell culture system and in vivo and were compared with those of VLX50.\n\nVLX60 showed \u2265 3-fold higher cytotoxic activity than VLX50 in 2-D cultures and, in contrast to VLX50, retained its activity in the presence of additional iron. VLX60 was effective against non-proliferative spheroids and against tumor xenografts in vivo in a murine model. In contrast to VLX50, gene expression analysis demonstrated that genes associated with oxidative stress were considerably enriched in cells exposed to VLX60 as was induction of reactive oxygen. VLX60 compromised the ubiquitin-proteasome system and was more active in BRAF mutated versus BRAF wild-type colon cancer cells.\n\nThe cytotoxic effects of the copper thiosemicarbazone VLX60 differ from those of VLX50 and shows interesting features as a potential antitumor drug, notably against BRAF mutated colorectal cancer.", "doi": "10.18632/oncotarget.16324", "pmid": "28415818", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "16324"}, {"db": "pmc", "key": "PMC5444738"}], "notes": [], "created": "2020-12-10T12:20:32.634Z", "modified": "2025-10-17T13:05:08.928Z"}, {"entity": "publication", "iuid": "f829cf93069349bbbb14966afed52937", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f829cf93069349bbbb14966afed52937.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f829cf93069349bbbb14966afed52937"}}, "title": "Glioblastoma Cell Malignancy and Drug Sensitivity Are Affected by the Cell of Origin.", "authors": [{"family": "Jiang", "given": "Yiwen", "initials": "Y"}, {"family": "Marinescu", "given": "Voichita Dana", "initials": "VD"}, {"family": "Xie", "given": "Yuan", "initials": "Y"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Maturi", "given": "Naga Prathyusha", "initials": "NP"}, {"family": "Haglund", "given": "Caroline", "initials": "C"}, {"family": "Olofsson", "given": "Sara", "initials": "S"}, {"family": "Lindberg", "given": "Nanna", "initials": "N"}, {"family": "Olofsson", "given": "Tommie", "initials": "T"}, {"family": "Leijonmarck", "given": "Caroline", "initials": "C"}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Uhrbom", "given": "Lene", "initials": "L"}], "type": "journal article", "published": "2017-05-02", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "19", "issue": "5", "pages": "1080-1081", "issn-l": null}, "abstract": null, "doi": "10.1016/j.celrep.2017.04.053", "pmid": "28467901", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(17)30564-8"}], "notes": [], "created": "2020-12-10T12:20:33.832Z", "modified": "2025-10-17T13:05:08.939Z"}, {"entity": "publication", "iuid": "181c30fb74a842d1b820ac8da5faf40c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/181c30fb74a842d1b820ac8da5faf40c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/181c30fb74a842d1b820ac8da5faf40c"}}, "title": "Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.", "authors": [{"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Sch\u00f6ning", "given": "Caspar", "initials": "C"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Hasselmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "5", "pages": "e1006792", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies.", "doi": "10.1371/journal.pgen.1006792", "pmid": "28542163", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00165"}, {"db": "pmc", "key": "PMC5444601"}, {"db": "BioProject", "description": "Population-scale sequencing of Apis mellifera monticola and scutellata from Kenya", "key": "PRJNA357367"}, {"db": "Dryad", "description": "Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees", "key": "https://doi.org/10.5061/dryad.jn630"}], "notes": [], "created": "2017-10-27T06:59:44.233Z", "modified": "2024-01-16T13:48:48.005Z"}, {"entity": "publication", "iuid": "3932c9f238004aaa8daf5320158c70ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff"}}, "title": "Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.", "authors": [{"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Wojdacz", "given": "Tomasz K", "initials": "TK"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Prezza", "given": "Nicola", "initials": "N"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "91", "issn": "1432-0738", "issue": "5", "pages": "2067-2078", "title": "Arch. Toxicol.", "issn-l": "0340-5761"}, "abstract": "Arsenic, a carcinogen with immunotoxic effects, is a common contaminant of drinking water and certain food worldwide. We hypothesized that chronic arsenic exposure alters gene expression, potentially by altering DNA methylation of genes encoding central components of the immune system. We therefore analyzed the transcriptomes (by RNA sequencing) and methylomes (by target-enrichment next-generation sequencing) of primary CD4-positive T cells from matched groups of four women each in the Argentinean Andes, with fivefold differences in urinary arsenic concentrations (median concentrations of urinary arsenic in the lower- and high-arsenic groups: 65 and 276 \u03bcg/l, respectively). Arsenic exposure was associated with genome-wide alterations of gene expression; principal component analysis indicated that the exposure explained 53% of the variance in gene expression among the top variable genes and 19% of 28,351 genes were differentially expressed (false discovery rate <0.05) between the exposure groups. Key genes regulating the immune system, such as tumor necrosis factor alpha and interferon gamma, as well as genes related to the NF-kappa-beta complex, were significantly downregulated in the high-arsenic group. Arsenic exposure was associated with genome-wide DNA methylation; the high-arsenic group had 3% points higher genome-wide full methylation (>80% methylation) than the lower-arsenic group. Differentially methylated regions that were hyper-methylated in the high-arsenic group showed enrichment for immune-related gene ontologies that constitute the basic functions of CD4-positive T cells, such as isotype switching and lymphocyte activation and differentiation. In conclusion, chronic arsenic exposure from drinking water was related to changes in the transcriptome and methylome of CD4-positive T cells, both genome wide and in specific genes, supporting the hypothesis that arsenic causes immunotoxicity by interfering with gene expression and regulation.", "doi": "10.1007/s00204-016-1879-4", "pmid": "27838757", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00204-016-1879-4"}, {"db": "pmc", "key": "PMC5399044"}], "notes": [], "created": "2017-05-03T12:59:46.128Z", "modified": "2024-01-16T13:48:48.019Z"}, {"entity": "publication", "iuid": "c66fd4d2712b4701a01b8f862deca4fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c66fd4d2712b4701a01b8f862deca4fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c66fd4d2712b4701a01b8f862deca4fb"}}, "title": "Three-dimensional functional human neuronal networks in uncompressed low-density electrospun fiber scaffolds.", "authors": [{"family": "Jakobsson", "given": "Albin", "initials": "A"}, {"family": "Ottosson", "given": "Maximilian", "initials": "M"}, {"family": "Zalis", "given": "Marina Castro", "initials": "MC"}, {"family": "O'Carroll", "given": "David", "initials": "D"}, {"family": "Johansson", "given": "Ulrica Englund", "initials": "UE"}, {"family": "Johansson", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2017-05-00", "journal": {"title": "Nanomedicine", "issn": "1748-6963", "volume": "13", "issue": "4", "pages": "1563-1573", "issn-l": "1743-5889"}, "abstract": "We demonstrate an artificial three-dimensional (3D) electrical active human neuronal network system, by the growth of brain neural progenitors in highly porous low density electrospun poly-\u03b5-caprolactone (PCL) fiber scaffolds. In neuroscience research cell-based assays are important experimental instruments for studying neuronal function in health and disease. Traditional cell culture at 2D-surfaces induces abnormal cell-cell contacts and network formation. Hence, there is a tremendous need to explore in vivo-resembling 3D neural cell culture approaches. We present an improved electrospinning method for fabrication of scaffolds that promote neuronal differentiation into highly 3D integrated networks, formation of inhibitory and excitatory synapses and extensive neurite growth. Notably, in 3D scaffolds in vivo-resembling intermixed neuronal and glial cell network were formed, whereas in parallel 2D cultures a neuronal cell layer grew separated from an underlying glial cell layer. Hence, the use of the 3D cell assay presented will most likely provide more physiological relevant results.", "doi": "10.1016/j.nano.2016.12.023", "pmid": "28064005", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S1549-9634(17)30002-3"}], "notes": [], "created": "2021-12-02T14:12:42.899Z", "modified": "2021-12-02T14:12:42.916Z"}, {"entity": "publication", "iuid": "c380b6d52d4c4864a440da08d6b90b4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c380b6d52d4c4864a440da08d6b90b4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c380b6d52d4c4864a440da08d6b90b4a"}}, "title": "The effect of temperature and substrate quality on the carbon use efficiency of saprotrophic decomposition", "authors": [{"family": "\u00d6quist", "given": "Mats G", "initials": "MG"}, {"family": "Erhagen", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Haei", "given": "Mahsa", "initials": "M"}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Ilstedt", "given": "Ulrik", "initials": "U"}, {"family": "Schleucher", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Nilsson", "given": "Mats B", "initials": "MB"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "414", "issn": "0032-079X", "issue": "1-2", "pages": "113-125", "title": "Plant Soil", "issn-l": null}, "abstract": null, "doi": "10.1007/s11104-016-3104-x", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:11:17.219Z", "modified": "2025-10-17T13:03:59.868Z"}, {"entity": "publication", "iuid": "a03bd7f66d9048c8b0bc3e8e576bd31e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a03bd7f66d9048c8b0bc3e8e576bd31e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a03bd7f66d9048c8b0bc3e8e576bd31e"}}, "title": "The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.", "authors": [{"family": "Hou", "given": "Chen", "initials": "C"}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "28", "issn": "2470-1408", "issue": "3", "pages": "330-331", "title": "Mitochondrial DNA A DNA Mapp Seq Anal", "issn-l": "2470-1394"}, "abstract": "This study presents the chloroplast genome of Ephedra foeminea, an entomophilous gymnosperm, sister to the remaining (wind-pollinated) species of Ephedra (Ephedraceae, Gnetales). Based on the reference-guided assembly, the length of the chloroplast genome was estimated to be 109\u00a0584\u2009bp, comprising a large single copy region of 60\u2009027\u2009bp, a small single copy 8079\u2009bp, and inverted repeat regions of 20\u00a0739\u2009bp. In total, 118 genes were detected, including 73 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene density is 1.076 (genes/kb) and the GC content is 36.7%. The genomic sequence of the entomophilous, Mediterranean species E. foeminea, differs from that of the anemophilous, Asian species E. equisetina by 1018 point mutations and 1334 indels. The detected variation is useful for future development of new plastid markers for phylogenetic purposes. Our phylogenetic analysis based on 55 protein-coding chloroplast genes resolve Ephedra as monophyletic and sister to a Gnetum-Welwitschia clade. The Gnetales are sister to Cupressophytes.", "doi": "10.3109/19401736.2015.1122768", "pmid": "26713841", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:18.729Z", "modified": "2024-01-16T13:48:48.033Z"}, {"entity": "publication", "iuid": "b63bed2e74cc427a8f132e656e586cec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b63bed2e74cc427a8f132e656e586cec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b63bed2e74cc427a8f132e656e586cec"}}, "title": "Structural Diversity of Human Gastric Mucin Glycans.", "authors": [{"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Kenny", "given": "Diarmuid T", "initials": "DT"}, {"family": "Skoog", "given": "Emma C", "initials": "EC"}, {"family": "Padra", "given": "M\u00e9dea", "initials": "M"}, {"family": "Adamczyk", "given": "Barbara", "initials": "B"}, {"family": "Vitizeva", "given": "Varvara", "initials": "V"}, {"family": "Thorell", "given": "Anders", "initials": "A"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V"}, {"family": "Lind\u00e9n", "given": "Sara K", "initials": "SK"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "16", "issn": "1535-9484", "issue": "5", "pages": "743-758", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The mucin O-glycosylation of 10 individuals with and without gastric disease was examined in depth in order to generate a structural map of human gastric glycosylation. In the stomach, these mucins and their O-glycosylation protect the epithelial surface from the acidic gastric juice and provide the first point of interaction for pathogens such as Helicobacter pylori, reported to cause gastritis, gastric and duodenal ulcers and gastric cancer. The rational of the present study was to map the O-glycosylation that the pathogen may come in contact with. An enormous diversity in glycosylation was found, which varied both between individuals and within mucins from a single individual: mucin glycan chain length ranged from 2-13 residues, each individual carried 34-103 O-glycan structures and in total over 258 structures were identified. The majority of gastric O-glycans were neutral and fucosylated. Blood group I antigens, as well as terminal \u03b11,4-GlcNAc-like and GalNAc\u03b21-4GlcNAc-like (LacdiNAc-like), were common modifications of human gastric O-glycans. Furthemore, each individual carried 1-14 glycan structures that were unique for that individual. The diversity and alterations in gastric O-glycosylation broaden our understanding of the human gastric O-glycome and its implications for gastric cancer research and emphasize that the high individual variation makes it difficult to identify gastric cancer specific structures. However, despite the low number of individuals, we could verify a higher level of sialylation and sulfation on gastric O-glycans from cancerous tissue than from healthy stomachs.", "doi": "10.1074/mcp.M116.067983", "pmid": "28461410", "labels": {"PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service", "Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "16/5/743"}, {"db": "pmc", "key": "PMC5417818"}], "notes": [], "created": "2020-01-07T14:46:52.447Z", "modified": "2024-01-16T13:46:32.704Z"}, {"entity": "publication", "iuid": "f6741ded19a843938682cf6b4a642326", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6741ded19a843938682cf6b4a642326.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6741ded19a843938682cf6b4a642326"}}, "title": "Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men", "authors": [{"family": "Forsberg", "given": "Lars A", "initials": "LA"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "136", "issn": "0340-6717", "issue": "5", "pages": "657-663", "title": "Hum Genet", "issn-l": "0340-6717"}, "abstract": null, "doi": "10.1007/s00439-017-1799-2", "pmid": "28424864", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:34.236Z", "modified": "2020-01-21T13:56:11.730Z"}, {"entity": "publication", "iuid": "a5b832bb673d4fdbae2def001be65d76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5b832bb673d4fdbae2def001be65d76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5b832bb673d4fdbae2def001be65d76"}}, "title": "Inflammatory markers in late pregnancy in association with postpartum depression-A nested case-control study.", "authors": [{"family": "Br\u00e4nn", "given": "Emma", "initials": "E"}, {"family": "Papadopoulos", "given": "Fotios", "initials": "F"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "White", "given": "Richard", "initials": "R"}, {"family": "Edvinsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Hellgren", "given": "Charlotte", "initials": "C"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Bostr\u00f6m", "given": "Adrian", "initials": "A"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Sundstr\u00f6m-Poromaa", "given": "Inger", "initials": "I"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "79", "issn": "1873-3360", "issue": null, "pages": "146-159", "title": "Psychoneuroendocrinology", "issn-l": "0306-4530"}, "abstract": "Recent studies indicate that the immune system adaptation during pregnancy could play a significant role in the pathophysiology of perinatal depression. The aim of this study was to investigate if inflammation markers in a late pregnancy plasma sample can predict the presence of depressive symptoms at eight weeks postpartum. Blood samples from 291 pregnant women (median and IQR for days to delivery, 13 and 7-23days respectively) comprising 63 individuals with postpartum depressive symptoms, as assessed by the Edinburgh postnatal depression scale (EPDS\u226512) and/or the Mini International Neuropsychiatric Interview (M.I.N.I.) and 228 controls were analyzed with an inflammation protein panel using multiplex proximity extension assay technology, comprising of 92 inflammation-associated markers. A summary inflammation variable was also calculated. Logistic regression, LASSO and Elastic net analyses were implemented. Forty markers were lower in late pregnancy among women with depressive symptoms postpartum. The difference remained statistically significant for STAM-BP (or otherwise AMSH), AXIN-1, ADA, ST1A1 and IL-10, after Bonferroni correction. The summary inflammation variable was ranked as the second best variable, following personal history of depression, in predicting depressive symptoms postpartum. The protein-level findings for STAM-BP and ST1A1 were validated in relation to methylation status of loci in the respective genes in a different population, using openly available data. This explorative approach revealed differences in late pregnancy levels of inflammation markers between women presenting with depressive symptoms postpartum and controls, previously not described in the literature. Despite the fact that the results do not support the use of a single inflammation marker in late pregnancy for assessing risk of postpartum depression, the use of STAM-BP or the novel notion of a summary inflammation variable developed in this work might be used in combination with other biological markers in the future.", "doi": "10.1016/j.psyneuen.2017.02.029", "pmid": "28285186", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0306-4530(16)30787-9"}], "notes": [], "created": "2017-10-30T12:37:46.988Z", "modified": "2023-04-14T13:56:15.105Z"}, {"entity": "publication", "iuid": "9fa1f34c27fa45719956c93209b8bf51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fa1f34c27fa45719956c93209b8bf51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fa1f34c27fa45719956c93209b8bf51"}}, "title": "Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model.", "authors": [{"family": "Rivetti di Val Cervo", "given": "Pia", "initials": "P"}, {"family": "Romanov", "given": "Roman A", "initials": "RA"}, {"family": "Spigolon", "given": "Giada", "initials": "G"}, {"family": "Masini", "given": "D\u00e9bora", "initials": "D"}, {"family": "Mart\u00edn-Monta\u00f1ez", "given": "Elisa", "initials": "E"}, {"family": "Toledo", "given": "Enrique M", "initials": "EM"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Feyder", "given": "Michael", "initials": "M"}, {"family": "Pifl", "given": "Christian", "initials": "C"}, {"family": "Ng", "given": "Yi-Han", "initials": "YH"}, {"family": "S\u00e1nchez", "given": "Sara Padrell", "initials": "SP"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Wernig", "given": "Marius", "initials": "M"}, {"family": "Harkany", "given": "Tibor", "initials": "T"}, {"family": "Fisone", "given": "Gilberto", "initials": "G"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "35", "issn": "1546-1696", "issue": "5", "pages": "444-452", "title": "Nat. Biotechnol.", "issn-l": "1087-0156"}, "abstract": "Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here we describe an alternative strategy for Parkinson's disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, we reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs). Reprogramming efficiency in vitro is improved by small molecules that promote chromatin remodeling and activate the TGF\u03b2, Shh and Wnt signaling pathways. The reprogramming efficiency of human astrocytes reaches up to 16%, resulting in iDANs with appropriate midbrain markers and excitability. In a mouse model of Parkinson's disease, NeAL218 alone reprograms adult striatal astrocytes into iDANs that are excitable and correct some aspects of motor behavior in vivo, including gait impairments. With further optimization, this approach may enable clinical therapies for Parkinson's disease by delivery of genes rather than cells.", "doi": "10.1038/nbt.3835", "pmid": "28398344", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nbt.3835"}], "notes": [], "created": "2017-11-03T16:21:17.986Z", "modified": "2024-01-16T13:48:48.046Z"}, {"entity": "publication", "iuid": "476bae4d77a6412ca34d278f2d99f088", "links": {"self": {"href": "https://publications.scilifelab.se/publication/476bae4d77a6412ca34d278f2d99f088.json"}, "display": {"href": "https://publications.scilifelab.se/publication/476bae4d77a6412ca34d278f2d99f088"}}, "title": "Immune Biomarkers on the Radar\u2014Comprehensive \u201cImmunograms\u201d for Multimodal Treatment Prediction", "authors": [{"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Sandelin", "given": "Martin", "initials": "M"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "12", "issn": "1556-0864", "issue": "5", "pages": "770-772", "title": "Journal of Thoracic Oncology", "issn-l": "1556-0864"}, "abstract": null, "doi": "10.1016/j.jtho.2017.03.009", "pmid": "28434508", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-12-21T12:56:39.258Z", "modified": "2018-12-10T12:29:34.046Z"}, {"entity": "publication", "iuid": "c529de8b48a84d6f81825d24ba3f9dd6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c529de8b48a84d6f81825d24ba3f9dd6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c529de8b48a84d6f81825d24ba3f9dd6"}}, "title": "High levels of the AR-V7 Splice Variant and Co-Amplification of the Golgi Protein Coding YIPF6 in AR Amplified Prostate Cancer Bone Metastases.", "authors": [{"family": "Djusberg", "given": "Erik", "initials": "E"}, {"family": "Jernberg", "given": "Emma", "initials": "E"}, {"family": "Thysell", "given": "Elin", "initials": "E"}, {"family": "Golovleva", "given": "Irina", "initials": "I"}, {"family": "Lundberg", "given": "Pia", "initials": "P"}, {"family": "Crnalic", "given": "Sead", "initials": "S"}, {"family": "Widmark", "given": "Anders", "initials": "A"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Brattsand", "given": "Maria", "initials": "M"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P"}], "type": "journal article", "published": "2017-05-00", "journal": {"title": "Prostate", "issn": "1097-0045", "volume": "77", "issue": "6", "pages": "625-638", "issn-l": "0270-4137"}, "abstract": "The relation between androgen receptor (AR) gene amplification and other mechanisms behind castration-resistant prostate cancer (CRPC), such as expression of constitutively active AR variants and steroid-converting enzymes has been poorly examined. Specific aim was to examine AR amplification in PC bone metastases and to explore molecular and functional consequences of this, with the long-term goal of identifying novel molecular targets for treatment.\n\nGene amplification was assessed by fluorescence in situ hybridization in cryo-sections of clinical PC bone metastases (n = 40) and by PCR-based copy number variation analysis. Whole genome mRNA expression was analyzed using H12 Illumina Beadchip arrays and specific transcript levels were quantified by qRT-PCR. Protein localization was analyzed using immunohistochemistry and confocal microscopy. The YIPF6 mRNA expression was transiently knocked down and stably overexpressed in the 22Rv1 cell line as representative for CRPC, and effects on cell proliferation, colony formation, migration, and invasion were determined in vitro. Extracellular vesicles (EVs) were isolated from cell cultures using size-exclusion chromatography and enumerated by nanoparticle tracking analysis. Protein content was identified by LC-MS/MS analysis. Blood coagulation was measured as activated partial thromboplastin time (APTT). Functional enrichment analysis was performed using the MetaCore software.\n\nAR amplification was detected in 16 (53%) of the bone metastases examined from CRPC patients (n = 30), and in none from the untreated patients (n = 10). Metastases with AR amplification showed high AR and AR-V7 mRNA levels, increased nuclear AR immunostaining, and co-amplification of genes such as YIPF6 in the AR proximity at Xq12. The YIPF6 protein was localized to the Golgi apparatus. YIPF6 overexpression in 22Rv1 cells resulted in reduced cell proliferation and colony formation, and in enhanced EV secretion. EVs from YIPF6 overproducing 22Rv1 cells were enriched for proteins involved in blood coagulation and, accordingly, decreased the APTT in a dose-dependent fashion.\n\nAR amplified CRPC bone metastases show high AR-V7 expression that probably gives resistance to AR-targeting drugs. Co-amplification of the Golgi protein coding YIPF6 gene with the AR may enhance the secretion of pro-coagulative EVs from cancer cells and thereby stimulate tumor progression and increase the coagulopathy risk in CRPC patients. Prostate 77: 625-638, 2017. \u00a9 2017 Wiley Periodicals, Inc.", "doi": "10.1002/pros.23307", "pmid": "28144969", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-30T16:00:22.776Z", "modified": "2024-01-16T13:46:32.725Z"}, {"entity": "publication", "iuid": "7923c641b6424277bea132a885eac76f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7923c641b6424277bea132a885eac76f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7923c641b6424277bea132a885eac76f"}}, "title": "Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments.", "authors": [{"family": "Mu\u00dfmann", "given": "Marc", "initials": "M"}, {"family": "Pjevac", "given": "Petra", "initials": "P"}, {"family": "Kr\u00fcger", "given": "Karen", "initials": "K"}, {"family": "Dyksma", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "5", "pages": "1276-1281", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments. The analysis of a single-cell genome, metagenomic bins and the genome of the next cultured relative Woeseia oceani indicated a broad physiological range, including heterotrophy and facultative autotrophy. All tested (meta)genomes encode a truncated denitrification pathway to nitrous oxide. The broad range of energy-yielding metabolisms possibly explains the ubiquity and high abundance of Woeseiaceae/JTB255 in marine sediments, where they carry out diverse, but yet unknown ecological functions.", "doi": "10.1038/ismej.2016.185", "pmid": "28060363", "labels": {"Microbial Single Cell Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "ismej2016185"}, {"db": "pmc", "key": "PMC5437919"}], "notes": [], "created": "2017-10-31T12:04:25.595Z", "modified": "2017-10-31T12:05:46.816Z"}, {"entity": "publication", "iuid": "4eab694bf7e14ca5a71b01cb978a023a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4eab694bf7e14ca5a71b01cb978a023a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4eab694bf7e14ca5a71b01cb978a023a"}}, "title": "Further evidence for specific IFIH1 mutation as a cause of Singleton-Merten syndrome with phenotypic heterogeneity.", "authors": [{"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Bergendal", "given": "Birgitta", "initials": "B"}, {"family": "Norderyd", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "173", "issn": "1552-4833", "issue": "5", "pages": "1396-1399", "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": "Singleton-Merten syndrome (MIM 182250) is an autosomal dominant inherited disorder characterized by early onset periodontitis, root resorption, osteopenia, osteoporosis, and aortic valve or thoracic aorta calcification. The disorder can have significant intrafamilial phenotypic variability. Here, we present a mother and daughter with Singleton-Merten syndrome harboring a previously described pathogenic missense mutation, c.2465G>A p.(Arg822Gln), in IFIH1 (interferon induced with helicase C domain 1), encoding MDA5 (Melanoma Differentiation-Associated protein 5). These data confirm the pathogenicity of IFIH1 c.2465G>A p.(Arg822Gln) for Singleton-Merten syndrome and affirm the striking phenotypic heterogeneity of this disorder. In addition, we expand the Singleton-Merten phenotype by adding severe systemic lupus erythematosus (SLE) to the clinical picture. Investigations of known SLE genes as well as a single nucleotide polymorphism suggested to be involved in development of SLE were normal.", "doi": "10.1002/ajmg.a.38214", "pmid": "28319323", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:19:24.520Z", "modified": "2024-01-16T13:48:48.059Z"}, {"entity": "publication", "iuid": "c9afdafcff6c4dfc8af08f774f704d8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9afdafcff6c4dfc8af08f774f704d8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9afdafcff6c4dfc8af08f774f704d8d"}}, "title": "FADD, Caspase-3, and Caspase-8 and Incidence of Coronary Events.", "authors": [{"family": "Xue", "given": "Ling", "initials": "L"}, {"family": "Born\u00e9", "given": "Yan", "initials": "Y"}, {"family": "Mattisson", "given": "Ingrid Yao", "initials": "IY"}, {"family": "Wigren", "given": "Maria", "initials": "M"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Ohro-Melander", "given": "Marju", "initials": "M"}, {"family": "Bengtsson", "given": "Eva", "initials": "E"}, {"family": "Fredrikson", "given": "Gunilla Nordin", "initials": "GN"}, {"family": "Nilsson", "given": "Jan", "initials": "J"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2017-05-00", "journal": {"title": "Arterioscler. Thromb. Vasc. Biol.", "issn": "1524-4636", "issn-l": "1079-5642", "volume": "37", "issue": "5", "pages": "983-989"}, "abstract": "To investigate the relationship between 3 markers of apoptosis, that is, FADD (Fas-associated death domain-containing protein), caspase-3, and caspase-8, and incidence of coronary events (CEs) in a population-based cohort study.\n\nIn vitro experiments were performed to assess the response of the apoptotic biomarkers after Fas stimulation of peripheral blood mononuclear cells. The experiments showed significantly increased releases of FADD, caspase-3, and caspase-8 after Fas stimulation. The relationship between FADD, caspase-3, and caspase-8, respectively, and incidence of CEs was studied in 4284 subjects from the population-based Malm\u00f6 Diet and Cancer Study. Cox' proportional hazards regression was used to examine the association between the apoptotic biomarkers and incidence of CE over a mean follow-up of 19 years. A total of 381 individuals had CE during the follow-up. High FADD at baseline was significantly associated with incident CE. In the highest compared with the lowest quartile of FADD, the risk factor adjusted hazards ratio for CE was 1.82 (95% confidence interval, 1.35-2.46; P for trend <0.001). A significant association was also found between caspase-8 and CE; the hazards ratio (Q4 versus Q1) was 1.90 (95% confidence interval, 1.39-2.60; P for trend <0.001) after adjustment for risk factors. No association was found between caspase-3 and CEs.\n\nHigh levels of FADD and caspase-8, but not caspase-3, were associated with increased incidence of CE in subjects from the general population. The in vitro experiments support the view that these biomarkers could reflect activation of the extrinsic apoptotic pathway.", "doi": "10.1161/ATVBAHA.117.308995", "pmid": "28302628", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "ATVBAHA.117.308995"}], "notes": [], "created": "2017-10-30T12:09:00.110Z", "modified": "2023-04-14T13:56:15.290Z"}, {"entity": "publication", "iuid": "1f2bf23387de42ca8c43de3d1878ea7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f2bf23387de42ca8c43de3d1878ea7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f2bf23387de42ca8c43de3d1878ea7a"}}, "title": "Contrasting patterns of cytokinins between years in senescing aspen leaves", "authors": [{"family": "Edlund", "given": "Erik", "initials": "E"}, {"family": "Novak", "given": "Ondrej", "initials": "O"}, {"family": "Karady", "given": "Michal", "initials": "M"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "40", "issn": "0140-7791", "issue": "5", "pages": "622-634", "title": "Plant, Cell & Environment", "issn-l": "0140-7791"}, "abstract": null, "doi": "10.1111/pce.12899", "pmid": "28042677", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:30:53.279Z", "modified": "2025-10-17T13:03:18.850Z"}, {"entity": "publication", "iuid": "dffab84ac9294147adf1ae2039ff814d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dffab84ac9294147adf1ae2039ff814d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dffab84ac9294147adf1ae2039ff814d"}}, "title": "Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.", "authors": [{"family": "Rineau", "given": "F", "initials": "F"}, {"family": "Lmalem", "given": "H", "initials": "H"}, {"family": "Ahren", "given": "D", "initials": "D"}, {"family": "Shah", "given": "F", "initials": "F"}, {"family": "Johansson", "given": "T", "initials": "T"}, {"family": "Coninx", "given": "L", "initials": "L"}, {"family": "Ruytinx", "given": "J", "initials": "J"}, {"family": "Nguyen", "given": "H", "initials": "H"}, {"family": "Grigoriev", "given": "I", "initials": "I"}, {"family": "Kuo", "given": "A", "initials": "A"}, {"family": "Kohler", "given": "A", "initials": "A"}, {"family": "Morin", "given": "E", "initials": "E"}, {"family": "Vangronsveld", "given": "J", "initials": "J"}, {"family": "Martin", "given": "F", "initials": "F"}, {"family": "Colpaert", "given": "J V", "initials": "JV"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "27", "issn": "1432-1890", "issue": "4", "pages": "383-396", "title": "Mycorrhiza", "issn-l": "0940-6360"}, "abstract": "Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.", "doi": "10.1007/s00572-016-0758-4", "pmid": "28066872", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00572-016-0758-4"}], "notes": [], "created": "2019-01-15T08:43:01.539Z", "modified": "2020-01-21T13:53:22.530Z"}, {"entity": "publication", "iuid": "8fdeb5a6200148f7b6db35cc74332911", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fdeb5a6200148f7b6db35cc74332911.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fdeb5a6200148f7b6db35cc74332911"}}, "title": "Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.", "authors": [{"family": "Weissensteiner", "given": "Matthias H", "initials": "MH"}, {"family": "Pang", "given": "Andy W C", "initials": "AWC"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Vinnere-Petterson", "given": "Olga", "initials": "O"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "27", "issn": "1549-5469", "issue": "5", "pages": "697-708", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (\u03c1) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.", "doi": "10.1101/gr.215095.116", "pmid": "28360231", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gr.215095.116"}, {"db": "pmc", "key": "PMC5411765"}], "notes": [], "created": "2017-10-17T09:42:42.055Z", "modified": "2024-01-16T13:48:48.069Z"}, {"entity": "publication", "iuid": "f79c9da07aed47b2804036d638253d45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f79c9da07aed47b2804036d638253d45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f79c9da07aed47b2804036d638253d45"}}, "title": "Brodie vs Hummers graphite oxides for preparation of multi-layered materials", "authors": [{"family": "Talyzin", "given": "Alexandr V", "initials": "AV", "orcid": "0000-0002-3320-8487", "researcher": {"href": "https://publications.scilifelab.se/researcher/88fd0ac58d1940cab006fa22599720ba.json"}}, {"family": "Mercier", "given": "Guillaume", "initials": "G"}, {"family": "Klechikov", "given": "Alexey", "initials": "A"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Johnels", "given": "Dan", "initials": "D"}, {"family": "Wei", "given": "Di", "initials": "D"}, {"family": "Cotton", "given": "Darryl", "initials": "D"}, {"family": "Opitz", "given": "Andreas", "initials": "A"}, {"family": "Moons", "given": "Ellen", "initials": "E"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "115", "issn": "0008-6223", "issue": null, "pages": "430-440", "title": "Carbon", "issn-l": null}, "abstract": null, "doi": "10.1016/j.carbon.2016.12.097", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:00:51.213Z", "modified": "2025-10-17T13:03:59.886Z"}, {"entity": "publication", "iuid": "728551f2381b43668a2a2516d07437aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/728551f2381b43668a2a2516d07437aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/728551f2381b43668a2a2516d07437aa"}}, "title": "Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations", "authors": [{"family": "Wang", "given": "Mi", "initials": "M"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "9", "issn": "1759-6653", "issue": "5", "pages": "1266-1279", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evx080", "pmid": "28453623", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:57:46.835Z", "modified": "2020-01-21T13:56:11.723Z"}, {"entity": "publication", "iuid": "9546e6c6d2a04b82b56377bedc0d7cb6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9546e6c6d2a04b82b56377bedc0d7cb6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9546e6c6d2a04b82b56377bedc0d7cb6"}}, "title": "Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast", "authors": [{"family": "Lahtvee", "given": "Petri Jaan", "initials": "PJ", "orcid": "0000-0002-3327-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/8043cd36bb0e4cf3bc8a526dd45fa311.json"}}, {"family": "S\u00e1nchez", "given": "Benjam\u00edn J", "initials": "BJ"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Kasvandik", "given": "Sergo", "initials": "S"}, {"family": "Elsemman", "given": "Ibrahim E", "initials": "IE"}, {"family": "Gatto", "given": "Francesco", "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": "2017-05-00", "journal": {"volume": "4", "issn": "2405-4712", "issue": "5", "pages": "495-504.e5", "title": "Cell Syst", "issn-l": null}, "abstract": "Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n = 202), the median mRNA-protein correlation was 0.88. We used these data to model translation efficiencies and found that they vary more than 400-fold between genes. Non-linear regression analysis detected that mRNA abundance and translation elongation were the dominant factors controlling protein synthesis, explaining 61% and 15% of its variance. Metabolic flux balance analysis further showed that only mitochondrial fluxes were positively associated with changes at the transcript level. The present dataset represents a crucial expansion to the current resources for future studies on yeast physiology.", "doi": "10.1016/j.cels.2017.03.003", "pmid": "28365149", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2405-4712(17)30088-1"}], "notes": [], "created": "2017-11-02T12:15:40.774Z", "modified": "2023-06-19T11:48:00.857Z"}, {"entity": "publication", "iuid": "ffaed83ff04c4f058b2fb20f13022ba5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffaed83ff04c4f058b2fb20f13022ba5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffaed83ff04c4f058b2fb20f13022ba5"}}, "title": "A Preliminary Report: Radical Surgery and Stem Cell Transplantation for the Treatment of Patients With Pancreatic Cancer.", "authors": [{"family": "Omazic", "given": "Brigitta", "initials": "B"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "L\u00f6hr", "given": "Matthias", "initials": "M"}, {"family": "Segersv\u00e4rd", "given": "Ralf", "initials": "R"}, {"family": "Verbeke", "given": "Caroline", "initials": "C"}, {"family": "Magalhaes", "given": "Isabelle", "initials": "I"}, {"family": "Potacova", "given": "Zuzana", "initials": "Z"}, {"family": "Mattsson", "given": "Jonas", "initials": "J"}, {"family": "Terman", "given": "Alexei", "initials": "A"}, {"family": "Ghazi", "given": "Sam", "initials": "S"}, {"family": "Albiin", "given": "Nils", "initials": "N"}, {"family": "Kartalis", "given": "Nikolaos", "initials": "N"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Poiret", "given": "Thomas", "initials": "T"}, {"family": "Zhenjiang", "given": "Liu", "initials": "L"}, {"family": "Heuchel", "given": "Rainer", "initials": "R"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Permert", "given": "Johan", "initials": "J"}, {"family": "Maeurer", "given": "Markus J", "initials": "MJ"}, {"family": "Ringden", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "40", "issn": "1537-4513", "issue": "4", "title": "J. Immunother.", "pages": "132-139", "issn-l": "1524-9557"}, "abstract": "We examined the immunologic effects of allogeneic hematopoietic stem cell transplantation (HSCT) in the treatment of pancreatic ductal adenocarcinoma, a deadly disease with a median survival of 24 months for resected tumors and a 5-year survival rate of 6%. After adjuvant chemotherapy, 2 patients with resected pancreatic ductal adenocarcinoma underwent HSCT with HLA-identical sibling donors. Comparable patients who underwent radical surgery, but did not have a donor, served as controls (n=6). Both patients developed humoral and cellular (ie, HLA-A*01:01-restricted) immune responses directed against 2 novel tumor-associated antigens (TAAs), INO80E and UCLH3 after HSCT. Both TAAs were highly expressed in the original tumor tissue suggesting that HSCT promoted a clinically relevant, long-lasting cellular immune response. In contrast to untreated controls, who succumbed to progressive disease, both patients are tumor-free 9 years after diagnosis. Radical surgery combined with HSCT may cure pancreatic adenocarcinoma and change the cellular immune repertoire capable of responding to clinically and biologically relevant TAAs.", "doi": "10.1097/CJI.0000000000000164", "pmid": "28338506", "labels": {"Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:39:38.489Z", "modified": "2021-07-08T12:07:34.361Z"}, {"entity": "publication", "iuid": "9c9d3150115a4c5fafc029f1f5279164", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c9d3150115a4c5fafc029f1f5279164.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c9d3150115a4c5fafc029f1f5279164"}}, "title": "Mitochondrial genome divergence between beluga whales in Baffin Bay and the Sea of Okhotsk.", "authors": [{"family": "Skovrind", "given": "Mikkel", "initials": "M", "orcid": "0000-0002-5430-5884", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d66c99ebd514dc98230f3e636100050.json"}}, {"family": "Samaniego Castruita", "given": "Jose Alfredo", "initials": "JA", "orcid": "0000-0001-5904-1198", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c719c4a3e3d4c2fa886d0837dc353df.json"}}, {"family": "Heide-J\u00f8rgensen", "given": "Mads Peter", "initials": "MP", "orcid": "0000-0003-4846-7622", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9e5faf23cc44a0cb5d1c122a4e30ce1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Lorenzen", "given": "Eline", "initials": "E", "orcid": "0000-0002-6353-2819", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2671a526ba54081889f378be5efba1e.json"}}], "type": "journal article", "published": "2017-04-28", "journal": {"volume": "2", "issn": "2380-2359", "issue": "1", "pages": "257-258", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "The beluga whale is one of three endemic Arctic whales. The species is philopatric, and its migration patterns are passed from mother to calf. Management of the species is informed by the levels of genetic structuring among summer aggregation sites based on mitochondrial D-Loop data. To assess the levels of differentiation across the entire mitochondrial genome within belugas, we present a comparison between the first two complete mitochondrial genomes from opposite sides of their distribution range: Baffin Bay and the Russian Far East. Our analyses reveal that additional phylogenetic insights can be gained from expanding the genetic region analyzed. Further, we estimate the divergence time between the two mitochondrial genomes to be 0.469 MYA.", "doi": "10.1080/23802359.2017.1318686", "pmid": "33473790", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1318686"}, {"db": "pmc", "key": "PMC7800697"}], "notes": [], "created": "2017-11-03T15:53:38.584Z", "modified": "2021-06-21T15:47:55.199Z"}, {"entity": "publication", "iuid": "5a18fd49e87041caa8d096732e5282cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a18fd49e87041caa8d096732e5282cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a18fd49e87041caa8d096732e5282cd"}}, "title": "Genetic Profile of Ductal Adenocarcinoma of the Prostate.", "authors": [{"family": "Seipel", "given": "Amanda H", "initials": "AH"}, {"family": "Whitington", "given": "Thomas", "initials": "T"}, {"family": "Delahunt", "given": "Brett", "initials": "B"}, {"family": "Samaratunga", "given": "Hemamali", "initials": "H"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Wiklund", "given": "Peter", "initials": "P"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Egevad", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2017-04-27", "journal": {"volume": null, "issn": "1532-8392", "issue": null, "title": "Hum. Pathol.", "issn-l": "0046-8177"}, "abstract": "Despite being discovered almost 50years ago little is known regarding the genetic profile of ductal adenocarcinoma of the prostate (DAC). In recent years, progress has been made in the understanding of the genetics of acinar adenocarcinomas and at least seven genetically different subtypes have been identified. DAC is known to present at an advanced stage with a high rate of extraprostatic extension and seminal vesicle invasion, and a decreased interval to biochemical recurrence and the development of metastatic disease, when compared to acinar adenocarcinoma. Our aim was to investigate the genetic profile of DAC to determine whether there is a genomic rationale for the aggressive behaviour associated with this tumor type. Frozen tissue from 11 cases of DAC with paired benign tissue was analysed. After DNA extraction, copy-number alteration analysis was performed, as well as identification of mutations and indels. We compared the fraction of the DAC genome with copy-number alteration to previous results from 74 primary acinar adenocarcinomas of the prostate. The alteration rate in DAC was comparable to that of acinar adenocarcinoma of high Gleason score. DAC harbored somatic changes seen in advanced and/or metastatic castration-resistant acinar adenocarcinoma, which likely accounts for its aggressive biological behavior.", "doi": "10.1016/j.humpath.2017.04.015", "pmid": "28457729", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0046-8177(17)30133-8"}], "notes": [], "created": "2017-11-03T12:53:32.379Z", "modified": "2017-11-03T14:10:15.511Z"}, {"entity": "publication", "iuid": "9405f119832b4231a5f50c1dff6cd6c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9405f119832b4231a5f50c1dff6cd6c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9405f119832b4231a5f50c1dff6cd6c5"}}, "title": "Does the sex of one's co-twin affect height and BMI in adulthood? A study of dizygotic adult twins from 31 cohorts.", "authors": [{"family": "Bogl", "given": "Leonie H", "initials": "LH"}, {"family": "Jelenkovic", "given": "Aline", "initials": "A"}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Ahrenfeldt", "given": "Linda", "initials": "L"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Stazi", "given": "Maria A", "initials": "MA"}, {"family": "Fagnani", "given": "Corrado", "initials": "C"}, {"family": "D'Ippolito", "given": "Cristina", "initials": "C"}, {"family": "Hur", "given": "Yoon-Mi", "initials": "YM"}, {"family": "Jeong", "given": "Hoe-Uk", "initials": "HU"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Eaves", "given": "Lindon J", "initials": "LJ"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Bayasgalan", "given": "Gombojav", "initials": "G"}, {"family": "Narandalai", "given": "Danshiitsoodol", "initials": "D"}, {"family": "Cutler", "given": "Tessa L", "initials": "TL"}, {"family": "Kandler", "given": "Christian", "initials": "C"}, {"family": "Jang", "given": "Kerry L", "initials": "KL"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Skytthe", "given": "Axel", "initials": "A"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Hwang", "given": "Amie E", "initials": "AE"}, {"family": "Mack", "given": "Thomas M", "initials": "TM"}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Nelson", "given": "Tracy L", "initials": "TL"}, {"family": "Whitfield", "given": "Keith E", "initials": "KE"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM"}, {"family": "McAdams", "given": "Tom A", "initials": "TA"}, {"family": "Eley", "given": "Thalia C", "initials": "TC"}, {"family": "Gregory", "given": "Alice M", "initials": "AM"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "van Beijsterveldt", "given": "Toos C E M", "initials": "TCEM"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Tan", "given": "Qihua", "initials": "Q"}, {"family": "Zhang", "given": "Dongfeng", "initials": "D"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Hjelmborg", "given": "Jacob V B", "initials": "JVB"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "Krasnow", "given": "Ruth", "initials": "R"}, {"family": "Busjahn", "given": "Andreas", "initials": "A"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Siribaddana", "given": "Sisira H", "initials": "SH"}, {"family": "Hotopf", "given": "Matthew", "initials": "M"}, {"family": "Sumathipala", "given": "Athula", "initials": "A"}, {"family": "Rijsdijk", "given": "Fruhling", "initials": "F"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Aslan", "given": "Anna K Dahl", "initials": "AKD"}, {"family": "Ordo\u00f1ana", "given": "Juan R", "initials": "JR"}, {"family": "S\u00e1nchez-Romera", "given": "Juan F", "initials": "JF"}, {"family": "Colodro-Conde", "given": "Lucia", "initials": "L"}, {"family": "Duncan", "given": "Glen E", "initials": "GE"}, {"family": "Buchwald", "given": "Dedra", "initials": "D"}, {"family": "Tarnoki", "given": "Adam D", "initials": "AD"}, {"family": "Tarnoki", "given": "David L", "initials": "DL"}, {"family": "Yokoyama", "given": "Yoshie", "initials": "Y"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Silventoinen", "given": "Karri", "initials": "K"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}], "type": "journal article", "published": "2017-04-27", "journal": {"volume": "8", "issn": "2042-6410", "issue": null, "pages": "14", "title": "Biol Sex Differ", "issn-l": "2042-6410"}, "abstract": "The comparison of traits in twins from opposite-sex (OS) and same-sex (SS) dizygotic twin pairs is considered a proxy measure of prenatal hormone exposure. To examine possible prenatal hormonal influences on anthropometric traits, we compared mean height, body mass index (BMI), and the prevalence of being overweight or obese between men and women from OS and SS dizygotic twin pairs.\n\nThe data were derived from the COllaborative project of Development of Anthropometrical measures in Twins (CODATwins) database, and included 68,494 SS and 53,808 OS dizygotic twin individuals above the age of 20\u00a0years from 31 twin cohorts representing 19 countries. Zygosity was determined by questionnaires or DNA genotyping depending on the study. Multiple regression and logistic regression models adjusted for cohort, age, and birth year with the twin type as a predictor were carried out to compare height and BMI in twins from OS pairs with those from SS pairs and to calculate the adjusted odds ratios and 95% confidence intervals for being overweight or obese.\n\nOS females were, on average, 0.31\u00a0cm (95% confidence interval (CI) 0.20, 0.41) taller than SS females. OS males were also, on average, taller than SS males, but this difference was only 0.14\u00a0cm (95% CI 0.02, 0.27). Mean BMI and the prevalence of overweight or obesity did not differ between males and females from SS and OS twin pairs. The statistically significant differences between OS and SS twins for height were small and appeared to reflect our large sample size rather than meaningful differences of public health relevance.\n\nWe found no evidence to support the hypothesis that prenatal hormonal exposure or postnatal socialization (i.e., having grown up with a twin of the opposite sex) has a major impact on height and BMI in adulthood.", "doi": "10.1186/s13293-017-0134-x", "pmid": "28465822", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "134"}, {"db": "pmc", "key": "PMC5408365"}], "notes": [], "created": "2017-10-25T15:27:45.038Z", "modified": "2024-01-16T13:48:48.078Z"}, {"entity": "publication", "iuid": "307148582507404896332168f5379674", "links": {"self": {"href": "https://publications.scilifelab.se/publication/307148582507404896332168f5379674.json"}, "display": {"href": "https://publications.scilifelab.se/publication/307148582507404896332168f5379674"}}, "title": "Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits", "authors": [{"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Graff", "given": "Misa", "initials": "M"}, {"family": "Fisher", "given": "Virginia A", "initials": "VA"}, {"family": "Young", "given": "Kristin", "initials": "K"}, {"family": "Barata", "given": "Llilda", "initials": "L"}, {"family": "Deng", "given": "Xuan", "initials": "X"}, {"family": "Czajkowski", "given": "Jacek", "initials": "J"}, {"family": "Hadley", "given": "David", "initials": "D"}, {"family": "Ngwa", "given": "Julius S", "initials": "JS"}, {"family": 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"David P", "initials": "DP"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Marchini", "given": "Jonathan", "initials": "J"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}], "type": "journal-article", "published": "2017-04-26", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "14977", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/ncomms14977", "pmid": "28443625", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:33.062Z", "modified": "2020-01-21T13:56:11.704Z"}, {"entity": "publication", "iuid": "a54451a7ba4f4e42b547db6d29ef15fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a54451a7ba4f4e42b547db6d29ef15fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a54451a7ba4f4e42b547db6d29ef15fa"}}, "title": "Corrigendum: MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.", "authors": [{"family": "Gad", "given": "Helge", "initials": "H"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Eshtad", "given": "Saeed", "initials": "S"}, {"family": "Jacques", "given": "Sylvain A", "initials": "SA"}, {"family": "Str\u00f6m", "given": "Cecilia E", "initials": "CE"}, {"family": "Svensson", "given": "Linda M", "initials": "LM"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Einarsdottir", "given": "Berglind Osk", "initials": "BO"}, {"family": "Saleh", "given": "Aljona", "initials": "A"}, {"family": "G\u00f6kt\u00fcrk", "given": "Camilla", "initials": "C"}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Berntsson", "given": "Ronnie P-A", "initials": "RP"}, {"family": "Gustafsson", "given": "Robert", "initials": "R"}, {"family": "Str\u00f6mberg", "given": "Kia", "initials": "K"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Jacques-Cordonnier", "given": "Marie-Caroline", "initials": "MC"}, {"family": "Desroses", "given": "Matthieu", "initials": "M"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Olofsson", "given": "Roger", "initials": "R"}, {"family": "Johansson", "given": "Fredrik", "initials": "F"}, {"family": "Homan", "given": "Evert J", "initials": "EJ"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "H\u00f6glund", "given": "Andreas", "initials": "A"}, {"family": "Hagenkort", "given": "Anna", "initials": "A"}, {"family": "Pham", "given": "Therese", "initials": "T"}, {"family": "Altun", "given": "Mikael", "initials": "M"}, {"family": "Gaugaz", "given": "Fabienne Z", "initials": "FZ"}, {"family": "Vikingsson", "given": "Svante", "initials": "S"}, {"family": "Evers", "given": "Bastiaan", "initials": "B"}, {"family": "Henriksson", "given": "Martin", "initials": "M"}, {"family": "Vallin", "given": "Karl S A", "initials": "KSA"}, {"family": "Wallner", "given": "Olov A", "initials": "OA"}, {"family": "Hammarstr\u00f6m", "given": "Lars G J", "initials": "LGJ"}, {"family": "Wiita", "given": "Elisee", "initials": "E"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Kalder\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Axelsson", "given": "Hanna", "initials": "H"}, {"family": "Djureinovic", "given": "Tatjana", "initials": "T"}, {"family": "Carreras Puigvert", "given": "Jordi", "initials": "J"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Jeppsson", "given": "Fredrik", "initials": "F"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Lundin", "given": "Cecilia", "initials": "C"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Granelli", "given": "Ingrid", "initials": "I"}, {"family": "Jenmalm Jensen", "given": "Annika", "initials": "A"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Nilsson", "given": "Jonas A", "initials": "JA"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Ulrika Warpman Berglund &Thomas Helleday", "given": "", "initials": ""}], "type": "journal article", "published": "2017-04-26", "journal": {"volume": "544", "issn": "1476-4687", "issue": "7651", "pages": "508", "title": "Nature", "issn-l": "0028-0836"}, "abstract": null, "doi": "10.1038/nature22083", "pmid": "28447629", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "nature22083"}], "notes": "Biochemical and Cellular Screening", "created": "2017-11-01T09:58:56.990Z", "modified": "2025-10-17T13:05:08.951Z"}, {"entity": "publication", "iuid": "9e0113f48d1045808092b59ff370869d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e0113f48d1045808092b59ff370869d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e0113f48d1045808092b59ff370869d"}}, "title": "Correlation of histopathologic characteristics to protein expression and function in malignant melanoma.", "authors": [{"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Paw\u0142owski", "given": "Krzysztof", "initials": "K"}, {"family": "Szasz", "given": "A Marcell", "initials": "AM"}, {"family": "Yakovleva", "given": "Maria", "initials": "M"}, {"family": "Sugihara", "given": "Yutaka", "initials": "Y"}, {"family": "Malm", "given": "Johan", "initials": "J"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ingvar", "given": "Christian", "initials": "C"}, {"family": "Lundgren", "given": "Lotta", "initials": "L"}, {"family": "Baldetorp", "given": "Bo", "initials": "B"}, {"family": "Olsson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Laurell", "given": "Thomas", "initials": "T"}, {"family": "Wieslander", "given": "Elisabet", "initials": "E"}, {"family": "Marko-Varga", "given": "Gy\u00f6rgy", "initials": "G"}], "type": "journal article", "published": "2017-04-26", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "12", "issue": "4", "pages": "e0176167", "issn-l": "1932-6203"}, "abstract": "Metastatic melanoma is still one of the most prevalent skin cancers, which upon progression has neither a prognostic marker nor a specific and lasting treatment. Proteomic analysis is a versatile approach with high throughput data and results that can be used for characterizing tissue samples. However, such analysis is hampered by the complexity of the disease, heterogeneity of patients, tumors, and samples themselves. With the long term aim of quest for better diagnostics biomarkers, as well as predictive and prognostic markers, we focused on relating high resolution proteomics data to careful histopathological evaluation of the tumor samples and patient survival information.\n\nRegional lymph node metastases obtained from ten patients with metastatic melanoma (stage III) were analyzed by histopathology and proteomics using mass spectrometry. Out of the ten patients, six had clinical follow-up data. The protein deep mining mass spectrometry data was related to the histopathology tumor tissue sections adjacent to the area used for deep-mining. Clinical follow-up data provided information on disease progression which could be linked to protein expression aiming to identify tissue-based specific protein markers for metastatic melanoma and prognostic factors for prediction of progression of stage III disease.\n\nIn this feasibility study, several proteins were identified that positively correlated to tumor tissue content including IF6, ARF4, MUC18, UBC12, CSPG4, PCNA, PMEL and MAGD2. The study also identified MYC, HNF4A and TGFB1 as top upstream regulators correlating to tumor tissue content. Other proteins were inversely correlated to tumor tissue content, the most significant being; TENX, EHD2, ZA2G, AOC3, FETUA and THRB. A number of proteins were significantly related to clinical outcome, among these, HEXB, PKM and GPNMB stood out, as hallmarks of processes involved in progression from stage III to stage IV disease and poor survival.\n\nIn this feasibility study, promising results show the feasibility of relating proteomics to histopathology and clinical outcome, and insight thus can be gained into the molecular processes driving the disease. The combined analysis of histological features including the sample cellular composition with protein expression of each metastasis enabled the identification of novel, differentially expressed proteins. Further studies are necessary to determine whether these putative biomarkers can be utilized in diagnostics and prognostic prediction of metastatic melanoma.", "doi": "10.1371/journal.pone.0176167", "pmid": "28445515", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-43238"}, {"db": "pmc", "key": "PMC5405986"}], "notes": [], "created": "2020-01-27T10:10:26.212Z", "modified": "2021-05-24T15:39:50.321Z"}, {"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": "52531998261243be9fc159120f4e6afd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52531998261243be9fc159120f4e6afd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52531998261243be9fc159120f4e6afd"}}, "title": "Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.", "authors": [{"family": "Tobiasson", "given": "Magnus", "initials": "M"}, {"family": "Abdulkadir", "given": "Hani", "initials": "H"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "De Paepe", "given": "Ayla", "initials": "A"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Krjutskov", "given": "Kaarel", "initials": "K"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Gr\u00f6vdal", "given": "Michael", "initials": "M"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Ben Azenkoud", "given": "Asmaa", "initials": "A"}, {"family": "Corddedu", "given": "Lina", "initials": "L"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2017-04-25", "journal": {"volume": "8", "issn": "1949-2553", "issue": "17", "pages": "28812-28825", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the histone modifications H3K18ac and H3K9me3 (ChIP seq). Aza induced a general increase in gene expression with 924 significantly upregulated genes but this increase showed no correlation with changes in DNA methylation or H3K18ac, and only a weak association with changes in H3K9me3. Interestingly, we observed activation of transcripts containing 15 endogenous retroviruses (ERVs) confirming previous cell line studies. DNA methylation decreased moderately in 99% of all genes, with a median \u03b2-value reduction of 0.018; the most pronounced effects seen in heterochromatin. Aza-induced hypomethylation correlated significantly with change in H3K9me3. The pattern of H3K18ac and H3K9me3 displayed large differences between patients and healthy controls without any consistent pattern induced by Aza. We conclude that the marked induction of gene expression only partly could be explained by epigenetic changes, and propose that activation of ERVs may contribute to the clinical effects of Aza in MDS.", "doi": "10.18632/oncotarget.15807", "pmid": "28427179", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "15807"}, {"db": "pmc", "key": "PMC5438694"}], "notes": [], "created": "2019-01-15T07:50:51.953Z", "modified": "2020-01-21T13:53:22.301Z"}, {"entity": "publication", "iuid": "a5e691e92e3f4249958e79986879afaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5e691e92e3f4249958e79986879afaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5e691e92e3f4249958e79986879afaf"}}, "title": "Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk", "authors": [{"family": "Day", "given": "Felix R", "initials": "FR"}, {"family": "Thompson", "given": "Deborah J", "initials": "DJ"}, {"family": "Helgason", "given": "Hannes", "initials": "H"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Finucane", "given": "Hilary", "initials": "H"}, {"family": "Sulem", "given": "Patrick", "initials": "P"}, {"family": "Ruth", "given": "Katherine S", "initials": "KS"}, {"family": "Whalen", "given": "Sean", "initials": "S"}, {"family": "Sarkar", "given": "Abhishek K", "initials": "AK"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Altmaier", "given": "Elisabeth", "initials": "E"}, {"family": "Amini", "given": "Marzyeh", "initials": "M"}, {"family": "Barbieri", "given": "Caterina M", "initials": "CM"}, {"family": "Boutin", "given": "Thibaud", "initials": "T"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Demerath", "given": "Ellen", "initials": "E"}, {"family": "Giri", "given": "Ayush", "initials": "A"}, {"family": "He", "given": "Chunyan", "initials": "C"}, {"family": "Hottenga", "given": "Jouke J", "initials": "JJ"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Loh", "given": "Po Ru", "initials": "PR"}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Marco", "given": "Brumat", "initials": "B"}, {"family": "McMahon", "given": "George", "initials": "G"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Paternoster", "given": "Lavinia", "initials": "L"}, {"family": "Perjakova", "given": "Natalia", "initials": "N"}, {"family": "Porcu", "given": "Eleonora", "initials": "E"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Schraut", "given": "Katharina E", "initials": "KE"}, {"family": "Segr\u00e8", "given": "Ayellet V", "initials": "AV"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Stolk", "given": "Lisette", "initials": "L"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Andrulis", "given": "Irene L", "initials": "IL"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Beckmann", "given": "Matthias W", "initials": "MW"}, {"family": "Benitez", "given": "Javier", "initials": "J"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bojesen", "given": "Stig E", "initials": "SE"}, {"family": "Bolla", "given": "Manjeet K", "initials": "MK"}, {"family": "Brand", "given": "Judith S", "initials": "JS"}, {"family": "Brauch", "given": "Hiltrud", "initials": "H"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Br\u00fcning", "given": "Thomas", "initials": "T"}, {"family": "Buring", "given": "Julie E", "initials": "JE"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Catamo", "given": "Eulalia", "initials": "E"}, {"family": "Chanock", "given": "Stephen", "initials": "S"}, {"family": "Chenevix-Trench", "given": "Georgia", "initials": "G"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Couch", "given": "Fergus J", "initials": "FJ"}, {"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Cox", "given": "Angela", "initials": "A"}, {"family": "Crisponi", "given": "Laura", "initials": "L"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Davey Smith", "given": "George", "initials": "G"}, {"family": "de Geus", "given": "Eco J C N", "initials": "EJCN"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "De Vivo", "given": "Immaculata", "initials": "I"}, {"family": "Dennis", "given": "Joe", "initials": "J"}, {"family": "Devilee", "given": "Peter", "initials": "P"}, {"family": "dos-Santos-Silva", "given": "Isabel", "initials": "I"}, {"family": "Dunning", "given": "Alison M", "initials": "AM"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Fasching", "given": "Peter A", "initials": "PA"}, {"family": "Fern\u00e1ndez-Rhodes", "given": "Lindsay", "initials": "L"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Flesch-Janys", "given": "Dieter", "initials": "D"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Gabrielson", "given": "Marike", "initials": "M"}, {"family": "Gandin", "given": "Ilaria", "initials": "I"}, {"family": "Giles", "given": "Graham G", "initials": "GG"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Gu\u00e9nel", "given": "Pascal", "initials": "P"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Hallberg", "given": "Emily", "initials": "E"}, {"family": "Hamann", "given": "Ute", "initials": "U"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Heiss", "given": "Gerardo", "initials": "G"}, {"family": "Hooning", "given": "Maartje J", "initials": "MJ"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Hu", "given": "Frank", "initials": "F"}, {"family": "Hunter", "given": "David J", "initials": "DJ"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Im", "given": "Hae Kyung", "initials": "HK"}, {"family": "J\u00e4rvelin", "given": "Marjo Riitta", "initials": "MR"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Kellis", "given": "Manolis", "initials": "M"}, {"family": "Kutalik", "given": "Zoltan", "initials": "Z"}, {"family": "LaChance", "given": "Genevieve", "initials": "G"}, {"family": "Lambrechts", "given": "Diether", "initials": "D"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Laven", "given": "Joop S E", "initials": "JSE"}, {"family": "Lenarduzzi", "given": "Stefania", "initials": "S"}, {"family": "Li", "given": "Jingmei", "initials": "J"}, {"family": "Lind", "given": "Penelope A", "initials": "PA"}, {"family": "Lindstrom", "given": "Sara", "initials": "S"}, {"family": "Liu", "given": "YongMei", "initials": "Y"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Mannermaa", "given": "Arto", "initials": "A"}, {"family": "Mbarek", "given": "Hamdi", "initials": "H"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Menni", "given": "Cristina", "initials": "C"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Michailidou", "given": "Kyriaki", "initials": "K"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Milne", "given": "Roger L", "initials": "RL"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Mulligan", "given": "Anna M", "initials": "AM"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Nevanlinna", "given": "Heli", "initials": "H"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "O'Mara", "given": "Tracy A", "initials": "TA"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Pedersen", "given": "Nancy", "initials": "N"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Peto", "given": "Julian", "initials": "J"}, {"family": "Pharoah", "given": "Paul D P", "initials": "PDP"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Radice", "given": "Paolo", "initials": "P"}, {"family": "Rahman", "given": "Iffat", "initials": "I"}, {"family": "Ring", "given": "Susan M", "initials": "SM"}, {"family": "Robino", "given": "Antonietta", "initials": "A"}, {"family": "Rosendaal", "given": "Frits R", "initials": "FR"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Rueedi", "given": "Rico", "initials": "R"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Sala", "given": "Cinzia F", "initials": "CF"}, {"family": "Schmidt", "given": "Marjanka K", "initials": "MK"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Shah", "given": "Mitul", "initials": "M"}, {"family": "Sorice", "given": "Rossella", "initials": "R"}, {"family": "Southey", "given": "Melissa C", "initials": "MC"}, {"family": "Sovio", "given": "Ulla", "initials": "U"}, {"family": "Stampfer", "given": "Meir", "initials": "M"}, {"family": "Steri", "given": "Maristella", "initials": "M"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Traglia", "given": "Michela", "initials": "M"}, {"family": "Truong", "given": "Th\u00e9r\u00e8se", "initials": "T"}, {"family": "Tyrer", "given": "Jonathan P", "initials": "JP"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Edwards", "given": "Digna R Velez", "initials": "DRV"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wang", "given": "Qin", "initials": "Q"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "van Dijk", "given": "Ko Willems", "initials": "KW"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Winqvist", "given": "Robert", "initials": "R"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Zoledziewska", "given": "Magdalena", "initials": "M"}, {"family": "Zygmunt", "given": "Marek", "initials": "M"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Lawlor", "given": "Debbie A", "initials": "DA"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Nohr", "given": "Ellen A", "initials": "EA"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Porteous", "given": "David", "initials": "D"}, {"family": "Price", "given": "Alkes L", "initials": "AL"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "St\u00f6ckl", "given": "Doris", "initials": "D"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "Visser", "given": "Jenny A", "initials": "JA"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Spurdle", "given": "Amanda B", "initials": "AB"}, {"family": "Thorsteindottir", "given": "Unnur", "initials": "U"}, {"family": "Pollard", "given": "Katherine S", "initials": "KS"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Tung", "given": "Joyce Y", "initials": "JY"}, {"family": "Chang-Claude", "given": "Jenny", "initials": "J"}, {"family": "Hinds", "given": "David", "initials": "D"}, {"family": "Murray", "given": "Anna", "initials": "A"}, {"family": "Murabito", "given": "Joanne M", "initials": "JM"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}], "type": "journal-article", "published": "2017-04-24", "journal": {"volume": "49", "issn": "1061-4036", "issue": "6", "pages": "834-841", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/ng.3841", "pmid": "28436984", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:33.659Z", "modified": "2020-01-21T13:56:11.689Z"}, {"entity": "publication", "iuid": "bef52d22554945fcb511d0de18e687d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bef52d22554945fcb511d0de18e687d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bef52d22554945fcb511d0de18e687d9"}}, "title": "The Influence of Hydroxyapatite Nanoparticle Morphology on Embryonic Development in a Zebrafish Exposure Model.", "authors": [{"family": "Pujari-Palmer", "given": "Shiuli", "initials": "S"}, {"family": "Lu", "given": "Xi", "initials": "X"}, {"family": "Karlsson Ott", "given": "Marjam", "initials": "M"}], "type": "journal article", "published": "2017-04-22", "journal": {"title": "Nanomaterials (Basel)", "issn": "2079-4991", "volume": "7", "issue": "4", "issn-l": "2079-4991"}, "abstract": "Nanomaterials are used in many different industries such as cosmetics, food, clothing, and electronics. There is increasing concern that exposure to nanoparticles (NPs) during pregnancy can adversely affect fetal development. It is well known that the size, charge, and chemistry of a nanoparticle can modulate embryological development. The role that particle morphology plays on early development, however, is still widely unknown. The present study aims to investigate the effect of hydroxyapatite nanoparticle (HANP) morphology on embryological development in a zebrafish exposure model. Four distinct HANP morphologies (dots, long rods, sheets, and fibers) were fabricated and characterized. Zebrafish embryos were exposed to HANPs (0-100 mg/L), and viability and developmental deformities were evaluated for up to 5 days post-fertilization (dpf). Malformations such as pericardial edema and axial curvature were apparent in embryos as early as 1 dpf, following exposure to the dot and fiber particles, and developed in embryos by 3 dpf in the sheet and long rod particle groups. Minimal death was observed in response to dot, long rod, and sheet particles (\u226425%), while fiber particles induced overwhelming toxicity (\u226460%) after 1 dpf, and complete toxicity during all subsequent time points. Collectively, these results suggest that nanoparticle morphology can significantly impact embryological development and should be a required consideration when designing nanomaterials for commercial use.", "doi": "10.3390/nano7040089", "pmid": "28441729", "labels": {"Genome Engineering Zebrafish": "Service"}, "xrefs": [{"db": "pii", "key": "nano7040089"}, {"db": "pmc", "key": "PMC5408181"}], "notes": [], "created": "2017-10-26T09:43:20.938Z", "modified": "2017-10-26T09:43:20.952Z"}, {"entity": "publication", "iuid": "ef873ebb1c55436395968a885ee5232b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef873ebb1c55436395968a885ee5232b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef873ebb1c55436395968a885ee5232b"}}, "title": "Respiratory chain complex III deficiency due to mutated BCS1L: a novel phenotype with encephalomyopathy, partially phenocopied in a Bcs1l mutant mouse model.", "authors": [{"family": "Tegelberg", "given": "Saara", "initials": "S"}, {"family": "Toma\u0161i\u0107", "given": "Nikica", "initials": "N"}, {"family": "Kallij\u00e4rvi", "given": "Jukka", "initials": "J"}, {"family": "Purhonen", "given": "Janne", "initials": "J"}, {"family": "Elm\u00e9r", "given": "Eskil", "initials": "E"}, {"family": "Lindberg", "given": "Eva", "initials": "E"}, {"family": "Nord", "given": "David Gisselsson", "initials": "DG"}, {"family": "Soller", "given": "Maria", "initials": "M"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Bruhn", "given": "Helene", "initials": "H"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}, {"family": "Eklund", "given": "Erik A", "initials": "EA"}, {"family": "Fellman", "given": "Vineta", "initials": "V"}], "type": "journal article", "published": "2017-04-20", "journal": {"volume": "12", "issn": "1750-1172", "issue": "1", "pages": "73", "title": "Orphanet J Rare Dis", "issn-l": "1750-1172"}, "abstract": "Mitochondrial diseases due to defective respiratory chain complex III (CIII) are relatively uncommon. The assembly of the eleven-subunit CIII is completed by the insertion of the Rieske iron-sulfur protein, a process for which BCS1L protein is indispensable. Mutations in the BCS1L gene constitute the most common diagnosed cause of CIII deficiency, and the phenotypic spectrum arising from mutations in this gene is wide.