{"entity": "publications", "timestamp": "2026-06-15T15:06:42.596Z", "year": "2010", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publications/2010.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publications/2010"}}, "publications_count": 70, "full": true, "publications": [{"entity": "publication", "iuid": "8928699933514a0ba1cae17c3de6f9d9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8928699933514a0ba1cae17c3de6f9d9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8928699933514a0ba1cae17c3de6f9d9"}}, "title": "Paraneoplastic antigen Ma2 autoantibodies as specific blood biomarkers for detection of early recurrence of small intestine neuroendocrine tumors.", "authors": [{"family": "Cui", "given": "Tao", "initials": "T"}, {"family": "Hurtig", "given": "Monica", "initials": "M"}, {"family": "Elgue", "given": "Graciela", "initials": "G"}, {"family": "Li", "given": "Su-Chen", "initials": "SC"}, {"family": "Veronesi", "given": "Giulia", "initials": "G"}, {"family": "Essaghir", "given": "Ahmed", "initials": "A"}, {"family": "Demoulin", "given": "Jean-Baptiste", "initials": "JB"}, {"family": "Pelosi", "given": "Giuseppe", "initials": "G"}, {"family": "Alimohammadi", "given": "Mohammad", "initials": "M"}, {"family": "\u00d6berg", "given": "Kjell", "initials": "K"}, {"family": "Giandomenico", "given": "Valeria", "initials": "V"}], "type": "journal article", "published": "2010-12-30", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "5", "issue": "12", "pages": "e16010", "issn-l": "1932-6203"}, "abstract": "Small intestine neuroendocrine tumors (SI-NETs) belong to a rare group of cancers. Most patients have developed metastatic disease at the time of diagnosis, for which there is currently no cure. The delay in diagnosis is a major issue in the clinical management of the patients and new markers are urgently needed. We have previously identified paraneoplastic antigen Ma2 (PNMA2) as a novel SI-NET tissue biomarker. Therefore, we evaluated whether Ma2 autoantibodies detection in the blood stream is useful for the clinical diagnosis and recurrence of SI-NETs.\n\nA novel indirect ELISA was set up to detect Ma2 autoantibodies in blood samples of patients with SI-NET at different stages of disease. The analysis was extended to include typical and atypical lung carcinoids (TLC and ALC), to evaluate whether Ma2 autoantibodies in the blood stream become a general biomarker for NETs. In total, 124 blood samples of SI-NET patients at different stages of disease were included in the study. The novel Ma2 autoantibody ELISA showed high sensitivity, specificity and accuracy with ROC curve analysis underlying an area between 0.734 and 0.816. Ma2 autoantibodies in the blood from SI-NET patients were verified by western blot and sequential immunoprecipitation. Serum antibodies of patients stain Ma2 in the tumor tissue and neurons. We observed that SI-NET patients expressing Ma2 autoantibody levels below the cutoff had a longer progression and recurrence-free survival compared to those with higher titer. We also detected higher levels of Ma2 autoantibodies in blood samples from TLC and ALC patients than from healthy controls, as previously shown in small cell lung carcinoma samples.\n\nHere we show that high Ma2 autoantibody titer in the blood of SI-NET patients is a sensitive and specific biomarker, superior to chromogranin A (CgA) for the risk of recurrence after radical operation of these tumors.", "doi": "10.1371/journal.pone.0016010", "pmid": "21209860", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC3012732"}], "notes": [], "created": "2018-12-05T09:14:16.102Z", "modified": "2018-12-05T09:14:16.124Z"}, {"entity": "publication", "iuid": "52e371915b2a42b4a1c1b3c2908d50fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/52e371915b2a42b4a1c1b3c2908d50fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/52e371915b2a42b4a1c1b3c2908d50fb"}}, "title": "Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates", "authors": [{"family": "Globisch", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4526-5788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd75219d6894d6b851e202eaa40fc5f.json"}}, {"family": "M\u00fcnzel", "given": "Martin", "initials": "M"}, {"family": "M\u00fcller", "given": "Markus", "initials": "M"}, {"family": "Michalakis", "given": "Stylianos", "initials": "S"}, {"family": "Wagner", "given": "Mirko", "initials": "M"}, {"family": "Koch", "given": "Susanne", "initials": "S"}, {"family": "Br\u00fcckl", "given": "Tobias", "initials": "T"}, {"family": "Biel", "given": "Martin", "initials": "M"}, {"family": "Carell", "given": "Thomas", "initials": "T"}], "type": "journal-article", "published": "2010-12-23", "journal": {"volume": "5", "issn": "1932-6203", "issue": "12", "pages": "e15367", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "5-Hydroxymethylcytosine (hmC) was recently detected as the sixth base in mammalian tissue at so far controversial levels. The function of the modified base is currently unknown, but it is certain that the base is generated from 5-methylcytosine (mC). This fuels the hypothesis that it represents an intermediate of an active demethylation process, which could involve further oxidation of the hydroxymethyl group to a formyl or carboxyl group followed by either deformylation or decarboxylation. Here, we use an ultra-sensitive and accurate isotope based LC-MS method to precisely determine the levels of hmC in various mouse tissues and we searched for 5-formylcytosine (fC), 5-carboxylcytosine (caC), and 5-hydroxymethyluracil (hmU) as putative active demethylation intermediates. Our data suggest that an active oxidative mC demethylation pathway is unlikely to occur. Additionally, we show using HPLC-MS analysis and immunohistochemistry that hmC is present in all tissues and cell types with highest concentrations in neuronal cells of the CNS.", "doi": "10.1371/journal.pone.0015367", "pmid": "21203455", "labels": {"Daniel Globisch": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:30.839Z", "modified": "2022-11-07T11:30:57.268Z"}, {"entity": "publication", "iuid": "a12cffd777a54df0a475e65e56f4b4bc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a12cffd777a54df0a475e65e56f4b4bc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a12cffd777a54df0a475e65e56f4b4bc"}}, "title": "Non-toxic dry-coated nanosilver for plasmonic biosensors.", "authors": [{"family": "Sotiriou", "given": "Georgios A", "initials": "GA"}, {"family": "Sannomiya", "given": "Takumi", "initials": "T"}, {"family": "Teleki", "given": "Alexandra", "initials": "A"}, {"family": "Krumeich", "given": "Frank", "initials": "F"}, {"family": "V\u00f6r\u00f6s", "given": "Janos", "initials": "J"}, {"family": "Pratsinis", "given": "Sotiris E", "initials": "SE"}], "type": "journal article", "published": "2010-12-21", "journal": {"title": "Adv. Funct. Mater.", "issn": "1616-301X", "volume": "20", "issue": "24", "pages": "4250-4257", "issn-l": null}, "abstract": "The plasmonic properties of noble metals facilitate their use for in-vivo bio-applications such as targeted drug delivery and cancer cell therapy. Nanosilver is best suited for such applications as it has the lowest plasmonic losses among all such materials in the UV-visible spectrum. Its toxicity, however, can destroy surrounding healthy tissues and thus, hinders its safe use. Here, that toxicity against a model biological system ( Escherichia coli) is \"cured\" or blocked by coating nanosilver hermetically with a about 2 nm thin SiO2 layer in one-step by a scalable flame aerosol method followed by swirl injection of a silica precursor vapor (hexamethyldisiloxane) without reducing the plasmonic performance of the enclosed or encapsulated silver nanoparticles (20 - 40 nm in diameter as determined by X-ray diffraction and microscopy). This creates the opportunity to safely use powerful nanosilver for intracellular bio-applications. The label-free biosensing and surface bio-functionalization of these ready-to-use, non-toxic (benign) Ag nanoparticles is presented by measuring the adsorption of bovine serum albumin (BSA) in a model sensing experiment. Furthermore, the silica coating around nanosilver prevents its agglomeration or flocculation (as determined by thermal annealing, optical absorption spectroscopy and microscopy) and thus, enhances its biosensitivity, including bioimaging as determined by dark field illumination.", "doi": "10.1002/adfm.201000985", "pmid": "23730266", "labels": {"Alexandra Teleki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC3667503"}, {"db": "mid", "key": "EMS53032"}], "notes": [], "created": "2020-11-30T21:42:01.431Z", "modified": "2022-11-07T11:29:43.558Z"}, {"entity": "publication", "iuid": "01d68c44cf114a2e9d45bcef5676e2c5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/01d68c44cf114a2e9d45bcef5676e2c5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/01d68c44cf114a2e9d45bcef5676e2c5"}}, "title": "Defining the transcriptome and proteome in three functionally different human cell lines.", "authors": [{"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Matic", "given": "Ivan", "initials": "I"}, {"family": "Geiger", "given": "Tamar", "initials": "T"}, {"family": "Cox", "given": "Juergen", "initials": "J"}, {"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Mann", "given": "Matthias", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}], "type": "journal article", "published": "2010-12-21", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "6", "issue": null, "pages": "450", "issn-l": "1744-4292"}, "abstract": "An essential question in human biology is how cells and tissues differ in gene and protein expression and how these differences delineate specific biological function. Here, we have performed a global analysis of both mRNA and protein levels based on sequence-based transcriptome analysis (RNA-seq), SILAC-based mass spectrometry analysis and antibody-based confocal microscopy. The study was performed in three functionally different human cell lines and based on the global analysis, we estimated the fractions of mRNA and protein that are cell specific or expressed at similar/different levels in the cell lines. A highly ubiquitous RNA expression was found with >60% of the gene products detected in all cells. The changes of mRNA and protein levels in the cell lines using SILAC and RNA ratios show high correlations, even though the genome-wide dynamic range is substantially higher for the proteins as compared with the transcripts. Large general differences in abundance for proteins from various functional classes are observed and, in general, the cell-type specific proteins are low abundant and highly enriched for cell-surface proteins. Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins.", "doi": "10.1038/msb.2010.106", "pmid": "21179022", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "msb2010106"}, {"db": "pmc", "key": "PMC3018165"}], "notes": [], "created": "2018-12-05T08:27:03.720Z", "modified": "2018-12-05T08:27:03.738Z"}, {"entity": "publication", "iuid": "5d904b4ae89f40f5900471cd675d7b7f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5d904b4ae89f40f5900471cd675d7b7f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5d904b4ae89f40f5900471cd675d7b7f"}}, "title": "Efficient Synthesis of 5-Hydroxymethylcytosine Containing DNA", "authors": [{"family": "Mu\u0308nzel", "given": "Martin", "initials": "M"}, {"family": "Globisch", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4526-5788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd75219d6894d6b851e202eaa40fc5f.json"}}, {"family": "Trindler", "given": "Christian", "initials": "C"}, {"family": "Carell", "given": "Thomas", "initials": "T"}], "type": "journal-article", "published": "2010-12-17", "journal": {"volume": "12", "issn": "1523-7060", "issue": "24", "pages": "5671-5673", "title": "Org. Lett.", "issn-l": "1523-7052"}, "abstract": "5-Hydroxymethylcytosine ((5-HOMe)dC) was recently discovered as the sixth base in the mammalian genome. The development of a new phosphoramidite building block is reported, which allows efficient synthesis of (5-HOMe)dC containing DNA. Key steps of the synthesis are a palladium-catalyzed formylation and the simultaneous protection of a hydroxyl and amino group as a cyclic carbamate. DNA synthesis is possible under standard conditions, and deprotection can be carried out with dilute NaOH.", "doi": "10.1021/ol102408t", "pmid": "21082782", "labels": {"Daniel Globisch": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:27.451Z", "modified": "2022-11-07T11:30:57.281Z"}, {"entity": "publication", "iuid": "c038949a42d94397ab9e718ef3701028", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c038949a42d94397ab9e718ef3701028.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c038949a42d94397ab9e718ef3701028"}}, "title": "The SNAP25 gene is linked to working memory capacity and maturation of the posterior cingulate cortex during childhood.", "authors": [{"family": "S\u00f6derqvist", "given": "Stina", "initials": "S"}, {"family": "McNab", "given": "Fiona", "initials": "F"}, {"family": "Peyrard-Janvid", "given": "Myriam", "initials": "M"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Humphreys", "given": "Keith", "initials": "K"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}], "type": "journal article", "published": "2010-12-15", "journal": {"title": "Biol. Psychiatry", "issn": "1873-2402", "volume": "68", "issue": "12", "pages": "1120-1125", "issn-l": "0006-3223"}, "abstract": "Working memory (WM) is the ability to retain task relevant information. This ability is important for a wide range of cognitive tasks, and WM deficits are a central cognitive impairment in neurodevelopment disorders such as attention-deficit/hyperactivity disorder (ADHD). Although WM capacity is known to be highly heritable, most genes involved remain unidentified.\n\nSingle nucleotide polymorphisms in genes previously associated with cognitive functions or ADHD were selected for genotyping. Associations of these with WM tasks were investigated in a community sample of 330 children and young adults. One single nucleotide polymorphisms was also investigated in an independent sample of 88 4-year-old children. Furthermore, association between brain structure and activity, as measured by magnetic resonance imaging techniques, and single nucleotide polymorphisms alleles were estimated in 88 participants.\n\nGenotype at rs363039, located in the gene coding for synaptosomal-associated protein, 25 kDa (SNAP25) was associated to WM capacity in both samples. Associations in the community sample were also found with measures of other cognitive functions. In addition, this polymorphism affected the gray matter and brain activity in the posterior cingulate cortex, an area included in the so-called default mode network previously correlated to regulation of attention and hypothesized to be implicated in ADHD.\n\nA novel gene-brain-behavior network was identified in which a genotype located in SNAP25 affects WM and has age-dependent effects on both brain structure and brain activity. Identifying such networks could be a key to better understanding cognitive development as well as some of its disorders.", "doi": "10.1016/j.biopsych.2010.07.036", "pmid": "20950795", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S0006-3223(10)00885-1"}], "notes": [], "created": "2018-12-05T09:02:35.200Z", "modified": "2018-12-05T09:02:35.220Z"}, {"entity": "publication", "iuid": "65a0c50e177143e4981e77ee9cff5bee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/65a0c50e177143e4981e77ee9cff5bee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/65a0c50e177143e4981e77ee9cff5bee"}}, "title": "Analysis of transcript and protein overlap in a human osteosarcoma cell line.", "authors": [{"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2010-12-02", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "11", "issue": null, "pages": "684", "issn-l": "1471-2164"}, "abstract": "An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF).\n\nA large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies.\n\nThis suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.", "doi": "10.1186/1471-2164-11-684", "pmid": "21126332", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-684"}, {"db": "pmc", "key": "PMC3014981"}], "notes": [], "created": "2018-12-05T10:22:09.857Z", "modified": "2018-12-05T10:22:09.875Z"}, {"entity": "publication", "iuid": "938f321612b244bba5558b3cc5463cda", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/938f321612b244bba5558b3cc5463cda.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/938f321612b244bba5558b3cc5463cda"}}, "title": "RNAs actively cycle on the Sm-like protein Hfq.", "authors": [{"family": "Fender", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Elf", "given": "Johan", "initials": "J"}, {"family": "Hampel", "given": "Kornelia", "initials": "K"}, {"family": "Zimmermann", "given": "Bastian", "initials": "B"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EG"}], "type": "journal article", "published": "2010-12-01", "journal": {"title": "Genes Dev.", "issn": "1549-5477", "volume": "24", "issue": "23", "pages": "2621-2626", "issn-l": "0890-9369"}, "abstract": "Hfq, a protein required for small RNA (sRNA)-mediated regulation in bacteria, binds RNA with low-nanomolar K(d) values and long half-lives of complexes (>100 min). This cannot be reconciled with the 1- 2-min response time of regulation in vivo. We show that RNAs displace each other on Hfq on a short time scale by RNA concentration-driven (active) cycling. Already at submicromolar concentrations of competitor RNA, half-lives of RNA-Hfq complexes are \u22481 min. We propose that competitor RNA associates transiently with RNA-Hfq complexes, RNAs exchange binding sites, and one of the RNAs eventually dissociates. This solves the \"strong binding-high turnover\" paradox and permits efficient use of the Hfq pool.", "doi": "10.1101/gad.591310", "pmid": "21123649", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "24/23/2621"}, {"db": "pmc", "key": "PMC2994036"}], "notes": [], "created": "2018-12-05T08:38:24.562Z", "modified": "2018-12-05T08:38:24.595Z"}, {"entity": "publication", "iuid": "9aee955361384e5c99b20a18dc896095", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9aee955361384e5c99b20a18dc896095.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9aee955361384e5c99b20a18dc896095"}}, "title": "A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.", "authors": [{"family": "Willing", "given": "Ben P", "initials": "BP"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lucio", "given": "Marianna", "initials": "M"}, {"family": "Zheng", "given": "Zongli", "initials": "Z"}, {"family": "J\u00e4rnerot", "given": "Gunnar", "initials": "G"}, {"family": "Tysk", "given": "Curt", "initials": "C"}, {"family": "Jansson", "given": "Janet K", "initials": "JK"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2010-12-00", "journal": {"title": "Gastroenterology", "issn": "1528-0012", "volume": "139", "issue": "6", "pages": "1844-1854.e1", "issn-l": "0016-5085"}, "abstract": "The composition of the gastrointestinal microbiota is thought to have an important role in the etiology of inflammatory bowel diseases (IBDs) such as Crohn's disease (CD) and ulcerative colitis (UC). Interindividual variation and an inability to detect less abundant bacteria have made it difficult to correlate specific bacteria with disease.\n\nWe used 454 pyrotag sequencing to determine the compositions of microbial communities in feces samples collected from a cohort of 40 twin pairs who were concordant or discordant for CD or UC, and in mucosal samples from a subset of the cohort. The cohort primarily comprised patients who were in remission, but also some with active disease.\n\nThe profiles of the microbial community differed with disease phenotypes; relative amounts of bacterial populations correlated with IBD phenotypes. The microbial compositions of individuals with CD differed from those of healthy individuals, but were similar between healthy individuals and individuals with UC. Profiles from individuals with CD that predominantly involved the ileum differed from those with CD that predominantly involved the colon; several bacterial populations increased or decreased with disease type. Changes specific to patients with ileal CD included the disappearance of core bacteria, such as Faecalibacterium and Roseburia, and increased amounts of Enterobacteriaceae and Ruminococcus gnavus.