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

Sent on Friday, 2014 February 28
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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Item 1 of 1

1.	Nat Med. 2013 Dec;19(12):1638-42. doi: 10.1038/nm.3408. Epub 2013 Nov 24. Subinfectious hepatitis C virus exposures suppress T cell responses against subsequent acute infection. Park SH1, Veerapu NS, Shin EC, Biancotto A, McCoy JP, Capone S, Folgori A, Rehermann B. Author information: 1Immunology Section, Liver Diseases Branch, NIDDK, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, Maryland, USA. Comment in Viral hepatitis: Subinfectious HCV exposure. [Nat Rev Gastroenterol Hepatol. 2014] Viral hepatitis: Subinfectious HCV exposure.Leake I. Nat Rev Gastroenterol Hepatol. 2014 Jan; 11(1):4. Epub 2013 Dec 3. Abstract Hepatitis C virus (HCV) is endemic in many countries due to its high propensity for establishing persistence. The presence of HCV-specific T cells in subjects repeatedly exposed to HCV who test negative for HCV RNA and antibodies and who do not have any history of HCV infection has been interpreted as T cell-mediated protection. Here, we show in nonhuman primates that repeated exposure to human plasma with trace amounts of HCV induced HCV-specific T cells without seroconversion and systemic viremia but did not protect upon subsequent HCV challenge. Rather, HCV-specific recall and de novo T cell responses, as well as intrahepatic T cell recruitment and interferon-γ (IFN-γ) production, were suppressed upon HCV challenge, concomitant with quantitative and qualitative changes in regulatory T cells (T(reg) cells) that occurred after subinfectious HCV exposure and increased after HCV challenge. In vitro T(reg) cell depletion restored HCV-specific T cell responses. Thus, T cells primed by trace amounts of HCV do not generate effective recall responses upon subsequent HCV infection. Subinfectious HCV exposure predisposes to T(reg) cell expansion, which suppresses effector T cells during subsequent infection. Strategies to reverse this exposure-induced immune suppression should be examined to aid in the development of T cell-based vaccines against HCV and other endemic pathogens.
	PMID: 24270546 [PubMed - indexed for MEDLINE]

