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  • 1.
    Huang, Hailiang
    et al.
    Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston MA, United States; Broad Institute of MIT and Harvard, Cambridge MA, United States.
    Halfvarson, Jonas
    Örebro University, School of Medical Sciences. Department of Gastroenterology, Faculty of Health and Medical Sciences, Örebro University, Örebro, Sweden.
    Barrett, Jeffrey C.
    Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.
    Fine-mapping inflammatory bowel disease loci to single-variant resolution2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 547, no 7662, p. 173-+Article in journal (Refereed)
    Abstract [en]

    Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty. These 45 variants are significantly enriched for protein-coding changes (n = 13), direct disruption of transcription-factor binding sites (n = 3), and tissue-specific epigenetic marks (n = 10), with the last category showing enrichment in specific immune cells among associations stronger in Crohn's disease and in gut mucosa among associations stronger in ulcerative colitis. The results of this study suggest that high-resolution fine-mapping in large samples can convert many discoveries from genome-wide association studies into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms.

  • 2.
    Husu, Liisa
    et al.
    Örebro University, School of Humanities, Education and Social Sciences.
    Al-Gazali, Lihadh
    United Arab Emirates Univ, Al Ain, United Arab Emirates.
    Valian, Virginia
    CUNY Hunter Coll, New York, USA; CUNY, Graduate Center, New York NY, USA.
    Barres, Ben
    Stanford Univ, Stanford, USA.
    Wu, Ling-An
    Inst Phys, Chinese Acad Sci, Beijing, China.
    Andrei, Eva Y.
    Rutgers State Univ, Piscataway Township NJ, USA.
    Handelsman, Jo
    Yale Univ, New Haven, USA.
    Moss-Racusin, Corinne
    Yale Univ, New Haven, USA.
    Scientists of the world speak up for equality2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 495, no 7439, p. 35-38Article in journal (Refereed)
    Abstract [en]

    Eight experts give their prescriptions for measures that will help to close the gender gap in national from China to Sweden

  • 3. Högberg, Peter
    et al.
    Nordgren, Anders
    Buchmann, Nina
    Taylor, Andrew F. S.
    Ekblad, Alf
    Örebro University, Department of Natural Sciences.
    Högberg, Mona N.
    Nyberg, Gert
    Ottosson-Löfvenius, Mikaell
    Read, David J.
    Large-scale forest girdling shows that current photosynthesis drives soil respiration2001In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 411, no 6839, p. 789-792Article in journal (Refereed)
    Abstract [en]

    The respiratory activities of plant roots, of their mycorrhizal fungi and of the free-living microbial heterotrophs (decomposers) in soils are significant components of the global carbon balance, but their relative contributions remain uncertain. To separate mycorrhizal root respiration from heterotrophic respiration in a boreal pine forest, we conducted a large-scale tree-girdling experiment, comprising 9 plots each containing about 120 trees. Tree-girdling involves stripping the stem bark to the depth of the current xylem at breast height terminating the supply of current photosynthates to roots and their mycorrhizal fungi without physically disturbing the delicate root-microbe-soil system. Here we report that girdling reduced soil respiration within 1-2 months by about 54% relative to respiration on ungirdled control plots, and that decreases of up to 37% were detected within 5 days. These values clearly show that the flux of current assimilates to roots is a key driver of soil respiration; they are conservative estimates of root respiration, however, because girdling increased the use of starch reserves in the roots. Our results indicate that models of soil respiration should incorporate measures of photosynthesis and of seasonal patterns of photosynthate allocation to roots.

  • 4.
    Jostins, Luke
    et al.
    Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
    Halfvarson, Jonas
    Örebro University Hospital. Örebro University, School of Medical Sciences.
    Cho, Judy H.
    Department of Genetics, Yale School of Medicine, New Haven CT, United States; Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven CT, United States.
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease2012In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 491, no 7422, p. 119-124Article in journal (Refereed)
    Abstract [en]

    Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations(1). Genome-wide association studies and subsequent meta-analyses of these two diseases(2,3) as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy(4), in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases(5). Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