\n\nBacterial populations differ in abundance among individuals with different phenotypes of CD. Specific species of bacteria are associated with ileal CD; further studies should investigate their role in pathogenesis.", "doi": "10.1053/j.gastro.2010.08.049", "pmid": "20816835", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S0016-5085(10)01299-0"}], "notes": [], "created": "2018-12-05T08:19:33.980Z", "modified": "2018-12-05T08:19:34.010Z"}, {"entity": "publication", "iuid": "752cf824c79244dea2d2c301a275ddfd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/752cf824c79244dea2d2c301a275ddfd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/752cf824c79244dea2d2c301a275ddfd"}}, "title": "High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5.", "authors": [{"family": "Ching", "given": "Yung-Hao", "initials": "YH"}, {"family": "Munroe", "given": "Robert J", "initials": "RJ"}, {"family": "Moran", "given": "Jennifer L", "initials": "JL"}, {"family": "Barker", "given": "Anna K", "initials": "AK"}, {"family": "Mauceli", "given": "Evan", "initials": "E"}, {"family": "Fennell", "given": "Tim", "initials": "T"}, {"family": "Dipalma", "given": "Frederica", "initials": "F"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Abcunas", "given": "Lindsay M", "initials": "LM"}, {"family": "Gilmour", "given": "Joyanna F", "initials": "JF"}, {"family": "Harris", "given": "Tanya P", "initials": "TP"}, {"family": "Kloet", "given": "Susan L", "initials": "SL"}, {"family": "Luo", "given": "Yunhai", "initials": "Y"}, {"family": "McElwee", "given": "John L", "initials": "JL"}, {"family": "Mu", "given": "Weipeng", "initials": "W"}, {"family": "Park", "given": "Hyo K", "initials": "HK"}, {"family": "Rogal", "given": "David L", "initials": "DL"}, {"family": "Schimenti", "given": "Kerry J", "initials": "KJ"}, {"family": "Shen", "given": "Lishuang", "initials": "L"}, {"family": "Shindo", "given": "Mami", "initials": "M"}, {"family": "Shou", "given": "James Y", "initials": "JY"}, {"family": "Stenson", "given": "Erin K", "initials": "EK"}, {"family": "Stover", "given": "Patrick J", "initials": "PJ"}, {"family": "Schimenti", "given": "John C", "initials": "JC"}], "type": "journal article", "published": "2010-11-30", "journal": {"title": "BMC Genet.", "issn": "1471-2156", "volume": "11", "issue": null, "pages": "106", "issn-l": "1471-2156"}, "abstract": "Forward genetic screens in mice provide an unbiased means to identify genes and other functional genetic elements in the genome. Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a ~50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals.\n\nWe report the high resolution genetic mapping, complementation analyses, and positional cloning of mutations in the target region. The collection of identified alleles include several with known or presumed functions for which no mutant models have been reported (Tbc1d14, Nol14, Tyms, Cad, Fbxl5, Haus3), and mutations in genes we or others previously reported (Tapt1, Rest, Ugdh, Paxip1, Hmx1, Otoe, Nsun7). We also confirmed the causative nature of a homeotic mutation with a targeted allele, mapped a lethal mutation to a large gene desert, and localized a spermiogenesis mutation to a region in which no annotated genes have coding mutations. The mutation in Tbc1d14 provides the first implication of a critical developmental role for RAB-GAP-mediated protein transport in early embryogenesis.\n\nThis collection of alleles contributes to the goal of assigning biological functions to all known genes, as well as identifying novel functional elements that would be missed by reverse genetic approaches.", "doi": "10.1186/1471-2156-11-106", "pmid": "21118569", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "1471-2156-11-106"}, {"db": "pmc", "key": "PMC3009607"}], "notes": [], "created": "2018-12-05T10:08:55.473Z", "modified": "2018-12-05T10:08:55.491Z"}, {"entity": "publication", "iuid": "3d3d3dd48ba34bd9b3b6534c14ffe2e1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d3d3dd48ba34bd9b3b6534c14ffe2e1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d3d3dd48ba34bd9b3b6534c14ffe2e1"}}, "title": "Stochastic reaction-diffusion kinetics in the microscopic limit.", "authors": [{"family": "Fange", "given": "David", "initials": "D"}, {"family": "Berg", "given": "Otto G", "initials": "OG"}, {"family": "Sj\u00f6berg", "given": "Paul", "initials": "P"}, {"family": "Elf", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2010-11-16", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "107", "issue": "46", "pages": "19820-19825", "issn-l": "0027-8424"}, "abstract": "Quantitative analysis of biochemical networks often requires consideration of both spatial and stochastic aspects of chemical processes. Despite significant progress in the field, it is still computationally prohibitive to simulate systems involving many reactants or complex geometries using a microscopic framework that includes the finest length and time scales of diffusion-limited molecular interactions. For this reason, spatially or temporally discretized simulations schemes are commonly used when modeling intracellular reaction networks. The challenge in defining such coarse-grained models is to calculate the correct probabilities of reaction given the microscopic parameters and the uncertainty in the molecular positions introduced by the spatial or temporal discretization. In this paper we have solved this problem for the spatially discretized Reaction-Diffusion Master Equation; this enables a seamless and physically consistent transition from the microscopic to the macroscopic frameworks of reaction-diffusion kinetics. We exemplify the use of the methods by showing that a phosphorylation-dephosphorylation motif, commonly observed in eukaryotic signaling pathways, is predicted to display fluctuations that depend on the geometry of the system.", "doi": "10.1073/pnas.1006565107", "pmid": "21041672", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "1006565107"}, {"db": "pmc", "key": "PMC2993376"}], "notes": [], "created": "2018-12-05T08:45:33.143Z", "modified": "2018-12-05T08:45:33.163Z"}, {"entity": "publication", "iuid": "77bece0890534055bffdd5e655d84af5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/77bece0890534055bffdd5e655d84af5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/77bece0890534055bffdd5e655d84af5"}}, "title": "A Complete Set of Nascent Transcription Rates for Yeast Genes", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal-article", "published": "2010-11-16", "journal": {"volume": "5", "issn": "1932-6203", "issue": "11", "pages": "e15442", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) and the RNA pol ChIP-on-chip methods we generated a new, more accurate nascent transcription rate dataset. By comparing this dataset with the indirect ones obtained from the mRNA stabilities and mRNA amount datasets, we are able to obtain biological information about posttranscriptional regulation processes and a genomic snapshot of the location of the active transcriptional machinery. We have obtained nascent transcription rates for 4,670 yeast genes. The median RNA polymerase II density in the genes is 0.078 molecules/kb, which corresponds to an average of 0.096 molecules/gene. Most genes have transcription rates of between 2 and 30 mRNAs/hour and less than 1% of yeast genes have >1 RNA polymerase molecule/gene. Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell.", "doi": "10.1371/journal.pone.0015442", "pmid": "21103382", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:20.719Z", "modified": "2022-11-07T11:38:35.250Z"}, {"entity": "publication", "iuid": "5d15ca6865b04500a8a52447bbceaf2c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5d15ca6865b04500a8a52447bbceaf2c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5d15ca6865b04500a8a52447bbceaf2c"}}, "title": "A Novel Synthetic Route for the Anti-HIV Drug MC-1220 and its Analogues", "authors": [{"family": "Loksha", "given": "Yasser M", "initials": "YM"}, {"family": "Globisch", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4526-5788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd75219d6894d6b851e202eaa40fc5f.json"}}, {"family": "Loddo", "given": "Roberta", "initials": "R"}, {"family": "Collu", "given": "Gabriella", "initials": "G"}, {"family": "La\u2005Colla", "given": "Paolo", "initials": "P"}, {"family": "Pedersen", "given": "Erik B", "initials": "EB"}], "type": "journal-article", "published": "2010-11-08", "journal": {"volume": "5", "issn": "1860-7179", "issue": "11", "pages": "1847-1849", "title": "ChemMedChem", "issn-l": null}, "abstract": null, "doi": "10.1002/cmdc.201000244", "pmid": "20715285", "labels": {"Daniel Globisch": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:24.105Z", "modified": "2022-11-07T11:30:57.293Z"}, {"entity": "publication", "iuid": "98c8a2d52d244f4c8d3c08ca5baa5ff7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/98c8a2d52d244f4c8d3c08ca5baa5ff7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/98c8a2d52d244f4c8d3c08ca5baa5ff7"}}, "title": "Heat shock transcription factor 1 localizes to sex chromatin during meiotic repression.", "authors": [{"family": "Akerfelt", "given": "Malin", "initials": "M"}, {"family": "Vihervaara", "given": "Anniina", "initials": "A"}, {"family": "Laiho", "given": "Asta", "initials": "A"}, {"family": "Conter", "given": "Annie", "initials": "A"}, {"family": "Christians", "given": "Elisabeth S", "initials": "ES"}, {"family": "Sistonen", "given": "Lea", "initials": "L"}, {"family": "Henriksson", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2010-11-05", "journal": {"title": "J Biol Chem", "issn": "1083-351X", "volume": "285", "issue": "45", "pages": "34469-34476", "issn-l": "0021-9258"}, "abstract": "Heat shock factor 1 (HSF1) is an important transcription factor in cellular stress responses, cancer, aging, and developmental processes including gametogenesis. Disruption of Hsf1, together with another HSF family member, Hsf2, causes male sterility and complete lack of mature sperm in mice, but the specific role of HSF1 in spermatogenesis has remained unclear. Here, we show that HSF1 is transiently expressed in meiotic spermatocytes and haploid round spermatids in mouse testis. The Hsf1(-/-) male mice displayed regions of seminiferous tubules containing only spermatogonia and increased morphological abnormalities in sperm heads. In search for HSF1 target genes, we identified 742 putative promoters in mouse testis. Among them, the sex chromosomal multicopy genes that are expressed in postmeiotic cells were occupied by HSF1. Given that the sex chromatin mostly is repressed during and after meiosis, it is remarkable that HSF1 directly regulates the transcription of sex-linked multicopy genes during postmeiotic repression. In addition, our results show that HSF1 localizes to the sex body prior to the meiotic divisions and to the sex chromocenter after completed meiosis. To the best of our knowledge, HSF1 is the first known transcription factor found at the repressed sex chromatin during meiosis.", "doi": "10.1074/jbc.M110.157552", "pmid": "20802198", "labels": {"Anniina Vihervaara": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC2966061"}, {"db": "pii", "key": "S0021-9258(20)46987-X"}], "notes": [], "created": "2023-12-03T19:33:02.901Z", "modified": "2023-12-03T19:33:02.905Z"}, {"entity": "publication", "iuid": "d78df8b2977044edb81dac3692bfcae0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d78df8b2977044edb81dac3692bfcae0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d78df8b2977044edb81dac3692bfcae0"}}, "title": "Incorporation of Mg and Ca into nanostructured Fe2O3 improves Fe solubility in dilute acid and sensory characteristics in foods.", "authors": [{"family": "Hilty", "given": "Florentine M", "initials": "FM"}, {"family": "Knijnenburg", "given": "Jesper T N", "initials": "JT"}, {"family": "Teleki", "given": "Alexandra", "initials": "A"}, {"family": "Krumeich", "given": "Frank", "initials": "F"}, {"family": "Hurrell", "given": "Richard F", "initials": "RF"}, {"family": "Pratsinis", "given": "Sotiris E", "initials": "SE"}, {"family": "Zimmermann", "given": "Michael B", "initials": "MB"}], "type": "journal article", "published": "2010-11-04", "journal": {"title": "J Food Sci", "issn": "1750-3841", "volume": "76", "issue": "1", "pages": "N2-10", "issn-l": null}, "abstract": "Iron deficiency is one of the most common micronutrient deficiencies worldwide. Food fortification can be an effective and sustainable strategy to reduce Fe deficiency but selection of iron fortificants remains a challenge. Water-soluble compounds, for example, FeSO(4), usually demonstrate high bioavailability but they often cause unacceptable sensory changes in foods. On the other hand, poorly acid-soluble Fe compounds, for example FePO(4), may cause fewer adverse sensory changes in foods but are usually not well bioavailable since they need to be dissolved in the stomach prior to absorption. The solubility and the bioavailability of poorly acid-soluble Fe compounds can be improved by decreasing their primary particle size and thereby increasing their specific surface area. Here, Fe oxide-based nanostructured compounds with added Mg or Ca were produced by scalable flame aerosol technology. The compounds were characterized by nitrogen adsorption, X-ray diffraction, transmission electron microscopy, and Fe solubility in dilute acid. Sensory properties of the Fe-based compounds were tested in 2 highly reactive, polyphenol-rich food matrices: chocolate milk and fruit yoghurt. The Fe solubility of nanostructured Fe(2)O(3) doped with Mg or Ca was higher than that of pure Fe(2)O(3). Since good solubility in dilute acid was obtained despite the inhomogeneity of the powders, inexpensive precursors, for example Fe- and Ca-nitrates, can be used for their manufacture. Adding Mg or Ca lightened powder color, while sensory changes when added to foods were less pronounced than for FeSO(4). The combination of high Fe solubility and low reactivity in foods makes these flame-made nanostructured compounds promising for food fortification. Practical Application: The nanostructured iron-containing compounds presented here may prove useful for iron fortification of certain foods; they are highly soluble in dilute acid and likely to be well absorbed in the gut but cause less severe color changes than FeSO(4) when added to difficult-to-fortify foods.", "doi": "10.1111/j.1750-3841.2010.01885.x", "pmid": "21535701", "labels": {"Alexandra Teleki": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-30T21:41:45.245Z", "modified": "2022-11-07T11:29:43.570Z"}, {"entity": "publication", "iuid": "6a9be1e5d3024b00853844855e4fbead", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6a9be1e5d3024b00853844855e4fbead.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6a9be1e5d3024b00853844855e4fbead"}}, "title": "Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Langen", "given": "Hanno", "initials": "H"}, {"family": "Becker", "given": "Charlotte", "initials": "C"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}], "type": "evaluation studies", "published": "2010-11-00", "journal": {"title": "Mol. Cell Proteomics", "issn": "1535-9484", "volume": "9", "issue": "11", "pages": "2497-2507", "issn-l": "1535-9476"}, "abstract": "There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal altered protein profiles upon epitope retrieval at elevated temperatures with limits of detection improving into lower ng/ml ranges. In a study based on prostate cancer patients, several proteins with differential profiles were discovered and subsequently validated in an independent cohort. For one of the potential biomarkers, the human carnosine dipeptidase 1 protein (CNDP1), the differences were determined to be related to the glycosylation status of the targeted protein. The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format.", "doi": "10.1074/mcp.M110.001560", "pmid": "20682762", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "M110.001560"}, {"db": "pmc", "key": "PMC2984230"}], "notes": [], "created": "2018-12-05T09:04:20.845Z", "modified": "2018-12-05T09:04:20.866Z"}, {"entity": "publication", "iuid": "bd1ee41155054ef797605ad7f3a89932", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bd1ee41155054ef797605ad7f3a89932.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bd1ee41155054ef797605ad7f3a89932"}}, "title": "Synthesis of novel analogues of zanamivir as neuraminidase inhibitors", "authors": [{"family": "Xiong", "given": "Rui Sheng", "initials": "RS"}, {"family": "Zhao", "given": "Qing Jie", "initials": "QJ"}, {"family": "Zhu", "given": "Hang Hang", "initials": "HH"}, {"family": "Liu", "given": "Zheng", "initials": "Z"}, {"family": "Wei", "given": "Ya Bing", "initials": "YB"}, {"family": "Shen", "given": "Jing Shan", "initials": "JS"}], "type": "journal-article", "published": "2010-11-00", "journal": {"title": "Chinese Chemical Letters", "issn": "1001-8417", "volume": "21", "issue": "11", "pages": "1338-1341", "issn-l": null}, "abstract": null, "doi": "10.1016/j.cclet.2010.06.021", "pmid": null, "labels": {"Ruisheng Xiong": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2025-11-27T17:39:40.667Z", "modified": "2025-12-05T10:17:03.766Z"}, {"entity": "publication", "iuid": "3d3ec8e079b34942b2c32300f4c04a75", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d3ec8e079b34942b2c32300f4c04a75.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d3ec8e079b34942b2c32300f4c04a75"}}, "title": "Effect of Sensor Domain Mutations on the Properties of Voltage-Gated Ion Channels: Molecular Dynamics Studies of the Potassium Channel Kv1.2", "authors": [{"family": "Delemotte", "given": "Lucie", "initials": "L"}, {"family": "Treptow", "given": "Werner", "initials": "W"}, {"family": "Klein", "given": "Michael L", "initials": "ML"}, {"family": "Tarek", "given": "Mounir", "initials": "M"}], "type": "journal-article", "published": "2010-11-00", "journal": {"volume": "99", "issn": "0006-3495", "issue": "9", "pages": "L72-L74", "title": "Biophysical Journal", "issn-l": "0006-3495"}, "abstract": "The effects on the structural and functional properties of the Kv1.2 voltage-gated ion channel, caused by selective mutation of voltage sensor domain residues, have been investigated using classical molecular dynamics simulations. Following experiments that have identified mutations of voltage-gated ion channels involved in state-dependent omega currents, we observe for both the open and closed conformations of the Kv1.2 that specific mutations of S4 gating-charge residues destabilize the electrostatic network between helices of the voltage sensor domain, resulting in the formation of hydrophilic pathways linking the intra- and extracellular media. When such mutant channels are subject to transmembrane potentials, they conduct cations via these so-called \"omega pores.\" This study provides therefore further insight into the molecular mechanisms that lead to omega currents, which have been linked to certain channelopathies.", "doi": "10.1016/j.bpj.2010.08.069", "pmid": "21044565", "labels": {"Lucie Delemotte": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:13.845Z", "modified": "2022-11-07T11:34:52.729Z"}, {"entity": "publication", "iuid": "a537fc9df9af49218f99f41e65159399", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a537fc9df9af49218f99f41e65159399.