What's new for 'JKB_daily1' in PubMed

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

Sent on Wednesday, 2014 February 26
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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1.	N Engl J Med. 2014 Feb 20;370(8):753-62. doi: 10.1056/NEJMcpc1208155. Case records of the Massachusetts General Hospital. Case 6-2014. A 35-day-old boy with fever, vomiting, mottled skin, and severe anemia. Yager PH, Luginbuhl LM, Dekker JP.
	PMID: 24552323 [PubMed - indexed for MEDLINE]
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2.	N Engl J Med. 2014 Feb 13;370(7):678. doi: 10.1056/NEJMc1315498#SA1. Absence of HIV-1 after treatment cessation in an infant. De Maria A. Comment in Absence of HIV-1 after treatment cessation in an infant. [N Engl J Med. 2014] Absence of HIV-1 after treatment cessation in an infant.Persaud D, Luzuriaga K. N Engl J Med. 2014 Feb 13; 370(7):678. Comment on Absence of detectable HIV-1 viremia after treatment cessation in an infant. [N Engl J Med. 2013] Absence of detectable HIV-1 viremia after treatment cessation in an infant.Persaud D, Gay H, Ziemniak C, Chen YH, Piatak M Jr, Chun TW, Strain M, Richman D, Luzuriaga K. N Engl J Med. 2013 Nov 7; 369(19):1828-35. Epub 2013 Oct 23.
	PMID: 24521124 [PubMed - indexed for MEDLINE]
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3.	N Engl J Med. 2014 Feb 13;370(7):678. doi: 10.1056/NEJMc1315498. Absence of HIV-1 after treatment cessation in an infant. Persaud D, Luzuriaga K. Comment on Absence of HIV-1 after treatment cessation in an infant. [N Engl J Med. 2014] Absence of HIV-1 after treatment cessation in an infant.De Maria A. N Engl J Med. 2014 Feb 13; 370(7):678. Absence of detectable HIV-1 viremia after treatment cessation in an infant. [N Engl J Med. 2013] Absence of detectable HIV-1 viremia after treatment cessation in an infant.Persaud D, Gay H, Ziemniak C, Chen YH, Piatak M Jr, Chun TW, Strain M, Richman D, Luzuriaga K. N Engl J Med. 2013 Nov 7; 369(19):1828-35. Epub 2013 Oct 23. Free Article
	PMID: 24521123 [PubMed - indexed for MEDLINE]
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4.	Science. 2014 Feb 7;343(6171):626. doi: 10.1126/science.1251005. Retrospective. Janet Rowley (1925-2013). Greaves M. Author information: The Institute of Cancer Research, London SM2 5NG, UK.
	PMID: 24503847 [PubMed - indexed for MEDLINE]
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5.	Science. 2014 Feb 7;343(6171):617-8. doi: 10.1126/science.1250173. Geochemistry. Limits of soil production? Heimsath AM. Author information: School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA. Comment on Rapid soil production and weathering in the Southern Alps, New Zealand. [Science. 2014] Rapid soil production and weathering in the Southern Alps, New Zealand.Larsen IJ, Almond PC, Eger A, Stone JO, Montgomery DR, Malcolm B. Science. 2014 Feb 7; 343(6171):637-40. Epub 2014 Jan 16.
	PMID: 24503841 [PubMed - indexed for MEDLINE]
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6.	Science. 2014 Feb 7;343(6171):637-40. doi: 10.1126/science.1244908. Epub 2014 Jan 16. Rapid soil production and weathering in the Southern Alps, New Zealand. Larsen IJ1, Almond PC, Eger A, Stone JO, Montgomery DR, Malcolm B. Author information: 1Department of Earth and Space Sciences and Quaternary Research Center, University of Washington, Seattle, WA 98195-1310, USA. Comment in Geochemistry. Limits of soil production? [Science. 2014] Geochemistry. Limits of soil production?Heimsath AM. Science. 2014 Feb 7; 343(6171):617-8. Abstract Evaluating conflicting theories about the influence of mountains on carbon dioxide cycling and climate requires understanding weathering fluxes from tectonically uplifting landscapes. The lack of soil production and weathering rate measurements in Earth's most rapidly uplifting mountains has made it difficult to determine whether weathering rates increase or decline in response to rapid erosion. Beryllium-10 concentrations in soils from the western Southern Alps, New Zealand, demonstrate that soil is produced from bedrock more rapidly than previously recognized, at rates up to 2.5 millimeters per year. Weathering intensity data further indicate that soil chemical denudation rates increase proportionally with erosion rates. These high weathering rates support the view that mountains play a key role in global-scale chemical weathering and thus have potentially important implications for the global carbon cycle.
	PMID: 24436184 [PubMed - indexed for MEDLINE]
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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Tuesday, 2014 February 25
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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1.	Science. 2014 Jan 24;343(6169):1236573. doi: 10.1126/science.1236573. A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Shapiro B1, Hofreiter M. Author information: 1Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA. Abstract The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.
	PMID: 24458647 [PubMed - indexed for MEDLINE]
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2.	Science. 2014 Jan 24;343(6169):437-40. doi: 10.1126/science.1247167. Transmissible dog cancer genome reveals the origin and history of an ancient cell lineage. Murchison EP1, Wedge DC, Alexandrov LB, Fu B, Martincorena I, Ning Z, Tubio JM, Werner EI, Allen J, De Nardi AB, Donelan EM, Marino G, Fassati A, Campbell PJ, Yang F, Burt A, Weiss RA, Stratton MR. Author information: 1Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. Comment in Cancer. Hiding in plain view--an ancient dog in the modern world. [Science. 2014] Cancer. Hiding in plain view--an ancient dog in the modern world.Parker HG, Ostrander EA. Science. 2014 Jan 24; 343(6169):376-8. Abstract Canine transmissible venereal tumor (CTVT) is the oldest known somatic cell lineage. It is a transmissible cancer that propagates naturally in dogs. We sequenced the genomes of two CTVT tumors and found that CTVT has acquired 1.9 million somatic substitution mutations and bears evidence of exposure to ultraviolet light. CTVT is remarkably stable and lacks subclonal heterogeneity despite thousands of rearrangements, copy-number changes, and retrotransposon insertions. More than 10,000 genes carry nonsynonymous variants, and 646 genes have been lost. CTVT first arose in a dog with low genomic heterozygosity that may have lived about 11,000 years ago. The cancer spawned by this individual dispersed across continents about 500 years ago. Our results provide a genetic identikit of an ancient dog and demonstrate the robustness of mammalian somatic cells to survive for millennia despite a massive mutation burden. PMCID: PMC3918581 [Available on 2014/7/24]
	PMID: 24458646 [PubMed - indexed for MEDLINE]
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3.	Science. 2014 Jan 24;343(6169):361-3. doi: 10.1126/science.343.6169.361. The epigenetics heretic. Kaiser J.
	PMID: 24458620 [PubMed - indexed for MEDLINE]
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4.	Science. 2014 Jan 24;343(6169):356-7. doi: 10.1126/science.343.6169.356. Clinical research. Divulging DNA secrets of dead stirs debate. Couzin-Frankel J.
	PMID: 24458615 [PubMed - indexed for MEDLINE]
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Sent on Wednesday, 2014 February 19
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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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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Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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1.	Nat Genet. 2013 Dec;45(12):1431-8. doi: 10.1038/ng.2811. Epub 2013 Oct 27. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, Wang T, Yeung CK, Chen L, Ma J, Zhang J, Jiang A, Li J, Zhou C, Zhang J, Liu Y, Sun X, Zhao H, Niu Z, Lou P, Xian L, Shen X, Liu S, Zhang S, Zhang M, Zhu L, Shuai S, Bai L, Tang G, Liu H, Jiang Y, Mai M, Xiao J, Wang X, Zhou Q, Wang Z, Stothard P, Xue M, Gao X, Luo Z, Gu Y, Zhu H, Hu X, Zhao Y, Plastow GS, Wang J, Jiang Z, Li K, Li N, Li X, Li R. Author information: 1] Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China. [2] Biodynamic Optical Imaging Center (BIOPIC), Peking-Tsinghua Center for Life Sciences and School of Life Sciences, Peking University, Beijing, China. [3]. Abstract We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched for genomic regions under selection, which includes genes that are involved in hypoxia, olfaction, energy metabolism and drug response. Comparing the genome of Tibetan wild boar with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig. We also report genetic adaptations in Tibetan wild boar that are associated with high altitudes and characterize the genetic basis of increased salivation in domestic pig.
	PMID: 24162736 [PubMed - indexed for MEDLINE]