\n\nA case of CIII deficiency was investigated in depth to assess respiratory chain function and assembly, and brain, skeletal muscle and liver histology. Exome sequencing was performed to search for the causative mutation(s). The patient's platelets and muscle mitochondria showed respiration defects and defective assembly of CIII was detected in fibroblast mitochondria. The patient was compound heterozygous for two novel mutations in BCS1L, c.306A\u2009>\u2009T and c.399delA. In the cerebral cortex a specific pattern of astrogliosis and widespread loss of microglia was observed. Further analysis showed loss of Kupffer cells in the liver. These changes were not found in infants suffering from GRACILE syndrome, the most severe BCS1L-related disorder causing early postnatal mortality, but were partially corroborated in a knock-in mouse model of BCS1L deficiency.\n\nWe describe two novel compound heterozygous mutations in BCS1L causing CIII deficiency. The pathogenicity of one of the mutations was unexpected and points to the importance of combining next generation sequencing with a biochemical approach when investigating these patients. We further show novel manifestations in brain, skeletal muscle and liver, including abnormality in specialized resident macrophages (microglia and Kupffer cells). These novel phenotypes forward our understanding of CIII deficiencies caused by BCS1L mutations.", "doi": "10.1186/s13023-017-0624-2", "pmid": "28427446", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13023-017-0624-2"}, {"db": "pmc", "key": "PMC5399415"}], "notes": [], "created": "2017-11-03T12:53:36.734Z", "modified": "2017-11-03T12:55:39.216Z"}, {"entity": "publication", "iuid": "3ab08f7ce0d64e499b1282411ce8639c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ab08f7ce0d64e499b1282411ce8639c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ab08f7ce0d64e499b1282411ce8639c"}}, "title": "Persistent Effects of Developmental Exposure to 17\u03b1-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior", "authors": [{"family": "Porseryd", "given": "Tove", "initials": "T"}, {"family": "Volkova", "given": "Kristina", "initials": "K"}, {"family": "Reyhanian Caspillo", "given": "Nasim", "initials": "N"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Dinnetz", "given": "Patrik", "initials": "P"}, {"family": "Porsh H\u00e4llstr\u00f6m", "given": "Inger", "initials": "I"}], "type": "journal-article", "published": "2017-04-20", "journal": {"volume": "11", "issn": "1662-5153", "issue": null, "pages": null, "title": "Front. Behav. Neurosci.", "issn-l": "1662-5153"}, "abstract": "The synthetic estrogen 17\u03b1-ethinylestradiol (EE\n            2) is an endocrine disrupting compound of concern due to its persistence and widespread presence in the aquatic environment. Effects of developmental exposure to low concentrations of EE2 in fish on reproduction and behavior not only persisted to adulthood, but have also been observed to be transmitted to several generations of unexposed progeny. To investigate the possible biological mechanisms of the persistent anxiogenic phenotype, we exposed zebrafish embryos for 80 days post fertilization to 0, 3, and 10 ng/L EE2 (measured concentrations 2.14 and 7.34 ng/L). After discontinued exposure, the animals were allowed to recover for 120 days in clean water. Adult males and females were later tested for changes in stress response and shoal cohesion, and whole-brain gene expression was analyzed with RNA sequencing. The results show increased anxiety in the novel tank and scototaxis tests, and increased shoal cohesion in fish exposed during development to EE2. RNA sequencing revealed 34 coding genes differentially expressed in male brains and 62 in female brains as a result of EE2 exposure. Several differences were observed between males and females in differential gene expression, with only one gene, sv2b, coding for a synaptic vesicle protein, that was affected by EE2 in both sexes. Functional analyses showed that in female brains, EE2 had significant effects on pathways connected to the circadian rhythm, cytoskeleton and motor proteins and synaptic proteins. A large number of non-coding sequences including 19 novel miRNAs were also differentially expressed in the female brain. The largest treatment effect in male brains was observed in pathways related to cholesterol biosynthesis and synaptic proteins. Circadian rhythm and cholesterol biosynthesis, previously implicated in anxiety behavior, might represent possible candidate pathways connecting the transcriptome changes to the alterations to behavior. Further the observed alteration in expression of genes involved in synaptogenesis and synaptic function may be important for the developmental modulations resulting in an anxiety phenotype. This study represents an initial survey of the fish brain transcriptome by RNA sequencing after long-term recovery from developmental exposure to an estrogenic compound.", "doi": "10.3389/fnbeh.2017.00069", "pmid": "28473760", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:35:55.751Z", "modified": "2020-01-21T13:56:17.414Z"}, {"entity": "publication", "iuid": "0fc10e2a8e984be2a2db97949bcb3821", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fc10e2a8e984be2a2db97949bcb3821.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fc10e2a8e984be2a2db97949bcb3821"}}, "title": "In muro deacetylation of xylan affects lignin properties and improves saccharification of aspen wood.", "authors": [{"family": "Pawar", "given": "Prashant Mohan-Anupama", "initials": "PM"}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M"}, {"family": "Chong", "given": "Sun-Li", "initials": "SL"}, {"family": "Gandla", "given": "Madhavi Latha", "initials": "ML"}, {"family": "Bashar", "given": "Shamrat Shafiul", "initials": "SS"}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Ahvenainen", "given": "Patrik", "initials": "P"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "\u00d6zparpucu", "given": "Merve", "initials": "M"}, {"family": "R\u00fcggeberg", "given": "Markus", "initials": "M"}, {"family": "Serimaa", "given": "Ritva", "initials": "R"}, {"family": "Lawoko", "given": "Martin", "initials": "M"}, {"family": "Tenkanen", "given": "Maija", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}], "type": "journal article", "published": "2017-04-20", "journal": {"volume": "10", "issn": "1754-6834", "issue": "1", "pages": "98", "title": "Biotechnol Biofuels", "issn-l": "1754-6834"}, "abstract": "Lignocellulose from fast growing hardwood species is a preferred source of polysaccharides for advanced biofuels and \"green\" chemicals. However, the extensive acetylation of hardwood xylan hinders lignocellulose saccharification by obstructing enzymatic xylan hydrolysis and causing inhibitory acetic acid concentrations during microbial sugar fermentation. To optimize lignocellulose for cost-effective saccharification and biofuel production, an acetyl xylan esterase AnAXE1 from Aspergillus niger was introduced into aspen and targeted to cell walls.\n\nAnAXE1-expressing plants exhibited reduced xylan acetylation and grew normally. Without pretreatment, their lignocellulose yielded over 25% more glucose per unit mass of wood (dry weight) than wild-type plants. Glucose yields were less improved (+7%) after acid pretreatment, which hydrolyses xylan. The results indicate that AnAXE1 expression also reduced the molecular weight of xylan, and xylan-lignin complexes and/or lignin co-extracted with xylan, increased cellulose crystallinity, altered the lignin composition, reducing its syringyl to guaiacyl ratio, and increased lignin solubility in dioxane and hot water. Lignin-associated carbohydrates became enriched in xylose residues, indicating a higher content of xylo-oligosaccharides.\n\nThis work revealed several changes in plant cell walls caused by deacetylation of xylan. We propose that deacetylated xylan is partially hydrolyzed in the cell walls, liberating xylo-oligosaccharides and their associated lignin oligomers from the cell wall network. Deacetylating xylan thus not only increases its susceptibility to hydrolytic enzymes during saccharification but also changes the cell wall architecture, increasing the extractability of lignin and xylan and facilitating saccharification.", "doi": "10.1186/s13068-017-0782-4", "pmid": "28428822", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "782"}, {"db": "pmc", "key": "PMC5397736"}], "notes": [], "created": "2017-10-31T12:05:27.764Z", "modified": "2025-10-17T13:03:59.901Z"}, {"entity": "publication", "iuid": "d07f80e9ae9c420d82d3a29d34c31f42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07f80e9ae9c420d82d3a29d34c31f42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07f80e9ae9c420d82d3a29d34c31f42"}}, "title": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms.", "authors": [{"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Davidsson", "given": "Josef", "initials": "J"}, {"family": "Voss", "given": "Matthias", "initials": "M"}, {"family": "Rahikkala", "given": "Elisa", "initials": "E"}, {"family": "Holmes", "given": "Tim D", "initials": "TD"}, {"family": "Chiang", "given": "Samuel C C", "initials": "SCC"}, {"family": "Komulainen-Ebrahim", "given": "Jonna", "initials": "J"}, {"family": "Gorcenco", "given": "Sorina", "initials": "S"}, {"family": "Rundberg Nilsson", "given": "Alexandra", "initials": "A"}, {"family": "Ripperger", "given": "Tim", "initials": "T"}, {"family": "Kokkonen", "given": "Hannaleena", "initials": "H"}, {"family": "Bryder", "given": "David", "initials": "D"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Henter", "given": "Jan-Inge", "initials": "JI"}, {"family": "M\u00f6tt\u00f6nen", "given": "Merja", "initials": "M"}, {"family": "Niinim\u00e4ki", "given": "Riitta", "initials": "R"}, {"family": "Nilsson", "given": "Lars", "initials": "L"}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ"}, {"family": "Puschmann", "given": "Andreas", "initials": "A"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Uusimaa", "given": "Johanna", "initials": "J"}, {"family": "Moilanen", "given": "Jukka", "initials": "J"}, {"family": "Tedg\u00e5rd", "given": "Ulf", "initials": "U"}, {"family": "Cammenga", "given": "J\u00f6rg", "initials": "J"}, {"family": "Bryceson", "given": "Yenan T", "initials": "YT"}], "type": "journal article", "published": "2017-04-20", "journal": {"volume": "129", "issn": "1528-0020", "issue": "16", "pages": "2266-2279", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Several monogenic causes of familial myelodysplastic syndrome (MDS) have recently been identified. We studied 2 families with cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction. Genetic studies uncovered heterozygous missense mutations in SAMD9L, a tumor suppressor gene located on chromosome arm 7q. Consistent with a gain-of-function effect, ectopic expression of the 2 identified SAMD9L mutants decreased cell proliferation relative to wild-type protein. Of the 10 individuals identified who were heterozygous for either SAMD9L mutation, 3 developed MDS upon loss of the mutated SAMD9L allele following intracellular infections associated with myeloid, B-, and natural killer (NK)-cell deficiency. Five other individuals, 3 with spontaneously resolved cytopenic episodes in infancy, harbored hematopoietic revertant mosaicism by uniparental disomy of 7q, with loss of the mutated allele or additional in cisSAMD9L truncating mutations. Examination of 1 individual indicated that somatic reversions were postnatally selected. Somatic mutations were tracked to CD34+ hematopoietic progenitor cell populations, being further enriched in B and NK cells. Stimulation of these cell types with interferon (IFN)-\u03b1 or IFN-\u03b3 induced SAMD9L expression. Clinically, revertant mosaicism was associated with milder disease, yet neurological manifestations persisted in 3 individuals. Two carriers also harbored a rare, in trans germ line SAMD9L missense loss-of-function variant, potentially counteracting the SAMD9L mutation. Our results demonstrate that gain-of-function mutations in the tumor suppressor SAMD9L cause cytopenia, immunodeficiency, variable neurological presentation, and predisposition to MDS with -7/del(7q), whereas hematopoietic revertant mosaicism commonly ameliorated clinical manifestations. The findings suggest a role for SAMD9L in regulating IFN-driven, demand-adapted hematopoiesis.", "doi": "10.1182/blood-2016-10-743302", "pmid": "28202457", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)33461-3"}, {"db": "pmc", "key": "PMC5399482"}], "notes": [], "created": "2017-10-13T14:45:25.923Z", "modified": "2021-07-06T15:41:35.342Z"}, {"entity": "publication", "iuid": "21c76b86d39f445bbe0e41910513b2e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21c76b86d39f445bbe0e41910513b2e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21c76b86d39f445bbe0e41910513b2e3"}}, "title": "Adenovirus-mediated CD40L gene transfer increases Teffector/Tregulatory cell ratio and upregulates death receptors in metastatic melanoma patients.", "authors": [{"family": "Schiza", "given": "A", "initials": "A"}, {"family": "Wenthe", "given": "J", "initials": "J"}, {"family": "Mangsbo", "given": "S", "initials": "S"}, {"family": "Eriksson", "given": "E", "initials": "E"}, {"family": "Nilsson", "given": "Anders", "initials": "A"}, {"family": "T\u00f6tterman", "given": "T H", "initials": "TH"}, {"family": "Loskog", "given": "A", "initials": "A"}, {"family": "Ullenhag", "given": "G", "initials": "G", "orcid": "0000-0003-4949-3267", "researcher": {"href": "https://publications.scilifelab.se/researcher/c500b5e092af439fb28a7ec1d26fe53d.json"}}], "type": "clinical trial, phase i", "published": "2017-04-20", "journal": {"title": "J Transl Med", "issn": "1479-5876", "issn-l": "1479-5876", "volume": "15", "issue": "1", "pages": "79"}, "abstract": "Malignant melanoma is an aggressive tumor sensitive for immunotherapy such as checkpoint blockade antibodies. Still, most patients with late stage disease do not respond, and the side effects can be severe. Stimulation of the CD40 pathway to initiate anti-tumor immunity is a promising alternative. Herein, we demonstrate immune profiling data from melanoma patients treated with an adenovirus-based CD40 ligand gene therapy (AdCD40L).\n\nPeripheral blood mononuclear cells and plasma were collected from malignant melanoma patients (n = 15) enrolled in a phase I/IIa study investigating intratumoral delivery of AdCD40L with or without low dose cyclophosphamide. Cells were analyzed by flow cytometry while plasma samples were analyzed by a multi-array proteomics.\n\nAll patients had an increased Teffector/Tregulatory cell ratio post therapy. Simultaneously, the death receptors TNFR1 and TRAIL-R2 were significantly up-regulated post treatment. Stem cell factor (SCF), E-selectin, and CD6 correlated to enhanced overall survival while a high level of granulocytic myeloid-derived suppressor cells (gMDSCs), IL8, IL10, TGFb1, CCL4, PlGF and Fl3t ligand was highest in patients with short survival.\n\nAdCD40L intratumoral injection induced desirable systemic immune effects that correlated to prolonged survival. Further studies using CD40 stimulation in malignant melanoma are warranted. Trial registration The 002:CD40L trial \"Phase I/IIa AdCD40L Immunogene Therapy for Malignant Melanoma and Other Solid Tumors\" (clinicalTrials.gov identifier: NCT01455259) was registered at September 2011.", "doi": "10.1186/s12967-017-1182-z", "pmid": "28427434", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12967-017-1182-z"}, {"db": "pmc", "key": "PMC5399418"}, {"db": "ClinicalTrials.gov", "key": "NCT01455259"}, {"db": "ClinicalTrials.gov", "key": "NCT01455259"}], "notes": [], "created": "2020-01-23T15:08:30.707Z", "modified": "2023-04-14T13:56:15.463Z"}, {"entity": "publication", "iuid": "d842cb7efe394cd3bba52313dcaffca6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d842cb7efe394cd3bba52313dcaffca6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d842cb7efe394cd3bba52313dcaffca6"}}, "title": "Synthesis and characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole: investigation on backbone/pendant interactions in a conducting redox polymer.", "authors": [{"family": "Huang", "given": "Hao", "initials": "H"}, {"family": "Karlsson", "given": "Christoffer", "initials": "C"}, {"family": "Str\u00f8mme", "given": "Maria", "initials": "M"}, {"family": "Gogoll", "given": "Adolf", "initials": "A"}, {"family": "Sj\u00f6din", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-04-19", "journal": {"volume": "19", "issn": "1463-9084", "issue": "16", "pages": "10427-10435", "title": "Phys Chem Chem Phys", "issn-l": "1463-9076"}, "abstract": "We herein report the synthesis and electrochemical characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole, consisting of a polypyrrole backbone derivatized at the beta position by a vinyl-hydroquinone pendant group. The structure of the polymer was characterized by solid state NMR spectroscopy. The interactions between the polypyrrole backbone and the oxidized quinone or reduced hydroquinone pendant groups are probed by several in situ methods. In situ attenuated total reflectance-Fourier transform infrared spectroscopy shows a spectroscopic response from both the doping of the polymer backbone and the redox activity of the pendant groups. Using an in situ Electrochemical Quartz Crystal Microbalance we reveal that the polymer doping is unaffected by the pendant group redox chemistry, as opposed to previous reports. Despite the continuous doping the electrochemical conversion from the hydroquinone state to the quinone state results in a significant conductance drop, as observed by in situ conductivity measurements using an Interdigitated Array electrode set-up. Twisting of the conducting polymer backbone as a result of a decreased separation between pendant groups due to \u03c0-\u03c0 stacking in the oxidized state is suggested as the cause of this conductance drop.", "doi": "10.1039/c6cp08736a", "pmid": "28379225", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:46:04.800Z", "modified": "2025-10-17T13:03:59.919Z"}, {"entity": "publication", "iuid": "b3c2828b051d47ae956b948e54288eb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3c2828b051d47ae956b948e54288eb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3c2828b051d47ae956b948e54288eb4"}}, "title": "Histology-Compatible MALDI Mass Spectrometry Based Imaging of Neuronal Lipids for Subsequent Immunofluorescent Staining.", "authors": [{"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Michno", "given": "Wojciech", "initials": "W"}, {"family": "Brinet", "given": "Dimitri", "initials": "D"}, {"family": "Iacone", "given": "Yasmine", "initials": "Y"}, {"family": "Zanni", "given": "Giulia", "initials": "G"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Hanrieder", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0001-6059-198X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e65454100674f98bf8f2575093f2441.json"}}], "type": "journal article", "published": "2017-04-18", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "89", "issue": "8", "pages": "4685-4694", "issn-l": "0003-2700"}, "abstract": "Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) enables acquisition of spatial distribution maps for molecular species in situ. This can provide comprehensive insights on the pathophysiology of different diseases. However, current sample preparation and MALDI-IMS acquisition methods have limitations in preserving molecular and histological tissue morphology, resulting in interfered correspondence of MALDI-IMS data with subsequently acquired immunofluorescent staining results. We here investigated the histology compatibility of MALDI-IMS to image neuronal lipids in rodent brain tissue with subsequent immunohistochemistry and fluorescent staining of histological features. This was achieved by sublimation of a low ionization energy matrix compound, 1,5-diaminonapthalene (1,5-DAN), minimizing the number of low-energy laser shots. This yielded improved lipid spectral quality and speed of data acquisition and reduced matrix cluster formation along with preservation of specific histological information at cellular levels. This gentle, histology-compatible MALDI-IMS protocol also diminished thermal effects and mechanical stress created during nanosecond laser ablation processes that were prominent in subsequent immunofluorescent staining images but not with classical hematoxylin and eosin (H&E) staining on the same tissue section. Furthermore, this methodology proved to be a powerful strategy for investigating \u03b2-amyloid (A\u03b2) plaque-associated neuronal lipids as exemplified by performing high-resolution MALDI-IMS with subsequent fluorescent amyloid staining in a transgenic mouse model of Alzheimer's disease (tgSwe).", "doi": "10.1021/acs.analchem.7b00313", "pmid": "28318232", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-23T16:35:14.859Z", "modified": "2021-06-21T15:39:50.308Z"}, {"entity": "publication", "iuid": "6d4a68165ff04eec80951890bf4c1c81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d4a68165ff04eec80951890bf4c1c81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d4a68165ff04eec80951890bf4c1c81"}}, "title": "Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis.", "authors": [{"family": "Kalantari", "given": "Aida", "initials": "A"}, {"family": "Chen", "given": "Tao", "initials": "T"}, {"family": "Ji", "given": "Boyang", "initials": "B"}, {"family": "Stancik", "given": "Ivan A", "initials": "IA"}, {"family": "Ravikumar", "given": "Vaishnavi", "initials": "V"}, {"family": "Franjevic", "given": "Damjan", "initials": "D"}, {"family": "Saulou-B\u00e9rion", "given": "Claire", "initials": "C"}, {"family": "Goelzer", "given": "Anne", "initials": "A"}, {"family": "Mijakovic", "given": "Ivan", "initials": "I"}], "type": "journal article", "published": "2017-04-18", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "8", "issue": null, "pages": "638", "issn-l": "1664-302X"}, "abstract": "3-Hydroxypropanoic acid (3-HP) is an important biomass-derivable platform chemical that can be converted into a number of industrially relevant compounds. There have been several attempts to produce 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae, and Saccharomyces cerevisiae. Despite the significant progress made in this field, commercially exploitable large-scale production of 3-HP in microbial strains has still not been achieved. In this study, we investigated the potential of Bacillus subtilis as a microbial platform for bioconversion of glycerol into 3-HP. Our recombinant B. subtilis strains overexpress the two-step heterologous pathway containing glycerol dehydratase and aldehyde dehydrogenase from K. pneumoniae. Genetic engineering, driven by in silico optimization, and optimization of cultivation conditions resulted in a 3-HP titer of 10 g/L, in a standard batch cultivation. Our findings provide the first report of successful introduction of the biosynthetic pathway for conversion of glycerol into 3-HP in B. subtilis. With this relatively high titer in batch, and the robustness of B. subtilis in high density fermentation conditions, we expect that our production strains may constitute a solid basis for commercial production of 3-HP.", "doi": "10.3389/fmicb.2017.00638", "pmid": "28458661", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5394112"}], "notes": [], "created": "2020-01-30T16:00:44.322Z", "modified": "2024-01-16T13:46:32.733Z"}, {"entity": "publication", "iuid": "b83d3f5716514cdaa183c816b5cd5e0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b83d3f5716514cdaa183c816b5cd5e0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b83d3f5716514cdaa183c816b5cd5e0c"}}, "title": "Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage", "authors": [{"family": "Kaucka", "given": "Marketa", "initials": "M"}, {"family": "Zikmund", "given": "Tomas", "initials": "T"}, {"family": "Tesarova", "given": "Marketa", "initials": "M"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Hellander", "given": "Andreas", "initials": "A"}, {"family": "Jaros", "given": "Josef", "initials": "J"}, {"family": "Kaiser", "given": "Jozef", "initials": "J"}, {"family": "Petersen", "given": "Julian", "initials": "J"}, {"family": "Szarowska", "given": "Bara", "initials": "B"}, {"family": "Newton", "given": "Phillip T", "initials": "PT"}, {"family": "Dyachuk", "given": "Vyacheslav", "initials": "V"}, {"family": "Li", "given": "Lei", "initials": "L"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Johansson", "given": "Anne Sofie", "initials": "AS"}, {"family": "Mishina", "given": "Yuji", "initials": "Y"}, {"family": "Currie", "given": "Joshua D", "initials": "JD"}, {"family": "Tanaka", "given": "Elly M", "initials": "EM"}, {"family": "Erickson", "given": "Alek", "initials": "A"}, {"family": "Dudley", "given": "Andrew", "initials": "A"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Southam", "given": "Paul", "initials": "P"}, {"family": "Coen", "given": "Enrico", "initials": "E"}, {"family": "Chen", "given": "Min", "initials": "M"}, {"family": "Weinstein", "given": "Lee S", "initials": "LS"}, {"family": "Hampl", "given": "Ales", "initials": "A"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}, {"family": "Chagin", "given": "Andrei S", "initials": "AS"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}], "type": "journal-article", "published": "2017-04-17", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "Cartilaginous structures are at the core of embryo growth and shaping before the bone forms. Here we report a novel principle of vertebrate cartilage growth that is based on introducing transversally-oriented clones into pre-existing cartilage. This mechanism of growth uncouples the lateral expansion of curved cartilaginous sheets from the control of cartilage thickness, a process which might be the evolutionary mechanism underlying adaptations of facial shape. In rod-shaped cartilage structures (Meckel, ribs and skeletal elements in developing limbs), the transverse integration of clonal columns determines the well-defined diameter and resulting rod-like morphology. We were able to alter cartilage shape by experimentally manipulating clonal geometries. Using in silico modeling, we discovered that anisotropic proliferation might explain cartilage bending and groove formation at the macro-scale.", "doi": "10.7554/elife.25902", "pmid": "28414273", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-20T07:19:40.676Z", "modified": "2021-07-05T13:44:34.775Z"}, {"entity": "publication", "iuid": "facbe48db3184e3b81e8b86eddbf9324", "links": {"self": {"href": "https://publications.scilifelab.se/publication/facbe48db3184e3b81e8b86eddbf9324.json"}, "display": {"href": "https://publications.scilifelab.se/publication/facbe48db3184e3b81e8b86eddbf9324"}}, "title": "Anaerobic Methanotrophic Archaea of the ANME-2d Cluster Are Active in a Low-sulfate, Iron-rich Freshwater Sediment.", "authors": [{"family": "Weber", "given": "Hannah S", "initials": "HS"}, {"family": "Habicht", "given": "Kirsten S", "initials": "KS"}, {"family": "Thamdrup", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2017-04-12", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": "619", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "ANaerobic MEthanotrophic (ANME) archaea remove the greenhouse gas methane from anoxic environments and diminish its flux to the atmosphere. High methane removal efficiencies are well documented in marine environments, whereas anaerobic oxidation of methane (AOM) was only recently indicated as an important methane sink in freshwater systems. Freshwater AOM-mediating microorganisms lack taxonomic identification and only little is known about metabolic adaptions to prevailing biogeochemical conditions. One of the first study sites providing information about AOM activity in freshwater sediment is Lake \u00d8rn, a low-sulfate, iron-rich Danish lake. With the aim to identify freshwater AOM-mediating archaea, we incubated AOM-active anoxic, nitrate-free freshwater sediment from Lake \u00d8rn with (13)C-labeled methane ((13)CCH4) and (13)C-labeled bicarbonate ((13)CDIC) and followed the assimilation of (13)C into RNA by stable isotope probing. While AOM was active, (13)CCH4 and probably also (13)CDIC were incorporated into uncultured archaea of the Methanosarcinales-related cluster ANME-2d, whereas other known ANME lineages were not detected. This finding strongly suggests that ANME-2d archaea perform AOM coupled to sulfate and/or iron reduction and may have the capability of mixed assimilation of CH4 and DIC. ANME-2d archaea may thus play an important role in controlling methane emissions from nitrate-depleted and low-sulfate freshwater systems.", "doi": "10.3389/fmicb.2017.00619", "pmid": "28446901", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5389135"}], "notes": [], "created": "2017-10-17T09:42:16.356Z", "modified": "2020-01-21T13:56:06.574Z"}, {"entity": "publication", "iuid": "b065ba93cc264109a62c401b02ac7cd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b065ba93cc264109a62c401b02ac7cd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b065ba93cc264109a62c401b02ac7cd9"}}, "title": "Adaptation to infectious disease exposure in indigenous Southern African populations.", "authors": [{"family": "Owers", "given": "Katharine A", "initials": "KA", "orcid": "0000-0002-5323-5079", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4357c52141940a1a68b6a241f4aa100.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-04-12", "journal": {"volume": "284", "issn": "1471-2954", "issue": "1852", "pages": "20170226", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the \u2021Khomani who had abundant contact with other people migrating into the region and the more isolated Ju|'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the \u2021Khomani than in the Ju|'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the \u2021Khomani, whereas in the Ju|'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the \u2021Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.", "doi": "10.1098/rspb.2017.0226", "pmid": "28381615", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "rspb.2017.0226"}, {"db": "pmc", "key": "PMC5394675"}], "notes": [], "created": "2018-01-09T14:01:35.720Z", "modified": "2021-07-07T10:32:33.473Z"}, {"entity": "publication", "iuid": "5b3c0a685bee4780824ad53cccfcd08c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b3c0a685bee4780824ad53cccfcd08c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b3c0a685bee4780824ad53cccfcd08c"}}, "title": "SnoN Stabilizes the SMAD3/SMAD4 Protein Complex", "authors": [{"family": "Walld\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Nyman", "given": "Tomas", "initials": "T"}, {"family": "H\u00e4llberg", "given": "B Martin", "initials": "BM"}], "type": "journal-article", "published": "2017-04-11", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "46370", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/srep46370", "pmid": "28397834", "labels": {"Protein Science Facility (PSF)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:18.362Z", "modified": "2017-11-09T13:17:11.248Z"}, {"entity": "publication", "iuid": "a08f9ad01e8e4304bb3dbff907529404", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a08f9ad01e8e4304bb3dbff907529404.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a08f9ad01e8e4304bb3dbff907529404"}}, "title": "Serglycin as a potential biomarker for glioma: association of serglycin expression, extent of mast cell recruitment and glioblastoma progression.", "authors": [{"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Attarha", "given": "Sanaz", "initials": "S"}, {"family": "Weishaupt", "given": "Holger", "initials": "H"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Siebzehnrubl", "given": "Florian A", "initials": "FA"}, {"family": "Smits", "given": "Anja", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Tchougounova", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2017-04-11", "journal": {"title": "Oncotarget", "issn": "1949-2553", "volume": "8", "issue": "15", "pages": "24815-24827", "issn-l": "1949-2553"}, "abstract": "Serglycin is an intracellular proteoglycan with a unique ability to adopt highly divergent structures by glycosylation with variable types of glycosaminoglycans (GAGs) when expressed by different cell types. Serglycin is overexpressed in aggressive cancers suggesting its protumorigenic role. In this study, we explored the expression of serglycin in human glioma and its correlation with survival and immune cell infiltration. We demonstrate that serglycin is expressed in glioma and that increased expression predicts poor survival of patients. Analysis of serglycin expression in a large cohort of low- and high-grade human glioma samples reveals that its expression is grade dependent and is positively correlated with mast cell (MC) infiltration. Moreover, serglycin expression in patient-derived glioma cells is significantly increased upon MC co-culture. This is also accompanied by increased expression of CXCL12, CXCL10, as well as markers of cancer progression, including CD44, ZEB1 and vimentin.In conclusion, these findings indicate the importance of infiltrating MCs in glioma by modulating signaling cascades involving serglycin, CD44 and ZEB1. The present investigation reveals serglycin as a potential prognostic marker for glioma and demonstrates an association with the extent of MC recruitment and glioma progression, uncovering potential future therapeutic opportunities for patients.", "doi": "10.18632/oncotarget.15820", "pmid": "28445977", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "15820"}, {"db": "pmc", "key": "PMC5421891"}], "notes": [], "created": "2017-11-05T12:41:32.340Z", "modified": "2017-11-05T12:41:32.358Z"}, {"entity": "publication", "iuid": "44ca59576a2f4e99813194b5701a4712", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44ca59576a2f4e99813194b5701a4712.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44ca59576a2f4e99813194b5701a4712"}}, "title": "Multi-label prediction of subcellular localization in confocal images using deep neural networks", "authors": [{"family": "Winsnes", "given": "C. F.", "initials": "CF", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a64c707c8b54b6bbd31dae6485a1392.json"}}, {"family": "Sullivan", "given": "D. P.", "initials": "DP", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a96138841741f9acff4a50100c2a25.json"}}, {"family": "Smith", "given": "Kevin", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}], "type": null, "published": "2017-04-10", "journal": {"title": "Molecular Biology of the Cell", "issn": "1059-1524", "issn-l": null, "volume": "27", "issue": null, "pages": null}, "abstract": null, "doi": null, "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": "https://www.diva-portal.org/smash/record.jsf?pid=diva2%3A1087739&dswid=2219", "created": "2017-11-03T07:24:53.118Z", "modified": "2025-11-17T09:58:12.856Z"}, {"entity": "publication", "iuid": "4e03b1140bb94f24a5dfc579a2902505", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e03b1140bb94f24a5dfc579a2902505.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e03b1140bb94f24a5dfc579a2902505"}}, "title": "Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function", "authors": [{"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Schillert", "given": "Arne", "initials": "A"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Chen", "given": "Ming Huei", "initials": "MH"}, {"family": "Leening", "given": "Maarten J G", "initials": "MJG"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Gro\u00dfmann", "given": "Vera", "initials": "V"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Shah", "given": "Sanjiv J", "initials": "SJ"}, {"family": "Pramana", "given": "Setia", "initials": "S"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Stanton", "given": "Alice V", "initials": "AV"}, {"family": "Malzahn", "given": "D\u00f6rthe", "initials": "D"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Minelli", "given": "Cosetta", "initials": "C"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Tiller", "given": "Daniel", "initials": "D"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Monnereau", "given": "Claire", "initials": "C"}, {"family": "Di Tullio", "given": "Marco R", "initials": "MR"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Morley", "given": "Michael", "initials": "M"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Aragam", "given": "Jayashri", "initials": "J"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Bisping", "given": "Egbert", "initials": "E"}, {"family": "Broeckel", "given": "Ulrich", "initials": "U"}, {"family": "Cheng", "given": "Susan", "initials": "S"}, {"family": "Deckers", "given": "Jaap W", "initials": "JW"}, {"family": "Del Greco M", "given": "Fabiola", "initials": "F"}, {"family": "Edelmann", "given": "Frank", "initials": "F"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Friedrich", "given": "Nele", "initials": "N"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Hughes", "given": "Alun D", "initials": "AD"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "investigators", "given": "KNHI", "initials": "K"}, {"family": "Kruppa", "given": "Jochen", "initials": "J"}, {"family": "Lackner", "given": "Karl J", "initials": "KJ"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Laskowski", "given": "Rafael", "initials": "R"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leosdottir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Lin", "given": "Honghuang", "initials": "H"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Loley", "given": "Christina", "initials": "C"}, {"family": "MacRae", "given": "Calum A", "initials": "CA"}, {"family": "Mascalzoni", "given": "Deborah", "initials": "D"}, {"family": "Mayet", "given": "Jamil", "initials": "J"}, {"family": "Medenwald", "given": "Daniel", "initials": "D"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "M\u00fcller", "given": "Christian", "initials": "C"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Nappo", "given": "Stefania", "initials": "S"}, {"family": "Nilsson", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Nuding", "given": "Sebastian", "initials": "S"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Pfeufer", "given": "Arne", "initials": "A"}, {"family": "Pietzner", "given": "Diana", "initials": "D"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Ruohonen", "given": "Saku T", "initials": "ST"}, {"family": "Sacco", "given": "Ralph L", "initials": "RL"}, {"family": "Samdarshi", "given": "Tandaw E", "initials": "TE"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Sharp", "given": "Andrew S P", "initials": "ASP"}, {"family": "Shields", "given": "Denis C", "initials": "DC"}, {"family": "Sorice", "given": "Rossella", "initials": "R"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "Thom", "given": "Simon", "initials": "S"}, {"family": "T\u00f6glhofer", "given": "Anna M", "initials": "AM"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wachter", "given": "Rolf", "initials": "R"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Ziegler", "given": "Andreas", "initials": "A"}, {"family": "M\u00fcnzel", "given": "Thomas", "initials": "T"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Cappola", "given": "Thomas P", "initials": "TP"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Mitchell", "given": "Gary F", "initials": "GF"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Dueker", "given": "Nicole D", "initials": "ND"}, {"family": "Jaddoe", "given": "Vincent W V", "initials": "VWV"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Russ", "given": "Martin", "initials": "M"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Pieske", "given": "Burkert", "initials": "B"}, {"family": "Barron", "given": "Anthony J", "initials": "AJ"}, {"family": "Zweiker", "given": "Robert", "initials": "R"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Liu", "given": "Kiang", "initials": "K"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Larson", "given": "Martin G", "initials": "MG"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}], "type": "journal-article", "published": "2017-04-10", "journal": {"volume": "127", "issn": "0021-9738", "issue": "5", "pages": "1798-1812", "title": "J Clin Invest.", "issn-l": null}, "abstract": null, "doi": "10.1172/jci84840", "pmid": "28394258", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:35.302Z", "modified": "2021-07-07T15:50:03.445Z"}, {"entity": "publication", "iuid": "f6ff44cbb6cb43d4ad682c875c41495c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6ff44cbb6cb43d4ad682c875c41495c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6ff44cbb6cb43d4ad682c875c41495c"}}, "title": "SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing.", "authors": [{"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Manlig", "given": "Erika", "initials": "E"}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2017-04-07", "journal": {"volume": "45", "issn": "1362-4962", "issue": "6", "pages": "e36", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.", "doi": "10.1093/nar/gkw1110", "pmid": "27899585", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gkw1110"}, {"db": "pmc", "key": "PMC5389478"}], "notes": [], "created": "2017-10-30T09:31:42.942Z", "modified": "2024-01-16T13:48:48.095Z"}, {"entity": "publication", "iuid": "9fd7c4c065ca4249814b1ab5b42d8246", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fd7c4c065ca4249814b1ab5b42d8246.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fd7c4c065ca4249814b1ab5b42d8246"}}, "title": "Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana", "authors": [{"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "Pendle", "given": "Ali", "initials": "A"}, {"family": "Irish", "given": "Vivian F", "initials": "VF"}, {"family": "Shaw", "given": "Peter", "initials": "P"}, {"family": "Nakayama", "given": "Naomi", "initials": "N"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}], "type": "journal-article", "published": "2017-04-07", "journal": {"volume": "45", "issn": "0305-1048", "issue": "6", "pages": "3253-3265", "title": "Nucleic Acids Res", "issn-l": null}, "abstract": null, "doi": "10.1093/nar/gkx087", "pmid": "28175342", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-04T15:14:48.141Z", "modified": "2020-01-21T13:53:21.841Z"}, {"entity": "publication", "iuid": "28528687ee0e4b6baf2aa786d22d9983", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28528687ee0e4b6baf2aa786d22d9983.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28528687ee0e4b6baf2aa786d22d9983"}}, "title": "Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.", "authors": [{"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Gonzales-Sil\u00e8s", "given": "Lucia", "initials": "L"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ER"}], "type": "journal article", "published": "2017-04-06", "journal": {"volume": "5", "issn": "2169-8287", "issue": "14", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Streptococcus pneumoniae is a pathogenic bacterium found most commonly in the respiratory tract of humans and is a common cause of pneumonia and bacterial meningitis. Here, we report the draft genome sequences of six S.\u00a0pneumoniae strains: CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG 35272.", "doi": "10.1128/genomeA.00125-17", "pmid": "28385844", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5/14/e00125-17"}, {"db": "pmc", "key": "PMC5383892"}], "notes": [], "created": "2017-11-03T16:21:51.107Z", "modified": "2024-01-16T13:48:48.105Z"}, {"entity": "publication", "iuid": "65cb7e1c59e54b4bb89c0517bccfa04f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65cb7e1c59e54b4bb89c0517bccfa04f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65cb7e1c59e54b4bb89c0517bccfa04f"}}, "title": "Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 4715", "authors": [{"family": "Moreno", "given": "Antonio D", "initials": "AD"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Olsson", "given": "Lisbeth", "initials": "L"}, {"family": "Geijer", "given": "Cecilia", "initials": "C"}], "type": "journal-article", "published": "2017-04-06", "journal": {"volume": "5", "issn": "2169-8287", "issue": "14", "pages": "e00138-17", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": null, "doi": "10.1128/genomea.00138-17", "pmid": "28385851", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:33:33.171Z", "modified": "2024-01-16T13:48:48.116Z"}, {"entity": "publication", "iuid": "e7393cb4fb5c445394eba1f7b1b6f31f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7393cb4fb5c445394eba1f7b1b6f31f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7393cb4fb5c445394eba1f7b1b6f31f"}}, "title": "dUTPase inhibition augments replication defects of 5-Fluorouracil.", "authors": [{"family": "Hagenkort", "given": "Anna", "initials": "A"}, {"family": "Paulin", "given": "Cynthia B J", "initials": "CBJ"}, {"family": "Desroses", "given": "Matthieu", "initials": "M"}, {"family": "Sarno", "given": "Antonio", "initials": "A"}, {"family": "Wiita", "given": "Elis\u00e9e", "initials": "E"}, {"family": "Mortusewicz", "given": "Oliver", "initials": "O"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "A"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "A", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-04-04", "journal": {"volume": "8", "issn": "1949-2553", "issue": "14", "pages": "23713-23726", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "The antimetabolite 5-Fluorouracil (5-FU) is used in the treatment of various forms of cancer and has a complex mode of action. Despite 6 decades in clinical application the contribution of 5-FdUTP and dUTP [(5-F)dUTP] and 5-FUTP misincorporation into DNA and RNA respectively, for 5-FU-induced toxicity is still under debate.This study investigates DNA replication defects induced by 5-FU treatment and how (5-F)dUTP accumulation contributes to this effect. We reveal that 5-FU treatment leads to extensive problems in DNA replication fork progression, causing accumulation of cells in S-phase, DNA damage and ultimately cell death. Interestingly, these effects can be reinforced by either depletion or inhibition of the deoxyuridine triphosphatase (dUTPase, also known as DUT), highlighting the importance of (5-F)dUTP accumulation for cytotoxicity.With this study, we not only extend the current understanding of the mechanism of action of 5-FU, but also contribute to the characterization of dUTPase inhibitors. We demonstrate that pharmacological inhibition of dUTPase is a promising approach that may improve the efficacy of 5-FU treatment in the clinic.", "doi": "10.18632/oncotarget.15785", "pmid": "28423595", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "15785"}, {"db": "pmc", "key": "PMC5410339"}], "notes": [], "created": "2017-10-20T15:11:22.720Z", "modified": "2025-10-17T13:04:29.288Z"}, {"entity": "publication", "iuid": "cc9a907e212c47deb1bf893bc47087c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc9a907e212c47deb1bf893bc47087c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc9a907e212c47deb1bf893bc47087c6"}}, "title": "Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia.", "authors": [{"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Olsson-Str\u00f6mberg", "given": "Ulla", "initials": "U"}, {"family": "Siart", "given": "Benjamin", "initials": "B"}, {"family": "Jansson", "given": "Mattias", "initials": "M"}, {"family": "Dahlin", "given": "Joakim S", "initials": "JS", "orcid": "0000-0003-3007-9875", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d022071f86a451aba84b18fb0774461.json"}}, {"family": "Th\u00f6rn", "given": "Ingrid", "initials": "I"}, {"family": "Christiansson", "given": "Lisa", "initials": "L"}, {"family": "Hermansson", "given": "Monica", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Ahlstrand", "given": "Erik", "initials": "E"}, {"family": "W\u00e5linder", "given": "G\u00f6ran", "initials": "G"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications.scilifelab.se/researcher/87392e51288f4ef9a38fe3989d10d180.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2017-04-04", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "623", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Chronic myeloid leukemia (CML) is characterized in the majority of cases by a t(9;22)(q34;q11) translocation, also called the Philadelphia chromosome, giving rise to the BCR-ABL1 fusion protein. Current treatment with tyrosine kinase inhibitors is directed against the constitutively active ABL1 domain of the fusion protein, and minimal residual disease (MRD) after therapy is monitored by real-time quantitative PCR (RQ-PCR) of the fusion transcript. Here, we describe a novel approach to detect and enumerate cells positive for the BCR-ABL1 fusion protein by combining the in situ proximity ligation assay with flow cytometry as readout (PLA-flow). By targeting of the BCR and ABL1 parts of the fusion protein with one antibody each, and creating strong fluorescent signals through rolling circle amplification, PLA-flow allowed sensitive detection of cells positive for the BCR-ABL1 fusion at frequencies as low as one in 10,000. Importantly, the flow cytometric results correlated strongly to those of RQ-PCR, both in diagnostic testing and for MRD measurements over time. In summary, we believe this flow cytometry-based method can serve as an attractive approach for routine measurement of cells harboring BCR-ABL1 fusions, also allowing simultaneously assessment of other cell surface markers as well as sensitive longitudinal follow-up.", "doi": "10.1038/s41598-017-00755-y", "pmid": "28377570", "labels": {"PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-00755-y"}, {"db": "pmc", "key": "PMC5429594"}], "notes": [], "created": "2017-11-02T14:39:48.739Z", "modified": "2023-04-14T13:56:15.652Z"}, {"entity": "publication", "iuid": "d312bb900a934511bde690e957e8ae4d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d312bb900a934511bde690e957e8ae4d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d312bb900a934511bde690e957e8ae4d"}}, "title": "Sulfonimidamides in Medicinal and Agricultural Chemistry", "authors": [{"family": "Chinthakindi", "given": "Praveen K", "initials": "PK"}, {"family": "Naicker", "given": "Tricia", "initials": "T"}, {"family": "Thota", "given": "Niranjan", "initials": "N"}, {"family": "Govender", "given": "Thavendran", "initials": "T"}, {"family": "Kruger", "given": "Hendrik G", "initials": "HG"}, {"family": "Arvidsson", "given": "Per I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}], "type": "journal-article", "published": "2017-04-03", "journal": {"volume": "56", "issn": "1433-7851", "issue": "15", "pages": "4100-4109", "title": "Angew. Chem. Int. Ed.", "issn-l": "1433-7851"}, "abstract": null, "doi": "10.1002/anie.201610456", "pmid": "27958674", "labels": {"Drug Discovery and Development": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T08:36:11.989Z", "modified": "2025-10-17T13:05:08.969Z"}, {"entity": "publication", "iuid": "280aae409a56481ab2cf2f46ae4d91fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/280aae409a56481ab2cf2f46ae4d91fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/280aae409a56481ab2cf2f46ae4d91fc"}}, "title": "Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.", "authors": [{"family": "Nielsen", "given": "Jens Christian", "initials": "JC", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Grijseels", "given": "Sietske", "initials": "S"}, {"family": "Prigent", "given": "Sylvain", "initials": "S"}, {"family": "Ji", "given": "Boyang", "initials": "B"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Nielsen", "given": "Kristian Fog", "initials": "KF"}, {"family": "Frisvad", "given": "Jens Christian", "initials": "JC"}, {"family": "Workman", "given": "Mhairi", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2017-04-03", "journal": {"volume": "2", "issn": "2058-5276", "issue": null, "pages": "17044", "title": "Nat Microbiol", "issn-l": "2058-5276"}, "abstract": "Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were identified, and polyketide synthase and non-ribosomal peptide synthetase based BGCs were grouped into gene cluster families and mapped to known pathways. The grouping of BGCs allowed us to study the evolutionary trajectory of pathways based on 6-methylsalicylic acid (6-MSA) synthases. Finally, we cross-referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic diversity of Penicillia and highlights the potential of these species as a source of new antibiotics and other pharmaceuticals.", "doi": "10.1038/nmicrobiol.2017.44", "pmid": "28368369", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nmicrobiol201744"}], "notes": [], "created": "2019-01-15T07:55:00.878Z", "modified": "2021-07-05T13:05:37.577Z"}, {"entity": "publication", "iuid": "0f57098db42146e397e63e366a3d1347", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f57098db42146e397e63e366a3d1347.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f57098db42146e397e63e366a3d1347"}}, "title": "Total body fat, abdominal fat, body fat distribution and surrogate markers for health related to adipocyte fatty acid-binding protein (FABP4) in children.", "authors": [{"family": "Dencker", "given": "Magnus", "initials": "M"}, {"family": "Danielson", "given": "Anton", "initials": "A"}, {"family": "Karlsson", "given": "Magnus K", "initials": "MK"}, {"family": "Wollmer", "given": "Per", "initials": "P"}, {"family": "Andersen", "given": "Lars B", "initials": "LB"}, {"family": "Thorsson", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2017-04-01", "journal": {"title": "J Pediatr Endocrinol Metab", "issn": "2191-0251", "issn-l": null, "volume": "30", "issue": "4", "pages": "375-382"}, "abstract": "The aim of the study was to assess possible relationships between adipocyte fatty acid-binding protein (FABP4) and total body fat (TBF), abdominal fat, body fat distribution, aerobic fitness, blood pressure, cardiac dimensions and the increase in body fat over 2 years in a community sample of children.\n\nA cross-sectional study was used in a community sample of 170 (92 boys and 78 girls) children aged 8-11 years. TBF and abdominal fat (AFM) were measured by dual-energy X-ray absorptiometry (DXA). TBF was also expressed as percentage of total body mass (BF%), and body fat distribution was calculated as AFM/TBF. Maximal oxygen uptake (VO2PEAK) was assessed by indirect calorimetry during a maximal exercise test and scaled to body mass. Systolic and diastolic blood pressure (SBP and DBP) and pulse pressure (PP) were measured. Echocardiography was performed. Left atrial (LA) size was measured, and left ventricular mass (LVM) was calculated. A follow-up DXA scan was available in 152 children (84 boys and 68 girls). Frozen serum samples were analyzed for FABP4.\n\nPartial correlations, with adjustment for sex, between FABP4 vs. ln TBF, ln BF%, ln AFM, AFM/TBF and VO2PEAK were (r=0.69, 0.68, 0.69, 0.49 and -0.39, p<0.05 for all). Moreover, SBP, PP, LVM and LA were also weakly correlated with FABP4 (r=0.23, 0.22, 0.28 and 0.21, p<0.05 for all). Correlations between FABP4 vs. increase in TBF and AFM over 2 years were 0.29 and 0.26, p<0.05, for both. (Increase in percent body fat or change in fat distribution were not correlated.) Conclusions: Findings from this community-based cohort of young children show that increased body fat and abdominal fat, more abdominal body fat distribution, low fitness, more LVM and increased LA, increased SBP and PP were all associated with increased levels of FABP4. Increase in TBF and abdominal fat over 2 years were also associated with increased levels of FABP4.", "doi": "10.1515/jpem-2016-0278", "pmid": "28085673", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "/j/jpem.2017.30.issue-4/jpem-2016-0278/jpem-2016-0278.xml"}], "notes": [], "created": "2020-01-23T15:13:41.578Z", "modified": "2023-04-14T13:56:15.847Z"}, {"entity": "publication", "iuid": "e59d31431a4d47d4a41b71c2023ffce6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e59d31431a4d47d4a41b71c2023ffce6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e59d31431a4d47d4a41b71c2023ffce6"}}, "title": "Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer.", "authors": [{"family": "Mathot", "given": "Lucy", "initials": "L"}, {"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Svedlund", "given": "Jessica", "initials": "J"}, {"family": "Moens", "given": "Lotte", "initials": "L"}, {"family": "Adlerteg", "given": "Tom", "initials": "T"}, {"family": "Falk-S\u00f6rqvist", "given": "Elin", "initials": "E"}, {"family": "Rendo", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Bellomo", "given": "Claudia", "initials": "C"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Cortina", "given": "Carme", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Magnus", "initials": "M"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A"}, {"family": "Batlle", "given": "Eduard", "initials": "E"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2017-04-01", "journal": {"volume": "77", "issn": "1538-7445", "issue": "7", "pages": "1730-1740", "title": "Cancer Res.", "issn-l": "0008-5472"}, "abstract": "The contribution of somatic mutations to metastasis of colorectal cancers is currently unknown. To find mutations involved in the colorectal cancer metastatic process, we performed deep mutational analysis of 676 genes in 107 stages II to IV primary colorectal cancer, of which half had metastasized. The mutation prevalence in the ephrin (EPH) family of tyrosine kinase receptors was 10-fold higher in primary tumors of metastatic colorectal than in nonmetastatic cases and preferentially occurred in stage III and IV tumors. Mutational analyses in situ confirmed expression of mutant EPH receptors. To enable functional studies of EPHB1 mutations, we demonstrated that DLD-1 colorectal cancer cells expressing EPHB1 form aggregates upon coculture with ephrin B1 expressing cells. When mutations in the fibronectin type III and kinase domains of EPHB1 were compared with wild-type EPHB1 in DLD-1 colorectal cancer cells, they decreased ephrin B1-induced compartmentalization. These observations provide a mechanistic link between EPHB receptor mutations and metastasis in colorectal cancer. Cancer Res; 77(7); 1730-40. \u00a92017 AACR.", "doi": "10.1158/0008-5472.CAN-16-1921", "pmid": "28108514", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-16-1921"}], "notes": [], "created": "2017-10-31T09:02:56.400Z", "modified": "2021-07-07T13:54:46.167Z"}, {"entity": "publication", "iuid": "b672cfafccdb450093604f54c0d0dc48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b672cfafccdb450093604f54c0d0dc48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b672cfafccdb450093604f54c0d0dc48"}}, "title": "Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses.", "authors": [{"family": "Niklasson", "given": "Mia", "initials": "M"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Sramkova", "given": "Zuzana", "initials": "Z"}, {"family": "Mutlu", "given": "Ercan", "initials": "E"}, {"family": "Wee", "given": "Shimei", "initials": "S"}, {"family": "Sekyrova", "given": "Petra", "initials": "P"}, {"family": "Schmidt", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Fritz", "given": "Nicolas", "initials": "N"}, {"family": "Dehnisch", "given": "Ivar", "initials": "I"}, {"family": "Kyriatzis", "given": "Gregorios", "initials": "G"}, {"family": "Krafcikova", "given": "Michaela", "initials": "M"}, {"family": "Carson", "given": "Brittany B", "initials": "BB"}, {"family": "Feenstra", "given": "Jennifer M", "initials": "JM"}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD"}, {"family": "Segerman", "given": "Anna", "initials": "A"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Hammarstr\u00f6m", "given": "Lars G J", "initials": "LG"}, {"family": "Jenmalm Jensen", "given": "Annika", "initials": "A"}, {"family": "Uhrbom", "given": "Lene", "initials": "L"}, {"family": "Altelaar", "given": "A F Maarten", "initials": "AF"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P"}, {"family": "Trantirek", "given": "Lukas", "initials": "L"}, {"family": "Vincent", "given": "C Theresa", "initials": "CT"}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Enger", "given": "Per \u00d8yvind", "initials": "P\u00d8"}, {"family": "And\u00e4ng", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2017-04-01", "journal": {"volume": "77", "issn": "1538-7445", "issue": "7", "pages": "1741-1752", "title": "Cancer Res.", "issn-l": "0008-5472"}, "abstract": "Glioma-initiating cells (GIC) are considered the underlying cause of recurrences of aggressive glioblastomas, replenishing the tumor population and undermining the efficacy of conventional chemotherapy. Here we report the discovery that inhibiting T-type voltage-gated Ca2+ and KCa channels can effectively induce selective cell death of GIC and increase host survival in an orthotopic mouse model of human glioma. At present, the precise cellular pathways affected by the drugs affecting these channels are unknown. However, using cell-based assays and integrated proteomics, phosphoproteomics, and transcriptomics analyses, we identified the downstream signaling events these drugs affect. Changes in plasma membrane depolarization and elevated intracellular Na+, which compromised Na+-dependent nutrient transport, were documented. Deficits in nutrient deficit acted in turn to trigger the unfolded protein response and the amino acid response, leading ultimately to nutrient starvation and GIC cell death. Our results suggest new therapeutic targets to attack aggressive gliomas. Cancer Res; 77(7); 1741-52. \u00a92017 AACR.", "doi": "10.1158/0008-5472.CAN-16-2274", "pmid": "28087597", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-16-2274"}], "notes": [], "created": "2017-10-20T15:10:26.209Z", "modified": "2025-10-17T13:04:29.305Z"}, {"entity": "publication", "iuid": "8315872149d64774893689fec33af1a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8315872149d64774893689fec33af1a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8315872149d64774893689fec33af1a5"}}, "title": "Interactions of Freshwater Cyanobacteria with Bacterial Antagonists", "authors": [{"family": "Osman", "given": "Omneya Ahmed", "initials": "OA"}, {"family": "Beier", "given": "Sara", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2017-04-01", "journal": {"volume": "83", "issn": "1098-5336", "issue": "7", "pages": "e02634-16", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": null, "doi": "10.1128/aem.02634-16", "pmid": "28115385", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:28:59.730Z", "modified": "2024-01-16T13:48:48.128Z"}, {"entity": "publication", "iuid": "ba007b2d5ca14d3984538e92b244bfa6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba007b2d5ca14d3984538e92b244bfa6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba007b2d5ca14d3984538e92b244bfa6"}}, "title": "Identification and quantification of even and odd chained 5-n alkylresorcinols, branched chain-alkylresorcinols and methylalkylresorcinols in Quinoa (Chenopodium quinoa).", "authors": [{"family": "Ross", "given": "Alastair B", "initials": "AB"}, {"family": "Svelander", "given": "Cecilia", "initials": "C"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1821-4715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6463abd05b415696c52be577ca2be6.json"}}, {"family": "Savolainen", "given": "Otto I", "initials": "OI"}], "type": "journal article", "published": "2017-04-01", "journal": {"volume": "220", "issn": "1873-7072", "issue": null, "pages": "344-351", "title": "Food Chem", "issn-l": "0308-8146"}, "abstract": "Quinoa is a pseudocereal grown in the Andean region of South America that is of increasing interest worldwide as an alternative staple food. We have detected a complex mixture of both odd- and even-alkyl chain alkylresorcinols (AR), branched-chain alkylresorcinols (bcAR) and methylalkylresorcinols (mAR) in ethyl acetate extracts of quinoa. We quantified the content of AR in 17 commercial samples of quinoa, and found that the mean\u00b1SD content of AR was 58\u00b116\u03bcg/g, bcAR was 182\u00b152\u03bcg/g, and mAR was 136\u00b140\u03bcg/g. AR from quinoa could also be detected in plasma after eating quinoa, indicating that some of these unique AR could be used as biomarkers of quinoa intake in humans. Further work is required to understand the role of these ARs in the quinoa plant and whether any of the novel ARs may be of particular interest in human nutrition.", "doi": "10.1016/j.foodchem.2016.10.020", "pmid": "27855910", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0308-8146(16)31637-5"}], "notes": [], "created": "2017-05-03T13:02:48.593Z", "modified": "2025-10-17T13:03:59.940Z"}, {"entity": "publication", "iuid": "f9e58a2d79d54634826b3cb1e0ee42c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9e58a2d79d54634826b3cb1e0ee42c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9e58a2d79d54634826b3cb1e0ee42c6"}}, "title": "Green listed\u2014a CRISPR screen tool", "authors": [{"family": "Panda", "given": "Sudeepta Kumar", "initials": "SK"}, {"family": "Boddul", "given": "Sanjay V", "initials": "SV"}, {"family": "Jim\u00e9nez-Andrade", "given": "Guillermina Yanek", "initials": "GY"}, {"family": "Jiang", "given": "Long", "initials": "L"}, {"family": "Kasza", "given": "Zsolt", "initials": "Z"}, {"family": "Fernandez-Ricaud", "given": "Luciano", "initials": "L"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F"}], "type": "journal-article", "published": "2017-04-01", "journal": {"volume": "33", "issn": "1367-4803", "issue": "7", "pages": "1099-1100", "title": "Bioinformatics", "issn-l": null}, "abstract": null, "doi": "10.1093/bioinformatics/btw739", "pmid": "28414855", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:35:56.233Z", "modified": "2020-01-21T13:53:22.688Z"}, {"entity": "publication", "iuid": "99c4a012bd934c289bd13c457c63189a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99c4a012bd934c289bd13c457c63189a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99c4a012bd934c289bd13c457c63189a"}}, "title": "Discrimination of pancreatic cancer and pancreatitis by LC-MS metabolomics.", "authors": [{"family": "Lindahl", "given": "Anna", "initials": "A"}, {"family": "Heuchel", "given": "Rainer", "initials": "R"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "L\u00f6hr", "given": "Matthias", "initials": "M"}, {"family": "Nordstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0003-3676-817X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b1803a3f7624f0d82abd552448bdaed.json"}}], "type": "journal article", "published": "2017-04-01", "journal": {"volume": "13", "issn": "1573-3882", "issue": "5", "pages": "61", "title": "Metabolomics", "issn-l": null}, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is the fifth most common cause of cancer-related death in Europe with a 5-year survival rate of <5%. Chronic pancreatitis (CP) is a risk factor for PDAC development, but in the majority of cases malignancy is discovered too late for curative treatment. There is at present no reliable diagnostic marker for PDAC available.\n\nThe aim of the study was to identify single blood-based metabolites or a panel of metabolites discriminating PDAC and CP using liquid chromatography-mass spectrometry (LC-MS).\n\nA discovery cohort comprising PDAC (n = 44) and CP (n = 23) samples was analyzed by LC-MS followed by univariate (Student's t test) and multivariate (orthogonal partial least squares-discriminant analysis (OPLS-DA)) statistics. Discriminative metabolite features were subject to raw data examination and identification to ensure high feature quality. Their discriminatory power was then confirmed in an independent validation cohort including PDAC (n = 20) and CP (n = 31) samples.\n\nGlycocholic acid, N-palmitoyl glutamic acid and hexanoylcarnitine were identified as single markers discriminating PDAC and CP by univariate analysis. OPLS-DA resulted in a panel of five metabolites including the aforementioned three metabolites as well as phenylacetylglutamine (PAGN) and chenodeoxyglycocholate.\n\nUsing LC-MS-based metabolomics we identified three single metabolites and a five-metabolite panel discriminating PDAC and CP in two independent cohorts. Although further study is needed in larger cohorts, the metabolites identified are potentially of use in PDAC diagnostics.", "doi": "10.1007/s11306-017-1199-6", "pmid": "28413374", "labels": {"Clinical Proteomics Mass spectrometry": "Service", "Global Proteomics and Proteogenomics": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "1199"}, {"db": "pmc", "key": "PMC5376388"}], "notes": [], "created": "2017-12-05T16:14:27.928Z", "modified": "2025-10-17T13:03:18.911Z"}, {"entity": "publication", "iuid": "805eaa34c87f47998780736a864788c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/805eaa34c87f47998780736a864788c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/805eaa34c87f47998780736a864788c7"}}, "title": "Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis", "authors": [{"family": "Volkov", "given": "Petr", "initials": "P"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "Ofori", "given": "Jones K", "initials": "JK"}, {"family": "Esguerra", "given": "Jonathan Lou S", "initials": "JLS"}, {"family": "Eliasson", "given": "Lena", "initials": "L"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "66", "issn": "1939-327X", "issue": "4", "pages": "1074-1085", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": null, "doi": "10.2337/db16-0996", "pmid": "28052964", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:37:34.478Z", "modified": "2024-01-16T13:48:48.141Z"}, {"entity": "publication", "iuid": "fa9dc30e92324f51a6af8689a8b622fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa9dc30e92324f51a6af8689a8b622fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa9dc30e92324f51a6af8689a8b622fc"}}, "title": "The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data.", "authors": [{"family": "Liu", "given": "Yan", "initials": "Y"}, {"family": "McBride", "given": "Ryan", "initials": "R"}, {"family": "Stoll", "given": "Mark", "initials": "M"}, {"family": "Palma", "given": "Angelina S", "initials": "AS"}, {"family": "Silva", "given": "Lisete", "initials": "L"}, {"family": "Agravat", "given": "Sanjay", "initials": "S"}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF"}, {"family": "Campbell", "given": "Matthew P", "initials": "MP"}, {"family": "Costello", "given": "Catherine E", "initials": "CE"}, {"family": "Dell", "given": "Anne", "initials": "A"}, {"family": "Haslam", "given": "Stuart M", "initials": "SM"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Khoo", "given": "Kay-Hooi", "initials": "KH"}, {"family": "Kolarich", "given": "Daniel", "initials": "D"}, {"family": "Novotny", "given": "Milos V", "initials": "MV"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "Ranzinger", "given": "Rene", "initials": "R"}, {"family": "Rapp", "given": "Erdmann", "initials": "E"}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}, {"family": "Struwe", "given": "Weston B", "initials": "WB"}, {"family": "Tiemeyer", "given": "Michael", "initials": "M"}, {"family": "Wells", "given": "Lance", "initials": "L"}, {"family": "York", "given": "William S", "initials": "WS"}, {"family": "Zaia", "given": "Joseph", "initials": "J"}, {"family": "Kettner", "given": "Carsten", "initials": "C"}, {"family": "Paulson", "given": "James C", "initials": "JC"}, {"family": "Feizi", "given": "Ten", "initials": "T"}, {"family": "Smith", "given": "David F", "initials": "DF"}], "type": "editorial", "published": "2017-04-00", "journal": {"volume": "27", "issn": "1460-2423", "issue": "4", "pages": "280-284", "title": "Glycobiology", "issn-l": "0959-6658"}, "abstract": "MIRAGE (Minimum Information Required for A Glycomics Experiment) is an initiative that was created by experts in the fields of glycobiology, glycoanalytics and glycoinformatics to produce guidelines for reporting results from the diverse types of experiments and analyses used in structural and functional studies of glycans in the scientific literature. As a sequel to the guidelines for sample preparation (Struwe et al. 2016, Glycobiology, 26:907-910) and mass spectrometry data (Kolarich et al. 2013, Mol. Cell Proteomics, 12:991-995), here we present the first version of guidelines intended to improve the standards for reporting data from glycan microarray analyses. For each of eight areas in the workflow of a glycan microarray experiment, we provide guidelines for the minimal information that should be provided in reporting results. We hope that the MIRAGE glycan microarray guidelines proposed here will gain broad acceptance by the community, and will facilitate interpretation and reproducibility of the glycan microarray results with implications in comparison of data from different laboratories and eventual deposition of glycan microarray data in international databases.", "doi": "10.1093/glycob/cww118", "pmid": "27993942", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "cww118"}, {"db": "pmc", "key": "PMC5444268"}], "notes": [], "created": "2020-01-30T16:19:32.804Z", "modified": "2024-01-16T13:46:32.762Z"}, {"entity": "publication", "iuid": "96d79977d425484089c430c1e76e7b73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96d79977d425484089c430c1e76e7b73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96d79977d425484089c430c1e76e7b73"}}, "title": "The anti-inflammatory compound palmitoylethanolamide inhibits prostaglandin and hydroxyeicosatetraenoic acid production by a macrophage cell line", "authors": [{"family": "Gabrielsson", "given": "Linda", "initials": "L"}, {"family": "Gouveia-Figueira", "given": "Sandra", "initials": "S"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jenny", "initials": "J"}, {"family": "Alhouayek", "given": "Mireille", "initials": "M"}, {"family": "Fowler", "given": "Christopher J", "initials": "CJ"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "5", "issn": "2052-1707", "issue": "2", "pages": "e00300", "title": "Pharmacol Res Perspect", "issn-l": "2052-1707"}, "abstract": null, "doi": "10.1002/prp2.300", "pmid": "28357126", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:31:56.969Z", "modified": "2025-10-17T13:03:18.950Z"}, {"entity": "publication", "iuid": "6667a9d478164c91a94c46639106a5c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6667a9d478164c91a94c46639106a5c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6667a9d478164c91a94c46639106a5c3"}}, "title": "Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands", "authors": [{"family": "Kyaschenko", "given": "Julia", "initials": "J"}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE"}, {"family": "Hagenbo", "given": "Andreas", "initials": "A"}, {"family": "Karltun", "given": "Erik", "initials": "E"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "4", "pages": "863-874", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": null, "doi": "10.1038/ismej.2016.184", "pmid": "28085155", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T16:09:20.930Z", "modified": "2024-01-16T13:48:48.149Z"}, {"entity": "publication", "iuid": "1576c2ab0a0b437b901c47aed34c1475", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1576c2ab0a0b437b901c47aed34c1475.