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a537fc9df9af49218f99f41e65159399"}}, "title": "A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1.", "authors": [{"family": "Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2", "given": "", "initials": ""}, {"family": "Strange", "given": "Amy", "initials": "A"}, {"family": "Capon", "given": "Francesca", "initials": "F"}, {"family": "Spencer", "given": "Chris C A", "initials": "CC"}, {"family": "Knight", "given": "Jo", "initials": "J"}, {"family": "Weale", "given": "Michael E", "initials": "ME"}, {"family": "Allen", "given": "Michael H", "initials": "MH"}, {"family": "Barton", "given": "Anne", "initials": "A"}, {"family": "Band", "given": "Gavin", "initials": "G"}, {"family": "Bellenguez", "given": "C\u00e9line", "initials": "C"}, {"family": "Bergboer", "given": "Judith G M", "initials": "JG"}, {"family": "Blackwell", "given": "Jenefer M", "initials": "JM"}, {"family": "Bramon", "given": "Elvira", "initials": "E"}, {"family": "Bumpstead", "given": "Suzannah J", "initials": "SJ"}, {"family": "Casas", "given": "Juan P", "initials": "JP"}, {"family": "Cork", "given": "Michael J", "initials": "MJ"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Dilthey", "given": "Alexander", "initials": "A"}, {"family": "Duncanson", "given": "Audrey", "initials": "A"}, {"family": "Edkins", "given": "Sarah", "initials": "S"}, {"family": "Estivill", "given": "Xavier", "initials": "X"}, {"family": "Fitzgerald", "given": "Oliver", "initials": "O"}, {"family": "Freeman", "given": "Colin", "initials": "C"}, {"family": "Giardina", "given": "Emiliano", "initials": "E"}, {"family": "Gray", "given": "Emma", "initials": "E"}, {"family": "Hofer", "given": "Angelika", "initials": "A"}, {"family": "H\u00fcffmeier", "given": "Ulrike", "initials": "U"}, {"family": "Hunt", "given": "Sarah E", "initials": "SE"}, {"family": "Irvine", "given": "Alan D", "initials": "AD"}, {"family": "Jankowski", "given": "Janusz", "initials": "J"}, {"family": "Kirby", "given": "Brian", "initials": "B"}, {"family": "Langford", "given": "Cordelia", "initials": "C"}, {"family": "Lascorz", "given": "Jes\u00fas", "initials": "J"}, {"family": "Leman", "given": "Joyce", "initials": "J"}, {"family": "Leslie", "given": "Stephen", "initials": "S"}, {"family": "Mallbris", "given": "Lotus", "initials": "L"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Mathew", "given": "Christopher G", "initials": "CG"}, {"family": "McLean", "given": "W H Irwin", "initials": "WH"}, {"family": "McManus", "given": "Ross", "initials": "R"}, {"family": "M\u00f6ssner", "given": "Rotraut", "initials": "R"}, {"family": "Moutsianas", "given": "Loukas", "initials": "L"}, {"family": "Naluai", "given": "Asa T", "initials": "AT"}, {"family": "Nestle", "given": "Frank O", "initials": "FO"}, {"family": "Novelli", "given": "Giuseppe", "initials": "G"}, {"family": "Onoufriadis", "given": "Alexandros", "initials": "A"}, {"family": "Palmer", "given": "Colin N A", "initials": "CN"}, {"family": "Perricone", "given": "Carlo", "initials": "C"}, {"family": "Pirinen", "given": "Matti", "initials": "M"}, {"family": "Plomin", "given": "Robert", "initials": "R"}, {"family": "Potter", "given": "Simon C", "initials": "SC"}, {"family": "Pujol", "given": "Ramon M", "initials": "RM"}, {"family": "Rautanen", "given": "Anna", "initials": "A"}, {"family": "Riveira-Munoz", "given": "Eva", "initials": "E"}, {"family": "Ryan", "given": "Anthony W", "initials": "AW"}, {"family": "Salmhofer", "given": "Wolfgang", "initials": "W"}, {"family": "Samuelsson", "given": "Lena", "initials": "L"}, {"family": "Sawcer", "given": "Stephen J", "initials": "SJ"}, {"family": "Schalkwijk", "given": "Joost", "initials": "J"}, {"family": "Smith", "given": "Catherine H", "initials": "CH"}, {"family": "St\u00e5hle", "given": "Mona", "initials": "M"}, {"family": "Su", "given": "Zhan", "initials": "Z"}, {"family": "Tazi-Ahnini", "given": "Rachid", "initials": "R"}, {"family": "Traupe", "given": "Heiko", "initials": "H"}, {"family": "Viswanathan", "given": "Ananth C", "initials": "AC"}, {"family": "Warren", "given": "Richard B", "initials": "RB"}, {"family": "Weger", "given": "Wolfgang", "initials": "W"}, {"family": "Wolk", "given": "Katarina", "initials": "K"}, {"family": "Wood", "given": "Nicholas", "initials": "N"}, {"family": "Worthington", "given": "Jane", "initials": "J"}, {"family": "Young", "given": "Helen S", "initials": "HS"}, {"family": "Zeeuwen", "given": "Patrick L J M", "initials": "PL"}, {"family": "Hayday", "given": "Adrian", "initials": "A"}, {"family": "Burden", "given": "A David", "initials": "AD"}, {"family": "Griffiths", "given": "Christopher E M", "initials": "CE"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Reis", "given": "Andr\u00e9", "initials": "A"}, {"family": "McVean", "given": "Gilean", "initials": "G"}, {"family": "Evans", "given": "David M", "initials": "DM"}, {"family": "Brown", "given": "Matthew A", "initials": "MA"}, {"family": "Barker", "given": "Jonathan N", "initials": "JN"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Donnelly", "given": "Peter", "initials": "P"}, {"family": "Trembath", "given": "Richard C", "initials": "RC"}], "type": "journal article", "published": "2010-11-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "42", "issue": "11", "pages": "985-990", "issn-l": "1061-4036"}, "abstract": "To identify new susceptibility loci for psoriasis, we undertook a genome-wide association study of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls. We identified associations at eight previously unreported genomic loci. Seven loci harbored genes with recognized immune functions (IL28RA, REL, IFIH1, ERAP1, TRAF3IP2, NFKBIA and TYK2). These associations were replicated in 9,079 European samples (six loci with a combined P < 5 \u00d7 10\u207b\u2078 and two loci with a combined P < 5 \u00d7 10\u207b\u2077). We also report compelling evidence for an interaction between the HLA-C and ERAP1 loci (combined P = 6.95 \u00d7 10\u207b\u2076). ERAP1 plays an important role in MHC class I peptide processing. ERAP1 variants only influenced psoriasis susceptibility in individuals carrying the HLA-C risk allele. Our findings implicate pathways that integrate epidermal barrier dysfunction with innate and adaptive immune dysregulation in psoriasis pathogenesis.", "doi": "10.1038/ng.694", "pmid": "20953190", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "ng.694"}, {"db": "pmc", "key": "PMC3749730"}, {"db": "mid", "key": "EMS48359"}], "notes": [], "created": "2018-12-05T08:19:18.870Z", "modified": "2018-12-05T08:19:18.910Z"}, {"entity": "publication", "iuid": "90f448fd1676456abf75f0ae5e584889", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/90f448fd1676456abf75f0ae5e584889.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/90f448fd1676456abf75f0ae5e584889"}}, "title": "Far-Field Autofluorescence Nanoscopy", "authors": [{"family": "Bierwagen", "given": "Jakob", "initials": "J"}, {"family": "Testa", "given": "Ilaria", "initials": "I"}, {"family": "Fo\u0308lling", "given": "Jonas", "initials": "J"}, {"family": "Wenzel", "given": "Dirk", "initials": "D"}, {"family": "Jakobs", "given": "Stefan", "initials": "S"}, {"family": "Eggeling", "given": "Christian", "initials": "C"}, {"family": "Hell", "given": "Stefan W", "initials": "SW"}], "type": "journal-article", "published": "2010-10-13", "journal": {"volume": "10", "issn": "1530-6984", "issue": "10", "pages": "4249-4252", "title": "Nano Lett.", "issn-l": null}, "abstract": "We demonstrate far-field optical imaging at the nanoscale with unlabeled samples. Subdiffraction resolution images of autofluorescent samples are obtained by depleting the ground state of natural fluorophores by transferring them to a metastable dark state and simultaneously localizing those fluorophores that are transiently returning. Our approach is based on the insight that nanoscopy methods relying on stochastic single-molecule switching require only a single fluorescence on-off cycle to yield an image, a condition fulfilled by various biomolecules. The method is exemplified by recording label-free nanoscopy images of thylakoid membranes of spinach chloroplasts.", "doi": "10.1021/nl1027638", "pmid": "20831171", "labels": {"Ilaria Testa": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:03.736Z", "modified": "2022-11-07T11:32:31.691Z"}, {"entity": "publication", "iuid": "a8fa45d6bad3476c8cb30d963ea4ffd8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a8fa45d6bad3476c8cb30d963ea4ffd8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a8fa45d6bad3476c8cb30d963ea4ffd8"}}, "title": "Semiconductor gas sensors: dry synthesis and application.", "authors": [{"family": "Tricoli", "given": "Antonio", "initials": "A"}, {"family": "Righettoni", "given": "Marco", "initials": "M"}, {"family": "Teleki", "given": "Alexandra", "initials": "A"}], "type": "journal article", "published": "2010-10-11", "journal": {"title": "Angew. Chem. Int. Ed. Engl.", "issn": "1521-3773", "volume": "49", "issue": "42", "pages": "7632-7659", "issn-l": "1433-7851"}, "abstract": "Since the development of the first chemoresistive metal oxide based gas sensors, transducers with innovative properties have been prepared by a variety of wet- and dry-deposition methods. Among these, direct assembly of nanostructured films from the gas phase promises simple fabrication and control and with the appropriate synthesis and deposition methods nm to \u03bcm thick films, can be prepared. Dense structures are achieved by tuning chemical or vapor deposition methods whereas particulate films are obtained by deposition of airborne, mono- or polydisperse, aggregated or agglomerated nanoparticles. Innovative materials in non-equilibrium or sub-stoichiometric states are captured by rapid cooling during their synthesis. This Review presents some of the most common chemical and vapor-deposition methods for the synthesis of semiconductor metal oxide based detectors for chemical gas sensors. In addition, the synthesis of highly porous films by novel aerosol methods is discussed. A direct comparison of structural and chemical properties with sensing performance is given.", "doi": "10.1002/anie.200903801", "pmid": "20718055", "labels": {"Alexandra Teleki": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-30T21:42:09.354Z", "modified": "2022-11-07T11:29:43.583Z"}, {"entity": "publication", "iuid": "43383d3efa764ee9a8243db8b3c202f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/43383d3efa764ee9a8243db8b3c202f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/43383d3efa764ee9a8243db8b3c202f5"}}, "title": "Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate.", "authors": [{"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Ankarklev", "given": "Johan", "initials": "J"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Noh\u00fdnkov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Andersson", "given": "Jan O", "initials": "JO"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "comparative study", "published": "2010-10-07", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "11", "issue": null, "pages": "543", "issn-l": "1471-2164"}, "abstract": "Giardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the Giardia intestinalis species, we have performed genome sequencing and analysis of a wild-type Giardia intestinalis sample from the assemblage E group, isolated from a pig.\n\nWe identified 5012 protein coding genes, the majority of which are conserved compared to the previously sequenced genomes of the WB and GS strains in terms of microsynteny and sequence identity. Despite this, there is an unexpectedly large number of chromosomal rearrangements and several smaller structural changes that are present in all chromosomes. Novel members of the VSP, NEK Kinase and HCMP gene families were identified, which may reveal possible mechanisms for host specificity and new avenues for antigenic variation. We used comparative genomics of the three diverse Giardia intestinalis isolates P15, GS and WB to define a core proteome for this species complex and to identify lineage-specific genes. Extensive analyses of polymorphisms in the core proteome of Giardia revealed differential rates of divergence among cellular processes.\n\nOur results indicate that despite a well conserved core of genes there is significant genome variation between Giardia isolates, both in terms of gene content, gene polymorphisms, structural chromosomal variations and surface molecule repertoires. This study improves the annotation of the Giardia genomes and enables the identification of functionally important variation.", "doi": "10.1186/1471-2164-11-543", "pmid": "20929575", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-543"}, {"db": "pmc", "key": "PMC3091692"}], "notes": [], "created": "2018-12-05T08:45:52.729Z", "modified": "2018-12-05T08:45:52.747Z"}, {"entity": "publication", "iuid": "33958fdaba7a489b9d0204b8b59053ed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/33958fdaba7a489b9d0204b8b59053ed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/33958fdaba7a489b9d0204b8b59053ed"}}, "title": "Neuroticism-related personality traits are related to symptom severity in patients with premenstrual dysphoric disorder and to the serotonin transporter gene-linked polymorphism 5-HTTPLPR.", "authors": [{"family": "Gingnell", "given": "Malin", "initials": "M"}, {"family": "Comasco", "given": "Erika", "initials": "E"}, {"family": "Oreland", "given": "Lars", "initials": "L"}, {"family": "Fredrikson", "given": "Mats", "initials": "M"}, {"family": "Sundstr\u00f6m-Poromaa", "given": "Inger", "initials": "I"}], "type": "journal article", "published": "2010-10-00", "journal": {"title": "Arch Womens Ment Health", "issn": "1435-1102", "volume": "13", "issue": "5", "pages": "417-423", "issn-l": "1434-1816"}, "abstract": "Neuroticism has been linked to a functional polymorphism in the serotonin transporter gene (5-HTTLPR), with short-allele carriers being overrepresented among high-scorers on neuroticism. Studies evaluating neuroticism-related personality traits in relation to the 5-HTTLPR polymorphism among patients with premenstrual dysphoric disorder (PMDD) and are lacking. The primary aim of this study was to evaluate the relationship between PMDD and neuroticism-related personality traits, and secondly, to relate the personality trait scores of PMDD patients to experienced symptom severity and to the 5-HTTLPR short allele. Thirty PMDD patients and 55 asymptomatic healthy controls were included in the study. The Swedish Universities Scale of Personality was used to evaluate personality traits. Genotype analyses were available in 27 PMDD patients and 18 healthy controls. Women with PMDD displayed higher levels of neuroticism-related personality traits (psychic trait anxiety, somatic trait anxiety, embitterment, stress susceptibility and mistrust) than healthy controls, and these effects were most prominent in women with more severe luteal phase symptoms. Furthermore, PMDD patients with at least one copy of the short allele of the 5-HTTLPR polymorphism scored higher on psychic trait anxiety and lack of assertiveness than PMDD patients who were homozygous for the long allele. PMDD patients who suffer from more severe luteal phase symptoms also display increased scores of neuroticism-related personality traits in comparison with healthy controls. Within the group of PMDD patients, differences in certain personality trait scores are associated with the short allele of the 5-HTTLPR polymorphism.", "doi": "10.1007/s00737-010-0164-4", "pmid": "20440524", "labels": {"Erika Comasco": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC2941046"}], "notes": [], "created": "2020-11-20T09:31:27.762Z", "modified": "2024-10-24T08:56:53.342Z"}, {"entity": "publication", "iuid": "e5d6432b42d843648f1b384b4174992d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e5d6432b42d843648f1b384b4174992d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e5d6432b42d843648f1b384b4174992d"}}, "title": "Multicolor Fluorescence Nanoscopy in Fixed and Living Cells by Exciting Conventional Fluorophores with a Single Wavelength", "authors": [{"family": "Testa", "given": "Ilaria", "initials": "I"}, {"family": "Wurm", "given": "Christian A", "initials": "CA"}, {"family": "Medda", "given": "Rebecca", "initials": "R"}, {"family": "Rothermel", "given": "Ellen", "initials": "E"}, {"family": "von Middendorf", "given": "Claas", "initials": "C"}, {"family": "F\u00f6lling", "given": "Jonas", "initials": "J"}, {"family": "Jakobs", "given": "Stefan", "initials": "S"}, {"family": "Sch\u00f6nle", "given": "Andreas", "initials": "A"}, {"family": "Hell", "given": "Stefan W", "initials": "SW"}, {"family": "Eggeling", "given": "Christian", "initials": "C"}], "type": "journal-article", "published": "2010-10-00", "journal": {"volume": "99", "issn": "0006-3495", "issue": "8", "pages": "2686-2694", "title": "Biophysical Journal", "issn-l": "0006-3495"}, "abstract": "Current far-field fluorescence nanoscopes provide subdiffraction resolution by exploiting a mechanism of fluorescence inhibition. This mechanism is implemented such that features closer than the diffraction limit emit separately when simultaneously exposed to excitation light. A basic mechanism for such transient fluorescence inhibition is the depletion of the fluorophore ground state by transferring it (via a triplet) in a dark state, a mechanism which is workable in most standard dyes. Here we show that microscopy based on ground state depletion followed by individual molecule return (GSDIM) can effectively provide multicolor diffraction-unlimited resolution imaging of immunolabeled fixed and SNAP-tag labeled living cells. Implemented with standard labeling techniques, GSDIM is demonstrated to separate up to four different conventional fluorophores using just two detection channels and a single laser line. The method can be expanded to even more colors by choosing optimized dichroic mirrors and selecting marker molecules with negligible inhomogeneous emission broadening.", "doi": "10.1016/j.bpj.2010.08.012", "pmid": "20959110", "labels": {"Ilaria Testa": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:07.113Z", "modified": "2022-11-07T11:32:31.703Z"}, {"entity": "publication", "iuid": "a12aeef5e6c1452d81c42b0ee0e04800", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a12aeef5e6c1452d81c42b0ee0e04800.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a12aeef5e6c1452d81c42b0ee0e04800"}}, "title": "Clinical and experimental pancreatic islet transplantation to striated muscle: establishment of a vascular system similar to that in native islets.", "authors": [{"family": "Christoffersson", "given": "Gustaf", "initials": "G"}, {"family": "Henriksn\u00e4s", "given": "Johanna", "initials": "J"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Rolny", "given": "Charlotte", "initials": "C"}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H"}, {"family": "Caballero-Corbalan", "given": "Jos\u00e9", "initials": "J"}, {"family": "Segersv\u00e4rd", "given": "Ralf", "initials": "R"}, {"family": "Permert", "given": "Johan", "initials": "J"}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Carlsson", "given": "Per-Ola", "initials": "PO"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}], "type": "journal article", "published": "2010-10-00", "journal": {"title": "Diabetes", "issn": "0012-1797", "volume": "59", "issue": "10", "pages": "2569-2578", "issn-l": null}, "abstract": "Curing type 1 diabetes by transplanting pancreatic islets into the liver is associated with poor long-term outcome and graft failure at least partly due to inadequate graft revascularization. The aim of the current study was to evaluate striated muscle as a potential angiogenic site for islet transplantation.\n\nThe current study presents a new experimental model that is found to be applicable to clinical islet transplantation. Islets were implanted into striated muscle and intraislet vascular density and blood flow were visualized with intravital and confocal microscopy in mice and by magnetic resonance imaging in three autotransplanted pancreatectomized patients. Mice were rendered neutropenic by repeated injections of Gr-1 antibody, and diabetes was induced by alloxan treatment.\n\nContrary to liver-engrafted islets, islets transplanted to mouse muscle were revascularized with vessel densities and blood flow entirely comparable with those of islets within intact pancreas. Initiation of islet revascularization at the muscular site was dependent on neutrophils, and the function of islets transplanted to muscle was proven by curing diabetic mice. The experimental data were confirmed in autotransplanted patients where higher plasma volumes were measured in islets engrafted in forearm muscle compared with adjacent muscle tissue through high-resolution magnetic resonance imaging.\n\nThis study presents a novel paradigm in islet transplantation whereby recruited neutrophils are crucial for the functionally restored intraislet blood perfusion following transplantation to striated muscle under experimental and clinical situations.", "doi": "10.2337/db10-0205", "pmid": "20651296", "labels": {"Gustaf Christoffersson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "db10-0205"}, {"db": "pmc", "key": "PMC3279536"}], "notes": [], "created": "2020-11-04T09:45:19.678Z", "modified": "2022-11-07T11:32:18.582Z"}, {"entity": "publication", "iuid": "1371468bb99b4b939714862710c891d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1371468bb99b4b939714862710c891d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1371468bb99b4b939714862710c891d0"}}, "title": "Light entrained rhythmic gene expression in the sea anemone Nematostella vectensis: the evolution of the animal circadian clock.", "authors": [{"family": "Reitzel", "given": "Adam M", "initials": "AM"}, {"family": "Behrendt", "given": "Lars", "initials": "L"}, {"family": "Tarrant", "given": "Ann M", "initials": "AM"}], "type": "journal article", "published": "2010-09-21", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "5", "issue": "9", "pages": "e12805", "issn-l": "1932-6203"}, "abstract": "Circadian rhythms in behavior and physiology are the observable phenotypes from cycles in expression of, interactions between, and degradation of the underlying molecular components. In bilaterian animals, the core molecular components include Timeless-Timeout, photoreceptive cryptochromes, and several members of the basic-loop-helix-Per-ARNT-Sim (bHLH-PAS) family. While many of core circadian genes are conserved throughout the Bilateria, their specific roles vary among species. Here, we identify and experimentally study the rhythmic gene expression of conserved circadian clock members in a sea anemone in order to characterize this gene network in a member of the phylum Cnidaria and to infer critical components of the clockwork used in the last common ancestor of cnidarians and bilaterians.