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1.	Nature. 2014 Jan 16;505(7483):286-7. Regulation: The FDA is overcautious on consumer genomics. Green RC, Farahany NA.
	PMID: 24436984 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Jan 16;505(7483):412-6. doi: 10.1038/nature12807. Epub 2013 Dec 8. Muc5b is required for airway defence. Roy MG1, Livraghi-Butrico A2, Fletcher AA3, McElwee MM4, Evans SE4, Boerner RM5, Alexander SN4, Bellinghausen LK4, Song AS4, Petrova YM4, Tuvim MJ4, Adachi R4, Romo I6, Bordt AS7, Bowden MG8, Sisson JH9, Woodruff PG10, Thornton DJ11, Rousseau K11, De la Garza MM4, Moghaddam SJ4, Karmouty-Quintana H 5, Blackburn MR5, Drouin SM5, Davis CW12, Terrell KA12, Grubb BR12, O'Neal WK12, Flores SC13, Cota-Gomez A13, Lozupone CA13, Donnelly JM13, Watson AM13, Hennessy CE13, Keith RC13, Yang IV13, Barthel L14, Henson PM14, Janssen WJ14, Schwartz DA13, Boucher RC12, Dickey BF4, Evans CM15. Author information: 11] University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2]. 21] University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA [2]. 31] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA [2]. 4University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. 5University of Texas Health Science Center-Houston Medical School, 6431 Fannin Street, Houston, Texas 77030, USA. 61] University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] Instituto Tecnológico y de Estudios Superiores de Monterrey, Avenida Eugenio Garza Sada 2501 Sur Colonia Tecnológico, Monterrey, Nuevo León 64849, Mexico. 7Texas A&M Health Science Center, 2121 W. Holcombe Boulevard, Houston, Texas 77030, USA. 81] Texas A&M Health Science Center, 2121 W. Holcombe Boulevard, Houston, Texas 77030, USA [2] University of Houston-Downtown, 1 Main Street, Houston, Texas 77002, USA. 9University of Nebraska Medical Center, 985910 Nebraska Medical Center, Omaha, Nebraska 68198, USA. 10University of California San Francisco, 505 Parnassus Avenue, San Francisco, California 27599, USA. 11University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. 12University of North Carolina-Chapel Hill, 7011 Thurston-Bowles Building, Chapel Hill, North Carolina 27599, USA. 13University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. 141] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA [2] National Jewish Health, Denver, Colorado 80206, USA. 151] University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] University of Colorado School of Medicine, 12700 East 19th Avenue, Aurora, Colorado 80045, USA. Abstract Respiratory surfaces are exposed to billions of particulates and pathogens daily. A protective mucus barrier traps and eliminates them through mucociliary clearance (MCC). However, excessive mucus contributes to transient respiratory infections and to the pathogenesis of numerous respiratory diseases. MUC5AC and MUC5B are evolutionarily conserved genes that encode structurally related mucin glycoproteins, the principal macromolecules in airway mucus. Genetic variants are linked to diverse lung diseases, but specific roles for MUC5AC and MUC5B in MCC, and the lasting effects of their inhibition, are unknown. Here we show that mouse Muc5b (but not Muc5ac) is required for MCC, for controlling infections in the airways and middle ear, and for maintaining immune homeostasis in mouse lungs, whereas Muc5ac is dispensable. Muc5b deficiency caused materials to accumulate in upper and lower airways. This defect led to chronic infection by multiple bacterial species, including Staphylococcus aureus, and to inflammation that failed to resolve normally. Apoptotic macrophages accumulated, phagocytosis was impaired, and interleukin-23 (IL-23) production was reduced in Muc5b(-/-) mice. By contrast, in mice that transgenically overexpress Muc5b, macrophage functions improved. Existing dogma defines mucous phenotypes in asthma and chronic obstructive pulmonary disease (COPD) as driven by increased MUC5AC, with MUC5B levels either unaffected or increased in expectorated sputum. However, in many patients, MUC5B production at airway surfaces decreases by as much as 90%. By distinguishing a specific role for Muc5b in MCC, and by determining its impact on bacterial infections and inflammation in mice, our results provide a refined framework for designing targeted therapies to control mucin secretion and restore MCC.
	PMID: 24317696 [PubMed - indexed for MEDLINE]
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Items 1 - 6 of 6