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1576c2ab0a0b437b901c47aed34c1475"}}, "title": "Porosity investigation of yttria-stabilized zirconia topcoats using NMR cryoporometry", "authors": [{"family": "Ekberg", "given": "Johanna", "initials": "J", "orcid": "0000-0001-9572-1780", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ce9ca9900fa40d5bb11971b06ff1db2.json"}}, {"family": "Nordstierna", "given": "Lars", "initials": "L"}, {"family": "Klement", "given": "Uta", "initials": "U", "orcid": "0000-0002-8945-3799", "researcher": {"href": "https://publications.scilifelab.se/researcher/e37ab9d01d334c049d2ed7d3042734e1.json"}}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "315", "issn": "0257-8972", "issue": null, "pages": "468-474", "title": "Surface and Coatings Technology", "issn-l": null}, "abstract": null, "doi": "10.1016/j.surfcoat.2017.02.067", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T11:01:04.892Z", "modified": "2025-10-17T13:03:59.952Z"}, {"entity": "publication", "iuid": "6687d42602c44a1cb27d7f8eef8b418c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6687d42602c44a1cb27d7f8eef8b418c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6687d42602c44a1cb27d7f8eef8b418c"}}, "title": "Neonatal Cord Blood Oxylipins and Exposure to Particulate Matter in the Early-Life Environment: An ENVIRONAGE Birth Cohort Study.", "authors": [{"family": "Martens", "given": "Dries S", "initials": "DS"}, {"family": "Gouveia", "given": "Sandra", "initials": "S"}, {"family": "Madhloum", "given": "Narjes", "initials": "N"}, {"family": "Janssen", "given": "Bram G", "initials": "BG"}, {"family": "Plusquin", "given": "Michelle", "initials": "M"}, {"family": "Vanpoucke", "given": "Charlotte", "initials": "C"}, {"family": "Lefebvre", "given": "Wouter", "initials": "W"}, {"family": "Forsberg", "given": "Bertil", "initials": "B"}, {"family": "Nording", "given": "Malin", "initials": "M"}, {"family": "Nawrot", "given": "Tim S", "initials": "TS"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "125", "issn": "1552-9924", "issue": "4", "pages": "691-698", "title": "Environ. Health Perspect.", "issn-l": "0091-6765"}, "abstract": "As part of the lipidome, oxylipins are bioactive lipid compounds originating from oxidation of different fatty acids. Oxylipins could provide a new target in the developmental origins model or the ability of early life exposure to change biology.\r\n\r\nWe studied the association between in utero PM2.5 (particulate matter with aerodynamic diameter < 2.5 \u03bcm) exposure and oxylipin profiles in newborns.\r\n\r\nThirty-seven oxylipins reflecting the cyclooxygenase (COX), lipoxygenase (5-LOX and 12/15-LOX), and cytochrome P450 (CYP) pathways were assayed in 197 cord blood plasma samples from the ENVIRONAGE birth cohort. Principal component (PC) analysis and multiple regression models were used to estimate associations of in utero PM2.5 exposure with oxylipin pathways and individual metabolites.\r\n\r\nA principal component representing the 5-LOX pathway (6 metabolites) was significantly positively associated with PM2.5 exposure during the entire (multiple testing-adjusted q-value = 0.05) and second trimester of pregnancy (q = 0.05). A principal component representing the 12/15-LOX pathway (11 metabolites) was positively associated with PM2.5 exposure during the second trimester of pregnancy (q = 0.05). PM2.5 was not significantly associated with the COX pathway during any time period. There was a positive but nonsignificant association between second-trimester PM2.5 and the CYP pathway (q = 0.16).\r\n\r\nIn utero exposure to particulate matter, particularly during the second trimester, was associated with differences in the cord blood levels of metabolites derived from the lipoxygenase pathways. These differences may indicate an effect of air pollution during in utero life on the inflammatory state of the newborn at birth. Oxylipins may be important mediators between early life exposures and health outcomes later in life.", "doi": "10.1289/EHP291", "pmid": "27814242", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "EHP291"}, {"db": "pmc", "key": "PMC5381981"}], "notes": [], "created": "2017-05-03T12:59:41.769Z", "modified": "2025-10-17T13:03:18.959Z"}, {"entity": "publication", "iuid": "3833bdb907964e41b9acfb00520e1629", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3833bdb907964e41b9acfb00520e1629.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3833bdb907964e41b9acfb00520e1629"}}, "title": "Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease.", "authors": [{"family": "Folkersen", "given": "Lasse", "initials": "L", "orcid": "0000-0003-0708-9530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7202a83ff6484d5c9d77f448f93c6520.json"}}, {"family": "Fauman", "given": "Eric", "initials": "E", "orcid": "0000-0002-9739-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/33640d6d585f4715ad0754af256954fd.json"}}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M", "orcid": "0000-0002-0128-379X", "researcher": {"href": "https://publications.scilifelab.se/researcher/588239fdbde94de0b5de738fd9c7a8a9.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D", "orcid": "0000-0002-2766-8882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c131cad5784434eb16cf720f7964ecb.json"}}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Humphries", "given": "Steve E", "initials": "SE", "orcid": "0000-0002-8221-6547", "researcher": {"href": "https://publications.scilifelab.se/researcher/7669b620701f4ebd97f91594c9a4989e.json"}}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}, {"family": "Enroth", "given": "Sofia Bosdotter", "initials": "SB"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "IMPROVE study group", "given": "", "initials": ""}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Brunak", "given": "S\u00f8ren", "initials": "S"}, {"family": "Eriksson", "given": "Per", "initials": "P", "orcid": "0000-0002-5635-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/247b26c7360d4032b9cecc81bfac3ed0.json"}}, {"family": "Ziemek", "given": "Daniel", "initials": "D"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "13", "issue": "4", "pages": "e1006706"}, "abstract": "Recent advances in highly multiplexed immunoassays have allowed systematic large-scale measurement of hundreds of plasma proteins in large cohort studies. In combination with genotyping, such studies offer the prospect to 1) identify mechanisms involved with regulation of protein expression in plasma, and 2) determine whether the plasma proteins are likely to be causally implicated in disease. We report here the results of genome-wide association (GWA) studies of 83 proteins considered relevant to cardiovascular disease (CVD), measured in 3,394 individuals with multiple CVD risk factors. We identified 79 genome-wide significant (p<5e-8) association signals, 55 of which replicated at P<0.0007 in separate validation studies (n = 2,639 individuals). Using automated text mining, manual curation, and network-based methods incorporating information on expression quantitative trait loci (eQTL), we propose plausible causal mechanisms for 25 trans-acting loci, including a potential post-translational regulation of stem cell factor by matrix metalloproteinase 9 and receptor-ligand pairs such as RANK-RANK ligand. Using public GWA study data, we further evaluate all 79 loci for their causal effect on coronary artery disease, and highlight several potentially causal associations. Overall, a majority of the plasma proteins studied showed evidence of regulation at the genetic level. Our results enable future studies of the causal architecture of human disease, which in turn should aid discovery of new drug targets.", "doi": "10.1371/journal.pgen.1006706", "pmid": "28369058", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-16-01965"}, {"db": "pmc", "key": "PMC5393901"}], "notes": [], "created": "2017-10-25T15:18:21.171Z", "modified": "2024-01-16T13:48:48.159Z"}, {"entity": "publication", "iuid": "3732dbfca4754a68811b2c295b9cc6d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3732dbfca4754a68811b2c295b9cc6d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3732dbfca4754a68811b2c295b9cc6d2"}}, "title": "Lipid response patterns in acute phase paediatric Plasmodium falciparum malaria", "authors": [{"family": "Orikiiriza", "given": "Judy", "initials": "J"}, {"family": "Surowiec", "given": "Izabella", "initials": "I"}, {"family": "Lindquist", "given": "Elisabeth", "initials": "E"}, {"family": "Bonde", "given": "Mari", "initials": "M"}, {"family": "Magambo", "given": "Jimmy", "initials": "J"}, {"family": "Muhinda", "given": "Charles", "initials": "C"}, {"family": "Bergstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Normark", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "13", "issn": "1573-3882", "issue": "4", "pages": null, "title": "Metabolomics", "issn-l": null}, "abstract": null, "doi": "10.1007/s11306-017-1174-2", "pmid": "28286460", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:34:17.045Z", "modified": "2025-10-17T13:03:18.973Z"}, {"entity": "publication", "iuid": "982044cf67514ddeb9751b625529811b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/982044cf67514ddeb9751b625529811b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/982044cf67514ddeb9751b625529811b"}}, "title": "Intranasal C3a treatment ameliorates cognitive impairment in a mouse model of neonatal hypoxic-ischemic brain injury.", "authors": [{"family": "Mor\u00e1n", "given": "Javier", "initials": "J"}, {"family": "Stokowska", "given": "Anna", "initials": "A", "orcid": "0000-0001-5237-3341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba5e258c6d934db08ed52a70cf6da7b9.json"}}, {"family": "Walker", "given": "Frederik R", "initials": "FR"}, {"family": "Mallard", "given": "Carina", "initials": "C", "orcid": "0000-0001-8953-919X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d0fa7de10554b5bb5a0e1ee64902aa1.json"}}, {"family": "Hagberg", "given": "Henrik", "initials": "H"}, {"family": "Pekna", "given": "Marcela", "initials": "M", "orcid": "0000-0003-2734-8237", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf0f51a8f05b4e659ba192642603a7d6.json"}}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "Exp. Neurol.", "issn": "1090-2430", "volume": "290", "issue": null, "pages": "74-84", "issn-l": "0014-4886"}, "abstract": "Perinatal asphyxia-induced brain injury is often associated with irreversible neurological complications such as intellectual disability and cerebral palsy but available therapies are limited. Novel neuroprotective therapies as well as approaches stimulating neural plasticity mechanism that can compensate for cell death after hypoxia-ischemia (HI) are urgently needed. We previously reported that single i.c.v. injection of complement-derived peptide C3a 1h after HI induction prevented HI-induced cognitive impairment when mice were tested as adults. Here, we tested the effects of intranasal treatment with C3a on HI-induced cognitive deficit. Using the object recognition test, we found that intranasal C3a treated mice were protected from HI-induced impairment of memory function assessed 6weeks after HI induction. C3a treatment ameliorated HI-induced reactive gliosis in the hippocampus, while it did not affect the extent of hippocampal tissue loss, neuronal cell density, expression of the pan-synaptic marker synapsin I or the expression of growth associated protein 43. In conclusion, our results reveal that brief pharmacological treatment with C3a using a clinically feasible non-invasive mode of administration ameliorates HI-induced cognitive impairment. Intranasal administration is a plausible route to deliver C3a into the brain of asphyxiated infants at high risk of developing hypoxic-ischemic encephalopathy.", "doi": "10.1016/j.expneurol.2017.01.001", "pmid": "28062175", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4886(17)30001-8"}], "notes": [], "created": "2020-01-23T16:35:48.152Z", "modified": "2021-06-21T15:40:51.853Z"}, {"entity": "publication", "iuid": "169c93a475fe4ef59a84000416d5f96c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/169c93a475fe4ef59a84000416d5f96c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/169c93a475fe4ef59a84000416d5f96c"}}, "title": "Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.", "authors": [{"family": "Kalanxhi", "given": "Erta", "initials": "E"}, {"family": "Risberg", "given": "Karianne", "initials": "K"}, {"family": "Barua", "given": "Imon S", "initials": "IS"}, {"family": "Dueland", "given": "Svein", "initials": "S"}, {"family": "Waagene", "given": "Stein", "initials": "S"}, {"family": "Andersen", "given": "Solveig Norheim", "initials": "SN"}, {"family": "Pettersen", "given": "Solveig J", "initials": "SJ"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Redalen", "given": "Kathrine R\u00f8e", "initials": "KR"}, {"family": "Flatmark", "given": "Kjersti", "initials": "K"}, {"family": "Ree", "given": "Anne Hansen", "initials": "AH"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "49", "issn": "2005-9256", "issue": "2", "pages": "374-386", "title": "Cancer Res Treat", "issn-l": "1598-2998"}, "abstract": "When integrating molecularly targeted compounds in radiotherapy, synergistic effects of the systemic agent and radiation may extend the limits of patient tolerance, increasing the demand for understanding the pathophysiological mechanisms of treatment toxicity. In this Pelvic Radiation and Vorinostat (PRAVO) study, we investigated mechanisms of adverse effects in response to the histone deacetylase (HDAC) inhibitor vorinostat (suberoylanilide hydroxamic acid, SAHA) when administered as a potential radiosensitiser.\n\nThis phase I study for advanced gastrointestinal carcinoma was conducted in sequential patient cohorts exposed to escalating doses of vorinostat combined with standard-fractionated palliative radiotherapy to pelvic target volumes. Gene expression microarray analysis of the study patient peripheral blood mononuclear cells (PBMC) was followed by functional validation in cultured cell lines and mice treated with SAHA.\n\nPBMC transcriptional responses to vorinostat, including induction of apoptosis, were confined to the patient cohort reporting dose-limiting intestinal toxicities. At relevant SAHA concentrations, apoptotic features (annexin V staining and caspase 3/7 activation, but not poly-(ADP-ribose)-polymerase cleavage) were observed in cultured intestinal epithelial cells. Moreover, SAHA-treated mice displayed significant weight loss.\n\nThe PRAVO study design implemented a strategy to explore treatment toxicity caused by an HDAC inhibitor when combined with radiotherapy and enabled the identification of apoptosis as a potential mechanism responsible for the dose-limiting effects of vorinostat. To the best of our knowledge, this is the first report deciphering mechanisms of normal tissue adverse effects in response to an HDAC inhibitor within a combined-modality treatment regimen.", "doi": "10.4143/crt.2016.080", "pmid": "27488871", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "crt.2016.080"}], "notes": [], "created": "2017-05-03T13:00:51.305Z", "modified": "2021-07-05T12:48:15.941Z"}, {"entity": "publication", "iuid": "5eb65d942fee44e4ba15ee7af3f02ee3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eb65d942fee44e4ba15ee7af3f02ee3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eb65d942fee44e4ba15ee7af3f02ee3"}}, "title": "HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.", "authors": [{"family": "Davies", "given": "Helen", "initials": "H"}, {"family": "Glodzik", "given": "Dominik", "initials": "D"}, {"family": "Morganella", "given": "Sandro", "initials": "S"}, {"family": "Yates", "given": "Lucy R", "initials": "LR"}, {"family": "Staaf", "given": "Johan", "initials": "J"}, {"family": "Zou", "given": "Xueqing", "initials": "X"}, {"family": "Ramakrishna", "given": "Manasa", "initials": "M"}, {"family": "Martin", "given": "Sancha", "initials": "S"}, {"family": "Boyault", "given": "Sandrine", "initials": "S"}, {"family": "Sieuwerts", "given": "Anieta M", "initials": "AM"}, {"family": "Simpson", "given": "Peter T", "initials": "PT"}, {"family": "King", "given": "Tari A", "initials": "TA"}, {"family": "Raine", "given": "Keiran", "initials": "K"}, {"family": "Eyfjord", "given": "Jorunn E", "initials": "JE"}, {"family": "Kong", "given": "Gu", "initials": "G"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Birney", "given": "Ewan", "initials": "E"}, {"family": "Stunnenberg", "given": "Hendrik G", "initials": "HG"}, {"family": "van de Vijver", "given": "Marc J", "initials": "MJ"}, {"family": "B\u00f8rresen-Dale", "given": "Anne-Lise", "initials": "A"}, {"family": "Martens", "given": "John W M", "initials": "JWM"}, {"family": "Span", "given": "Paul N", "initials": "PN"}, {"family": "Lakhani", "given": "Sunil R", "initials": "SR"}, {"family": "Vincent-Salomon", "given": "Anne", "initials": "A"}, {"family": "Sotiriou", "given": "Christos", "initials": "C"}, {"family": "Tutt", "given": "Andrew", "initials": "A"}, {"family": "Thompson", "given": "Alastair M", "initials": "AM"}, {"family": "Van Laere", "given": "Steven", "initials": "S"}, {"family": "Richardson", "given": "Andrea L", "initials": "AL"}, {"family": "Viari", "given": "Alain", "initials": "A"}, {"family": "Campbell", "given": "Peter J", "initials": "PJ"}, {"family": "Stratton", "given": "Michael R", "initials": "MR"}, {"family": "Nik-Zainal", "given": "Serena", "initials": "S"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "23", "issn": "1546-170X", "issue": "4", "pages": "517-525", "title": "Nat. Med.", "issn-l": "1078-8956"}, "abstract": "Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (\u223c1-5%) who could have selective therapeutic sensitivity to PARP inhibition.", "doi": "10.1038/nm.4292", "pmid": "28288110", "labels": {"Clinical Genomics Lund": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nm.4292"}], "notes": [], "created": "2017-12-22T13:13:02.271Z", "modified": "2018-01-09T10:07:55.166Z"}, {"entity": "publication", "iuid": "5c60d95ec1144a3f84f4f35dbac8f469", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c60d95ec1144a3f84f4f35dbac8f469.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c60d95ec1144a3f84f4f35dbac8f469"}}, "title": "Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species.", "authors": [{"family": "Zangenah", "given": "S", "initials": "S"}, {"family": "Andersson", "given": "A F", "initials": "AF"}, {"family": "\u00d6zenci", "given": "V", "initials": "V"}, {"family": "Bergman", "given": "P", "initials": "P"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "36", "issn": "1435-4373", "issue": "4", "pages": "657-662", "title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn-l": "0934-9723"}, "abstract": "Capnocytophga canimorsus and Capnocytophga cynodegmi can be transmitted from cats and dogs to humans, and can cause a wide range of infections including wound infections, sepsis, or endocarditis. We and others recently discovered two new Capnocytophaga species, C. canis and C. stomatis, mainly associated with wound infections. The first-line treatment of animal bite related infections is penicillin, and in case of allergy, doxycycline and trimethoprim/sulfamethoxazole. However, there is a lack of antibiotic susceptibility patterns for animal bite associated Capnocytophaga species. Thus, we \ufeffset out to study the antibiotic profiles against animal bite associated Capnocytophaga species isolated from wound and blood cultures after cat and dog bites and coupled the findings to whole genome sequencing data. A total of 24 strains were included in the study. Phenotypic analysis of antibiotic resistance was performed with E-tests. The web-based tool 'Resfinder' was used to identify resistance genes in the whole genome dataset. Two strains of C. cynodegmi and two strains of the recently discovered C. stomatis were resistant to penicillin (MIC\u2009> 24 mg\ufeff/L) and cephalosporins (MIC\u2009>\u200924 mg/\ufeffL), and three out of these strains also exhibited resistance to imipenem (MIC\u2009=\u200932 mg/\ufeffL). Genomic analysis revealed that these strains carried a class D beta-lactamase gene, which has not previously been found in Capnocytophaga spp. A class D beta lactamase with broad substrate specificity was found in animal bite associated Capnocytophaga species, which could have important implications when treating wound infections after cat and dog bites. It also suggests that pet animal bacteria can harbour resistance genes with relevance for human infections.", "doi": "10.1007/s10096-016-2842-2", "pmid": "27909820", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s10096-016-2842-2"}, {"db": "pmc", "key": "PMC5366173"}], "notes": [], "created": "2017-05-03T12:58:58.451Z", "modified": "2024-01-16T13:48:48.169Z"}, {"entity": "publication", "iuid": "9861fe84e8714daba4df313b6aa9fe1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9861fe84e8714daba4df313b6aa9fe1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9861fe84e8714daba4df313b6aa9fe1b"}}, "title": "Gene co-expression network connectivity is an important determinant of selective constraint.", "authors": [{"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "4", "pages": "e1006402", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure. Here we utilised RNA-Sequencing to assay gene expression in winter buds undergoing bud flush in a natural population of Populus tremula, an outbreeding forest tree species. We performed expression Quantitative Trait Locus (eQTL) mapping and identified 164,290 significant eQTLs associating 6,241 unique genes (eGenes) with 147,419 unique SNPs (eSNPs). We found approximately four times as many local as distant eQTLs, with local eQTLs having significantly higher effect sizes. eQTLs were primarily located in regulatory regions of genes (UTRs or flanking regions), regardless of whether they were local or distant. We used the gene expression data to infer a co-expression network and investigated the relationship between network topology, the genetic architecture of gene expression and signatures of selection. Within the co-expression network, eGenes were underrepresented in network module cores (hubs) and overrepresented in the periphery of the network, with a negative correlation between eQTL effect size and network connectivity. We additionally found that module core genes have experienced stronger selective constraint on coding and non-coding sequence, with connectivity associated with signatures of selection. Our integrated genetics and genomics results suggest that purifying selection is the primary mechanism underlying the genetic architecture of natural variation in gene expression assayed in flushing leaf buds of P. tremula and that connectivity within the co-expression network is linked to the strength of purifying selection.", "doi": "10.1371/journal.pgen.1006402", "pmid": "28406900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-16-02227"}, {"db": "pmc", "key": "PMC5407845"}], "notes": [], "created": "2017-11-03T16:22:16.369Z", "modified": "2024-01-16T13:48:48.178Z"}, {"entity": "publication", "iuid": "a096ccc00d02499da3af87b2dd611be6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a096ccc00d02499da3af87b2dd611be6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a096ccc00d02499da3af87b2dd611be6"}}, "title": "Frequent low-level mutations of protein kinase D2 in angiolipoma", "authors": [{"family": "Hofvander", "given": "Jakob", "initials": "J"}, {"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Stenkula", "given": "Karin G", "initials": "KG"}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "von Steyern", "given": "Fredrik Vult", "initials": "FV"}, {"family": "Rissler", "given": "Pehr", "initials": "P"}, {"family": "Hornick", "given": "Jason L", "initials": "JL"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "241", "issn": "0022-3417", "issue": "5", "pages": "578-582", "title": "J. Pathol", "issn-l": "0022-3417"}, "abstract": null, "doi": "10.1002/path.4865", "pmid": "28139834", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:35:56.912Z", "modified": "2020-01-21T13:53:21.835Z"}, {"entity": "publication", "iuid": "f45ab5374259462a85a914ce26350231", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f45ab5374259462a85a914ce26350231.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f45ab5374259462a85a914ce26350231"}}, "title": "FZD10-G\u03b113 signalling axis points to a role of FZD10 in CNS angiogenesis.", "authors": [{"family": "Hot", "given": "Belma", "initials": "B"}, {"family": "Valnohova", "given": "Jana", "initials": "J"}, {"family": "Arthofer", "given": "Elisa", "initials": "E"}, {"family": "Simon", "given": "Katharina", "initials": "K"}, {"family": "Shin", "given": "Jaekyung", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Kostenis", "given": "Evi", "initials": "E"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schulte", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "Cell. Signal.", "issn": "1873-3913", "volume": "32", "issue": null, "pages": "93-103", "issn-l": "0898-6568"}, "abstract": "Among the 10 Frizzled (FZD) isoforms belonging to the Class F of G protein-coupled receptors (GPCRs), FZD10 remains the most enigmatic. FZD10 shows homology to FZD4 and FZD9 and was previously implicated in both \u03b2-catenin-dependent and -independent signalling. In normal tissue, FZD10 levels are generally very low; however, its upregulation in synovial carcinoma has attracted some attention for therapy. Our findings identify FZD10 as a receptor interacting with and signalling through the heterotrimeric G protein G\u03b113 but not G\u03b112, G\u03b1i1, G\u03b1oA, G\u03b1s, or G\u03b1q. Stimulation with the FZD agonist WNT induced the dissociation of the G\u03b113 protein from FZD10, and led to global G\u03b112/13-dependent cell changes assessed by dynamic mass redistribution measurements. Furthermore, we show that FZD10 mediates G\u03b112/13 activation-dependent induction of YAP/TAZ transcriptional activity. In addition, we show a distinct expression of FZD10 in embryonic CNS endothelial cells at E11.5-E14.5. Given the well-known importance of G\u03b113 signalling for the development of the vascular system, the selective expression of FZD10 in brain vascular endothelial cells points at a potential role of FZD10-G\u03b113 signalling in CNS angiogenesis.", "doi": "10.1016/j.cellsig.2017.01.023", "pmid": "28126591", "labels": {"Fluorescence Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0898-6568(17)30029-3"}], "notes": [], "created": "2017-10-30T14:58:32.429Z", "modified": "2021-07-08T13:44:33.744Z"}, {"entity": "publication", "iuid": "033b5a0bde204450b47ca9e89437b1fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/033b5a0bde204450b47ca9e89437b1fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/033b5a0bde204450b47ca9e89437b1fe"}}, "title": "Epigenome-wide DNA methylation study of IgE concentration in relation to self-reported allergies.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Moffatt", "given": "Miriam F", "initials": "MF"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "9", "issn": "1750-192X", "issue": "4", "pages": "407-418", "title": "Epigenomics", "issn-l": null}, "abstract": "Epigenetic mechanisms are critical for normal immune development and epigenetic alterations might therefore be possible contributors to immune diseases. To investigate if DNA methylation in whole blood is associated with total and allergen-specific IgE levels.\n\nWe performed an epigenome-wide association study to investigate the association between DNA methylation and IgE level, allergen-specific IgE and self-reported immune diseases and allergies in 728 individuals.\n\nWe identified and replicated 15 CpG sites associated with IgE, mapping to biologically relevant genes, including ACOT7, ILR5A, KCNH2, PRG2 and EPX. A total of 331 loci were associated with allergen-specific IgE, but none of these CpG sites were associated with self-reported allergies and immune diseases.\n\nThis study shows that IgE levels are associated with DNA methylation levels at numerous CpG sites, which might provide new leads for investigating the links between IgE and allergic inflammation.", "doi": "10.2217/epi-2016-0158", "pmid": "28322575", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-25T15:18:20.445Z", "modified": "2024-01-16T13:48:48.187Z"}, {"entity": "publication", "iuid": "582a1ec0dba34f4f83e8c24ff80a6284", "links": {"self": {"href": "https://publications.scilifelab.se/publication/582a1ec0dba34f4f83e8c24ff80a6284.json"}, "display": {"href": "https://publications.scilifelab.se/publication/582a1ec0dba34f4f83e8c24ff80a6284"}}, "title": "Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout", "authors": [{"family": "Huyben", "given": "David", "initials": "D", "orcid": "0000-0001-7913-851X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e03b5f5591824373a7eb756f21a93001.json"}}, {"family": "Nyman", "given": "Andreas", "initials": "A"}, {"family": "Vidakovi\u0107", "given": "Aleksandar", "initials": "A"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}, {"family": "Moccia", "given": "Richard", "initials": "R"}, {"family": "Kiessling", "given": "Anders", "initials": "A"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Lundh", "given": "Torbj\u00f6rn", "initials": "T"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "473", "issn": "0044-8486", "issue": null, "pages": "528-537", "title": "Aquaculture", "issn-l": null}, "abstract": null, "doi": "10.1016/j.aquaculture.2017.03.024", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:41.442Z", "modified": "2024-01-16T13:48:48.198Z"}, {"entity": "publication", "iuid": "503a479740074fe8bfe99d3476e3be89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/503a479740074fe8bfe99d3476e3be89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/503a479740074fe8bfe99d3476e3be89"}}, "title": "Editorial for the special issue on \"Golgi-related human disorders\".", "authors": [{"family": "Micaroni", "given": "Massimo", "initials": "M"}], "type": "editorial", "published": "2017-04-00", "journal": {"title": "Tissue and Cell", "issn": "1532-3072", "volume": "49", "issue": "2 Pt A", "pages": "131-132", "issn-l": "0040-8166"}, "abstract": null, "doi": "10.1016/j.tice.2017.03.004", "pmid": "28342448", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0040-8166(17)30084-8"}], "notes": [], "created": "2020-01-23T16:35:31.615Z", "modified": "2021-06-21T15:41:15.849Z"}, {"entity": "publication", "iuid": "3828c52e01cd47828d156b9fcc1dfcdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3828c52e01cd47828d156b9fcc1dfcdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3828c52e01cd47828d156b9fcc1dfcdb"}}, "title": "Combined immunodeficiency and hypoglycemia associated with mutations in hypoxia upregulated 1.", "authors": [{"family": "Haapaniemi", "given": "Emma M", "initials": "EM"}, {"family": "Fogarty", "given": "Christopher L", "initials": "CL"}, {"family": "Keskitalo", "given": "Salla", "initials": "S"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Vihinen", "given": "Helena", "initials": "H"}, {"family": "Ilander", "given": "Mette", "initials": "M"}, {"family": "Mustjoki", "given": "Satu", "initials": "S"}, {"family": "Krjut\u0161kov", "given": "Kaarel", "initials": "K"}, {"family": "Lehto", "given": "Markku", "initials": "M"}, {"family": "Hautala", "given": "Timo", "initials": "T"}, {"family": "Eriksson", "given": "Ove", "initials": "O"}, {"family": "Jokitalo", "given": "Eija", "initials": "E"}, {"family": "Velagapudi", "given": "Vidya", "initials": "V"}, {"family": "Varjosalo", "given": "Markku", "initials": "M"}, {"family": "Sepp\u00e4nen", "given": "Mikko", "initials": "M"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "139", "issn": "1097-6825", "issue": "4", "pages": "1391-1393.e11", "title": "J. Allergy Clin. Immunol.", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2016.09.050", "pmid": "27913302", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0091-6749(16)31375-6"}], "notes": [], "created": "2017-05-03T12:58:58.149Z", "modified": "2024-01-16T13:48:48.209Z"}, {"entity": "publication", "iuid": "b9d5f822620d40a596cc8d3c94c75dc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9d5f822620d40a596cc8d3c94c75dc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9d5f822620d40a596cc8d3c94c75dc2"}}, "title": "Cardiometabolic biomarkers are predictors of readmission and death in patients hospitalized for acute dyspnea.", "authors": [{"family": "Lund", "given": "Nathalie", "initials": "N"}, {"family": "Gr\u00e4nsbo", "given": "Klas", "initials": "K"}, {"family": "Wernersson", "given": "Camilla", "initials": "C"}, {"family": "Melander", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "The American Journal of Emergency Medicine", "issn": "1532-8171", "issn-l": "0735-6757", "volume": "35", "issue": "4", "pages": "610-614"}, "abstract": "Acute dyspnea affects a large heterogeneous patient group with high mortality and readmission rates.\n\nTo investigate if cardiometabolic biomarkers and clinical characteristics predict readmission and death in patients hospitalized for acute dyspnea.\n\n65 dyspnea patients at a general internal medicine ward were followed for six months. The combined endpoint was readmission or death.\n\nCardiometabolic biomarkers at admission were related to the endpoint in Cox proportional hazard models (adjusted for sex, age, oxygen saturation, respiratory rate and C-reactive protein (CRP)). The biomarkers tissue-type plasminogen activator (tPA), prolactin (PRL), tumor necrosis factor receptor superfamily member 6 (FAS) and C-C motif chemokine 3 (CCL3) were independently and significantly related to the endpoint and combined into a biomarker risk score (BRS). Each SD increment of the BRS conferred a hazard ratio (HR) of 2.13 (1.39-3.27) P=0.001. The top vs bottom tertile of the BRS conferred a HR of 4.75 (1.93-11.68) P=0.001. Dyspnea severity was also associated with worse outcome, HR=3.43 (1.28-9.20) P=0.014. However, when mutually adjusted the BRS remained significant (P=0.004) whereas dyspnea severity was not. The BRS was related to the endpoint among patients with mild to moderate dyspnea (P=0.016) but not among those with severe dyspnea.\n\nA score of tPA, PRL, FAS and CCL3 predicts 6-month death and readmission in patients hospitalized for acute dyspnea and may prove useful to optimize length of stay and follow-up. Although the BRS outweighs dyspnea severity in prediction of the endpoint, its prognostic role is strongest in mild-moderate dyspnea.", "doi": "10.1016/j.ajem.2016.12.048", "pmid": "28062207", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S0735-6757(16)30948-2"}, {"db": "pmc", "key": "PMC5754318"}], "notes": [], "created": "2020-01-23T15:07:33.011Z", "modified": "2023-04-14T13:56:16.220Z"}, {"entity": "publication", "iuid": "837e52920ed54e07bb3af93391714b11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/837e52920ed54e07bb3af93391714b11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/837e52920ed54e07bb3af93391714b11"}}, "title": "An assessment of the importance of exposure routes to the uptake and internal localisation of fluorescent nanoparticles in zebrafish (Danio rerio), using light sheet microscopy.", "authors": [{"family": "Skjolding", "given": "L M", "initials": "LM"}, {"family": "A\u0161monait\u0117", "given": "G", "initials": "G"}, {"family": "J\u00f8lck", "given": "R I", "initials": "RI"}, {"family": "Andresen", "given": "T L", "initials": "TL"}, {"family": "Selck", "given": "H", "initials": "H"}, {"family": "Baun", "given": "A", "initials": "A"}, {"family": "Sturve", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "Nanotoxicology", "issn": "1743-5404", "volume": "11", "issue": "3", "pages": "351-359", "issn-l": "1743-5390"}, "abstract": "A major challenge in nanoecotoxicology is finding suitable methods to determine the uptake and localisation of nanoparticles on a whole-organism level. Some uptake methods have been associated with artefacts induced by sample preparation, including staining for electron microscopy. This study used light sheet microscopy (LSM) to define the uptake and localisation of fluorescently labelled nanoparticles in living organisms with minimal sample preparation. Zebrafish (Danio rerio) were exposed to fluorescent gold nanoparticles (Au NPs) and fluorescent polystyrene NPs via aqueous or dietary exposure. The in vivo uptake and localisation of NPs were investigated using LSM at different time points (1, 3 and 7 days). A time-dependent increase in fluorescence was observed in the gut after dietary exposure to both Au NPs and polystyrene NPs. No fluorescence was observed within gut epithelia regardless of the NP exposure route indicating no or limited uptake via intestinal villi. Fish exposed to polystyrene NPs through the aqueous phase emitted fluorescence signals from the gills and intestine. Fluorescence was also detected in the head region of the fish after aqueous exposure to polystyrene NPs. This was not observed for Au NPs. Aqueous exposure to Au NPs resulted in increased relative swimming distance, while no effect was observed for other exposures. This study supports that the route of exposure is essential for the uptake and subsequent localisation of nanoparticles in zebrafish. Furthermore, it demonstrates that the localisation of NPs in whole living organisms can be visualised in real-time, using LSM.", "doi": "10.1080/17435390.2017.1306128", "pmid": "28286999", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-23T16:36:11.183Z", "modified": "2021-06-21T15:41:45.799Z"}, {"entity": "publication", "iuid": "3a1cc06125b84310aade5d4e82d2ae12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a1cc06125b84310aade5d4e82d2ae12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a1cc06125b84310aade5d4e82d2ae12"}}, "title": "A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gs\u03b1 Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).", "authors": [{"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Nevalainen", "given": "Pasi I", "initials": "PI"}, {"family": "Reyes", "given": "Monica", "initials": "M"}, {"family": "Thiele", "given": "Susanne", "initials": "S"}, {"family": "Tafaj", "given": "Olta", "initials": "O"}, {"family": "Molinaro", "given": "Angelo", "initials": "A"}, {"family": "Takatani", "given": "Rieko", "initials": "R"}, {"family": "Ala-Houhala", "given": "Marja", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Kottler", "given": "Marie-Laure", "initials": "ML"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "J\u00fcppner", "given": "Harald", "initials": "H"}], "type": "case reports", "published": "2017-04-00", "journal": {"volume": "32", "issn": "1523-4681", "issue": "4", "pages": "776-783", "title": "J. Bone Miner. Res.", "issn-l": "0884-0431"}, "abstract": "Pseudohypoparathyroidism type Ib (PHP1B) is characterized primarily by resistance to parathyroid hormone (PTH) and thus hypocalcemia and hyperphosphatemia, in most cases without evidence for Albright hereditary osteodystrophy (AHO). PHP1B is associated with epigenetic changes at one or several differentially-methylated regions (DMRs) within GNAS, which encodes the \u03b1-subunit of the stimulatory G protein (Gs\u03b1) and splice variants thereof. Heterozygous, maternally inherited STX16 or GNAS deletions leading to isolated loss-of-methylation (LOM) at exon A/B alone or at all maternal DMRs are the cause of autosomal dominant PHP1B (AD-PHP1B). In this study, we analyzed three affected individuals, the female proband and her two sons. All three revealed isolated LOM at GNAS exon A/B, whereas the proband's healthy maternal grandmother and uncle showed normal methylation at this locus. Haplotype analysis was consistent with linkage to the STX16/GNAS region, yet no deletion could be identified. Whole-genome sequencing of one of the patients revealed a large heterozygous inversion (1,882,433 bp). The centromeric breakpoint of the inversion is located 7,225 bp downstream of GNAS exon XL, but its DMR showed no methylation abnormality, raising the possibility that the inversion disrupts a regulatory element required only for establishing or maintaining exon A/B methylation. Because our three patients presented phenotypes consistent with PHP1B, and not with PHP1A, the Gs\u03b1 promoter is probably unaffected by the inversion. Our findings expand the spectrum of genetic mutations that lead to LOM at exon A/B alone and thus biallelic expression of the transcript derived from this alternative first GNAS exon. \u00a9 2017 American Society for Bone and Mineral Research.", "doi": "10.1002/jbmr.3083", "pmid": "28084650", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5395346"}, {"db": "mid", "key": "NIHMS843464"}], "notes": [], "created": "2017-11-03T12:53:35.193Z", "modified": "2024-01-16T13:48:48.221Z"}, {"entity": "publication", "iuid": "66e2871d10da49c9a15ec3ccaf63231e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66e2871d10da49c9a15ec3ccaf63231e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66e2871d10da49c9a15ec3ccaf63231e"}}, "title": "Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology", "authors": [{"family": "Vi\u013cuma", "given": "Agnese", "initials": "A"}, {"family": "Mikko", "given": "Sofia", "initials": "S"}, {"family": "Hahn", "given": "Daniela", "initials": "D"}, {"family": "Skow", "given": "Loren", "initials": "L"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF"}], "type": "journal-article", "published": "2017-03-31", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "45518", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region. The final assembly resulted in a 1,165,328\u2009bp continuous gap free sequence with 35 manually curated genomic loci of which 23 were considered to be functional and 12 to be pseudogenes. In comparison to the MHC class II region in other mammals, the corresponding region in horse shows extraordinary copy number variation and different relative location and directionality of the Eqca-DRB, -DQA, -DQB and -DOB loci. This is the first long-read sequence assembly of the horse MHC class II region with rigorous manual gene annotation, and it will serve as an important resource for association studies of immune-mediated equine diseases and for evolutionary analysis of genetic diversity in this region.", "doi": "10.1038/srep45518", "pmid": "28361880", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:40:57.204Z", "modified": "2024-01-16T13:48:48.234Z"}, {"entity": "publication", "iuid": "4329e9402acb48b795c634b93c76be4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4329e9402acb48b795c634b93c76be4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4329e9402acb48b795c634b93c76be4b"}}, "title": "Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches.", "authors": [{"family": "Lamei", "given": "Sepideh", "initials": "S"}, {"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Olofsson", "given": "Tobias C", "initials": "TC"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Forsgren", "given": "Eva", "initials": "E"}, {"family": "V\u00e1squez", "given": "Alejandra", "initials": "A"}], "type": "journal article", "published": "2017-03-27", "journal": {"volume": "12", "issn": "1932-6203", "issue": "3", "pages": "e0174614", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Honeybees face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. The crop microbiota of Apis mellifera, composed of 13 Lactic Acid Bacterial (LAB) species within the genera Lactobacillus and Bifidobacterium, form a beneficial symbiotic relationship with each other and the honeybee to protect their niche and their host. Possibly playing a vital role in honeybee health, it is important that these honeybee specific Lactic Acid Bacterial (hbs-LAB) symbionts can be correctly identified, isolated and cultured, to further investigate their health promoting properties. We have previously reported successful identification to the strain level by culture-dependent methods and we recently sequenced and annotated the genomes of the 13 hbs-LAB. However, the hitherto applied techniques are unfortunately very time consuming, expensive and not ideal when analyzing a vast quantity of samples. In addition, other researchers have constantly failed to identify the 13 hbs-LAB from honeybee samples by using inadequate media and/or molecular techniques based on 16S rRNA gene sequencing with insufficient discriminatory power. The aim of this study was to develop better and more suitable methods for the identification and cultivation of hbs-LAB. We compared currently used bacterial cultivation media and could for the first time demonstrate a significant variation in the hbs-LAB basic requirements for optimal growth. We also present a new bacterial identification approach based on amplicon sequencing of a region of the 16S rRNA gene using the Illumina platform and an error correction software that can be used to successfully differentiate and rapidly identify the 13 hbs-LAB to the strain level.", "doi": "10.1371/journal.pone.0174614", "pmid": "28346815", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-47026"}, {"db": "pmc", "key": "PMC5367889"}], "notes": [], "created": "2017-11-03T16:11:40.176Z", "modified": "2024-01-16T13:48:48.244Z"}, {"entity": "publication", "iuid": "ce4c21c5846e448796cea17aa113b78f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce4c21c5846e448796cea17aa113b78f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce4c21c5846e448796cea17aa113b78f"}}, "title": "Light-sensing via hydrogen peroxide and a peroxiredoxin.", "authors": [{"family": "Bodvard", "given": "Kristofer", "initials": "K"}, {"family": "Peeters", "given": "Ken", "initials": "K"}, {"family": "Roger", "given": "Friederike", "initials": "F"}, {"family": "Romanov", "given": "Natalie", "initials": "N"}, {"family": "Igbaria", "given": "Aeid", "initials": "A"}, {"family": "Welkenhuysen", "given": "Niek", "initials": "N"}, {"family": "Palais", "given": "Ga\u00ebl", "initials": "G"}, {"family": "Reiter", "given": "Wolfgang", "initials": "W"}, {"family": "Toledano", "given": "Michel B", "initials": "MB"}, {"family": "K\u00e4ll", "given": "Mikael", "initials": "M"}, {"family": "Molin", "given": "Mikael", "initials": "M", "orcid": "0000-0002-3903-8503", "researcher": {"href": "https://publications.scilifelab.se/researcher/12e9dc11d1b047d88913ea3bcb2694be.json"}}], "type": "journal article", "published": "2017-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "8", "issue": "1", "pages": "14791", "issn-l": "2041-1723"}, "abstract": "Yeast lacks dedicated photoreceptors; however, blue light still causes pronounced oscillations of the transcription factor Msn2 into and out of the nucleus. Here we show that this poorly understood phenomenon is initiated by a peroxisomal oxidase, which converts light into a hydrogen peroxide (H 2O2) signal that is sensed by the peroxiredoxin Tsa1 and transduced to thioredoxin, to counteract PKA-dependent Msn2 phosphorylation. Upon H2O2, the nuclear retention of PKA catalytic subunits, which contributes to delayed Msn2 nuclear concentration, is antagonized in a Tsa1-dependent manner. Conversely, peroxiredoxin hyperoxidation interrupts the H2O2 signal and drives Msn2 oscillations by superimposing on PKA feedback regulation. Our data identify a mechanism by which light could be sensed in all cells lacking dedicated photoreceptors. In particular, the use of H2O2 as a second messenger in signalling is common to Msn2 oscillations and to light-induced entrainment of circadian rhythms and suggests conserved roles for peroxiredoxins in endogenous rhythms.", "doi": "10.1038/ncomms14791", "pmid": "28337980", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms14791"}, {"db": "pmc", "key": "PMC5376668"}], "notes": [], "created": "2020-01-23T16:34:25.369Z", "modified": "2021-06-21T15:40:28.799Z"}, {"entity": "publication", "iuid": "a9f6d02505334fa7bdeddc62f4a05039", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9f6d02505334fa7bdeddc62f4a05039.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9f6d02505334fa7bdeddc62f4a05039"}}, "title": "Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.", "authors": [{"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Pedersen", "given": "Karsten", "initials": "K"}, {"family": "Edlund", "given": "Johanna", "initials": "J"}, {"family": "Eriksson", "given": "Lena", "initials": "L"}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-03-23", "journal": {"volume": "5", "issn": "2049-2618", "issue": "1", "pages": "37", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere.\n\nIn this study, flow cells were attached to boreholes containing either \"modern marine\" or \"old saline\" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria.\n\nPopulations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.", "doi": "10.1186/s40168-017-0253-y", "pmid": "28335808", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0253-y"}, {"db": "pmc", "key": "PMC5364579"}], "notes": [], "created": "2017-11-03T16:11:41.099Z", "modified": "2024-01-16T13:48:48.253Z"}, {"entity": "publication", "iuid": "f184b14667ce421baf3bef07a0046a67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f184b14667ce421baf3bef07a0046a67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f184b14667ce421baf3bef07a0046a67"}}, "title": "NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.", "authors": [{"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}], "type": "journal article", "published": "2017-03-23", "journal": {"volume": "18", "issn": "1471-2105", "issue": "Suppl 5", "pages": "118", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "The statistical evaluation of pathway enrichment, i.e. of gene profiles' confluence to the pathway level, allows exploring molecular landscapes using functionally annotated gene sets. However, pathway scores can also be used as predictive features in machine learning. That requires, firstly, increasing statistical power and biological relevance via a network enrichment analysis (NEA) and, secondly, a fast and convenient procedure for rendering the original data into a space of pathway scores. However, previous implementations of NEA involved multiple runs of network randomization and were therefore slow.\n\nHere, we present a new R package NEArender which can transform raw 'omics' features of experimental or clinical samples into matrices describing the same samples with many fewer NEA-based pathway scores. This is done via a parametric estimation of the null binomial distribution and is thus much faster and less biased than randomization procedures. Further, we compare estimates from these two alternative procedures and demonstrate that the summarization of individual genes to pathways increases the statistical power compared to both the default differential expression analysis on individual genes and the state-of-the-art gene set enrichment analysis. The package also contains functions for preparing input, modeling null distributions, and evaluating alternative versions of the global network.\n\nBeyond the state-of-the-art exploration of molecular data through pathway enrichment, score matrices produced by NEArender can be used in larger bioinformatics pipelines as input for phenotype modeling, predicting disease outcomes etc. This approach is often more sensitive and robust than using the original data. The package NEArender is complementary to the online NEA tool EviNet ( https://www.evinet.org ) and, unlike of the latter, enables high performance of computations off-line. The R package NEArender version 1.4 is available at CRAN repository https://cran.r-project.org/web/packages/NEArender/.", "doi": "10.1186/s12859-017-1534-y", "pmid": "28361684", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-017-1534-y"}, {"db": "pmc", "key": "PMC5374688"}], "notes": [], "created": "2019-01-15T07:43:39.403Z", "modified": "2020-01-21T13:53:22.281Z"}, {"entity": "publication", "iuid": "9199b6ea51d04aa2b2f5f831a3d4e154", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9199b6ea51d04aa2b2f5f831a3d4e154.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9199b6ea51d04aa2b2f5f831a3d4e154"}}, "title": "Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.", "authors": [{"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2017-03-23", "journal": {"volume": "5", "issn": "2169-8287", "issue": "12", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "The oomycete Pythium periplocum is an aggressive mycoparasite of a number of plant pathogenic fungi and oomycetes and therefore has potential as a biological control agent. Here, we report the first draft genome sequence of P. periplocum, which comprises 35.89\u00a0Mb. It contains 1,043 scaffolds and 14,399 predicted protein-coding genes.", "doi": "10.1128/genomeA.00057-17", "pmid": "28336598", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5/12/e00057-17"}, {"db": "pmc", "key": "PMC5364223"}], "notes": [], "created": "2017-11-03T16:21:53.141Z", "modified": "2020-01-21T13:56:17.350Z"}, {"entity": "publication", "iuid": "0990de43373146d69c60334dffbe0590", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0990de43373146d69c60334dffbe0590.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0990de43373146d69c60334dffbe0590"}}, "title": "The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.", "authors": [{"family": "Chang", "given": "Dan", "initials": "D"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Enk", "given": "Jacob", "initials": "J"}, {"family": "Lippold", "given": "Sebastian", "initials": "S"}, {"family": "Kircher", "given": "Martin", "initials": "M"}, {"family": "Lister", "given": "Adrian", "initials": "A"}, {"family": "MacPhee", "given": "Ross D E", "initials": "RD"}, {"family": "Widga", "given": "Christopher", "initials": "C"}, {"family": "Czechowski", "given": "Paul", "initials": "P"}, {"family": "Sommer", "given": "Robert", "initials": "R"}, {"family": "Hodges", "given": "Emily", "initials": "E"}, {"family": "St\u00fcmpel", "given": "Nikolaus", "initials": "N"}, {"family": "Barnes", "given": "Ian", "initials": "I"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Derevianko", "given": "Anatoly", "initials": "A"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Hillebrand-Voiculescu", "given": "Alexandra", "initials": "A"}, {"family": "Constantin", "given": "Silviu", "initials": "S"}, {"family": "Kuznetsova", "given": "Tatyana", "initials": "T"}, {"family": "Mol", "given": "Dick", "initials": "D"}, {"family": "Rathgeber", "given": "Thomas", "initials": "T"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Tikhonov", "given": "Alexey N", "initials": "AN"}, {"family": "Willerslev", "given": "Eske", "initials": "E"}, {"family": "Hannon", "given": "Greg", "initials": "G"}, {"family": "Lalueza-Fox", "given": "Carles", "initials": "C"}, {"family": "Joger", "given": "Ulrich", "initials": "U"}, {"family": "Poinar", "given": "Hendrik", "initials": "H"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}], "type": "journal article", "published": "2017-03-22", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "44585", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.", "doi": "10.1038/srep44585", "pmid": "28327635", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep44585"}, {"db": "pmc", "key": "PMC5361112"}], "notes": [], "created": "2017-11-03T16:21:50.396Z", "modified": "2021-07-07T20:31:10.689Z"}, {"entity": "publication", "iuid": "be33ec0e3ee447298b828ebbd839157a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be33ec0e3ee447298b828ebbd839157a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be33ec0e3ee447298b828ebbd839157a"}}, "title": "Atrophin controls developmental signaling pathways via interactions with Trithorax-like", "authors": [{"family": "Yeung", "given": "Kelvin", "initials": "K"}, {"family": "Boija", "given": "Ann", "initials": "A"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Holmqvist", "given": "Per Henrik", "initials": "PH"}, {"family": "Tsatskis", "given": "Yonit", "initials": "Y"}, {"family": "Nisoli", "given": "Ilaria", "initials": "I"}, {"family": "Yap", "given": "Damian", "initials": "D"}, {"family": "Lorzadeh", "given": "Alireza", "initials": "A"}, {"family": "Moksa", "given": "Michelle", "initials": "M"}, {"family": "Hirst", "given": "Martin", "initials": "M"}, {"family": "Aparicio", "given": "Samuel", "initials": "S"}, {"family": "Fanto", "given": "Manolis", "initials": "M"}, {"family": "Stenberg", "given": "Per", "initials": "P"}, {"family": "Mannervik", "given": "Mattias", "initials": "M"}, {"family": "McNeill", "given": "Helen", "initials": "H"}], "type": "journal-article", "published": "2017-03-22", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": null, "doi": "10.7554/elife.23084", "pmid": "28327288", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T13:26:13.308Z", "modified": "2024-01-16T13:48:48.263Z"}, {"entity": "publication", "iuid": "19386a58bf7d4e2a9800337227fe6871", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19386a58bf7d4e2a9800337227fe6871.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19386a58bf7d4e2a9800337227fe6871"}}, "title": "Quantification of HER2 and estrogen receptor heterogeneity in breast cancer by single-molecule RNA fluorescence in situ hybridization.", "authors": [{"family": "Annaratone", "given": "Laura", "initials": "L"}, {"family": "Simonetti", "given": "Michele", "initials": "M"}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Garnerone", "given": "Silvano", "initials": "S"}, {"family": "Scalzo", "given": "Maria Stella", "initials": "MS"}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Chiarle", "given": "Roberto", "initials": "R"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}], "type": "journal article", "published": "2017-03-21", "journal": {"volume": "8", "issn": "1949-2553", "issue": "12", "pages": "18680-18698", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Intra-tumor heterogeneity is a pervasive property of human cancers that poses a major clinical challenge. Here, we describe the characterization, at the transcriptional level, of the intra-tumor topography of two prominent breast cancer biomarkers and drug targets, epidermal growth factor receptor 2 (HER2) and estrogen receptor 1 (ER) in 49 archival breast cancer samples. We developed a protocol for single-molecule RNA FISH in formalin-fixed, paraffin-embedded tissue sections (FFPE-smFISH), which enabled us to simultaneously detect and perform absolute quantification of HER2 and ER mature transcripts in single cells and multiple tumor regions. We benchmarked our method with standard diagnostic techniques, demonstrating that FFPE-smFISH is able to correctly classify breast cancers into well-established molecular subgroups. By counting transcripts in thousands of single cells, we identified different expression modes and levels of inter-cellular variability. In samples expressing both HER2 and ER, many cells co-expressed both genes, although expression levels were typically uncorrelated. Finally, we applied diversity metrics from the field of ecology to assess the intra-tumor topography of HER2 and ER gene expression, revealing that the spatial distribution of these key biomarkers can vary substantially even among breast cancers of the same subtype. Our results demonstrate that FFPE-smFISH is a reliable diagnostic assay and a powerful method for quantification of intra-tumor transcriptional heterogeneity of selected biomarkers in clinical samples.", "doi": "10.18632/oncotarget.15727", "pmid": "28423635", "labels": {"Advanced FISH Technologies": "Collaborative"}, "xrefs": [{"db": "pii", "key": "15727"}, {"db": "pmc", "key": "PMC5386639"}], "notes": [], "created": "2020-01-21T12:35:31.029Z", "modified": "2020-02-12T15:16:35.184Z"}, {"entity": "publication", "iuid": "462837a655434c04a22ffd076f56c646", "links": {"self": {"href": "https://publications.scilifelab.se/publication/462837a655434c04a22ffd076f56c646.json"}, "display": {"href": "https://publications.scilifelab.se/publication/462837a655434c04a22ffd076f56c646"}}, "title": "Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.", "authors": [{"family": "Zhu", "given": "Yafeng", "initials": "Y", "orcid": "0000-0003-1947-9026", "researcher": {"href": "https://publications.scilifelab.se/researcher/d464b30bf5174a8fb456601d75aecb14.json"}}, {"family": "Engstr\u00f6m", "given": "P\u00e4r G", "initials": "PG", "orcid": "0000-0001-5265-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce330ec225f4a8595932d092ab8c8d1.json"}}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Baudo", "given": "Charles D", "initials": "CD"}, {"family": "Kennell", "given": "John C", "initials": "JC"}, {"family": "Sun", "given": "Sheng", "initials": "S"}, {"family": "Billmyre", "given": "R Blake", "initials": "RB"}, {"family": "Schr\u00f6der", "given": "Markus S", "initials": "MS"}, {"family": "Andersson", "given": "Anna", "initials": "A"}, {"family": "Holm", "given": "Tina", "initials": "T"}, {"family": "Sigurgeirsson", "given": "Benjamin", "initials": "B"}, {"family": "Wu", "given": "Guangxi", "initials": "G"}, {"family": "Sankaranarayanan", "given": "Sundar Ram", "initials": "SR"}, {"family": "Siddharthan", "given": "Rahul", "initials": "R"}, {"family": "Sanyal", "given": "Kaustuv", "initials": "K"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Boekhout", "given": "Teun", "initials": "T"}, {"family": "Dawson", "given": "Thomas L", "initials": "TL"}, {"family": "Heitman", "given": "Joseph", "initials": "J"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2017-03-17", "journal": {"volume": "45", "issn": "1362-4962", "issue": "5", "pages": "2629-2643", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome. We also sequenced and assembled four M. sympodialis clinical isolates, and showed their value for understanding Malassezia reproduction by confirming four alternative allele combinations at the two mating-type loci. Importantly, we demonstrated how proteomics data could be readily integrated with transcriptomics data in standard annotation tools. This increased the number of annotated protein-coding genes by 14% (from 3612 to 4113), compared to using transcriptomics evidence alone. Manual curation further increased the number of protein-coding genes by 9% (to 4493). All of these genes have RNA-seq evidence and 87% were confirmed by proteomics. The M. sympodialis genome assembly and annotation presented here is at a quality yet achieved only for a few eukaryotic organisms, and constitutes an important reference for future host-microbe interaction studies.", "doi": "10.1093/nar/gkx006", "pmid": "28100699", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Clinical Proteomics Mass spectrometry": "Technology development", "National Genomics Infrastructure": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "gkx006"}, {"db": "pmc", "key": "PMC5389616"}], "notes": [], "created": "2017-08-23T14:28:34.856Z", "modified": "2024-01-16T13:48:48.270Z"}, {"entity": "publication", "iuid": "6ba3241f53fa4f55aa4eec0a4f518f18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ba3241f53fa4f55aa4eec0a4f518f18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ba3241f53fa4f55aa4eec0a4f518f18"}}, "title": "PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.", "authors": [{"family": "Pan", "given": "Gang", "initials": "G"}, {"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": "Bysani", "given": "Madhusudhan", "initials": "M"}, {"family": "Nord", "given": "Helena", "initials": "H"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Essand", "given": "Magnus", "initials": "M"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2017-03-17", "journal": {"volume": "45", "issn": "1362-4962", "issue": "5", "pages": "2408-2422", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The FADS1 and FADS2 genes in the FADS cluster encode the rate-limiting enzymes in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFAs). Genetic variation in this region has been associated with a large number of diseases and traits many of them correlated to differences in metabolism of PUFAs. However, the causative variants leading to these associations have not been identified. Here we find that the multiallelic rs174557 located in an AluYe5 element in intron 1 of FADS1 is functional and lies within a PATZ1 binding site. The derived allele of rs174557, which is the common variant in most populations, diminishes binding of PATZ1, a transcription factor conferring allele-specific downregulation of FADS1. The PATZ1 binding site overlaps with a SP1 site. The competitive binding between the suppressive PATZ1 and the activating complex of SP1 and SREBP1c determines the enhancer activity of this region, which regulates expression of FADS1.", "doi": "10.1093/nar/gkw1186", "pmid": "27932482", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gkw1186"}, {"db": "pmc", "key": "PMC5389558"}], "notes": [], "created": "2017-05-03T13:01:46.011Z", "modified": "2024-01-16T13:48:48.278Z"}, {"entity": "publication", "iuid": "08960a8cdc4e4e808ee5e6bd933bdd43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08960a8cdc4e4e808ee5e6bd933bdd43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08960a8cdc4e4e808ee5e6bd933bdd43"}}, "title": "Chromosome and Megaplasmid Sequences of Borrelia anserina (Sakharoff 1891), the Agent of Avian Spirochetosis and Type Species of the Genus", "authors": [{"family": "Elbir", "given": "Haitham", "initials": "H"}, {"family": "Sitlani", "given": "Parth", "initials": "P"}, {"family": "Bergstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "Barbour", "given": "Alan G", "initials": "AG"}], "type": "journal-article", "published": "2017-03-16", "journal": {"volume": "5", "issn": "2169-8287", "issue": "11", "pages": "e00018-17", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": null, "doi": "10.1128/genomea.00018-17", "pmid": "28302772", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:52:10.210Z", "modified": "2020-01-21T13:56:09.945Z"}, {"entity": "publication", "iuid": "f5376f721608439b957f4647da281e62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5376f721608439b957f4647da281e62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5376f721608439b957f4647da281e62"}}, "title": "Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration", "authors": [{"family": "Sun", "given": "Xiaohuan", "initials": "X"}, {"family": "Cahill", "given": "James", "initials": "J"}, {"family": "Van Hautegem", "given": "Tom", "initials": "T"}, {"family": "Feys", "given": "Kim", "initials": "K"}, {"family": "Whipple", "given": "Clinton", "initials": "C"}, {"family": "Nov\u00e1k", "given": "Ondrej", "initials": "O"}, {"family": "Delbare", "given": "Sofie", "initials": "S"}, {"family": "Versteele", "given": "Charlot", "initials": "C"}, {"family": "Demuynck", "given": "Kirin", "initials": "K"}, {"family": "De Block", "given": "Jolien", "initials": "J"}, {"family": "Storme", "given": "Veronique", "initials": "V"}, {"family": "Claeys", "given": "Hannes", "initials": "H"}, {"family": "Van Lijsebettens", "given": "Mieke", "initials": "M"}, {"family": "Coussens", "given": "Griet", "initials": "G"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "De Vliegher", "given": "Alex", "initials": "A"}, {"family": "Muszynski", "given": "Michael", "initials": "M"}, {"family": "Inz\u00e9", "given": "Dirk", "initials": "D"}, {"family": "Nelissen", "given": "Hilde", "initials": "H"}], "type": "journal-article", "published": "2017-03-16", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "14752", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/ncomms14752", "pmid": "28300078", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:35:22.230Z", "modified": "2025-10-17T13:03:19.001Z"}, {"entity": "publication", "iuid": "924daf3262a24d6aac43a6ad82ae9e16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/924daf3262a24d6aac43a6ad82ae9e16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/924daf3262a24d6aac43a6ad82ae9e16"}}, "title": "Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26.", "authors": [{"family": "Gudmundsson", "given": "Sanna", "initials": "S"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Cahill", "given": "Nicola", "initials": "N"}, {"family": "Alexandrov", "given": "Ludmil B", "initials": "LB"}, {"family": "Virtanen", "given": "Marie", "initials": "M"}, {"family": "Hellstr\u00f6m Pigg", "given": "Maritta", "initials": "M"}, {"family": "Vahlquist", "given": "Anders", "initials": "A"}, {"family": "T\u00f6rm\u00e4", "given": "Hans", "initials": "H"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}], "type": "journal article", "published": "2017-03-15", "journal": {"volume": "26", "issn": "1460-2083", "issue": "6", "pages": "1070-1077", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Revertant mosaicism (RM) is a naturally occurring phenomenon where the pathogenic effect of a germline mutation is corrected by a second somatic event. Development of healthy-looking skin due to RM has been observed in patients with various inherited skin disorders, but not in connexin-related disease. We aimed to clarify the underlying molecular mechanisms of suspected RM in the skin of a patient with keratitis-ichthyosis-deafness (KID) syndrome. The patient was diagnosed with KID syndrome due to characteristic skin lesions, hearing deficiency and keratitis. Investigation of GJB2 encoding connexin (Cx) 26 revealed heterozygosity for the recurrent de novo germline mutation, c.148G > A, p.Asp50Asn. At age 20, the patient developed spots of healthy-looking skin that grew in size and number within widespread erythrokeratodermic lesions. Ultra-deep sequencing of two healthy-looking skin biopsies identified five somatic nonsynonymous mutations, independently present in cis with the p.Asp50Asn mutation. Functional studies of Cx26 in HeLa cells revealed co-expression of Cx26-Asp50Asn and wild-type Cx26 in gap junction channel plaques. However, Cx26-Asp50Asn with the second-site mutations identified in the patient displayed no formation of gap junction channel plaques. We argue that the second-site mutations independently inhibit Cx26-Asp50Asn expression in gap junction channels, reverting the dominant negative effect of the p.Asp50Asn mutation. To our knowledge, this is the first time RM has been reported to result in the development of healthy-looking skin in a patient with KID syndrome.", "doi": "10.1093/hmg/ddx017", "pmid": "28158657", "labels": {"National Genomics Infrastructure": "Collaborative", "Clinical Genomics Uppsala": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "2965926"}, {"db": "pmc", "key": "PMC5409067"}], "notes": [], "created": "2017-10-17T08:08:10.708Z", "modified": "2024-01-16T13:48:48.302Z"}, {"entity": "publication", "iuid": "1efc9e8a5f12496091a749b6a455d5b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1efc9e8a5f12496091a749b6a455d5b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1efc9e8a5f12496091a749b6a455d5b0"}}, "title": "Endocytic turnover of Rab8 controls cell polarization.", "authors": [{"family": "Vidal-Quadras", "given": "Maite", "initials": "M"}, {"family": "Holst", "given": "Mikkel R", "initials": "MR"}, {"family": "Francis", "given": "Monika K", "initials": "MK", "orcid": "0000-0002-6806-0515", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbfa343ff09d4e7095fced73be91df51.json"}}, {"family": "Larsson", "given": "Elin", "initials": "E"}, {"family": "Hachimi", "given": "Mariam", "initials": "M"}, {"family": "Yau", "given": "Wai-Lok", "initials": "WL"}, {"family": "Per\u00e4nen", "given": "Johan", "initials": "J"}, {"family": "Mart\u00edn-Belmonte", "given": "Fernando", "initials": "F"}, {"family": "Lundmark", "given": "Richard", "initials": "R", "orcid": "0000-0001-9104-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e1b756caa79468dab0f960e43cd61d3.json"}}], "type": "journal article", "published": "2017-03-15", "journal": {"title": "J. Cell. Sci.", "issn": "1477-9137", "volume": "130", "issue": "6", "pages": "1147-1157", "issn-l": "0021-9533"}, "abstract": "Adaptation of cell shape and polarization through the formation and retraction of cellular protrusions requires balancing of endocytosis and exocytosis combined with fine-tuning of the local activity of small GTPases like Rab8. Here, we show that endocytic turnover of the plasma membrane at protrusions is directly coupled to surface removal and inactivation of Rab8. Removal is induced by reduced membrane tension and mediated by the GTPase regulator associated with focal adhesion kinase-1 (GRAF1, also known as ARHGAP26), a regulator of clathrin-independent endocytosis. GRAF1-depleted cells were deficient in multi-directional spreading and displayed elevated levels of GTP-loaded Rab8, which was accumulated at the tips of static protrusions. Furthermore, GRAF1 depletion impaired lumen formation and spindle orientation in a 3D cell culture system, indicating that GRAF1 activity regulates polarity establishment. Our data suggest that GRAF1-mediated removal of Rab8 from the cell surface restricts its activity during protrusion formation, thereby facilitating dynamic adjustment of the polarity axis.", "doi": "10.1242/jcs.195420", "pmid": "28137756", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "jcs.195420"}, {"db": "pmc", "key": "PMC5358338"}], "notes": [], "created": "2020-01-23T16:36:50.803Z", "modified": "2021-06-21T15:44:32.527Z"}, {"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"}, {"entity": "publication", "iuid": "6dfbcba9d844443089d4824b4331e464", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dfbcba9d844443089d4824b4331e464.