\n\nWe identified homologs of circadian regulatory genes in the sea anemone Nematostella vectensis, including a gene most similar to Timeout, three cryptochromes, and several key bHLH-PAS transcription factors. We then maintained N. vectensis either in complete darkness or in a 12 hour light: 12 hour dark cycle in three different light treatments (blue only, full spectrum, blue-depleted). Gene expression varied in response to light cycle and light treatment, with a particularly strong pattern observed for NvClock. The cryptochromes more closely related to the light-sensitive clade of cryptochromes were upregulated in light treatments that included blue wavelengths. With co-immunoprecipitation, we determined that heterodimerization between CLOCK and CYCLE is conserved within N. vectensis. Additionally, we identified E-box motifs, DNA sequences recognized by the CLOCK:CYCLE heterodimer, upstream of genes showing rhythmic expression.\n\nThis study reveals conserved molecular and functional components of the circadian clock that were in place at the divergence of the Cnidaria and Bilateria, suggesting the animal circadian clockwork is more ancient than previous data suggest. Characterizing circadian regulation in a cnidarian provides insight into the early origins of animal circadian rhythms and molecular regulation of environmentally cued behaviors.", "doi": "10.1371/journal.pone.0012805", "pmid": "20877728", "labels": {"SciLifeLab Fellow": null, "Lars Behrendt": null}, "xrefs": [{"db": "pmc", "key": "PMC2943474"}, {"db": "pii", "key": "e12805"}], "notes": [], "created": "2023-05-12T11:54:02.737Z", "modified": "2023-05-12T11:54:02.751Z"}, {"entity": "publication", "iuid": "2f780a21bc594197b90449fa90659787", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2f780a21bc594197b90449fa90659787.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2f780a21bc594197b90449fa90659787"}}, "title": "A chemotactic gradient sequestered on endothelial heparan sulfate induces directional intraluminal crawling of neutrophils.", "authors": [{"family": "Massena", "given": "Sara", "initials": "S"}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G"}, {"family": "Hjertstr\u00f6m", "given": "Elina", "initials": "E"}, {"family": "Zcharia", "given": "Eyal", "initials": "E"}, {"family": "Vlodavsky", "given": "Israel", "initials": "I"}, {"family": "Ausmees", "given": "Nora", "initials": "N"}, {"family": "Rolny", "given": "Charlotte", "initials": "C"}, {"family": "Li", "given": "Jin-Ping", "initials": "JP"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}], "type": "journal article", "published": "2010-09-16", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "116", "issue": "11", "pages": "1924-1931", "issn-l": "0006-4971"}, "abstract": "During infection, chemokines sequestered on endothelium induce recruitment of circulating leukocytes into the tissue where they chemotax along chemokine gradients toward the afflicted site. The aim of this in vivo study was to determine whether a chemokine gradient was formed intravascularly and influenced intraluminal neutrophil crawling and transmigration. A chemokine gradient was induced by placing a macrophage inflammatory protein-2 (MIP-2)-containing (CXCL2) gel on the cremaster muscle of anesthetized wild-type mice or heparanase-overexpressing transgenic mice (hpa-tg) with truncated heparan sulfate (HS) side chains. Neutrophil-endothelial interactions were visualized by intravital microscopy and chemokine gradients detected by confocal microscopy. Localized extravascular chemokine release (MIP-2 gel) induced directed neutrophil crawling along a chemotactic gradient immobilized on the endothelium and accelerated their recruitment into the target tissue compared with homogeneous extravascular chemokine concentration (MIP-2 superfusion). Endothelial chemokine sequestration occurred exclusively in venules and was HS-dependent, and neutrophils in hpa-tg mice exhibited random crawling. Despite similar numbers of adherent neutrophils in hpa-tg and wild-type mice, the altered crawling in hpa-tg mice was translated into decreased number of emigrated neutrophils and ultimately decreased the ability to clear bacterial infections. In conclusion, an intravascular chemokine gradient sequestered by endothelial HS effectively directs crawling leukocytes toward transmigration loci close to the infection site.", "doi": "10.1182/blood-2010-01-266072", "pmid": "20530797", "labels": {"Gustaf Christoffersson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "blood-2010-01-266072"}, {"db": "pmc", "key": "PMC3173988"}], "notes": [], "created": "2020-11-04T09:45:24.421Z", "modified": "2022-11-07T11:32:18.594Z"}, {"entity": "publication", "iuid": "3d92a22723be44629fbeb380b6fa2e0b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d92a22723be44629fbeb380b6fa2e0b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d92a22723be44629fbeb380b6fa2e0b"}}, "title": "Chk1 promotes replication fork progression by controlling replication initiation.", "authors": [{"family": "Petermann", "given": "Eva", "initials": "E"}, {"family": "Woodcock", "given": "Mick", "initials": "M"}, {"family": "Helleday", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2010-09-14", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "107", "issue": "37", "pages": "16090-16095", "issn-l": "0027-8424"}, "abstract": "DNA replication starts at initiation sites termed replication origins. Metazoan cells contain many more potential origins than are activated (fired) during each S phase. Origin activation is controlled by the ATR checkpoint kinase and its downstream effector kinase Chk1, which suppresses origin firing in response to replication blocks and during normal S phase by inhibiting the cyclin-dependent kinase Cdk2. In addition to increased origin activation, cells deficient in Chk1 activity display reduced rates of replication fork progression. Here we investigate the causal relationship between increased origin firing and reduced replication fork progression. We use the Cdk inhibitor roscovitine or RNAi depletion of Cdc7 to inhibit origin firing in Chk1-inhibited or RNAi-depleted cells. We report that Cdk inhibition and depletion of Cdc7 can alleviate the slow replication fork speeds in Chk1-deficient cells. Our data suggest that increased replication initiation leads to slow replication fork progression and that Chk1 promotes replication fork progression during normal S phase by controlling replication origin activity.", "doi": "10.1073/pnas.1005031107", "pmid": "20805465", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "1005031107"}, {"db": "pmc", "key": "PMC2941317"}], "notes": [], "created": "2018-12-05T08:34:59.222Z", "modified": "2018-12-05T08:34:59.241Z"}, {"entity": "publication", "iuid": "92df46cd26ba4d6b9836fe1b7ec90c02", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/92df46cd26ba4d6b9836fe1b7ec90c02.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/92df46cd26ba4d6b9836fe1b7ec90c02"}}, "title": "Lung cancer proteomics, clinical and technological considerations.", "authors": [{"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "De Petris", "given": "Luigi", "initials": "L"}], "type": "journal article", "published": "2010-09-10", "journal": {"title": "J Proteomics", "issn": "1876-7737", "volume": "73", "issue": "10", "pages": "1851-1863", "issn-l": "1874-3919"}, "abstract": "The overall survival of lung cancer patients is disappointingly low. This is due to several factors, including the lack of an effective screening strategy to detect tumors at a potentially curable early stage, a marked resistance of lung cancer cells to drug treatment and a still superficial knowledge about the multifactorial cellular networks that are activated or suppressed during cancer progression. Furthermore, the armamentarium of clinicians and researchers in the field does not yet include reliable biomarkers to predict tumor response to treatment and foresee the natural history of the disease. In the present situation, a potential breakthrough is presented by proteomics technologies with the potential to discover relevant biomarkers which can be accurately quantified in multiplexed assays. Proteomics field can also contribute greatly in the understanding of mechanisms in tumor progression and treatment response. In this review we will describe the work that is being done in the field of lung cancer proteomics, focusing on clinically relevant questions that need to be addressed and on the possible applications of novel technologies.", "doi": "10.1016/j.jprot.2010.05.015", "pmid": "20685322", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(10)00174-0"}], "notes": [], "created": "2018-12-05T09:14:19.814Z", "modified": "2018-12-05T09:14:19.833Z"}, {"entity": "publication", "iuid": "665cd7c18d7d4d169578d68059ed4957", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/665cd7c18d7d4d169578d68059ed4957.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/665cd7c18d7d4d169578d68059ed4957"}}, "title": "Substance graphs are optimal simple-graph representations of metabolism", "authors": [{"family": "Holme", "given": "Petter", "initials": "P"}, {"family": "Huss", "given": "Mikael", "initials": "M"}], "type": "journal-article", "published": "2010-09-00", "journal": {"title": "Chin. Sci. Bull.", "issn": "1001-6538", "volume": "55", "issue": "27-28", "pages": "3161-3168", "issn-l": null}, "abstract": null, "doi": "10.1007/s11434-010-4086-3", "pmid": null, "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T13:11:21.656Z", "modified": "2021-07-09T09:32:17.046Z"}, {"entity": "publication", "iuid": "03ad6c43f6694db29fe3d4e4fee773b3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/03ad6c43f6694db29fe3d4e4fee773b3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/03ad6c43f6694db29fe3d4e4fee773b3"}}, "title": "Introduction into the analysis of high-throughput-sequencing based epigenome data.", "authors": [{"family": "Huss", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2010-09-00", "journal": {"title": "Brief. Bioinformatics", "issn": "1477-4054", "volume": "11", "issue": "5", "pages": "512-523", "issn-l": "1467-5463"}, "abstract": "Sequencing-based approaches now allow high-resolution, genome-scale investigation of cellular epigenetic landscapes. For example, mapping of open chromatin regions, post-translational histone modifications and DNA methylation across a whole genome is now feasible, and new non-coding regulatory RNAs can be sensitively identified via RNA sequencing. The resulting large-scale data sets promise to contribute towards a more precise and complete understanding of gene regulation and to yield insights into the interplay between genomes and the environment. In this article, I review some of the conceptual issues and currently available software tools for the analysis of sequencing-based whole-genome epigenetics data.", "doi": "10.1093/bib/bbq014", "pmid": "20457755", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "bbq014"}], "notes": [], "created": "2018-12-05T10:01:20.105Z", "modified": "2018-12-05T10:01:20.123Z"}, {"entity": "publication", "iuid": "3d081d28787d49ceb53840e744c1d4b3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d081d28787d49ceb53840e744c1d4b3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d081d28787d49ceb53840e744c1d4b3"}}, "title": "Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres", "authors": [{"family": "Lewis", "given": "P W", "initials": "PW"}, {"family": "Elsaesser", "given": "S J", "initials": "SJ"}, {"family": "Noh", "given": "K M", "initials": "KM"}, {"family": "Stadler", "given": "S C", "initials": "SC"}, {"family": "Allis", "given": "C D", "initials": "CD"}], "type": "journal-article", "published": "2010-08-10", "journal": {"volume": "107", "issn": "0027-8424", "issue": "32", "pages": "14075-14080", "title": "Proceedings of the National Academy of Sciences", "issn-l": "0027-8424"}, "abstract": "The histone variant H3.3 is implicated in the formation and maintenance of specialized chromatin structure in metazoan cells. H3.3-containing nucleosomes are assembled in a replication-independent manner by means of dedicated chaperone proteins. We previously identified the death domain associated protein (Daxx) and the alpha-thalassemia X-linked mental retardation protein (ATRX) as H3.3-associated proteins. Here, we report that the highly conserved N terminus of Daxx interacts directly with variant-specific residues in the H3.3 core. Recombinant Daxx assembles H3.3/H4 tetramers on DNA templates, and the ATRX-Daxx complex catalyzes the deposition and remodeling of H3.3-containing nucleosomes. We find that the ATRX-Daxx complex is bound to telomeric chromatin, and that both components of this complex are required for H3.3 deposition at telomeres in murine embryonic stem cells (ESCs). These data demonstrate that Daxx functions as an H3.3-specific chaperone and facilitates the deposition of H3.3 at heterochromatin loci in the context of the ATRX-Daxx complex.", "doi": "10.1073/pnas.1008850107", "pmid": "20651253", "labels": {"Simon Els\u00e4sser": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:56.806Z", "modified": "2022-11-07T11:38:06.858Z"}, {"entity": "publication", "iuid": "aa43c646a6414ffe8c1cf56f80ba7402", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa43c646a6414ffe8c1cf56f80ba7402.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa43c646a6414ffe8c1cf56f80ba7402"}}, "title": "Genome-Wide Evidence for Efficient Positive and Purifying Selection in Capsella grandiflora, a Plant Species with a Large Effective Population Size", "authors": [{"family": "Slotte", "given": "T", "initials": "T"}, {"family": "Foxe", "given": "J P", "initials": "JP"}, {"family": "Hazzouri", "given": "K M", "initials": "KM"}, {"family": "Wright", "given": "S I", "initials": "SI"}], "type": "journal-article", "published": "2010-08-01", "journal": {"volume": "27", "issn": "0737-4038", "issue": "8", "pages": "1813-1821", "title": "Molecular Biology and Evolution", "issn-l": "0737-4038"}, "abstract": "Recent studies comparing genome-wide polymorphism and divergence in Drosophila have found evidence for a surprisingly high proportion of adaptive amino acid fixations, but results for other taxa are mixed. In particular, few studies have found convincing evidence for adaptive amino acid substitution in plants. To assess the generality of this finding, we have sequenced 257 loci in the outcrossing crucifer Capsella grandiflora, which has a large effective population size and low population structure. Using a new method that jointly infers selective and demographic effects, we estimate that 40% of amino acid substitutions were fixed by positive selection in this species, and we also infer a low proportion of slightly deleterious amino acid mutations. We contrast these estimates with those for a similar data set from the closely related Arabidopsis thaliana and find significantly higher rates of adaptive evolution and fewer nearly neutral mutations in C. grandiflora. In agreement with results for other taxa, genes involved in reproduction show the strongest evidence for positive selection in C. grandiflora. Taken together, these results imply that both positive and purifying selection are more effective in C. grandiflora than in A. thaliana, consistent with the contrasting demographic history and effective population sizes of these species.", "doi": "10.1093/molbev/msq062", "pmid": "20194429", "labels": {"Tanja Slotte": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:49.864Z", "modified": "2022-11-07T11:38:19.887Z"}, {"entity": "publication", "iuid": "ff2730a697d443b799be3b97a8f9faa2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ff2730a697d443b799be3b97a8f9faa2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ff2730a697d443b799be3b97a8f9faa2"}}, "title": "6-thioguanine selectively kills BRCA2-defective tumors and overcomes PARP inhibitor resistance.", "authors": [{"family": "Issaeva", "given": "Natalia", "initials": "N"}, {"family": "Thomas", "given": "Huw D", "initials": "HD"}, {"family": "Djureinovic", "given": "Tatjana", "initials": "T"}, {"family": "Djurenovic", "given": "Tatjana", "initials": "T"}, {"family": "Jaspers", "given": "Janneke E", "initials": "JE"}, {"family": "Stoimenov", "given": "Ivaylo", "initials": "I"}, {"family": "Kyle", "given": "Suzanne", "initials": "S"}, {"family": "Pedley", "given": "Nicholas", "initials": "N"}, {"family": "Gottipati", "given": "Ponnari", "initials": "P"}, {"family": "Zur", "given": "Rafal", "initials": "R"}, {"family": "Sleeth", "given": "Kate", "initials": "K"}, {"family": "Chatzakos", "given": "Vicky", "initials": "V"}, {"family": "Mulligan", "given": "Evan A", "initials": "EA"}, {"family": "Lundin", "given": "Cecilia", "initials": "C"}, {"family": "Gubanova", "given": "Evgenia", "initials": "E"}, {"family": "Kersbergen", "given": "Ariena", "initials": "A"}, {"family": "Harris", "given": "Adrian L", "initials": "AL"}, {"family": "Sharma", "given": "Ricky A", "initials": "RA"}, {"family": "Rottenberg", "given": "Sven", "initials": "S"}, {"family": "Curtin", "given": "Nicola J", "initials": "NJ"}, {"family": "Helleday", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2010-08-01", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "70", "issue": "15", "pages": "6268-6276", "issn-l": "0008-5472"}, "abstract": "Familial breast and ovarian cancers are often defective in homologous recombination (HR) due to mutations in the BRCA1 or BRCA2 genes. Cisplatin chemotherapy or poly(ADP-ribose) polymerase (PARP) inhibitors were tested for these tumors in clinical trials. In a screen for novel drugs that selectively kill BRCA2-defective cells, we identified 6-thioguanine (6TG), which induces DNA double-strand breaks (DSB) that are repaired by HR. Furthermore, we show that 6TG is as efficient as a PARP inhibitor in selectively killing BRCA2-defective tumors in a xenograft model. Spontaneous BRCA1-defective mammary tumors gain resistance to PARP inhibitors through increased P-glycoprotein expression. Here, we show that 6TG efficiently kills such BRCA1-defective PARP inhibitor-resistant tumors. We also show that 6TG could kill cells and tumors that have gained resistance to PARP inhibitors or cisplatin through genetic reversion of the BRCA2 gene. Although HR is reactivated in PARP inhibitor-resistant BRCA2-defective cells, it is not fully restored for the repair of 6TG-induced lesions. This is likely to be due to several recombinogenic lesions being formed after 6TG. We show that BRCA2 is also required for survival from mismatch repair-independent lesions formed by 6TG, which do not include DSBs. This suggests that HR is involved in the repair of 6TG-induced DSBs as well as mismatch repair-independent 6TG-induced DNA lesion. Altogether, our data show that 6TG efficiently kills BRCA2-defective tumors and suggest that 6TG may be effective in the treatment of advanced tumors that have developed resistance to PARP inhibitors or platinum-based chemotherapy.", "doi": "10.1158/0008-5472.CAN-09-3416", "pmid": "20631063", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-09-3416"}, {"db": "pmc", "key": "PMC2913123"}, {"db": "mid", "key": "UKMS31228"}], "notes": [], "created": "2018-12-05T08:51:24.464Z", "modified": "2018-12-05T08:51:24.483Z"}, {"entity": "publication", "iuid": "5a88f0c63cd94972a4ad9f89d91505c4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5a88f0c63cd94972a4ad9f89d91505c4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5a88f0c63cd94972a4ad9f89d91505c4"}}, "title": "Why do adolescents drink? Motivational patterns related to alcohol consumption and alcohol-related problems.", "authors": [{"family": "Comasco", "given": "Erika", "initials": "E"}, {"family": "Berglund", "given": "Kenneth", "initials": "K"}, {"family": "Oreland", "given": "Lars", "initials": "L"}, {"family": "Nilsson", "given": "Kent W", "initials": "KW"}], "type": "journal article", "published": "2010-08-00", "journal": {"title": "Subst Use Misuse", "issn": "1532-2491", "volume": "45", "issue": "10", "pages": "1589-1604", "issn-l": "1082-6084"}, "abstract": "The present study was designed to investigate motivational patterns for drinking alcohol and their relation about alcohol consumption and problems related to alcohol consumption. Data were collected by semistructured interviews and questionnaires, containing questions about reasons for drinking, alcohol consumption, and problems related to alcohol consumption during the years 2001, 