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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Wednesday, 2014 February 19
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PubMed Results

Items 1 - 4 of 4

1.	Nature. 2014 Feb 6;506(7486):21-2. doi: 10.1038/506020a. Winter Olympics: downhill forecast. Morello L.
	PMID: 24499901 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Feb 6;506(7486):58-62. doi: 10.1038/nature12959. Epub 2014 Jan 29. An environmental bacterial taxon with a large and distinct metabolic repertoire. Wilson MC1, Mori T2, Rückert C3, Uria AR4, Helf MJ4, Takada K5, Gernert C6, Steffens UA7, Heycke N7, Schmitt S8, Rinke C9, Helfrich EJ4, Brachmann AO10, Gurgui C7, Wakimoto T11, Kracht M7, Crüsemann M7, Hentschel U6, Abe I11, Matsunaga S5, Kalinowski J3, Takeyama H12, Piel J4. Author information: 11] Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland [2] Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany [3]. 21] Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan [2]. 3Institute for Genome Research and Systems Biology, Center for Biotechnology, Universität Bielefeld, Universitätstrasse 25, 33594 Bielefeld, Germany. 41] Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland [2] Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany. 5Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. 6Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany. 7Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany. 8Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig Maximilians University Munich, Richard-Wagner-Strasse 10, 80333 Munich, Germany. 9Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA. 10Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland. 11Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. 12Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Comment in Microbiology: a talented genus. [Nature. 2014] Microbiology: a talented genus.Jaspars M, Challis G. Nature. 2014 Feb 6; 506(7486):38-9. Epub 2014 Jan 29. Abstract Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such 'talented' producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus 'Entotheonella' with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. 'Entotheonella' spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum 'Tectomicrobia'. The pronounced bioactivities and chemical uniqueness of 'Entotheonella' compounds provide significant opportunities for ecological studies and drug discovery.
	PMID: 24476823 [PubMed - indexed for MEDLINE]
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3.	Nature. 2014 Jan 30;505(7485):635-40. doi: 10.1038/nature12943. Epub 2014 Jan 19. The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A1, Soumillon M1, Warnefors M2, Liechti A2, Daish T3, Zeller U4, Baker JC5, Grützner F3, Kaessmann H2. Author information: 11] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland [3] Laboratory of Developmental Genomics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.); Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA (M.S.). 21] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. 3The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia. 4Department of Systematic Zoology, Faculty of Agriculture and Horticulture, Humboldt University Berlin, 10099 Berlin, Germany. 5Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA. Abstract Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.
	PMID: 24463510 [PubMed - indexed for MEDLINE]
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4.	Nature. 2014 Feb 6;506(7486):89-92. doi: 10.1038/nature12872. Epub 2013 Dec 22. Three keys to the radiation of angiosperms into freezing environments. Zanne AE1, Tank DC2, Cornwell WK3, Eastman JM2, Smith SA4, FitzJohn RG5, McGlinn DJ6, O'Meara BC7, Moles AT8, Reich PB9, Royer DL10, Soltis DE11, Stevens PF12, Westoby M13, Wright IJ13, Aarssen L14, Bertin RI15, Calaminus A16, Govaerts R17, Hemmings F8, Leishman MR13, Oleksyn J18, Soltis PS19, Swenson NG20, Warman L21, Beaulieu JM22. Author information: 11] Department of Biological Sciences, George Washington University, Washington DC 20052, USA [2] Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, Missouri 63121, USA. 21] Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA [2] Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844, USA. 31] Department of Ecological Sciences, Systems Ecology, de Boelelaan 1085, 1081 HV Amsterdam, the Netherlands [2] Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia. 4Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA. 51] Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada [2] Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia. 6Department of Biology and the Ecology Center, Utah State University, Logan, Utah 84322, USA. 7Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA. 8Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia. 91] Department of Forest Resources, University of Minnesota, St Paul, Minnesota 55108, USA [2] Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, New South Wales 2751, Australia. 10Department of Earth and Environmental Sciences, Wesleyan University, Middletown, Connecticut 06459, USA. 111] Department of Biology, University of Florida, Gainesville, Florida 32611, USA [2] Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA [3] Genetics Institute, University of Florida, Gainesville, Florida 32611, USA. 12Department of Biology, University of Missouri-St Louis, St Louis, Missouri 63121, USA. 13Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia. 14Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada. 15Department of Biology, College of the Holy Cross, Worcester, Massachusetts 01610, USA. 16Department of Biology, University of Florida, Gainesville, Florida 32611, USA. 17Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. 181] Department of Forest Resources, University of Minnesota, St Paul, Minnesota 55108, USA [2] Polish Academy of Sciences, Institute of Dendrology, 62-035 Kornik, Poland. 191] Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA [2] Genetics Institute, University of Florida, Gainesville, Florida 32611, USA. 20Department of Plant Biology and Ecology, Evolutionary Biology and Behavior, Program, Michigan State University, East Lansing, Michigan 48824, USA. 211] Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia [2] Institute of Pacific Islands Forestry, USDA Forest Service, Hilo, Hawaii 96720, USA. 22National Institute for Mathematical & Biological Synthesis, University of Tennessee, Knoxville, Tennessee 37996, USA. Abstract Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species' traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.
	PMID: 24362564 [PubMed - indexed for MEDLINE]
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