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

Sent on Saturday, 2014 October 04
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 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Gire SK1, Goba A2, Andersen KG3, Sealfon RS4, Park DJ5, Kanneh L6, Jalloh S6, Momoh M7, Fullah M7, Dudas G8, Wohl S9, Moses LM10, Yozwiak NL1, Winnicki S1, Matranga CB5, Malboeuf CM5, Qu J5, Gladden AD5, Schaffner SF1, Yang X5, Jiang PP1, Nekoui M1, Colubri A11, Coomber MR6, Fonnie M6, Moigboi A6, Gbakie M6, Kamara FK6, Tucker V6, Konuwa E6, Saffa S6, Sellu J6, Jalloh AA6, Kovoma A6, Koninga J6, Mustapha I6, Kargbo K6, Foday M6, Yillah M6, Kanneh F6, Robert W6, Massally JL6, Chapman SB5, Bochicchio J5, Murphy C5, Nusbaum C5, Young S5, Birren BW5, Grant DS6, Scheiffelin JS10, Lander ES12, Happi C13, Gevao SM14, Gnirke A5, Rambaut A15, Garry RF10, Khan SH6, Sabeti PC3. Author information: 1Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. 2Kenema Government Hospital, Kenema, Sierra Leone. andersen@broadinstitute.org augstgoba@yahoo.com psabeti@oeb.harvard.edu. 3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. andersen@broadinstitute.org augstgoba@yahoo.com psabeti@oeb.harvard.edu. 4Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. 5Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. 6Kenema Government Hospital, Kenema, Sierra Leone. 7Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone. 8Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. 9Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA. 10Tulane University Medical Center, New Orleans, LA 70112, USA. 11Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. 12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. 13Redeemer's University, Ogun State, Nigeria. 14University of Sierra Leone, Freetown, Sierra Leone. 15Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK. Abstract In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response. Copyright © 2014, American Association for the Advancement of Science.
	PMID: 25214632 [PubMed - indexed for MEDLINE]
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2.	Science. 2014 Sep 12;345(6202):1346-9. doi: 10.1126/science.1254421. Biogeographic patterns in ocean microbes emerge in a neutral agent-based model. Hellweger FL1, van Sebille E2, Fredrick ND3. Author information: 1Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA. ferdi@coe.neu.edu. 2Australian Research Council (ARC) Centre of Excellence for Climate System Science and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia. 3Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA. Comment in Ecology. Microbes ride the current. [Science. 2014] Ecology. Microbes ride the current.Giovannoni S, Nemergut D. Science. 2014 Sep 12; 345(6202):1246-7. Abstract A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection. Copyright © 2014, American Association for the Advancement of Science.
	PMID: 25214628 [PubMed - indexed for MEDLINE]
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