2004, and 2005. Three independent population samples from two different counties of central Sweden were included. A total of 11,167 adolescents participated. Data on reasons for drinking were analyzed by factor analysis to extract components explaining drinking motives. Relationships between motivational patterns and alcohol use were examined with correlation analysis. Three drinking motives emerged (social-enhancement, coping, and dominance motives) and related to alcohol consumption and problems related to alcohol consumption. Limitations of the study are noted and discussed.", "doi": "10.3109/10826081003690159", "pmid": "20590377", "labels": {"Erika Comasco": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-20T09:31:26.527Z", "modified": "2024-10-24T08:56:52.272Z"}, {"entity": "publication", "iuid": "09d29e0e98594b0d8caef0a2d989d04a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09d29e0e98594b0d8caef0a2d989d04a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09d29e0e98594b0d8caef0a2d989d04a"}}, "title": "The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors", "authors": [{"family": "Rodr\u00edguez-Gil", "given": "Alfonso", "initials": "A"}, {"family": "Garc\u00eda-Mart\u00ednez", "given": "Jos\u00e9", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Mu\u00f1oz-Centeno", "given": "Mar\u00eda de la Cruz", "initials": "MdlC"}, {"family": "Geli", "given": "Vincent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}, {"family": "Ch\u00e1vez", "given": "Sebasti\u00e1n", "initials": "S"}], "type": "journal-article", "published": "2010-08-00", "journal": {"volume": "38", "issn": "1362-4962", "issue": "14", "pages": "4651-4664", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3'/5' RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in both cases. We detected a subset of elongation-related factors that are important for maintaining the wild-type profiles of active transcription, including DSIF, Mediator, factors related to the methylation of histone H3-lysine 4, the Bur CDK and the RNA polymerase II subunit Rpb9. We conducted a more detailed investigation of the alterations caused by rpb9Delta to find that Rpb9 contributes to the intragenic profiles of active transcription by influencing the probability of arrest of RNA polymerase II.", "doi": "10.1093/nar/gkq215", "pmid": "20385590", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:00.358Z", "modified": "2022-11-07T11:38:35.263Z"}, {"entity": "publication", "iuid": "b923bb427ba14e3f9125a8d10c03fc7b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b923bb427ba14e3f9125a8d10c03fc7b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b923bb427ba14e3f9125a8d10c03fc7b"}}, "title": "Many particle magnetic dipole\u2013dipole and hydrodynamic interactions in magnetizable stent assisted magnetic drug targeting", "authors": [{"family": "Cregg", "given": "P J", "initials": "PJ"}, {"family": "Murphy", "given": "Kieran", "initials": "K"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Prina-Mello", "given": "Adriele", "initials": "A"}], "type": "journal-article", "published": "2010-08-00", "journal": {"title": "Journal of Magnetism and Magnetic Materials", "issn": "0304-8853", "volume": "322", "issue": "15", "pages": "2087-2094", "issn-l": null}, "abstract": null, "doi": "10.1016/j.jmmm.2010.01.038", "pmid": null, "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:22.533Z", "modified": "2025-12-04T17:08:52.052Z"}, {"entity": "publication", "iuid": "08c163f2500e470da96ad64b04dbfba9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/08c163f2500e470da96ad64b04dbfba9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/08c163f2500e470da96ad64b04dbfba9"}}, "title": "Replication-biased genome organisation in the crenarchaeon Sulfolobus.", "authors": [{"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pelve", "given": "Erik A", "initials": "EA"}, {"family": "Lindeberg", "given": "Stefan", "initials": "S"}, {"family": "Lundgren", "given": "Magnus", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Bernander", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2010-07-28", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "11", "issue": null, "pages": "454", "issn-l": "1471-2164"}, "abstract": "Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication.\n\nWe demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements.\n\nThe strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.", "doi": "10.1186/1471-2164-11-454", "pmid": "20667100", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-454"}, {"db": "pmc", "key": "PMC3091651"}], "notes": [], "created": "2018-12-05T09:40:10.109Z", "modified": "2018-12-05T09:40:10.128Z"}, {"entity": "publication", "iuid": "0dbc927530c24f56973a7a4a0facf0e5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0dbc927530c24f56973a7a4a0facf0e5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0dbc927530c24f56973a7a4a0facf0e5"}}, "title": "Impacts of added dissolved organic carbon on boreal freshwater pelagic metabolism and food webs in mesocosm experiments", "authors": [{"family": "Kankaala", "given": "Paula", "initials": "P"}, {"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Nyk\u00e4nen", "given": "Hannu", "initials": "H"}, {"family": "Sonninen", "given": "Eloni", "initials": "E"}, {"family": "Taipale", "given": "Sami", "initials": "S"}, {"family": "Tiirola", "given": "Marja", "initials": "M"}, {"family": "Jones", "given": "Roger I", "initials": "RI"}], "type": "journal-article", "published": "2010-07-09", "journal": {"title": "Fund. App. Lim.", "issn": "1863-9135", "volume": "177", "issue": "3", "pages": "161-176", "issn-l": null}, "abstract": null, "doi": "10.1127/1863-9135/2010/0177-0161", "pmid": null, "labels": {"Sari Peura": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-10-08T14:54:22.135Z", "modified": "2025-12-04T17:03:33.973Z"}, {"entity": "publication", "iuid": "d7063589c86544e5b236109757b2324f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d7063589c86544e5b236109757b2324f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d7063589c86544e5b236109757b2324f"}}, "title": "Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.", "authors": [{"family": "Hedskog", "given": "Charlotte", "initials": "C"}, {"family": "Mild", "given": "Mattias", "initials": "M"}, {"family": "Jernberg", "given": "Johanna", "initials": "J"}, {"family": "Sherwood", "given": "Ellen", "initials": "E"}, {"family": "Bratt", "given": "G\u00f6ran", "initials": "G"}, {"family": "Leitner", "given": "Thomas", "initials": "T"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Albert", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2010-07-07", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "5", "issue": "7", "pages": "e11345", "issn-l": "1932-6203"}, "abstract": "Ultra-deep pyrosequencing (UDPS) allows identification of rare HIV-1 variants and minority drug resistance mutations, which are not detectable by standard sequencing.\n\nHere, UDPS was used to analyze the dynamics of HIV-1 genetic variation in reverse transcriptase (RT) (amino acids 180-220) in six individuals consecutively sampled before, during and after failing 3TC and AZT containing antiretroviral treatment. Optimized UDPS protocols and bioinformatic software were developed to generate, clean and analyze the data. The data cleaning strategy reduced the error rate of UDPS to an average of 0.05%, which is lower than previously reported. Consequently, the cut-off for detection of resistance mutations was very low. A median of 16,016 (range 2,406-35,401) sequence reads were obtained per sample, which allowed detection and quantification of minority resistance mutations at amino acid position 181, 184, 188, 190, 210, 215 and 219 in RT. In four of five pre-treatment samples low levels (0.07-0.09%) of the M184I mutation were observed. Other resistance mutations, except T215A and T215I were below the detection limit. During treatment failure, M184V replaced M184I and dominated the population in combination with T215Y, while wild-type variants were rarely detected. Resistant virus disappeared rapidly after treatment interruption and was undetectable as early as after 3 months. In most patients, drug resistant variants were replaced by wild-type variants identical to those present before treatment, suggesting rebound from latent reservoirs.\n\nWith this highly sensitive UDPS protocol preexisting drug resistance was infrequently observed; only M184I, T215A and T215I were detected at very low levels. Similarly, drug resistant variants in plasma quickly decreased to undetectable levels after treatment interruption. The study gives important insights into the dynamics of the HIV-1 quasispecies and is of relevance for future research and clinical use of the UDPS technology.", "doi": "10.1371/journal.pone.0011345", "pmid": "20628644", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC2898805"}], "notes": [], "created": "2018-12-05T08:39:51.604Z", "modified": "2018-12-05T08:39:51.626Z"}, {"entity": "publication", "iuid": "ec968f80cc6c4b49be35c167e4f06c76", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ec968f80cc6c4b49be35c167e4f06c76.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ec968f80cc6c4b49be35c167e4f06c76"}}, "title": "Classification of DNA sequences using Bloom filters.", "authors": [{"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M"}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Arvestad", "given": "Lars", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2010-07-01", "journal": {"title": "Bioinformatics", "issn": "1367-4803", "volume": "26", "issue": "13", "pages": "1595-1600", "issn-l": null}, "abstract": "New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed.\n\nA novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can accurately and rapidly classify sequences as belonging or not belonging to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS achieves comparable accuracy as BLAT and SSAHA2 but is at least 21 times faster in classifying sequences.\n\nSource code for FACS, Bloom filters and MetaSim dataset used is available at http://facs.biotech.kth.se. The Bloom::Faster 1.6 Perl module can be downloaded from CPAN at http://search.cpan.org/ approximately palvaro/Bloom-Faster-1.6/\n\nhenrik.stranneheim@biotech.kth.se; joakiml@biotech.kth.se\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btq230", "pmid": "20472541", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "btq230"}, {"db": "pmc", "key": "PMC2887045"}], "notes": [], "created": "2018-12-05T09:30:21.135Z", "modified": "2018-12-05T09:30:21.155Z"}, {"entity": "publication", "iuid": "89b9bc65a411441ebc979c37d83225c8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/89b9bc65a411441ebc979c37d83225c8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/89b9bc65a411441ebc979c37d83225c8"}}, "title": "Upregulated Op18/stathmin activity causes chromosomal instability through a mechanism that evades the spindle assembly checkpoint", "authors": [{"family": "Holmfeldt", "given": "Per", "initials": "P"}, {"family": "Sellin", "given": "Mikael E", "initials": "ME"}, {"family": "Gullberg", "given": "Martin", "initials": "M"}], "type": "journal-article", "published": "2010-07-00", "journal": {"volume": "316", "issn": "0014-4827", "issue": "12", "pages": "2017-2026", "title": "Experimental Cell Research", "issn-l": "0014-4827"}, "abstract": "Op18/stathmin (Op18) is a microtubule-destabilizing protein that is phosphorylation-inactivated during mitosis and its normal function is to govern tubulin subunit partitioning during interphase. Human tumors frequently overexpress Op18 and a tumor-associated Q18-->E mutation has been identified that confers hyperactivity, destabilizes spindle microtubules, and causes mitotic aberrancies, polyploidization, and chromosome loss in K562 leukemia cells. Here we determined whether wild-type and mutant Op18 have the potential to cause chromosomal instability by some means other than interference with spindle assembly, and thereby bypassing the spindle assembly checkpoint. Our approach was based on Op18 derivatives with distinct temporal order of activity during mitosis, conferred either by differential phosphorylation inactivation or by anaphase-specific degradation through fusion with the destruction box of cyclin B1. We present evidence that excessive Op18 activity generates chromosomal instability through interference occurring subsequent to the metaphase-to-anaphase transition, which reduces the fidelity of chromosome segregation to spindle poles during anaphase. Similar to uncorrected merotelic attachment, this mechanism evades detection by the spindle assembly checkpoint and thus provides an additional route to chromosomal instability.", "doi": "10.1016/j.yexcr.2010.04.008", "pmid": "20399773", "labels": {"Mikael Sellin": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:42.954Z", "modified": "2022-11-07T11:35:38.102Z"}, {"entity": "publication", "iuid": "6416bb8fb3174de3a340b0c5ff12860c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6416bb8fb3174de3a340b0c5ff12860c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6416bb8fb3174de3a340b0c5ff12860c"}}, "title": "Quantification of the Sixth DNA Base Hydroxymethylcytosine in the Brain", "authors": [{"family": "M\u00fcnzel", "given": "Martin", "initials": "M"}, {"family": "Globisch", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4526-5788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cd75219d6894d6b851e202eaa40fc5f.json"}}, {"family": "Br\u00fcckl", "given": "Tobias", "initials": "T"}, {"family": "Wagner", "given": "Mirko", "initials": "M"}, {"family": "Welzmiller", "given": "Veronika", "initials": "V"}, {"family": "Michalakis", "given": "Stylianos", "initials": "S"}, {"family": "M\u00fcller", "given": "Markus", "initials": "M"}, {"family": "Biel", "given": "Martin", "initials": "M"}, {"family": "Carell", "given": "Thomas", "initials": "T"}], "type": "journal-article", "published": "2010-06-25", "journal": {"volume": "49", "issn": "1433-7851", "issue": "31", "pages": "5375-5377", "title": "Angewandte Chemie International Edition", "issn-l": "1433-7851"}, "abstract": null, "doi": "10.1002/anie.201002033", "pmid": "20583021", "labels": {"Daniel Globisch": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:53.418Z", "modified": "2022-11-07T11:30:57.306Z"}, {"entity": "publication", "iuid": "18c81c48ef9e4fd4b3c53ac87983dcbf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/18c81c48ef9e4fd4b3c53ac87983dcbf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/18c81c48ef9e4fd4b3c53ac87983dcbf"}}, "title": "Control of membrane protein topology by a single C-terminal residue.", "authors": [{"family": "Sepp\u00e4l\u00e4", "given": "Susanna", "initials": "S"}, {"family": "Slusky", "given": "Joanna S", "initials": "JS"}, {"family": "Lloris-Garcer\u00e1", "given": "Pilar", "initials": "P"}, {"family": "Rapp", "given": "Mikaela", "initials": "M"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2010-06-25", "journal": {"title": "Science", "issn": "0036-8075", "volume": "328", "issue": "5986", "pages": "1698-1700", "issn-l": "0036-8075"}, "abstract": "The mechanism by which multispanning helix-bundle membrane proteins are inserted into their target membrane remains unclear. In both prokaryotic and eukaryotic cells, membrane proteins are inserted cotranslationally into the lipid bilayer. Positively charged residues flanking the transmembrane helices are important topological determinants, but it is not known whether they act strictly locally, affecting only the nearest transmembrane helices, or can act globally, affecting the topology of the entire protein. Here we found that the topology of an Escherichia coli inner membrane protein with four or five transmembrane helices could be controlled by a single positively charged residue placed in different locations throughout the protein, including the very C terminus. This observation points to an unanticipated plasticity in membrane protein insertion mechanisms.", "doi": "10.1126/science.1188950", "pmid": "20508091", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "science.1188950"}], "notes": [], "created": "2018-12-05T08:37:57.825Z", "modified": "2018-12-05T08:37:57.849Z"}, {"entity": "publication", "iuid": "e822b5ba609648f7b225180458559f6a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e822b5ba609648f7b225180458559f6a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e822b5ba609648f7b225180458559f6a"}}, "title": "Induction of cytochrome P450 1 genes and stress response genes in developing zebrafish exposed to ultraviolet radiation.", "authors": [{"family": "Behrendt", "given": "Lars", "initials": "L"}, {"family": "J\u00f6nsson", "given": "Maria E", "initials": "ME"}, {"family": "Goldstone", "given": "Jared V", "initials": "JV"}, {"family": "Stegeman", "given": "John J", "initials": "JJ"}], "type": "journal article", "published": "2010-06-01", "journal": {"title": "Aquat Toxicol", "issn": "1879-1514", "volume": "98", "issue": "1", "pages": "74-82", "issn-l": null}, "abstract": "Ultraviolet (UV) radiation damages cell molecules, and has been suggested to up-regulate mammalian cytochrome P4501 (CYP1) genes through an aryl hydrocarbon receptor (AHR) mediated mechanism. In this study, embryos and larvae of zebrafish (Danio rerio) were exposed to UV to determine the effects on expression of CYP1 and stress response genes in vivo in these fish. Zebrafish embryos were exposed for varying times to UV on two consecutive days, with exposure beginning at 24 and 48h post-fertilization (hpf). Embryos exposed for 2, 4 or 6h twice over 2 days to UVB (0.62 W/m(2); 8.9-26.7 kJ/m(2)) plus UVA (2.05 W/m(2); 29.5-144.6 kJ/m(2)) had moderately (2.4+/-0.8-fold) but significantly up-regulated levels of CYP1A. UVA alone had no effect on CYP1A expression. Proliferating cellular nuclear antigen (PCNA) and Cu-Zn superoxide dismutase (SOD1) transcript levels were induced (2.1+/-0.2 and 2.3+/-0.5-fold, respectively) in embryos exposed to two 6-h pulses of 0.62 W/m(2) UVB (26.8 kJ/m(2)). CYP1A was induced also in embryos exposed to higher intensity UVB (0.93 W/m(2)) for two 3-h or two 4-h pulses (20.1 or 26.8 kJ/m(2)). CYP1B1, SOD1 and PCNA expression was induced by the two 3-h pulses of the higher intensity UVB, but not after two 4-h pulses of the higher intensity UVB, possibly due to impaired condition of surviving embryos, reflected in a mortality of 34% at that UVB dose. A single 8-h long exposure of zebrafish larvae (8dpf) to UVB at 0.93 W/m(2) (26.8 kJ/m(2)) significantly induced CYP1A and CYP1B1 expression, but other CYP1 genes (CYP1C1, CYP1C2 and CYP1D1) showed no significant increase. The results show that UVB can induce expression of CYP1 genes as well stress response genes in developing zebrafish, and that UVB intensity and duration influence the responses.", "doi": "10.1016/j.aquatox.2010.01.008", "pmid": "20189255", "labels": {"SciLifeLab Fellow": null, "Lars Behrendt": null}, "xrefs": [{"db": "mid", "key": "NIHMS176609"}, {"db": "pmc", "key": "PMC2864789"}, {"db": "pii", "key": "S0166-445X(10)00020-2"}], "notes": [], "created": "2023-05-12T11:54:05.262Z", "modified": "2023-05-12T11:54:05.292Z"}, {"entity": "publication", "iuid": "d9126e7fe59f4525a83c36be46506e36", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d9126e7fe59f4525a83c36be46506e36.