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dfbcba9d844443089d4824b4331e464"}}, "title": "Identification of Triazolothiadiazoles as Potent Inhibitors of the dCTP Pyrophosphatase 1.", "authors": [{"family": "Llona-Minguez", "given": "Sabin", "initials": "S", "orcid": "0000-0003-3187-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/437b1f98ad21471f884226ed89a3da12.json"}}, {"family": "H\u00f6glund", "given": "Andreas", "initials": "A"}, {"family": "Wiita", "given": "Elisee", "initials": "E"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Calder\u00f3n-Monta\u00f1o", "given": "Jos\u00e9 Manuel", "initials": "JM"}, {"family": "Cazares-K\u00f6rner", "given": "Cindy", "initials": "C"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Baranczewski", "given": "Pawel", "initials": "P"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Jenmalm Jensen", "given": "Annika", "initials": "A"}, {"family": "Warpman Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2017-03-09", "journal": {"volume": "60", "issn": "1520-4804", "issue": "5", "pages": "2148-2154", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "The dCTP pyrophosphatase 1 (dCTPase) is involved in the regulation of the cellular dNTP pool and has been linked to cancer progression. Here we report on the discovery of a series of 3,6-disubstituted triazolothiadiazoles as potent dCTPase inhibitors. Compounds 16 and 18 display good correlation between enzymatic inhibition and target engagement, together with efficacy in a cellular synergy model, deeming them as a promising starting point for hit-to-lead development.", "doi": "10.1021/acs.jmedchem.6b01786", "pmid": "28145708", "labels": {"Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [], "notes": "Biochemical and Cellular Screening", "created": "2017-10-25T12:41:01.158Z", "modified": "2025-10-17T13:05:08.987Z"}, {"entity": "publication", "iuid": "d2131eeeed404689b6cf4dba0f546d6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2131eeeed404689b6cf4dba0f546d6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2131eeeed404689b6cf4dba0f546d6e"}}, "title": "Discovery of circulating proteins associated to knee radiographic osteoarthritis.", "authors": [{"family": "Lourido", "given": "Luc\u00eda", "initials": "L"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Fern\u00e1ndez-Tajes", "given": "Juan", "initials": "J"}, {"family": "Oreiro", "given": "Natividad", "initials": "N"}, {"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ruiz-Romero", "given": "Cristina", "initials": "C"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Blanco", "given": "Francisco J", "initials": "FJ"}], "type": "journal article", "published": "2017-03-09", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "137", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Currently there are no sufficiently sensitive biomarkers able to reflect changes in joint remodelling during osteoarthritis (OA). In this work, we took an affinity proteomic approach to profile serum samples for proteins that could serve as indicators for the diagnosis of radiographic knee OA. Antibody suspension bead arrays were applied to analyze serum samples from patients with OA (n\u2009=\u2009273), control subjects (n\u2009=\u200976) and patients with rheumatoid arthritis (RA, n\u2009=\u2009244). For verification, a focused bead array was built and applied to an independent set of serum samples from patients with OA (n\u2009=\u2009188), control individuals (n\u2009=\u200983) and RA (n\u2009=\u2009168) patients. A linear regression analysis adjusting for sex, age and body mass index (BMI) revealed that three proteins were significantly elevated (P\u2009<\u20090.05) in serum from OA patients compared to controls: C3, ITIH1 and S100A6. A panel consisting of these three proteins had an area under the curve of 0.82 for the classification of OA and control samples. Moreover, C3 and ITIH1 levels were also found to be significantly elevated (P\u2009<\u20090.05) in OA patients compared to RA patients. Upon validation in additional study sets, the alterations of these three candidate serum biomarker proteins could support the diagnosis of radiographic knee OA.", "doi": "10.1038/s41598-017-00195-8", "pmid": "28273936", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-00195-8"}, {"db": "pmc", "key": "PMC5427840"}], "notes": [], "created": "2017-10-30T10:15:33.970Z", "modified": "2021-07-08T12:07:34.275Z"}, {"entity": "publication", "iuid": "1f477773d0a9429885c8dab2a73981b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f477773d0a9429885c8dab2a73981b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f477773d0a9429885c8dab2a73981b1"}}, "title": "Peptide Functionalized Gold Nanoparticles as a Stimuli Responsive Contrast Medium in Multiphoton Microscopy.", "authors": [{"family": "Borglin", "given": "Johan", "initials": "J"}, {"family": "Seleg\u00e5rd", "given": "Robert", "initials": "R"}, {"family": "Aili", "given": "Daniel", "initials": "D", "orcid": "0000-0002-7001-9415", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc760610215a4dee9061f28723b97e62.json"}}, {"family": "Ericson", "given": "Marica B", "initials": "MB", "orcid": "0000-0002-5987-5915", "researcher": {"href": "https://publications.scilifelab.se/researcher/af1f53e7cd234c36bdde7121e7204ed5.json"}}], "type": "journal article", "published": "2017-03-08", "journal": {"title": "Nano Lett.", "issn": "1530-6992", "volume": "17", "issue": "3", "pages": "2102-2108", "issn-l": "1530-6984"}, "abstract": "There is a need for biochemical contrast mediators with high signal-to-noise ratios enabling noninvasive biomedical sensing, for example, for neural sensing and protein-protein interactions, in addition to cancer diagnostics. The translational challenge is to develop a biocompatible approach ensuring high biochemical contrast while avoiding a raise of the background signal. We here present a concept where gold nanoparticles (AuNPs) can be utilized as a stimuli responsive contrast medium by chemically triggering their ability to exhibit multiphoton-induced luminescence (MIL) when performing multiphoton laser scanning microscopy (MPM). Proof-of-principle is demonstrated using peptide-functionalized AuNPs sensitive to zinc ions (Zn 2+). Dispersed particles are invisible in the MPM until addition of millimolar concentrations of Zn2+ upon which MIL is enabled through particle aggregation caused by specific peptide interactions and folding. The process can be reversed by removal of the Zn2+ using a chelator, thereby resuspending the AuNPs. In addition, the concept was demonstrated by exposing the particles to matrix metalloproteinase-7 (MMP-7) causing peptide digestion resulting in AuNP aggregation, significantly elevating the MIL signal from the background. The approach is based on the principle that aggregation shifts the plasmon resonance, elevating the absorption cross section in the near-infrared wavelength region enabling onset of MIL. This Letter demonstrates how biochemical sensing can be obtained in far-field MPM and should be further exploited as a future tool for noninvasive optical biosensing.", "doi": "10.1021/acs.nanolett.7b00611", "pmid": "28215085", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-23T16:34:34.853Z", "modified": "2021-06-21T15:41:57.977Z"}, {"entity": "publication", "iuid": "b17338b5c9244e6cbebb0ecfb29ea1b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b17338b5c9244e6cbebb0ecfb29ea1b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b17338b5c9244e6cbebb0ecfb29ea1b7"}}, "title": "Life-Saving Degeneracy in the Human Immune System.", "authors": [{"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2017-03-08", "journal": {"title": "Cell Host Microbe", "issn": "1934-6069", "issn-l": "1931-3128", "volume": "21", "issue": "3", "pages": "309-310"}, "abstract": "Different human immune system components coordinate to ensure effective control of pathogens. Israel et al. (2017) examine the immune system of a patient with an inborn genetic error, presenting as impaired TLR signaling and staphylococcal disease, and uncover a beautiful example of degeneracy between innate and adaptive branches of immunity.", "doi": "10.1016/j.chom.2017.02.018", "pmid": "28279338", "labels": {"Cellular Immunomonitoring": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1931-3128(17)30080-X"}], "notes": [], "created": "2019-03-25T19:57:35.258Z", "modified": "2023-11-28T12:54:03.150Z"}, {"entity": "publication", "iuid": "233b062d1f5d47e5ac0971cd9ea0a47f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f"}}, "title": "Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG"}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Sinika", "given": "Vitaly", "initials": "V"}, {"family": "Piontek", "given": "Janusz", "initials": "J"}, {"family": "Ivanova", "given": "Svetlana", "initials": "S"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2017-03-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43950", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.", "doi": "10.1038/srep43950", "pmid": "28266657", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep43950"}, {"db": "pmc", "key": "PMC5339713"}], "notes": [], "created": "2017-11-03T16:18:39.704Z", "modified": "2021-07-07T10:48:05.331Z"}, {"entity": "publication", "iuid": "fb83d71ce8b34d139466e43e8e7f58f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb83d71ce8b34d139466e43e8e7f58f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb83d71ce8b34d139466e43e8e7f58f6"}}, "title": "Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121.", "authors": [{"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "Martinez Molledo", "given": "Maria", "initials": "M"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C", "orcid": "0000-0003-0764-7483", "researcher": {"href": "https://publications.scilifelab.se/researcher/2edefbe4254a4d16b2dafe375995ef29.json"}}], "type": "journal article", "published": "2017-03-06", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "12", "issue": "3", "pages": "e0173126", "issn-l": "1932-6203"}, "abstract": "Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed. Here we report in detail the detergent screening, crystallization, experimental MIRAS phasing, and refinement of the peptide transporter PepTSt from Streptococcus thermophilus. The space group is P3121, and the protein is crystallized in a monomeric inward facing form. The binding site is likely to be somewhat occluded, as the lobe encompassing transmembrane helices 10 and 11 is markedly bent towards the central pore of the protein, but the extent of this potential occlusion could not be determined due to disorder at the apex of the lobe. Based on structural comparisons with the seven previously determined P212121 and C2221 structures of inward facing PepTSt, the structural flexibility as well as the conformational changes mediating transition between the inward open and inward facing occluded states are discussed. In conclusion, this report improves our understanding of the structure and conformational cycle of PepTSt, and can furthermore serve as a case study, which may aid in supporting future structure determinations of additional MFS transporters or other integral membrane proteins.", "doi": "10.1371/journal.pone.0173126", "pmid": "28264013", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5338821"}, {"db": "pii", "key": "PONE-D-16-49596"}], "notes": [], "created": "2024-04-03T13:38:19.982Z", "modified": "2024-04-03T13:38:20.214Z"}, {"entity": "publication", "iuid": "71cb03a7aa104761b89ada3693fad56c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71cb03a7aa104761b89ada3693fad56c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71cb03a7aa104761b89ada3693fad56c"}}, "title": "Postnatal development of the small intestinal mucosa drives age-dependent, regio-selective susceptibility to Escherichia coli K1 infection.", "authors": [{"family": "Birchenough", "given": "George M H", "initials": "GM"}, {"family": "Dalgakiran", "given": "Fatma", "initials": "F"}, {"family": "Witcomb", "given": "Luci A", "initials": "LA"}, {"family": "Johansson", "given": "Malin E V", "initials": "ME", "orcid": "0000-0002-4237-6677", "researcher": {"href": "https://publications.scilifelab.se/researcher/520dab35c19049c8b3f1083a92e60d56.json"}}, {"family": "McCarthy", "given": "Alex J", "initials": "AJ"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC", "orcid": "0000-0002-1900-1869", "researcher": {"href": "https://publications.scilifelab.se/researcher/44b3815603154322a6dac16f2fc1c1e9.json"}}, {"family": "Taylor", "given": "Peter W", "initials": "PW"}], "type": "journal article", "published": "2017-03-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "7", "issue": "1", "pages": "83", "issn-l": "2045-2322"}, "abstract": "The strong age dependency of neonatal systemic infection with Escherichia coli K1 can be replicated in the neonatal rat. Gastrointestinal (GI) colonization of two-day-old (P2) rats leads to invasion of the blood within 48 h of initiation of colonization; pups become progressively less susceptible to infection over the P2-P9 period. We show that, in animals colonized at P2 but not at P9, E. coli K1 bacteria gain access to the enterocyte surface in the mid-region of the small intestine and translocate through the epithelial cell monolayer by an intracellular pathway to the submucosa. In this region of the GI tract, the protective mucus barrier is poorly developed but matures to full thickness over P2-P9, coincident with the development of resistance to invasion. At P9, E. coli K1 bacteria are physically separated from villi by the mucus layer and their numbers controlled by mucus-embedded antimicrobial peptides, preventing invasion of host tissues.", "doi": "10.1038/s41598-017-00123-w", "pmid": "28250440", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-00123-w"}, {"db": "pmc", "key": "PMC5427930"}], "notes": [], "created": "2020-01-23T16:34:09.203Z", "modified": "2021-06-21T14:59:19.303Z"}, {"entity": "publication", "iuid": "87340c9a3cf84389a738d51e8c157012", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87340c9a3cf84389a738d51e8c157012.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87340c9a3cf84389a738d51e8c157012"}}, "title": "Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy", "authors": [{"family": "B. Kumar", "given": "Ramakrishnan", "initials": "R"}, {"family": "Zhu", "given": "Lin", "initials": "L"}, {"family": "Hebert", "given": "Hans", "initials": "H"}, {"family": "Jegersch\u00f6ld", "given": "Caroline", "initials": "C"}], "type": "journal-article", "published": "2017-03-05", "journal": {"volume": null, "issn": "1940-087X", "issue": "121", "pages": null, "title": "J Vis Exp", "issn-l": "1940-087X"}, "abstract": null, "doi": "10.3791/55148", "pmid": "28287545", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:18.006Z", "modified": "2017-11-09T13:16:21.586Z"}, {"entity": "publication", "iuid": "21ac326da0ee45f5bd33bf1335b9fa92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21ac326da0ee45f5bd33bf1335b9fa92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21ac326da0ee45f5bd33bf1335b9fa92"}}, "title": "Antibody Validation by Immunoprecipitation Followed by Mass Spectrometry Analysis.", "authors": [{"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Preger", "given": "Charlotta", "initials": "C"}, {"family": "Marcon", "given": "Edyta", "initials": "E"}, {"family": "Lengqvist", "given": "Johan", "initials": "J"}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2017-03-04", "journal": {"volume": "1575", "issn": "1940-6029", "issue": null, "pages": "175-187", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "We describe a mass spectrometry-based approach for validation of antibody specificity. This method allows validation of antibodies or antibody fragments, against their endogenous targets. It can assess if the antibody is able to bind to its native antigen in cell lysates among thousands of other proteins, DNA, RNA, and other cellular components. In addition, it identifies other proteins the antibody is able to immunoprecipitate allowing for the assessment of antibody specificity and selectivity. This method is easily scalable, adaptable to different cell lines and conditions and has been shown to be reproducible between multiple laboratories.", "doi": "10.1007/978-1-4939-6857-2_10", "pmid": "28255880", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-25T06:05:37.967Z", "modified": "2025-10-17T13:05:08.997Z"}, {"entity": "publication", "iuid": "442e355248544b87a31a6f4208cade10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/442e355248544b87a31a6f4208cade10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/442e355248544b87a31a6f4208cade10"}}, "title": "Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy.", "authors": [{"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "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"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}], "type": "journal article", "published": "2017-03-03", "journal": {"volume": "16", "issn": "1535-3907", "issue": "3", "pages": "1300-1314", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The underlying molecular mechanisms of autoimmune diseases are poorly understood. To unravel the autoimmune processes across diseases, comprehensive and unbiased analyses of proteins targets recognized by the adaptive immune system are needed. Here we present an approach starting from high-density peptide arrays to characterize autoantibody repertoires and to identify new autoantigens. A set of ten plasma and serum samples from subjects with multiple sclerosis, narcolepsy, and without any disease diagnosis were profiled on a peptide array representing the whole proteome, hosting 2.2 million 12-mer peptides with a six amino acid lateral shift. On the basis of the IgG reactivities found on these whole-proteome peptide microarrays, a set of 23 samples was then studied on a targeted array with 174\u202f000 12-mer peptides of single amino acid lateral shift. Finally, verification of IgG reactivities was conducted with a larger sample set (n = 448) using the bead-based peptide microarrays. The presented workflow employed three different peptide microarray formats to discover and resolve the epitopes of human autoantibodies and revealed two potentially new autoantigens: MAP3K7 in multiple sclerosis and NRXN1 in narcolepsy. The presented strategy provides insights into antibody repertoire reactivity at a peptide level and may accelerate the discovery and validation of autoantigens in human diseases.", "doi": "10.1021/acs.jproteome.6b00916", "pmid": "28121444", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:40:32.221Z", "modified": "2021-07-08T13:44:33.196Z"}, {"entity": "publication", "iuid": "358994257989494b85e108f04b2dd78d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/358994257989494b85e108f04b2dd78d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/358994257989494b85e108f04b2dd78d"}}, "title": "Evidence of both systemic inflammation and neuroinflammation in fibromyalgia patients, as assessed by a multiplex protein panel applied to the cerebrospinal fluid and to plasma.", "authors": [{"family": "B\u00e4ckryd", "given": "Emmanuel", "initials": "E"}, {"family": "Tanum", "given": "Lars", "initials": "L"}, {"family": "Lind", "given": "Anne-Li", "initials": "AL"}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3161-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/2276de26382b402aa384ac231f30f156.json"}}, {"family": "Gordh", "given": "Torsten", "initials": "T"}], "type": "journal article", "published": "2017-03-03", "journal": {"title": "J Pain Res", "issn": "1178-7090", "issn-l": "1178-7090", "volume": "10", "issue": null, "pages": "515-525"}, "abstract": "In addition to central hyperexcitability and impaired top-down modulation, chronic inflammation probably plays a role in the pathophysiology of fibromyalgia (FM). Indeed, on the basis of both animal experiments and human studies involving the analysis of cytokines and other inflammation-related proteins in different body fluids, neuroinflammatory mechanisms are considered to be central to the pathophysiology of many chronic pain conditions. However, concerning FM, previous human plasma/serum and/or cerebrospinal fluid (CSF) cytokine studies have looked only at a few predetermined cytokine candidates. Instead of analyzing only a few substances at a time, we used a new multiplex protein panel enabling simultaneous analysis of 92 inflammation-related proteins. Hence, we investigated the CSF and plasma inflammatory profiles of 40 FM patients compared with CSF from healthy controls (n=10) and plasma from blood donor controls (n=46). Using multivariate data analysis by projection, we found evidence of both neuroinflammation (as assessed in CSF) and chronic systemic inflammation (as assessed in plasma). Two groups of proteins (one for CSF and one for plasma) highly discriminating between patients and controls are presented. Notably, we found high levels of CSF chemokine CX3CL1 (also known as fractalkine). In addition, previous findings concerning IL-8 in FM were replicated, in both CSF and plasma. This is the first time that such an extensive inflammatory profile has been described for FM patients. Hence, FM seems to be characterized by objective biochemical alterations, and the lingering characterization of its mechanisms as essentially idiopathic or even psychogenic should be seen as definitively outdated.", "doi": "10.2147/JPR.S128508", "pmid": "28424559", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "jpr-10-515"}, {"db": "pmc", "key": "PMC5344444"}], "notes": [], "created": "2020-01-23T15:13:40.778Z", "modified": "2023-04-14T13:56:16.599Z"}, {"entity": "publication", "iuid": "ecbaa43f8e1f4ee0accd6bafac629dce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecbaa43f8e1f4ee0accd6bafac629dce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecbaa43f8e1f4ee0accd6bafac629dce"}}, "title": "Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.", "authors": [{"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Hettling", "given": "Hannes", "initials": "H"}, {"family": "Condamine", "given": "Fabien L", "initials": "FL"}, {"family": "Vos", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Sanderson", "given": "Michael J", "initials": "MJ"}, {"family": "Sauquet", "given": "Herv\u00e9", "initials": "H"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Oxelman", "given": "Bengt", "initials": "B"}, {"family": "Vos", "given": "Rutger A", "initials": "RA"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "66", "issn": "1076-836X", "issue": "2", "pages": "152-166", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a \"Dated Tree of Life\" where all node ages are directly comparable. [Bayesian phylogenetics; data mining; divide-and-conquer methods; GenBank; multilocus multispecies coalescent; next-generation sequencing; palms; primates; tree calibration.].", "doi": "10.1093/sysbio/syw066", "pmid": "27616324", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "syw066"}, {"db": "pmc", "key": "PMC5410925"}, {"db": "Dryad", "key": "10.5061/dryad.sk81k"}], "notes": [], "created": "2019-01-14T19:03:30.954Z", "modified": "2021-06-21T15:55:31.210Z"}, {"entity": "publication", "iuid": "0d5fa939ffd84f5eb9884fe38f94ad39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d5fa939ffd84f5eb9884fe38f94ad39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d5fa939ffd84f5eb9884fe38f94ad39"}}, "title": "SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.", "authors": [{"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Zizka", "given": "Alexander", "initials": "A"}, {"family": "Cali\u00f3", "given": "Maria Fernanda", "initials": "MF"}, {"family": "Scharn", "given": "Ruud", "initials": "R"}, {"family": "Silvestro", "given": "Daniele", "initials": "D"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "66", "issn": "1076-836X", "issue": "2", "pages": "145-151", "title": "Syst. Biol.", "issn-l": "1063-5157"}, "abstract": "Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. [ancestral area reconstruction; biodiversity patterns; ecology; evolution; point in polygon; species distribution data.].", "doi": "10.1093/sysbio/syw064", "pmid": "27486181", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "syw064"}, {"db": "pmc", "key": "PMC5410971"}, {"db": "Dryad", "key": "10.5061/dryad.tm32k"}], "notes": [], "created": "2019-01-14T19:02:47.673Z", "modified": "2021-06-21T15:56:01.806Z"}, {"entity": "publication", "iuid": "6bc70b0130924ae9bc7190acaeb79387", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6bc70b0130924ae9bc7190acaeb79387.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6bc70b0130924ae9bc7190acaeb79387"}}, "title": "Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus.", "authors": [{"family": "Immonen", "given": "Elina", "initials": "E"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Bayram", "given": "Helen", "initials": "H"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "3", "pages": "677-699", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Sexually dimorphic phenotypes arise largely from sex-specific gene expression, which has mainly been characterized in sexually na\u00efve adults. However, we expect sexual dimorphism in transcription to be dynamic and dependent on factors such as reproductive status. Mating induces many behavioral and physiological changes distinct to each sex and is therefore expected to activate regulatory changes in many sex-biased genes. Here, we first characterized sexual dimorphism in gene expression in Callosobruchus maculatus seed beetles. We then examined how females and males respond to mating and how it affects sex-biased expression, both in sex-limited (abdomen) and sex-shared (head and thorax) tissues. Mating responses were largely sex-specific and, as expected, females showed more genes responding compared with males (\u223c2,000 vs. \u223c300 genes in the abdomen, \u223c500 vs. \u223c400 in the head and thorax, respectively). Of the sex-biased genes present in virgins, 16% (1,041 genes) in the abdomen and 17% (243 genes) in the head and thorax altered their relative expression between the sexes as a result of mating. Sex-bias status changed in 2% of the genes in the abdomen and 4% in the head and thorax following mating. Mating responses involved de-feminization of females and, to a lesser extent, de-masculinization of males relative to their virgin state: mating decreased rather than increased dimorphic expression of sex-biased genes. The fact that regulatory changes of both types of sex-biased genes occurred in both sexes suggests that male- and female-specific selection is not restricted to male- and female-biased genes, respectively, as is sometimes assumed.", "doi": "10.1093/gbe/evx029", "pmid": "28391318", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3039479"}], "notes": [], "created": "2017-10-17T09:27:20.453Z", "modified": "2024-01-16T13:48:48.324Z"}, {"entity": "publication", "iuid": "d76c5dadcc0f4b3a8c4a2839d6667beb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d76c5dadcc0f4b3a8c4a2839d6667beb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d76c5dadcc0f4b3a8c4a2839d6667beb"}}, "title": "Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae).", "authors": [{"family": "Haddad", "given": "Nizar Jamal", "initials": "NJ", "orcid": "0000-0003-0250-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ff610b5673c4050a4e4377c48b2a372.json"}}, {"family": "Al-Nakeeb", "given": "Kosai", "initials": "K", "orcid": "0000-0003-3432-3628", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d87f93200b4f0ba3480a0f975e9cd9.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Blom", "given": "Nikolaj", "initials": "N", "orcid": "0000-0001-8012-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd245cd9d02443f4814e6fb1e949265d.json"}}, {"family": "Sicheritz-Pont\u00e9n", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "2", "issn": "2380-2359", "issue": "1", "pages": "139-140", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "The Oriental Hornet ( Vespa orientalis) is a social insect belonging to the Vespiade family (Wasps, Hornets, Yellowjackets), genus Vespa (true Hornets). The oriental hornet is a scavenger and an agricultural pest, especially to bee farmers, but is also recently described as a harvester of solar energy. Here, we report the mitochondrial genome sequence of the Oriental Hornet, Vespa orientalis F., which may play a vital role in understanding this wasp biology, light trapping and generation of electricity. The mitochondrial genome of this hornet is 16,099 bp in length, containing 13 protein-coding genes, 21 transfer RNA genes, and 2 ribosomal RNA genes. The overall base composition of the heavy-strand is 40.3% A, 5.9% C, 13.2% G, and 40.6% T, the percentages of A and T being higher than that of G and C. The mitochondrial genome of the Oriental Hornet, Vespa orientalis F. represents the first mitogenome of a solar energy harvesting insect.", "doi": "10.1080/23802359.2017.1292480", "pmid": "33473744", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1292480"}, {"db": "pmc", "key": "PMC7800523"}], "notes": [], "created": "2017-11-03T15:53:38.192Z", "modified": "2021-06-21T15:47:32.461Z"}, {"entity": "publication", "iuid": "da7cdc7b5fb04abeb8a08c52ea256402", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da7cdc7b5fb04abeb8a08c52ea256402.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da7cdc7b5fb04abeb8a08c52ea256402"}}, "title": "Use of a proximity extension assay proteomics chip to discover new biomarkers associated with albuminuria.", "authors": [{"family": "Carlsson", "given": "Axel C", "initials": "AC"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Carrero", "given": "Juan Jesus", "initials": "JJ"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Stenemo", "given": "Markus", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-03-00", "journal": {"title": "Eur J Prev Cardiol", "issn": "2047-4881", "issn-l": "2047-4873", "volume": "24", "issue": "4", "pages": "340-348"}, "abstract": "Background The underlying mechanisms for the development of albuminuria and the increased cardiovascular risk in patients with elevated albuminuria levels are incompletely understood. We therefore investigated the associations between 80 cardiovascular proteins and the urinary albumin to creatinine ratio (ACR). Methods We used a discovery/replication approach in two independent community-based cohorts of elderly patients: the Uppsala Longitudinal Study of Adult Men ( n = 662; mean age 78 years) and the Prospective Investigation of the Vasculature in Uppsala Seniors ( n = 757; mean age 75 years; 51% women). A proteomic chip with a panel of 80 plasma proteins associated with different aspects of cardiovascular disease was analysed. In the discovery cohort, we used a false discovery rate of 5% to take into account the multiple statistical testing. Nominal p values were used in the replication. Results Higher levels of T-cell immunoglobulin mucin-1, placenta growth factor, growth/differentiation factor-15, urokinase plasminogen activator surface receptor and kallikrein-11 were robustly associated with a higher ACR in both cohorts in multivariable linear regression models adjusted for sex, established cardiovascular risk factors, antihypertensive treatment, prevalent cardiovascular disease and glomerular filtration rate ( p < 0.02 for all). All associations were also significant in separate analyses of patients without diabetes. Conclusions We discovered and replicated associations between ACR and five cardiovascular proteins involved in tubular injury, atherosclerosis, endothelial function, heart failure, inflammation, glomerulosclerosis and podocyte injury. Our findings put forward multiplex proteomics as a promising approach to explore novel aspects of the complex detrimental interplay between kidney function and the cardiovascular system.", "doi": "10.1177/2047487316676134", "pmid": "27794105", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "2047487316676134"}], "notes": [], "created": "2017-05-03T13:02:18.732Z", "modified": "2023-04-14T13:56:16.778Z"}, {"entity": "publication", "iuid": "82328e28bb30498ca7414a9ad5c2ecf2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82328e28bb30498ca7414a9ad5c2ecf2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82328e28bb30498ca7414a9ad5c2ecf2"}}, "title": "Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays", "authors": [{"family": "Larssen", "given": "Pia", "initials": "P"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Eldh", "given": "Maria", "initials": "M"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Ronquist", "given": "K G\u00f6ran", "initials": "KG"}, {"family": "Dubois", "given": "Louise", "initials": "L"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Oelrich", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Ronquist", "given": "Gunnar", "initials": "G"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Gabrielsson", "given": "Susanne", "initials": "S"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "16", "issn": "1535-9476", "issue": "3", "pages": "502-511", "title": "Mol Cell Proteomics", "issn-l": "1535-9476"}, "abstract": null, "doi": "10.1074/mcp.m116.064725", "pmid": "28111361", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:55:02.303Z", "modified": "2023-04-14T13:56:17.086Z"}, {"entity": "publication", "iuid": "0d12224d115c4264913af93ddf48ea97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d12224d115c4264913af93ddf48ea97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d12224d115c4264913af93ddf48ea97"}}, "title": "Towards a whole-genome sequence for rye (Secale cereale L.).", "authors": [{"family": "Bauer", "given": "Eva", "initials": "E"}, {"family": "Schmutzer", "given": "Thomas", "initials": "T"}, {"family": "Barilar", "given": "Ivan", "initials": "I"}, {"family": "Mascher", "given": "Martin", "initials": "M"}, {"family": "Gundlach", "given": "Heidrun", "initials": "H"}, {"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Twardziok", "given": "Sven O", "initials": "SO"}, {"family": "Hackauf", "given": "Bernd", "initials": "B"}, {"family": "Gordillo", "given": "Andres", "initials": "A"}, {"family": "Wilde", "given": "Peer", "initials": "P"}, {"family": "Schmidt", "given": "Malthe", "initials": "M"}, {"family": "Korzun", "given": "Viktor", "initials": "V"}, {"family": "Mayer", "given": "Klaus F X", "initials": "KF"}, {"family": "Schmid", "given": "Karl", "initials": "K"}, {"family": "Sch\u00f6n", "given": "Chris-Carolin", "initials": "CC"}, {"family": "Scholz", "given": "Uwe", "initials": "U"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "89", "issn": "1365-313X", "issue": "5", "pages": "853-869", "title": "Plant J.", "issn-l": "0960-7412"}, "abstract": "We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8\u00a0Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27\u00a0784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S.\u00a0vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600\u00a0843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.", "doi": "10.1111/tpj.13436", "pmid": "27888547", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "GENBANK", "key": "ERS455621"}, {"db": "GENBANK", "key": "ERS455631"}, {"db": "GENBANK", "key": "ERS1115868"}], "notes": [], "created": "2017-05-03T13:00:45.334Z", "modified": "2020-01-21T13:53:21.218Z"}, {"entity": "publication", "iuid": "812e665e561c421f97d2887a450329ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/812e665e561c421f97d2887a450329ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/812e665e561c421f97d2887a450329ab"}}, "title": "Strain improvement of Pichia kudriavzevii TY13 for raised phytase production and reduced phosphate repression.", "authors": [{"family": "Qvirist", "given": "Linnea", "initials": "L"}, {"family": "Vorontsov", "given": "Egor", "initials": "E"}, {"family": "Veide Vilg", "given": "Jenny", "initials": "J"}, {"family": "Andlid", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2017-03-00", "journal": {"title": "Microb Biotechnol", "issn": "1751-7915", "volume": "10", "issue": "2", "pages": "341-353", "issn-l": "1751-7915"}, "abstract": "In this work, we present the development and characterization of a strain of Pichia kudriavzevii (TY1322), with highly improved phytate-degrading capacity. The mutant strain TY1322 shows a biomass-specific phytate degradation of 1.26 mmol g -1 h-1 after 8 h of cultivation in a high-phosphate medium, which is about 8 times higher compared with the wild-type strain. Strain TY1322 was able to grow at low pH (pH 2), at high temperature (46\u00b0C) and in the presence of ox bile (2% w/v), indicating this strain's ability to survive passage through the gastrointestinal tract. The purified phytase showed two pH optima, at pH 3.5 and 5.5, and one temperature optimum at 55\u00b0C. The lower pH optimum of 3.5 matches the reported pH of the pig stomach, meaning that TY1322 and/or its phytase is highly suitable for use in feed production. Furthermore, P. kudriavzevii TY1322 tolerates ethanol up to 6% (v/v) and shows high osmotic stress tolerance. Owing to the phenotypic characteristics and non-genetically modified organisms nature of TY1322, this strain show great potential for future uses in (i) cereal fermentations for increased mineral bioavailability, and (ii) feed production to increase the phosphate bioavailability for monogastric animals to reduce the need for artificial phosphate fortification.", "doi": "10.1111/1751-7915.12427", "pmid": "27790831", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5328827"}], "notes": [], "created": "2020-01-30T15:58:19.867Z", "modified": "2024-01-16T13:46:32.776Z"}, {"entity": "publication", "iuid": "edc13d5d3d614305b2c9c16e2d3529b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edc13d5d3d614305b2c9c16e2d3529b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edc13d5d3d614305b2c9c16e2d3529b6"}}, "title": "Stool frequency is associated with gut microbiota composition.", "authors": [{"family": "Hadizadeh", "given": "Fatemeh", "initials": "F"}, {"family": "Walter", "given": "Susanna", "initials": "S"}, {"family": "Belheouane", "given": "Meriem", "initials": "M"}, {"family": "Bonfiglio", "given": "Ferdinando", "initials": "F"}, {"family": "Heinsen", "given": "Femke-Anouska", "initials": "FA"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Agreus", "given": "Lars", "initials": "L"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Baines", "given": "John F", "initials": "JF"}, {"family": "Rafter", "given": "Joseph", "initials": "J"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}], "type": "letter", "published": "2017-03-00", "journal": {"volume": "66", "issn": "1468-3288", "issue": "3", "pages": "559-560", "title": "Gut", "issn-l": "0017-5749"}, "abstract": null, "doi": "10.1136/gutjnl-2016-311935", "pmid": "27196592", "labels": {"Clinical Genomics Stockholm": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "gutjnl-2016-311935"}], "notes": [], "created": "2017-05-03T13:02:21.337Z", "modified": "2017-09-06T11:51:11.992Z"}, {"entity": "publication", "iuid": "e91441b2860b4da08bfcee67837224b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e91441b2860b4da08bfcee67837224b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e91441b2860b4da08bfcee67837224b4"}}, "title": "Signs of ongoing inflammation in female patients with chronic widespread pain: A multivariate, explorative, cross-sectional study of blood samples.", "authors": [{"family": "Gerdle", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ghafouri", "given": "Bijar", "initials": "B"}, {"family": "Ghafouri", "given": "Nazdar", "initials": "N"}, {"family": "B\u00e4ckryd", "given": "Emmanuel", "initials": "E"}, {"family": "Gordh", "given": "Torsten", "initials": "T"}], "type": "journal article", "published": "2017-03-00", "journal": {"title": "Medicine", "issn": "1536-5964", "issn-l": "0025-7974", "volume": "96", "issue": "9", "pages": "e6130"}, "abstract": "This cross-sectional study investigates the plasma inflammatory profile of chronic widespread pain (CWP) patients compared to healthy controls (CON). Rather than analyzing a relatively few substances at a time, we used a new multiplex proximity extension assay (PEA) panel that enabled the simultaneous analysis of 92 inflammation-related proteins, mainly cytokines and chemokines.Seventeen women with CWP and 21 female CON participated and a venous blood sample was drawn from all subjects. Pain intensity and pain thresholds for pressure, heat, and cold were registered. A PEA panel (92 proteins) was used to analyze the blood samples. Multivariate data analysis by projection was used in the statistical analyses.Eleven proteins significantly differentiated the CON and CWP subjects (R = 0.58, Q = 0.37, analysis of variance of cross-validated predictive residuals P = 0.006). It was not possible to significantly regress pain thresholds within each group (CON or CWP). Positive significant correlations existed between several proteins and pain intensities in CWP, but the model reliability of the regression was poor.CWP was associated with systemic low-grade inflammation. Larger studies are needed to confirm the results and to investigate which alterations are condition-specific and which are common across chronic pain conditions. The presence of inflammation could promote the spreading of pain, a hallmark sign of CWP. As it has been suggested that prevalent comorbidities to pain (e.g., depression and anxiety, poor sleep, and tiredness) also are associated with inflammation, it will be important to determine whether inflammation may be a common mediator.", "doi": "10.1097/MD.0000000000006130", "pmid": "28248866", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "00005792-201703030-00017"}, {"db": "pmc", "key": "PMC5340439"}], "notes": [], "created": "2020-01-23T15:13:40.445Z", "modified": "2023-04-14T13:56:17.294Z"}, {"entity": "publication", "iuid": "43db2f8fcbdb41a4b435ac0e229e7a41", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43db2f8fcbdb41a4b435ac0e229e7a41.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43db2f8fcbdb41a4b435ac0e229e7a41"}}, "title": "Reducing VEGF-B Signaling Ameliorates Renal Lipotoxicity and Protects against Diabetic Kidney Disease", "authors": [{"family": "Falkevall", "given": "Annelie", "initials": "A"}, {"family": "Mehlem", "given": "Annika", "initials": "A"}, {"family": "Palombo", "given": "Isolde", "initials": "I"}, {"family": "Heller Sahlgren", "given": "Benjamin", "initials": "B"}, {"family": "Ebarasi", "given": "Lwaki", "initials": "L"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Ytterberg", "given": "A Jimmy", "initials": "AJ"}, {"family": "Olauson", "given": "Hannes", "initials": "H"}, {"family": "Axelsson", "given": "Jonas", "initials": "J"}, {"family": "Sundelin", "given": "Birgitta", "initials": "B"}, {"family": "Patrakka", "given": "Jaakko", "initials": "J"}, {"family": "Scotney", "given": "Pierre", "initials": "P"}, {"family": "Nash", "given": "Andrew", "initials": "A"}, {"family": "Eriksson", "given": "Ulf", "initials": "U"}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "25", "issn": "1550-4131", "issue": "3", "pages": "713-726", "title": "Cell Metabolism", "issn-l": "1550-4131"}, "abstract": null, "doi": "10.1016/j.cmet.2017.01.004", "pmid": "28190774", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:31:15.466Z", "modified": "2025-10-17T13:03:19.022Z"}, {"entity": "publication", "iuid": "7a3a7dc0fde540518b370680b462c0a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a3a7dc0fde540518b370680b462c0a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a3a7dc0fde540518b370680b462c0a9"}}, "title": "Phylogenetic analysis of  Monascus  and new species from honey, pollen and nests of stingless bees", "authors": [{"family": "Barbosa", "given": "R N", "initials": "RN"}, {"family": "Leong", "given": "S L", "initials": "SL"}, {"family": "Vinnere-Pettersson", "given": "O", "initials": "O"}, {"family": "Chen", "given": "A J", "initials": "AJ"}, {"family": "Souza-Motta", "given": "C M", "initials": "CM"}, {"family": "Frisvad", "given": "J C", "initials": "JC"}, {"family": "Samson", "given": "R A", "initials": "RA"}, {"family": "Oliveira", "given": "N T", "initials": "NT"}, {"family": "Houbraken", "given": "J", "initials": "J"}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "86", "issn": "0166-0616", "issue": null, "pages": "29-51", "title": "Studies in Mycology", "issn-l": null}, "abstract": null, "doi": "10.1016/j.simyco.2017.04.001", "pmid": "28539687", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:30:33.063Z", "modified": "2020-01-21T13:56:11.674Z"}, {"entity": "publication", "iuid": "e6e4e79409034a12a92271d4450846c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6e4e79409034a12a92271d4450846c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6e4e79409034a12a92271d4450846c2"}}, "title": "Overexpression of protein kinase STK25 in mice exacerbates ectopic lipid accumulation, mitochondrial dysfunction and insulin resistance in skeletal muscle.", "authors": [{"family": "Chursa", "given": "Urszula", "initials": "U"}, {"family": "Nu\u00f1ez-Dur\u00e1n", "given": "Esther", "initials": "E"}, {"family": "Cansby", "given": "Emmelie", "initials": "E"}, {"family": "Amrutkar", "given": "Manoj", "initials": "M"}, {"family": "S\u00fctt", "given": "Silva", "initials": "S"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Olsson", "given": "Britt-Marie", "initials": "BM"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Johansson", "given": "Maria E", "initials": "ME"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Johansson", "given": "Bengt R", "initials": "BR"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Mahlapuu", "given": "Margit", "initials": "M"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "60", "issn": "1432-0428", "issue": "3", "pages": "553-567", "title": "Diabetologia", "issn-l": "0012-186X"}, "abstract": "Understanding the molecular networks controlling ectopic lipid deposition and insulin responsiveness in skeletal muscle is essential for developing new strategies to treat type 2 diabetes. We recently identified serine/threonine protein kinase 25 (STK25) as a critical regulator of liver steatosis, hepatic lipid metabolism and whole body glucose and insulin homeostasis. Here, we assessed the role of STK25 in control of ectopic fat storage and insulin responsiveness in skeletal muscle.\n\nSkeletal muscle morphology was studied by histological examination, exercise performance and insulin sensitivity were assessed by treadmill running and euglycaemic-hyperinsulinaemic clamp, respectively, and muscle lipid metabolism was analysed by ex vivo assays in Stk25 transgenic and wild-type mice fed a high-fat diet. Lipid accumulation and mitochondrial function were also studied in rodent myoblasts overexpressing STK25. Global quantitative phosphoproteomics was performed in skeletal muscle of Stk25 transgenic and wild-type mice fed a high-fat diet to identify potential downstream mediators of STK25 action.\n\nWe found that overexpression of STK25 in transgenic mice fed a high-fat diet increases intramyocellular lipid accumulation, impairs skeletal muscle mitochondrial function and sarcomeric ultrastructure, and induces perimysial and endomysial fibrosis, thereby reducing endurance exercise capacity and muscle insulin sensitivity. Furthermore, we observed enhanced lipid accumulation and impaired mitochondrial function in rodent myoblasts overexpressing STK25, demonstrating an autonomous action for STK25 within cells. Global phosphoproteomic analysis revealed alterations in the total abundance and phosphorylation status of different target proteins located predominantly to mitochondria and sarcomeric contractile elements in Stk25 transgenic vs wild-type muscle, respectively, providing a possible molecular mechanism for the observed phenotype.\n\nSTK25 emerges as a new regulator of the complex interplay between lipid storage, mitochondrial energetics and insulin action in skeletal muscle, highlighting the potential of STK25 antagonists for type 2 diabetes treatment.", "doi": "10.1007/s00125-016-4171-5", "pmid": "27981357", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00125-016-4171-5"}, {"db": "pmc", "key": "PMC6518105"}], "notes": [], "created": "2020-01-27T22:46:09.731Z", "modified": "2024-01-16T13:46:32.787Z"}, {"entity": "publication", "iuid": "8b4b362f5f4b417c937c972e94b1ace8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b4b362f5f4b417c937c972e94b1ace8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b4b362f5f4b417c937c972e94b1ace8"}}, "title": "Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Ekstam", "given": "B\u00f6rje", "initials": "B"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "19", "issn": "1462-2920", "issue": "3", "pages": "1222-1236", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.", "doi": "10.1111/1462-2920.13650", "pmid": "28028880", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:11:41.751Z", "modified": "2024-01-16T13:48:48.333Z"}, {"entity": "publication", "iuid": "725b691fbefb457a9acd5f5fd689c118", "links": {"self": {"href": "https://publications.scilifelab.se/publication/725b691fbefb457a9acd5f5fd689c118.json"}, "display": {"href": "https://publications.scilifelab.se/publication/725b691fbefb457a9acd5f5fd689c118"}}, "title": "Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences", "authors": [{"family": "Kardos", "given": "Marty", "initials": "M"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "205", "issn": "1943-2631", "issue": "3", "pages": "1319-1334", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": null, "doi": "10.1534/genetics.116.198861", "pmid": "28100590", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genetic variation in Ficedula flycatchers", "key": "PRJEB7359"}, {"db": "BioProject", "description": "Detecting QTL in natural populations", "key": "PRJEB11502"}], "notes": [], "created": "2017-10-19T20:22:23.226Z", "modified": "2024-01-16T13:48:48.342Z"}, {"entity": "publication", "iuid": "9d31db38ff3e46ff85f710dfcf4c086c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d31db38ff3e46ff85f710dfcf4c086c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d31db38ff3e46ff85f710dfcf4c086c"}}, "title": "High GC content causes orphan proteins to be intrinsically disordered.", "authors": [{"family": "Basile", "given": "Walter", "initials": "W"}, {"family": "Sachenkova", "given": "Oxana", "initials": "O"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "13", "issn": "1553-7358", "issue": "3", "pages": "e1005375", "title": "PLoS Comput. Biol.", "issn-l": "1553-734X"}, "abstract": "De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population. These orphan proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported. In Drosophila young proteins are more disordered than ancient ones, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed. To solve this riddle we studied structural properties and age of proteins in 187 eukaryotic organisms. We find that, with the exception of length, there are only small differences in the properties between proteins of different ages. However, when we take the GC content into account we noted that it could explain the opposite trends observed for orphans in yeast (low GC) and Drosophila (high GC). GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins. Instead these proteins largely resemble random proteins given a particular GC level. During evolution the properties of a protein change faster than the GC level causing the relationship between disorder and GC to gradually weaken.", "doi": "10.1371/journal.pcbi.1005375", "pmid": "28355220", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PCOMPBIOL-D-16-01242"}, {"db": "pmc", "key": "PMC5389847"}], "notes": [], "created": "2017-11-10T13:08:08.198Z", "modified": "2020-01-21T13:53:21.871Z"}, {"entity": "publication", "iuid": "d184f17edf224ccfa2872001d101e3aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d184f17edf224ccfa2872001d101e3aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d184f17edf224ccfa2872001d101e3aa"}}, "title": "Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes.", "authors": [{"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "Andersson", "given": "Sofia", "initials": "S"}, {"family": "Winiecka-Krusnell", "given": "Jadwiga", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Alsmark", "given": "Cecilia", "initials": "C"}, {"family": "Troell", "given": "Karin", "initials": "K"}, {"family": "Beser", "given": "Jessica", "initials": "J"}, {"family": "Arrighi", "given": "Romanico B G", "initials": "RB"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "55", "issn": "1098-660X", "issue": "3", "pages": "844-858", "title": "J. Clin. Microbiol.", "issn-l": "0095-1137"}, "abstract": "In order to improve genotyping and epidemiological analysis of Cryptosporidium spp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 different Cryptosporidium hominis patient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17\u00d7 and 490\u00d7 coverage. Sequence homology-based functional annotation identified several genes of interest, including the gene encoding Cryptosporidium oocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to the Cryptosporidium parvum reference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in the C. hominis tree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencing Cryptosporidium directly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes of Cryptosporidium from human fecal samples, while alluding to the potential for a higher degree of genotyping within Cryptosporidium epidemiology.", "doi": "10.1128/JCM.01798-16", "pmid": "28003424", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "JCM.01798-16"}, {"db": "pmc", "key": "PMC5328452"}], "notes": [], "created": "2018-01-19T17:11:46.625Z", "modified": "2021-07-06T14:53:44.798Z"}, {"entity": "publication", "iuid": "cad7ac8c65a143ce922d87d02dc1d5e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cad7ac8c65a143ce922d87d02dc1d5e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cad7ac8c65a143ce922d87d02dc1d5e5"}}, "title": "Discovery of new biomarkers for atrial fibrillation using a custom-made proteomics chip.", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Stenemo", "given": "Markus", "initials": "M"}, {"family": "Hagstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-03-00", "journal": {"title": "Heart", "issn": "1468-201X", "issn-l": "1355-6037", "volume": "103", "issue": "5", "pages": "377-382"}, "abstract": "Apart from several established clinical risk factors for atrial fibrillation (AF), a number of biomarkers have also been identified as potential risk factors for AF. None of these have so far been adopted in clinical practice.\n\nTo use a novel custom-made proteomics chip to discover new prognostic biomarkers for AF risk.\n\nIn two independent community-based cohorts (Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study (978 participants without AF, mean age 70.1 years, 50% women, median follow-up 10.0 years) and Uppsala Longitudinal Study of Adult Men (ULSAM) (n=725, mean age 77.5 years, median follow-up 7.9 years)), ninety-two plasma proteins were assessed at baseline by a proximity extension assay (PEA) chip. Of those, 85 proteins showed a call rate >70% in both cohorts.\n\nThirteen proteins were related to incident AF in PIVUS (148 events) using a false discovery rate of 5%. Of those, five were replicated in ULSAM at nominal multivariable p value (123 events, N-terminal pro-B-type natriuretic peptide (NT-pro-BNP), fibroblast growth factor 23 (FGF-23), fatty acid-binding protein 4 (FABP4), growth differentiation factor 15 (GDF-15) and interleukin-6 (IL-6)). Of those, NT-pro-BNP and FGF-23 were also associated with AF after adjusting for established AF risk factors. In a prespecified secondary analysis pooling the two data sets, T-cell immunoglobulin and mucin domain 1 (TIM-1) and adrenomedullin (AM) were also significantly related to incident AF in addition to the aforementioned five proteins (Bonferroni-adjustment). The addition of NT-pro-BNP to a model with established risk factors increased the C-statistic from 0.605 to 0.676 (p<0.0001).\n\nUsing a novel proteomics approach, we confirmed the previously reported association between NT-pro-BNP, FGF-23, GDF-15 and incident AF, and also discovered four proteins (FABP4, IL-6, TIM-1 and AM) that could be of importance in the development of AF.", "doi": "10.1136/heartjnl-2016-309764", "pmid": "27609943", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "heartjnl-2016-309764"}], "notes": [], "created": "2017-05-03T13:02:17.936Z", "modified": "2023-04-14T13:56:17.464Z"}, {"entity": "publication", "iuid": "4dc11902700e4529b5a144a21c561101", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4dc11902700e4529b5a144a21c561101.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4dc11902700e4529b5a144a21c561101"}}, "title": "Development of [(11)C]/[(3)H]THK-5351 - A potential novel carbon-11 tau imaging PET radioligand.", "authors": [{"family": "Stepanov", "given": "Vladimir", "initials": "V"}, {"family": "Svedberg", "given": "Marie", "initials": "M"}, {"family": "Jia", "given": "Zhisheng", "initials": "Z"}, {"family": "Krasikova", "given": "Raisa", "initials": "R"}, {"family": "Lemoine", "given": "Laetitia", "initials": "L"}, {"family": "Okamura", "given": "Nobujuki", "initials": "N"}, {"family": "Furumoto", "given": "Shozo", "initials": "S"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "L\u00e5ngstr\u00f6m", "given": "Bengt", "initials": "B"}, {"family": "Nordberg", "given": "Agneta", "initials": "A"}, {"family": "Halldin", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "46", "issn": "1872-9614", "issue": null, "pages": "50-53", "title": "Nucl. Med. Biol.", "issn-l": "0969-8051"}, "abstract": "Due to the rise in the number of patients with dementia the imperative for finding new diagnostic and treatment options becomes ever more pressing. While significant progress has been made in PET imaging of A\u03b2 aggregates both in vitro and in vivo, options for imaging tau protein aggregates selectively are still limited. Based on the work previously published by researchers from the Tohoku University, Japan, that resulted in the development of [(18)F]THK-5351, we have undertaken an effort to develop a carbon-11 version of the identical structure - [(11)C]THK-5351. In parallel, THK-5351 was also labeled with tritium ([(3)H]THK-5351) for use in in vitro autoradiography (ARG).\n\nThe carbon-11 labeling was performed starting with di-protected enantiomeric pure precursor - tert-butyl 5-(6-((2S)-3-fluoro-2-(tetrahydro-2H-pyran-2-yloxy)propoxy)quinolin-2-yl)pyridin-2-yl carbamate, which was reacted with [(11)C]MeI, using DMF as the solvent and NaH as base, followed by deprotection with trifluoroacetic acid/water mixture, resulting in enantiomerically pure carbon-11 radioligand, [(11)C]THK-5351 - (S)-1-fluoro-3-(2-(6-([(11)C]methylamino)pyridin-3-yl)quinolin-6-yloxy)propan-2-ol. Tritium labeling and purification of [(3)H]THK-5351 were undertaken using similar approach, resulting in [(3)H]THK-5351 with RCP >99.8% and specific radioactivity of 1.3GBq/\u03bcmol.\n\n[(11)C]THK-5351 was produced in good yield (1900\u00b1355MBq), specific radioactivity (SRA) (361\u00b1119GBq/\u03bcmol at EOS+20min) and radiochemical purity (RCP) (>99.8%), with enantiomeric purity of 98.7%. [(3)H]THK-5351 was evaluated for ARG of tau binding in post-mortem human brain tissue using cortical sections from one AD patient and one control subject. [(3)H]THK-5351 binding density was higher in the AD patient compared to the control subject, the binding was displaced by unlabeled THK-5351 confirming specific [(3)H]THK-5351 binding.", "doi": "10.1016/j.nucmedbio.2016.12.004", "pmid": "28013122", "labels": {"Fluorescence Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0969-8051(16)30381-X"}], "notes": [], "created": "2017-05-03T12:58:51.897Z", "modified": "2017-06-12T11:37:16.312Z"}, {"entity": "publication", "iuid": "3174c50b7f7444a1bf2978b567b3a401", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3174c50b7f7444a1bf2978b567b3a401.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3174c50b7f7444a1bf2978b567b3a401"}}, "title": "Damaged reward areas in human alcoholics: neuronal proportion decline and astrocyte activation.", "authors": [{"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Bazov", "given": "Igor", "initials": "I"}, {"family": "Watanabe", "given": "Hiroyuki", "initials": "H"}, {"family": "Kononenko", "given": "Olga", "initials": "O"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Yakovleva", "given": "Tatiana", "initials": "T"}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}], "type": "letter", "published": "2017-03-00", "journal": {"volume": "133", "issn": "1432-0533", "issue": "3", "pages": "485-487", "title": "Acta Neuropathol.", "issn-l": "0001-6322"}, "abstract": null, "doi": "10.1007/s00401-017-1675-0", "pmid": "28097436", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00401-017-1675-0"}], "notes": [], "created": "2017-10-25T15:54:12.769Z", "modified": "2024-01-16T13:48:48.352Z"}, {"entity": "publication", "iuid": "46c57c089f404bc792706ca3baa9d9be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46c57c089f404bc792706ca3baa9d9be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46c57c089f404bc792706ca3baa9d9be"}}, "title": "DNA methylation profiling of pediatric B-cell lymphoblastic leukemia with KMT2A rearrangement identifies hypomethylation at enhancer sites.", "authors": [{"family": "Bergmann", "given": "Anke K", "initials": "AK"}, {"family": "Castellano", "given": "Giancarlo", "initials": "G"}, {"family": "Alten", "given": "Julia", "initials": "J"}, {"family": "Ammerpohl", "given": "Ole", "initials": "O"}, {"family": "Kolarova", "given": "Julia", "initials": "J"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Martin-Subero", "given": "Jose Ignacio", "initials": "JI"}, {"family": "Schrappe", "given": "Martin", "initials": "M"}, {"family": "Siebert", "given": "Reiner", "initials": "R"}], "type": "comparative study", "published": "2017-03-00", "journal": {"volume": "64", "issn": "1545-5017", "issue": "3", "title": "Pediatr Blood Cancer", "issn-l": "1545-5009"}, "abstract": "Deregulation of the epigenome is an important pathogenetic mechanism in acute lymphoblastic leukemia (ALL) with lysine (K)-specific methyltransferase 2A rearrangement (KMT2Ar). We performed array-based DNA methylation profiling of KMT2Ar ALL cells from 26 children in comparison to normal B-cell precursors. Significant changes in DNA methylation in KMT2Ar ALL were identified in 2,545 CpG loci, influenced by age and the translocation partners AFF1 and MLLT1. In KMT2Ar ALL, DNA methylation loss was enriched at enhancers and for certain transcription factor binding sites such as BCL11A, EBF, and MEF2A. In summary, DNA methylation changes in KMT2Ar ALL target enhancers, genes involved in leukemogenesis and normal hematopoiesis, as well as transcription factor networks.", "doi": "10.1002/pbc.26251", "pmid": "27786413", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:45.837Z", "modified": "2024-01-16T13:48:48.363Z"}, {"entity": "publication", "iuid": "869550206f244adb8ca27e7b6a01cbfe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/869550206f244adb8ca27e7b6a01cbfe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/869550206f244adb8ca27e7b6a01cbfe"}}, "title": "Binding and processing of \u03b2-lactam antibiotics by the transpeptidase LdtMt2fromMycobacterium tuberculosis", "authors": [{"family": "Steiner", "given": "Eva Maria", "initials": "EM"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}, {"family": "Schnell", "given": "Robert", "initials": "R"}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "284", "issn": "1742-464X", "issue": "5", "pages": "725-741", "title": "FEBS J", "issn-l": "1742-464X"}, "abstract": null, "doi": "10.1111/febs.14010", "pmid": "28075068", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:17.628Z", "modified": "2017-11-09T13:16:18.882Z"}, {"entity": "publication", "iuid": "3e47041311a44189b48417dec4292e33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e47041311a44189b48417dec4292e33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e47041311a44189b48417dec4292e33"}}, "title": "Antibody-encoding repertoires of bone marrow and peripheral blood\u2014a focus on IgE", "authors": [{"family": "Levin", "given": "Mattias", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Palmason", "given": "Robert", "initials": "R"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "139", "issn": "1085-8725", "issue": "3", "pages": "1026-1030", "title": "Journal of Allergy and Clinical Immunology", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2016.06.040", "pmid": "27521279", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0091-6749(16)30779-5"}], "notes": [], "created": "2017-05-03T12:59:52.904Z", "modified": "2024-01-16T13:48:48.371Z"}, {"entity": "publication", "iuid": "0ff8303caf2746efb3bd07ea3471a45f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ff8303caf2746efb3bd07ea3471a45f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ff8303caf2746efb3bd07ea3471a45f"}}, "title": "Anaesthetic-induced cardioprotection in an experimental model of the Takotsubo syndrome - isoflurane vs. propofol.", "authors": [{"family": "Oras", "given": "J", "initials": "J"}, {"family": "Redfors", "given": "B", "initials": "B"}, {"family": "Ali", "given": "A", "initials": "A"}, {"family": "Lundgren", "given": "J", "initials": "J"}, {"family": "Sihlbom", "given": "C", "initials": "C"}, {"family": "Thorsell", "given": "A", "initials": "A"}, {"family": "Seeman-Lodding", "given": "H", "initials": "H"}, {"family": "Omerovic", "given": "E", "initials": "E"}, {"family": "Ricksten", "given": "S-E", "initials": "SE"}], "type": "comparative study", "published": "2017-03-00", "journal": {"volume": "61", "issn": "1399-6576", "issue": "3", "pages": "309-321", "title": "Acta Anaesthesiol Scand", "issn-l": "0001-5172"}, "abstract": "Takotsubo syndrome (TS) is an acute cardiac condition with a substantial mortality for which no specific treatment is available. We have previously shown that isoflurane attenuates the development of left ventricular (LV) dysfunction in an experimental TS-model. We compared the effects of equi-anaesthetic doses of isoflurane, propofol and ketamine+midazolam on haemodynamics, global and regional LV systolic function and the activation of intracellular metabolic pathways in experimental TS. We hypothesized that cardioprotection in experimental TS is specific for isoflurane.\n\nForty-five rats were randomized to isoflurane (0.6 MAC, n = 15), propofol (bolus 200 mg/kg+360 mg/kg/h, n = 15) or ketamine (100 mg/kg)+midazolam (10 mg/kg, n = 15) anaesthesia. Arterial pressure, heart rate and body temperature were continuously measured and arterial blood gas analysis was performed intermittently. TS was induced by intraperitoneal injection of isoprenaline, 50 mg/kg. LV echocardiography was performed 90 min after isoprenaline injection. Apical cardiac tissue was analysed by global discovery proteomics and pathway analysis.\n\nIsoprenaline-induced changes in arterial blood pressure, heart rate or body temperature did not differ between groups. LV ejection fraction was higher and extent of LV akinesia was lower with isoflurane, when compared with the propofol and the ketamine+midazolam groups. In this TS-model, the proteomic analysis revealed an up-regulation of pathways involved in inflammation, coagulation, endocytosis and lipid metabolism. This up-regulation was clearly attenuated with isoflurane compared to propofol.\n\nIn an experimental model of TS, isoflurane, but not propofol, exerts a cardioprotective effect. The proteomic analysis suggests that inflammation might be involved in pathogenesis of TS.", "doi": "10.1111/aas.12857", "pmid": "28111740", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-27T22:45:18.764Z", "modified": "2024-01-16T13:46:32.815Z"}, {"entity": "publication", "iuid": "bbeba960120c414dbe625693fba033dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbeba960120c414dbe625693fba033dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbeba960120c414dbe625693fba033dd"}}, "title": "Amino acid transporter mutants of Arabidopsis provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil.", "authors": [{"family": "Ganeteg", "given": "Ulrika", "initials": "U"}, {"family": "Ahmad", "given": "Iftikhar", "initials": "I"}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S"}, {"family": "Aguetoni-Cambui", "given": "Camila", "initials": "C"}, {"family": "Inselsbacher", "given": "Erich", "initials": "E"}, {"family": "Svennerstam", "given": "Henrik", "initials": "H"}, {"family": "Schmidt", "given": "Susanne", "initials": "S"}, {"family": "N\u00e4sholm", "given": "Torgny", "initials": "T"}], "type": "journal article", "published": "2017-03-00", "journal": {"title": "Plant Cell Environ.", "issn": "1365-3040", "volume": "40", "issue": "3", "pages": "413-423", "issn-l": "0140-7791"}, "abstract": "Although organic nitrogen (N) compounds are ubiquitous in soil solutions, their potential role in plant N nutrition has been questioned. We performed a range of experiments on Arabidopsis thaliana genetically modified to enhance or reduce root uptake of amino acids. Plants lacking expression of the Lysine Histidine Transporter 1 (LHT1) displayed significantly lower contents of 13 C and 15 N label and of U-13 C5 ,15 N2 L-glutamine, as determined by liquid chromatography-mass spectrometry when growing in pots and supplied with dually labelled L-glutamine compared to wild type plants and LHT1-overexpressing plants. Slopes of regressions between accumulation of 13 C-labelled carbon and 15 N-labelled N were higher for LHT1-overexpressing plants than wild type plants, while plants lacking expression of LHT1 did not display a significant regression between the two isotopes. Uptake of labelled organic N from soil tallied with that of labelled ammonium for wild type plants and LHT1-overexpressing plants but was significantly lower for plants lacking expression of LHT1. When grown on agricultural soil plants lacking expression of LHT1 had the lowest, and plants overexpressing LHT1 the highest C/N ratios and natural \u03b415 N abundance suggesting their dependence on different N pools. Our data show that LHT1 expression is crucial for plant uptake of organic N from soil.", "doi": "10.1111/pce.12881", "pmid": "27943312", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2023-04-12T14:14:36.776Z", "modified": "2025-10-17T13:03:19.035Z"}, {"entity": "publication", "iuid": "6306f0bfadd949feaecbcd33e05f999b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6306f0bfadd949feaecbcd33e05f999b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6306f0bfadd949feaecbcd33e05f999b"}}, "title": "A genetic risk score is significantly associated with statin therapy response in the elderly population.", "authors": [{"family": "Ciuculete", "given": "D M", "initials": "DM"}, {"family": "Bandstein", "given": "M", "initials": "M"}, {"family": "Benedict", "given": "C", "initials": "C"}, {"family": "Waeber", "given": "G", "initials": "G"}, {"family": "Vollenweider", "given": "P", "initials": "P"}, {"family": "Lind", "given": "L", "initials": "L"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}, {"family": "Mwinyi", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "91", "issn": "1399-0004", "issue": "3", "pages": "379-385", "title": "Clin. Genet.", "issn-l": "0009-9163"}, "abstract": "The ability of statins to strongly reduce low-density lipoprotein cholesterol (LDL-C) varies interindividually and is partially influenced by genetic variants. Based on a comprehensive analysis of 23 single nucleotide polymorphisms (SNPs) known to be associated with pharmacokinetics and dynamics of statins, we developed a genetic risk score to study its impact on the therapy outcome in elderly individuals under at least 5 years statin therapy. The study was performed in a population-based cohort of 1016 elderly individuals, which comprised 168 statin users investigated at age 75 and 80. Using random forest models, the major variants influencing LDL-C levels were summarized in a weighted GRS (wGRS). The wGRS was tested with lipid and glucose outcomes and validated in an independent population-based cohort including 221 statin users. Four SNPs within the APOE cluster (rs7412, rs4420638), ABCC2 (rs2002042) and CELSR/SORT1/PSRC1 (rs646776), displayed a major impact on statin efficacy. The wGRS was significantly associated with lower LDL-C at age 75 and 80. This association was replicated displaying similar results. GRS analysis is a powerful tool to evaluate the additive effects of genetic variants on statin response and to estimate the magnitude of LDL-C reduction to a considerable extent in the older population.", "doi": "10.1111/cge.12890", "pmid": "27943270", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:58:53.688Z", "modified": "2024-01-16T13:48:48.381Z"}, {"entity": "publication", "iuid": "4e3c7f59473c4977898194697572f4d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e3c7f59473c4977898194697572f4d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e3c7f59473c4977898194697572f4d2"}}, "title": "Assessing the Ability of Spectroscopic Methods to Determine the Difference in the Folding Propensities of Highly Similar \u03b2-Hairpins", "authors": [{"family": "Andersson", "given": "Hanna", "initials": "H"}, {"family": "Danelius", "given": "Emma", "initials": "E"}, {"family": "Jarvoll", "given": "Patrik", "initials": "P"}, {"family": "Niebling", "given": "Stephan", "initials": "S"}, {"family": "Hughes", "given": "Ashley J", "initials": "AJ"}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S"}, {"family": "Brath", "given": "Ulrika", "initials": "U"}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M"}], "type": "journal-article", "published": "2017-02-28", "journal": {"volume": "2", "issn": "2470-1343", "issue": "2", "pages": "508-516", "title": "ACS Omega", "issn-l": "2470-1343"}, "abstract": null, "doi": "10.1021/acsomega.6b00484", "pmid": "28261689", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T10:46:28.687Z", "modified": "2025-10-17T13:03:59.962Z"}, {"entity": "publication", "iuid": "29a8d9d36c394e308816b4dce4810e24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29a8d9d36c394e308816b4dce4810e24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29a8d9d36c394e308816b4dce4810e24"}}, "title": "Measuring true localization accuracy in super resolution microscopy with DNA-origami nanostructures", "authors": [{"family": "Reuss", "given": "Matthias", "initials": "M", "orcid": "0000-0001-8914-3830", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2f2150863764c5dab34567c8a6adbcb.json"}}, {"family": "F\u00f6rd\u0151s", "given": "Ferenc", "initials": "F"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "\u00d6ktem", "given": "Ozan", "initials": "O", "orcid": "0000-0002-1118-6483", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c9a098e97474b84bfeb2208665d9a28.json"}}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications.scilifelab.se/researcher/13b88210e9b64000a27d2eb914fb519c.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}], "type": "journal-article", "published": "2017-02-27", "journal": {"volume": "19", "issn": "1367-2630", "issue": "2", "pages": "025013", "title": "New J. Phys.", "issn-l": "1367-2630"}, "abstract": "A common method to assess the performance of (super resolution) microscopes is to use the localization precision of emitters as an estimate for the achieved resolution. Naturally, this is widely used in super resolution methods based on single molecule stochastic switching. This concept suffers from the fact that it is hard to calibrate measures against a real sample (a phantom), because true absolute positions of emitters are almost always unknown. For this reason, resolution estimates are potentially biased in an image since one is blind to true position accuracy, i.e. deviation in position measurement from true positions. We have solved this issue by imaging nanorods fabricated with DNA-origami. The nanorods used are designed to have emitters attached at each end in a well-defined and highly conserved distance. These structures are widely used to gauge localization precision. Here, we additionally determined the true achievable localization accuracy and compared this figure of merit to localization precision values for two common super resolution microscope methods STED and STORM.", "doi": "10.1088/1367-2630/aa5f74", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-05T09:05:57.228Z", "modified": "2021-06-21T15:42:39.918Z"}, {"entity": "publication", "iuid": "8a7781e0bd8f4bb08cfb479a681554c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a7781e0bd8f4bb08cfb479a681554c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a7781e0bd8f4bb08cfb479a681554c1"}}, "title": "Flavonoids fromErythrina schliebenii", "authors": [{"family": "Nyandoro", "given": "Stephen S", "initials": "SS"}, {"family": "Munissi", "given": "Joan J E", "initials": "JJE"}, {"family": "Kombo", "given": "Msim", "initials": "M"}, {"family": "Mgina", "given": "Clarence A", "initials": "CA"}, {"family": "Pan", "given": "Fangfang", "initials": "F"}, {"family": "Gruhonjic", "given": "Amra", "initials": "A"}, {"family": "Fitzpatrick", "given": "Paul", "initials": "P"}, {"family": "Lu", "given": "Yu", "initials": "Y"}, {"family": "Wang", "given": "Bin", "initials": "B"}, {"family": "Rissanen", "given": "Kari", "initials": "K"}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M"}], "type": "journal-article", "published": "2017-02-24", "journal": {"volume": "80", "issn": "1520-6025", "issue": "2", "pages": "377-383", "title": "J. Nat. Prod.", "issn-l": "0163-3864"}, "abstract": null, "doi": "10.1021/acs.jnatprod.6b00839", "pmid": "28112509", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:46:06.058Z", "modified": "2025-10-17T13:03:59.973Z"}, {"entity": "publication", "iuid": "bd94aea05d1b4f7da7b5165ed48d553a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd94aea05d1b4f7da7b5165ed48d553a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd94aea05d1b4f7da7b5165ed48d553a"}}, "title": "Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.", "authors": [{"family": "Sandmann", "given": "Sarah", "initials": "S"}, {"family": "de Graaf", "given": "Aniek O", "initials": "AO"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "van der Reijden", "given": "Bert A", "initials": "BA"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Jansen", "given": "Joop H", "initials": "JH"}, {"family": "Dugas", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43169", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322\u2009bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.", "doi": "10.1038/srep43169", "pmid": "28233799", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "srep43169"}, {"db": "pmc", "key": "PMC5324109"}], "notes": [], "created": "2018-01-10T09:44:12.939Z", "modified": "2020-01-21T13:56:10.961Z"}, {"entity": "publication", "iuid": "4463761683c544979c68bd54d04d4690", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4463761683c544979c68bd54d04d4690.