1.	Nature. 2014 Jan 23;505(7484):484. doi: 10.1038/505484a. Janet Rowley (1925-2013). Druker BJ. Author information: Knight Cancer Institute at Oregon Health & Science University, Portland, Oregon, and a Howard Hughes Medical Institute investigator. He shared the 2012 Japan Prize with Janet Rowley and Nicholas Lydon.
	PMID: 24451535 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Jan 23;505(7484):468-71. doi: 10.1038/505468a. Cloning comeback. Cyranoski D.
	PMID: 24451524 [PubMed - indexed for MEDLINE]
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3.	N Engl J Med. 2014 Jan 23;370(4):379-80. doi: 10.1056/NEJMcibr1314577. Immunotherapy for HIV Infection. Weiss RA.
	PMID: 24450898 [PubMed - indexed for MEDLINE]
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4.	Science. 2014 Jan 17;343(6168):262. doi: 10.1126/science.1249912. Retrospective. Frederick Sanger (1918-2013). Brenner S. Author information: Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673.
	PMID: 24436413 [PubMed - indexed for MEDLINE]
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5.	Nature. 2014 Jan 23;505(7484):495-501. doi: 10.1038/nature12912. Epub 2014 Jan 5. Discovery and saturation analysis of cancer genes across 21 tumour types. Lawrence MS1, Stojanov P2, Mermel CH3, Robinson JT1, Garraway LA4, Golub TR5, Meyerson M4, Gabriel SB1, Lander ES6, Getz G7. Author information: 1Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. 21] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA. 31] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital, Cancer Center and Department of Pathology, 55 Fruit Street, Boston, Massachusetts 02114, USA. 41] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA. 51] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [4] Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815, USA. 61] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [3] Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4]. 71] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital, Cancer Center and Department of Pathology, 55 Fruit Street, Boston, Massachusetts 02114, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [4]. Abstract Although a few cancer genes are mutated in a high proportion of tumours of a given type (>20%), most are mutated at intermediate frequencies (2-20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600-5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics.
	PMID: 24390350 [PubMed - indexed for MEDLINE]
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6.	Nature. 2014 Jan 23;505(7484):546-9. doi: 10.1038/nature12817. Epub 2013 Dec 18. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Dohm JC1, Minoche AE1, Holtgräwe D2, Capella-Gutiérrez S3, Zakrzewski F4, Tafer H5, Rupp O2, Sörensen TR2, Stracke R2, Reinhardt R6, Goesmann A2, Kraft T7, Schulz B8, Stadler PF5, Schmidt T4, Gabaldón T9, Lehrach H10, Weisshaar B2, Himmelbauer H11. Author information: 11] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [4]. 2Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany. 31] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain. 4TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany. 5University of Leipzig, Department of Computer Science, Härtelstraße 16-18, 04107 Leipzig, Germany. 6Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Köln, Germany. 7Syngenta, Box 302, 26123 Landskrona, Sweden. 8KWS SAAT AG, Grimsehlstraße 31, 37574 Einbeck, Germany. 91] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain. 10Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany. 111] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain. Abstract Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.
	PMID: 24352233 [PubMed - indexed for MEDLINE]
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