  • 5. Näsholm, Torgny
    et al.
    Ekblad, Alf
    Örebro University, Department of Natural Sciences.
    Nordin, Annika
    Giesler, Reiner
    Högberg, Mona
    Högberg, Peter
    Boreal forest plants take up organic nitrogen1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 392, no 6679, p. 914-916Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    Plant growth in the boreal forest, the largest terrestrial biome, is generally limited by the availability of nitrogen. The presumed cause of this limitation is slow mineralization of soil organic nitrogen1,2. Here we demonstrate, to our knowledge for the first time, the uptake of organic nitrogen in the field by the trees Pinus sylvestris and Picea abies, the dwarf shrub Vaccinium myrtillus and the grass Deschampsia flexuosa. These results show that these plants, irrespective of their different types of root–fungal associations (mycorrhiza), bypass nitrogen mineralization. A trace of the amino acid glycine, labelled with the stable isotopes 13C and 15N, was injected into the organic (mor) layer of an old successional boreal coniferous forest. Ratios of 13C:15N in the roots showed that at least 91, 64 and 42% of the nitrogen from the absorbed glycine was taken up in intact glycine by the dwarf shrub, the grass and the trees, respectively. Rates of glycine uptake were similar to those of 15N-ammonium. Our data indicate that organic nitrogen is important for these different plants, even when they are competing with each other and with non-symbiotic microorganisms. This has major implications for our understanding of the effects of nitrogen deposition, global warming and intensified forestry.

  • 6.
    Pedersen, Helle Krogh
    et al.
    Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
    Gudmundsdottir, Valborg
    Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
    Nielsen, Henrik Bjorn
    Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
    Hyötyläinen, Tuulia
    Örebro University, School of Science and Technology. Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland; Turku Centre for Biotechnology, University of Turku, Turku, Finland; VTT Technical Research Centre of Finland, Espoo, Finland.
    Nielsen, Trine
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
    Jensen, Benjamin A. H.
    Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
    Forslund, Kristoffer
    European Molecular Biology Laboratory, Heidelberg, Germany.
    Hildebrand, Falk
    European Molecular Biology Laboratory, Heidelberg, Germany; Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium; Center for the Biology of Disease, VIB, Leuven, Belgium.
    Prifti, Edi
    MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France; Institute of Cardiometabolism and Nutrition (ICAN), Paris, France.
    Falony, Gwen
    Center for the Biology of Disease, VIB, Leuven, Belgium; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
    Le Chatelier, Emmanuelle
    MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.
    Levenez, Florence
    MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.
    Dore, Joel
    MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France; Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
    Mattila, Ismo
    VTT Technical Research Centre of Finland, Espoo, Finland; Steno Diabetes Center, Gentofte, Denmark.
    Plichta, Damian R.
    Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens, Lyngby, Denmark.
    Pöhö, Paivi
    VTT Technical Research Centre of Finland, Espoo, Finland; Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
    Hellgren, Lars I.
    Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens, Lyngby, Denmark.
    Arumugam, Manimozhiyan
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
    Sunagawa, Shinichi
    European Molecular Biology Laboratory, Heidelberg, Germany; Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
    Vieira-Silva, Sara
    Center for the Biology of Disease, VIB, Leuven, Belgium; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
    Jørgensen, Torben
    Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Research Centre for Prevention and Health, Centre for Health, Capital Region, Glostrup Hospital, Glostrup, Denmark.
    Holm, Jacob Bak
    Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
    Trost, Kajetan
    Steno Diabetes Center, Gentofte, Denmark.
    Kristiansen, Karsten
    Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; BGI-Shenzhen, Shenzhen, China.
    Brix, Susanne
    Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens, Lyngby, Denmark.
    Raes, Jeroen
    Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium; Center for the Biology of Disease, VIB, Leuven, Belgium; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
    Wang, Jun
    Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; BGI-Shenzhen, Shenzhen, China; Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia; Macau University of Science and Technology, Taipa, China; Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.
    Hansen, Torben
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.
    Bork, Peer
    European Molecular Biology Laboratory, Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, Berlin, Germany; Department of Bioinformatics, University of Wuerzburg, Würzburg, Germany.
    Brunak, Søren
    Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens, Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
    Oresic, Matej
    Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland; VTT Technical Research Centre of Finland, Espoo, Finland; Steno Diabetes Center, Gentofte, Denmark.
    Ehrlich, S. Dusko
    Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark; University of Örebro, Örebro, Sweden.
    Pedersen, Oluf
    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
    Human gut microbes impact host serum metabolome and insulin sensitivity2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 535, no 7612, p. 376-381Article in journal (Refereed)
    Abstract [en]

    Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus are identified as the main species driving the association between biosynthesis of BCAAs and insulin resistance, and in mice we demonstrate that P. copri can induce insulin resistance, aggravate glucose intolerance and augment circulating levels of BCAAs. Our findings suggest that microbial targets may have the potential to diminish insulin resistance and reduce the incidence of common metabolic and cardiovascular disorders.

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