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4463761683c544979c68bd54d04d4690"}}, "title": "Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing.", "authors": [{"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Sirel", "given": "Madle", "initials": "M"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Del Pilar Quintana", "given": "Maria", "initials": "M"}, {"family": "Chun Leung Chan", "given": "Sherwin", "initials": "S"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Tellgren-Roth", "given": "Asa", "initials": "A"}, {"family": "Nilsson", "given": "IngMarie", "initials": "I"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43190", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.", "doi": "10.1038/srep43190", "pmid": "28233866", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "srep43190"}, {"db": "pmc", "key": "PMC5324397"}], "notes": [], "created": "2017-11-02T11:40:03.653Z", "modified": "2021-07-07T15:50:03.085Z"}, {"entity": "publication", "iuid": "2499bc475aae42a59bcc144af936e76f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2499bc475aae42a59bcc144af936e76f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2499bc475aae42a59bcc144af936e76f"}}, "title": "Characterization of the Ruler Protein Interaction Interface on the Substrate Specificity Switch Protein in the Yersinia Type III Secretion System.", "authors": [{"family": "Ho", "given": "Oanh", "initials": "O"}, {"family": "Rogne", "given": "Per", "initials": "P"}, {"family": "Edgren", "given": "Tomas", "initials": "T"}, {"family": "Wolf-Watz", "given": "Hans", "initials": "H"}, {"family": "Login", "given": "Fr\u00e9d\u00e9ric H", "initials": "FH"}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "292", "issn": "1083-351X", "issue": "8", "pages": "3299-3311", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Many pathogenic Gram-negative bacteria use the type III secretion system (T3SS) to deliver effector proteins into eukaryotic host cells. In Yersinia, the switch to secretion of effector proteins is induced first after intimate contact between the bacterium and its eukaryotic target cell has been established, and the T3SS proteins YscP and YscU play a central role in this process. Here we identify the molecular details of the YscP binding site on YscU by means of nuclear magnetic resonance (NMR) spectroscopy. The binding interface is centered on the C-terminal domain of YscU. Disrupting the YscU-YscP interaction by introducing point mutations at the interaction interface significantly reduced the secretion of effector proteins and HeLa cell cytotoxicity. Interestingly, the binding of YscP to the slowly self-cleaving YscU variant P264A conferred significant protection against autoproteolysis. The YscP-mediated inhibition of YscU autoproteolysis suggests that the cleavage event may act as a timing switch in the regulation of early versus late T3SS substrates. We also show that YscUC binds to the inner rod protein YscI with a dissociation constant (K ) of 3.8 \u03bcm and with 1:1 stoichiometry. The significant similarity among different members of the YscU, YscP, and YscI families suggests that the protein-protein interactions discussed in this study are also relevant for other T3SS-containing Gram-negative bacteria.d", "doi": "10.1074/jbc.M116.770255", "pmid": "28039361", "labels": {"Protein Science Facility (PSF)": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5336164"}, {"db": "pii", "key": "S0021-9258(20)41927-1"}, {"db": "PDB", "key": "2JLI"}], "notes": [], "created": "2017-10-23T10:56:36.771Z", "modified": "2025-10-17T13:03:59.984Z"}, {"entity": "publication", "iuid": "85bc4b574c6f4dda8c31eb30f086f852", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85bc4b574c6f4dda8c31eb30f086f852.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85bc4b574c6f4dda8c31eb30f086f852"}}, "title": "Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors", "authors": [{"family": "Thorsell", "given": "Ann Gerd", "initials": "AG"}, {"family": "Ekblad", "given": "Torun", "initials": "T"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "L\u00f6w", "given": "Mirjam", "initials": "M"}, {"family": "Pinto", "given": "Ana Filipa", "initials": "AF"}, {"family": "Tr\u00e9saugues", "given": "Lionel", "initials": "L"}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Cohen", "given": "Michael S", "initials": "MS"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}], "type": "journal-article", "published": "2017-02-23", "journal": {"volume": "60", "issn": "1520-4804", "issue": "4", "pages": "1262-1271", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": null, "doi": "10.1021/acs.jmedchem.6b00990", "pmid": "28001384", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-16T14:50:00.266Z", "modified": "2017-11-09T13:15:57.872Z"}, {"entity": "publication", "iuid": "8a981796d792400d95224a22b3d2a76a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a981796d792400d95224a22b3d2a76a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a981796d792400d95224a22b3d2a76a"}}, "title": "Intracellular drug bioavailability: a new predictor of system dependent drug disposition.", "authors": [{"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Treyer", "given": "Andrea", "initials": "A"}, {"family": "Wegler", "given": "Christine", "initials": "C"}, {"family": "Karlgren", "given": "Maria", "initials": "M"}, {"family": "Matsson", "given": "P\u00e4r", "initials": "P"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2017-02-22", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43047", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Intracellular drug exposure is influenced by cell- and tissue-dependent expression of drug-transporting proteins and metabolizing enzymes. Here, we introduce the concept of intracellular bioavailability (Fic) as the fraction of extracellular drug available to bind intracellular targets, and we assess how Fic is affected by cellular drug disposition processes. We first investigated the impact of two essential drug transporters separately, one influx transporter (OATP1B1; SLCO1B1) and one efflux transporter (P-gp; ABCB1), in cells overexpressing these proteins. We showed that OATP1B1 increased Fic of its substrates, while P-gp decreased Fic. We then investigated the impact of the concerted action of multiple transporters and metabolizing enzymes in freshly-isolated human hepatocytes in culture configurations with different levels of expression and activity of these proteins. We observed that Fic was up to 35-fold lower in the configuration with high expression of drug-eliminating transporters and enzymes. We conclude that Fic provides a measurement of the net impact of all cellular drug disposition processes on intracellular bioavailable drug levels. Importantly, no prior knowledge of the involved drug distribution pathways is required, allowing for high-throughput determination of drug access to intracellular targets in highly defined cell systems (e.g., single-transporter transfectants) or in complex ones (including primary human cells).", "doi": "10.1038/srep43047", "pmid": "28225057", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "srep43047"}, {"db": "pmc", "key": "PMC5320532"}], "notes": [], "created": "2017-10-24T12:55:23.366Z", "modified": "2025-10-17T13:05:09.017Z"}, {"entity": "publication", "iuid": "052b591e68464a66bde48f99012b379e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/052b591e68464a66bde48f99012b379e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/052b591e68464a66bde48f99012b379e"}}, "title": "Defining the human copper proteome and analysis of its expression variation in cancers.", "authors": [{"family": "Blockhuys", "given": "S", "initials": "S"}, {"family": "Celauro", "given": "E", "initials": "E"}, {"family": "Hildesj\u00f6", "given": "C", "initials": "C"}, {"family": "Feizi", "given": "A", "initials": "A"}, {"family": "St\u00e5l", "given": "O", "initials": "O"}, {"family": "Fierro-Gonz\u00e1lez", "given": "J C", "initials": "JC"}, {"family": "Wittung-Stafshede", "given": "P", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2017-02-22", "journal": {"volume": "9", "issn": "1756-591X", "issue": "2", "pages": "112-123", "title": "Metallomics", "issn-l": "1756-5901"}, "abstract": "Copper (Cu) is essential for living organisms, and acts as a cofactor in many metabolic enzymes. To avoid the toxicity of free Cu, organisms have specific transport systems that 'chaperone' the metal to targets. Cancer progression is associated with increased cellular Cu concentrations, whereby proliferative immortality, angiogenesis and metastasis are cancer hallmarks with defined requirements for Cu. The aim of this study is to gather all known Cu-binding proteins and reveal their putative involvement in cancers using the available database resources of RNA transcript levels. Using the database along with manual curation, we identified a total of 54 Cu-binding proteins (named the human Cu proteome). Next, we retrieved RNA expression levels in cancer versus normal tissues from the TCGA database for the human Cu proteome in 18 cancer types, and noted an intricate pattern of up- and downregulation of the genes in different cancers. Hierarchical clustering in combination with bioinformatics and functional genomics analyses allowed for the prediction of cancer-related Cu-binding proteins; these were specifically inspected for the breast cancer data. Finally, for the Cu chaperone ATOX1, which is the only Cu-binding protein proposed to have transcription factor activities, we validated its predicted over-expression in patient breast cancer tissue at the protein level. This collection of Cu-binding proteins, with RNA expression patterns in different cancers, will serve as an excellent resource for mechanistic-molecular studies of Cu-dependent processes in cancer.", "doi": "10.1039/c6mt00202a", "pmid": "27942658", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-15T08:23:52.183Z", "modified": "2021-06-16T16:16:13.314Z"}, {"entity": "publication", "iuid": "c6f37a4cb0494adab40df449aa3f4707", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6f37a4cb0494adab40df449aa3f4707.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6f37a4cb0494adab40df449aa3f4707"}}, "title": "Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting", "authors": [{"family": "Dutoit", "given": "Ludovic", "initials": "L"}, {"family": "Vijay", "given": "Nagarjun", "initials": "N"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Bossu", "given": "Christen M", "initials": "CM"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Wolf", "given": "Jochen", "initials": "J"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-02-22", "journal": {"volume": "284", "issn": "0962-8452", "issue": "1849", "pages": "20162756", "title": "Proc. R. Soc. B", "issn-l": "0962-8452"}, "abstract": null, "doi": "10.1098/rspb.2016.2756", "pmid": "28202815", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:24:44.458Z", "modified": "2024-01-16T13:48:48.388Z"}, {"entity": "publication", "iuid": "29c7f4009ca84ed19064680dc486ca73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29c7f4009ca84ed19064680dc486ca73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29c7f4009ca84ed19064680dc486ca73"}}, "title": "Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate.", "authors": [{"family": "Wahlestedt", "given": "Martin", "initials": "M"}, {"family": "Erlandsson", "given": "Eva", "initials": "E"}, {"family": "Kristiansen", "given": "Trine", "initials": "T"}, {"family": "Lu", "given": "Rong", "initials": "R"}, {"family": "Brakebusch", "given": "Cord", "initials": "C"}, {"family": "Weissman", "given": "Irving L", "initials": "IL"}, {"family": "Yuan", "given": "Joan", "initials": "J"}, {"family": "Martin-Gonzalez", "given": "Javier", "initials": "J"}, {"family": "Bryder", "given": "David", "initials": "D"}], "type": "journal article", "published": "2017-02-22", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "14533", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Ageing associates with significant alterations in somatic/adult stem cells and therapies to counteract these might have profound benefits for health. In the blood, haematopoietic stem cell (HSC) ageing is linked to several functional shortcomings. However, besides the recent realization that individual HSCs might be preset differentially already from young age, HSCs might also age asynchronously. Evaluating the prospects for HSC rejuvenation therefore ultimately requires approaching those HSCs that are functionally affected by age. Here we combine genetic barcoding of aged murine HSCs with the generation of induced pluripotent stem (iPS) cells. This allows us to specifically focus on aged HSCs presenting with a pronounced lineage skewing, a hallmark of HSC ageing. Functional and molecular evaluations reveal haematopoiesis from these iPS clones to be indistinguishable from that associating with young mice. Our data thereby provide direct support to the notion that several key functional attributes of HSC ageing can be reversed.", "doi": "10.1038/ncomms14533", "pmid": "28224997", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms14533"}, {"db": "pmc", "key": "PMC5322498"}], "notes": [], "created": "2017-10-17T09:41:51.769Z", "modified": "2024-01-16T13:48:48.396Z"}, {"entity": "publication", "iuid": "2f60cc890070451880d67bdcfb11753f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f60cc890070451880d67bdcfb11753f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f60cc890070451880d67bdcfb11753f"}}, "title": "RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.", "authors": [{"family": "Alkasalias", "given": "Twana", "initials": "T"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Hennig", "given": "Katharina", "initials": "K"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Lebbink", "given": "Robert Jan", "initials": "RJ"}, {"family": "Fielden", "given": "Matthew", "initials": "M"}, {"family": "Turunen", "given": "S Pauliina", "initials": "SP"}, {"family": "Lehti", "given": "Kaisa", "initials": "K"}, {"family": "Kashuba", "given": "Vladimir", "initials": "V"}, {"family": "Madapura", "given": "Harsha S", "initials": "HS"}, {"family": "Bozoky", "given": "Benedek", "initials": "B"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Balland", "given": "Martial", "initials": "M"}, {"family": "Guv\u00e9n", "given": "Hayrettin", "initials": "H"}, {"family": "Klein", "given": "George", "initials": "G"}, {"family": "Gad", "given": "Annica K B", "initials": "AK"}, {"family": "Pavlova", "given": "Tatiana", "initials": "T"}], "type": "journal article", "published": "2017-02-21", "journal": {"volume": "114", "issn": "1091-6490", "issue": "8", "pages": "E1413-E1421", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Fibroblasts are a main player in the tumor-inhibitory microenvironment. Upon tumor initiation and progression, fibroblasts can lose their tumor-inhibitory capacity and promote tumor growth. The molecular mechanisms that underlie this switch have not been defined completely. Previously, we identified four proteins overexpressed in cancer-associated fibroblasts and linked to Rho GTPase signaling. Here, we show that knocking out the Ras homolog family member A (RhoA) gene in normal fibroblasts decreased their tumor-inhibitory capacity, as judged by neighbor suppression in vitro and accompanied by promotion of tumor growth in vivo. This also induced PC3 cancer cell motility and increased colony size in 2D cultures. RhoA knockout in fibroblasts induced vimentin intermediate filament reorganization, accompanied by reduced contractile force and increased stiffness of cells. There was also loss of wide F-actin stress fibers and large focal adhesions. In addition, we observed a significant loss of \u03b1-smooth muscle actin, which indicates a difference between RhoA knockout fibroblasts and classic cancer-associated fibroblasts. In 3D collagen matrix, RhoA knockout reduced fibroblast branching and meshwork formation and resulted in more compactly clustered tumor-cell colonies in coculture with PC3 cells, which might boost tumor stem-like properties. Coculturing RhoA knockout fibroblasts and PC3 cells induced expression of proinflammatory genes in both. Inflammatory mediators may induce tumor cell stemness. Network enrichment analysis of transcriptomic changes, however, revealed that the Rho signaling pathway per se was significantly triggered only after coculturing with tumor cells. Taken together, our findings in vivo and in vitro indicate that Rho signaling governs the inhibitory effects by fibroblasts on tumor-cell growth.", "doi": "10.1073/pnas.1621161114", "pmid": "28174275", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Spatial Proteomics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1621161114"}, {"db": "pmc", "key": "PMC5338371"}], "notes": [], "created": "2017-10-30T12:42:04.006Z", "modified": "2021-07-05T16:33:38.606Z"}, {"entity": "publication", "iuid": "44d5cdcaf7f74b68991bab0d20c5fac3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44d5cdcaf7f74b68991bab0d20c5fac3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44d5cdcaf7f74b68991bab0d20c5fac3"}}, "title": "Three Chalconoids and a Pterocarpene from the Roots of Tephrosia aequilata.", "authors": [{"family": "Atilaw", "given": "Yoseph", "initials": "Y"}, {"family": "Duffy", "given": "Sandra", "initials": "S"}, {"family": "Heydenreich", "given": "Matthias", "initials": "M"}, {"family": "Muiva-Mutisya", "given": "Lois", "initials": "L"}, {"family": "Avery", "given": "Vicky M", "initials": "VM"}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M"}, {"family": "Yenesew", "given": "Abiy", "initials": "A"}], "type": "journal article", "published": "2017-02-20", "journal": {"volume": "22", "issn": "1420-3049", "issue": "2", "pages": "318", "title": "Molecules", "issn-l": "1420-3049"}, "abstract": "In our search for new antiplasmodial agents, the CH\u2082Cl\u2082/CH\u2083OH (1:1) extract of the roots of Tephrosia aequilata was investigated, and observed to cause 100% mortality of the chloroquine-sensitive (3D7) strain of Plasmodium falciparum at a 10 mg/mL concentration. From this extract three new chalconoids, E-2',6'-dimethoxy-3',4'-(2'',2''-dimethyl)pyranoretrochalcone (1, aequichalcone A), Z-2',6'-dimethoxy-3',4'-(2'',2''-dimethyl)pyranoretrochalcone (2, aequichalcone B), 4''-ethoxy-3''-hydroxypraecansone B (3, aequichalcone C) and a new pterocarpene, 3,4:8,9-dimethylenedioxy-6a,11a-pterocarpene (4), along with seven known compounds were isolated. The purified compounds were characterized by NMR spectroscopic and mass spectrometric analyses. Compound 1 slowly converts into 2 in solution, and thus the latter may have been enriched, or formed, during the extraction and separation process. The isomeric compounds 1 and 2 were both observed in the crude extract. Some of the isolated constituents showed good to moderate antiplasmodial activity against the chloroquine-sensitive (3D7) strain of Plasmodium falciparum.", "doi": "10.3390/molecules22020318", "pmid": "28230755", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "molecules22020318"}, {"db": "pmc", "key": "PMC6155904"}], "notes": [], "created": "2017-11-03T16:52:26.802Z", "modified": "2025-10-17T13:04:00.010Z"}, {"entity": "publication", "iuid": "7168b95dce2a405386fcbade449d4999", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7168b95dce2a405386fcbade449d4999.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7168b95dce2a405386fcbade449d4999"}}, "title": "Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.", "authors": [{"family": "Danielsson", "given": "Rebecca", "initials": "R"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Gonda", "given": "Horacio", "initials": "H"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Bertilsson", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2017-02-17", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": "226", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Methane (CH4) is produced as an end product from feed fermentation in the rumen. Yield of CH4 varies between individuals despite identical feeding conditions. To get a better understanding of factors behind the individual variation, 73 dairy cows given the same feed but differing in CH4 emissions were investigated with focus on fiber digestion, fermentation end products and bacterial and archaeal composition. In total 21 cows (12 Holstein, 9 Swedish Red) identified as persistent low, medium or high CH4 emitters over a 3 month period were furthermore chosen for analysis of microbial community structure in rumen fluid. This was assessed by sequencing the V4 region of 16S rRNA gene and by quantitative qPCR of targeted Methanobrevibacter groups. The results showed a positive correlation between low CH4 emitters and higher abundance of Methanobrevibacter ruminantium clade. Principal coordinate analysis (PCoA) on operational taxonomic unit (OTU) level of bacteria showed two distinct clusters (P < 0.01) that were related to CH4 production. One cluster was associated with low CH4 production (referred to as cluster L) whereas the other cluster was associated with high CH4 production (cluster H) and the medium emitters occurred in both clusters. The differences between clusters were primarily linked to differential abundances of certain OTUs belonging to Prevotella. Moreover, several OTUs belonging to the family Succinivibrionaceae were dominant in samples belonging to cluster L. Fermentation pattern of volatile fatty acids showed that proportion of propionate was higher in cluster L, while proportion of butyrate was higher in cluster H. No difference was found in milk production or organic matter digestibility between cows. Cows in cluster L had lower CH4/kg energy corrected milk (ECM) compared to cows in cluster H, 8.3 compared to 9.7 g CH4/kg ECM, showing that low CH4 cows utilized the feed more efficient for milk production which might indicate a more efficient microbial population or host genetic differences that is reflected in bacterial and archaeal (or methanogens) populations.", "doi": "10.3389/fmicb.2017.00226", "pmid": "28261182", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5313486"}], "notes": [], "created": "2017-11-03T16:20:56.020Z", "modified": "2024-01-16T13:48:48.405Z"}, {"entity": "publication", "iuid": "f35c109acf9743b79cb359d6a7b17c91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91"}}, "title": "The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.", "authors": [{"family": "Adrian-Kalchhauser", "given": "Irene", "initials": "I"}, {"family": "Svensson", "given": "Ola", "initials": "O"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "Schloissnig", "given": "Siegfried", "initials": "S"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Burkhardt-Holm", "given": "Patricia", "initials": "P"}], "type": "journal article", "published": "2017-02-16", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "177", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb).\n\nDuring genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4\u00a0kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19\u00a0kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies.\n\nOur results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.", "doi": "10.1186/s12864-017-3550-8", "pmid": "28209125", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3550-8"}, {"db": "pmc", "key": "PMC5314710"}], "notes": [], "created": "2017-11-01T12:54:58.955Z", "modified": "2024-01-16T13:48:48.415Z"}, {"entity": "publication", "iuid": "171899c09f704f0499506bbae6f97a8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/171899c09f704f0499506bbae6f97a8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/171899c09f704f0499506bbae6f97a8e"}}, "title": "Comparison of whole genome amplification techniques for human single cell exome sequencing.", "authors": [{"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Paterlini", "given": "Marta", "initials": "M"}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Frisen", "given": "Jonas", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "comparative study", "published": "2017-02-16", "journal": {"volume": "12", "issn": "1932-6203", "issue": "2", "pages": "e0171566", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly.\n\nThe largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells.\n\nIn this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.", "doi": "10.1371/journal.pone.0171566", "pmid": "28207771", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-34697"}, {"db": "pmc", "key": "PMC5313163"}], "notes": [], "created": "2017-11-03T16:21:22.034Z", "modified": "2024-01-16T13:48:48.426Z"}, {"entity": "publication", "iuid": "49e5872c79664d88937a1adc92d80dc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49e5872c79664d88937a1adc92d80dc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49e5872c79664d88937a1adc92d80dc4"}}, "title": "Genome-wide Association for Major Depression Through Age at Onset Stratification: Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium.", "authors": [{"family": "Power", "given": "Robert A", "initials": "RA"}, {"family": "Tansey", "given": "Katherine E", "initials": "KE"}, {"family": "Buttensch\u00f8n", "given": "Henriette N\u00f8rm\u00f8lle", "initials": "HN"}, {"family": "Cohen-Woods", "given": "Sarah", "initials": "S"}, {"family": "Bigdeli", "given": "Tim", "initials": "T"}, {"family": "Hall", "given": "Lynsey S", "initials": "LS"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Lee", "given": "S Hong", "initials": "SH"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Steinberg", "given": "Stacy", "initials": "S"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Viktorin", "given": "Alexander", "initials": "A"}, {"family": "Wray", "given": "Naomi R", "initials": "NR"}, {"family": "Arolt", "given": "Volker", "initials": "V"}, {"family": "Baune", "given": "Bernard T", "initials": "BT"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "B\u00f8rglum", "given": "Anders D", "initials": "AD"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Castelao", "given": "Enrique", "initials": "E"}, {"family": "Craddock", "given": "Nick", "initials": "N"}, {"family": "Craig", "given": "Ian W", "initials": "IW"}, {"family": "Dannlowski", "given": "Udo", "initials": "U"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Degenhardt", "given": "Franziska", "initials": "F"}, {"family": "Forstner", "given": "Andreas J", "initials": "AJ"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Grove", "given": "Jakob", "initials": "J"}, {"family": "Hamilton", "given": "Steven P", "initials": "SP"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hocking", "given": "Lynne J", "initials": "LJ"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hottenga", "given": "Jouke J", "initials": "JJ"}, {"family": "Kloiber", "given": "Stefan", "initials": "S"}, {"family": "Krogh", "given": "Jesper", "initials": "J"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Lang", "given": "Maren", "initials": "M"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "MacIntyre", "given": "Donald J", "initials": "DJ"}, {"family": "Madden", "given": "Pamela", "initials": "P"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Middeldorp", "given": "Christel M", "initials": "CM"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Oskarsson", "given": "Hogni", "initials": "H"}, {"family": "Owen", "given": "Michael J", "initials": "MJ"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BW"}, {"family": "Pergadia", "given": "Michele L", "initials": "ML"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Potash", "given": "James B", "initials": "JB"}, {"family": "Preisig", "given": "Martin", "initials": "M"}, {"family": "Rivera", "given": "Margarita", "initials": "M"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Shyn", "given": "Stanley I", "initials": "SI"}, {"family": "Sigurdsson", "given": "Engilbert", "initials": "E"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Stefansson", "given": "Hreinn", "initials": "H"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Thomson", "given": "Pippa", "initials": "P"}, {"family": "Thorgeirsson", "given": "Thorgeir E", "initials": "TE"}, {"family": "Van der Auwera", "given": "Sandra", "initials": "S"}, {"family": "Weissman", "given": "Myrna M", "initials": "MM"}, {"family": "CONVERGE Consortium, CARDIoGRAM Consortium, GERAD1 Consortium", "given": null, "initials": null}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}], "type": "journal article", "published": "2017-02-15", "journal": {"volume": "81", "issn": "1873-2402", "issue": "4", "pages": "325-335", "title": "Biol. Psychiatry", "issn-l": "0006-3223"}, "abstract": "Major depressive disorder (MDD) is a disabling mood disorder, and despite a known heritable component, a large meta-analysis of genome-wide association studies revealed no replicable genetic risk variants. Given prior evidence of heterogeneity by age at onset in MDD, we tested whether genome-wide significant risk variants for MDD could be identified in cases subdivided by age at onset.\n\nDiscovery case-control genome-wide association studies were performed where cases were stratified using increasing/decreasing age-at-onset cutoffs; significant single nucleotide polymorphisms were tested in nine independent replication samples, giving a total sample of 22,158 cases and 133,749 control subjects for subsetting. Polygenic score analysis was used to examine whether differences in shared genetic risk exists between earlier and adult-onset MDD with commonly comorbid disorders of schizophrenia, bipolar disorder, Alzheimer's disease, and coronary artery disease.\n\nWe identified one replicated genome-wide significant locus associated with adult-onset (>27 years) MDD (rs7647854, odds ratio: 1.16, 95% confidence interval: 1.11-1.21, p = 5.2 \u00d7 10(-11)). Using polygenic score analyses, we show that earlier-onset MDD is genetically more similar to schizophrenia and bipolar disorder than adult-onset MDD.\n\nWe demonstrate that using additional phenotype data previously collected by genetic studies to tackle phenotypic heterogeneity in MDD can successfully lead to the discovery of genetic risk factor despite reduced sample size. Furthermore, our results suggest that the genetic susceptibility to MDD differs between adult- and earlier-onset MDD, with earlier-onset cases having a greater genetic overlap with schizophrenia and bipolar disorder.", "doi": "10.1016/j.biopsych.2016.05.010", "pmid": "27519822", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-3223(16)32386-1"}, {"db": "pmc", "key": "PMC5262436"}], "notes": [], "created": "2017-05-03T12:59:49.338Z", "modified": "2024-01-16T13:48:48.438Z"}, {"entity": "publication", "iuid": "760b105c4c974b08bbf488f12adb4fcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/760b105c4c974b08bbf488f12adb4fcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/760b105c4c974b08bbf488f12adb4fcf"}}, "title": "Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios", "authors": [{"family": "Juottonen", "given": "Heli", "initials": "H"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Biasi", "given": "Christina", "initials": "C"}, {"family": "Tuittila", "given": "Eeva Stiina", "initials": "ES"}, {"family": "Yrj\u00e4l\u00e4", "given": "Kim", "initials": "K"}, {"family": "Fritze", "given": "Hannu", "initials": "H"}], "type": "journal-article", "published": "2017-02-15", "journal": {"volume": "83", "issn": "1098-5336", "issue": "4", "pages": "e02533-16", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Northern peatlands in general have high methane (CH\n                4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands.\n\nPeatlands are major sources of the greenhouse gas methane (CH\n                4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.", "doi": "10.1128/aem.02533-16", "pmid": "27913414", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP075161"}], "notes": [], "created": "2017-05-03T13:00:16.242Z", "modified": "2024-01-16T13:48:48.453Z"}, {"entity": "publication", "iuid": "1e2f5f5b41994ebe87f808d019813e2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2f5f5b41994ebe87f808d019813e2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2f5f5b41994ebe87f808d019813e2c"}}, "title": "Delineating Amyloid Plaque Associated Neuronal Sphingolipids in Transgenic Alzheimer's Disease Mice (tgArcSwe) Using MALDI Imaging Mass Spectrometry.", "authors": [{"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Brinet", "given": "Dimitri", "initials": "D"}, {"family": "Michno", "given": "Wojciech", "initials": "W"}, {"family": "Syv\u00e4nen", "given": "Stina", "initials": "S"}, {"family": "Sehlin", "given": "Dag", "initials": "D"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Hanrieder", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0001-6059-198X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e65454100674f98bf8f2575093f2441.json"}}], "type": "journal article", "published": "2017-02-15", "journal": {"title": "ACS Chem Neurosci", "issn": "1948-7193", "volume": "8", "issue": "2", "pages": "347-355", "issn-l": "1948-7193"}, "abstract": "The major pathological hallmarks of Alzheimer's disease (AD) are the progressive aggregation and accumulation of beta-amyloid (A\u03b2) and hyperphosphorylated tau protein into neurotoxic deposits. A\u03b2 aggregation has been suggested as the critical early inducer, driving the disease progression. However, the factors that promote neurotoxic A\u03b2 aggregation remain elusive. Imaging mass spectrometry (IMS) is a powerful technique to comprehensively elucidate the spatial distribution patterns of lipids, peptides, and proteins in biological tissue sections. In the present study, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS)-based imaging was used on transgenic Alzheimer's disease mouse (tgArcSwe) brain tissue to investigate the sphingolipid microenvironment of individual A\u03b2 plaques and elucidate plaque-associated sphingolipid alterations. Multivariate data analysis was used to interrogate the IMS data for identifying pathologically relevant, anatomical features based on their lipid chemical profile. This approach revealed sphingolipid species that distinctly located to cortical and hippocampal deposits, whose A\u03b2 identity was further verified using fluorescent amyloid staining and immunohistochemistry. Subsequent multivariate statistical analysis of the spectral data revealed significant localization of gangliosides and ceramides species to A\u03b2 positive plaques, which was accompanied by distinct local reduction of sulfatides. These plaque-associated changes in sphingolipid levels implicate a functional role of sphingolipid metabolism in A\u03b2 plaque pathology and AD pathogenesis. Taken together, the presented data highlight the potential of imaging mass spectrometry as a powerful approach for probing A\u03b2 plaque-associated lipid changes underlying AD pathology.", "doi": "10.1021/acschemneuro.6b00391", "pmid": "27984697", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5314428"}], "notes": [], "created": "2020-01-23T16:35:04.780Z", "modified": "2021-06-21T15:43:06.156Z"}, {"entity": "publication", "iuid": "ef4cc924f1e54f01bd4c84a213b5e5ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef4cc924f1e54f01bd4c84a213b5e5ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef4cc924f1e54f01bd4c84a213b5e5ec"}}, "title": "Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor.", "authors": [{"family": "Gustafsson", "given": "Robert", "initials": "R"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Gustafsson", "given": "Nina M S", "initials": "NM"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Wiita", "given": "Elis\u00e9e", "initials": "E"}, {"family": "Bonagas", "given": "Nadilly", "initials": "N"}, {"family": "Dahllund", "given": "Leif", "initials": "L"}, {"family": "Llona-Minguez", "given": "Sabin", "initials": "S"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Henriksson", "given": "Martin", "initials": "M"}, {"family": "Andersson", "given": "Yasmin", "initials": "Y"}, {"family": "Homan", "given": "Evert", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}], "type": "journal article", "published": "2017-02-15", "journal": {"volume": "77", "issn": "1538-7445", "issue": "4", "pages": "937-948", "title": "Cancer Res.", "issn-l": "0008-5472"}, "abstract": "To sustain their proliferation, cancer cells become dependent on one-carbon metabolism to support purine and thymidylate synthesis. Indeed, one of the most highly upregulated enzymes during neoplastic transformation is MTHFD2, a mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase involved in one-carbon metabolism. Because MTHFD2 is expressed normally only during embryonic development, it offers a disease-selective therapeutic target for eradicating cancer cells while sparing healthy cells. Here we report the synthesis and preclinical characterization of the first inhibitor of human MTHFD2. We also disclose the first crystal structure of MTHFD2 in complex with a substrate-based inhibitor and the enzyme cofactors NAD+ and inorganic phosphate. Our work provides a rationale for continued development of a structural framework for the generation of potent and selective MTHFD2 inhibitors for cancer treatment. Cancer Res; 77(4); 937-48. \u00a92017 AACR.", "doi": "10.1158/0008-5472.CAN-16-1476", "pmid": "27899380", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-16-1476"}], "notes": "Medicinal Chemistry \u2013 Hit2Lead\r\nProtein Expression and Characterization", "created": "2017-05-08T07:55:19.741Z", "modified": "2025-10-17T13:05:09.030Z"}, {"entity": "publication", "iuid": "00c05d1d2e00402b8d42acb6b2bc70a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00c05d1d2e00402b8d42acb6b2bc70a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00c05d1d2e00402b8d42acb6b2bc70a8"}}, "title": "Correlated/non-correlated ion dynamics of charge-neutral ion couples: the origin of ionicity in ionic liquids.", "authors": [{"family": "Driver", "given": "G W", "initials": "GW"}, {"family": "Huang", "given": "Y", "initials": "Y"}, {"family": "Laaksonen", "given": "A", "initials": "A"}, {"family": "Sparrman", "given": "T", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Wang", "given": "Y-L", "initials": "YL", "orcid": "0000-0003-3393-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/20011b26fd054aceabec7b86b66c0d79.json"}}, {"family": "Westlund", "given": "P-O", "initials": "PO", "orcid": "0000-0002-9277-4534", "researcher": {"href": "https://publications.scilifelab.se/researcher/18985f1db0b64da48e7805cf918c58b3.json"}}], "type": "journal article", "published": "2017-02-15", "journal": {"volume": "19", "issn": "1463-9084", "issue": "7", "pages": "4975-4988", "title": "Phys Chem Chem Phys", "issn-l": "1463-9076"}, "abstract": "Proton/fluoride spin-lattice (T1) nuclear magnetic relaxation dispersion (NMRD) measurements of 1-butyl-3-methyl-1H-imidazolium hexafluorophosphate, [C4mim][PF6], have been carried out using high field spectrometers and a fast-field-cycling instrument at proton Larmor frequencies ranging from 10 kHz to 40 MHz, at different temperatures. The NMRD profiles are interpreted by means of a simple relaxation model based on the inter- and intra-ionic dipole-dipole relaxation mechanism. Using an atomic molecular-ion dynamic simulation at 323 K the relevant spin dipole-dipole (DD) correlation functions are calculated. The results indicate that the NMRD profiles can be rationalized using intra- and inter-ionic spin DD interactions, however, anions are mainly modulated by ionic reorientation because of temporary correlations with cations, where modulation by translational diffusion plays a minor role. Reorientational dynamics of charge-neutral ion couples (i.e. [C4mim][PF6]) and [C4mim]+ ions are in the nano-second (ns) time range whereas the reorientation of [PF6]- is characterized by a reorientational correlation time in the pico-second (ps) regime. Based on the NMRD profiles we conclude that the main relaxation mechanism for [PF6]- is due to fast internal reorientational motion, a partially averaged F-F intra- and F-H inter-ionic DD coupling as the anion resides in close proximity to its temporary oppositely charged cation partner. The F-T1-NMRD data display a ns dispersion which is interpreted as being due to correlated reorientational modulations resulting from the H-containing charge-neutral ion couple [C4mim][PF6]. The analysis of ionicity is based on the free anion fraction, f, and it increases with temperature with f \u2192 1 at the highest temperatures investigated. The fraction is obtained from the H-F NMRD profiles as correlated-non-correlated dynamics of the ions. The analysis of T1 relaxation rates of C, H, F and P at high fields cannot generally give the fraction of ions but is consistent with the interpretation based on the NMRD profiles with relaxation contributions due to DD-intra and -inter, CSA-intra (and -inter for C), including spin rotation for P. The investigation has led to a description of the mechanics governing ion transport in the title ionic liquid via identification of transient correlated/non-correlated ion dynamics.", "doi": "10.1039/c6cp05801a", "pmid": "28074972", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:02:50.668Z", "modified": "2025-10-17T13:04:00.021Z"}, {"entity": "publication", "iuid": "209932748e35452f8c3277616f4a166f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/209932748e35452f8c3277616f4a166f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/209932748e35452f8c3277616f4a166f"}}, "title": "The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.", "authors": [{"family": "Zeigler Allen", "given": "Lisa", "initials": "L"}, {"family": "McCrow", "given": "John P", "initials": "JP"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Badger", "given": "Jonathan H", "initials": "JH"}, {"family": "Hoffman", "given": "Jeffery M", "initials": "JM"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Allen", "given": "Andrew E", "initials": "AE"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Venter", "given": "J Craig", "initials": "JC"}], "type": "journal article", "published": "2017-02-14", "journal": {"volume": "2", "issn": "2379-5077", "issue": "1", "title": "mSystems", "issn-l": "2379-5077"}, "abstract": "Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetr\u00e4sk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Tornetr\u00e4sk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.", "doi": "10.1128/mSystems.00125-16", "pmid": "28217745", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mSystems00125-16"}, {"db": "pmc", "key": "PMC5309335"}], "notes": [], "created": "2017-11-03T16:19:51.205Z", "modified": "2024-01-16T13:48:48.463Z"}, {"entity": "publication", "iuid": "93c782e1f0c14ff9a48a91185fb7eafb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93c782e1f0c14ff9a48a91185fb7eafb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93c782e1f0c14ff9a48a91185fb7eafb"}}, "title": "Longitudinal analysis of hepatic transcriptome and serum metabolome demonstrates altered lipid metabolism following the onset of hyperglycemia in spontaneously diabetic biobreeding rats.", "authors": [{"family": "Regnell", "given": "Simon E", "initials": "SE", "orcid": "0000-0002-6672-8972", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6aeb77eea2944dc8cfe44906d9c133e.json"}}, {"family": "Hessner", "given": "Martin J", "initials": "MJ"}, {"family": "Jia", "given": "Shuang", "initials": "S"}, {"family": "\u00c5kesson", "given": "Lina", "initials": "L"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "La Torre", "given": "Daria", "initials": "D"}, {"family": "Lernmark", "given": "\u00c5ke", "initials": "\u00c5"}], "type": "journal article", "published": "2017-02-13", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "12", "issue": "2", "pages": "e0171372"}, "abstract": "Type 1 diabetes is associated with abberations of fat metabolism before and after the clinical onset of disease. It has been hypothesized that the absence of the effect of insulin in the liver contributes to reduced hepatic fat synthesis. We measured hepatic gene expression and serum metabolites before and after the onset of hyperglycemia in a BioBreeding rat model of type 1 diabetes. Functional pathway annotation identified that lipid metabolism was differentially expressed in hyperglycemic rats and that these pathways significantly overlapped with genes regulated by insulin. 17 serum metabolites significantly changed in concentration. All but 2 of the identified metabolites had previously been reported in type 1 diabetes, and carbohydrates were overall the most upregulated class of metabolites. We conclude that lack of insulin in the liver contributes to the changes in fat metabolism observed in type 1 diabetes. Further studies are needed to understand the clinical consequences of a lack of insulin in the liver in patients with type 1 diabetes.", "doi": "10.1371/journal.pone.0171372", "pmid": "28192442", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5305198"}, {"db": "pii", "key": "PONE-D-16-35507"}], "notes": [], "created": "2023-04-12T14:19:30.516Z", "modified": "2025-10-17T13:03:19.061Z"}, {"entity": "publication", "iuid": "74fcedf830fe4da28feaf59862e5d126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74fcedf830fe4da28feaf59862e5d126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74fcedf830fe4da28feaf59862e5d126"}}, "title": "A novel RNA sequencing data analysis method for cell line authentication.", "authors": [{"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Raso", "given": "Cinzia", "initials": "C"}, {"family": "Kennedy", "given": "Susan", "initials": "S"}, {"family": "Rauch", "given": "Nora", "initials": "N"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Kolch", "given": "Walter", "initials": "W"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C", "orcid": "0000-0001-6990-1905", "researcher": {"href": "https://publications.scilifelab.se/researcher/cff94d8d749248d38f5da13c1f636c9d.json"}}], "type": "journal article", "published": "2017-02-13", "journal": {"volume": "12", "issn": "1932-6203", "issue": "2", "pages": "e0171435", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.", "doi": "10.1371/journal.pone.0171435", "pmid": "28192450", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-35145"}, {"db": "pmc", "key": "PMC5305277"}], "notes": [], "created": "2017-11-03T16:20:58.076Z", "modified": "2021-07-08T13:44:33.358Z"}, {"entity": "publication", "iuid": "52aeeba6f0b143fcbf6610d898639cbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52aeeba6f0b143fcbf6610d898639cbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52aeeba6f0b143fcbf6610d898639cbe"}}, "title": "Genetic and Functional Study of L-Type Amino Acid Transporter 1 in Schizophrenia.", "authors": [{"family": "Comasco", "given": "Erika", "initials": "E"}, {"family": "Vumma", "given": "Ravi", "initials": "R"}, {"family": "Toffoletto", "given": "Simone", "initials": "S"}, {"family": "Johansson", "given": "Jessica", "initials": "J"}, {"family": "Flyckt", "given": "Lena", "initials": "L"}, {"family": "Lewander", "given": "Tommy", "initials": "T"}, {"family": "Oreland", "given": "Lars", "initials": "L"}, {"family": "Bjerkenstedt", "given": "Lars", "initials": "L"}, {"family": "Andreou", "given": "Dimitrios", "initials": "D"}, {"family": "S\u00f6derman", "given": "Erik", "initials": "E"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Venizelos", "given": "Nikolaos", "initials": "N"}], "type": "journal article", "published": "2017-02-11", "journal": {"volume": "74", "issn": "1423-0224", "issue": "2", "pages": "96-103", "title": "Neuropsychobiology", "issn-l": "0302-282X"}, "abstract": "Schizophrenia involves neural catecholaminergic dysregulation. Tyrosine is the precursor of catecholamines, and its major transporter, according to studies on fibroblasts, in the brain is the L-type amino acid transporter 1 (LAT1). The present study assessed haplotype tag single-nucleotide polymorphisms (SNPs) of the SLC7A5/LAT1 gene in 315 patients with psychosis within the schizophrenia spectrum and 233 healthy controls to investigate genetic vulnerability to the disorder as well as genetic relationships to homovanillic acid (HVA) and 3-methoxy-4-hydroxyphenylglycol (MHPG), the major catecholamine metabolites in the cerebrospinal fluid (CSF). Moreover, the involvement of the different isoforms of the system L in tyrosine uptake and LAT1 tyrosine kinetics were studied in fibroblast cell lines of 10 patients with schizophrenia and 10 healthy controls. The results provide suggestive evidence of individual vulnerability to schizophrenia related to the LAT1 SNP rs9936204 genotype. A number of SNPs were nominally associated with CSF HVA and MHPG concentrations but did not survive correction for multiple testing. The LAT1 isoform was confirmed as the major tyrosine transporter in patients with schizophrenia. However, the kinetic parameters (maximal transport capacity, affinity of the binding sites, and diffusion constant of tyrosine transport through the LAT1 isoform) did not differ between patients with schizophrenia and controls. The present genetic findings call for independent replication in larger samples, while the functional study seems to exclude a role of LAT1 in the aberrant transport of tyrosine in fibroblasts of patients with schizophrenia.", "doi": "10.1159/000455234", "pmid": "28190014", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "000455234"}], "notes": [], "created": "2018-01-09T14:07:15.547Z", "modified": "2021-06-22T11:34:21.312Z"}, {"entity": "publication", "iuid": "fbc5fb6308f74c049a6285b5b4849133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbc5fb6308f74c049a6285b5b4849133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbc5fb6308f74c049a6285b5b4849133"}}, "title": "Detection of Somatic Mutations in Gastroenteropancreatic Neuroendocrine Tumors Using Targeted Deep Sequencing", "authors": [{"family": "BACKMAN", "given": "SAMUEL", "initials": "S"}, {"family": "NORL\u00c9N", "given": "OLOV", "initials": "O"}, {"family": "ERIKSSON", "given": "BARBRO", "initials": "B"}, {"family": "SKOGSEID", "given": "BRITT", "initials": "B"}, {"family": "ST\u00c5LBERG", "given": "PETER", "initials": "P"}, {"family": "CRONA", "given": "JOAKIM", "initials": "J"}], "type": "journal-article", "published": "2017-02-10", "journal": {"volume": "37", "issn": "0250-7005", "issue": "2", "pages": "705-712", "title": "AR", "issn-l": "0250-7005"}, "abstract": null, "doi": "10.21873/anticanres.11367", "pmid": "28179320", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:36:20.548Z", "modified": "2020-01-21T13:56:10.041Z"}, {"entity": "publication", "iuid": "1ca13a5dbc2c44329bbbefec4d917ee0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ca13a5dbc2c44329bbbefec4d917ee0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ca13a5dbc2c44329bbbefec4d917ee0"}}, "title": "microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.", "authors": [{"family": "Zhou", "given": "Y", "initials": "Y"}, {"family": "Frings", "given": "O", "initials": "O"}, {"family": "Branca", "given": "R M", "initials": "RM"}, {"family": "Boekel", "given": "J", "initials": "J"}, {"family": "le Sage", "given": "C", "initials": "C"}, {"family": "Fredlund", "given": "E", "initials": "E"}, {"family": "Agami", "given": "R", "initials": "R"}, {"family": "Orre", "given": "L M", "initials": "LM"}], "type": "journal article", "published": "2017-02-09", "journal": {"volume": "36", "issn": "1476-5594", "issue": "6", "pages": "731-745", "title": "Oncogene", "issn-l": "0950-9232"}, "abstract": "microRNA (miRNA) dysregulation is a common feature of cancer cells, but the complex roles of miRNAs in cancer are not fully elucidated. Here, we used functional genomics to identify oncogenic miRNAs in non-small cell lung cancer and evaluate their impact on response to epidermal growth factor (EGFR)-targeting therapy. Our data demonstrate that miRNAs with an AAGUGC motif in their seed sequence increase both cancer cell proliferation and sensitivity to EGFR inhibitors. Global transcriptomics, proteomics and target prediction resulted in the identification of several tumor suppressors involved in the G1/S transition as AAGUGC-miRNA targets. The clinical implications of our findings were evaluated by analysis of AAGUGC-miRNA expression in multiple cancer types, supporting the link between this miRNA seed family, their tumor suppressor targets and cancer cell proliferation. In conclusion, we propose the AAGUGC seed motif as an oncomotif and that oncomotif-miRNAs promote cancer cell proliferation. These findings have potential therapeutic implications, especially in selecting patients for EGFR-targeting therapy.", "doi": "10.1038/onc.2016.242", "pmid": "27477696", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "onc2016242"}, {"db": "pmc", "key": "PMC5311252"}], "notes": [], "created": "2017-05-03T13:00:40.536Z", "modified": "2020-01-21T13:56:16.909Z"}, {"entity": "publication", "iuid": "e16b1a021a0e42aea2eb4a9ed9d95719", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e16b1a021a0e42aea2eb4a9ed9d95719.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e16b1a021a0e42aea2eb4a9ed9d95719"}}, "title": "Rare and 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{"family": "'t Hart", "given": "Leen M", "initials": "LM", "orcid": "0000-0003-4401-2938", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cb1193c2ad3419899ec86d9d95bf25d.json"}}, {"family": "Tansey", "given": "Katherine E", "initials": "KE"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Thompson", "given": "Deborah J", "initials": "DJ"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Thuesen", "given": "Betina H", "initials": "BH"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tromp", "given": "Gerard", "initials": "G"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Tsafantakis", "given": "Emmanouil", "initials": "E"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Tybjaerg-Hansen", "given": "Anne", "initials": "A"}, {"family": "Tyrer", "given": "Jonathan P", "initials": "JP"}, {"family": "Uher", "given": "Rudolf", "initials": "R"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW"}, {"family": "Van Der Leij", "given": "Andries R", "initials": "AR"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "van Setten", "given": "Jessica", "initials": "J"}, {"family": "Varbo", "given": "Anette", "initials": "A"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Varma", "given": "Rohit", "initials": "R"}, {"family": "Edwards", "given": "Digna R Velez", "initials": "DR"}, {"family": "Vermeulen", "given": "Sita H", "initials": "SH"}, {"family": "Vestergaard", "given": "Henrik", "initials": "H"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Vogt", "given": "Thomas F", "initials": "TF"}, {"family": "Vozzi", "given": "Diego", "initials": "D"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Wang", "given": "Feijie", "initials": "F"}, {"family": "Wang", "given": "Carol A", "initials": "CA"}, {"family": "Wang", "given": "Shuai", "initials": "S"}, {"family": "Wang", "given": "Yiqin", "initials": "Y"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Witte", "given": "Daniel R", "initials": "DR"}, {"family": "Woods", "given": "Michael O", "initials": "MO"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yao", "given": "Pang", "initials": "P"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Young", "given": "Robin", "initials": "R"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zhan", "given": "Xiaowei", "initials": "X"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Zheng", "given": "He", "initials": "H"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "EPIC-InterAct Consortium", "given": "", "initials": ""}, {"family": "CHD Exome+ Consortium", "given": "", "initials": ""}, {"family": "ExomeBP Consortium", "given": "", "initials": ""}, {"family": "T2D-Genes Consortium", "given": "", "initials": ""}, {"family": "GoT2D Genes Consortium", "given": "", "initials": ""}, {"family": "Global Lipids Genetics Consortium", "given": "", "initials": ""}, {"family": "ReproGen Consortium", "given": "", "initials": ""}, {"family": "MAGIC Investigators", "given": "", "initials": ""}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Liu", "given": "Dajiang J", "initials": "DJ"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Oxvig", "given": "Claus", "initials": "C"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}], "type": "journal article", "published": "2017-02-09", "journal": {"volume": "542", "issn": "1476-4687", "issue": "7640", "pages": "186-190", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2\u2009centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height-increasing alleles of STC2 (giving an increase of 1-2\u2009centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.", "doi": "10.1038/nature21039", "pmid": "28146470", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nature21039"}, {"db": "pmc", "key": "PMC5302847"}, {"db": "mid", "key": "NIHMS834200"}], "notes": [], "created": "2017-10-25T15:54:16.444Z", "modified": "2024-01-16T13:48:48.470Z"}, {"entity": "publication", "iuid": "3ef89dc74e2648e6917a87d7e601859e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ef89dc74e2648e6917a87d7e601859e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ef89dc74e2648e6917a87d7e601859e"}}, "title": "IL-8 predicts early mortality in patients with acute hypercapnic respiratory failure treated with noninvasive positive pressure ventilation.", "authors": [{"family": "J\u00f3nsd\u00f3ttir", "given": "Brynja", "initials": "B"}, {"family": "Jaworowski", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "San Miguel", "given": "Carmen", "initials": "C"}, {"family": "Melander", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2017-02-08", "journal": {"title": "BMC Pulm Med", "issn": "1471-2466", "issn-l": "1471-2466", "volume": "17", "issue": "1", "pages": "35"}, "abstract": "Patients with Acute Hypercapnic Respiratory Failure (AHRF) who are unresponsive to appropriate medical treatment, are often treated with Noninvasive Positive Pressure Ventilation (NPPV). Clinical predictors of the outcome of this treatment are scarce. Therefore, we evaluated the role of the biomarkers IL-8 and GDF-15 in predicting 28-day mortality in patients with AHRF who receive treatment with NPPV.\n\nThe study population were 46 patients treated with NPPV for AHRF. Clinical and background data was registered and blood samples taken for analysis of inflammatory biomarkers. IL-8 and GDF-15 were selected for analysis, and related to risk of 28-day mortality (primary endpoint) using Cox proportional hazard models adjusted for gender, age and various clinical parameters.\n\nOf the 46 patients, there were 3 subgroup in regards to primary diagnosis: Acute Exacerbation of COPD (AECOPD, n = 34), Acute Heart Failure (AHF, n = 8) and Acute Exacerbation in Obesity Hypoventilation Syndrome (AEOHS, n = 4). There was significant difference in the basic characteristic of the subgroups, but not in the clinical parameters that were used in treatment decisions. 13 patients died within 28 days of admission (28%). The Hazard Ratio for 28-days mortality per 1-SD increment of IL-8 was 3.88 (95% CI 1.86-8.06, p < 0.001). When IL-8 values were divided into tertiles, the highest tertile had a significant association with 28 days mortality, HR 10.02 (95% CI 1.24-80.77, p for trend 0.03), compared with the lowest tertile. This correlation was maintained when the largest subgroup with AECOPD was analyzed. GDF-15 was correlated in the same way, but when put into the same model as IL-8, the significance disappeared.\n\nIL-8 is a target to explore further as a predictor of 28 days mortality, in patients with AHRF treated with NPPV.", "doi": "10.1186/s12890-017-0377-7", "pmid": "28178959", "labels": {"Clinical Biomarkers": "Service", "Affinity Proteomics Stockholm": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12890-017-0377-7"}, {"db": "pmc", "key": "PMC5299680"}], "notes": [], "created": "2020-01-23T15:13:41.234Z", "modified": "2023-04-14T13:56:17.622Z"}, {"entity": "publication", "iuid": "24344bb489604ac38a35c61b68e2a68c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24344bb489604ac38a35c61b68e2a68c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24344bb489604ac38a35c61b68e2a68c"}}, "title": "SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics.", "authors": [{"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}, {"family": "Aarsland", "given": "Dag", "initials": "D"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2017-02-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "41929", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The human blood proteome is frequently assessed by protein abundance profiling using a combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS). In traditional sequence database search, many good-quality MS/MS data remain unassigned. Here we uncover the hidden part of the blood proteome via novel SpotLight approach. This method combines de novo MS/MS sequencing of enriched antibodies and co-extracted proteins with subsequent label-free quantification of new and known peptides in both enriched and unfractionated samples. In a pilot study on differentiating early stages of Alzheimer's disease (AD) from Dementia with Lewy Bodies (DLB), on peptide level the hidden proteome contributed almost as much information to patient stratification as the apparent proteome. Intriguingly, many of the new peptide sequences are attributable to antibody variable regions, and are potentially indicative of disease etiology. When the hidden and apparent proteomes are combined, the accuracy of differentiating AD (n = 97) and DLB (n = 47) increased from \u224885% to \u224895%. The low added burden of SpotLight proteome analysis makes it attractive for use in clinical settings.", "doi": "10.1038/srep41929", "pmid": "28167817", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "srep41929"}, {"db": "pmc", "key": "PMC5294601"}], "notes": [], "created": "2020-01-23T13:29:59.536Z", "modified": "2021-07-08T08:58:46.741Z"}, {"entity": "publication", "iuid": "b155d01aad66436bbb4048569af0b228", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b155d01aad66436bbb4048569af0b228.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b155d01aad66436bbb4048569af0b228"}}, "title": "MASTL is essential for anaphase entry of proliferating primordial germ cells and establishment of female germ cells in mice.", "authors": [{"family": "Risal", "given": "Sanjiv", "initials": "S"}, {"family": "Zhang", "given": "Jingjing", "initials": "J"}, {"family": "Adhikari", "given": "Deepak", "initials": "D"}, {"family": "Liu", "given": "Xiaoman", "initials": "X"}, {"family": "Shao", "given": "Jingchen", "initials": "J"}, {"family": "Hu", "given": "Mengwen", "initials": "M"}, {"family": "Busayavalasa", "given": "Kiran", "initials": "K"}, {"family": "Tu", "given": "Zhaowei", "initials": "Z"}, {"family": "Chen", "given": "Zijiang", "initials": "Z"}, {"family": "Kaldis", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7247-7591", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7faea8844574f828b494445e5f64bc4.json"}}, {"family": "Liu", "given": "Kui", "initials": "K"}], "type": "journal article", "published": "2017-02-07", "journal": {"title": "Cell Discov", "issn": "2056-5968", "volume": "3", "issue": "1", "pages": "16052", "issn-l": "2056-5968"}, "abstract": "In mammals, primordial germ cells (PGCs) are the embryonic cell population that serve as germ cell precursors in both females and males. During mouse embryonic development, the majority of PGCs are arrested at the G2 phase when they migrate into the hindgut at 7.75-8.75 dpc (days post coitum). It is after 9.5 dpc that the PGCs undergo proliferation with a doubling time of 12.6 h. The molecular mechanisms underlying PGC proliferation are however not well studied. In this work. Here we studied how MASTL (microtubule-associated serine/threonine kinase-like)/Greatwall kinase regulates the rapid proliferation of PGCs. We generated a mouse model where we specifically deleted Mastl in PGCs and found a significant loss of PGCs before the onset of meiosis in female PGCs. We further revealed that the deletion of Mastl in PGCs did not prevent mitotic entry, but led to a failure of the cells to proceed beyond metaphase-like stage, indicating that MASTL-mediated molecular events are indispensable for anaphase entry in PGCs. These mitotic defects further led to the death of Mastl-null PGCs by 12.5 dpc. Moreover, the defect in mitotic progression observed in the Mastl-null PGCs was rescued by simultaneous deletion of Ppp2r1a (\u03b1 subunit of PP2A). Thus, our results demonstrate that MASTL, PP2A, and therefore regulated phosphatase activity have a fundamental role in establishing female germ cell population in gonads by controlling PGC proliferation during embryogenesis.", "doi": "10.1038/celldisc.2016.52", "pmid": "28224044", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5301161"}], "notes": [], "created": "2020-01-23T16:36:04.019Z", "modified": "2021-06-21T14:58:15.153Z"}, {"entity": "publication", "iuid": "8d06af19583b4649aaf237da6391fc27", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d06af19583b4649aaf237da6391fc27.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d06af19583b4649aaf237da6391fc27"}}, "title": "The Arabidopsis bZIP11 transcription factor links low-energy signalling to auxin-mediated control of primary root growth", "authors": [{"family": "Weiste", "given": "Christoph", "initials": "C"}, {"family": "Pedrotti", "given": "Lorenzo", "initials": "L"}, {"family": "Selvanayagam", "given": "Jebasingh", "initials": "J"}, {"family": "Muralidhara", "given": "Prathibha", "initials": "P"}, {"family": "Fr\u00f6schel", "given": "Christian", "initials": "C"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Hanson", "given": "Johannes", "initials": "J"}, {"family": "Dr\u00f6ge-Laser", "given": "Wolfgang", "initials": "W"}], "type": "journal-article", "published": "2017-02-03", "journal": {"volume": "13", "issn": "1553-7404", "issue": "2", "pages": "e1006607", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": null, "doi": "10.1371/journal.pgen.1006607", "pmid": "28158182", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:36:46.921Z", "modified": "2025-10-17T13:03:19.071Z"}, {"entity": "publication", "iuid": "5d81df2251e447e591576b835a99b31a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d81df2251e447e591576b835a99b31a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d81df2251e447e591576b835a99b31a"}}, "title": "Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes", "authors": [{"family": "Samad", "given": "Md Sainur", "initials": "MS"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2017-02-03", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": null, "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": null, "doi": "10.3389/fmicb.2017.00142", "pmid": "28217121", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:36:43.319Z", "modified": "2024-01-16T13:48:48.483Z"}, {"entity": "publication", "iuid": "c50b3617005b4f488783938e7540a7d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c50b3617005b4f488783938e7540a7d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c50b3617005b4f488783938e7540a7d5"}}, "title": "Posttranscriptional Regulation in Adenovirus Infected Cells.", "authors": [{"family": "Zhao", "given": "Hongxing", "initials": "H"}, {"family": "Konzer", "given": "Anne", "initials": "A"}, {"family": "Mi", "given": "Jia", "initials": "J"}, {"family": "Chen", "given": "Moashan", "initials": "M"}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB", "orcid": "0000-0002-9510-3816", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c2549b838d7416ea5823767aff3ef30.json"}}], "type": "journal article", "published": "2017-02-03", "journal": {"volume": "16", "issn": "1535-3907", "issue": "2", "pages": "872-888", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "A deeper understanding of how viruses reprogram their hosts for production of progeny is needed to combat infections. Most knowledge on the regulation of cellular gene expression during adenovirus infection is derived from mRNA studies. Here, we investigated the changes in protein expression during the late phase of adenovirus type 2 (Ad2) infection of the IMR-90 cell line by stable isotope labeling in cell culture with subsequent liquid chromatography-high resolution tandem mass spectrometric analysis. Two biological replicates of samples collected at 24 and 36 h post-infection (hpi) were investigated using swapped labeling. In total, 2648 and 2394 proteins were quantified at 24 and 36 hpi, respectively. Among them, 659 and 645 were deregulated >1.6-fold at the two time points. The protein expression was compared with RNA expression using cDNA sequencing data. The correlation was surprisingly low (r = 0.3), and several examples of posttranscriptional regulation were observed; e.g., proteins related to carbohydrate metabolism were up-regulated at the protein level but unchanged at the RNA level, whereas histone proteins were down-regulated at the protein level but up-regulated at the RNA level. The deregulation of cellular gene expression by adenovirus is mediated at multiple levels and more complex than hitherto believed.", "doi": "10.1021/acs.jproteome.6b00834", "pmid": "27959563", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:25:19.054Z", "modified": "2024-01-16T13:48:48.490Z"}, {"entity": "publication", "iuid": "07f943c602224528812fe68f04e4fa03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07f943c602224528812fe68f04e4fa03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07f943c602224528812fe68f04e4fa03"}}, "title": "Photochemically Induced Aryl Azide Rearrangement: Solution NMR Spectroscopic Identification of the Rearrangement Product", "authors": [{"family": "Andersson", "given": "Hanna", "initials": "H"}, {"family": "Gr\u00e4fenstein", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Isobe", "given": "Minoru", "initials": "M"}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M"}, {"family": "Sydnes", "given": "Magne O", "initials": "MO"}], "type": "journal-article", "published": "2017-02-03", "journal": {"volume": "82", "issn": "1520-6904", "issue": "3", "pages": "1812-1816", "title": "J. Org. Chem.", "issn-l": "0022-3263"}, "abstract": null, "doi": "10.1021/acs.joc.6b02555", "pmid": "28068094", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:52:26.456Z", "modified": "2025-10-17T13:04:00.037Z"}, {"entity": "publication", "iuid": "70b0cd44ec9c439cab867cbc5d28636c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70b0cd44ec9c439cab867cbc5d28636c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70b0cd44ec9c439cab867cbc5d28636c"}}, "title": "A Synthesis of \u201cDual Warhead\u201d \u03b2-Aryl Ethenesulfonyl Fluorides and One-Pot Reaction to \u03b2-Sultams", "authors": [{"family": "Chinthakindi", "given": "Praveen K", "initials": "PK"}, {"family": "Govender", "given": "Kimberleigh B", "initials": "KB"}, {"family": "Kumar", "given": "A Sanjeeva", "initials": "AS"}, {"family": "Kruger", "given": "Hendrik G", "initials": "HG"}, {"family": "Govender", "given": "Thavendran", "initials": "T"}, {"family": "Naicker", "given": "Tricia", "initials": "T"}, {"family": "Arvidsson", "given": "Per I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}], "type": "journal-article", "published": "2017-02-03", "journal": {"volume": "19", "issn": "1523-7060", "issue": "3", "pages": "480-483", "title": "Org. Lett.", "issn-l": "1523-7052"}, "abstract": null, "doi": "10.1021/acs.orglett.6b03634", "pmid": "28075600", "labels": {"Drug Discovery and Development": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T08:36:12.341Z", "modified": "2025-10-17T13:05:09.061Z"}, {"entity": "publication", "iuid": "8e9f2942aae54865a9b27b0869aeffb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e9f2942aae54865a9b27b0869aeffb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e9f2942aae54865a9b27b0869aeffb0"}}, "title": "The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.", "authors": [{"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2017-02-01", "journal": {"volume": "158", "issn": "1945-7170", "issue": "2", "pages": "239-251", "title": "Endocrinology", "issn-l": "0013-7227"}, "abstract": "The adrenal gland is a composite endocrine organ with vital functions that include the synthesis and release of glucocorticoids and catecholamines. To define the molecular landscape that underlies the specific functions of the adrenal gland, we combined a genome-wide transcriptomics approach using messenger RNA sequencing of human tissues with immunohistochemistry-based protein profiling on tissue microarrays. Approximately two-thirds of all putative protein coding genes were expressed in the adrenal gland, and the analysis identified 253 genes with an elevated pattern of expression in the adrenal gland, with only 37 genes showing a markedly greater expression level (more than fivefold) in the adrenal gland compared with 31 other normal human tissue types analyzed. The analyses allowed for an assessment of the relative expression levels for well-known proteins involved in adrenal gland function but also identified previously poorly characterized proteins in the adrenal cortex, such as the FERM (4.1 protein, ezrin, radixin, moesin) domain containing 5 and the nephroblastoma overexpressed (NOV) protein homolog. We have provided a global analysis of the adrenal gland transcriptome and proteome, with a comprehensive list of genes with elevated expression in the adrenal gland and spatial information with examples of protein expression patterns for corresponding proteins. These genes and proteins constitute important starting points for an improved understanding of the normal function and pathophysiology of the adrenal glands.", "doi": "10.1210/en.2016-1758", "pmid": "27901589", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:56:06.552Z", "modified": "2024-01-16T13:48:48.500Z"}, {"entity": "publication", "iuid": "852f20143a4546a9bbabf51403a46d9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/852f20143a4546a9bbabf51403a46d9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/852f20143a4546a9bbabf51403a46d9e"}}, "title": "Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster.", "authors": [{"family": "Schou", "given": "Mads F", "initials": "MF"}, {"family": "Kristensen", "given": "Torsten N", "initials": "TN"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}, {"family": "Karlsson", "given": "B G\u00f6ran", "initials": "BG"}, {"family": "Loeschcke", "given": "Volker", "initials": "V"}, {"family": "Malmendal", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-02-01", "journal": {"volume": "312", "issn": "1522-1490", "issue": "2", "pages": "R211-R222", "title": "Am. J. Physiol. Regul. Integr. Comp. Physiol.", "issn-l": "0363-6119"}, "abstract": "The ability of ectotherms to respond to changes in their thermal environment through plastic mechanisms is central to their adaptive capability. However, we still lack knowledge on the physiological and functional responses by which ectotherms acclimate to temperatures during development, and in particular, how physiological stress at extreme temperatures may counteract beneficial acclimation responses at benign temperatures. We exposed Drosophila melanogaster to 10 developmental temperatures covering their entire permissible temperature range. We obtained metabolic profiles and reaction norms for several functional traits: egg-to-adult viability, developmental time, and heat and cold tolerance. Females were more heat tolerant than males, whereas no sexual dimorphism was found in cold tolerance. A group of metabolites, mainly free amino acids, had linear reaction norms. Several energy-carrying molecules, as well as some sugars, showed distinct inverted U-shaped norms of reaction across the thermal range, resulting in a positive correlation between metabolite intensities and egg-to-adult viability. At extreme temperatures, low levels of these metabolites were interpreted as a response characteristic of costs of homeostatic perturbations. Our results provide novel insights into a range of metabolites reported to be central for the acclimation response and suggest several new candidate metabolites. Low and high temperatures result in different adaptive physiological responses, but they also have commonalities likely to be a result of the failure to compensate for the physiological stress. We suggest that the regulation of metabolites that are tightly connected to the performance curve is important for the ability of ectotherms to cope with variation in temperature.", "doi": "10.1152/ajpregu.00268.2016", "pmid": "27927623", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ajpregu.00268.2016"}, {"db": "pmc", "key": "PMC5336569"}], "notes": [], "created": "2017-05-03T12:58:52.806Z", "modified": "2025-10-17T13:04:00.046Z"}, {"entity": "publication", "iuid": "ffb4e02791ba47ac883a6415b0338549", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffb4e02791ba47ac883a6415b0338549.