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d9126e7fe59f4525a83c36be46506e36"}}, "title": "Local release of highly loaded antibodies from functionalized nanoporous support for cancer immunotherapy.", "authors": [{"family": "Lei", "given": "Chenghong", "initials": "C"}, {"family": "Liu", "given": "Pu", "initials": "P"}, {"family": "Chen", "given": "Baowei", "initials": "B"}, {"family": "Mao", "given": "Yumeng", "initials": "Y"}, {"family": "Engelmann", "given": "Heather", "initials": "H"}, {"family": "Shin", "given": "Yongsoon", "initials": "Y"}, {"family": "Jaffar", "given": "Jade", "initials": "J"}, {"family": "Hellstrom", "given": "Ingegerd", "initials": "I"}, {"family": "Liu", "given": "Jun", "initials": "J"}, {"family": "Hellstrom", "given": "Karl Erik", "initials": "KE"}], "type": "journal article", "published": "2010-05-26", "journal": {"title": "Journal of the American Chemical Society", "issn": "1520-5126", "volume": "132", "issue": "20", "pages": "6906-6907", "issn-l": "0002-7863"}, "abstract": "We report that antibodies can be spontaneously loaded in functionalized mesoporous silica (FMS) with superhigh density (0.4-0.8 mg of antibody/mg of FMS) due to their comprehensive noncovalent interaction. The superhigh loading density and noncovalent interaction between FMS and antibodies allow long-lasting local release of the immunoregulatory molecules from FMS under physiological conditions. Preliminary data indicate that FMS-anti-CTLA4 antibody injected directly into a mouse melanoma induces much greater and extended inhibition of tumor growth than the antibody given systemically. Our findings open up a novel approach for local delivery of therapeutically active proteins to tumors and, potentially, other diseases.", "doi": "10.1021/ja102414t", "pmid": "20433206", "labels": {"SciLifeLab Fellow": null, "Yumeng Mao": null}, "xrefs": [{"db": "mid", "key": "NIHMS201379"}, {"db": "pmc", "key": "PMC2874126"}], "notes": [], "created": "2023-05-12T11:57:39.765Z", "modified": "2023-05-12T11:57:39.778Z"}, {"entity": "publication", "iuid": "9d80ba9cdb89414db0800f8ce2c1b17b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9d80ba9cdb89414db0800f8ce2c1b17b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9d80ba9cdb89414db0800f8ce2c1b17b"}}, "title": "Amplified fragment length polymorphism (AFLP) analysis of closely related wild and captive tsetse fly (Glossina morsitans morsitans) populations.", "authors": [{"family": "Lall", "given": "Gurdeep K", "initials": "GK"}, {"family": "Darby", "given": "Alistair C", "initials": "AC"}, {"family": "Nystedt", "given": "Bjorn", "initials": "B"}, {"family": "Macleod", "given": "Ewan T", "initials": "ET"}, {"family": "Bishop", "given": "Richard P", "initials": "RP"}, {"family": "Welburn", "given": "Susan C", "initials": "SC"}], "type": "journal article", "published": "2010-05-26", "journal": {"title": "Parasit Vectors", "issn": "1756-3305", "volume": "3", "issue": null, "pages": "47", "issn-l": "1756-3305"}, "abstract": "Tsetse flies (Diptera: Glossinidae) are vectors of trypanosomes that cause sleeping sickness in humans and nagana in livestock across sub-Saharan Africa. Tsetse control strategies rely on a detailed understanding of the epidemiology and ecology of tsetse together with genetic variation within and among populations. High-resolution nuclear genetic markers are useful tools for elucidation of the genetic basis of phenotypic traits. In this study amplified fragment length polymorphism (AFLP) markers were developed to analyze genetic variation in Glossina morsitans morsitans from laboratory and field-collected populations from Zimbabwe.\n\nA total of seven hundred and fifty one loci from laboratory and field populations of G. m. morsitans from Zimbabwe were genotyped using AFLP with seven primer combinations. Analysis identified 335 polymorphic loci. The two populations could be distinguished by cluster and principal components analysis (PCA) analysis, indicating that AFLP markers can be used to separate genetically similar populations; at the same time differences observed between laboratory and field populations were not very great. Among the techniques investigated, the use of acetone was the most reliable method of preservation of tsetse for subsequent extraction of high molecular weight DNA. An interesting finding was that AFLP also enabled robust within-population discrimination of male and female tsetse flies due to their different X chromosome DNA complements.\n\nAFLP represents a useful additional tool to add to the suite of techniques currently available for the genetic analysis of tsetse populations and represents a useful resource for identification of the genetic basis of important phenotypic traits.", "doi": "10.1186/1756-3305-3-47", "pmid": "20504326", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "1756-3305-3-47"}, {"db": "pmc", "key": "PMC2893174"}], "notes": [], "created": "2018-12-05T11:35:21.998Z", "modified": "2018-12-05T11:35:22.029Z"}, {"entity": "publication", "iuid": "3c66678ebfae42c0852c5474aa2f4553", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3c66678ebfae42c0852c5474aa2f4553.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3c66678ebfae42c0852c5474aa2f4553"}}, "title": "Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding", "authors": [{"family": "Schmidt", "given": "D", "initials": "D"}, {"family": "Wilson", "given": "M D", "initials": "MD"}, {"family": "Ballester", "given": "B", "initials": "B"}, {"family": "Schwalie", "given": "P C", "initials": "PC"}, {"family": "Brown", "given": "G D", "initials": "GD"}, {"family": "Marshall", "given": "A", "initials": "A"}, {"family": "Kutter", "given": "C", "initials": "C"}, {"family": "Watt", "given": "S", "initials": "S"}, {"family": "Martinez-Jimenez", "given": "C P", "initials": "CP"}, {"family": "Mackay", "given": "S", "initials": "S"}, {"family": "Talianidis", "given": "I", "initials": "I"}, {"family": "Flicek", "given": "P", "initials": "P"}, {"family": "Odom", "given": "D T", "initials": "DT"}], "type": "journal-article", "published": "2010-05-21", "journal": {"volume": "328", "issn": "0036-8075", "issue": "5981", "pages": "1036-1040", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Transcription factors (TFs) direct gene expression by binding to DNA regulatory regions. To explore the evolution of gene regulation, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of two TFs, CCAAT/enhancer-binding protein alpha and hepatocyte nuclear factor 4 alpha, in the livers of five vertebrates. Although each TF displays highly conserved DNA binding preferences, most binding is species-specific, and aligned binding events present in all five species are rare. Regions near genes with expression levels that are dependent on a TF are often bound by the TF in multiple species yet show no enhanced DNA sequence constraint. Binding divergence between species can be largely explained by sequence changes to the bound motifs. Among the binding events lost in one lineage, only half are recovered by another binding event within 10 kilobases. Our results reveal large interspecies differences in transcriptional regulation and provide insight into regulatory evolution.", "doi": "10.1126/science.1186176", "pmid": "20378774", "labels": {"Claudia Kutter": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:29.306Z", "modified": "2022-11-07T11:30:38.582Z"}, {"entity": "publication", "iuid": "1dae97cce7ee489e9bea44da26c2e3d4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1dae97cce7ee489e9bea44da26c2e3d4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1dae97cce7ee489e9bea44da26c2e3d4"}}, "title": "Structure-Based Discovery of A2A Adenosine Receptor Ligands", "authors": [{"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Yoo", "given": "Lena", "initials": "L"}, {"family": "Gao", "given": "Zhan Guo", "initials": "ZG"}, {"family": "Irwin", "given": "John J", "initials": "JJ"}, {"family": "Shoichet", "given": "Brian K", "initials": "BK"}, {"family": "Jacobson", "given": "Kenneth A", "initials": "KA"}], "type": "journal-article", "published": "2010-05-13", "journal": {"volume": "53", "issn": "0022-2623", "issue": "9", "pages": "3748-3755", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "The recent determination of X-ray structures of pharmacologically relevant GPCRs has made these targets accessible to structure-based ligand discovery. Here we explore whether novel chemotypes may be discovered for the A(2A) adenosine receptor, based on complementarity to its recently determined structure. The A(2A) adenosine receptor signals in the periphery and the CNS, with agonists explored as anti-inflammatory drugs and antagonists explored for neurodegenerative diseases. We used molecular docking to screen a 1.4 million compound database against the X-ray structure computationally and tested 20 high-ranking, previously unknown molecules experimentally. Of these 35% showed substantial activity with affinities between 200 nM and 9 microM. For the most potent of these new inhibitors, over 50-fold specificity was observed for the A(2A) versus the related A(1) and A(3) subtypes. These high hit rates and affinities at least partly reflect the bias of commercial libraries toward GPCR-like chemotypes, an issue that we attempt to investigate quantitatively. Despite this bias, many of the most potent new ligands were novel, dissimilar from known ligands, providing new lead structures for modulation of this medically important target.", "doi": "10.1021/jm100240h", "pmid": "20405927", "labels": {"Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:25.905Z", "modified": "2022-11-07T11:33:17.688Z"}, {"entity": "publication", "iuid": "972a802c23e44a2cb9415179e2b376c5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/972a802c23e44a2cb9415179e2b376c5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/972a802c23e44a2cb9415179e2b376c5"}}, "title": "Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression", "authors": [{"family": "Git", "given": "A", "initials": "A"}, {"family": "Dvinge", "given": "H", "initials": "H"}, {"family": "Salmon-Divon", "given": "M", "initials": "M"}, {"family": "Osborne", "given": "M", "initials": "M"}, {"family": "Kutter", "given": "C", "initials": "C"}, {"family": "Hadfield", "given": "J", "initials": "J"}, {"family": "Bertone", "given": "P", "initials": "P"}, {"family": "Caldas", "given": "C", "initials": "C"}], "type": "journal-article", "published": "2010-05-01", "journal": {"volume": "16", "issn": "1355-8382", "issue": "5", "pages": "991-1006", "title": "RNA", "issn-l": null}, "abstract": "RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a \"gold standard.\" Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.", "doi": "10.1261/rna.1947110", "pmid": "20360395", "labels": {"Claudia Kutter": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:15.788Z", "modified": "2022-11-07T11:30:38.593Z"}, {"entity": "publication", "iuid": "967d06684bbe44d2b0823df7ac4c194e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/967d06684bbe44d2b0823df7ac4c194e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/967d06684bbe44d2b0823df7ac4c194e"}}, "title": "Understanding biological dynamics: following cells and molecules to track functions and mechanisms", "authors": [{"family": "Palamidessi", "given": "A", "initials": "A"}, {"family": "Testa", "given": "I", "initials": "I"}, {"family": "Frittoli", "given": "E", "initials": "E"}, {"family": "Barozzi", "given": "S", "initials": "S"}, {"family": "Garr\u00e8", "given": "M", "initials": "M"}, {"family": "Mazza", "given": "D", "initials": "D"}, {"family": "Di Fiore", "given": "P P", "initials": "PP"}, {"family": "Diaspro", "given": "A", "initials": "A"}, {"family": "Scita", "given": "G", "initials": "G"}, {"family": "Faretta", "given": "Mario", "initials": "M"}], "type": "journal-article", "published": "2010-05-00", "journal": {"volume": "39", "issn": "0175-7571", "issue": "6", "pages": "947-957", "title": "Eur Biophys J", "issn-l": null}, "abstract": "The dissection of the molecular circuitries at the base of cell life and the identification of their abnormal transformation during carcinogenesis rely on the characterization of biological phenotypes generated by targeted overexpression or deletion of gene products through genetic manipulation. Fluorescence microscopy provides a wide variety of tools to monitor cell life with minimal perturbations. The observation of living cells requires the selection of a correct balance between temporal, spatial and \"statistical\" resolution according to the process to be analyzed. In the following paper ad hoc developed optical tools for dynamical tracking from cellular to molecular resolution will be presented. Particular emphasis will be devoted to discuss how to exploit light-matter interaction to selectively target specific molecular species, understanding the relationships between their intracellular compartmentalization and function.", "doi": "10.1007/s00249-009-0461-x", "pmid": "19455321", "labels": {"Ilaria Testa": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:19.163Z", "modified": "2022-11-07T11:32:31.719Z"}, {"entity": "publication", "iuid": "f38ef41358af40eaaa269bb4ac66b4af", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f38ef41358af40eaaa269bb4ac66b4af.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f38ef41358af40eaaa269bb4ac66b4af"}}, "title": "Iron from nanocompounds containing iron and zinc is highly bioavailable in rats without tissue accumulation.", "authors": [{"family": "Hilty", "given": "Florentine M", "initials": "FM"}, {"family": "Arnold", "given": "Myrtha", "initials": "M"}, {"family": "Hilbe", "given": "Monika", "initials": "M"}, {"family": "Teleki", "given": "Alexandra", "initials": "A"}, {"family": "Knijnenburg", "given": "Jesper T N", "initials": "JT"}, {"family": "Ehrensperger", "given": "Felix", "initials": "F"}, {"family": "Hurrell", "given": "Richard F", "initials": "RF"}, {"family": "Pratsinis", "given": "Sotiris E", "initials": "SE"}, {"family": "Langhans", "given": "Wolfgang", "initials": "W"}, {"family": "Zimmermann", "given": "Michael B", "initials": "MB"}], "type": "journal article", "published": "2010-05-00", "journal": {"title": "Nat Nanotechnol", "issn": "1748-3395", "volume": "5", "issue": "5", "pages": "374-380", "issn-l": null}, "abstract": "Effective iron fortification of foods is difficult, because water-soluble compounds that are well absorbed, such as ferrous sulphate (FeSO(4)), often cause unacceptable changes in the colour or taste of foods. Poorly water-soluble compounds, on the other hand, cause fewer sensory changes, but are not well absorbed. Here, we show that poorly water-soluble nanosized Fe and Fe/Zn compounds (specific surface area approximately 190 m(2) g(-1)) made by scalable flame aerosol technology have in vivo iron bioavailability in rats comparable to FeSO(4) and cause less colour change in reactive food matrices than conventional iron fortificants. The addition of Zn to FePO(4) and Mg to Fe/Zn oxide increases Fe absorption from the compounds, and doping with Mg also improves their colour. After feeding rats with nanostructured iron-containing compounds, no stainable Fe was detected in their gut wall, gut-associated lymphatics or other tissues, suggesting no adverse effects. Nanosizing of poorly water-soluble Fe compounds sharply increases their absorption and nutritional value.", "doi": "10.1038/nnano.2010.79", "pmid": "20418865", "labels": {"Alexandra Teleki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "nnano.2010.79"}], "notes": [], "created": "2020-11-30T21:42:16.807Z", "modified": "2022-11-07T11:29:43.594Z"}, {"entity": "publication", "iuid": "a811ffa81e324c87970995465ed551e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a811ffa81e324c87970995465ed551e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a811ffa81e324c87970995465ed551e4"}}, "title": "Continuous surface functionalization of flame-made TiO2 nanoparticles.", "authors": [{"family": "Teleki", "given": "Alexandra", "initials": "A"}, {"family": "Bjelobrk", "given": "Nada", "initials": "N"}, {"family": "Pratsinis", "given": "Sotiris E", "initials": "SE"}], "type": "journal article", "published": "2010-04-20", "journal": {"title": "Langmuir", "issn": "1520-5827", "volume": "26", "issue": "8", "pages": "5815-5822", "issn-l": "0743-7463"}, "abstract": "Hydrophilic TiO(2) particles made in a flame aerosol reactor were converted in situ to hydrophobic ones by silylation of their surface hydroxyl groups. So the freshly formed titania aerosol was mixed with a fine spray of octyltriethoxysilane (OTES) in water/ethanol solution and functionalized continuously at high temperature. The extent of functionalization and structure of that surface layer were assessed by thermogravimetric analysis (TGA) coupled to mass spectroscopy (MS), differential scanning calorimetry (DSC), Fourier transform infrared (FTIR), and Raman spectroscopy. Product particles were characterized also by transmission electron microscopy (TEM), X-ray diffraction, and nitrogen adsorption. The influence of titania specific surface area (SSA) and OTES solution concentration on the functional group surface density was investigated. The titanium dioxide surface was covered with functional groups (up to 2.9 wt %) that were thermally stable up to 300 degrees C in air at an average density of 2 OTES/nm(2). Such surface-functionalized particle suspensions in 2-ethylhexanoic acid and xylene were stable over several weeks. In contrast, as-prepared hydrophilic TiO(2) precipitated within days in these solvents.", "doi": "10.1021/la9037149", "pmid": "20192157", "labels": {"Alexandra Teleki": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-30T21:42:29.429Z", "modified": "2022-11-07T11:29:43.606Z"}, {"entity": "publication", "iuid": "9c9aa12e58154dfeba62822212950b4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c9aa12e58154dfeba62822212950b4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c9aa12e58154dfeba62822212950b4d"}}, "title": "International network of cancer genome projects.", "authors": [{"family": "International Cancer Genome Consortium", "given": "", "initials": ""}, {"family": "Hudson", "given": "Thomas J", "initials": "TJ"}, {"family": "Anderson", "given": "Warwick", "initials": "W"}, {"family": "Artez", "given": "Axel", "initials": "A"}, {"family": "Barker", "given": "Anna D", "initials": "AD"}, {"family": "Bell", "given": "Cindy", "initials": "C"}, {"family": "Bernab\u00e9", "given": "Rosa R", "initials": "RR"}, {"family": "Bhan", "given": "M K", "initials": "MK"}, {"family": "Calvo", "given": "Fabien", "initials": "F"}, {"family": "Eerola", "given": "Iiro", "initials": "I"}, {"family": "Gerhard", "given": "Daniela S", "initials": "DS"}, {"family": "Guttmacher", "given": "Alan", "initials": "A"}, {"family": "Guyer", "given": "Mark", "initials": "M"}, {"family": "Hemsley", "given": "Fiona M", "initials": "FM"}, {"family": "Jennings", "given": "Jennifer L", "initials": "JL"}, {"family": "Kerr", "given": "David", "initials": "D"}, {"family": "Klatt", "given": "Peter", "initials": "P"}, {"family": "Kolar", "given": "Patrik", "initials": "P"}, {"family": "Kusada", "given": "Jun", "initials": "J"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Laplace", "given": "Frank", "initials": "F"}, {"family": "Youyong", "given": "Lu", "initials": "L"}, {"family": "Nettekoven", "given": "Gerd", "initials": "G"}, {"family": "Ozenberger", "given": "Brad", "initials": "B"}, {"family": "Peterson", "given": "Jane", "initials": "J"}, {"family": "Rao", "given": "T S", "initials": "TS"}, {"family": "Remacle", "given": "Jacques", "initials": "J"}, {"family": "Schafer", "given": "Alan J", "initials": "AJ"}, {"family": "Shibata", "given": "Tatsuhiro", "initials": "T"}, {"family": "Stratton", "given": "Michael R", "initials": "MR"}, {"family": "Vockley", "given": "Joseph G", "initials": "JG"}, {"family": "Watanabe", "given": "Koichi", "initials": "K"}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Yuen", "given": "Matthew M F", "initials": "MM"}, {"family": "Knoppers", "given": "Bartha M", "initials": "BM"}, {"family": "Bobrow", "given": "Martin", "initials": "M"}, {"family": "Cambon-Thomsen", "given": "Anne", "initials": "A"}, {"family": "Dressler", "given": "Lynn G", "initials": "LG"}, {"family": "Dyke", "given": "Stephanie O M", "initials": "SO"}, {"family": "Joly", "given": "Yann", "initials": "Y"}, {"family": "Kato", "given": "Kazuto", "initials": "K"}, {"family": "Kennedy", "given": "Karen L", "initials": "KL"}, {"family": "Nicol\u00e1s", "given": "Pilar", "initials": "P"}, {"family": "Parker", "given": "Michael J", "initials": "MJ"}, {"family": "Rial-Sebbag", "given": "Emmanuelle", "initials": "E"}, {"family": "Romeo-Casabona", "given": "Carlos M", "initials": "CM"}, {"family": "Shaw", "given": "Kenna M", "initials": "KM"}, {"family": "Wallace", "given": "Susan", "initials": "S"}, {"family": "Wiesner", "given": "Georgia L", "initials": "GL"}, {"family": "Zeps", "given": "Nikolajs", "initials": "N"}, {"family": "Lichter", "given": "Peter", "initials": "P"}, {"family": "Biankin", "given": "Andrew V", "initials": "AV"}, {"family": "Chabannon", "given": "Christian", "initials": "C"}, {"family": "Chin", "given": "Lynda", "initials": "L"}, {"family": "Cl\u00e9ment", "given": "Bruno", "initials": "B"}, {"family": "de Alava", "given": "Enrique", "initials": "E"}, {"family": "Degos", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Ferguson", "given": "Martin L", "initials": "ML"}, {"family": "Geary", "given": "Peter", "initials": "P"}, {"family": "Hayes", "given": "D Neil", "initials": "DN"}, {"family": "Johns", "given": "Amber L", "initials": "AL"}, {"family": "Kasprzyk", "given": "Arek", "initials": "A"}, {"family": "Nakagawa", "given": "Hidewaki", "initials": "H"}, {"family": "Penny", "given": "Robert", "initials": "R"}, {"family": "Piris", "given": "Miguel A", "initials": "MA"}, {"family": "Sarin", "given": "Rajiv", "initials": "R"}, {"family": "Scarpa", "given": "Aldo", "initials": "A"}, {"family": "van de Vijver", "given": "Marc", "initials": "M"}, {"family": "Futreal", "given": "P Andrew", "initials": "PA"}, {"family": "Aburatani", "given": "Hiroyuki", "initials": "H"}, {"family": "Bay\u00e9s", "given": "M\u00f3nica", "initials": "M"}, {"family": "Botwell", "given": "David D