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffb4e02791ba47ac883a6415b0338549"}}, "title": "Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels.", "authors": [{"family": "Sennblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-4360-8003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c991150beec46ba8886379193d6037b.json"}}, {"family": "Basu", "given": "Saonli", "initials": "S"}, {"family": "Mazur", "given": "Johanna", "initials": "J"}, {"family": "Suchon", "given": "Pierre", "initials": "P"}, {"family": "Martinez-Perez", "given": "Angel", "initials": "A"}, {"family": "van Hylckama Vlieg", "given": "Astrid", "initials": "A"}, {"family": "Truong", "given": "Vinh", "initials": "V"}, {"family": "Li", "given": "Yuhuang", "initials": "Y"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "Grossman", "given": "Vera", "initials": "V"}, {"family": "de Haan", "given": "Hugoline G", "initials": "HG"}, {"family": "Handin", "given": "Niklas", "initials": "N"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Souto", "given": "Juan Carlos", "initials": "JC"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE"}, {"family": "Gagnon", "given": "France", "initials": "F"}, {"family": "Soria", "given": "Jose Manuel", "initials": "JM"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Maegdefessel", "given": "Lars", "initials": "L", "orcid": "0000-0001-5228-2634", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bb494450154c51a70281d20fb07f81.json"}}, {"family": "Rosendaal", "given": "Frits R", "initials": "FR"}, {"family": "Wild", "given": "Philipp", "initials": "P"}, {"family": "Folsom", "given": "Aaron R", "initials": "AR"}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb3fe1a732b41d79a4a165a64c322d1.json"}}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M", "orcid": "0000-0002-0128-379X", "researcher": {"href": "https://publications.scilifelab.se/researcher/588239fdbde94de0b5de738fd9c7a8a9.json"}}], "type": "journal article", "published": "2017-02-01", "journal": {"volume": "26", "issn": "1460-2083", "issue": "3", "pages": "637-649", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Coagulation factor XI (FXI) has become increasingly interesting for its role in pathogenesis of thrombosis. While elevated plasma levels of FXI have been associated with venous thromboembolism and ischemic stroke, its deficiency is associated with mild bleeding. We aimed to determine novel genetic and post-transcriptional plasma FXI regulators.We performed a genome-wide association study (GWAS) for plasma FXI levels, using novel data imputed to the 1000 Genomes reference panel. Individual GWAS analyses, including a total of 16,169 European individuals from the ARIC, GHS, MARTHA and PROCARDIS studies, were meta-analysed and further replicated in 2,045 individuals from the F5L family, GAIT2 and MEGA studies. Additional association with activated partial thromboplastin time (aPTT) was tested for the top SNPs. In addition, a study on the effect of miRNA on FXI regulation was performed using in silico prediction tools and in vitro luciferase assays.Three loci showed robust, replicating association with circulating FXI levels: KNG1 (rs710446, P-value = 2.07 \u00d7 10-302), F11 (rs4253417, P-value = 2.86 \u00d7 10-193), and a novel association in GCKR (rs780094, P-value = 3.56 \u00d710-09), here for the first time implicated in FXI regulation. The two first SNPs (rs710446 and rs4253417) also associated with aPTT. Conditional and haplotype analyses demonstrated a complex association signal, with additional novel SNPs modulating plasma FXI levels in both the F11 and KNG1 loci. Finally, eight miRNAs were predicted to bind F11 mRNA. Over-expression of either miR-145 or miR-181 significantly reduced the luciferase activity in cells transfected with a plasmid containing FXI-3'UTR.These results should open the door to new therapeutic targets for thrombosis prevention.", "doi": "10.1093/hmg/ddw401", "pmid": "28053049", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5703348"}, {"db": "pii", "key": "ddw401"}], "notes": [], "created": "2018-01-09T14:03:03.562Z", "modified": "2023-06-19T13:11:02.644Z"}, {"entity": "publication", "iuid": "86fcf3738a9b44aa929319fab8c2be01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86fcf3738a9b44aa929319fab8c2be01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86fcf3738a9b44aa929319fab8c2be01"}}, "title": "Dysregulated fatty acid metabolism in coronary ectasia: An extended lipidomic analysis.", "authors": [{"family": "Boles", "given": "Usama", "initials": "U"}, {"family": "Pinto", "given": "Rui Climaco", "initials": "RC"}, {"family": "David", "given": "Santosh", "initials": "S"}, {"family": "Abdullah", "given": "Abdullah S", "initials": "AS"}, {"family": "Henein", "given": "Michael Y", "initials": "MY"}], "type": "journal article", "published": "2017-02-01", "journal": {"title": "Int. J. Cardiol.", "issn": "1874-1754", "volume": "228", "pages": "303-308", "issn-l": "0167-5273"}, "abstract": "Coronary artery ectasia (CAE) is not an uncommon clinical condition, which could be associated with adverse outcome. The exact pathophysiology of the disease is poorly understood and is commonly interpreted as a variant of atherosclerosis. In this study, we sought to undertake lipidomic profiling of a group of CAE patients in an attempt to achieve better understanding of its disturbed metabolism.\n\nUntargeted lipid profiling and complementary modelling strategies were employed to compare serum samples from 16 patients with CAE (mean age 63.5\u00b110.1years, 6 female) and 26 controls with normal smooth coronary arteries (mean age 59.2\u00b16.6years and 7 female). Sample preparation, LC-MS analysis and metabolite identification were performed at the Swedish Metabolomics Centre, Ume\u00e5, Sweden.\n\nPhosphatidylcholine levels were significantly distorted in the CAE patients (p=0.001-0.04). Specifically, 16-carbon fatty acyl chain phosphatidylcholines (PC) were detected in lower levels. Similarly, 11 meioties of Sphyngomyelin (SM) species were detected at lower concentrations (p=0.000001-0.01) in the same group. However, only three metabolites were significantly higher in the pure CAE subgroup (6 patients) when compared with the 10 mixed CAE patients (two meioties of SM species and one of PC). Atherosclerosis risk factors were not different between groups.\n\nThis is the first lipid profiling study reported in coronary artery ectasia. While the lower concentration and dysregulation of sphyngomyelin suggests an evidence for premature apoptosis, that of phosphatidylcholines suggests perturbed fatty acid elongation/desaturation, thus may be indicative of non-atherogenic process in CAE.", "doi": "10.1016/j.ijcard.2016.11.093", "pmid": "27866019", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0167-5273(16)33549-5"}], "notes": [], "created": "2023-04-12T14:15:02.488Z", "modified": "2025-10-17T13:03:19.084Z"}, {"entity": "publication", "iuid": "40ef56b7f0b94b45a0d7bf27297e8a0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/40ef56b7f0b94b45a0d7bf27297e8a0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/40ef56b7f0b94b45a0d7bf27297e8a0d"}}, "title": "Design, synthesis and in vitro biological evaluation of oligopeptides targeting E. coli type I signal peptidase (LepB).", "authors": [{"family": "De Rosa", "given": "Maria", "initials": "M"}, {"family": "Lu", "given": "Lu", "initials": "L"}, {"family": "Zamaratski", "given": "Edouard", "initials": "E"}, {"family": "Sza\u0142aj", "given": "Natalia", "initials": "N"}, {"family": "Cao", "given": "Sha", "initials": "S"}, {"family": "Wadensten", "given": "Henrik", "initials": "H"}, {"family": "Lenhammar", "given": "Lena", "initials": "L"}, {"family": "Gising", "given": "Johan", "initials": "J"}, {"family": "Roos", "given": "Annette K", "initials": "AK"}, {"family": "Huseby", "given": "Douglas L", "initials": "DL"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "Hughes", "given": "Diarmaid", "initials": "D"}, {"family": "Brandt", "given": "Peter", "initials": "P"}, {"family": "Mowbray", "given": "Sherry L", "initials": "SL"}, {"family": "Karl\u00e9n", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-02-01", "journal": {"title": "Bioorg. Med. Chem.", "issn": "1464-3391", "volume": "25", "issue": "3", "pages": "897-911", "issn-l": "0968-0896"}, "abstract": "Type I signal peptidases are potential targets for the development of new antibacterial agents. Here we report finding potent inhibitors of E. coli type I signal peptidase (LepB), by optimizing a previously reported hit compound, decanoyl-PTANA-CHO, through modifications at the N- and C-termini. Good improvements of inhibitory potency were obtained, with IC 50s in the low nanomolar range. The best inhibitors also showed good antimicrobial activity, with MICs in the low \u03bcg/mL range for several bacterial species. The selection of resistant mutants provided strong support for LepB as the target of these compounds. The cytotoxicity and hemolytic profiles of these compounds are not optimal but the finding that minor structural changes cause the large effects on these properties suggests that there is potential for optimization in future studies.", "doi": "10.1016/j.bmc.2016.12.003", "pmid": "28038943", "labels": {"Spatial Mass Spectrometry": "Service"}, "xrefs": [{"db": "pii", "key": "S0968-0896(16)31360-8"}], "notes": [], "created": "2020-01-24T08:53:33.528Z", "modified": "2021-05-17T08:47:18.668Z"}, {"entity": "publication", "iuid": "8647f49647c04b678c4e64e993003d70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8647f49647c04b678c4e64e993003d70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8647f49647c04b678c4e64e993003d70"}}, "title": "Causal Effect of Genetic Variants Associated With Body Mass Index on Multiple Sclerosis Susceptibility.", "authors": [{"family": "Gianfrancesco", "given": "Milena A", "initials": "MA"}, {"family": "Glymour", "given": "M Maria", "initials": "MM"}, {"family": "Walter", "given": "Stefan", "initials": "S"}, {"family": "Rhead", "given": "Brooke", "initials": "B"}, {"family": "Shao", "given": "Xiaorong", "initials": "X"}, {"family": "Shen", "given": "Ling", "initials": "L"}, {"family": "Quach", "given": "Hong", "initials": "H"}, {"family": "Hubbard", "given": "Alan", "initials": "A"}, {"family": "J\u00f3nsd\u00f3ttir", "given": "Ingileif", "initials": "I"}, {"family": "Stef\u00e1nsson", "given": "K\u00e1ri", "initials": "K"}, {"family": "Strid", "given": "Pernilla", "initials": "P"}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Hedstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Schaefer", "given": "Catherine", "initials": "C"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Barcellos", "given": "Lisa F", "initials": "LF"}], "type": "journal article", "published": "2017-02-01", "journal": {"volume": "185", "issn": "1476-6256", "issue": "3", "pages": "162-171", "title": "Am. J. Epidemiol.", "issn-l": "0002-9262"}, "abstract": "Multiple sclerosis (MS) is an autoimmune disease with both genetic and environmental risk factors. Recent studies indicate that childhood and adolescent obesity double the risk of MS, but this association may reflect unmeasured confounders rather than causal effects of obesity. We used separate-sample Mendelian randomization to estimate the causal effect of body mass index (BMI) on susceptibility to MS. Using data from non-Hispanic white members of the Kaiser Permanente Medical Care Plan of Northern California (KPNC) (2006-2014; 1,104 cases of MS and 10,536 controls) and a replication data set from Sweden (the Epidemiological Investigation of MS (EIMS) and the Genes and Environment in MS (GEMS) studies, 2005-2013; 5,133 MS cases and 4,718 controls), we constructed a weighted genetic risk score using 97 variants previously established to predict BMI. Results were adjusted for birth year, sex, education, smoking status, ancestry, and genetic predictors of MS. Estimates in KPNC and Swedish data sets suggested that higher genetically induced BMI predicted greater susceptibility to MS (odds ratio = 1.13, 95% confidence interval: 1.04, 1.22 for the KPNC sample; odds ratio = 1.09, 95% confidence interval: 1.03, 1.15 for the Swedish sample). Although the mechanism remains unclear, to our knowledge, these findings support a causal effect of increased BMI on susceptibility to MS for the first time, and they suggest a role for inflammatory pathways that characterize both obesity and the MS disease process.", "doi": "10.1093/aje/kww120", "pmid": "28073764", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "kww120"}, {"db": "pmc", "key": "PMC5391720"}], "notes": [], "created": "2017-10-25T15:54:17.223Z", "modified": "2024-01-16T13:48:48.512Z"}, {"entity": "publication", "iuid": "7de7ae9e75fe4fa281ab300f10a19c69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7de7ae9e75fe4fa281ab300f10a19c69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7de7ae9e75fe4fa281ab300f10a19c69"}}, "title": "Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation.", "authors": [{"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Gustavsson", "given": "Peter", "initials": "P"}, {"family": "F\u00f6rster", "given": "Alisa", "initials": "A"}, {"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Lupski", "given": "James R", "initials": "JR"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Lundberg", "given": "Elisabeth Syk", "initials": "ES"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "38", "issn": "1098-1004", "issue": "2", "pages": "180-192", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.", "doi": "10.1002/humu.23146", "pmid": "27862604", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5225243"}, {"db": "mid", "key": "NIHMS830031"}], "notes": [], "created": "2017-05-03T12:59:45.241Z", "modified": "2024-01-16T13:48:48.524Z"}, {"entity": "publication", "iuid": "c63ea0fe49dd453798aca844add7e849", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c63ea0fe49dd453798aca844add7e849.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c63ea0fe49dd453798aca844add7e849"}}, "title": "The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.", "authors": [{"family": "Abrouk", "given": "Michael", "initials": "M"}, {"family": "Balc\u00e1rkov\u00e1", "given": "Barbora", "initials": "B"}, {"family": "\u0160imkov\u00e1", "given": "Hana", "initials": "H"}, {"family": "Kom\u00ednkova", "given": "Eva", "initials": "E"}, {"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Jakobson", "given": "Irena", "initials": "I"}, {"family": "Timofejeva", "given": "Ljudmilla", "initials": "L"}, {"family": "Rey", "given": "Elodie", "initials": "E"}, {"family": "Vr\u00e1na", "given": "Jan", "initials": "J"}, {"family": "Kilian", "given": "Andrzej", "initials": "A"}, {"family": "J\u00e4rve", "given": "Kadri", "initials": "K"}, {"family": "Dole\u017eel", "given": "Jaroslav", "initials": "J"}, {"family": "Val\u00e1rik", "given": "Miroslav", "initials": "M"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "15", "issn": "1467-7652", "issue": "2", "pages": "249-256", "title": "Plant Biotechnol. J.", "issn-l": "1467-7644"}, "abstract": "The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. T\u00e4hti\u00a0\u00d7\u00a0T.\u00a0militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.", "doi": "10.1111/pbi.12610", "pmid": "27510270", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5259550"}], "notes": [], "created": "2017-05-03T13:00:44.730Z", "modified": "2020-01-21T13:53:21.406Z"}, {"entity": "publication", "iuid": "a2da1ab0ebad4db8ba25618746d60e2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2da1ab0ebad4db8ba25618746d60e2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2da1ab0ebad4db8ba25618746d60e2a"}}, "title": "Targeting SAMHD1 with the Vpx protein to improve cytarabine therapy for hematological malignancies.", "authors": [{"family": "Herold", "given": "Nikolas", "initials": "N", "orcid": "0000-0001-9468-4543", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2af6f17f76457680908c36693f2de5.json"}}, {"family": "Rudd", "given": "Sean G", "initials": "SG"}, {"family": "Ljungblad", "given": "Linda", "initials": "L"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Myrberg", "given": "Ida Hed", "initials": "IH"}, {"family": "Paulin", "given": "Cynthia B J", "initials": "CB"}, {"family": "Heshmati", "given": "Yaser", "initials": "Y"}, {"family": "Hagenkort", "given": "Anna", "initials": "A"}, {"family": "Kutzner", "given": "Juliane", "initials": "J"}, {"family": "Page", "given": "Brent D G", "initials": "BD"}, {"family": "Calder\u00f3n-Monta\u00f1o", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Bulli", "given": "Lorenzo", "initials": "L"}, {"family": "Axelsson", "given": "Hanna", "initials": "H"}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Valerie", "given": "Nicholas C K", "initials": "NC", "orcid": "0000-0002-9423-964X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d90c5a1f924c8b97409934dec74b0b.json"}}, {"family": "H\u00f6glund", "given": "Andreas", "initials": "A"}, {"family": "Bladh", "given": "Julia", "initials": "J"}, {"family": "Wiita", "given": "Elis\u00e9e", "initials": "E"}, {"family": "Sundin", "given": "Mikael", "initials": "M"}, {"family": "Uhlin", "given": "Michael", "initials": "M"}, {"family": "Rassidakis", "given": "Georgios", "initials": "G"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP"}, {"family": "Warpman-Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Walfridsson", "given": "Julian", "initials": "J"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Henter", "given": "Jan-Inge", "initials": "JI"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Schaller", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9597-4112", "researcher": {"href": "https://publications.scilifelab.se/researcher/c74944db1b4f4fe4a09079f417f8eec6.json"}}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "23", "issn": "1546-170X", "issue": "2", "pages": "256-263", "title": "Nat. Med.", "issn-l": "1078-8956"}, "abstract": "The cytostatic deoxycytidine analog cytarabine (ara-C) is the most active agent available against acute myelogenous leukemia (AML). Together with anthracyclines, ara-C forms the backbone of AML treatment for children and adults. In AML, both the cytotoxicity of ara-C in vitro and the clinical response to ara-C therapy are correlated with the ability of AML blasts to accumulate the active metabolite ara-C triphosphate (ara-CTP), which causes DNA damage through perturbation of DNA synthesis. Differences in expression levels of known transporters or metabolic enzymes relevant to ara-C only partially account for patient-specific differential ara-CTP accumulation in AML blasts and response to ara-C treatment. Here we demonstrate that the deoxynucleoside triphosphate (dNTP) triphosphohydrolase SAM domain and HD domain 1 (SAMHD1) promotes the detoxification of intracellular ara-CTP pools. Recombinant SAMHD1 exhibited ara-CTPase activity in vitro, and cells in which SAMHD1 expression was transiently reduced by treatment with the simian immunodeficiency virus (SIV) protein Vpx were dramatically more sensitive to ara-C-induced cytotoxicity. CRISPR-Cas9-mediated disruption of the gene encoding SAMHD1 sensitized cells to ara-C, and this sensitivity could be abrogated by ectopic expression of wild-type (WT), but not dNTPase-deficient, SAMHD1. Mouse models of AML lacking SAMHD1 were hypersensitive to ara-C, and treatment ex vivo with Vpx sensitized primary patient-derived AML blasts to ara-C. Finally, we identified SAMHD1 as a risk factor in cohorts of both pediatric and adult patients with de novo AML who received ara-C treatment. Thus, SAMHD1 expression levels dictate patient sensitivity to ara-C, providing proof-of-concept that the targeting of SAMHD1 by Vpx could be an attractive therapeutic strategy for potentiating ara-C efficacy in hematological malignancies.", "doi": "10.1038/nm.4265", "pmid": "28067901", "labels": {"Protein Science Facility (PSF)": "Service", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nm.4265"}], "notes": [], "created": "2017-10-05T06:44:17.119Z", "modified": "2025-10-17T13:04:29.327Z"}, {"entity": "publication", "iuid": "ea64623217244bc2bcf2b887b655475c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea64623217244bc2bcf2b887b655475c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea64623217244bc2bcf2b887b655475c"}}, "title": "PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study.", "authors": [{"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "Swerdlow", "given": "Daniel I", "initials": "DI"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Patel", "given": "Riyaz S", "initials": "RS"}, {"family": "Fairhurst-Hunter", "given": "Zammy", "initials": "Z"}, {"family": "Lyall", "given": "Donald M", "initials": "DM"}, {"family": "Hartwig", "given": "Fernando Pires", "initials": "FP"}, {"family": "Horta", "given": "Bernardo Lessa", "initials": "BL"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Power", "given": "Christine", "initials": "C"}, {"family": "Moldovan", "given": "Max", "initials": "M"}, {"family": "van Iperen", "given": "Erik", "initials": "E"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Demuth", "given": "Ilja", "initials": "I"}, {"family": "Norman", "given": "Kristina", "initials": "K"}, {"family": "Steinhagen-Thiessen", "given": "Elisabeth", "initials": "E"}, {"family": "Demuth", "given": "Juri", "initials": "J"}, {"family": "Bertram", "given": "Lars", "initials": "L"}, {"family": "Liu", "given": "Tian", "initials": "T"}, {"family": "Coassin", "given": "Stefan", "initials": "S"}, {"family": "Willeit", "given": "Johann", "initials": "J"}, {"family": "Kiechl", "given": "Stefan", "initials": "S"}, {"family": "Willeit", "given": "Karin", "initials": "K"}, {"family": "Mason", "given": "Dan", "initials": "D"}, {"family": "Wright", "given": "John", "initials": "J"}, {"family": "Morris", "given": "Richard", "initials": "R"}, {"family": "Wanamethee", "given": "Goya", "initials": "G"}, {"family": "Whincup", "given": "Peter", "initials": "P"}, {"family": "Ben-Shlomo", "given": "Yoav", "initials": "Y"}, {"family": "McLachlan", "given": "Stela", "initials": "S"}, {"family": "Price", "given": "Jackie F", "initials": "JF"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Welch", "given": "Catherine", "initials": "C"}, {"family": "Sanchez-Galvez", "given": "Adelaida", "initials": "A"}, {"family": "Marques-Vidal", "given": "Pedro", "initials": "P"}, {"family": "Nicolaides", "given": "Andrew", "initials": "A"}, {"family": "Panayiotou", "given": "Andrie G", "initials": "AG"}, {"family": "Onland-Moret", "given": "N Charlotte", "initials": "NC"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "Matullo", "given": "Giuseppe", "initials": "G"}, {"family": "Fiorito", "given": "Giovanni", "initials": "G"}, {"family": "Guarrera", "given": "Simonetta", "initials": "S"}, {"family": "Sacerdote", "given": "Carlotta", "initials": "C"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Scott", "given": "Robert", "initials": "R"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Bobak", "given": "Martin", "initials": "M"}, {"family": "Malyutina", "given": "Sofia", "initials": "S"}, {"family": "Paj\u0105k", "given": "Andrzej", "initials": "A"}, {"family": "Kubinova", "given": "Ruzena", "initials": "R"}, {"family": "Tamosiunas", "given": "Abdonas", "initials": "A"}, {"family": "Pikhart", "given": "Hynek", "initials": "H"}, {"family": "Husemoen", "given": "Lise Lotte Nystrup", "initials": "LL"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Simonsen", "given": "Kenneth Starup", "initials": "KS"}, {"family": "Cooper", "given": "Jackie", "initials": "J"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Brilliant", "given": "Murray", "initials": "M"}, {"family": "Kitchner", "given": "Terrie", "initials": "T"}, {"family": "Hakonarson", "given": "Hakon", "initials": "H"}, {"family": "Carrell", "given": "David S", "initials": "DS"}, {"family": "McCarty", "given": "Catherine A", "initials": "CA"}, {"family": "Kirchner", "given": "H Lester", "initials": "HL"}, {"family": "Larson", "given": "Eric B", "initials": "EB"}, {"family": "Crosslin", "given": "David R", "initials": "DR"}, {"family": "de Andrade", "given": "Mariza", "initials": "M"}, {"family": "Roden", "given": "Dan M", "initials": "DM"}, {"family": "Denny", "given": "Joshua C", "initials": "JC"}, {"family": "Carty", "given": "Cara", "initials": "C"}, {"family": "Hancock", "given": "Stephen", "initials": "S"}, {"family": "Attia", "given": "John", "initials": "J"}, {"family": "Holliday", "given": "Elizabeth", "initials": "E"}, {"family": "O'Donnell", "given": "Martin", "initials": "M"}, {"family": "Yusuf", "given": "Salim", "initials": "S"}, {"family": "Chong", "given": "Michael", "initials": "M"}, {"family": "Pare", "given": "Guillaume", "initials": "G"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Said", "given": "M Abdullah", "initials": "MA"}, {"family": "Eppinga", "given": "Ruben N", "initials": "RN"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "LifeLines Cohort study group", "given": null, "initials": null}, {"family": "Christen", "given": "Tim", "initials": "T"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Pazoki", "given": "Raha", "initials": "R"}, {"family": "Franco", "given": "Oscar", "initials": "O"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Uitterlinden", "given": "Andre", "initials": "A"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Baumeister", "given": "Sebastian", "initials": "S"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Lerch", "given": "Markus M", "initials": "MM"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Ward", "given": "Joey", "initials": "J"}, {"family": "Pell", "given": "Jill P", "initials": "JP"}, {"family": "Smith", "given": "Daniel J", "initials": "DJ"}, {"family": "Meade", "given": "Tom", "initials": "T"}, {"family": "Maitland-van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "Baranova", "given": "Ekaterina V", "initials": "EV"}, {"family": "Young", "given": "Robin", "initials": "R"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Bots", "given": "Michiel L", "initials": "ML"}, {"family": "Grobbee", "given": "Diederick E", "initials": "DE"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Thuillier", "given": "Doroth\u00e9e", "initials": "D"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Bonnefond", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Cariou", "given": "Bertrand", "initials": "B"}, {"family": "Smart", "given": "Melissa", "initials": "M"}, {"family": "Bao", "given": "Yanchun", "initials": "Y"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Ritchie", "given": "Marylyn D", "initials": "MD"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Casas", "given": "Juan-Pablo", "initials": "JP"}, {"family": "Keating", "given": "Brendan J", "initials": "BJ"}, {"family": "Preiss", "given": "David", "initials": "D"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "UCLEB consortium", "given": null, "initials": null}, {"family": "Sattar", "given": "Naveed", "initials": "N"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "5", "issn": "2213-8595", "issue": "2", "pages": "97-105", "title": "Lancet Diabetes Endocrinol", "issn-l": "2213-8587"}, "abstract": "Statin treatment and variants in the gene encoding HMG-CoA reductase are associated with reductions in both the concentration of LDL cholesterol and the risk of coronary heart disease, but also with modest hyperglycaemia, increased bodyweight, and modestly increased risk of type 2 diabetes, which in no way offsets their substantial benefits. We sought to investigate the associations of LDL cholesterol-lowering PCSK9 variants with type 2 diabetes and related biomarkers to gauge the likely effects of PCSK9 inhibitors on diabetes risk.\n\nIn this mendelian randomisation study, we used data from cohort studies, randomised controlled trials, case control studies, and genetic consortia to estimate associations of PCSK9 genetic variants with LDL cholesterol, fasting blood glucose, HbA1c, fasting insulin, bodyweight, waist-to-hip ratio, BMI, and risk of type 2 diabetes, using a standardised analysis plan, meta-analyses, and weighted gene-centric scores.\n\nData were available for more than 550\u2008000 individuals and 51\u2008623 cases of type 2 diabetes. Combined analyses of four independent PCSK9 variants (rs11583680, rs11591147, rs2479409, and rs11206510) scaled to 1 mmol/L lower LDL cholesterol showed associations with increased fasting glucose (0\u00b709 mmol/L, 95% CI 0\u00b702 to 0\u00b715), bodyweight (1\u00b703 kg, 0\u00b724 to 1\u00b782), waist-to-hip ratio (0\u00b7006, 0\u00b7003 to 0\u00b7010), and an odds ratio for type diabetes of 1\u00b729 (1\u00b711 to 1\u00b750). Based on the collected data, we did not identify associations with HbA1c (0\u00b703%, -0\u00b701 to 0\u00b708), fasting insulin (0\u00b700%, -0\u00b706 to 0\u00b707), and BMI (0\u00b711 kg/m(2), -0\u00b709 to 0\u00b730).\n\nPCSK9 variants associated with lower LDL cholesterol were also associated with circulating higher fasting glucose concentration, bodyweight, and waist-to-hip ratio, and an increased risk of type 2 diabetes. In trials of PCSK9 inhibitor drugs, investigators should carefully assess these safety outcomes and quantify the risks and benefits of PCSK9 inhibitor treatment, as was previously done for statins.\n\nBritish Heart Foundation, and University College London Hospitals NHS Foundation Trust (UCLH) National Institute for Health Research (NIHR) Biomedical Research Centre.", "doi": "10.1016/S2213-8587(16)30396-5", "pmid": "27908689", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2213-8587(16)30396-5"}, {"db": "pmc", "key": "PMC5266795"}], "notes": [], "created": "2017-05-03T12:59:53.796Z", "modified": "2024-01-16T13:48:48.535Z"}, {"entity": "publication", "iuid": "f6e933bcf3b04b0fb8bd753cf0d3dc90", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6e933bcf3b04b0fb8bd753cf0d3dc90.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6e933bcf3b04b0fb8bd753cf0d3dc90"}}, "title": "Opioid precursor protein isoform is targeted to the cell nuclei in the human brain.", "authors": [{"family": "Kononenko", "given": "Olga", "initials": "O"}, {"family": "Bazov", "given": "Igor", "initials": "I"}, {"family": "Watanabe", "given": "Hiroyuki", "initials": "H"}, {"family": "Gerashchenko", "given": "Ganna", "initials": "G"}, {"family": "Dyachok", "given": "Oleg", "initials": "O"}, {"family": "Verbeek", "given": "Dineke S", "initials": "DS"}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Druid", "given": "Henrik", "initials": "H"}, {"family": "Andersson", "given": "Malin", "initials": "M"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Svenningsen", "given": "\u00c5sa Fex", "initials": "\u00c5F"}, {"family": "Rajkowska", "given": "Grazyna", "initials": "G"}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA"}, {"family": "Krishtal", "given": "Oleg", "initials": "O"}, {"family": "Yakovleva", "given": "Tatiana", "initials": "T"}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "1861", "issn": "0304-4165", "issue": "2", "pages": "246-255", "title": "Biochimica et Biophysica Acta (BBA) - General Subjects", "issn-l": null}, "abstract": "Neuropeptide precursors are traditionally viewed as proteins giving rise to small neuropeptide molecules. Prodynorphin (PDYN) is the precursor protein to dynorphins, endogenous ligands for the \u03ba-opioid receptor. Alternative mRNA splicing of neuropeptide genes may regulate cell- and tissue-specific neuropeptide expression and produce novel protein isoforms. We here searched for novel PDYN mRNA and their protein product in the human brain.\n\nNovel PDYN transcripts were identified using nested PCR amplification of oligo(dT) selected full-length capped mRNA. Gene expression was analyzed by qRT-PCR, PDYN protein by western blotting and confocal imaging, dynorphin peptides by radioimmunoassay. Neuronal nuclei were isolated using fluorescence-activated nuclei sorting (FANS) from postmortem human striatal tissue. Immunofluorescence staining and confocal microscopy was performed for human caudate nucleus.\n\nTwo novel human PDYN mRNA splicing variants were identified. Expression of one of them was confined to the striatum where its levels constituted up to 30% of total PDYN mRNA. This transcript may be translated into \u2206SP-PDYN protein lacking 13 N-terminal amino acids, a fragment of signal peptide (SP). \u2206SP-PDYN was not processed to mature dynorphins and surprisingly, was targeted to the cell nuclei in a model cellular system. The endogenous PDYN protein was identified in the cell nuclei in human striatum by western blotting of isolated neuronal nuclei, and by confocal imaging.\n\nHigh levels of alternatively spliced \u2206SP-PDYN mRNA and nuclear localization of PDYN protein suggests a nuclear function for this isoform of the opioid peptide precursor in human striatum.", "doi": "10.1016/j.bbagen.2016.11.002", "pmid": "27838394", "labels": {"Fluorescence Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "mid", "key": "NIHMS847462"}, {"db": "pmc", "key": "PMC5323248"}, {"db": "pii", "key": "S0304-4165(16)30405-6"}], "notes": [], "created": "2017-05-03T12:59:10.450Z", "modified": "2023-06-08T08:27:14.666Z"}, {"entity": "publication", "iuid": "612ec8baa90d4adb85aac60df882db88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/612ec8baa90d4adb85aac60df882db88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/612ec8baa90d4adb85aac60df882db88"}}, "title": "Novel seminal fluid proteins in the seed beetle Callosobruchus maculatus identified by a proteomic and transcriptomic approach.", "authors": [{"family": "Bayram", "given": "H", "initials": "H"}, {"family": "Sayadi", "given": "A", "initials": "A"}, {"family": "Goenaga", "given": "J", "initials": "J"}, {"family": "Immonen", "given": "E", "initials": "E"}, {"family": "Arnqvist", "given": "G", "initials": "G"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "26", "issn": "1365-2583", "issue": "1", "pages": "58-73", "title": "Insect Mol. Biol.", "issn-l": "0962-1075"}, "abstract": "The seed beetle Callosobruchus maculatus is a significant agricultural pest and increasingly studied model of sexual conflict. Males possess genital spines that increase the transfer of seminal fluid proteins (SFPs) into the female body. As SFPs alter female behaviour and physiology, they are likely to modulate reproduction and sexual conflict in this species. Here, we identified SFPs using proteomics combined with a de novo transcriptome. A prior 2D-sodium dodecyl sulphate polyacrylamide gel electrophoresis analysis identified male accessory gland protein spots that were probably transferred to the female at mating. Proteomic analysis of these spots identified 98 proteins, a majority of which were also present within ejaculates collected from females. Standard annotation workflows revealed common functional groups for SFPs, including proteases and metabolic proteins. Transcriptomic analysis found 84 transcripts differentially expressed between the sexes. Notably, genes encoding 15 proteins were highly expressed in male abdomens and only negligibly expressed within females. Most of these sequences corresponded to 'unknown' proteins (nine of 15) and may represent rapidly evolving SFPs novel to seed beetles. Our combined analyses highlight 44 proteins for which there is strong evidence that they are SFPs. These results can inform further investigation, to better understand the molecular mechanisms of sexual conflict in seed beetles.", "doi": "10.1111/imb.12271", "pmid": "27779332", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Mass Spectrometry-based Proteomics, Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:02:36.229Z", "modified": "2024-01-16T13:48:48.544Z"}, {"entity": "publication", "iuid": "6eeb153d4072463db806a9bd79c398d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6eeb153d4072463db806a9bd79c398d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6eeb153d4072463db806a9bd79c398d5"}}, "title": "Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes.", "authors": [{"family": "Romanov", "given": "Roman A", "initials": "RA"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Bakker", "given": "Joanne", "initials": "J"}, {"family": "Girach", "given": "Fatima", "initials": "F"}, {"family": "Hellysaz", "given": "Arash", "initials": "A"}, {"family": "Tomer", "given": "Raju", "initials": "R"}, {"family": "Alp\u00e1r", "given": "Al\u00e1n", "initials": "A"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Clotman", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}, {"family": "Keimpema", "given": "Erik", "initials": "E"}, {"family": "Hsueh", "given": "Brian", "initials": "B"}, {"family": "Crow", "given": "Ailey K", "initials": "AK"}, {"family": "Martens", "given": "Henrik", "initials": "H"}, {"family": "Schwindling", "given": "Christian", "initials": "C"}, {"family": "Calvigioni", "given": "Daniela", "initials": "D"}, {"family": "Bains", "given": "Jaideep S", "initials": "JS"}, {"family": "M\u00e1t\u00e9", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Szab\u00f3", "given": "G\u00e1bor", "initials": "G"}, {"family": "Yanagawa", "given": "Yuchio", "initials": "Y"}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD"}, {"family": "Rendeiro", "given": "Andre", "initials": "A", "orcid": "0000-0001-9362-5373", "researcher": {"href": "https://publications.scilifelab.se/researcher/e714399288874d1097d0d8c13123f756.json"}}, {"family": "Farlik", "given": "Matthias", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Wulff", "given": "Peer", "initials": "P"}, {"family": "Bock", "given": "Christoph", "initials": "C", "orcid": "0000-0001-6091-3088", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab95ee1c8284fa7bf2e5a2ee987c835.json"}}, {"family": "Broberger", "given": "Christian", "initials": "C"}, {"family": "Deisseroth", "given": "Karl", "initials": "K"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Horvath", "given": "Tamas L", "initials": "TL"}, {"family": "Harkany", "given": "Tibor", "initials": "T"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "20", "issn": "1546-1726", "issue": "2", "pages": "176-188", "title": "Nat. Neurosci.", "issn-l": "1097-6256"}, "abstract": "The hypothalamus contains the highest diversity of neurons in the brain. Many of these neurons can co-release neurotransmitters and neuropeptides in a use-dependent manner. Investigators have hitherto relied on candidate protein-based tools to correlate behavioral, endocrine and gender traits with hypothalamic neuron identity. Here we map neuronal identities in the hypothalamus by single-cell RNA sequencing. We distinguished 62 neuronal subtypes producing glutamatergic, dopaminergic or GABAergic markers for synaptic neurotransmission and harboring the ability to engage in task-dependent neurotransmitter switching. We identified dopamine neurons that uniquely coexpress the Onecut3 and Nmur2 genes, and placed these in the periventricular nucleus with many synaptic afferents arising from neuromedin S+ neurons of the suprachiasmatic nucleus. These neuroendocrine dopamine cells may contribute to the dopaminergic inhibition of prolactin secretion diurnally, as their neuromedin S+ inputs originate from neurons expressing Per2 and Per3 and their tyrosine hydroxylase phosphorylation is regulated in a circadian fashion. Overall, our catalog of neuronal subclasses provides new understanding of hypothalamic organization and function.", "doi": "10.1038/nn.4462", "pmid": "27991900", "labels": {"Fluorescence Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nn.4462"}], "notes": [], "created": "2017-05-03T12:58:52.200Z", "modified": "2021-07-08T13:44:33.346Z"}, {"entity": "publication", "iuid": "f501789b43404e2bab18536f512912c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f501789b43404e2bab18536f512912c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f501789b43404e2bab18536f512912c3"}}, "title": "Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.", "authors": [{"family": "Celepli", "given": "Narin", "initials": "N"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Dupont", "given": "Chris L", "initials": "CL"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "19", "issn": "1462-2920", "issue": "2", "pages": "673-686", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16\u00a0psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.", "doi": "10.1111/1462-2920.13592", "pmid": "27871145", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:10.996Z", "modified": "2024-01-16T13:48:48.558Z"}, {"entity": "publication", "iuid": "52e6b8f5adc249aaac10a6fd81033e5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52e6b8f5adc249aaac10a6fd81033e5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52e6b8f5adc249aaac10a6fd81033e5b"}}, "title": "Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy", "authors": [{"family": "Dalin", "given": "Martin G", "initials": "MG"}, {"family": "Engstr\u00f6m", "given": "P\u00e4r G", "initials": "PG", "orcid": "0000-0001-5265-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce330ec225f4a8595932d092ab8c8d1.json"}}, {"family": "Ivarsson", "given": "Emil G", "initials": "EG"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Schaufelberger", "given": "Maria", "initials": "M"}, {"family": "Gilljam", "given": "Thomas", "initials": "T"}, {"family": "Andersson", "given": "Bert", "initials": "B", "orcid": "0000-0001-7957-2463", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf5a4c61accb4c7b93bca8e713be3694.json"}}, {"family": "Bergo", "given": "Martin O", "initials": "MO"}], "type": "journal-article", "published": "2017-02-00", "journal": {"volume": "228", "issn": "0167-5273", "issue": null, "pages": "742-748", "title": "International Journal of Cardiology", "issn-l": "0167-5273"}, "abstract": "Germline genetic variants are an important cause of dilated cardiomyopathy (DCM). However, recent sequencing studies have revealed rare variants in DCM-associated genes also in individuals without known heart disease. In this study, we investigate variant prevalence and genotype-phenotype correlations in Swedish DCM patients, and compare their genetic variants to those detected in reference cohorts.\n\nWe sequenced the coding regions of 41 DCM-associated genes in 176 unrelated patients with idiopathic DCM and found 102 protein-altering variants with an allele frequency of <0.04% in reference cohorts; the majority were missense variants not previously described in DCM. Fifty-five (31%) patients had one variant, and 24 (14%) patients had two or more variants in the analysed genes. Detection of genetic variants in any gene, and in LMNA, MYH7 or TTN alone, was associated with early onset disease and reduced transplant-free survival. As expected, nonsense and frameshift variants were more common in DCM patients than in healthy individuals of the reference cohort 1000 Genomes Europeans. Surprisingly however, the prevalence, conservation and pathogenicity scores, and localization of missense variants were similar in DCM patients and healthy reference individuals.\n\nTo our knowledge, this is the first study to identify correlations between genotype and prognosis when sequencing a large number of genes in unselected DCM patients. The similar distribution of missense variants in DCM patients and healthy reference individuals questions the pathogenic role of many variants, and suggests that results from genetic testing of DCM patients should be interpreted with caution.", "doi": "10.1016/j.ijcard.2016.11.066", "pmid": "27886618", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0167-5273(16)33512-4"}], "notes": [], "created": "2017-05-03T12:58:56.344Z", "modified": "2024-01-16T13:48:48.570Z"}, {"entity": "publication", "iuid": "b555f13298ec4a75b25a26825eb7af97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b555f13298ec4a75b25a26825eb7af97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b555f13298ec4a75b25a26825eb7af97"}}, "title": "Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism.", "authors": [{"family": "Bramswig", "given": "Nuria C", "initials": "NC"}, {"family": "L\u00fcdecke", "given": "H-J", "initials": "HJ"}, {"family": "Pettersson", "given": "M", "initials": "M"}, {"family": "Albrecht", "given": "B", "initials": "B"}, {"family": "Bernier", "given": "R A", "initials": "RA"}, {"family": "Cremer", "given": "K", "initials": "K"}, {"family": "Eichler", "given": "E E", "initials": "EE"}, {"family": "Falkenstein", "given": "D", "initials": "D"}, {"family": "Gerdts", "given": "J", "initials": "J"}, {"family": "Jansen", "given": "S", "initials": "S"}, {"family": "Kuechler", "given": "A", "initials": "A"}, {"family": "Kvarnung", "given": "M", "initials": "M"}, {"family": "Lindstrand", "given": "A", "initials": "A"}, {"family": "Nilsson", "given": "D", "initials": "D"}, {"family": "Nordgren", "given": "A", "initials": "A"}, {"family": "Pfundt", "given": "R", "initials": "R"}, {"family": "Spruijt", "given": "L", "initials": "L"}, {"family": "Surowy", "given": "H M", "initials": "HM"}, {"family": "de Vries", "given": "B B A", "initials": "BB"}, {"family": "Wieland", "given": "T", "initials": "T"}, {"family": "Engels", "given": "H", "initials": "H"}, {"family": "Strom", "given": "T M", "initials": "TM"}, {"family": "Kleefstra", "given": "T", "initials": "T"}, {"family": "Wieczorek", "given": "D", "initials": "D"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "136", "issn": "1432-1203", "issue": "2", "pages": "179-192", "title": "Hum. Genet.", "issn-l": "0340-6717"}, "abstract": "The ubiquitin pathway is an enzymatic cascade including activating E1, conjugating E2, and ligating E3 enzymes, which governs protein degradation and sorting. It is crucial for many physiological processes. Compromised function of members of the ubiquitin pathway leads to a wide range of human diseases, such as cancer, neurodegenerative diseases, and neurodevelopmental disorders. Mutations in the thyroid hormone receptor interactor 12 (TRIP12) gene (OMIM 604506), which encodes an E3 ligase in the ubiquitin pathway, have been associated with autism spectrum disorder (ASD). In addition to autistic features, TRIP12 mutation carriers showed intellectual disability (ID). More recently, TRIP12 was postulated as a novel candidate gene for intellectual disability in a meta-analysis of published ID cohorts. However, detailed clinical information characterizing the phenotype of these individuals was not provided. In this study, we present seven novel individuals with private TRIP12 mutations including two splice site mutations, one nonsense mutation, three missense mutations, and one translocation case with a breakpoint in intron 1 of the TRIP12 gene and clinically review four previously published cases. The TRIP12 mutation-positive individuals presented with mild to moderate ID (10/11) or learning disability [intelligence quotient (IQ) 76 in one individual], ASD (8/11) and some of them with unspecific craniofacial dysmorphism and other anomalies. In this study, we provide detailed clinical information of 11 TRIP12 mutation-positive individuals and thereby expand the clinical spectrum of the TRIP12 gene in non-syndromic intellectual disability with or without ASD.", "doi": "10.1007/s00439-016-1743-x", "pmid": "27848077", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00439-016-1743-x"}], "notes": [], "created": "2017-05-03T12:59:46.726Z", "modified": "2024-01-16T13:48:48.579Z"}, {"entity": "publication", "iuid": "982ce1b1530f4c3299d9d6e35ea44358", "links": {"self": {"href": "https://publications.scilifelab.se/publication/982ce1b1530f4c3299d9d6e35ea44358.json"}, "display": {"href": "https://publications.scilifelab.se/publication/982ce1b1530f4c3299d9d6e35ea44358"}}, "title": "Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication", "authors": [{"family": "Fallahsharoudi", "given": "Amir", "initials": "A"}, {"family": "de Kock", "given": "Neil", "initials": "N"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Bektic", "given": "Lejla", "initials": "L"}, {"family": "Ubhayasekera", "given": "S J Kumari A", "initials": "SJKA"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Jensen", "given": "Per", "initials": "P"}], "type": "journal-article", "published": "2017-02-00", "journal": {"volume": "7", "issn": "2160-1836", "issue": "2", "pages": "497-504", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": null, "doi": "10.1534/g3.116.037721", "pmid": "27974436", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:03:03.924Z", "modified": "2020-01-21T13:56:11.667Z"}, {"entity": "publication", "iuid": "8481694649d0451d9ec4dd22f32b30e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8481694649d0451d9ec4dd22f32b30e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8481694649d0451d9ec4dd22f32b30e2"}}, "title": "Evolution of bird genomes-a transposon's-eye view.", "authors": [{"family": "Kapusta", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Suh", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "1389", "issn": "1749-6632", "issue": "1", "pages": "164-185", "title": "Ann. N. Y. Acad. Sci.", "issn-l": "0077-8923"}, "abstract": "Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE \"arms races\" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.", "doi": "10.1111/nyas.13295", "pmid": "27997700", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T09:29:02.852Z", "modified": "2024-01-16T13:48:48.586Z"}, {"entity": "publication", "iuid": "0128976e8d8d46669f7aca7b8d36aa37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0128976e8d8d46669f7aca7b8d36aa37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0128976e8d8d46669f7aca7b8d36aa37"}}, "title": "Evidence for three genetic loci involved in both anorexia nervosa risk and variation of body mass index.", "authors": [{"family": "Hinney", "given": "A", "initials": "A"}, {"family": "Kesselmeier", "given": "M", "initials": "M"}, {"family": "Jall", "given": "S", "initials": "S"}, {"family": "Volckmar", "given": "A-L", "initials": "AL"}, {"family": "F\u00f6cker", "given": "M", "initials": "M"}, {"family": "Antel", "given": "J", "initials": "J"}, {"family": "GCAN", "given": null, "initials": null}, {"family": "WTCCC3", "given": null, "initials": null}, {"family": "Heid", "given": "I M", "initials": "IM"}, {"family": "Winkler", "given": "T W", "initials": "TW"}, {"family": "GIANT", "given": null, "initials": null}, {"family": "Grant", "given": "S F A", "initials": "SF"}, {"family": "EGG", "given": null, "initials": null}, {"family": "Guo", "given": "Y", "initials": "Y"}, {"family": "Bergen", "given": "A W", "initials": "AW"}, {"family": "Kaye", "given": "W", "initials": "W"}, {"family": "Berrettini", "given": "W", "initials": "W"}, {"family": "Hakonarson", "given": "H", "initials": "H"}, {"family": "Price Foundation Collaborative Group", "given": null, "initials": null}, {"family": "Children\u2019s Hospital of Philadelphia/Price Foundation", "given": null, "initials": null}, {"family": "Herpertz-Dahlmann", "given": "B", "initials": "B"}, {"family": "de Zwaan", "given": "M", "initials": "M"}, {"family": "Herzog", "given": "W", "initials": "W"}, {"family": "Ehrlich", "given": "S", "initials": "S"}, {"family": "Zipfel", "given": "S", "initials": "S"}, {"family": "Egberts", "given": "K M", "initials": "KM"}, {"family": "Adan", "given": "R", "initials": "R"}, {"family": "Brandys", "given": "M", "initials": "M"}, {"family": "van Elburg", "given": "A", "initials": "A"}, {"family": "Boraska Perica", "given": "V", "initials": "V"}, {"family": "Franklin", "given": "C S", "initials": "CS"}, {"family": "Tsch\u00f6p", "given": "M H", "initials": "MH"}, {"family": "Zeggini", "given": "E", "initials": "E"}, {"family": "Bulik", "given": "C M", "initials": "CM"}, {"family": "Collier", "given": "D", "initials": "D"}, {"family": "Scherag", "given": "A", "initials": "A"}, {"family": "M\u00fcller", "given": "T D", "initials": "TD"}, {"family": "Hebebrand", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "22", "issn": "1476-5578", "issue": "2", "pages": "192-201", "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "The maintenance of normal body weight is disrupted in patients with anorexia nervosa (AN) for prolonged periods of time. Prior to the onset of AN, premorbid body mass index (BMI) spans the entire range from underweight to obese. After recovery, patients have reduced rates of overweight and obesity. As such, loci involved in body weight regulation may also be relevant for AN and vice versa. Our primary analysis comprised a cross-trait analysis of the 1000 single-nucleotide polymorphisms (SNPs) with the lowest P-values in a genome-wide association meta-analysis (GWAMA) of AN (GCAN) for evidence of association in the largest published GWAMA for BMI (GIANT). Subsequently we performed sex-stratified analyses for these 1000 SNPs. Functional ex vivo studies on four genes ensued. Lastly, a look-up of GWAMA-derived BMI-related loci was performed in the AN GWAMA. We detected significant associations (P-values <5 \u00d7 10(-5), Bonferroni-corrected P<0.05) for nine SNP alleles at three independent loci. Interestingly, all AN susceptibility alleles were consistently associated with increased BMI. None of the genes (chr. 10: CTBP2, chr. 19: CCNE1, chr. 2: CARF and NBEAL1; the latter is a region with high linkage disequilibrium) nearest to these SNPs has previously been associated with AN or obesity. Sex-stratified analyses revealed that the strongest BMI signal originated predominantly from females (chr. 10 rs1561589; Poverall: 2.47 \u00d7 10(-06)/Pfemales: 3.45 \u00d7 10(-07)/Pmales: 0.043). Functional ex vivo studies in mice revealed reduced hypothalamic expression of Ctbp2 and Nbeal1 after fasting. Hypothalamic expression of Ctbp2 was increased in diet-induced obese (DIO) mice as compared with age-matched lean controls. We observed no evidence for associations for the look-up of BMI-related loci in the AN GWAMA. A cross-trait analysis of AN and BMI loci revealed variants at three chromosomal loci with potential joint impact. The chromosome 10 locus is particularly promising given that the association with obesity was primarily driven by females. In addition, the detected altered hypothalamic expression patterns of Ctbp2 and Nbeal1 as a result of fasting and DIO implicate these genes in weight regulation.", "doi": "10.1038/mp.2016.71", "pmid": "27184124", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mp201671"}, {"db": "pmc", "key": "PMC5114162"}, {"db": "mid", "key": "NIHMS798415"}], "notes": [], "created": "2017-05-08T07:57:27.350Z", "modified": "2024-01-16T13:48:48.595Z"}, {"entity": "publication", "iuid": "571f5407c7cb4f8499d389e458b520d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/571f5407c7cb4f8499d389e458b520d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/571f5407c7cb4f8499d389e458b520d5"}}, "title": "Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr ( Salvelinus alpinus )", "authors": [{"family": "Nyman", "given": "Andreas", "initials": "A"}, {"family": "Huyben", "given": "David", "initials": "D"}, {"family": "Lundh", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-02-00", "journal": {"volume": "5", "issn": "2352-5134", "issue": null, "pages": "34-40", "title": "Aquaculture Reports", "issn-l": "2352-5134"}, "abstract": null, "doi": "10.1016/j.aqrep.2016.12.003", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:10:04.160Z", "modified": "2024-01-16T13:48:48.611Z"}, {"entity": "publication", "iuid": "179081d94ec4445399f3f2ddc36fac7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/179081d94ec4445399f3f2ddc36fac7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/179081d94ec4445399f3f2ddc36fac7e"}}, "title": "Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells.", "authors": [{"family": "Ullmark", "given": "Tove", "initials": "T"}, {"family": "J\u00e4rvstr\u00e5t", "given": "Linnea", "initials": "L"}, {"family": "Sand\u00e9n", "given": "Carl", "initials": "C"}, {"family": "Montano", "given": "Giorgia", "initials": "G"}, {"family": "Jernmark-Nilsson", "given": "Helena", "initials": "H"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Drott", "given": "Kristina", "initials": "K"}, {"family": "Vidovic", "given": "Karina", "initials": "K"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gullberg", "given": "Urban", "initials": "U"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "102", "issn": "1592-8721", "issue": "2", "pages": "336-345", "title": "Haematologica", "issn-l": "0390-6078"}, "abstract": "The zinc finger transcription factor Wilms tumor gene 1 (WT1) acts as an oncogene in acute myeloid leukemia. A naturally occurring alternative splice event between zinc fingers three and four, removing or retaining three amino acids (\u00b1KTS), is believed to change the DNA binding affinity of WT1, although there are conflicting data regarding the binding affinity and motifs of the different isoforms. Increased expression of the WT1 -KTS isoform at the expense of the WT1 +KTS isoform is associated with poor prognosis in acute myeloid leukemia. We determined the genome-wide binding pattern of WT1 -KTS and WT1 +KTS in leukemic K562 cells by chromatin immunoprecipitation and deep sequencing. We discovered that the WT1 -KTS isoform predominantly binds close to transcription start sites and to enhancers, in a similar fashion to other transcription factors, whereas WT1 +KTS binding is enriched within gene bodies. We observed a significant overlap between WT1 -KTS and WT1 +KTS target genes, despite the binding sites being distinct. Motif discovery revealed distinct binding motifs for the isoforms, some of which have been previously reported as WT1 binding sites. Additional analyses showed that both WT1 -KTS and WT1 +KTS target genes are more likely to be transcribed than non-targets, and are involved in cell proliferation, cell death, and development. Our study provides evidence that WT1 -KTS and WT1 +KTS share target genes yet still bind distinct locations, indicating isoform-specific regulation in transcription of genes related to cell proliferation and differentiation, consistent with the involvement of WT1 in acute myeloid leukemia.", "doi": "10.3324/haematol.2016.149815", "pmid": "27612989", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "haematol.2016.149815"}, {"db": "pmc", "key": "PMC5286941"}], "notes": [], "created": "2017-05-03T13:02:03.431Z", "modified": "2024-01-16T13:48:48.624Z"}, {"entity": "publication", "iuid": "98c5a5fab45440a39295dd0bcec235d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98c5a5fab45440a39295dd0bcec235d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98c5a5fab45440a39295dd0bcec235d3"}}, "title": "Defense Responses in Aspen with Altered Pectin Methylesterase Activity Reveal the Hormonal Inducers of Tyloses", "authors": [{"family": "Le\u015bniewska", "given": "Joanna", "initials": "J"}, {"family": "\u00d6hman", "given": "David", "initials": "D"}, {"family": "Krzes\u0142owska", "given": "Magdalena", "initials": "M"}, {"family": "Kushwah", "given": "Sunita", "initials": "S"}, {"family": "Barciszewska-Pacak", "given": "Maria", "initials": "M"}, {"family": "Kleczkowski", "given": "Leszek A", "initials": "LA"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ"}], "type": "journal-article", "published": "2017-02-00", "journal": {"volume": "173", "issn": "1532-2548", "issue": "2", "pages": "1409-1419", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": null, "doi": "10.1104/pp.16.01443", "pmid": "27923986", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:32:48.053Z", "modified": "2025-10-17T13:03:19.115Z"}, {"entity": "publication", "iuid": "b663df15bfdf4bfcacc56407fda3cb8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b663df15bfdf4bfcacc56407fda3cb8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b663df15bfdf4bfcacc56407fda3cb8a"}}, "title": "Complement peptide C3a stimulates neural plasticity after experimental brain ischaemia.", "authors": [{"family": "Stokowska", "given": "Anna", "initials": "A"}, {"family": "Atkins", "given": "Alison L", "initials": "AL"}, {"family": "Mor\u00e1n", "given": "Javier", "initials": "J"}, {"family": "Pekny", "given": "Tulen", "initials": "T"}, {"family": "Bulmer", "given": "Linda", "initials": "L"}, {"family": "Pascoe", "given": "Michaela C", "initials": "MC"}, {"family": "Barnum", "given": "Scott R", "initials": "SR"}, {"family": "Wetsel", "given": "Rick A", "initials": "RA"}, {"family": "Nilsson", "given": "Jonas A", "initials": "JA"}, {"family": "Dragunow", "given": "Mike", "initials": "M"}, {"family": "Pekna", "given": "Marcela", "initials": "M"}], "type": "journal article", "published": "2017-02-00", "journal": {"title": "Brain", "issn": "1460-2156", "volume": "140", "issue": "2", "pages": "353-369", "issn-l": "0006-8950"}, "abstract": "Ischaemic stroke induces endogenous repair processes that include proliferation and differentiation of neural stem cells and extensive rewiring of the remaining neural connections, yet about 50% of stroke survivors live with severe long-term disability. There is an unmet need for drug therapies to improve recovery by promoting brain plasticity in the subacute to chronic phase after ischaemic stroke. We previously showed that complement-derived peptide C3a regulates neural progenitor cell migration and differentiation in vitro and that C3a receptor signalling stimulates neurogenesis in unchallenged adult mice. To determine the role of C3a-C3a receptor signalling in ischaemia-induced neural plasticity, we subjected C3a receptor-deficient mice, GFAP-C3a transgenic mice expressing biologically active C3a in the central nervous system, and their respective wild-type controls to photothrombotic stroke. We found that C3a overexpression increased, whereas C3a receptor deficiency decreased post-stroke expression of GAP43 (P < 0.01), a marker of axonal sprouting and plasticity, in the peri-infarct cortex. To verify the translational potential of these findings, we used a pharmacological approach. Daily intranasal treatment of wild-type mice with C3a beginning 7 days after stroke induction robustly increased synaptic density (P < 0.01) and expression of GAP43 in peri-infarct cortex (P < 0.05). Importantly, the C3a treatment led to faster and more complete recovery of forepaw motor function (P < 0.05). We conclude that C3a-C3a receptor signalling stimulates post-ischaemic neural plasticity and intranasal treatment with C3a receptor agonists is an attractive approach to improve functional recovery after ischaemic brain injury.", "doi": "10.1093/brain/aww314", "pmid": "27956400", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "aww314"}], "notes": [], "created": "2020-01-23T16:36:17.901Z", "modified": "2021-06-21T15:43:36.124Z"}, {"entity": "publication", "iuid": "1f6f62aa9045409dbd1e3e2179eaa17c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f6f62aa9045409dbd1e3e2179eaa17c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f6f62aa9045409dbd1e3e2179eaa17c"}}, "title": "Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS.", "authors": [{"family": "Nilsson", "given": "Jonas", "initials": "J"}, {"family": "Noborn", "given": "Fredrik", "initials": "F"}, {"family": "Gomez Toledo", "given": "Alejandro", "initials": "A"}, {"family": "Nasir", "given": "Waqas", "initials": "W"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Larson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "28", "issn": "1879-1123", "issue": "2", "pages": "229-241", "title": "J. Am. Soc. Mass Spectrom.", "issn-l": "1044-0305"}, "abstract": "Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had \u0394HexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. However, it was not possible to exactly pinpoint sulfate attachment residues, for protonated precursors, due to extensive fragmentation of sulfate groups using high-energy collision induced dissociation (HCD). To circumvent the well-recognized sulfate instability, we now introduced Na + ions to form sodiated precursors, which protected sulfate groups from decomposition and facilitated the assignment of sulfate modifications. Sulfate groups were pinpointed to both Gal residues and to the GalNAc of the hexasaccharide structure. The intensities of protonated and sodiated saccharide oxonium ions were very prominent in the HCD-MS2 spectra, which provided complementary structural analysis of sulfate substituents of CS-glycopeptides. We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. The realization of these structural variants should be beneficial in studies aimed at investigating the importance of the CS linkage region with regards to the biosynthesis of CS and potential interactions to CS binding proteins. Also, the combined use of protonated and sodiated precursors for positive mode HCD fragmentation analysis will likely become useful for additional classes of sulfated glycopeptides. Graphical Abstract \u115f.", "doi": "10.1007/s13361-016-1539-1", "pmid": "27873218", "labels": {"Glycoproteomics and MS Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1007/s13361-016-1539-1"}, {"db": "pmc", "key": "PMC5227003"}], "notes": [], "created": "2020-01-27T22:46:42.220Z", "modified": "2024-01-16T13:46:32.889Z"}, {"entity": "publication", "iuid": "80df265c4d2b497f96f16322e923b55e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80df265c4d2b497f96f16322e923b55e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80df265c4d2b497f96f16322e923b55e"}}, "title": "Associations of defect mismatch repair genes with prognosis and heredity in sporadic colorectal cancer.", "authors": [{"family": "Ghanipour", "given": "L", "initials": "L"}, {"family": "Jirstr\u00f6m", "given": "K", "initials": "K"}, {"family": "Sundstr\u00f6m", "given": "M", "initials": "M"}, {"family": "Glimelius", "given": "B", "initials": "B"}, {"family": "Birgisson", "given": "H", "initials": "H"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "43", "issn": "1532-2157", "issue": "2", "pages": "311-321", "title": "Eur J Surg Oncol", "issn-l": "0748-7983"}, "abstract": "Microsatellite instability arises due to defect mismatch repair (MMR) and occurs in 10-20% of sporadic colorectal cancer. The purpose was to investigate correlations between defect MMR, prognosis and heredity for colorectal cancer in first-degree relatives.\n\nTumour tissues from 318 patients consecutively operated for colorectal cancer were analysed for immunohistochemical expression of MLH1, MSH2 and MSH6 on tissue microarrays. Information on KRAS and BRAF mutation status was available for selected cases.\n\nForty-seven (15%) tumours displayed MSI. No correlation was seen between patients exhibiting MSI in the tumour and heredity (p\u00a0=\u00a00.789). Patients with proximal colon cancer and MSI had an improved cancer-specific survival (p\u00a0=\u00a00.006) and prolonged time to recurrence (p\u00a0=\u00a00.037). In a multivariate analysis including MSI status, gender, CEA, vascular and neural invasion, patients with MSS and proximal colon cancer had an impaired cancer-specific survival compared with patients with MSI (HR, 4.32; CI, 1.46-12.78). The same prognostic information was also seen in distal colon cancer; no recurrences seen in the eight patients with stages II and III distal colon cancer and MSI, but the difference was not statistically significant.\n\nNo correlation between MSI and heredity for colorectal cancer in first-degree relatives was seen. Patients with MSI tumours had improved survival.", "doi": "10.1016/j.ejso.2016.10.013", "pmid": "27836416", "labels": {"Tissue Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "S0748-7983(16)30951-9"}], "notes": [], "created": "2017-05-03T12:59:18.221Z", "modified": "2017-06-12T11:37:32.856Z"}, {"entity": "publication", "iuid": "c3d1ea2fcb184dfa8d3078a38811a2ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3d1ea2fcb184dfa8d3078a38811a2ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3d1ea2fcb184dfa8d3078a38811a2ce"}}, "title": "Activation of myeloid and endothelial cells by CD40L gene therapy supports T-cell expansion and migration into the tumor microenvironment", "authors": [{"family": "Eriksson", "given": "E", "initials": "E"}, {"family": "Moreno", "given": "R", "initials": "R"}, {"family": "Milenova", "given": "I", "initials": "I"}, {"family": "Liljenfeldt", "given": "L", "initials": "L"}, {"family": "Dieterich", "given": "L C", "initials": "LC"}, {"family": "Christiansson", "given": "L", "initials": "L"}, {"family": "Karlsson", "given": "H", "initials": "H"}, {"family": "Ullenhag", "given": "G", "initials": "G"}, {"family": "Mangsbo", "given": "S M", "initials": "SM"}, {"family": "Dimberg", "given": "A", "initials": "A"}, {"family": "Alemany", "given": "R", "initials": "R"}, {"family": "Loskog", "given": "A", "initials": "A"}], "type": "journal-article", "published": "2017-02-00", "journal": {"volume": "24", "issn": "0969-7128", "issue": "2", "pages": "92-103", "title": "Gene Ther", "issn-l": null}, "abstract": null, "doi": "10.1038/gt.2016.80", "pmid": "27906162", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-17T08:06:57.401Z", "modified": "2024-01-16T13:48:48.635Z"}, {"entity": "publication", "iuid": "1acded0fd6a14542ab5ca0f60463b32b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1acded0fd6a14542ab5ca0f60463b32b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1acded0fd6a14542ab5ca0f60463b32b"}}, "title": "A meta-analysis of reflux genome-wide association studies in 6750 Northern Europeans from the general population.", "authors": [{"family": "Bonfiglio", "given": "F", "initials": "F"}, {"family": "Hysi", "given": "P G", "initials": "PG"}, {"family": "Ek", "given": "W", "initials": "W"}, {"family": "Karhunen", "given": "V", "initials": "V"}, {"family": "Rivera", "given": "N V", "initials": "NV"}, {"family": "M\u00e4nnikk\u00f6", "given": "M", "initials": "M"}, {"family": "Nordenstedt", "given": "H", "initials": "H"}, {"family": "Zucchelli", "given": "M", "initials": "M"}, {"family": "Bresso", "given": "F", "initials": "F"}, {"family": "Williams", "given": "F", "initials": "F"}, {"family": "Tornblom", "given": "H", "initials": "H"}, {"family": "Magnusson", "given": "P K", "initials": "PK"}, {"family": "Pedersen", "given": "N L", "initials": "NL"}, {"family": "Ronkainen", "given": "J", "initials": "J"}, {"family": "Schmidt", "given": "P T", "initials": "PT"}, {"family": "D'Amato", "given": "M", "initials": "M"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "29", "issn": "1365-2982", "issue": "2", "title": "Neurogastroenterol. Motil.", "issn-l": "1350-1925"}, "abstract": "Gastroesophageal reflux disease (GERD), the regurgitation of gastric acids often accompanied by heartburn, affects up to 20% of the general population. Genetic predisposition is suspected from twin and family studies but gene-hunting efforts have so far been scarce and no conclusive genome-wide study has been reported. We exploited data available from general population samples, and studied self-reported reflux symptoms in relation to genome-wide single nucleotide polymorphism (SNP) genotypes.\n\nWe performed a GWAS meta-analysis of three independent population-based cohorts from Sweden, Finland, and UK. GERD cases (n=2247) and asymptomatic controls (n=4503) were identified using questionnaire-derived symptom data. Upon stringent quality controls, genotype data for more than 2.5M markers were used for association testing. Bioinformatic characterization of genomic regions associated with GERD included gene-set enrichment analysis (GSEA), in silico prediction of genetic risk effects on gene expression, and computational analysis of drug-induced gene expression signatures using Connectivity Map (cMap).\n\nWe identified 30 GERD suggestive risk loci (P\u22645\u00d710(-5) ), with concordant risk effects in all cohorts, and predicted functional effects on gene expression in relevant tissues. GSEA revealed involvement of GERD risk genes in biological processes associated with the regulation of ion channel and cell adhesion. From cMap analysis, omeprazole had significant effects on GERD risk gene expression, while antituberculosis and anti-inflammatory drugs scored highest among the repurposed compounds.\n\nWe report a large-scale genetic study of GERD, and highlight genes and pathways that contribute to further our understanding of its pathogenesis and therapeutic opportunities.", "doi": "10.1111/nmo.12923", "pmid": "27485664", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:14.837Z", "modified": "2024-01-16T13:48:48.644Z"}, {"entity": "publication", "iuid": "77013ba616c2495e8f68bf6a247e26f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77013ba616c2495e8f68bf6a247e26f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77013ba616c2495e8f68bf6a247e26f2"}}, "title": "Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection.", "authors": [{"family": "Svedberg", "given": "Gustav", "initials": "G"}, {"family": "Jeong", "given": "Yunjin", "initials": "Y"}, {"family": "Na", "given": "Hunjong", "initials": "H"}, {"family": "Jang", "given": "Jisung", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Kwon", "given": "Sunghoon", "initials": "S"}, {"family": "Gantelius", "given": "Jesper", "initials": "J"}, {"family": "Svahn", "given": "Helene Andersson", "initials": "HA"}], "type": "journal article", "published": "2017-01-31", "journal": {"volume": "17", "issn": "1473-0189", "issue": "3", "pages": "549-556", "title": "Lab Chip", "issn-l": null}, "abstract": "Highly multiplexed point of care tests could improve diagnostic accuracy and differential diagnostic capacity in for instance emergency medicine and low resource environments. Available technology platforms for POC biomarker detection are typically simplex or low-plexed, whereas common lab-based microarray systems allow for the simultaneous detection of thousands of DNA or protein biomarkers. In this study, we demonstrate a novel suspension particle array platform that utilizes 900 \u03bcm bricks for POC amenable colorimetric biomarker detection with an encoding capacity of over two million. Due to the mm-scale size, both the lithographic codes and colorimetric signals of individual particles can be visualized using a consumer grade office flatbed scanner, with a potential for simultaneous imaging of around 19\u2009000 particles per scan. The analytical sensitivity of the assay was determined to be 4 ng ml(-1) using an antibody model system. As a proof of concept, autoantibodies toward anoctamin 2 were detected in order to discriminate between multiple sclerosis plasma samples and healthy controls with p < 0.0001 and an inter-assay % CV of 9.44%.", "doi": "10.1039/c6lc01358a", "pmid": "28102419", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:41:16.257Z", "modified": "2021-07-07T15:50:03.198Z"}, {"entity": "publication", "iuid": "a606501cd092464a84df30e0303ff7ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a606501cd092464a84df30e0303ff7ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a606501cd092464a84df30e0303ff7ad"}}, "title": "Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.", "authors": [{"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2017-01-31", "journal": {"volume": "114", "issn": "1091-6490", "issue": "5", "pages": "1087-1092", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.", "doi": "10.1073/pnas.1612561114", "pmid": "28096395", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1612561114"}, {"db": "pmc", "key": "PMC5293047"}], "notes": [], "created": "2017-08-23T14:19:03.168Z", "modified": "2024-01-16T13:48:48.655Z"}, {"entity": "publication", "iuid": "68d241823fb44e4d999225e98aff042d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68d241823fb44e4d999225e98aff042d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68d241823fb44e4d999225e98aff042d"}}, "title": "Copper chaperone Atox1 plays role in breast cancer cell migration.", "authors": [{"family": "Blockhuys", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2017-01-29", "journal": {"title": "Biochem. Biophys. Res. Commun.", "issn": "1090-2104", "volume": "483", "issue": "1", "pages": "301-304", "issn-l": "0006-291X"}, "abstract": "Copper (Cu) is an essential transition metal ion required as cofactor in many key enzymes. After cell uptake of Cu, the metal is transported by the cytoplasmic Cu chaperone Atox1 to P 1B-type ATPases in the Golgi network for incorporation into Cu-dependent enzymes in the secretory path. Cu is vital for many steps of cancer progression and Atox1 was recently suggested to have additional functionality as a nuclear transcription factor. We here investigated the expression level, cellular localization and role in cell migration of Atox1 in an aggressive breast cancer cell line upon combining immunostaining, microscopy and a wound healing assay. We made the unexpected discovery that Atox1 accumulates at lamellipodia borders of migrating cancer cells and Atox1 silencing resulted in migration defects as evidenced from reduced wound closure. Therefore, we have discovered an unknown role of the Cu chaperone Atox1 in breast cancer cell migration.", "doi": "10.1016/j.bbrc.2016.12.148", "pmid": "28027931", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-291X(16)32208-2"}], "notes": [], "created": "2020-01-23T16:34:17.371Z", "modified": "2021-06-21T15:48:50.807Z"}, {"entity": "publication", "iuid": "ecbb9eedad564312b53c2998afae42cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecbb9eedad564312b53c2998afae42cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecbb9eedad564312b53c2998afae42cf"}}, "title": "Polyoxygenated Cyclohexenes and Other Constituents of Cleistochlamys kirkii Leaves", "authors": [{"family": "Nyandoro", "given": "Stephen S", "initials": "SS"}, {"family": "Munissi", "given": "Joan J E", "initials": "JJE"}, {"family": "Gruhonjic", "given": "Amra", "initials": "A"}, {"family": "Duffy", "given": "Sandra", "initials": "S"}, {"family": "Pan", "given": "Fangfang", "initials": "F"}, {"family": "Puttreddy", "given": "Rakesh", "initials": "R"}, {"family": "Holleran", "given": "John P", "initials": "JP"}, {"family": "Fitzpatrick", "given": "Paul A", "initials": "PA"}, {"family": "Pelletier", "given": "Jerry", "initials": "J"}, {"family": "Avery", "given": "Vicky M", "initials": "VM"}, {"family": "Rissanen", "given": "Kari", "initials": "K"}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M"}], "type": "journal-article", "published": "2017-01-27", "journal": {"volume": "80", "issn": "1520-6025", "issue": "1", "pages": "114-125", "title": "J. Nat. Prod.", "issn-l": "0163-3864"}, "abstract": null, "doi": "10.1021/acs.jnatprod.6b00759", "pmid": "28001067", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:46:07.686Z", "modified": "2025-10-17T13:04:00.082Z"}, {"entity": "publication", "iuid": "0b27d073b90240b18860ecc4d243d200", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b27d073b90240b18860ecc4d243d200.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b27d073b90240b18860ecc4d243d200"}}, "title": "Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.", "authors": [{"family": "Cimdins", "given": "Annika", "initials": "A"}, {"family": "L\u00fcthje", "given": "Petra", "initials": "P"}, {"family": "Li", "given": "Fengyang", "initials": "F"}, {"family": "Ahmad", "given": "Irfan", "initials": "I"}, {"family": "Brauner", "given": "Annelie", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}], "type": "journal article", "published": "2017-01-26", "journal": {"volume": "5", "issn": "2169-8287", "issue": "4", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Strains of Escherichia coli exhibit diverse biofilm formation capabilities. E.\u00a0coli K-12 expresses the red, dry, and rough (rdar) morphotype below 30\u00b0C, whereas clinical isolates frequently display the rdar morphotype semiconstitutively. We sequenced the genomes of eight E.\u00a0coli strains to subsequently investigate the molecular basis of semiconstitutive rdar morphotype expression.", "doi": "10.1128/genomeA.01249-16", "pmid": "28126929", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "5/4/e01249-16"}, {"db": "pmc", "key": "PMC5270688"}], "notes": [], "created": "2017-10-17T07:55:03.116Z", "modified": "2020-01-21T13:56:17.431Z"}, {"entity": "publication", "iuid": "3be6d8132ef84bd8a601931855600a3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3be6d8132ef84bd8a601931855600a3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3be6d8132ef84bd8a601931855600a3a"}}, "title": "Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level.", "authors": [{"family": "Dolatabadi", "given": "Soheila", "initials": "S"}, {"family": "Candia", "given": "Juli\u00e1n", "initials": "J"}, {"family": "Akrap", "given": "Nina", "initials": "N"}, {"family": "Vannas", "given": "Christoffer", "initials": "C"}, {"family": "Tesan Tomic", "given": "Tajana", "initials": "T"}, {"family": "Losert", "given": "Wolfgang", "initials": "W"}, {"family": "Landberg", "given": "G\u00f6ran", "initials": "G"}, {"family": "\u00c5man", "given": "Pierre", "initials": "P"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-01-25", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "8", "issue": null, "pages": "1", "issn-l": "1664-8021"}, "abstract": "Cell proliferation includes a series of events that is tightly regulated by several checkpoints and layers of control mechanisms. Most studies have been performed on large cell populations, but detailed understanding of cell dynamics and heterogeneity requires single-cell analysis. Here, we used quantitative real-time PCR, profiling the expression of 93 genes in single-cells from three different cell lines. Individual unsynchronized cells from three different cell lines were collected in different cell cycle phases (G0/G1 - S - G2/M) with variable cell sizes. We found that the total transcript level per cell and the expression of most individual genes correlated with progression through the cell cycle, but not with cell size. By applying the random forests algorithm, a supervised machine learning approach, we show how a multi-gene signature that classifies individual cells into their correct cell cycle phase and cell size can be generated. To identify the most predictive genes we used a variable selection strategy. Detailed analysis of cell cycle predictive genes allowed us to define subpopulations with distinct gene expression profiles and to calculate a cell cycle index that illustrates the transition of cells between cell cycle phases. In conclusion, we provide useful experimental approaches and bioinformatics to identify informative and predictive genes at the single-cell level, which opens up new means to describe and understand cell proliferation and subpopulation dynamics.", "doi": "10.3389/fgene.2017.00001", "pmid": "28179914", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5263129"}], "notes": [], "created": "2020-01-23T16:34:51.889Z", "modified": "2021-06-21T15:44:54.553Z"}, {"entity": "publication", "iuid": "81d0505b646149a0a161e493843996b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81d0505b646149a0a161e493843996b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81d0505b646149a0a161e493843996b7"}}, "title": "In vitro and in vivo anti-leukemic activity of the peptidase-potentiated alkylator melflufen in acute myeloid leukemia.", "authors": [{"family": "Strese", "given": "Sara", "initials": "S"}, {"family": "Hassan", "given": "Saadia Bashir", "initials": "SB"}, {"family": "Velander", "given": "Ebba", "initials": "E"}, {"family": "Haglund", "given": "Caroline", "initials": "C"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}], "type": "comparative study", "published": "2017-01-24", "journal": {"title": "Oncotarget", "issn": "1949-2553", "volume": "8", "issue": "4", "pages": "6341-6352", "issn-l": "1949-2553"}, "abstract": "The novel aminopeptidase potentiated alkylating agent melflufen, was evaluated for activity in acute myeloid leukemia in a range of in vitro models, as well as in a patient derived xenograft study. All tested AML cell lines were highly sensitive to melflufen while melphalan was considerably less potent. In the HL-60 cell line model, synergy was observed for the combination of melflufen and cytarabine, an interaction that appeared sequence dependent with increased synergy when melflufen was added before cytarabine. Also, in primary cultures of AML cells from patients melflufen was highly active, while normal PBMC cultures appeared less sensitive, indicating a 7-fold in vitro therapeutic index. Melphalan, on the other hand, was only 2-fold more potent in the AML patient samples compared with PBMCs. Melflufen was equally active against non-malignant, immature CD34+ progenitor cells and a more differentiated CD34+ derived cell population (GM14), whereas the stem cell like cells were less sensitive to melphalan. Finally, melflufen treatment showed significant anti-leukemia activity and increased survival in a patient derived xenograft of AML in mice. In conclusion, melflufen demonstrates high and significant preclinical activity in AML and further clinical evaluation seem warranted in this disease.", "doi": "10.18632/oncotarget.13856", "pmid": "27974676", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "13856"}, {"db": "pmc", "key": "PMC5351636"}], "notes": [], "created": "2020-12-10T12:20:30.199Z", "modified": "2025-10-17T13:05:09.073Z"}, {"entity": "publication", "iuid": "5cd81ab25d5347f49efbc2f7906190f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cd81ab25d5347f49efbc2f7906190f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cd81ab25d5347f49efbc2f7906190f7"}}, "title": "Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages", "authors": [{"family": "Vizlin-Hodzic", "given": "D", "initials": "D"}, {"family": "Zhai", "given": "Q", "initials": "Q"}, {"family": "Illes", "given": "S", "initials": "S"}, {"family": "S\u00f6dersten", "given": "K", "initials": "K"}, {"family": "Truv\u00e9", "given": "K", "initials": "K"}, {"family": "Parris", "given": "T Z", "initials": "TZ"}, {"family": "Sobhan", "given": "P K", "initials": "PK"}, {"family": "Salmela", "given": "S", "initials": "S"}, {"family": "Kosalai", "given": "S T", "initials": "ST"}, {"family": "Kanduri", "given": "C", "initials": "C"}, {"family": "Strandberg", "given": "J", "initials": "J"}, {"family": "Seth", "given": "H", "initials": "H"}, {"family": "Bontell", "given": "T O", "initials": "TO"}, {"family": "Hanse", "given": "E", "initials": "E"}, {"family": "\u00c5gren", "given": "H", "initials": "H"}, {"family": "Funa", "given": "K", "initials": "K"}], "type": "journal-article", "published": "2017-01-24", "journal": {"volume": "7", "issn": "2158-3188", "issue": "1", "pages": "e1010", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": null, "doi": "10.1038/tp.2016.284", "pmid": "28117838", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T12:55:00.969Z", "modified": "2020-01-21T13:53:21.828Z"}, {"entity": "publication", "iuid": "492ba50b5ed74cb395df955515ddd51e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/492ba50b5ed74cb395df955515ddd51e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/492ba50b5ed74cb395df955515ddd51e"}}, "title": "Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts", "authors": [{"family": "Terriac", "given": "Emmanuel", "initials": "E"}, {"family": "Coceano", "given": "Giovanna", "initials": "G", "orcid": "0000-0001-9391-1476", "researcher": {"href": "https://publications.scilifelab.se/researcher/80a080afe1ee495f9f75f8e6be3ddc10.json"}}, {"family": "Mavajian", "given": "Zahra", "initials": "Z"}, {"family": "Hageman", "given": "Tijmen", "initials": "T"}, {"family": "Christ", "given": "Andreas", "initials": "A"}, {"family": "Testa", "given": "Ilaria", "initials": "I"}, {"family": "Lautenschl\u00e4ger", "given": "Franziska", "initials": "F"}, {"family": "Gad", "given": "Annica", "initials": "A"}], "type": "journal-article", "published": "2017-01-22", "journal": {"volume": "6", "issn": "2073-4409", "issue": "1", "pages": "2", "title": "Cells", "issn-l": "2073-4409"}, "abstract": "Metastasizing tumor cells show increased expression of the intermediate filament (IF) protein vimentin, which has been used to diagnose invasive tumors for decades. Recent observations indicate that vimentin is not only a passive marker for carcinoma, but may also induce tumor cell invasion. To clarify how vimentin IFs control cell adhesions and migration, we analyzed the nanoscale (30-50 nm) spatial organization of vimentin IFs and cell-matrix adhesions in metastatic fibroblast cells, using three-color stimulated emission depletion (STED) microscopy. We also studied whether wild-type and phospho-deficient or -mimicking mutants of vimentin changed the size and lifetime of focal adhesions (FAs), cell shape, and cell migration, using live-cell total internal reflection imaging and confocal microscopy. We observed that vimentin exists in fragments of different lengths. Short fragments were mostly the size of a unit-length filament and were mainly localized close to small cell-matrix adhesions. Long vimentin filaments were found in the proximity of large FAs. Vimentin expression in these cells caused a reduction in FAs size and an elongated cell shape, but did not affect FA lifetime, or the speed or directionality of cell migration. Expression of a phospho-mimicking mutant (S71D) of vimentin increased the speed of cell migration. Taken together, our results suggest that in highly migratory, transformed mesenchymal cells, vimentin levels control the cell shape and FA size, but not cell migration, which instead is linked to the phosphorylation status of S71 vimentin. These observations are consistent with the possibility that not only levels, but also the assembly status of vimentin control cell migration.", "doi": "10.3390/cells6010002", "pmid": "28117759", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5371867"}, {"db": "pii", "key": "cells6010002"}], "notes": [], "created": "2017-10-05T09:26:47.153Z", "modified": "2023-06-19T11:06:42.387Z"}, {"entity": "publication", "iuid": "eab05309fc2d4f3f90c49cb25edf1953", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eab05309fc2d4f3f90c49cb25edf1953.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eab05309fc2d4f3f90c49cb25edf1953"}}, "title": "Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.", "authors": [{"family": "Jones", "given": "Gregory T", "initials": "GT"}, {"family": "Tromp", "given": "Gerard", "initials": "G"}, {"family": "Kuivaniemi", "given": "Helena", "initials": "H"}, {"family": "Gretarsdottir", "given": "Solveig", "initials": "S"}, {"family": "Baas", "given": "Annette F", "initials": "AF"}, {"family": "Giusti", "given": "Betti", "initials": "B"}, {"family": "Strauss", "given": "Ewa", "initials": "E"}, {"family": "Van't Hof", "given": "Femke N G", "initials": "FN"}, {"family": "Webb", "given": "Thomas R", "initials": "TR"}, {"family": "Erdman", "given": "Robert", "initials": "R"}, {"family": "Ritchie", "given": "Marylyn D", "initials": "MD"}, {"family": "Elmore", "given": "James R", "initials": "JR"}, {"family": "Verma", "given": "Anurag", "initials": "A"}, {"family": "Pendergrass", "given": "Sarah", "initials": "S"}, {"family": "Kullo", "given": "Iftikhar J", "initials": "IJ"}, {"family": "Ye", "given": "Zi", "initials": "Z"}, {"family": "Peissig", "given": "Peggy L", "initials": "PL"}, {"family": "Gottesman", "given": "Omri", "initials": "O"}, {"family": "Verma", "given": "Shefali S", "initials": "SS"}, {"family": "Malinowski", "given": "Jennifer", "initials": "J"}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Borthwick", "given": "Kenneth M", "initials": "KM"}, {"family": "Smelser", "given": "Diane T", "initials": "DT"}, {"family": "Crosslin", "given": "David R", "initials": "DR"}, {"family": "de Andrade", "given": "Mariza", "initials": "M"}, {"family": "Ryer", "given": "Evan J", "initials": "EJ"}, {"family": "McCarty", "given": "Catherine A", "initials": "CA"}, {"family": "B\u00f6ttinger", "given": "Erwin P", "initials": "EP"}, {"family": "Pacheco", "given": "Jennifer A", "initials": "JA"}, {"family": "Crawford", "given": "Dana C", "initials": "DC"}, {"family": "Carrell", "given": "David S", "initials": "DS"}, {"family": "Gerhard", "given": "Glenn S", "initials": "GS"}, {"family": "Franklin", "given": "David P", "initials": "DP"}, {"family": "Carey", "given": "David J", "initials": "DJ"}, {"family": "Phillips", "given": "Victoria L", "initials": "VL"}, {"family": "Williams", "given": "Michael J A", "initials": "MJ"}, {"family": "Wei", "given": "Wenhua", "initials": "W"}, {"family": "Blair", "given": "Ross", "initials": "R"}, {"family": "Hill", "given": "Andrew A", "initials": "AA"}, {"family": "Vasudevan", "given": "Thodor M", "initials": "TM"}, {"family": "Lewis", "given": "David R", "initials": "DR"}, {"family": "Thomson", "given": "Ian A", "initials": "IA"}, {"family": "Krysa", "given": "Jo", "initials": "J"}, {"family": "Hill", "given": "Geraldine B", "initials": "GB"}, {"family": "Roake", "given": "Justin", "initials": "J"}, {"family": "Merriman", "given": "Tony R", "initials": "TR"}, {"family": "Oszkinis", "given": "Grzegorz", "initials": "G"}, {"family": "Galora", "given": "Silvia", "initials": "S"}, {"family": "Saracini", "given": "Claudia", "initials": "C"}, {"family": "Abbate", "given": "Rosanna", "initials": "R"}, {"family": "Pulli", "given": "Raffaele", "initials": "R"}, {"family": "Pratesi", "given": "Carlo", "initials": "C"}, {"family": "Saratzis", "given": "Athanasios", "initials": "A"}, {"family": "Verissimo", "given": "Ana R", "initials": "AR"}, {"family": "Bumpstead", "given": "Suzannah", "initials": "S"}, {"family": "Badger", "given": "Stephen A", "initials": "SA"}, {"family": "Clough", "given": "Rachel E", "initials": "RE"}, {"family": "Cockerill", "given": "Gillian", "initials": "G"}, {"family": "Hafez", "given": "Hany", "initials": "H"}, {"family": "Scott", "given": "D Julian A", "initials": "DJ"}, {"family": "Futers", "given": "T Simon", "initials": "TS"}, {"family": "Romaine", "given": "Simon P R", "initials": "SP"}, {"family": "Bridge", "given": "Katherine", "initials": "K"}, {"family": "Griffin", "given": "Kathryn J", "initials": "KJ"}, {"family": "Bailey", "given": "Marc A", "initials": "MA"}, {"family": "Smith", "given": "Alberto", "initials": "A"}, {"family": "Thompson", "given": "Matthew M", "initials": "MM"}, {"family": "van Bockxmeer", "given": "Frank M", "initials": "FM"}, {"family": "Matthiasson", "given": "Stefan E", "initials": "SE"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Blankensteijn", "given": "Jan D", "initials": "JD"}, {"family": "Teijink", "given": "Joep A W", "initials": "JA"}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "de Graaf", "given": "Jacqueline", "initials": "J"}, {"family": "Kiemeney", "given": "Lambertus A", "initials": "LA"}, {"family": "Lindholt", "given": "Jes S", "initials": "JS"}, {"family": "Hughes", "given": "Anne", "initials": "A"}, {"family": "Bradley", "given": "Declan T", "initials": "DT"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "Golledge", "given": "Jonathan", "initials": "J"}, {"family": "Norman", "given": "Paul E", "initials": "PE"}, {"family": "Powell", "given": "Janet T", "initials": "JT"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Hamby", "given": "Stephen E", "initials": "SE"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Sakalihasan", "given": "Natzi", "initials": "N"}, {"family": "Courtois", "given": "Audrey", "initials": "A"}, {"family": "Ferrell", "given": "Robert E", "initials": "RE"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eicher", "given": "John D", "initials": "JD"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JL"}, {"family": "Lipovich", "given": "Leonard", "initials": "L"}, {"family": "Drolet", "given": "Anne M", "initials": "AM"}, {"family": "Verhoeven", "given": "Eric L", "initials": "EL"}, {"family": "Zeebregts", "given": "Clark J", "initials": "CJ"}, {"family": "Geelkerken", "given": "Robert H", "initials": "RH"}, {"family": "van Sambeek", "given": "Marc R", "initials": "MR"}, {"family": "van Sterkenburg", "given": "Steven M", "initials": "SM"}, {"family": "de Vries", "given": "Jean-Paul", "initials": "JP"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PI"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Sayers", "given": "Robert D", "initials": "RD"}, {"family": "Harrison", "given": "Seamus C", "initials": "SC"}, {"family": "van Rij", "given": "Andre M", "initials": "AM"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Bown", "given": "Matthew J", "initials": "MJ"}], "type": "journal article", "published": "2017-01-20", "journal": {"volume": "120", "issn": "1524-4571", "issue": "2", "pages": "341-353", "title": "Circ. Res.", "issn-l": "0009-7330"}, "abstract": "Abdominal aortic aneurysm (AAA) is a complex disease with both genetic and environmental risk factors. Together, 6 previously identified risk loci only explain a small proportion of the heritability of AAA.\n\nTo identify additional AAA risk loci using data from all available genome-wide association studies.\n\nThrough a meta-analysis of 6 genome-wide association study data sets and a validation study totaling 10\u2009204 cases and 107\u2009766 controls, we identified 4 new AAA risk loci: 1q32.3 (SMYD2), 13q12.11 (LINC00540), 20q13.12 (near PCIF1/MMP9/ZNF335), and 21q22.2 (ERG). In various database searches, we observed no new associations between the lead AAA single nucleotide polymorphisms and coronary artery disease, blood pressure, lipids, or diabetes mellitus. Network analyses identified ERG, IL6R, and LDLR as modifiers of MMP9, with a direct interaction between ERG and MMP9.\n\nThe 4 new risk loci for AAA seem to be specific for AAA compared with other cardiovascular diseases and related traits suggesting that traditional cardiovascular risk factor management may only have limited value in preventing the progression of aneurysmal disease.", "doi": "10.1161/CIRCRESAHA.116.308765", "pmid": "27899403", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "CIRCRESAHA.116.308765"}, {"db": "pmc", "key": "PMC5253231"}, {"db": "mid", "key": "EMS70602"}], "notes": [], "created": "2017-05-03T13:01:54.332Z", "modified": "2024-01-16T13:48:48.666Z"}, {"entity": "publication", "iuid": "f38b315a15584e4396559e01b8376b10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f38b315a15584e4396559e01b8376b10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f38b315a15584e4396559e01b8376b10"}}, "title": "Novel genetic loci associated with hippocampal volume.", "authors": [{"family": "Hibar", "given": "Derrek P", "initials": "DP"}, {"family": "Adams", "given": "Hieab H H", "initials": "HH"}, {"family": "Jahanshad", "given": "Neda", "initials": "N"}, {"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Stein", "given": "Jason L", "initials": "JL"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Renteria", "given": "Miguel E", "initials": "ME"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Arias-Vasquez", "given": "Alejandro", "initials": "A"}, {"family": "Ikram", "given": "M Kamran", "initials": "MK"}, {"family": "Desrivi\u00e8res", "given": "Sylvane", "initials": "S"}, {"family": "Vernooij", "given": "Meike W", "initials": "MW"}, {"family": "Abramovic", "given": "Lucija", "initials": "L"}, {"family": "Alhusaini", "given": "Saud", "initials": "S"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Andersson", "given": "Micael", "initials": "M"}, {"family": "Arfanakis", "given": "Konstantinos", "initials": "K"}, {"family": "Aribisala", "given": "Benjamin S", "initials": "BS"}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ"}, {"family": "Athanasiu", "given": "Lavinia", "initials": "L"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Beecham", "given": "Ashley H", "initials": "AH"}, {"family": "Beiser", "given": "Alexa", "initials": "A"}, {"family": "Bernard", "given": "Manon", "initials": "M"}, {"family": "Blanton", "given": "Susan H", "initials": "SH"}, {"family": "Bohlken", "given": "Marc M", "initials": "MM"}, {"family": "Boks", "given": "Marco P", "initials": "MP"}, {"family": "Bralten", "given": "Janita", "initials": "J"}, {"family": "Brickman", "given": "Adam M", "initials": "AM"}, {"family": "Carmichael", "given": "Owen", "initials": "O"}, {"family": "Chakravarty", "given": "M Mallar", "initials": "MM"}, {"family": "Chen", "given": "Qiang", "initials": "Q"}, {"family": "Ching", "given": "Christopher R K", "initials": "CR"}, {"family": "Chouraki", "given": "Vincent", "initials": "V"}, {"family": "Cuellar-Partida", "given": "Gabriel", "initials": "G"}, {"family": "Crivello", "given": "Fabrice", "initials": "F"}, {"family": "Den Braber", "given": "Anouk", "initials": "A"}, {"family": "Doan", "given": "Nhat Trung", "initials": "NT"}, {"family": "Ehrlich", "given": "Stefan", "initials": "S"}, {"family": "Giddaluru", "given": "Sudheer", "initials": "S"}, {"family": "Goldman", "given": "Aaron L", "initials": "AL"}, {"family": "Gottesman", "given": "Rebecca F", "initials": "RF"}, {"family": "Grimm", "given": "Oliver", "initials": "O"}, {"family": "Griswold", "given": "Michael E", "initials": "ME"}, {"family": "Guadalupe", "given": "Tulio", "initials": "T"}, {"family": "Gutman", "given": "Boris A", "initials": "BA"}, {"family": "Hass", "given": "Johanna", "initials": "J"}, {"family": "Haukvik", "given": "Unn K", "initials": "UK"}, {"family": "Hoehn", "given": "David", "initials": "D"}, {"family": "Holmes", "given": "Avram J", "initials": "AJ"}, {"family": "Hoogman", "given": "Martine", "initials": "M"}, {"family": "Janowitz", "given": "Deborah", "initials": "D"}, {"family": "Jia", "given": "Tianye", "initials": "T"}, {"family": "J\u00f8rgensen", "given": "Kjetil N", "initials": "KN"}, {"family": "Karbalai", "given": "Nazanin", "initials": "N"}, {"family": "Kasperaviciute", "given": "Dalia", "initials": "D"}, {"family": "Kim", "given": "Sungeun", "initials": "S"}, {"family": "Klein", "given": "Marieke", "initials": "M"}, {"family": "Kraemer", "given": "Bernd", "initials": "B"}, {"family": "Lee", "given": "Phil H", "initials": "PH"}, {"family": "Liewald", "given": "David C M", "initials": "DC"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "Luciano", "given": "Michelle", "initials": "M"}, {"family": "Macare", "given": "Christine", "initials": "C"}, {"family": "Marquand", "given": "Andre F", "initials": "AF"}, {"family": "Matarin", "given": "Mar", "initials": "M"}, {"family": "Mather", "given": "Karen A", "initials": "KA"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M"}, {"family": "McKay", "given": "David R", "initials": "DR"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mu\u00f1oz Maniega", "given": "Susana", "initials": "S"}, {"family": "Nho", "given": "Kwangsik", "initials": "K"}, {"family": "Nugent", "given": "Allison C", "initials": "AC"}, {"family": "Nyquist", "given": "Paul", "initials": "P"}, {"family": "Loohuis", "given": "Loes M Olde", "initials": "LM"}, {"family": "Oosterlaan", "given": "Jaap", "initials": "J"}, {"family": "Papmeyer", "given": "Martina", "initials": "M"}, {"family": "Pirpamer", "given": "Lukas", 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{"family": "Sachdev", "given": "Perminder S", "initials": "PS"}, {"family": "Saykin", "given": "Andrew J", "initials": "AJ"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schofield", "given": "Peter R", "initials": "PR"}, {"family": "Sigursson", "given": "Sigurdur", "initials": "S"}, {"family": "Simmons", "given": "Andrew", "initials": "A"}, {"family": "Singleton", "given": "Andrew", "initials": "A"}, {"family": "Sisodiya", "given": "Sanjay M", "initials": "SM"}, {"family": "Smith", "given": "Colin", "initials": "C"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "Soininen", "given": "Hilkka", "initials": "H"}, {"family": "Steen", "given": "Vidar M", "initials": "VM"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Sussmann", "given": "Jessika E", "initials": "JE"}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A"}, {"family": "Toga", "given": "Arthur W", "initials": "AW"}, {"family": "Traynor", "given": "Bryan J", "initials": "BJ"}, {"family": "Troncoso", "given": "Juan", "initials": "J"}, {"family": "Tsolaki", "given": "Magda", "initials": "M"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Hern\u00e1ndez", "given": "Maria C Vald\u00e9s", "initials": "MC"}, {"family": "Van der Brug", "given": "Marcel", "initials": "M"}, {"family": "van der Lugt", "given": "Aad", "initials": "A"}, {"family": "van der Wee", "given": "Nic J A", "initials": "NJ"}, {"family": "Van Haren", "given": "Neeltje E M", "initials": "NE"}, {"family": "van 't Ent", "given": "Dennis", "initials": "D"}, {"family": "Van Tol", "given": "Marie-Jose", "initials": "MJ"}, {"family": "Vardarajan", "given": "Badri N", "initials": "BN"}, {"family": "Vellas", "given": "Bruno", "initials": "B"}, {"family": "Veltman", "given": "Dick J", "initials": "DJ"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Walter", "given": "Henrik", "initials": "H"}, {"family": "Wardlaw", "given": "Joanna M", "initials": "JM"}, {"family": "Wassink", "given": "Thomas H", "initials": "TH"}, {"family": "Weale", "given": "Michael E", "initials": "ME"}, {"family": "Weinberger", "given": "Daniel R", "initials": "DR"}, {"family": "Weiner", "given": "Michael W", "initials": "MW"}, {"family": "Wen", "given": "Wei", "initials": "W"}, {"family": "Westman", "given": "Eric", "initials": "E"}, {"family": "White", "given": "Tonya", "initials": "T"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}, {"family": "Wright", "given": "Clinton B", "initials": "CB"}, {"family": "Zielke", "given": "Ronald H", "initials": "RH"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Longstreth", "given": "W T", "initials": "WT"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Franke", "given": "Barbara", "initials": "B"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Thompson", "given": "Paul M", "initials": "PM"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}], "type": "journal article", "published": "2017-01-18", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "13624", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200\u2009kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg=-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness.", "doi": "10.1038/ncomms13624", "pmid": "28098162", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms13624"}, {"db": "pmc", "key": "PMC5253632"}], "notes": [], "created": "2017-10-25T15:54:13.732Z", "modified": "2024-01-16T13:48:48.676Z"}, {"entity": "publication", "iuid": "07d6940ab1f84b6dbc83497d9ad3d3fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07d6940ab1f84b6dbc83497d9ad3d3fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07d6940ab1f84b6dbc83497d9ad3d3fd"}}, "title": "Perivascular PDGFR-\u03b2 is an independent marker for prognosis in renal cell carcinoma.", "authors": [{"family": "Fr\u00f6din", "given": "Magnus", "initials": "M"}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A"}, {"family": "Corvigno", "given": "Sara", "initials": "S"}, {"family": "Harmenberg", "given": "Ulrika", "initials": "U"}, {"family": "Sandstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Johansson", "given": "Martin", "initials": "M"}, {"family": "\u00d6stman", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2017-01-17", "journal": {"volume": "116", "issn": "1532-1827", "issue": "2", "pages": "195-201", "title": "Br. J. Cancer", "issn-l": "0007-0920"}, "abstract": "Renal cell carcinoma (RCC) is a highly vascularised tumour, where anti-angiogenic treatment with multi-tyrosine-kinase-inhibitor, is used for first-line treatment of metastatic disease. Variations in vascular characteristics are likely to contribute to variations in intrinsic aggressiveness of the disease. Emerging studies are identifying perivascular status, including perivascular PDGFR-\u03b2, as a determinant of prognosis in other tumour types.\n\nThis work explored the impact on prognosis of vascular characteristics in RCC through analyses of a population-based collection of tumours from surgery-alone-treated patients. The quantitative data from a panel of vascular metrics were obtained through computerised image analysis of sections double-stained for expression of the endothelial cell marker CD34 together with perivascular markers \u03b1-SMA or PDGFR-\u03b2.\n\nPerivascular expression of PDGFR-\u03b2 and \u03b1-SMA were positively correlated to each other, and negatively correlated to vessel density. High expression of PDGFR-\u03b2 and \u03b1-SMA as well as low vessel density was significantly associated with short survival in uni- and multivariate analyses. Subgroup analyses demonstrated that the prognostic impact of the perivascular markers was particularly prominent in the T4-subgroup. A novel metric, related to PDGFR-\u03b2 perivascular heterogeneity, was also associated with prognosis in uni-and multi-variate analyses. This novel metric also acted as a prognosis marker in ovarian cancer.\n\nThe study demonstrates previously unrecognised associations between RCC survival and the absolute levels, and variability, of perivascular PDGFR-\u03b2. This marker should be further explored in other RCC cohorts. Findings also suggest mechanistic analyses and studies on the relationship between perivascular status and efficacy of multi-tyrosine-kinase-inhibitors.", "doi": "10.1038/bjc.2016.407", "pmid": "27931046", "labels": {"Tissue Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "bjc2016407"}, {"db": "pmc", "key": "PMC5243993"}], "notes": [], "created": "2017-05-03T12:59:18.817Z", "modified": "2017-06-12T11:37:33.220Z"}, {"entity": "publication", "iuid": "b188912bce584c0f99fd1517873a63cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b188912bce584c0f99fd1517873a63cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b188912bce584c0f99fd1517873a63cd"}}, "title": "A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score.", "authors": [{"family": "Ciuculete", "given": "D M", "initials": "DM"}, {"family": "Bostr\u00f6m", "given": "A E", "initials": "AE"}, {"family": "Voisin", "given": "S", "initials": "S"}, {"family": "Philipps", "given": "H", "initials": "H"}, {"family": "Titova", "given": "O E", "initials": "OE"}, {"family": "Bandstein", "given": "M", "initials": "M"}, {"family": "Nikontovic", "given": "L", "initials": "L"}, {"family": "Williams", "given": "M J", "initials": "MJ"}, {"family": "Mwinyi", "given": "J", "initials": "J"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}], "type": "journal article", "published": "2017-01-17", "journal": {"volume": "7", "issn": "2158-3188", "issue": "1", "pages": "e1002", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "Genome-wide association studies have identified a number of single-nucleotide polymorphisms (SNPs) that are associated with psychiatric diseases. Increasing body of evidence suggests a complex connection of SNPs and the transcriptional and epigenetic regulation of gene expression, which is poorly understood. In the current study, we investigated the interplay between genetic risk variants, shifts in methylation and mRNA levels in whole blood from 223 adolescents distinguished by a risk for developing psychiatric disorders. We analyzed 37 SNPs previously associated with psychiatric diseases in relation to genome-wide DNA methylation levels using linear models, with Bonferroni correction and adjusting for cell-type composition. Associations between DNA methylation, mRNA levels and psychiatric disease risk evaluated by the Development and Well-Being Assessment (DAWBA) score were identified by robust linear models, Pearson's correlations and binary regression models. We detected five SNPs (in HCRTR1, GAD1, HADC3 and FKBP5) that were associated with eight CpG sites, validating five of these SNP-CpG pairs. Three of these CpG sites, that is, cg01089319 (GAD1), cg01089249 (GAD1) and cg24137543 (DIAPH1), manifest in significant gene expression changes and overlap with active regulatory regions in chromatin states of brain tissues. Importantly, methylation levels at cg01089319 were associated with the DAWBA score in the discovery group. These results show how distinct SNPs linked with psychiatric diseases are associated with epigenetic shifts with relevance for gene expression. Our findings give a novel insight on how genetic variants may modulate risks for the development of psychiatric diseases.", "doi": "10.1038/tp.2016.275", "pmid": "28094813", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "tp2016275"}, {"db": "pmc", "key": "PMC5545735"}], "notes": [], "created": "2017-10-25T15:18:15.377Z", "modified": "2024-01-16T13:48:48.687Z"}, {"entity": "publication", "iuid": "e7ef68a1bed844139e2810dea9b1fd70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7ef68a1bed844139e2810dea9b1fd70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7ef68a1bed844139e2810dea9b1fd70"}}, "title": "NLK-mediated phosphorylation of HDAC1 negatively regulates Wnt signaling.", "authors": [{"family": "Masoumi", "given": "Katarzyna Chmielarska", "initials": "KC"}, {"family": "Daams", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Sime", "given": "Wondossen", "initials": "W"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Ke", "given": "Hengning", "initials": "H"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Massoumi", "given": "Ramin", "initials": "R"}], "type": "journal article", "published": "2017-01-15", "journal": {"volume": "28", "issn": "1939-4586", "issue": "2", "pages": "346-355", "title": "Mol. Biol. Cell", "issn-l": "1059-1524"}, "abstract": "The Wnt signaling pathway is essential in regulating various cellular processes. Different mechanisms of inhibition for Wnt signaling have been proposed. Besides \u03b2-catenin degradation through the proteasome, nemo-like kinase (NLK) is another molecule that is known to negatively regulate Wnt signaling. However, the mechanism by which NLK mediates the inhibition of Wnt signaling was not known. In the present study, we used primary embryonic fibroblast cells isolated from NLK-deficient mice and showed that these cells proliferate faster and have a shorter cell cycle than wild-type cells. In NLK-knockout cells, we observed sustained interaction between Lef1 and \u03b2-catenin, leading to elevated luciferase reporter of \u03b2-catenin/Lef1-mediated transcriptional activation. The mechanism for the reduced \u03b2-catenin/Lef1 promoter activation was explained by phosphorylation of HDAC1 at serine 421 via NLK. The phosphorylation of HDAC1 was achieved only in the presence of wild-type NLK because a catalytically inactive mutant of NLK was unable to phosphorylate HDAC1 and reduced the luciferase reporter of \u03b2-catenin/Lef1-mediated transcriptional activation. This result suggests that NLK and HDAC1 together negatively regulate Wnt signaling, which is vital in preventing aberrant proliferation of nontransformed primary fibroblast cells.", "doi": "10.1091/mbc.E16-07-0547", "pmid": "27903773", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "mbc.E16-07-0547"}, {"db": "pmc", "key": "PMC5231902"}], "notes": [], "created": "2019-01-15T07:52:59.999Z", "modified": "2020-01-21T13:53:22.314Z"}, {"entity": "publication", "iuid": "7f747305169e493a98de0d03fb8b658a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f747305169e493a98de0d03fb8b658a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f747305169e493a98de0d03fb8b658a"}}, "title": "Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes", "authors": [{"family": "Le\u00a0Rhun", "given": "Ana\u00efs", "initials": "A"}, {"family": "L\u00e9crivain", "given": "Anne Laure", "initials": "AL"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Broglia", "given": "Laura", "initials": "L"}, {"family": "Della\u00a0Beffa", "given": "Cristina", "initials": "C"}, {"family": "Charpentier", "given": "Emmanuelle", "initials": "E"}], "type": "journal-article", "published": "2017-01-12", "journal": {"volume": null, "issn": "0305-1048", "issue": null, "pages": "gkw1316", "title": "Nucleic Acids Res", "issn-l": null}, "abstract": "A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5\u0384 and 3\u0384 ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3\u0384 overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.", "doi": "10.1093/nar/gkw1316", "pmid": "28082390", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-04T15:14:47.764Z", "modified": "2020-01-21T13:53:22.542Z"}, {"entity": "publication", "iuid": "ef8699b32cf64705852f712a062b95ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef8699b32cf64705852f712a062b95ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef8699b32cf64705852f712a062b95ad"}}, "title": "Asgard archaea illuminate the origin of eukaryotic cellular complexity", "authors": [{"family": "Zaremba-Niedzwiedzka", "given": "Katarzyna", "initials": "K"}, {"family": "Caceres", "given": "Eva F", "initials": "EF"}, {"family": "Saw", "given": "Jimmy H", "initials": "JH"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Disa", "initials": "D"}, {"family": "Juzokaite", "given": "Lina", "initials": "L"}, {"family": "Vancaester", "given": "Emmelien", "initials": "E"}, {"family": "Seitz", "given": "Kiley W", "initials": "KW"}, {"family": "Anantharaman", "given": "Karthik", "initials": "K"}, {"family": "Starnawski", "given": "Piotr", "initials": "P"}, {"family": "Kjeldsen", "given": "Kasper U", "initials": "KU"}, {"family": "Stott", "given": "Matthew B", "initials": "MB"}, {"family": "Nunoura", "given": "Takuro", "initials": "T"}, {"family": "Banfield", "given": "Jillian F", "initials": "JF"}, {"family": "Schramm", "given": "Andreas", "initials": "A"}, {"family": "Baker", "given": "Brett J", "initials": "BJ"}, {"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal-article", "published": "2017-01-11", "journal": {"volume": "541", "issn": "1476-4687", "issue": "7637", "pages": "353-358", "title": "Nature", "issn-l": "0028-0836"}, "abstract": null, "doi": "10.1038/nature21031", "pmid": "28077874", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Asgard archaea from sediments", "key": "PRJNA319486"}, {"db": "GENBANK", "description": "Candidatus Odinarchaeota archaeon LCB_4, whole genome shotgun sequencing project", "key": "MDVT00000000"}, {"db": "GENBANK", "description": "Candidatus Thorarchaeota archaeon AB_25, whole genome shotgun sequencing project", "key": "MEHG00000000"}, {"db": "BioProject", "description": "Terrestrial subsurface C, N, S and H cycles cross-linked by metabolic handoffs", "key": "PRJNA288027"}, {"db": "GENBANK", "description": "Candidatus Lokiarchaeota archaeon CR_4, whole genome shotgun sequencing project", "key": "MBAA00000000"}, {"db": "BioProject", "description": "Estuary Sediments Metagenome", "key": "PRJNA270657"}, {"db": "GENBANK", "description": "Candidatus Thorarchaeota archaeon SMTZ1-83, whole genome shotgun sequencing project", "key": "LRSK00000000"}, {"db": "GENBANK", "description": "Candidatus Thorarchaeota archaeon SMTZ1-45, whole genome shotgun sequencing project", "key": "LRSL00000000"}, {"db": "GENBANK", "description": "Candidatus Heimdallarchaeota archaeon AB_125, whole genome shotgun sequencing project", "key": "MEHH00000000"}, {"db": "GENBANK", "description": "Candidatus Heimdallarchaeota archaeon LC_3, whole genome shotgun sequencing project", "key": "MDVS00000000"}, {"db": "GENBANK", "description": "Candidatus Heimdallarchaeota archaeon LC_2, whole genome shotgun sequencing project", "key": "MDVR00000000"}], "notes": [], "created": "2017-10-19T20:18:18.013Z", "modified": "2024-01-16T13:48:48.694Z"}, {"entity": "publication", "iuid": "0eaade49c88145f3916df8e923cc24b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0eaade49c88145f3916df8e923cc24b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0eaade49c88145f3916df8e923cc24b4"}}, "title": "Proteomic analysis of enterotoxigenic Escherichia coli (ETEC) in neutral and alkaline conditions.", "authors": [{"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Kenny", "given": "Diarmuid", "initials": "D"}, {"family": "Karlsson", "given": "Anders", "initials": "A"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-01-07", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "17", "issue": "1", "pages": "11", "issn-l": "1471-2180"}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and travelers to endemic areas. Secretion of the heat labile AB 5 toxin (LT) is induced by alkaline conditions. In this study, we determined the surface proteome of ETEC exposed to alkaline conditions (pH 9) as compared to neutral conditions (pH 7) using a LPI Hexalane FlowCell combined with quantitative proteomics. Relative quantitation with isobaric labeling (TMT) was used to compare peptide abundance and their corresponding proteins in multiple samples at MS/MS level. For protein identification and quantification samples were analyzed using either a 1D-LCMS or a 2D-LCMS approach.\n\nStrong up-regulation of the ATP synthase operon encoding F1Fo ATP synthase and down-regulation of proton pumping proteins NuoF, NuoG, Ndh and WrbA were detected among proteins involved in regulating the proton and electron transport under alkaline conditions. Reduced expression of proteins involved in osmotic stress was found at alkaline conditions while the Sec-dependent transport over the inner membrane and outer membrane protein proteins such as OmpA and the \u03b2-Barrel Assembly Machinery (BAM) complex were up-regulated.\n\nETEC exposed to alkaline environments express a specific proteome profile characterized by up-regulation of membrane proteins and secretion of LT toxin. Alkaline microenvironments have been reported close to the intestinal epithelium and the alkaline proteome may hence represent a better view of ETEC during infection.", "doi": "10.1186/s12866-016-0914-1", "pmid": "28061865", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-016-0914-1"}, {"db": "pmc", "key": "PMC5219706"}], "notes": [], "created": "2020-01-30T16:00:21.978Z", "modified": "2024-01-16T13:46:32.900Z"}, {"entity": "publication", "iuid": "3d0cc871ee8644d1b9ecf349a1eb0965", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d0cc871ee8644d1b9ecf349a1eb0965.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d0cc871ee8644d1b9ecf349a1eb0965"}}, "title": "Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer.", "authors": [{"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Magnusson", "given": "Patrik", "initials": "P"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"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": "2017-01-06", "journal": {"volume": "16", "issn": "1535-3907", "issue": "1", "pages": "204-216", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "There is a demand for novel targets and approaches to diagnose and treat prostate cancer (PCA). In this context, serum and plasma samples from a total of 609 individuals from two independent patient cohorts were screened for IgG reactivity against a sum of 3833 human protein fragments. Starting from planar protein arrays with 3786 protein fragments to screen 80 patients with and without PCA diagnosis, 161 fragments (4%) were chosen for further analysis based on their reactivity profiles. Adding 71 antigens from literature, the selection of antigens was corroborated for their reactivity in a set of 550 samples using suspension bead arrays. The antigens prostein (SLC45A3), TATA-box binding protein (TBP), and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) showed higher reactivity in PCA patients with late disease compared with early disease. Because of its prostate tissue specificity, we focused on prostein and continued with mapping epitopes of the 66-mer protein fragment using patient samples. Using bead-based assays and 15-mer peptides, a minimal peptide epitope was identified and refined by alanine scanning to the KPxAPFP. Further sequence alignment of this motif revealed homology to transmembrane protein 79 (TMEM79) and TGF-beta-induced factor 2 (TGIF2), thus providing a reasoning for cross-reactivity found in females. A comprehensive workflow to discover and validate IgG reactivity against prostein and homologous targets in human serum and plasma was applied. This study provides useful information when searching for novel biomarkers or drug targets that are guided by the reactivity of the immune system against autoantigens.", "doi": "10.1021/acs.jproteome.6b00620", "pmid": "27700103", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:14.584Z", "modified": "2021-07-08T13:44:33.168Z"}, {"entity": "publication", "iuid": "90e126a31ae94eb29dcf7d80571f9573", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90e126a31ae94eb29dcf7d80571f9573.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90e126a31ae94eb29dcf7d80571f9573"}}, "title": "Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.", "authors": [{"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L"}, {"family": "Poser", "given": "Ina", "initials": "I"}, {"family": "Hyman", "given": "Anthony", "initials": "A"}, {"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": "2017-01-06", "journal": {"volume": "16", "issn": "1535-3907", "issue": "1", "pages": "147-155", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here we present a strategy to systematically validate antibodies for immunofluorescence (IF) applications using gene tagging. We have assessed the on- and off-target binding capabilities of 197 antibodies using 108 cell lines expressing EGFP-tagged target proteins at endogenous levels. Furthermore, we assessed batch-to-batch effects for 35 target proteins, showing that both the on- and off-target binding patterns vary significantly between antibody batches and that the proposed strategy serves as a reliable procedure for ensuring reproducibility upon production of new antibody batches. In summary, we present a systematic scheme for antibody validation in IF applications using endogenous expression of tagged proteins. This is an important step toward a reproducible approach for context- and application-specific antibody validation and improved reliability of antibody-based experiments and research data.", "doi": "10.1021/acs.jproteome.6b00821", "pmid": "27723985", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:09.252Z", "modified": "2021-07-08T13:44:33.422Z"}, {"entity": "publication", "iuid": "389c89b5cd9f4e68b0b97447e9fdcb93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/389c89b5cd9f4e68b0b97447e9fdcb93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/389c89b5cd9f4e68b0b97447e9fdcb93"}}, "title": "Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.", "authors": [{"family": "Kee", "given": "Nigel", "initials": "N"}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Kirkeby", "given": "Agnete", "initials": "A"}, {"family": "Dahl", "given": "Lina", "initials": "L"}, {"family": "Storvall", "given": "Helena", "initials": "H"}, {"family": "Nolbrant", "given": "Sara", "initials": "S"}, {"family": "Lahti", "given": "Laura", "initials": "L"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Joodmardi", "given": "Eliza", "initials": "E"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2017-01-05", "journal": {"volume": "20", "issn": "1875-9777", "issue": "1", "pages": "29-40", "title": "Cell Stem Cell", "issn-l": null}, "abstract": "Stem cell engineering and grafting of mesencephalic dopamine (mesDA) neurons is a promising strategy for brain repair in Parkinson's disease (PD). Refinement of differentiation protocols to optimize this approach will require deeper understanding of mesDA neuron development. Here, we studied this process using transcriptome-wide single-cell RNA sequencing of mouse neural progenitors expressing the mesDA neuron determinant Lmx1a. This approach resolved the differentiation of mesDA and neighboring neuronal lineages and revealed a remarkably close relationship between developing mesDA and subthalamic nucleus (STN) neurons, while also highlighting a distinct transcription factor set that can distinguish between them. While previous hESC mesDA differentiation protocols have relied on markers that are shared between the two lineages, we found that application of these highlighted markers can help to refine current stem cell engineering protocols, increasing the proportion of appropriately patterned mesDA progenitors. Our results, therefore, have important implications for cell replacement therapy in PD.", "doi": "10.1016/j.stem.2016.10.003", "pmid": "28094018", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1934-5909(16)30343-5"}], "notes": [], "created": "2017-05-03T13:00:32.781Z", "modified": "2021-07-07T11:46:33.581Z"}, {"entity": "publication", "iuid": "194ee9c55a104a2dbed74300d09dff7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/194ee9c55a104a2dbed74300d09dff7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/194ee9c55a104a2dbed74300d09dff7b"}}, "title": "Proteomic analyses of limbic regions in neonatal male, female and androgen receptor knockout mice.", "authors": [{"family": "Zettergren", "given": "Anna", "initials": "A"}, {"family": "Karlsson", "given": "Sara", "initials": "S"}, {"family": "Studer", "given": "Erik", "initials": "E"}, {"family": "Sarvim\u00e4ki", "given": "Anna", "initials": "A"}, {"family": "Kettunen", "given": "Petronella", "initials": "P"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Westberg", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2017-01-05", "journal": {"volume": "18", "issn": "1471-2202", "issue": "1", "pages": "9", "title": "BMC Neurosci", "issn-l": "1471-2202"}, "abstract": "It is well-established that organizational effects of sex steroids during early development are fundamental for sex-typical displays of, for example, mating and aggressive behaviors in rodents and other species. Male and female brains are known to differ with respect to neuronal morphology in particular regions of the brain, including the number and size of neurons, and the density and length of dendrites in nuclei of hypothalamus and amygdala. The aim of the present study was to use global proteomics to identify proteins differentially expressed in hypothalamus/amygdala during early development (postnatal day 8) of male, female and conditional androgen receptor knockout (AR NesDel) male mice, lacking androgen receptors specifically in the brain. Furthermore, verification of selected sexually dimorphic proteins was performed using targeted proteomics.\n\nOur proteomic approach, iTRAQ, allowed us to investigate expression differences in the 2998 most abundantly expressed proteins in our dissected tissues. Approximately 170 proteins differed between the sexes, and 38 proteins between AR NesDel and control males (p < 0.05). In line with previous explorative studies of sexually dimorphic gene expression we mainly detected subtle protein expression differences (fold changes <1.3). The protein MARCKS (myristoylated alanine rich C kinase substrate), having the largest fold change of the proteins selected from the iTRAQ analyses and of known importance for synaptic transmission and dendritic branching, was confirmed by targeted proteomics as differentially expressed between the sexes.\n\nOverall, our results provide solid evidence that a large number of proteins show sex differences in their brain expression and could potentially be involved in brain sexual differentiation. Furthermore, our finding of a sexually dimorphic expression of MARCKS in the brain during development warrants further investigation on the involvement in sexual differentiation of this protein.", "doi": "10.1186/s12868-016-0332-1", "pmid": "28056817", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12868-016-0332-1"}, {"db": "pmc", "key": "PMC5217640"}], "notes": [], "created": "2020-01-27T22:45:55.076Z", "modified": "2024-01-16T13:46:32.920Z"}, {"entity": "publication", "iuid": "5db1f3150d6c44788e37906fdb48c5bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5db1f3150d6c44788e37906fdb48c5bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5db1f3150d6c44788e37906fdb48c5bb"}}, "title": "Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus", "authors": [{"family": "Odhams", "given": "Christopher A", "initials": "CA"}, {"family": "Cortini", "given": "Andrea", "initials": "A"}, {"family": "Chen", "given": "Lingyan", "initials": "L"}, {"family": "Roberts", "given": "Amy L", "initials": "AL"}, {"family": "Vi\u00f1uela", "given": "Ana", "initials": "A"}, {"family": "Buil", "given": "Alfonso", "initials": "A"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET"}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}, {"family": "Cunninghame Graham", "given": "Deborah S", "initials": "DS"}], "type": "journal-article", "published": "2017-01-05", "journal": {"volume": null, "issn": "1460-2083", "issue": null, "pages": "ddw417", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": null, "doi": "10.1093/hmg/ddw417", "pmid": "28062664", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:23:52.678Z", "modified": "2020-01-21T13:56:10.000Z"}, {"entity": "publication", "iuid": "9ea2ff492e6647c18f98f1ec9698dd97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ea2ff492e6647c18f98f1ec9698dd97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ea2ff492e6647c18f98f1ec9698dd97"}}, "title": "Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci.", "authors": [{"family": "Brandt", "given": "Monika", "initials": "M"}, {"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}], "type": "journal article", "published": "2017-01-05", "journal": {"volume": "7", "issn": "2160-1836", "issue": "1", "pages": "119-128", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.", "doi": "10.1534/g3.116.036012", "pmid": "27799342", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "g3.116.036012"}, {"db": "pmc", "key": "PMC5217102"}], "notes": [], "created": "2017-10-25T15:18:14.406Z", "modified": "2020-01-21T13:56:08.009Z"}, {"entity": "publication", "iuid": "d696eb5a55e8441fa0660644f896cd63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d696eb5a55e8441fa0660644f896cd63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d696eb5a55e8441fa0660644f896cd63"}}, "title": "A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma.", "authors": [{"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Niinivirta", "given": "Marjut", "initials": "M"}, {"family": "Laird", "given": "Alexander", "initials": "A"}, {"family": "Ljungqvist", "given": "Oscar", "initials": "O"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Khan", "given": "Naila", "initials": "N"}, {"family": "Patil", "given": "Tushar", "initials": "T"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Harrison", "given": "David J", "initials": "DJ"}, {"family": "Ullenhag", "given": "Gustav J", "initials": "GJ"}, {"family": "Stewart", "given": "Grant D", "initials": "GD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2017-01-04", "journal": {"title": "BMC Cancer", "issn": "1471-2407", "volume": "17", "issue": "1", "pages": "9", "issn-l": "1471-2407"}, "abstract": "There is an unmet clinical need for better prognostic and diagnostic tools for renal cell carcinoma (RCC).\n\nHuman Protein Atlas data resources, including the transcriptomes and proteomes of normal and malignant human tissues, were searched for RCC-specific proteins and cubilin (CUBN) identified as a candidate. Patient tissue representing various cancer types was constructed into a tissue microarray (n = 940) and immunohistochemistry used to investigate the specificity of CUBN expression in RCC as compared to other cancers. Two independent RCC cohorts (n = 181; n = 114) were analyzed to further establish the sensitivity of CUBN as RCC-specific marker and to explore if the fraction of RCCs lacking CUBN expression could predict differences in patient survival.\n\nCUBN was identified as highly RCC-specific protein with 58% of all primary RCCs staining positive for CUBN using immunohistochemistry. In venous tumor thrombi and metastatic lesions, the frequency of CUBN expression was increasingly lost. Clear cell RCC (ccRCC) patients with CUBN positive tumors had a significantly better prognosis compared to patients with CUBN negative tumors, independent of T-stage, Fuhrman grade and nodal status (HR 0.382, CI 0.203-0.719, P = 0.003).\n\nCUBN expression is highly specific to RCC and loss of the protein is significantly and independently associated with poor prognosis. CUBN expression in ccRCC provides a promising positive prognostic indicator for patients with ccRCC. The high specificity of CUBN expression in RCC also suggests a role as a new diagnostic marker in clinical cancer differential diagnostics to confirm or rule out RCC.", "doi": "10.1186/s12885-016-3030-6", "pmid": "28052770", "labels": {"Tissue Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-016-3030-6"}, {"db": "pmc", "key": "PMC5215231"}], "notes": [], "created": "2017-11-05T12:38:11.316Z", "modified": "2021-07-08T13:44:33.674Z"}, {"entity": "publication", "iuid": "0237c96aa2a14dc0ae3a6b465cecfd6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0237c96aa2a14dc0ae3a6b465cecfd6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0237c96aa2a14dc0ae3a6b465cecfd6f"}}, "title": "Profile of upregulated inflammatory proteins in sera of Myasthenia Gravis patients.", "authors": [{"family": "Molin", "given": "Carl Johan", "initials": "CJ"}, {"family": "Westerberg", "given": "Elisabet", "initials": "E"}, {"family": "Punga", "given": "Anna Rostedt", "initials": "AR"}], "type": "journal article", "published": "2017-01-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "7", "issue": "1", "pages": "39716"}, "abstract": "This study describes specific patterns of elevated inflammatory proteins in clinical subtypes of myasthenia gravis (MG) patients. MG is a chronic, autoimmune neuromuscular disease with antibodies most commonly targeting the acetylcholine receptors (AChRab), which causes fluctuating skeletal muscle fatigue. MG pathophysiology includes a strong component of inflammation, and a large proportion of patients with early onset MG additionally present thymus hyperplasia. Due to the fluctuating nature and heterogeneity of the disease, there is a great need for objective biomarkers as well as novel potential inflammatory targets. We examined the sera of 45 MG patients (40 AChRab seropositive and 5 AChRab seronegative), investigating 92 proteins associated with inflammation. Eleven of the analysed proteins were significantly elevated compared to healthy controls, out of which the three most significant were: matrix metalloproteinase 10 (MMP-10; p = 0.0004), transforming growth factor alpha (TGF-\u03b1; p = 0.0017) and extracellular newly identified receptor for advanced glycation end-products binding protein (EN-RAGE) (also known as protein S100-A12; p = 0.0054). Further, levels of MMP-10, C-X-C motif ligand 1 (CXCL1) and brain derived neurotrophic factor (BDNF) differed between early and late onset MG. These novel targets provide valuable additional insight into the systemic inflammatory response in MG.", "doi": "10.1038/srep39716", "pmid": "28045063", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "srep39716"}, {"db": "pmc", "key": "PMC5206650"}], "notes": [], "created": "2020-01-23T15:13:42.026Z", "modified": "2023-04-14T13:56:17.836Z"}, {"entity": "publication", "iuid": "89a9f8ed7d814a7fbe77b48bc3699912", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89a9f8ed7d814a7fbe77b48bc3699912.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89a9f8ed7d814a7fbe77b48bc3699912"}}, "title": "Small Molecule Microarray Based Discovery of PARP14 Inhibitors", "authors": [{"family": "Peng", "given": "Bo", "initials": "B"}, {"family": "Thorsell", "given": "Ann Gerd", "initials": "AG"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}, {"family": "Yao", "given": "Shao Q", "initials": "SQ"}], "type": "journal-article", "published": "2017-01-02", "journal": {"volume": "56", "issn": "1433-7851", "issue": "1", "pages": "248-253", "title": "Angew. Chem. Int. Ed.", "issn-l": "1433-7851"}, "abstract": null, "doi": "10.1002/anie.201609655", "pmid": "27918638", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-05T06:44:16.745Z", "modified": "2017-11-09T13:14:50.035Z"}, {"entity": "publication", "iuid": "795978f5e49e4146bc9e7b6c2a0f4e67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/795978f5e49e4146bc9e7b6c2a0f4e67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/795978f5e49e4146bc9e7b6c2a0f4e67"}}, "title": "Epigenetic changes as prognostic predictors in endometrial carcinomas.", "authors": [{"family": "Farkas", "given": "Sanja A", "initials": "SA"}, {"family": "Sorbe", "given": "Bengt G", "initials": "BG"}, {"family": "Nilsson", "given": "Torbj\u00f6rn K", "initials": "TK"}], "type": "journal article", "published": "2017-01-02", "journal": {"volume": "12", "issn": "1559-2308", "issue": "1", "pages": "19-26", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively). We identified specific DNA methylation signature in high-risk endometrial tumors, and potential molecular biomarker genes (TBX2, CHST11, and NID2) associated with unfavorable clinical predictive and prognostic factors.", "doi": "10.1080/15592294.2016.1252891", "pmid": "27874289", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5270631"}], "notes": [], "created": "2017-05-03T13:01:43.385Z", "modified": "2020-01-21T13:56:03.152Z"}, {"entity": "publication", "iuid": "982fd0bf85684fa2b08e09e4171d860a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/982fd0bf85684fa2b08e09e4171d860a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/982fd0bf85684fa2b08e09e4171d860a"}}, "title": "Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.", "authors": [{"family": "Sigurgeirsson", "given": "Benjamin", "initials": "B"}, {"family": "\u00c5mark", "given": "Hanna", "initials": "H"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Ujvari", "given": "Dorina", "initials": "D"}, {"family": "Westgren", "given": "Magnus", "initials": "M"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gidl\u00f6f", "given": "Sebastian", "initials": "S"}], "type": "comparative study", "published": "2017-01-01", "journal": {"volume": "96", "issn": "1529-7268", "issue": "1", "pages": "24-33", "title": "Biol. Reprod.", "issn-l": "0006-3363"}, "abstract": "Endometrial receptivity is crucial for implantation and establishment of a normal pregnancy. The shift from proliferative to receptive endometrium is still far from being understood. In this paper, we comprehensively present the transcriptome of the human endometrium by comparing endometrial biopsies from proliferative phase with consecutive biopsies 7-9 days after ovulation. The results show a clear difference in expression between the two time points using both total and small RNA sequencing. A total of 3,297 messenger RNAs (mRNAs), 516 long noncoding RNAs (lncRNAs), and 102 small noncoding RNAs were identified as statistically differentially expressed between the two time points. We show a thorough description of the change in mRNA between the two time points and display lncRNAs, small nucleolar RNAs, and small nuclear RNAs not previously reported in the healthy human endometrium. In conclusion, this paper reports in detail the shift in RNA expression from the proliferative to receptive endometrium.", "doi": "10.1095/biolreprod.116.142547", "pmid": "28395321", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2725477"}, {"db": "GEO", "key": "GSE86491"}], "notes": [], "created": "2017-11-03T16:21:34.477Z", "modified": "2024-01-16T13:48:48.703Z"}, {"entity": "publication", "iuid": "2b720df7014c43089e56ee43a3dd1ce9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b720df7014c43089e56ee43a3dd1ce9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b720df7014c43089e56ee43a3dd1ce9"}}, "title": "cis-Cinnamic Acid Is a Novel, Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation", "authors": [{"family": "Steenackers", "given": "Ward", "initials": "W"}, {"family": "Kl\u00edma", "given": "Petr", "initials": "P"}, {"family": "Quareshy", "given": "Mussa", "initials": "M"}, {"family": "Cesarino", "given": "Igor", "initials": "I"}, {"family": "Kumpf", "given": "Robert P", "initials": "RP"}, {"family": "Corneillie", "given": "Sander", "initials": "S"}, {"family": "Ara\u00fajo", "given": "Pedro", "initials": "P"}, {"family": "Viaene", "given": "Tom", "initials": "T"}, {"family": "Goeminne", "given": "Geert", "initials": "G"}, {"family": "Nowack", "given": "Moritz K", "initials": "MK"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Friml", "given": "Ji\u0159\u00ed", "initials": "J"}, {"family": "Blakeslee", "given": "Joshua J", "initials": "JJ"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Za\u017e\u00edmalov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Napier", "given": "Richard", "initials": "R"}, {"family": "Boerjan", "given": "Wout", "initials": "W"}, {"family": "Vanholme", "given": "Bartel", "initials": "B"}], "type": "journal-article", "published": "2017-01-00", "journal": {"volume": "173", "issn": "1532-2548", "issue": "1", "pages": "552-565", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": null, "doi": "10.1104/pp.16.00943", "pmid": "27837086", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:35:07.585Z", "modified": "2025-10-17T13:03:19.131Z"}, {"entity": "publication", "iuid": "eb989235ef28426db5628c1f51c5dc4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb989235ef28426db5628c1f51c5dc4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb989235ef28426db5628c1f51c5dc4b"}}, "title": "VAV1 regulates experimental autoimmune arthritis and is associated with anti-CCP negative rheumatoid arthritis.", "authors": [{"family": "Guerreiro-Cacais", "given": "A O", "initials": "AO"}, {"family": "Norin", "given": "U", "initials": "U"}, {"family": "Gyllenberg", "given": "A", "initials": "A"}, {"family": "Berglund", "given": "R", "initials": "R"}, {"family": "Beyeen", "given": "A D", "initials": "AD"}, {"family": "Rheumatoid Arthritis Consortium International (RACI)", "given": "", "initials": ""}, {"family": "Petit-Teixeira", "given": "E", "initials": "E"}, {"family": "Corn\u00e9lis", "given": "F", "initials": "F"}, {"family": "Saoudi", "given": "A", "initials": "A"}, {"family": "Fourni\u00e9", "given": "G J", "initials": "GJ"}, {"family": "Holmdahl", "given": "R", "initials": "R"}, {"family": "Alfredsson", "given": "L", "initials": "L"}, {"family": "Klareskog", "given": "L", "initials": "L"}, {"family": "Jagodic", "given": "M", "initials": "M"}, {"family": "Olsson", "given": "T", "initials": "T"}, {"family": "Kockum", "given": "I", "initials": "I"}, {"family": "Padyukov", "given": "L", "initials": "L"}], "type": "comparative study", "published": "2017-01-00", "journal": {"volume": "18", "issn": "1476-5470", "issue": "1", "pages": "48-56", "title": "Genes Immun.", "issn-l": "1466-4879"}, "abstract": "Rheumatoid arthritis (RA) patients can be stratified into two subgroups defined by the presence or absence of antibodies against citrullinated circular peptides (anti-CCP) with most of the genetic association found in anti-CCP positive RA. Here we addressed the role of VAV1, previously associated to multiple sclerosis (MS), in the pathogenesis of RA in experimental models and in a genetic association study. Experimental arthritis triggered by pristane or collagen type II was induced in DA rats and in the DA.BN-R25 congenic line that carries a polymorphism in Vav1. Difference in arthritis severity was observed only after immunization with pristane. In a case-control study, 34 SNPs from VAV1 locus were analyzed by Immunochip genotyping in 11475 RA patients (7573 anti-CCP positive and 3902 negative) and 15,870 controls in six cohorts of European Caucasians. A combination of the previous MS-associated haplotype and two additional SNPs was associated with anti-CCP negative RA (alleles G-G-A-A of rs682626-rs2546133-rs2617822-rs12979659, OR=1.13, P=1.27 \u00d7 10 -5). The same markers also contributed to activity of RA at baseline with the strongest association in the anti-CCP negative group for the rs682626-rs12979659 G-A haplotype (\u03b2=-0.283, P=0.0048). Our study suggests a role for VAV1 and T-cell signaling in the pathology of anti-CCP-negative RA.", "doi": "10.1038/gene.2016.49", "pmid": "28053322", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gene201649"}], "notes": [], "created": "2017-10-25T15:18:16.559Z", "modified": "2024-01-16T13:48:48.714Z"}, {"entity": "publication", "iuid": "6251945fdc9249b4b7e5bf48d0f60705", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6251945fdc9249b4b7e5bf48d0f60705.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6251945fdc9249b4b7e5bf48d0f60705"}}, "title": "SHADE AVOIDANCE 4 Is Required for Proper Auxin Distribution in the Hypocotyl", "authors": [{"family": "Ge", "given": "Yanhua", "initials": "Y"}, {"family": "Yan", "given": "Fenglian", "initials": "F"}, {"family": "Zourelidou", "given": "Melina", "initials": "M"}, {"family": "Wang", "given": "Meiling", "initials": "M"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Fastner", "given": "Astrid", "initials": "A"}, {"family": "Hammes", "given": "Ulrich Z", "initials": "UZ"}, {"family": "Di Donato", "given": "Martin", "initials": "M"}, {"family": "Geisler", "given": "Markus", "initials": "M"}, {"family": "Schwechheimer", "given": "Claus", "initials": "C"}, {"family": "Tao", "given": "Yi", "initials": "Y"}], "type": "journal-article", "published": "2017-01-00", "journal": {"volume": "173", "issn": "1532-2548", "issue": "1", "pages": "788-800", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": null, "doi": "10.1104/pp.16.01491", "pmid": "27872246", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:32:11.460Z", "modified": "2025-10-17T13:03:19.153Z"}, {"entity": "publication", "iuid": "69d3f8ae22854c9087ae31716554c354", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69d3f8ae22854c9087ae31716554c354.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69d3f8ae22854c9087ae31716554c354"}}, "title": "Rye B chromosomes encode a functional Argonaute-like protein with in\u00a0vitro slicer activities similar to its A chromosome paralog.", "authors": [{"family": "Ma", "given": "Wei", "initials": "W"}, {"family": "Gabriel", "given": "Tobias Sebastian", "initials": "TS"}, {"family": "Martis", "given": "Mihaela Maria", "initials": "MM"}, {"family": "Gursinsky", "given": "Torsten", "initials": "T"}, {"family": "Schubert", "given": "Veit", "initials": "V"}, {"family": "Vr\u00e1na", "given": "Jan", "initials": "J"}, {"family": "Dole\u017eel", "given": "Jaroslav", "initials": "J"}, {"family": "Grundlach", "given": "Heidrun", "initials": "H"}, {"family": "Altschmied", "given": "Lothar", "initials": "L"}, {"family": "Scholz", "given": "Uwe", "initials": "U"}, {"family": "Himmelbach", "given": "Axel", "initials": "A"}, {"family": "Behrens", "given": "Sven-Erik", "initials": "SE"}, {"family": "Banaei-Moghaddam", "given": "Ali Mohammad", "initials": "AM"}, {"family": "Houben", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "213", "issn": "1469-8137", "issue": "2", "pages": "916-928", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In\u00a0vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.", "doi": "10.1111/nph.14110", "pmid": "27468091", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:44.433Z", "modified": "2020-01-21T13:53:21.320Z"}, {"entity": "publication", "iuid": "79209a0da0ed46bfac15fb20ace04226", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79209a0da0ed46bfac15fb20ace04226.