L", "initials": "DD"}, {"family": "Campbell", "given": "Peter J", "initials": "PJ"}, {"family": "Estivill", "given": "Xavier", "initials": "X"}, {"family": "Grimmond", "given": "Sean M", "initials": "SM"}, {"family": "Gut", "given": "Ivo", "initials": "I"}, {"family": "Hirst", "given": "Martin", "initials": "M"}, {"family": "L\u00f3pez-Ot\u00edn", "given": "Carlos", "initials": "C"}, {"family": "Majumder", "given": "Partha", "initials": "P"}, {"family": "Marra", "given": "Marco", "initials": "M"}, {"family": "McPherson", "given": "John D", "initials": "JD"}, {"family": "Ning", "given": "Zemin", "initials": "Z"}, {"family": "Puente", "given": "Xose S", "initials": "XS"}, {"family": "Ruan", "given": "Yijun", "initials": "Y"}, {"family": "Stunnenberg", "given": "Hendrik G", "initials": "HG"}, {"family": "Swerdlow", "given": "Harold", "initials": "H"}, {"family": "Velculescu", "given": "Victor E", "initials": "VE"}, {"family": "Wilson", "given": "Richard K", "initials": "RK"}, {"family": "Xue", "given": "Hong H", "initials": "HH"}, {"family": "Yang", "given": "Liu", "initials": "L"}, {"family": "Spellman", "given": "Paul T", "initials": "PT"}, {"family": "Bader", "given": "Gary D", "initials": "GD"}, {"family": "Boutros", "given": "Paul C", "initials": "PC"}, {"family": "Flicek", "given": "Paul", "initials": "P"}, {"family": "Getz", "given": "Gad", "initials": "G"}, {"family": "Guig\u00f3", "given": "Roderic", "initials": "R"}, {"family": "Guo", "given": "Guangwu", "initials": "G"}, {"family": "Haussler", "given": "David", "initials": "D"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "Hubbard", "given": "Tim J", "initials": "TJ"}, {"family": "Jiang", "given": "Tao", "initials": "T"}, {"family": "Jones", "given": "Steven M", "initials": "SM"}, {"family": "Li", "given": "Qibin", "initials": "Q"}, {"family": "L\u00f3pez-Bigas", "given": "Nuria", "initials": "N"}, {"family": "Luo", "given": "Ruibang", "initials": "R"}, {"family": "Muthuswamy", "given": "Lakshmi", "initials": "L"}, {"family": "Ouellette", "given": "B F Francis", "initials": "BF"}, {"family": "Pearson", "given": "John V", "initials": "JV"}, {"family": "Quesada", "given": "Victor", "initials": "V"}, {"family": "Raphael", "given": "Benjamin J", "initials": "BJ"}, {"family": "Sander", "given": "Chris", "initials": "C"}, {"family": "Speed", "given": "Terence P", "initials": "TP"}, {"family": "Stein", "given": "Lincoln D", "initials": "LD"}, {"family": "Stuart", "given": "Joshua M", "initials": "JM"}, {"family": "Teague", "given": "Jon W", "initials": "JW"}, {"family": "Totoki", "given": "Yasushi", "initials": "Y"}, {"family": "Tsunoda", "given": "Tatsuhiko", "initials": "T"}, {"family": "Valencia", "given": "Alfonso", "initials": "A"}, {"family": "Wheeler", "given": "David A", "initials": "DA"}, {"family": "Wu", "given": "Honglong", "initials": "H"}, {"family": "Zhao", "given": "Shancen", "initials": "S"}, {"family": "Zhou", "given": "Guangyu", 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"MA"}, {"family": "Waddell", "given": "Nicola J", "initials": "NJ"}, {"family": "Wilson", "given": "Peter J", "initials": "PJ"}, {"family": "Gallinger", "given": "Steve", "initials": "S"}, {"family": "Tsao", "given": "Ming-Sound", "initials": "MS"}, {"family": "Shaw", "given": "Patricia A", "initials": "PA"}, {"family": "Petersen", "given": "Gloria M", "initials": "GM"}, {"family": "Mukhopadhyay", "given": "Debabrata", "initials": "D"}, {"family": "DePinho", "given": "Ronald A", "initials": "RA"}, {"family": "Thayer", "given": "Sarah", "initials": "S"}, {"family": "Shazand", "given": "Kamran", "initials": "K"}, {"family": "Beck", "given": "Timothy", "initials": "T"}, {"family": "Sam", "given": "Michelle", "initials": "M"}, {"family": "Timms", "given": "Lee", "initials": "L"}, {"family": "Ballin", "given": "Vanessa", "initials": "V"}, {"family": "Lu", "given": "Youyong", "initials": "Y"}, {"family": "Ji", "given": "Jiafu", "initials": "J"}, {"family": "Zhang", "given": "Xiuqing", "initials": "X"}, {"family": "Chen", "given": "Feng", "initials": "F"}, {"family": "Hu", "given": "Xueda", "initials": "X"}, {"family": "Yang", "given": "Qi", "initials": "Q"}, {"family": "Tian", "given": "Geng", "initials": "G"}, {"family": "Zhang", "given": "Lianhai", "initials": "L"}, {"family": "Xing", "given": "Xiaofang", "initials": "X"}, {"family": "Li", "given": "Xianghong", "initials": "X"}, {"family": "Zhu", "given": "Zhenggang", "initials": "Z"}, {"family": "Yu", "given": "Yingyan", "initials": "Y"}, {"family": "Yu", "given": "Jun", "initials": "J"}, {"family": "Tost", "given": "J\u00f6rg", "initials": "J"}, {"family": "Brennan", "given": "Paul", "initials": "P"}, {"family": "Holcatova", "given": "Ivana", "initials": "I"}, {"family": "Zaridze", "given": "David", "initials": "D"}, {"family": "Brazma", "given": "Alvis", "initials": "A"}, {"family": "Egevard", "given": "Lars", "initials": "L"}, {"family": "Prokhortchouk", "given": "Egor", "initials": "E"}, {"family": "Banks", "given": "Rosamonde Elizabeth", "initials": "RE"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Viksna", "given": "Juris", "initials": "J"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Skryabin", "given": "Konstantin", "initials": "K"}, {"family": "Birney", "given": "Ewan", "initials": "E"}, {"family": "Borg", "given": "Ake", "initials": "A"}, {"family": "B\u00f8rresen-Dale", "given": "Anne-Lise", "initials": "AL"}, {"family": "Caldas", "given": "Carlos", "initials": "C"}, {"family": "Foekens", "given": "John A", "initials": "JA"}, {"family": "Martin", "given": "Sancha", "initials": "S"}, {"family": "Reis-Filho", "given": "Jorge S", "initials": "JS"}, {"family": "Richardson", "given": "Andrea L", "initials": "AL"}, {"family": "Sotiriou", "given": "Christos", "initials": "C"}, {"family": "Thoms", "given": "Giles", "initials": "G"}, {"family": "van't Veer", "given": "Laura", "initials": "L"}, {"family": "Birnbaum", "given": "Daniel", "initials": "D"}, {"family": "Blanche", "given": "H\u00e9l\u00e8ne", "initials": "H"}, {"family": "Boucher", "given": "Pascal", "initials": "P"}, {"family": "Boyault", "given": "Sandrine", "initials": "S"}, {"family": "Masson-Jacquemier", "given": "Jocelyne D", "initials": "JD"}, {"family": "Pauport\u00e9", "given": "Iris", "initials": "I"}, {"family": "Pivot", "given": "Xavier", "initials": "X"}, {"family": "Vincent-Salomon", "given": "Anne", "initials": "A"}, {"family": "Tabone", "given": "Eric", "initials": "E"}, {"family": "Theillet", "given": "Charles", "initials": "C"}, {"family": "Treilleux", "given": "Isabelle", "initials": "I"}, {"family": "Bioulac-Sage", "given": "Paulette", "initials": "P"}, {"family": "Decaens", "given": "Thomas", "initials": "T"}, {"family": "Franco", "given": "Dominique", "initials": "D"}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Samuel", "given": "Didier", "initials": "D"}, {"family": "Zucman-Rossi", "given": "Jessica", "initials": "J"}, {"family": "Eils", "given": "Roland", "initials": "R"}, {"family": "Brors", "given": "Benedikt", "initials": "B"}, {"family": "Korbel", "given": "Jan O", "initials": "JO"}, {"family": "Korshunov", "given": "Andrey", "initials": "A"}, {"family": "Landgraf", "given": "Pablo", "initials": "P"}, {"family": "Lehrach", "given": "Hans", "initials": "H"}, {"family": "Pfister", "given": "Stefan", "initials": "S"}, {"family": "Radlwimmer", "given": "Bernhard", "initials": "B"}, {"family": "Reifenberger", "given": "Guido", "initials": "G"}, {"family": "Taylor", "given": "Michael D", "initials": "MD"}, {"family": "von Kalle", "given": "Christof", "initials": "C"}, {"family": "Majumder", "given": "Partha P", "initials": "PP"}, {"family": "Pederzoli", "given": "Paolo", "initials": "P"}, {"family": "Lawlor", "given": "Rita A", "initials": "RA"}, {"family": "Delledonne", "given": "Massimo", "initials": "M"}, {"family": "Bardelli", "given": "Alberto", "initials": "A"}, {"family": "Gress", "given": "Thomas", "initials": "T"}, {"family": "Klimstra", "given": "David", "initials": "D"}, {"family": "Zamboni", "given": "Giuseppe", "initials": "G"}, {"family": "Nakamura", "given": "Yusuke", "initials": "Y"}, {"family": "Miyano", "given": "Satoru", "initials": "S"}, {"family": "Fujimoto", "given": "Akihiro", "initials": "A"}, {"family": "Campo", "given": "Elias", "initials": "E"}, {"family": "de Sanjos\u00e9", "given": "Silvia", "initials": "S"}, {"family": "Montserrat", "given": "Emili", "initials": "E"}, {"family": "Gonz\u00e1lez-D\u00edaz", "given": "Marcos", "initials": "M"}, {"family": "Jares", "given": "Pedro", "initials": "P"}, {"family": "Himmelbauer", "given": "Heinz", "initials": "H"}, {"family": "Himmelbaue", "given": "Heinz", "initials": "H"}, {"family": "Bea", "given": "Silvia", "initials": "S"}, {"family": "Aparicio", "given": "Samuel", "initials": "S"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Compton", "given": "Carolyn C", "initials": "CC"}, {"family": "Lander", "given": "Eric S", "initials": "ES"}, {"family": "Burke", "given": "Wylie", "initials": "W"}, {"family": "Green", "given": "Anthony R", "initials": "AR"}, {"family": "Hamilton", "given": "Stanley R", "initials": "SR"}, {"family": "Kallioniemi", "given": "Olli P", "initials": "OP"}, {"family": "Ley", "given": "Timothy J", "initials": "TJ"}, {"family": "Liu", "given": "Edison T", "initials": "ET"}, {"family": "Wainwright", "given": "Brandon J", "initials": "BJ"}], "type": "journal article", "published": "2010-04-15", "journal": {"title": "Nature", "issn": "0028-0836", "volume": "464", "issue": "7291", "pages": "993-998", "issn-l": null}, "abstract": "The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.", "doi": "10.1038/nature08987", "pmid": "20393554", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "nature08987"}, {"db": "pmc", "key": "PMC2902243"}, {"db": "mid", "key": "NIHMS187228"}], "notes": [], "created": "2018-12-05T08:18:46.806Z", "modified": "2018-12-05T08:18:46.851Z"}, {"entity": "publication", "iuid": "43916da0820a4ff6b694ef8b15e69a36", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/43916da0820a4ff6b694ef8b15e69a36.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/43916da0820a4ff6b694ef8b15e69a36"}}, "title": "Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes", "authors": [{"family": "Zelezniak", "given": "Aleksej", "initials": "A"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Soares", "given": "Sim\u00e3o", "initials": "S"}, {"family": "Patti", "given": "Mary Elizabeth", "initials": "ME"}, {"family": "Patil", "given": "Kiran Raosaheb", "initials": "KR"}], "type": "journal-article", "published": "2010-04-01", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "issn-l": "1553-734X", "volume": "6", "issue": "4", "pages": "e1000729"}, "abstract": null, "doi": "10.1371/journal.pcbi.1000729", "pmid": "20369014", "labels": {"Aleksej Zelezniak": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:39.560Z", "modified": "2022-11-04T11:54:39.499Z"}, {"entity": "publication", "iuid": "e37299fec1e4407a901b50c6f93bb3ef", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e37299fec1e4407a901b50c6f93bb3ef.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e37299fec1e4407a901b50c6f93bb3ef"}}, "title": "New functions for an old variant: no substitute for histone H3.3", "authors": [{"family": "Elsaesser", "given": "Simon J", "initials": "SJ"}, {"family": "Goldberg", "given": "Aaron D", "initials": "AD"}, {"family": "Allis", "given": "C David", "initials": "CD"}], "type": "journal-article", "published": "2010-04-00", "journal": {"volume": "20", "issn": "0959-437X", "issue": "2", "pages": "110-117", "title": "Current Opinion in Genetics & Development", "issn-l": "0959-437X"}, "abstract": "Histone proteins often come in different variants serving specialized functions in addition to their fundamental role in packaging DNA. The metazoan histone H3.3 has been most closely associated with active transcription. Its role in histone replacement at active genes and promoters is conserved to the single histone H3 in yeast. However, recent genetic studies in flies have challenged its importance as a mark of active chromatin, and revealed unexpected insights into essential functions of H3.3 in the germline. With strikingly little amino acid sequence difference to the canonical H3, H3.3 therefore accomplishes a surprising variety of cellular and developmental processes.", "doi": "10.1016/j.gde.2010.01.003", "pmid": "20153629", "labels": {"Simon Els\u00e4sser": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:36.053Z", "modified": "2022-11-07T11:38:06.870Z"}, {"entity": "publication", "iuid": "f4e0066284a0474790f19a2b65a6e0c2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f4e0066284a0474790f19a2b65a6e0c2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f4e0066284a0474790f19a2b65a6e0c2"}}, "title": "In vivo and in vitro characterization of [18F]-FE-(+)-DTBZ as a tracer for beta-cell mass.", "authors": [{"family": "Eriksson", "given": "Olof", "initials": "O"}, {"family": "Jahan", "given": "Mahabuba", "initials": "M"}, {"family": "Johnstr\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Sundin", "given": "Anders", "initials": "A"}, {"family": "Halldin", "given": "Christer", "initials": "C"}, {"family": "Johansson", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2010-04-00", "journal": {"title": "Nucl. Med. Biol.", "issn": "1872-9614", "volume": "37", "issue": "3", "pages": "357-363", "issn-l": "0969-8051"}, "abstract": "The positron emission tomography (PET) tracer 9-[(18)F]fluoroethyl-(+)-dihydrotetrabenazine ([(18)F]-FE-(+)-DTBZ) is a potential candidate for quantifying beta-cell mass in vivo. The purpose was to investigate in vitro and in vivo utility of this tracer for the assessment of beta-cell mass.\n\nThree pigs were intravenously administered [(18)F]-FE-(+)-DTBZ and examined by PET/computed tomography. Binding parameters were estimated by kinetic modeling. In vitro k(D) and B(max) were determined by saturation binding studies of endocrine and exocrine human tissue homogenates. In vitro pancreatic uptake was determined by tissue autoradiography with pancreases from patients with types 1 (T1DM) and 2 diabetes mellitus (T2DM) and healthy controls.\n\n[(18)F]-FE-(+)-DTBZ had a k(D) of 3.5+/-1.0 nM, a B(max) of 382+/-108 fmol/mg protein and a specificity of 89+/-1.8% in islet homogenates. The total exocrine uptake was lower and 65% was nondisplaceable. No uptake difference was observed in pancreatic tissue slices from patients with T1DM, T2DM or healthy controls. The in vivo porcine pancreatic uptake reached a peak of standardized uptake value (SUV) of 2.8 with a low distribution volume ratio in all animals. Moderate to high tracer uptake was identified in the bile system and in bone.\n\n[(18)F]-FE-(+)-DTBZ binds to vesicular monoamine transporter 2 (VMAT2) with high specificity in pure islet tissue in vitro. However, there is high nondisplaceable binding to exocrine tissue. In addition, in vivo tracer metabolism and dehalogenation result in severe underestimation of porcine pancreatic VMAT2 expression and BCM. The results do not support [(18)F]-FE-(+)-DTBZ as a suitable tracer for in vivo beta-cell imaging.", "doi": "10.1016/j.nucmedbio.2009.12.004", "pmid": "20346875", "labels": {"Olof Eriksson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0969-8051(09)00294-7"}], "notes": [], "created": "2020-10-06T14:08:15.665Z", "modified": "2022-11-07T11:35:51.883Z"}, {"entity": "publication", "iuid": "653ceadb4bdf481a87d5a1c19f84c158", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/653ceadb4bdf481a87d5a1c19f84c158.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/653ceadb4bdf481a87d5a1c19f84c158"}}, "title": "There is a steady-state transcriptome in exponentially growing yeast cells", "authors": [{"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "P\u00e9rez-Ort\u00edn", "given": "Jos\u00e9 E", "initials": "JE"}], "type": "journal-article", "published": "2010-03-17", "journal": {"volume": "27", "issn": "0749-503X", "issue": "7", "pages": "413-422", "title": "Yeast", "issn-l": null}, "abstract": "The growth of yeast cells in batches in glucose-based media is a standard condition in most yeast laboratories. Most gene expression experiments are done by taking this condition as a reference. Presumably, cells are in a stable physiological condition that can be easily reproduced in other laboratories. With this assumption, however, it is necessary to consider that the average amount of the mRNAs per cell for most genes does not change during exponential growth. That is to say, there is a steady-state condition for the transcriptome. However, this has not been rigorously demonstrated to date. In this work we take several cell samples during the exponential phase growth to perform a kinetic study using the genomic run-on (GRO) technique, which allows simultaneous measurement of the amount of mRNA and transcription rate variation at the genomic level. We show here that the steady-state condition is fulfilled for almost all the genes during most exponential growth in yeast extract-peptone-dextrose medium (YPD) and, therefore, that simultaneous measures of the transcription rates and the amounts of mRNA can be used for indirect mRNA stability calculations. With this kinetic approach, we were also able to determine the relative influence of the transcription rate and the mRNA stability changes for the mRNA variation for those genes that deviate from the steady state.", "doi": "10.1002/yea.1768", "pmid": "20301094", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:46.335Z", "modified": "2022-11-07T11:38:35.275Z"}, {"entity": "publication", "iuid": "c0ef67b1ce924c4ebba525f40160c09c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c0ef67b1ce924c4ebba525f40160c09c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c0ef67b1ce924c4ebba525f40160c09c"}}, "title": "Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation", "authors": [{"family": "Chao", "given": "Luke H", "initials": "LH"}, {"family": "Pellicena", "given": "Patricia", "initials": "P"}, {"family": "Deindl", "given": "Sebastian", "initials": "S"}, {"family": "Barclay", "given": "Lauren A", "initials": "LA"}, {"family": "Schulman", "given": "Howard", "initials": "H"}, {"family": "Kuriyan", "given": "John", "initials": "J"}], "type": "journal-article", "published": "2010-03-00", "journal": {"volume": "17", "issn": "1545-9993", "issue": "3", "pages": "264-272", "title": "Nat Struct Mol Biol", "issn-l": "1545-9985"}, "abstract": "The dodecameric holoenzyme of calcium-calmodulin-dependent protein kinase II (CaMKII) responds to high-frequency Ca(2+) pulses to become Ca(2+) independent. A simple coincidence-detector model for Ca(2+)-frequency dependency assumes noncooperative activation of kinase domains. We show that activation of CaMKII by Ca(2+)-calmodulin is cooperative, with a Hill coefficient of approximately 3.0, implying sequential kinase-domain activation beyond dimeric units. We present data for a model in which cooperative activation includes the intersubunit 'capture' of regulatory segments. Such a capture interaction is seen in a crystal structure that shows extensive contacts between the regulatory segment of one kinase and the catalytic domain of another. These interactions are mimicked by a natural inhibitor of CaMKII. Our results show that a simple coincidence-detection model cannot be operative and point to the importance of kinetic dissection of the frequency-response mechanism in future experiments.", "doi": "10.1038/nsmb.1751", "pmid": "20139983", "labels": {"Sebastian Deindl": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:08.979Z", "modified": "2022-11-07T11:37:50.918Z"}, {"entity": "publication", "iuid": "d1540c23c4dc42e2b78358283efa92b2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d1540c23c4dc42e2b78358283efa92b2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d1540c23c4dc42e2b78358283efa92b2"}}, "title": "Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions", "authors": [{"family": "Goldberg", "given": "Aaron D", "initials": "AD"}, {"family": "Banaszynski", "given": "Laura A", "initials": "LA"}, {"family": "Noh", "given": "Kyung Min", "initials": "KM"}, {"family": "Lewis", "given": "Peter W", "initials": "PW"}, {"family": "Elsaesser", "given": "Simon J", "initials": "SJ"}, {"family": "Stadler", "given": "Sonja", "initials": "S"}, {"family": "Dewell", "given": "Scott", "initials": "S"}, {"family": "Law", "given": "Martin", "initials": "M"}, {"family": "Guo", "given": "Xingyi", "initials": "X"}, {"family": "Li", "given": "Xuan", "initials": "X"}, {"family": "Wen", "given": "Duancheng", "initials": "D"}, {"family": "Chapgier", "given": "Ariane", "initials": "A"}, {"family": "DeKelver", "given": "Russell C", "initials": "RC"}, {"family": "Miller", "given": "Jeffrey C", "initials": "JC"}, {"family": "Lee", "given": "Ya Li", "initials": "YL"}, {"family": "Boydston", "given": "Elizabeth A", "initials": "EA"}, {"family": "Holmes", "given": "Michael C", "initials": "MC"}, {"family": "Gregory", "given": "Philip D", "initials": "PD"}, {"family": "Greally", "given": "John M", "initials": "JM"}, {"family": "Rafii", "given": "Shahin", "initials": "S"}, {"family": "Yang", "given": "Chingwen", "initials": "C"}, {"family": "Scambler", "given": "Peter J", "initials": "PJ"}, {"family": "Garrick", "given": "David", "initials": "D"}, {"family": "Gibbons", "given": "Richard J", "initials": "RJ"}, {"family": "Higgs", "given": "Douglas R", "initials": "DR"}, {"family": "Cristea", "given": "Ileana M", "initials": "IM"}, {"family": "Urnov", "given": "Fyodor D", "initials": "FD"}, {"family": "Zheng", "given": "Deyou", "initials": "D"}, {"family": "Allis", "given": "C David", "initials": "CD"}], "type": "journal-article", "published": "2010-03-00", "journal": {"volume": "140", "issn": "0092-8674", "issue": "5", "pages": "678-691", "title": "Cell", "issn-l": null}, "abstract": "The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.", "doi": "10.1016/j.cell.2010.01.003", "pmid": "20211137", "labels": {"Simon Els\u00e4sser": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:12.389Z", "modified": "2022-11-07T11:38:06.880Z"}, {"entity": "publication", "iuid": "cb7b616a39f54bdbae0a651641670822", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cb7b616a39f54bdbae0a651641670822.