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79209a0da0ed46bfac15fb20ace04226"}}, "title": "P1.02-063 Mutation Profiling by Targeted Next-Generation Sequencing of an Unselected NSCLC Cohort", "authors": [{"family": "La Fleur", "given": "Linnea", "initials": "L"}, {"family": "Falk-Sorqvist", "given": "Elin", "initials": "E"}, {"family": "Smeds", "given": "Patrik", "initials": "P"}, {"family": "Sundstrom", "given": "Magnus", "initials": "M"}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Sandelin", "given": "Martin", "initials": "M"}, {"family": "Lamberg", "given": "Kristina", "initials": "K"}, {"family": "Landelius", "given": "Per", "initials": "P"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Moens", "given": "Lotte", "initials": "L"}, {"family": "Botling", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-01-00", "journal": {"volume": "12", "issn": "1556-0864", "issue": "1", "pages": "S526-S527", "title": "Journal of Thoracic Oncology", "issn-l": "1556-0864"}, "abstract": null, "doi": "10.1016/j.jtho.2016.11.647", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:40.001Z", "modified": "2024-01-16T13:48:48.725Z"}, {"entity": "publication", "iuid": "3aee01e26d264c08ae8aa37108283a2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3aee01e26d264c08ae8aa37108283a2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3aee01e26d264c08ae8aa37108283a2d"}}, "title": "Multiethnic genome-wide meta-analysis of ectopic fat depots identifies loci associated with adipocyte development and differentiation.", "authors": [{"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Deng", "given": "Xuan", "initials": "X"}, {"family": "Fisher", "given": "Virginia A", "initials": "VA"}, {"family": "Drong", "given": "Alexander", "initials": "A"}, {"family": "Zhang", "given": "Yang", "initials": "Y"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Weeks", "given": "Olivia", "initials": "O"}, {"family": "Choh", "given": "Audrey C", "initials": "AC"}, {"family": "Duan", "given": "Qing", "initials": "Q"}, {"family": "Dyer", "given": "Thomas D", "initials": "TD"}, {"family": "Eicher", "given": "John D", "initials": "JD"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Kacprowski", "given": "Tim", "initials": "T"}, {"family": "Kent", "given": "Jack W", "initials": "JW"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Liu", "given": "Xinggang", "initials": "X"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "Lu", "given": "Lingyi", "initials": "L"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Parihar", "given": "Ankita", "initials": "A"}, {"family": "Peralta", "given": "Juan M", "initials": "JM"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Zhang", "given": "Yi", "initials": "Y"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Kissebah", "given": "Ahmed H", "initials": "AH"}, {"family": "Kullberg", "given": "Joel", "initials": "J"}, {"family": "Laqua", "given": "Ren\u00e9", "initials": "R"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Olivier", "given": "Michael", "initials": "M"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Terry", "given": "James G", "initials": "JG"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Carr", "given": "John Jeffrey", "initials": "JJ"}, {"family": "Czerwinski", "given": "Stefan A", "initials": "SA"}, {"family": "Ding", "given": "Jingzhong", "initials": "J"}, {"family": "Friedrich", "given": "Nele", "initials": "N"}, {"family": "Gudnason", "given": "Vilmunder", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SL"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Towne", "given": "Bradford", "initials": "B"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Allison", "given": "Matthew", "initials": "M"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Goessling", "given": "Wolfram", "initials": "W"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Steinhauser", "given": "Matthew L", "initials": "ML"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "1", "pages": "125-130", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Variation in body fat distribution contributes to the metabolic sequelae of obesity. The genetic determinants of body fat distribution are poorly understood. The goal of this study was to gain new insights into the underlying genetics of body fat distribution by conducting sample-size-weighted fixed-effects genome-wide association meta-analyses in up to 9,594 women and 8,738 men of European, African, Hispanic and Chinese ancestry, with and without sex stratification, for six traits associated with ectopic fat (hereinafter referred to as ectopic-fat traits). In total, we identified seven new loci associated with ectopic-fat traits (ATXN1, UBE2E2, EBF1, RREB1, GSDMB, GRAMD3 and ENSA; P < 5 \u00d7 10(-8); false discovery rate < 1%). Functional analysis of these genes showed that loss of function of either Atxn1 or Ube2e2 in primary mouse adipose progenitor cells impaired adipocyte differentiation, suggesting physiological roles for ATXN1 and UBE2E2 in adipogenesis. Future studies are necessary to further explore the mechanisms by which these genes affect adipocyte biology and how their perturbations contribute to systemic metabolic disease.", "doi": "10.1038/ng.3738", "pmid": "27918534", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3738"}], "notes": [], "created": "2017-05-03T13:00:00.288Z", "modified": "2024-01-16T13:48:48.735Z"}, {"entity": "publication", "iuid": "ae3d3cf425d84a4c8806b185c19a7a01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae3d3cf425d84a4c8806b185c19a7a01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae3d3cf425d84a4c8806b185c19a7a01"}}, "title": "Meta-GWAS Accuracy and Power (MetaGAP) Calculator Shows that Hiding Heritability Is Partially Due to Imperfect Genetic Correlations across Studies.", "authors": [{"family": "de Vlaming", "given": "Ronald", "initials": "R"}, {"family": "Okbay", "given": "Aysu", "initials": "A"}, {"family": "Rietveld", "given": "Cornelius A", "initials": "CA"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Rooij", "given": "Frank J A", "initials": "FJ"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Groenen", "given": "Patrick J F", "initials": "PJ"}, {"family": "Thurik", "given": "A Roy", "initials": "AR"}, {"family": "Koellinger", "given": "Philipp D", "initials": "PD"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "1", "pages": "e1006495", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Large-scale genome-wide association results are typically obtained from a fixed-effects meta-analysis of GWAS summary statistics from multiple studies spanning different regions and/or time periods. This approach averages the estimated effects of genetic variants across studies. In case genetic effects are heterogeneous across studies, the statistical power of a GWAS and the predictive accuracy of polygenic scores are attenuated, contributing to the so-called 'missing heritability'. Here, we describe the online Meta-GWAS Accuracy and Power (MetaGAP) calculator (available at www.devlaming.eu) which quantifies this attenuation based on a novel multi-study framework. By means of simulation studies, we show that under a wide range of genetic architectures, the statistical power and predictive accuracy provided by this calculator are accurate. We compare the predictions from the MetaGAP calculator with actual results obtained in the GWAS literature. Specifically, we use genomic-relatedness-matrix restricted maximum likelihood to estimate the SNP heritability and cross-study genetic correlation of height, BMI, years of education, and self-rated health in three large samples. These estimates are used as input parameters for the MetaGAP calculator. Results from the calculator suggest that cross-study heterogeneity has led to attenuation of statistical power and predictive accuracy in recent large-scale GWAS efforts on these traits (e.g., for years of education, we estimate a relative loss of 51-62% in the number of genome-wide significant loci and a relative loss in polygenic score R2 of 36-38%). Hence, cross-study heterogeneity contributes to the missing heritability.", "doi": "10.1371/journal.pgen.1006495", "pmid": "28095416", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-16-00815"}, {"db": "pmc", "key": "PMC5240919"}], "notes": [], "created": "2017-10-25T15:54:17.918Z", "modified": "2024-01-16T13:48:48.748Z"}, {"entity": "publication", "iuid": "86fb99b8bde44d8782114a6a0c9fbafe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86fb99b8bde44d8782114a6a0c9fbafe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86fb99b8bde44d8782114a6a0c9fbafe"}}, "title": "Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Bednarczyk", "given": "J\u00f3zef", "initials": "J"}, {"family": "Piontek", "given": "Janusz", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "26", "issn": "1878-0326", "issue": null, "pages": "30-39", "title": "Forensic Sci Int Genet", "issn-l": "1872-4973"}, "abstract": "We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq\u2122 Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS 14C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq\u2122 Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct maternal relationship in ancient individuals.", "doi": "10.1016/j.fsigen.2016.10.008", "pmid": "27771467", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1872-4973(16)30193-4"}], "notes": [], "created": "2017-05-08T07:57:17.839Z", "modified": "2024-01-16T13:48:48.760Z"}, {"entity": "publication", "iuid": "8a6fa76781b74bb8b0b580e3693aa9cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a6fa76781b74bb8b0b580e3693aa9cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a6fa76781b74bb8b0b580e3693aa9cc"}}, "title": "Identification of two distinct mesenchymal stromal cell populations in human malignant glioma.", "authors": [{"family": "Svensson", "given": "Andreas", "initials": "A"}, {"family": "Ramos-Moreno", "given": "Tania", "initials": "T"}, {"family": "Eberst\u00e5l", "given": "Sofia", "initials": "S"}, {"family": "Scheding", "given": "Stefan", "initials": "S"}, {"family": "Bengzon", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "131", "issn": "1573-7373", "issue": "2", "pages": "245-254", "title": "J. Neurooncol.", "issn-l": "0167-594X"}, "abstract": "Gene profiling has revealed that malignant gliomas can be divided into four distinct molecular subtypes, where tumors with a mesenchymal gene expression are correlated with short survival. The present investigation was undertaken to clarify whether human malignant gliomas contain endogenous mesenchymal stromal cells (MSC), fulfilling consensus criteria defined by The International Society for Cellular Therapy, recruited from the host. We found that MSC-like cells can be isolated from primary human malignant gliomas. Two distinct MSC-like cell populations, differing in their expression of the CD90 surface marker, were discovered after cell sorting. RNA sequencing revealed further genetic differences between these two cell populations and MSC-like cells lacking CD90 produced higher amounts of VEGF and PGE2 compared to cells with the true MSC phenotype, implying that the CD90(-) MSC-like cells most probably are more active in tumor vascularization and immunosuppression than their CD90(+) counterpart. The results highlight the CD90(-) subpopulation as an important tumor component, however, its functional effects in glioma remains to be resolved. Using the protocols presented here, it will be possible to isolate, characterize and analyze brain tumor-derived MSC-like cells in more detail and to further test their functions in vitro and in in vivo xenograft models of glioma.", "doi": "10.1007/s11060-016-2302-y", "pmid": "27757723", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s11060-016-2302-y"}, {"db": "pmc", "key": "PMC5306185"}], "notes": [], "created": "2017-10-31T13:05:41.055Z", "modified": "2017-10-31T13:15:02.890Z"}, {"entity": "publication", "iuid": "5157c9ed636a4d68950d96383ad8f826", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5157c9ed636a4d68950d96383ad8f826.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5157c9ed636a4d68950d96383ad8f826"}}, "title": "Human immune system variation.", "authors": [{"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Davis", "given": "Mark M", "initials": "MM"}], "type": "journal article", "published": "2017-01-00", "journal": {"title": "Nat. Rev. Immunol.", "issn": "1474-1741", "volume": "17", "issue": "1", "pages": "21-29", "issn-l": "1474-1733"}, "abstract": "The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual's immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases.", "doi": "10.1038/nri.2016.125", "pmid": "27916977", "labels": {"Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nri.2016.125"}, {"db": "pmc", "key": "PMC5328245"}, {"db": "mid", "key": "NIHMS846460"}], "notes": [], "created": "2019-03-25T19:57:58.123Z", "modified": "2021-07-08T09:18:09.831Z"}, {"entity": "publication", "iuid": "65de7f1a1ae041cbbd79874bfcc303e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65de7f1a1ae041cbbd79874bfcc303e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65de7f1a1ae041cbbd79874bfcc303e1"}}, "title": "Genetic and methylation variation in the CYP2B6 gene is related to circulating p,p'-dde levels in a population-based sample.", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ng", "given": "Esther", "initials": "E"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Salihovic", "given": "Samira", "initials": "S"}, {"family": "van Bavel", "given": "Bert", "initials": "B"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Lampa", "given": "Erik", "initials": "E"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Lind", "given": "P Monica", "initials": "PM"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "98", "issn": "1873-6750", "issue": null, "pages": "212-218", "title": "Environ Int", "issn-l": "0160-4120"}, "abstract": "Since the metabolism of the organochlorine pesticide dichlorodiphenyltrichloroethane (DDT) is not fully known in humans, we evaluated if circulating levels of a major breakdown product of DDT, p,p'-DDE, were related to genome-wide genetic and methylation variation in a population-based sample.\n\nIn the population-based Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study (1016 subjects all aged 70), circulating levels of p,p'-DDE were analyzed by high-resolution chromatography coupled to high-resolution mass spectrometry (HRGC/HRMS). Genetic variants were genotyped and imputed (1000 Genomes reference, March 2012 release). Methylation sites were assayed using the Illumina HumanMethylation450 array in whole blood. A genome-wide association study (GWAS) approach was applied.\n\nEvidence for genome-wide significant association with p,p'-DDE levels was observed only for a locus at chromosome 19 corresponding to the CYP2B6 gene (lead SNP rs7260538). Subjects being homozygote for the G allele showed a median level of 472ng/g lipid, while the corresponding level for those being homozygote for the T allele was 192ng/g lipid (p=1.5\u00d710(-31)). An analysis conditioned on the lead SNP disclosed a distinct signal in the same gene (rs7255374, position chr19:41520351; p=2.2\u00d710(-8)). A whole-genome methylation analysis showed one significant relationship vs. p,p'-DDE levels (p=6.2\u00d710(-9)) located 7kb downstream the CYP2B6 gene (cg27089200, position chr19:41531976). This CpG-site was also related to the lead SNP (p=3.8\u00d710(-35)), but mediated only 4% of the effect of the lead SNP on p,p'-DDE levels.\n\nCirculating levels of p,p'-DDE were related to genetic variation in the CYP2B6 gene in the general elderly population. DNA methylation in this gene is not closely linked to the p,p'-DDE levels.", "doi": "10.1016/j.envint.2016.11.010", "pmid": "27839851", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0160-4120(16)30761-9"}, {"db": "pmc", "key": "PMC5152752"}], "notes": [], "created": "2017-05-03T12:59:51.721Z", "modified": "2024-01-16T13:48:48.767Z"}, {"entity": "publication", "iuid": "0bc2c20401304b77954186e8a12287c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0bc2c20401304b77954186e8a12287c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0bc2c20401304b77954186e8a12287c3"}}, "title": "Expression of possible targets for new proteasome inhibitors in diffuse large B-cell lymphoma.", "authors": [{"family": "Delforoush", "given": "Maryam", "initials": "M"}, {"family": "Berglund", "given": "Mattias", "initials": "M"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Sundstr\u00f6m", "given": "Christer", "initials": "C"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "98", "issn": "1600-0609", "issue": "1", "pages": "52-56", "title": "Eur. J. Haematol.", "issn-l": "0902-4441"}, "abstract": "Investigating expression of possible targets for proteasome inhibitors in patients with diffuse large B-cell lymphoma (DLBCL) and correlating the findings to clinical parameters and outcome.\n\nTumour material from 92 patients with DLBCL treated with either R-CHOP like (n = 69) or CHOP like (n = 23) regimens were stained for possible targets of proteasome inhibitors.\n\nThe primary target molecule of bortezomib, proteasome subunit beta, type 5 (PSMB5), was not detected in the tumour cells in any of the cases but showed an abundant expression in cells in the microenvironment. However, the deubiquitinases (DUBs) of the proteasome, the ubiquitin carboxyl-terminal hydrolase L5 (UCHL5) and the ubiquitin specific peptidase 14 (USP14), were detected in the cytoplasm of the tumour cells in 77% and 74% of the cases, respectively. The adhesion regulating molecule 1 (ADRM1) was detected in 98% of the cases. There was no correlation between the expression of any of the studied markers and clinical outcome or GC/non-GC phenotype.\n\nWe suggest that UCHL5 and/or USP14 should be further evaluated as new targets for proteasome inhibitors in DLBCL. The lack of expression of PSMB5 on the tumour cells might provide an explanation of the relatively poor results of bortezomib in DLBCL.", "doi": "10.1111/ejh.12784", "pmid": "27301795", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:19.921Z", "modified": "2017-11-05T13:04:33.333Z"}, {"entity": "publication", "iuid": "02c9e94d276149cd93952ef5577ea324", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02c9e94d276149cd93952ef5577ea324.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02c9e94d276149cd93952ef5577ea324"}}, "title": "Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic \u03b2-Cells.", "authors": [{"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Islam", "given": "Md Shahidul", "initials": "MS"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "46", "issn": "1536-4828", "issue": "1", "pages": "97-101", "title": "Pancreas", "issn-l": "0885-3177"}, "abstract": "Members of the transient receptor potential (TRP) channels are involved in mediating the electrical excitability and stimulus-secretion coupling in the pancreatic \u03b2-cells. The expression and the relative abundance of different TRP channels in the human \u03b2-cells are unknown. The objective of this study was to examine the expression of the TRP channels and their relative abundance in the human \u03b2-cell.\n\nRNA sequencing data obtained from human islets, fluorescence-activated cell sorting-purified human \u03b2-cell and human pancreatic acinar cells were analyzed. Gene counts and fragments per kilobase per million mapped reads were obtained.\n\nAmong the TRPC family only the TRPC1 was expressed in the human \u03b2-cell. TRPV1 channels were not expressed in the human \u03b2-cells. Among the TRPM family, TRPM4, TRPM7, TRPM2, and TRPM3 were expressed in the human \u03b2-cell. Of the remaining TRP channels, TRPP2, TRPML1, and TRPML3 were expressed in these cells.\n\nBy analyzing the RNA sequencing data, we have detected for the first time the TRP channels that are expressed in the purified human \u03b2-cells, in comparison to the other relevant pancreatic cell types. Our study provides an opportunity to focus on these TRP channels for a better understanding of the electrophysiology and stimulus-secretion coupling in these cells.", "doi": "10.1097/MPA.0000000000000685", "pmid": "27464700", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:43.824Z", "modified": "2020-01-21T13:53:21.201Z"}, {"entity": "publication", "iuid": "15650b102c574ba3b445c90eef4e6c11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15650b102c574ba3b445c90eef4e6c11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15650b102c574ba3b445c90eef4e6c11"}}, "title": "Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.", "authors": [{"family": "Fletcher", "given": "Eugene", "initials": "E"}, {"family": "Feizi", "given": "Amir", "initials": "A"}, {"family": "Bisschops", "given": "Markus M M", "initials": "MMM"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Khoomrung", "given": "Sakda", "initials": "S"}, {"family": "Siewers", "given": "Verena", "initials": "V"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-01-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "39", "issue": null, "pages": "19-28"}, "abstract": "Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions. Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether these mechanisms will be similar for tolerance to both organic and inorganic acids is yet to be explored. We therefore evolved Saccharomyces cerevisiae to acquire tolerance to HCl (inorganic acid) and to 0.3M L-lactic acid (organic acid) at pH 2.8 and then isolated several low pH tolerant strains. Whole genome sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid lactate degradation was crucial for tolerance to high concentrations of lactic acid. Our findings highlight the contribution of both the selection pressure and nature of the acid as a driver for directing the evolutionary path towards tolerance to low pH. The choice of carbon source was also an important factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending on the acid of interest.", "doi": "10.1016/j.ymben.2016.10.010", "pmid": "27815194", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1096-7176(16)30175-6"}], "notes": [], "created": "2017-11-03T16:22:27.564Z", "modified": "2024-01-16T13:48:48.775Z"}, {"entity": "publication", "iuid": "5c715075ccd24738a7561b80be7a616c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c715075ccd24738a7561b80be7a616c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c715075ccd24738a7561b80be7a616c"}}, "title": "Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies.", "authors": [{"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Mendelson", "given": "Michael M", "initials": "MM"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Joehanes", "given": "Roby", "initials": "R"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Zhi", "given": "Degui", "initials": "D"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Yao", "given": "Chen", "initials": "C"}, {"family": "Liu", "given": "Chunyu", "initials": "C"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Huan", "given": "Tianxiao", "initials": "T"}, {"family": "McRae", "given": "Allan F", "initials": "AF"}, {"family": "Demissie", "given": "Serkalem", "initials": "S"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Krauss", "given": "Ronald M", "initials": "RM"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "10", "issn": "1942-3268", "issue": "1", "title": "Circ Cardiovasc Genet", "issn-l": null}, "abstract": "Genome-wide association studies have identified loci influencing circulating lipid concentrations in humans; further information on novel contributing genes, pathways, and biology may be gained through studies of epigenetic modifications.\n\nTo identify epigenetic changes associated with lipid concentrations, we assayed genome-wide DNA methylation at cytosine-guanine dinucleotides (CpGs) in whole blood from 2306 individuals from 2 population-based cohorts, with replication of findings in 2025 additional individuals. We identified 193 CpGs associated with lipid levels in the discovery stage (P<1.08E-07) and replicated 33 (at Bonferroni-corrected P<0.05), including 25 novel CpGs not previously associated with lipids. Genes at lipid-associated CpGs were enriched in lipid and amino acid metabolism processes. A differentially methylated locus associated with triglycerides and high-density lipoprotein cholesterol (HDL-C; cg27243685; P=8.1E-26 and 9.3E-19) was associated with cis-expression of a reverse cholesterol transporter (ABCG1; P=7.2E-28) and incident cardiovascular disease events (hazard ratio per SD increment, 1.38; 95% confidence interval, 1.15-1.66; P=0.0007). We found significant cis-methylation quantitative trait loci at 64% of the 193 CpGs with an enrichment of signals from genome-wide association studies of lipid levels (PTC=0.004, PHDL-C=0.008 and Ptriglycerides=0.00003) and coronary heart disease (P=0.0007). For example, genome-wide significant variants associated with low-density lipoprotein cholesterol and coronary heart disease at APOB were cis-methylation quantitative trait loci for a low-density lipoprotein cholesterol-related differentially methylated locus.\n\nWe report novel associations of DNA methylation with lipid levels, describe epigenetic mechanisms related to previous genome-wide association studies discoveries, and provide evidence implicating epigenetic regulation of reverse cholesterol transport in blood in relation to occurrence of cardiovascular disease events.", "doi": "10.1161/CIRCGENETICS.116.001487", "pmid": "28213390", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "CIRCGENETICS.116.001487"}, {"db": "pmc", "key": "PMC5331877"}, {"db": "mid", "key": "EMS71180"}], "notes": [], "created": "2017-10-25T15:54:15.486Z", "modified": "2024-01-16T13:48:48.782Z"}, {"entity": "publication", "iuid": "03dc9797a6124bb1b776d2fc9924726c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03dc9797a6124bb1b776d2fc9924726c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03dc9797a6124bb1b776d2fc9924726c"}}, "title": "Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad\u200b", "authors": [{"family": "S\u00f6derqvist", "given": "Karin", "initials": "K"}, {"family": "Ahmed Osman", "given": "Omneya", "initials": "O"}, {"family": "Wolff", "given": "Cecilia", "initials": "C"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "V\u00e5gsholm", "given": "Ivar", "initials": "I"}, {"family": "Boqvist", "given": "Sofia", "initials": "S"}], "type": "journal-article", "published": "2017-01-00", "journal": {"volume": "7", "issn": "2000-8686", "issue": "1", "pages": "1328963", "title": "Infect Ecol Epidemiol", "issn-l": "2000-8686"}, "abstract": null, "doi": "10.1080/20008686.2017.1328963", "pmid": "28649305", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:44.165Z", "modified": "2024-01-16T13:48:48.790Z"}, {"entity": "publication", "iuid": "bb9d97d33bd445a488b6c9a31e179703", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb9d97d33bd445a488b6c9a31e179703.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb9d97d33bd445a488b6c9a31e179703"}}, "title": "Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury.", "authors": [{"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Gry", "given": "Marcus", "initials": "M"}, {"family": "Bachmann", "given": "Julie", "initials": "J"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Yimer", "given": "Getnet", "initials": "G"}, {"family": "Aklillu", "given": "Eleni", "initials": "E"}, {"family": "Makonnen", "given": "Eyasu", "initials": "E"}, {"family": "Aderaye", "given": "Getachew", "initials": "G"}, {"family": "Roach", "given": "James", "initials": "J"}, {"family": "Fier", "given": "Ian", "initials": "I"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "G\u00f6pfert", "given": "Jens", "initials": "J"}, {"family": "Perazzo", "given": "Hugo", "initials": "H"}, {"family": "Poynard", "given": "Thierry", "initials": "T"}, {"family": "Stephens", "given": "Camilla", "initials": "C"}, {"family": "Andrade", "given": "Ra\u00fal J", "initials": "RJ"}, {"family": "Lucena", "given": "M Isabel", "initials": "MI"}, {"family": "Arber", "given": "Nadir", "initials": "N"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Watkins", "given": "Paul B", "initials": "PB"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "37", "issn": "1478-3231", "issue": "1", "pages": "132-140", "title": "Liver Int.", "issn-l": "1478-3223"}, "abstract": "The occurrence of drug-induced liver injury (DILI) is a major issue in all phases of drug development. To identify novel biomarker candidates associated with DILI, we utilised an affinity proteomics strategy, where antibody suspension bead arrays were applied to profile plasma and serum samples from human DILI cases and controls.\n\nAn initial screening was performed using 4594 randomly selected antibodies, representing 3450 human proteins. Resulting candidate proteins together with proposed DILI biomarker candidates generated a DILI array of 251 proteins for subsequent target analysis and verifications. In total, 1196 samples from 241 individuals across four independent cohorts were profiled: healthy volunteers receiving acetaminophen, patients with human immunodeficiency virus and/or tuberculosis receiving treatment, DILI cases originating from a wide spectrum of drugs, and healthy volunteers receiving heparins.\n\nWe observed elevated levels of cadherin 5, type 2 (CDH5) and fatty acid-binding protein 1 (FABP1) in DILI cases. In the two longitudinal cohorts, CDH5 was elevated already at baseline. FABP1 was elevated after treatment initiation and seemed to respond more rapidly than alanine aminotransferase (ALT). The elevations were verified in the DILI cases treated with various drugs. In the heparin cohort, CDH5 was stable over time whereas FABP1 was elevated.\n\nThese results suggest that CDH5 may have value as a susceptibility marker for DILI. FABP1 was identified as a biomarker candidate with superior characteristics regarding tissue distribution and kinetics compared to ALT but likely with limited predictive value for the development of severe DILI. Further studies are needed to determine the clinical utility of the proposed markers.", "doi": "10.1111/liv.13174", "pmid": "27224670", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5215406"}], "notes": [], "created": "2017-05-03T12:59:07.167Z", "modified": "2021-07-08T13:44:33.558Z"}, {"entity": "publication", "iuid": "0be663b8d3934de29814d3954f39725e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0be663b8d3934de29814d3954f39725e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0be663b8d3934de29814d3954f39725e"}}, "title": "Deep Fish: Deep Learning\u2013Based Classification of Zebrafish Deformation for High-Throughput Screening", "authors": [{"family": "Ishaq", "given": "Omer", "initials": "O"}, {"family": "Sadanandan", "given": "Sajith Kecheril", "initials": "SK"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal-article", "published": "2017-01-00", "journal": {"volume": "22", "issn": "2472-5552", "issue": "1", "pages": "102-107", "title": "SLAS DISCOVERY: Advancing Life Sciences R&D", "issn-l": null}, "abstract": null, "doi": "10.1177/1087057116667894", "pmid": "27613194", "labels": {"BioImage Informatics": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-01T08:23:55.870Z", "modified": "2021-07-05T14:18:24.278Z"}, {"entity": "publication", "iuid": "cf71c241fdcd4495960102aa540095b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf71c241fdcd4495960102aa540095b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf71c241fdcd4495960102aa540095b8"}}, "title": "Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change.", "authors": [{"family": "Comte", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Berga", "given": "Merc\u00e8", "initials": "M"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "19", "issn": "1462-2920", "issue": "1", "pages": "251-260", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Dispersal can modify how bacterial community composition (BCC) changes in response to environmental perturbations, yet knowledge about the functional consequences of dispersal is limited. Here we hypothesized that changes in bacterial community production in response to a salinity disturbance depend on the possibility to recruit cells from different dispersal sources. To investigate this, we conducted an in situ mesocosm experiment where bacterial communities of an oligotrophic lake were exposed to different salinities (0, 18, 36 psu) for 2 weeks and subjected to dispersal of cells originating from sediments, air (mesocosms open to air deposition), both or none. BCC was determined using 454 pyrosequencing of the 16S rRNA gene and bacterial production was measured by (3) H leucine uptake. Bacterial production differed significantly among salinity treatments and dispersal treatments, being highest at high salinity. These changes were associated with changes in BCC and it was found that the identity of the main functional contributors differed at different salinities. Our results further showed that after a salinity perturbation, the response of bacterial communities depended on the recruitment of taxa, including marine representatives (e.g., Alphaproteobacteria Loktanella, Erythrobacter and the Gammaproteobacterium Rheiheimera) from dispersal sources, in which atmospheric deposition appeared to play a major role.", "doi": "10.1111/1462-2920.13593", "pmid": "27871136", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP060458"}], "notes": [], "created": "2017-05-03T13:01:47.852Z", "modified": "2024-01-16T13:48:48.797Z"}, {"entity": "publication", "iuid": "f25fd87e63e24502843cd39b5c596172", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f25fd87e63e24502843cd39b5c596172.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f25fd87e63e24502843cd39b5c596172"}}, "title": "Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects.", "authors": [{"family": "Marshall", "given": "Christian R", "initials": "CR"}, {"family": "Howrigan", "given": "Daniel P", "initials": "DP"}, {"family": "Merico", "given": "Daniele", "initials": "D"}, {"family": "Thiruvahindrapuram", "given": "Bhooma", "initials": "B"}, {"family": "Wu", "given": "Wenting", "initials": "W"}, {"family": "Greer", "given": "Douglas S", "initials": "DS"}, {"family": "Antaki", "given": "Danny", "initials": "D"}, {"family": "Shetty", "given": "Aniket", "initials": "A"}, {"family": "Holmans", "given": "Peter A", "initials": "PA"}, {"family": "Pinto", "given": "Dalila", "initials": "D", "orcid": "0000-0002-8769-0846", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd1cc4756157463f9c18f03d10531a33.json"}}, {"family": "Gujral", "given": "Madhusudan", "initials": "M"}, {"family": "Brandler", "given": "William M", "initials": "WM"}, {"family": "Malhotra", "given": "Dheeraj", "initials": "D"}, {"family": "Wang", "given": "Zhouzhi", "initials": "Z"}, {"family": "Fajarado", "given": "Karin V Fuentes", "initials": "KVF"}, {"family": "Maile", "given": "Michelle S", "initials": "MS"}, {"family": "Ripke", "given": "Stephan", "initials": "S", "orcid": "0000-0003-3622-835X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2b56c2c5f534130b7fdc2b14d6b7f15.json"}}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Albus", "given": "Margot", "initials": "M"}, {"family": "Alexander", "given": "Madeline", "initials": "M"}, {"family": "Amin", "given": "Farooq", "initials": "F"}, {"family": "Atkins", "given": "Joshua", "initials": "J"}, {"family": "Bacanu", "given": "Silviu A", "initials": "SA"}, {"family": "Belliveau", "given": "Richard A", "initials": "RA"}, {"family": "Bergen", "given": "Sarah E", "initials": "SE"}, {"family": "Bertalan", "given": "Marcelo", "initials": "M"}, {"family": "Bevilacqua", "given": "Elizabeth", "initials": "E"}, {"family": "Bigdeli", "given": "Tim B", "initials": "TB"}, {"family": "Black", "given": "Donald W", "initials": "DW"}, {"family": "Bruggeman", "given": "Richard", "initials": "R"}, {"family": "Buccola", "given": "Nancy G", "initials": "NG"}, {"family": "Buckner", "given": "Randy L", "initials": "RL"}, {"family": "Bulik-Sullivan", "given": "Brendan", "initials": "B"}, {"family": "Byerley", "given": "William", "initials": "W"}, {"family": "Cahn", "given": "Wiepke", "initials": "W"}, {"family": "Cai", "given": "Guiqing", "initials": "G"}, {"family": "Cairns", "given": "Murray J", "initials": "MJ"}, {"family": "Campion", "given": "Dominique", "initials": "D"}, {"family": "Cantor", "given": "Rita M", "initials": "RM"}, {"family": "Carr", "given": "Vaughan J", "initials": "VJ"}, {"family": "Carrera", "given": "Noa", "initials": "N"}, {"family": "Catts", "given": "Stanley V", "initials": "SV"}, {"family": "Chambert", "given": "Kimberley D", "initials": "KD"}, {"family": "Cheng", "given": "Wei", "initials": "W"}, {"family": "Cloninger", "given": "C Robert", "initials": "CR", "orcid": "0000-0003-3096-4807", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5e4c1f290d408a9ccacdc298eabbc0.json"}}, {"family": "Cohen", "given": "David", "initials": "D"}, {"family": "Cormican", "given": "Paul", "initials": "P"}, {"family": "Craddock", "given": "Nick", "initials": "N"}, {"family": "Crespo-Facorro", "given": "Benedicto", "initials": "B"}, {"family": "Crowley", "given": "James J", "initials": "JJ"}, {"family": "Curtis", "given": "David", "initials": "D"}, {"family": "Davidson", "given": "Michael", "initials": "M"}, {"family": "Davis", "given": "Kenneth L", "initials": "KL"}, {"family": "Degenhardt", "given": "Franziska", "initials": "F"}, {"family": "Del Favero", "given": "Jurgen", "initials": "J"}, {"family": "DeLisi", "given": "Lynn E", "initials": "LE"}, {"family": "Dikeos", "given": "Dimitris", "initials": "D"}, {"family": "Dinan", "given": "Timothy", "initials": "T"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Donohoe", "given": "Gary", "initials": "G"}, {"family": "Drapeau", "given": "Elodie", "initials": "E"}, {"family": "Duan", "given": "Jubao", "initials": "J"}, {"family": "Dudbridge", "given": "Frank", "initials": "F"}, {"family": "Eichhammer", "given": "Peter", "initials": "P"}, {"family": "Eriksson", "given": "Johan", "initials": "J"}, {"family": "Escott-Price", "given": "Valentina", "initials": "V"}, {"family": "Essioux", "given": "Laurent", "initials": "L"}, {"family": "Fanous", "given": "Ayman H", "initials": "AH"}, {"family": "Farh", "given": "Kai-How", "initials": "KH"}, {"family": "Farrell", "given": "Martilias S", "initials": "MS", "orcid": "0000-0002-9520-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/20be04f56c474537ad8fa07cb17241cf.json"}}, {"family": "Frank", "given": "Josef", "initials": "J", "orcid": "0000-0003-4867-9465", "researcher": {"href": "https://publications.scilifelab.se/researcher/041d6a59ba7d4c2dab9706861964bce1.json"}}, {"family": "Franke", "given": "Lude", "initials": "L", "orcid": "0000-0002-5159-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee63161f78274a53b615c05555b81a10.json"}}, {"family": "Freedman", "given": "Robert", "initials": "R"}, {"family": "Freimer", "given": "Nelson B", "initials": "NB", "orcid": "0000-0003-3586-6587", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ab76a765d4b4f57a0720b3f680cd579.json"}}, {"family": "Friedman", "given": "Joseph I", "initials": "JI"}, {"family": "Forstner", "given": "Andreas J", "initials": "AJ"}, {"family": "Fromer", "given": "Menachem", "initials": "M"}, {"family": "Genovese", "given": "Giulio", "initials": "G"}, {"family": "Georgieva", "given": "Lyudmila", "initials": "L"}, {"family": "Gershon", "given": "Elliot S", "initials": "ES"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "Giusti-Rodr\u00edguez", "given": "Paola", "initials": "P"}, {"family": "Godard", "given": "Stephanie", "initials": "S"}, {"family": "Goldstein", "given": "Jacqueline I", "initials": "JI"}, {"family": "Gratten", "given": "Jacob", "initials": "J"}, {"family": "de Haan", "given": "Lieuwe", "initials": "L"}, {"family": "Hamshere", "given": "Marian L", "initials": "ML"}, {"family": "Hansen", "given": "Mark", "initials": "M"}, {"family": "Hansen", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6703-7762", "researcher": {"href": "https://publications.scilifelab.se/researcher/56994131a2ef4278b802dc55c838d88a.json"}}, {"family": "Haroutunian", "given": "Vahram", "initials": "V"}, {"family": "Hartmann", "given": "Annette M", "initials": "AM"}, {"family": "Henskens", "given": "Frans A", "initials": "FA"}, {"family": "Herms", "given": "Stefan", "initials": "S"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Hoffmann", "given": "Per", "initials": "P"}, {"family": "Hofman", "given": "Andrea", "initials": "A"}, {"family": "Huang", "given": "Hailiang", "initials": "H", "orcid": "0000-0003-1461-5762", "researcher": {"href": "https://publications.scilifelab.se/researcher/06d9e3a25fb04741a60e9474937fc346.json"}}, {"family": "Ikeda", "given": "Masashi", "initials": "M"}, {"family": "Joa", "given": "Inge", "initials": "I"}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Kahn", "given": "Ren\u00e9 S", "initials": "RS"}, {"family": "Kalaydjieva", "given": "Luba", "initials": "L"}, {"family": "Karjalainen", "given": "Juha", "initials": "J"}, {"family": "Kavanagh", "given": "David", "initials": "D"}, {"family": "Keller", "given": "Matthew C", "initials": "MC"}, {"family": "Kelly", "given": "Brian J", "initials": "BJ"}, {"family": "Kennedy", "given": "James L", "initials": "JL"}, {"family": "Kim", "given": "Yunjung", "initials": "Y"}, {"family": "Knowles", "given": "James A", "initials": "JA", "orcid": "0000-0002-3307-5741", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6441a1b462340f29954075fbb746004.json"}}, {"family": "Konte", "given": "Bettina", "initials": "B", "orcid": "0000-0001-5287-308X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cb7ee6c582a4c72ada0b350b8434aba.json"}}, {"family": "Laurent", "given": "Claudine", "initials": "C"}, {"family": "Lee", "given": "Phil", "initials": "P"}, {"family": "Lee", "given": "S Hong", "initials": "SH"}, {"family": "Legge", "given": "Sophie E", "initials": "SE"}, {"family": "Lerer", "given": "Bernard", "initials": "B"}, {"family": "Levy", "given": "Deborah L", "initials": "DL"}, {"family": "Liang", "given": "Kung-Yee", "initials": "KY"}, {"family": "Lieberman", "given": "Jeffrey", "initials": "J"}, {"family": "L\u00f6nnqvist", "given": "Jouko", "initials": "J"}, {"family": "Loughland", "given": "Carmel M", "initials": "CM"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Maher", "given": "Brion S", "initials": "BS"}, {"family": "Maier", "given": "Wolfgang", "initials": "W"}, {"family": "Mallet", "given": "Jacques", "initials": "J"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M", "orcid": "0000-0002-8442-493X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c38fef539c2c4cebb81eff917aa3d4ef.json"}}, {"family": "Mattingsdal", "given": "Morten", "initials": "M"}, {"family": "McCarley", "given": "Robert W", "initials": "RW"}, {"family": "McDonald", "given": "Colm", "initials": "C"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM", "orcid": "0000-0002-0198-4588", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbac1cee97084746b97442ec39efe91b.json"}}, {"family": "Meier", "given": "Sandra", "initials": "S"}, {"family": "Meijer", "given": "Carin J", "initials": "CJ"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Mesholam-Gately", "given": "Raquelle I", "initials": "RI"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Michie", "given": "Patricia T", "initials": "PT"}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec8d00c4b9d43458c5c895b164695d5.json"}}, {"family": "Milanova", "given": "Vihra", "initials": "V"}, {"family": "Mokrab", "given": "Younes", "initials": "Y"}, {"family": "Morris", "given": "Derek W", "initials": "DW"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Murphy", "given": "Kieran C", "initials": "KC"}, {"family": "Murray", "given": "Robin M", "initials": "RM"}, {"family": "Myin-Germeys", "given": "Inez", "initials": "I"}, {"family": "Nenadic", "given": "Igor", "initials": "I"}, {"family": "Nertney", "given": "Deborah A", "initials": "DA"}, {"family": "Nestadt", "given": "Gerald", "initials": "G"}, {"family": "Nicodemus", "given": "Kristin K", "initials": "KK"}, {"family": "Nisenbaum", "given": "Laura", "initials": "L"}, {"family": "Nordin", "given": "Annelie", "initials": "A"}, {"family": "O'Callaghan", "given": "Eadbhard", "initials": "E"}, {"family": "O'Dushlaine", "given": "Colm", "initials": "C"}, {"family": "Oh", "given": "Sang-Yun", "initials": "SY"}, {"family": "Olincy", "given": "Ann", "initials": "A"}, {"family": "Olsen", "given": "Line", "initials": "L"}, {"family": "O'Neill", "given": "F Anthony", "initials": "FA"}, {"family": "Van Os", "given": "Jim", "initials": "J"}, {"family": "Pantelis", "given": "Christos", "initials": "C"}, {"family": "Papadimitriou", "given": "George N", "initials": "GN"}, {"family": "Parkhomenko", "given": "Elena", "initials": "E"}, {"family": "Pato", "given": "Michele T", "initials": "MT"}, {"family": "Paunio", "given": "Tiina", "initials": "T"}, {"family": "Psychosis Endophenotypes International Consortium", "given": "", "initials": ""}, {"family": "Perkins", "given": "Diana O", "initials": "DO"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Pietil\u00e4inen", "given": "Olli", "initials": "O"}, {"family": "Pimm", "given": "Jonathan", "initials": "J"}, {"family": "Pocklington", "given": "Andrew J", "initials": "AJ"}, {"family": "Powell", "given": "John", "initials": "J"}, {"family": "Price", "given": "Alkes", "initials": "A"}, {"family": "Pulver", "given": "Ann E", "initials": "AE"}, {"family": "Purcell", "given": "Shaun M", "initials": "SM"}, {"family": "Quested", "given": "Digby", "initials": "D"}, {"family": "Rasmussen", "given": "Henrik B", "initials": "HB"}, {"family": "Reichenberg", "given": "Abraham", "initials": "A"}, {"family": "Reimers", "given": "Mark A", "initials": "MA"}, {"family": "Richards", "given": "Alexander L", "initials": "AL"}, {"family": "Roffman", "given": "Joshua L", "initials": "JL"}, {"family": "Roussos", "given": "Panos", "initials": "P"}, {"family": "Ruderfer", "given": "Douglas M", "initials": "DM"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sanders", "given": "Alan R", "initials": "AR"}, {"family": "Savitz", "given": "Adam", "initials": "A"}, {"family": "Schall", "given": "Ulrich", "initials": "U"}, {"family": "Schulze", "given": "Thomas G", "initials": "TG"}, {"family": "Schwab", "given": "Sibylle G", "initials": "SG"}, {"family": "Scolnick", "given": "Edward M", "initials": "EM"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Seidman", "given": "Larry J", "initials": "LJ"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Silverman", "given": "Jeremy M", "initials": "JM"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "S\u00f6derman", "given": "Erik", "initials": "E"}, {"family": "Spencer", "given": "Chris C A", "initials": "CCA"}, {"family": "Stahl", "given": "Eli A", "initials": "EA"}, {"family": "Strengman", "given": "Eric", "initials": "E"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Stroup", "given": "T Scott", "initials": "TS"}, {"family": "Suvisaari", "given": "Jaana", "initials": "J"}, {"family": "Svrakic", "given": "Dragan M", "initials": "DM"}, {"family": "Szatkiewicz", "given": "Jin P", "initials": "JP"}, {"family": "Thirumalai", "given": "Srinivas", "initials": "S"}, {"family": "Tooney", "given": "Paul A", "initials": "PA"}, {"family": "Veijola", "given": "Juha", "initials": "J"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Waddington", "given": "John", "initials": "J"}, {"family": "Walsh", "given": "Dermot", "initials": "D"}, {"family": "Webb", "given": "Bradley T", "initials": "BT"}, {"family": "Weiser", "given": "Mark", "initials": "M"}, {"family": "Wildenauer", "given": "Dieter B", "initials": "DB"}, {"family": "Williams", "given": "Nigel M", "initials": "NM"}, {"family": "Williams", "given": "Stephanie", "initials": "S"}, {"family": "Witt", "given": "Stephanie H", "initials": "SH"}, {"family": "Wolen", "given": "Aaron R", "initials": "AR"}, {"family": "Wormley", "given": "Brandon K", "initials": "BK"}, {"family": "Wray", "given": "Naomi R", "initials": "NR"}, {"family": "Wu", "given": "Jing Qin", "initials": "JQ"}, {"family": "Zai", "given": "Clement C", "initials": "CC"}, {"family": "Adolfsson", "given": "Rolf", "initials": "R"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Blackwood", "given": "Douglas H R", "initials": "DHR"}, {"family": "Bramon", "given": "Elvira", "initials": "E"}, {"family": "Buxbaum", "given": "Joseph D", "initials": "JD"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "Collier", "given": "David A", "initials": "DA"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}, {"family": "Darvasi", "given": "Ariel", "initials": "A"}, {"family": "Domenici", "given": "Enrico", "initials": "E"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Gejman", "given": "Pablo V", "initials": "PV"}, {"family": "Gill", "given": "Michael", "initials": "M"}, {"family": "Gurling", "given": "Hugh", "initials": "H"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Iwata", "given": "Nakao", "initials": "N"}, {"family": "Jablensky", "given": "Assen V", "initials": "AV"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Kendler", "given": "Kenneth S", "initials": "KS"}, {"family": "Kirov", "given": "George", "initials": "G"}, {"family": "Knight", "given": "Jo", "initials": "J"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF"}, {"family": "Li", "given": "Qingqin S", "initials": "QS"}, {"family": "McCarroll", "given": "Steven A", "initials": "SA"}, {"family": "McQuillin", "given": "Andrew", "initials": "A"}, {"family": "Moran", "given": "Jennifer L", "initials": "JL"}, {"family": "Mowry", "given": "Bryan J", "initials": "BJ"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Ophoff", "given": "Roel A", "initials": "RA"}, {"family": "Owen", "given": "Michael J", "initials": "MJ"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Pato", "given": "Carlos N", "initials": "CN"}, {"family": "Petryshen", "given": "Tracey L", "initials": "TL"}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Riley", "given": "Brien P", "initials": "BP"}, {"family": "Rujescu", "given": "Dan", "initials": "D"}, {"family": "Sklar", "given": "Pamela", "initials": "P"}, {"family": "St Clair", "given": "David", "initials": "D"}, {"family": "Walters", "given": "James T R", "initials": "JTR"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "O'Donovan", "given": "Michael C", "initials": "MC"}, {"family": "Scherer", "given": "Stephen W", "initials": "SW"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Sebat", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9087-526X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd6f99b76b62434e9deccbf84cb30d53.json"}}, {"family": "CNV and Schizophrenia Working Groups of the Psychiatric Genomics Consortium", "given": "", "initials": ""}], "type": "comparative study", "published": "2017-01-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "1", "pages": "27-35", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Copy number variants (CNVs) have been strongly implicated in the genetic etiology of schizophrenia (SCZ). However, genome-wide investigation of the contribution of CNV to risk has been hampered by limited sample sizes. We sought to address this obstacle by applying a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. A global enrichment of CNV burden was observed in cases (odds ratio (OR) = 1.11, P = 5.7 \u00d7 10 -15), which persisted after excluding loci implicated in previous studies (OR = 1.07, P = 1.7 \u00d7 10-6). CNV burden was enriched for genes associated with synaptic function (OR = 1.68, P = 2.8 \u00d7 10-11) and neurobehavioral phenotypes in mouse (OR = 1.18, P = 7.3 \u00d7 10-5). Genome-wide significant evidence was obtained for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. Suggestive support was found for eight additional candidate susceptibility and protective loci, which consisted predominantly of CNVs mediated by nonallelic homologous recombination.", "doi": "10.1038/ng.3725", "pmid": "27869829", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3725"}, {"db": "pmc", "key": "PMC5737772"}, {"db": "mid", "key": "NIHMS918949"}], "notes": [], "created": "2017-05-08T07:59:07.363Z", "modified": "2021-06-21T15:52:42.322Z"}, {"entity": "publication", "iuid": "32c370e02d384d7e896285e4a06530ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32c370e02d384d7e896285e4a06530ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32c370e02d384d7e896285e4a06530ad"}}, "title": "Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice.", "authors": [{"family": "Pauter", "given": "Anna M", "initials": "AM"}, {"family": "Trattner", "given": "Sofia", "initials": "S"}, {"family": "Gonzalez-Bengtsson", "given": "Amanda", "initials": "A"}, {"family": "Talamonti", "given": "Emanuela", "initials": "E"}, {"family": "Asadi", "given": "Abolfazl", "initials": "A"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Jacobsson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "58", "issn": "1539-7262", "issue": "1", "pages": "111-123", "title": "J. Lipid Res.", "issn-l": "0022-2275"}, "abstract": "The molecular details relevant to dietary supplementation of the omega-3 fatty acid DHA in mothers as well as in their offspring are not clear. The PUFA elongase, elongation of very long-chain fatty acid (ELOVL)2, is a critical enzyme in the formation of DHA in mammals. In order to address the question regarding the origin of DHA during perinatal life, we have used DHA-deficient Elovl2-ablated mice as a model system to analyze the maternal impact on the DHA level in their offspring of various genotypes. Elovl2(-/-) mothers maintained on control diet had significantly lower systemic levels of DHA compared with the Elovl2(+/-) and Elovl2(+/+) mothers. Dietary DHA administration during the pregnancy and lactation periods led to increased DHA accretion in maternal tissues and serum of all genotypes. The proportion of DHA in the liver and serum of the Elovl2(-/-) offspring was significantly lower than in the Elovl2(+/+) offspring. Remarkably, the DHA level in the Elovl2(+/-) offspring nursed by DHA-free-fed Elovl2(-/-) mothers was almost as high as in +/+ pups delivered by +/+ mothers, suggesting that endogenous synthesis in the offspring can compensate for maternal DHA deficiency. Maternal DHA supplementation had a strong impact on offspring hepatic gene expression, especially of the fatty acid transporter, Mfsd2a, suggesting a dynamic interplay between DHA synthesis and DHA uptake in the control of systemic levels in the offspring.", "doi": "10.1194/jlr.M070862", "pmid": "27864326", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jlr.M070862"}, {"db": "pmc", "key": "PMC5234714"}], "notes": [], "created": "2017-05-03T13:00:47.686Z", "modified": "2020-01-21T13:53:21.284Z"}, {"entity": "publication", "iuid": "33bd1e90ae2942cfb7f394e25b50819d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33bd1e90ae2942cfb7f394e25b50819d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33bd1e90ae2942cfb7f394e25b50819d"}}, "title": "Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.", "authors": [{"family": "Mendelson", "given": "Michael M", "initials": "MM"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Joehanes", "given": "Roby", "initials": "R"}, {"family": "Liu", "given": "Chunyu", "initials": "C"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Aslibekyan", "given": "Stella", "initials": "S"}, {"family": "Demerath", "given": "Ellen W", "initials": "EW"}, {"family": "Guan", "given": "Weihua", "initials": "W"}, {"family": "Zhi", "given": "Degui", "initials": "D"}, {"family": "Yao", "given": "Chen", "initials": "C"}, {"family": "Huan", "given": "Tianxiao", "initials": "T"}, {"family": "Willinger", "given": "Christine", "initials": "C"}, {"family": "Chen", "given": "Brian", "initials": "B"}, {"family": "Courchesne", "given": "Paul", "initials": "P"}, {"family": "Multhaup", "given": "Michael", "initials": "M"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Cohain", "given": "Ariella", "initials": "A"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Bressler", "given": "Jan", "initials": "J"}, {"family": "North", "given": "Kari", "initials": "K"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "McRae", "given": "Allan F", "initials": "AF"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Gibson", "given": "Jude", "initials": "J"}, {"family": "Redmond", "given": "Paul", "initials": "P"}, {"family": "Corley", "given": "Janie", "initials": "J"}, {"family": "Murphy", "given": "Lee", "initials": "L"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Kleinbrink", "given": "Erica", "initials": "E"}, {"family": "Lipovich", "given": "Leonard", "initials": "L"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Wray", "given": "Naomi R", "initials": "NR"}, {"family": "Krauss", "given": "Ronald M", "initials": "RM"}, {"family": "Fallin", "given": "Daniele", "initials": "D"}, {"family": "Feinberg", "given": "Andrew", "initials": "A"}, {"family": "Absher", "given": "Devin M", "initials": "DM"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Fox", "given": "Caroline", "initials": "C"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "14", "issn": "1549-1676", "issue": "1", "pages": "e1002215", "title": "PLoS Med.", "issn-l": "1549-1277"}, "abstract": "The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain.\n\nWe conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs that replicated across cohorts; BMI-related differential methylation was associated with concurrent changes in the expression of genes in lipid metabolism pathways. Genetic instrumental variable analysis of alterations in methylation at one of the 83 replicated CpGs, cg11024682 (intronic to sterol regulatory element binding transcription factor 1 [SREBF1]), demonstrated links to BMI, adiposity-related traits, and coronary artery disease. Independent genetic instruments for expression of SREBF1 supported the findings linking methylation to adiposity and cardiometabolic disease. Methylation at a substantial proportion (16 of 83) of the identified loci was found to be secondary to differences in BMI. However, the cross-sectional nature of the data limits definitive causal determination.\n\nWe present robust associations of BMI with differential DNA methylation at numerous loci in blood cells. BMI-related DNA methylation and gene expression provide mechanistic insights into the relationship between DNA methylation, obesity, and adiposity-related diseases.", "doi": "10.1371/journal.pmed.1002215", "pmid": "28095459", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PMEDICINE-D-16-00194"}, {"db": "pmc", "key": "PMC5240936"}], "notes": [], "created": "2017-10-25T15:54:14.632Z", "modified": "2024-01-16T13:48:48.807Z"}, {"entity": "publication", "iuid": "37442ab98d914bb1827ce6b803dae200", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37442ab98d914bb1827ce6b803dae200.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37442ab98d914bb1827ce6b803dae200"}}, "title": "A multi-step peptidolytic cascade for amino acid recovery in chloroplasts.", "authors": [{"family": "Teixeira", "given": "Pedro F", "initials": "PF", "orcid": "0000-0001-8638-7477", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b43730fe20b424db84f091333be7244.json"}}, {"family": "Kmiec", "given": "Beata", "initials": "B"}, {"family": "Branca", "given": "Rui M M", "initials": "RM"}, {"family": "Murcha", "given": "Monika W", "initials": "MW", "orcid": "0000-0002-3689-6158", "researcher": {"href": "https://publications.scilifelab.se/researcher/49b1e7e1fca74be090072ad2185c9827.json"}}, {"family": "Byzia", "given": "Anna", "initials": "A"}, {"family": "Ivanova", "given": "Aneta", "initials": "A"}, {"family": "Whelan", "given": "James", "initials": "J"}, {"family": "Drag", "given": "Marcin", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Glaser", "given": "Elzbieta", "initials": "E"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "13", "issn": "1552-4469", "issue": "1", "pages": "15-17", "title": "Nat. Chem. Biol.", "issn-l": "1552-4450"}, "abstract": "Plastids (including chloroplasts) are subcellular sites for a plethora of proteolytic reactions, required in functions ranging from protein biogenesis to quality control. Here we show that peptides generated from pre-protein maturation within chloroplasts of Arabidopsis thaliana are degraded to amino acids by a multi-step peptidolytic cascade consisting of oligopeptidases and aminopeptidases, effectively allowing the recovery of single amino acids within these organelles.", "doi": "10.1038/nchembio.2227", "pmid": "27820795", "labels": {"Clinical Proteomics Mass spectrometry": "Collaborative", "Global Proteomics and Proteogenomics": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "nchembio.2227"}], "notes": [], "created": "2017-05-03T12:59:39.078Z", "modified": "2025-10-17T13:03:19.180Z"}, {"entity": "publication", "iuid": "07224a0f92c44df3854986c75650daf3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07224a0f92c44df3854986c75650daf3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07224a0f92c44df3854986c75650daf3"}}, "title": "A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus.", "authors": [{"family": "M\u00e1rquez", "given": "Ana", "initials": "A"}, {"family": "Vidal-Bralo", "given": "Laura", "initials": "L"}, {"family": "Rodr\u00edguez-Rodr\u00edguez", "given": "Luis", "initials": "L"}, {"family": "Gonz\u00e1lez-Gay", "given": "Miguel A", "initials": "MA"}, {"family": "Balsa", "given": "Alejandro", "initials": "A"}, {"family": "Gonz\u00e1lez-\u00c1lvaro", "given": "Isidoro", "initials": "I"}, {"family": "Carreira", "given": "Patricia", "initials": "P"}, {"family": "Ortego-Centeno", "given": "Norberto", "initials": "N"}, {"family": "Ayala-Guti\u00e9rrez", "given": "Mar\u00eda M", "initials": "MM"}, {"family": "Garc\u00eda-Hern\u00e1ndez", "given": "Francisco Jos\u00e9", "initials": "FJ"}, {"family": "Gonz\u00e1lez-Escribano", "given": "M Francisca", "initials": "MF"}, {"family": "Sabio", "given": "Jos\u00e9 Mario", "initials": "JM"}, {"family": "Tolosa", "given": "Carles", "initials": "C"}, {"family": "Su\u00e1rez", "given": "Ana", "initials": "A"}, {"family": "Gonz\u00e1lez", "given": "Antonio", "initials": "A"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Worthington", "given": "Jane", "initials": "J"}, {"family": "Vyse", "given": "Timothy", "initials": "T"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}, {"family": "Mart\u00edn", "given": "Javier", "initials": "J"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "76", "issn": "1468-2060", "issue": "1", "pages": "286-294", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "During the last years, genome-wide association studies (GWASs) have identified a number of common genetic risk factors for rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). However, the genetic overlap between these two immune-mediated diseases has not been thoroughly examined so far. The aim of the present study was to identify additional risk loci shared between RA and SLE.\n\nWe performed a large-scale meta-analysis of GWAS data from RA (3911 cases and 4083 controls) and SLE (2237 cases and 6315 controls). The top-associated polymorphisms in the discovery phase were selected for replication in additional datasets comprising 13\u2005641 RA cases and 31\u2005921 controls and 1957 patients with SLE and 4588 controls.\n\nThe rs9603612 genetic variant, located nearby the COG6 gene, an established susceptibility locus for RA, reached genome-wide significance in the combined analysis including both discovery and replication sets (p value=2.95E-13). In silico expression quantitative trait locus analysis revealed that the associated polymorphism acts as a regulatory variant influencing COG6 expression. Moreover, protein-protein interaction and gene ontology enrichment analyses suggested the existence of overlap with specific biological processes, specially the type I interferon signalling pathway. Finally, genetic correlation and polygenic risk score analyses showed cross-phenotype associations between RA and SLE.\n\nIn conclusion, we have identified a new risk locus shared between RA and SLE through a meta-analysis including GWAS datasets of both diseases. This study represents the first comprehensive large-scale analysis on the genetic overlap between these two complex disorders.", "doi": "10.1136/annrheumdis-2016-209436", "pmid": "27193031", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2016-209436"}], "notes": [], "created": "2017-05-03T13:00:17.725Z", "modified": "2024-01-16T13:48:48.816Z"}, {"entity": "publication", "iuid": "7df99a6755c54531bdaad563d07835a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7df99a6755c54531bdaad563d07835a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7df99a6755c54531bdaad563d07835a6"}}, "title": "The 15N NMR chemical shift in the characterization of weak halogen bonding in solution", "authors": [{"family": "Hakkert", "given": "Sebastiaan B", "initials": "SB"}, {"family": "Gr\u00e4fenstein", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Erdelyi", "given": "Mate", "initials": "M"}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "203", "issn": "1359-6640", "issue": null, "pages": "333-346", "title": "Faraday Discuss.", "issn-l": null}, "abstract": null, "doi": "10.1039/c7fd00107j", "pmid": "28731100", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:52:27.689Z", "modified": "2025-10-17T13:04:00.107Z"}, {"entity": "publication", "iuid": "1d075a67a1794b31970012b079fe9f46", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d075a67a1794b31970012b079fe9f46.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d075a67a1794b31970012b079fe9f46"}}, "title": "Synthesis of phenanthridine spiropyrans and studies of their effects on G-quadruplex DNA", "authors": [{"family": "Livendahl", "given": "M", "initials": "M"}, {"family": "Jamroskovic", "given": "J", "initials": "J"}, {"family": "Hedenstr\u00f6m", "given": "M", "initials": "M"}, {"family": "G\u00f6rlich", "given": "T", "initials": "T"}, {"family": "Sabouri", "given": "N", "initials": "N"}, {"family": "Chorell", "given": "E", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "15", "issn": "1477-0539", "issue": "15", "pages": "3265-3275", "title": "Org. Biomol. Chem.", "issn-l": "1477-0520"}, "abstract": null, "doi": "10.1039/c7ob00300e", "pmid": "28349141", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:05:28.485Z", "modified": "2025-10-17T13:04:00.117Z"}, {"entity": "publication", "iuid": "0719d3f941c84308a223ca2bfb3343a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0719d3f941c84308a223ca2bfb3343a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0719d3f941c84308a223ca2bfb3343a0"}}, "title": "Lysozyme's lectin-like characteristics facilitates its immune defense function", "authors": [{"family": "Zhang", "given": "Ruiyan", "initials": "R"}, {"family": "Wu", "given": "Lisha", "initials": "L"}, {"family": "Eckert", "given": "Thomas", "initials": "T"}, {"family": "Burg-Roderfeld", "given": "Monika", "initials": "M"}, {"family": "Rojas-Macias", "given": "Miguel A", "initials": "MA"}, {"family": "L\u00fctteke", "given": "Thomas", "initials": "T"}, {"family": "Krylov", "given": "Vadim B", "initials": "VB"}, {"family": "Argunov", "given": "Dmitry A", "initials": "DA"}, {"family": "Datta", "given": "Aritreyee", "initials": "A"}, {"family": "Markart", "given": "Philipp", "initials": "P"}, {"family": "Guenther", "given": "Andreas", "initials": "A"}, {"family": "Norden", "given": "Bengt", "initials": "B"}, {"family": "Schauer", "given": "Roland", "initials": "R"}, {"family": "Bhunia", "given": "Anirban", "initials": "A"}, {"family": "Enani", "given": "Mushira Abdelaziz", "initials": "MA"}, {"family": "Billeter", "given": "Martin", "initials": "M"}, {"family": "Scheidig", "given": "Axel J", "initials": "AJ"}, {"family": "Nifantiev", "given": "Nikolay E", "initials": "NE"}, {"family": "Siebert", "given": "Hans Christian", "initials": "HC"}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "50", "issn": "0033-5835", "issue": null, "pages": null, "title": "Quart. Rev. Biophys.", "issn-l": null}, "abstract": null, "doi": "10.1017/s0033583517000075", "pmid": "29233221", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:52:27.202Z", "modified": "2025-10-17T13:04:00.134Z"}, {"entity": "publication", "iuid": "f2686424a22741ab9878c51370e438ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2686424a22741ab9878c51370e438ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2686424a22741ab9878c51370e438ea"}}, "title": "Low Rank Enhanced Matrix Recovery of Hybrid Time and Frequency Data in Fast Magnetic Resonance Spectroscopy", "authors": [{"family": "Lu", "given": "Hengfa", "initials": "H"}, {"family": "Zhang", "given": "Xinlin", "initials": "X"}, {"family": "Qiu", "given": "Tianyu", "initials": "T"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Ying", "given": "Jiaxi", "initials": "J"}, {"family": "Guo", "given": "Di", "initials": "D"}, {"family": "Chen", "given": "Zhong", "initials": "Z"}, {"family": "Qu", "given": "Xiaobo", "initials": "X"}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": null, "issn": "0018-9294", "issue": null, "pages": "1-1", "title": "IEEE Trans. Biomed. Eng.", "issn-l": null}, "abstract": null, "doi": "10.1109/tbme.2017.2719709", "pmid": "28682242", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:46:05.693Z", "modified": "2025-10-17T13:04:00.145Z"}, {"entity": "publication", "iuid": "fe30033c695f4ecb975524cdf7ebe58a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe30033c695f4ecb975524cdf7ebe58a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe30033c695f4ecb975524cdf7ebe58a"}}, "title": "Favored surface-limited oxidation of cellulose with Oxone\u00ae in water", "authors": [{"family": "Ruan", "given": "Chang Qing", "initials": "CQ"}, {"family": "Str\u00f8mme", "given": "Maria", "initials": "M"}, {"family": "Mihranyan", "given": "Albert", "initials": "A"}, {"family": "Lindh", "given": "Jonas", "initials": "J"}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "7", "issn": "2046-2069", "issue": "64", "pages": "40600-40607", "title": "RSC Adv.", "issn-l": "2046-2069"}, "abstract": null, "doi": "10.1039/c7ra06141b", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:46:06.870Z", "modified": "2025-10-17T13:04:00.162Z"}, {"entity": "publication", "iuid": "a30dbedd94c94e36a8ea47ce308374d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a30dbedd94c94e36a8ea47ce308374d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a30dbedd94c94e36a8ea47ce308374d4"}}, "title": "Differential Neuroprotective Effects of Interleukin-1 Receptor Antagonist on Spinal Cord Neurons after Excitotoxic Injury", "authors": [{"family": "Schizas", "given": "Nikos", "initials": "N"}, {"family": "Perry", "given": "Sharn", "initials": "S"}, {"family": "Andersson", "given": "Brittmarie", "initials": "B"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Kullander", "given": "Klas", "initials": "K"}, {"family": "Hailer", "given": "Nils P", "initials": "NP"}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "24", "issn": "1021-7401", "issue": "4-5", "pages": "220-230", "title": "Neuroimmunomodulation", "issn-l": null}, "abstract": null, "doi": "10.1159/000484607", "pmid": "29393213", "labels": {"BioImage Informatics": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-28T08:14:36.460Z", "modified": "2021-07-05T14:18:24.389Z"}, {"entity": "publication", "iuid": "9784434acb164d7f840bedaa69e012f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9784434acb164d7f840bedaa69e012f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9784434acb164d7f840bedaa69e012f1"}}, "title": "Decoding Gene Expression in 2D and 3D", "authors": [{"family": "Bombrun", "given": "Maxime", "initials": "M"}, {"family": "Ranefall", "given": "Petter", "initials": "P"}, {"family": "Lindblad", "given": "Joakim", "initials": "J"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Partel", "given": "Gabriele", "initials": "G"}, {"family": "Solorzano", "given": "Leslie", "initials": "L"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "book-chapter", "published": "2017-00-00", "journal": {"volume": null, "issn": "0302-9743", "issue": null, "pages": "257-268", "title": "Scandinavian Conference on Image Analysis 2017", "issn-l": null}, "abstract": null, "doi": "10.1007/978-3-319-59129-2_22", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-01T08:06:23.725Z", "modified": "2021-07-07T13:54:46.111Z"}, {"entity": "publication", "iuid": "d6c925f143764bd5817a614df1e58b1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6c925f143764bd5817a614df1e58b1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6c925f143764bd5817a614df1e58b1f"}}, "title": "Achieving enhanced ionic mobility in nanoporous silica by controlled surface interactions", "authors": [{"family": "Garaga", "given": "Mounesha Nagendrachar", "initials": "MN"}, {"family": "Aguilera", "given": "Luis", "initials": "L"}, {"family": "Yaghini", "given": "Negin", "initials": "N"}, {"family": "Matic", "given": "Aleksandar", "initials": "A"}, {"family": "Persson", "given": "Michael", "initials": "M"}, {"family": "Martinelli", "given": "Anna", "initials": "A"}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "19", "issn": "1463-9076", "issue": "8", "pages": "5727-5736", "title": "Phys. Chem. Chem. Phys.", "issn-l": "1463-9076"}, "abstract": null, "doi": "10.1039/c6cp07351d", "pmid": "27905602", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T11:01:05.257Z", "modified": "2025-10-17T13:04:00.172Z"}, {"entity": "publication", "iuid": "1b1c37e25c9d41df972527f70b414583", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b1c37e25c9d41df972527f70b414583.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b1c37e25c9d41df972527f70b414583"}}, "title": "A Fast Low Rank Hankel Matrix Factorization Reconstruction Method for Non-Uniformly Sampled Magnetic Resonance Spectroscopy", "authors": [{"family": "Guo", "given": "Di", "initials": "D"}, {"family": "Lu", "given": "Hengfa", "initials": "H"}, {"family": "Qu", "given": "Xiaobo", "initials": "X", "orcid": "0000-0002-8675-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0bbb61a58d4218ac29f5ec08ed3520.json"}}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "5", "issn": "2169-3536", "issue": null, "pages": "16033-16039", "title": "IEEE Access", "issn-l": "2169-3536"}, "abstract": null, "doi": "10.1109/access.2017.2731860", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T11:01:06.351Z", "modified": "2025-10-17T13:04:00.201Z"}, {"entity": "publication", "iuid": "37abbbed0f064fa1b4332cd280769e25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37abbbed0f064fa1b4332cd280769e25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37abbbed0f064fa1b4332cd280769e25"}}, "title": "124 CHANGES IN GENE EXPRESSION FOLLOWING EXPOSURE OF BOVINE ENDOMETRIAL EPITHELIAL CELLS (bEEC) TO ESCHERICHIA COLI LPS; THEIR POSSIBLE EFFECT ON IMPLANTATION", "authors": [{"family": "Guo", "given": "Y", "initials": "Y"}, {"family": "Jahmat", "given": "N", "initials": "N"}, {"family": "Van Shaik", "given": "T", "initials": "T"}, {"family": "Chanrot", "given": "M", "initials": "M"}, {"family": "Valarcher", "given": "J F", "initials": "JF"}, {"family": "Charpigny", "given": "G", "initials": "G"}, {"family": "Bongcam-Rudloff", "given": "E", "initials": "E"}, {"family": "Andersson", "given": "G", "initials": "G"}, {"family": "Humblot", "given": "P", "initials": "P"}], "type": "journal-article", "published": "2017-00-00", "journal": {"volume": "29", "issn": "1031-3613", "issue": "1", "pages": "170", "title": "Reprod. Fertil. Dev.", "issn-l": null}, "abstract": null, "doi": "10.1071/rdv29n1ab124", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:31:42.120Z", "modified": "2024-01-16T13:48:48.825Z"}]}