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cb7b616a39f54bdbae0a651641670822"}}, "title": "Unconventional Ubiquitin Recognition by the Ubiquitin-Binding Motif within the Y Family DNA Polymerases \u03b9 and Rev1", "authors": [{"family": "Bomar", "given": "Martha G", "initials": "MG"}, {"family": "D'Souza", "given": "Sanjay", "initials": "S"}, {"family": "Bienko", "given": "Marzena", "initials": "M"}, {"family": "Dikic", "given": "Ivan", "initials": "I"}, {"family": "Walker", "given": "Graham C", "initials": "GC"}, {"family": "Zhou", "given": "Pei", "initials": "P"}], "type": "journal-article", "published": "2010-02-00", "journal": {"volume": "37", "issn": "1097-2765", "issue": "3", "pages": "408-417", "title": "Molecular Cell", "issn-l": "1097-2765"}, "abstract": "Translesion synthesis is an essential cell survival strategy to promote replication after DNA damage. The accumulation of Y family polymerases (pol) iota and Rev1 at the stalled replication machinery is mediated by the ubiquitin-binding motifs (UBMs) of the polymerases and enhanced by PCNA monoubiquitination. We report the solution structures of the C-terminal UBM of human pol iota and its complex with ubiquitin. Distinct from other ubiquitin-binding domains, the UBM binds to the hydrophobic surface of ubiquitin centered at L8. Accordingly, mutation of L8A, but not I44A, of ubiquitin abolishes UBM binding. Human pol iota contains two functional UBMs, both contributing to replication foci formation. In contrast, only the second UBM of Saccharomyces cerevisiae Rev1 binds to ubiquitin and is essential for Rev1-dependent cell survival and mutagenesis. Point mutations disrupting the UBM-ubiquitin interaction also impair the accumulation of pol iota in replication foci and Rev1-mediated DNA damage tolerance in vivo.", "doi": "10.1016/j.molcel.2009.12.038", "pmid": "20159559", "labels": {"Magda Bienko": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:05.589Z", "modified": "2022-11-07T11:35:11.258Z"}, {"entity": "publication", "iuid": "ca62411b1e5445d89801037afa0d7fd9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ca62411b1e5445d89801037afa0d7fd9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ca62411b1e5445d89801037afa0d7fd9"}}, "title": "The clock gene PER2 and sleep problems: association with alcohol consumption among Swedish adolescents.", "authors": [{"family": "Comasco", "given": "Erika", "initials": "E"}, {"family": "Nordquist", "given": "Niklas", "initials": "N"}, {"family": "G\u00f6kt\u00fcrk", "given": "Camilla", "initials": "C"}, {"family": "Aslund", "given": "Cecilia", "initials": "C"}, {"family": "Hallman", "given": "Jarmila", "initials": "J"}, {"family": "Oreland", "given": "Lars", "initials": "L"}, {"family": "Nilsson", "given": "Kent W", "initials": "KW"}], "type": "journal article", "published": "2010-02-00", "journal": {"title": "Ups. J. Med. Sci.", "issn": "2000-1967", "volume": "115", "issue": "1", "pages": "41-48", "issn-l": "0300-9734"}, "abstract": "Alcohol abuse is associated with sleep problems, which are often linked to circadian rhythm disturbances. Previous studies have separately examined the effects of mutations in the clock gene PER2 on alcohol consumption and sleep problems. Here we hypothesized that an allelic variation in the PER2 gene is associated with alcohol consumption in interaction with sleep problems among adolescents.\n\nThe Survey of Adolescent Life and Health in V\u00e4stmanland 2006, a Swedish county, including 1254 students 17-18 years old, was used as a population-representative sample of adolescents. We investigated the PER2 Single Nucleotide polymorphism (SNP) 10870 (A/G) in the cohort together with an assessment of alcohol consumption according to the AUDIT-C questionnaire, and sleep problems using a survey consisting of 18 items. Furthermore, we carried out an exploratory analysis on the PER2 Single Nucleotide Polymorphism 10870 polymorphism in a group of severely alcoholic females.\n\nWe found a significant association of the SNP 10870 in adolescent boys, where the genotype AA, in the presence of several and frequent sleep problems, was associated with increased alcohol consumption. Among adolescent girls, only sleep problems were related to alcohol consumption. A non-significant trend was observed among the severely alcoholic females, with the G allele being over-represented in the severely alcoholic females group in comparision to the control females.\n\nThese results indicate that PER2 gene variation is associated with alcohol consumption in interaction with sleep problems among Swedish adolescent boys.", "doi": "10.3109/03009731003597127", "pmid": "20187847", "labels": {"Erika Comasco": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC2853353"}], "notes": [], "created": "2020-11-20T09:32:05.402Z", "modified": "2024-10-24T08:56:54.437Z"}, {"entity": "publication", "iuid": "6708e878a89b47f1941bed717b108d8c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6708e878a89b47f1941bed717b108d8c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6708e878a89b47f1941bed717b108d8c"}}, "title": "Regulation of Translesion Synthesis DNA Polymerase \u03b7 by Monoubiquitination", "authors": [{"family": "Bienko", "given": "Marzena", "initials": "M"}, {"family": "Green", "given": "Catherine M", "initials": "CM"}, {"family": "Sabbioneda", "given": "Simone", "initials": "S"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Matic", "given": "Ivan", "initials": "I"}, {"family": "Hibbert", "given": "Richard G", "initials": "RG"}, {"family": "Begovic", "given": "Tihana", "initials": "T"}, {"family": "Niimi", "given": "Atsuko", "initials": "A"}, {"family": "Mann", "given": "Matthias", "initials": "M"}, {"family": "Lehmann", "given": "Alan R", "initials": "AR"}, {"family": "Dikic", "given": "Ivan", "initials": "I"}], "type": "journal-article", "published": "2010-02-00", "journal": {"volume": "37", "issn": "1097-2765", "issue": "3", "pages": "396-407", "title": "Molecular Cell", "issn-l": "1097-2765"}, "abstract": "DNA polymerase eta is a Y family polymerase involved in translesion synthesis (TLS). Its action is initiated by simultaneous interaction between the PIP box in pol eta and PCNA and between the UBZ in pol eta and monoubiquitin attached to PCNA. Whereas monoubiquitination of PCNA is required for its interaction with pol eta during TLS, we now show that monoubiquitination of pol eta inhibits this interaction, preventing its functions in undamaged cells. Identification of monoubiquitination sites within pol eta nuclear localization signal (NLS) led to the discovery that pol eta NLS directly contacts PCNA, forming an extended pol eta-PCNA interaction surface. We name this the PCNA-interacting region (PIR) and show that its monoubiquitination is downregulated by various DNA-damaging agents. We propose that this mechanism ensures optimal availability of nonubiquitinated, TLS-competent pol eta after DNA damage. Our work shows how monoubiquitination can either positively or negatively regulate the assembly of a protein complex, depending on which substrates are targeted by ubiquitin.", "doi": "10.1016/j.molcel.2009.12.039", "pmid": "20159558", "labels": {"Magda Bienko": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:02.185Z", "modified": "2022-11-07T11:35:11.270Z"}, {"entity": "publication", "iuid": "94870a6cda6c4e2999c7cfe1f2f07fda", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/94870a6cda6c4e2999c7cfe1f2f07fda.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/94870a6cda6c4e2999c7cfe1f2f07fda"}}, "title": "Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella Typhimurium.", "authors": [{"family": "Jonas", "given": "Kristina", "initials": "K"}, {"family": "Edwards", "given": "Adrianne N", "initials": "AN"}, {"family": "Ahmad", "given": "Irfan", "initials": "I"}, {"family": "Romeo", "given": "Tony", "initials": "T"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}, {"family": "Melefors", "given": "Ojar", "initials": "O"}], "type": "journal article", "published": "2010-02-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "12", "issue": "2", "pages": "524-540", "issn-l": "1462-2912"}, "abstract": "Bacterial survival depends on the ability to switch between sessile and motile lifestyles in response to changing environmental conditions. In many species, this switch is governed by (3'-5')-cyclic-diguanosine monophosphate (c-di-GMP), a signalling molecule, which is metabolized by proteins containing GGDEF and/or EAL domains. Salmonella Typhimurium contains 20 such proteins. Here, we show that the RNA-binding protein CsrA regulates the expression of eight genes encoding GGDEF, GGDEF-EAL and EAL domain proteins. CsrA bound directly to the mRNA leaders of five of these genes, suggesting that it may regulate these genes post-transcriptionally. The c-di-GMP-specific phosphodiesterase STM3611, which reciprocally controls flagella function and production of biofilm matrix components, was regulated by CsrA binding to the mRNA, but was also indirectly regulated by CsrA through the FlhDC/FliA flagella cascade and STM1344. STM1344 is an unconventional (c-di-GMP-inactive) EAL domain protein, recently identified as a negative regulator of flagella gene expression. Here, we demonstrate that CsrA directly downregulates expression of STM1344, which in turn regulates STM3611 through fliA and thus reciprocally controls motility and biofilm factors. Altogether, our data reveal that the concerted and complex regulation of several genes encoding GGDEF/EAL domain proteins allows CsrA to control the motility-sessility switch in S. Typhimurium at multiple levels.", "doi": "10.1111/j.1462-2920.2009.02097.x", "pmid": "19919539", "labels": {"Kristina Jonas": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "EMI2097"}, {"db": "pmc", "key": "PMC2888478"}, {"db": "mid", "key": "NIHMS194244"}], "notes": [], "created": "2018-12-03T14:30:25.734Z", "modified": "2022-11-07T11:33:47.254Z"}, {"entity": "publication", "iuid": "8d454eaae96742e7a0a5d5ceb36c42dd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8d454eaae96742e7a0a5d5ceb36c42dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8d454eaae96742e7a0a5d5ceb36c42dd"}}, "title": "Structure Determination and Improved Model of Plant Photosystem I", "authors": [{"family": "Amunts", "given": "Alexey", "initials": "A"}, {"family": "Toporik", "given": "Hila", "initials": "H"}, {"family": "Borovikova", "given": "Anna", "initials": "A"}, {"family": "Nelson", "given": "Nathan", "initials": "N"}], "type": "journal-article", "published": "2010-01-29", "journal": {"volume": "285", "issn": "0021-9258", "issue": "5", "pages": "3478-3486", "title": "J. Biol. Chem.", "issn-l": null}, "abstract": "Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction. Our current understanding of the sophisticated mechanisms underlying these processes has profited greatly from elucidation of the crystal structures of the Photosystem I complex. In this report, we describe the developments that ultimately led to enhanced structural information of plant Photosystem I. In addition, we report an improved crystallographic model at 3.3-A resolution, which allows analysis of the structure in more detail. An improved electron density map yielded identification and tracing of subunit PsaK. The location of an additional ten beta-carotenes as well as five chlorophylls and several loop regions, which were previously uninterpretable, are now modeled. This represents the most complete plant Photosystem I structure obtained thus far, revealing the locations of and interactions among 17 protein subunits and 193 non-covalently bound photochemical cofactors. Using the new crystal structure, we examine the network of contacts among the protein subunits from the structural perspective, which provide the basis for elucidating the functional organization of the complex.", "doi": "10.1074/jbc.m109.072645", "pmid": "19923216", "labels": {"Alexey Amunts": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:24:55.350Z", "modified": "2022-11-07T11:30:20.501Z"}, {"entity": "publication", "iuid": "58c167e3e79e4eaaa09215d0ba320218", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/58c167e3e79e4eaaa09215d0ba320218.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/58c167e3e79e4eaaa09215d0ba320218"}}, "title": "Differential effects of anti-apoptotic Bcl-2 family members Mcl-1, Bcl-2, and Bcl-xL on Celecoxib-induced apoptosis", "authors": [{"family": "Rudner", "given": "Justine", "initials": "J"}, {"family": "Elsaesser", "given": "Simon Johannes", "initials": "SJ"}, {"family": "M\u00fcller", "given": "Arndt Christian", "initials": "AC"}, {"family": "Belka", "given": "Claus", "initials": "C"}, {"family": "Jendrossek", "given": "Verena", "initials": "V"}], "type": "journal-article", "published": "2010-01-00", "journal": {"volume": "79", "issn": "0006-2952", "issue": "1", "pages": "10-20", "title": "Biochemical Pharmacology", "issn-l": "0006-2952"}, "abstract": "The cyclooxygenase-2 inhibitor Celecoxib is a potent inducer of apoptosis in tumor cells. In most cellular systems Celecoxib induces apoptosis via an intrinsic, mitochondrial apoptosis pathway. We recently showed that in Bax-negative Jurkat cells expression of pro-apoptotic Bak is essential for Celecoxib-induced mitochondrial damage and apoptosis induction. Aim of the present study was to identify specific pro- and anti-apoptotic members of the Bcl-2 family involved in the regulation of Bak activation, and subsequent apoptosis upon treatment with Celecoxib in the Jurkat cell model. Our results show that apoptosis in response to Celecoxib required the presence of Noxa and downregulation of the anti-apoptotic protein Mcl-1. Celecoxib-induced Bak activation and subsequent apoptosis could be inhibited by overexpression of Bcl-xL but not by the very similar Bcl-2. In Bcl-xL-overexpressing cells neutralization of both, Mcl-1 and Bcl-xL, was prerequisite for an efficient induction of apoptosis. Our data reveal an important role of the Mcl-1/Noxa axis for Celecoxib-induced apoptosis and suggest that Celecoxib may be of value for treatment of tumors addicted to Mcl-1 and for combined treatment approaches targeting anti-apoptotic Bcl-2 family members.", "doi": "10.1016/j.bcp.2009.07.021", "pmid": "19665451", "labels": {"Simon Els\u00e4sser": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:24:51.916Z", "modified": "2022-11-07T11:38:06.892Z"}, {"entity": "publication", "iuid": "061a221627534ef9a6701847496b185c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/061a221627534ef9a6701847496b185c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/061a221627534ef9a6701847496b185c"}}, "title": "Novel and Practical Synthesis of Candesartan Cilexetil", "authors": [{"family": "Shen", "given": "Jingshan", "initials": "J"}, {"family": "Mao", "given": "Yongjun", "initials": "Y"}, {"family": "Xiong", "given": "Ruisheng", "initials": "R"}, {"family": "Liu", "given": "Zheng", "initials": "Z"}, {"family": "Li", "given": "Haihong", "initials": "H"}, {"family": "Shen", "given": "Jingkang", "initials": "J"}], "type": "journal-article", "published": "2010-00-00", "journal": {"title": "HETEROCYCLES", "issn": "0385-5414", "volume": "81", "issue": "6", "pages": "1503", "issn-l": null}, "abstract": null, "doi": "10.3987/com-10-11944", "pmid": null, "labels": {"Ruisheng Xiong": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2025-11-27T17:41:02.725Z", "modified": "2025-12-05T10:16:35.536Z"}, {"entity": "publication", "iuid": "91213e7b1035466cbecc54faef7fcb36", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/91213e7b1035466cbecc54faef7fcb36.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/91213e7b1035466cbecc54faef7fcb36"}}, "title": "Improved Total Synthesis of Racemic Rutamarin", "authors": [{"family": "Jiang", "given": "Xiangrui", "initials": "X"}, {"family": "Sun", "given": "Hongbin", "initials": "H"}, {"family": "Xiong", "given": "Ruisheng", "initials": "R"}, {"family": "Jiang", "given": "Hong", "initials": "H"}, {"family": "Tong", "given": "Ling", "initials": "L"}, {"family": "Jiang", "given": "Hualiang", "initials": "H"}, {"family": "Shen", "given": "Jingshan", "initials": "J"}], "type": "journal-article", "published": "2010-00-00", "journal": {"title": "HETEROCYCLES", "issn": "0385-5414", "volume": "81", "issue": "7", "pages": "1697", "issn-l": null}, "abstract": null, "doi": "10.3987/com-10-11962", "pmid": null, "labels": {"Ruisheng Xiong": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2025-11-27T17:40:31.033Z", "modified": "2025-12-05T10:16:05.690Z"}, {"entity": "publication", "iuid": "0d190989356947b9ab356bd6f5082206", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0d190989356947b9ab356bd6f5082206.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0d190989356947b9ab356bd6f5082206"}}, "title": "Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists", "authors": [{"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "Kudryavtsev", "given": "Alexander", "initials": "A"}, {"family": "Matz", "given": "Mikhail V", "initials": "MV"}, {"family": "Aglyamova", "given": "Galina V", "initials": "GV"}, {"family": "Bulman", "given": "Simon", "initials": "S"}, {"family": "Fiers", "given": "Mark", "initials": "M"}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ"}, {"family": "Pawlowski", "given": "Jan", "initials": "J"}], "type": "journal-article", "published": "2010-00-00", "journal": {"volume": "10", "issn": "1471-2148", "issue": "1", "pages": "377", "title": "BMC Evol Biol BMC Evolutionary Biology", "issn-l": "1471-2148"}, "abstract": "Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica).\n\n167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin insertion in Acantharea. Finally, this work reveals another possible rhizarian signature in the 60S ribosomal protein L10a.\n\nOur study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.", "doi": "10.1186/1471-2148-10-377", "pmid": "21126361", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:26:10.486Z", "modified": "2022-11-07T11:31:56.857Z"}, {"entity": "publication", "iuid": "90bfa6c0f3854c5590db6d0fe336af04", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/90bfa6c0f3854c5590db6d0fe336af04.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/90bfa6c0f3854c5590db6d0fe336af04"}}, "title": "Deciphering the porcine intestinal microRNA transcriptome", "authors": [{"family": "Sharbati", "given": "Soroush", "initials": "S"}, {"family": "Friedlander", "given": "Marc R", "initials": "MR"}, {"family": "Sharbati", "given": "Jutta", "initials": "J"}, {"family": "Hoeke", "given": "Lena", "initials": "L"}, {"family": "Chen", "given": "Wei", "initials": "W"}, {"family": "Keller", "given": "Andreas", "initials": "A"}, {"family": "Stahler", "given": "Peer F", "initials": "PF"}, {"family": "Rajewsky", "given": "Nikolaus", "initials": "N"}, {"family": "Einspanier", "given": "Ralf", "initials": "R"}], "type": "journal-article", "published": "2010-00-00", "journal": {"volume": "11", "issn": "1471-2164", "issue": "1", "pages": "275", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy.\n\nHere, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks.\n\nIn this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.", "doi": "10.1186/1471-2164-11-275", "pmid": "20433717", "labels": {"Marc Friedl\u00e4nder": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:25:32.659Z", "modified": "2022-11-07T11:35:26.357Z"}]}