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

Sent on Thursday, 2012 December 27
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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PubMed Results

Items 1 - 7 of 7

1.	Nature. 2012 Nov 1;491(7422):S4-6. Genetics: Searching for answers. Williams SC.
	PMID: 23136651 [PubMed - indexed for MEDLINE]
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2.	Nature. 2012 Nov 1;491(7422):143-7. doi: 10.1038/491143a. Epigenetics: Reading the second genomic code. Marx V.
	PMID: 23128234 [PubMed - indexed for MEDLINE]
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3.	Nature. 2012 Nov 1;491(7422):92-5. doi: 10.1038/nature11513. Epub 2012 Oct 24. Fluvial response to abrupt global warming at the Palaeocene/Eocene boundary. Foreman BZ, Heller PL, Clementz MT. University of Wyoming, Department of Geology and Geophysics, 1000 East University Avenue, Laramie, Wyoming 82071, USA. bforema1@uwyo.edu Abstract Climate strongly affects the production of sediment from mountain catchments as well as its transport and deposition within adjacent sedimentary basins. However, identifying climatic influences on basin stratigraphy is complicated by nonlinearities, feedback loops, lag times, buffering and convergence among processes within the sediment routeing system. The Palaeocene/Eocene thermal maximum (PETM) arguably represents the most abrupt and dramatic instance of global warming in the Cenozoic era and has been proposed to be a geologic analogue for anthropogenic climate change. Here we evaluate the fluvial response in western Colorado to the PETM. Concomitant with the carbon isotope excursion marking the PETM we document a basin-wide shift to thick, multistoried, sheets of sandstone characterized by variable channel dimensions, dominance of upper flow regime sedimentary structures, and prevalent crevasse splay deposits. This progradation of coarse-grained lithofacies matches model predictions for rapid increases in sediment flux and discharge, instigated by regional vegetation overturn and enhanced monsoon precipitation. Yet the change in fluvial deposition persisted long after the approximately 200,000-year-long PETM with its increased carbon dioxide levels in the atmosphere, emphasizing the strong role the protracted transmission of catchment responses to distant depositional systems has in constructing large-scale basin stratigraphy. Our results, combined with evidence for increased dissolved loads and terrestrial clay export to world oceans, indicate that the transient hyper-greenhouse climate of the PETM may represent a major geomorphic 'system-clearing event', involving a global mobilization of dissolved and solid sediment loads on Earth's surface.
	PMID: 23128230 [PubMed - indexed for MEDLINE]
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4.	Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632. An integrated map of genetic variation from 1,092 human genomes. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Collaborators: Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Donnelly P, Eichler EE, Flicek P, Gabriel SB, Gibbs RA, Green ED, Hurles ME, Knoppers BM, Korbel JO, Lander ES, Lee C, Lehrach H, Mardis ER, Marth GT, McVean GA, Nickerson DA, Schmidt JP, Sherry ST, Wang J, Wilson RK, Gibbs RA, Dinh H, Kovar C, Lee S, Lewis L, Muzny D, Reid J, Wang M, Wang J, Fang X, Guo X, Jian M, Jiang H, Jin X, Li G, Li J, Li Y, Li Z, Liu X, Lu Y, Ma X, Su Z, Tai S, Tang M, Wang B, Wang G, Wu H, Wu R, Yin Y, Zhang W, Zhao J, Zhao M, Zheng X, Zhou Y, Lander ES, Altshuler DM, Gabriel SB, Gupta N, Flicek P, Clarke L, Leinonen R, Smith RE, Zheng-Bradley X, Bentley DR, Grocock R, Humphray S, James T, Kingsbury Z, Lehrach H, Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Lienhard M, Mertes F, Sultan M, Timmermann B, Yaspo ML, Sherry ST, McVean GA, Mardis ER, Wilson RK, Fulton L, Fulton R, Weinstock GM, Durbin RM, Balasubramaniam S, Burton J, Danecek P, Keane TM, Kolb-Kokocinski A, McCarthy S, Stalker J, Quail M, Schmidt JP, Davies CJ, Gollub J, Webster T, Wong B, Zhan Y, Auton A, Gibbs RA, Yu F, Bainbridge M, Challis D, Evani US, Lu J, Muzny D, Nagaswamy U, Reid J, Sabo A, Wang Y, Yu J, Wang J, Coin LJ, Fang L, Guo X, Jin X, Li G, Li Q, Li Y, Li Z, Lin H, Liu B, Luo R, Qin N, Shao H, Wang B, Xie Y, Ye C, Yu C, Zhang F, Zheng H, Zhu H, Marth GT, Garrison EP, Kural D, Lee WP, Leong WF, Ward AN, Wu J, Zhang M, Lee C, Griffin L, Hsieh CH, Mills RE, Shi X, von Grotthuss M, Zhang C, Daly MJ, DePristo MA, Altshuler DM, Banks E, Bhatia G, Carneiro MO, del Angel G, Gabriel SB, Genovese G, Gupta N, Handsaker RE, Hartl C, Lander ES, McCarroll SA, Nemesh JC, Poplin RE, Schaffner SF, Shakir K, Yoon SC, Lihm J, Makarov V, Jin H, Kim W, Kim KC, Korbel JO, Rausch T, Flicek P, Beal K, Clarke L, Cunningham F, Herrero J, McLaren WM, Ritchie GR, Smith RE, Zheng-Bradley X, Clark AG, Gottipati S, Keinan A, Rodriguez-Flores JL, Sabeti PC, Grossman SR, Tabrizi S, Tariyal R, Cooper DN, Ball EV, Stenson PD, Bentley DR, Barnes B, Bauer M, Cheetham R, Cox T, Eberle M, Humphray S, Kahn S, Murray L, Peden J, Shaw R, Ye K, Batzer MA, Konkel MK, Walker JA, MacArthur DG, Lek M, Sudbrak R, Amstislavskiy VS, Herwig R, Shriver MD, Bustamante CD, Byrnes JK, De La Vega FM, Gravel S, Kenny EE, Kidd JM, Lacroute P, Maples BK, Moreno-Estrada A, Zakharia F, Halperin E, Baran Y, Craig DW, Christoforides A, Homer N, Izatt T, Kurdoglu AA, Sinari SA, Squire K, Sherry ST, Xiao C, Sebat J, Bafna V, Ye K, Burchard EG, Hernandez RD, Gignoux CR, Haussler D, Katzman SJ, Kent WJ, Howie B, Ruiz-Linares A, Dermitzakis ET, Lappalainen T, Devine SE, Liu X, Maroo A, Tallon LJ, Rosenfeld JA, Michelson LP, Abecasis GR, Kang HM, Anderson P, Angius A, Bigham A, Blackwell T, Busonero F, Cucca F, Fuchsberger C, Jones C, Jun G, Li Y, Lyons R, Maschio A, Porcu E, Reinier F, Sanna S, Schlessinger D, Sidore C, Tan A, Trost MK, Awadalla P, Hodgkinson A, Lunter G, McVean GA, Marchini JL, Myers S, Churchhouse C, Delaneau O, Gupta-Hinch A, Iqbal Z, Mathieson I, Rimmer A, Xifara DK, Oleksyk TK, Fu Y, Liu X, Xiong M, Jorde L, Witherspoon D, Xing J, Eichler EE, Browning BL, Alkan C, Hajirasouliha I, Hormozdiari F, Ko A, Sudmant PH, Mardis ER, Chen K, Chinwalla A, Ding L, Dooling D, Koboldt DC, McLellan MD, Wallis JW, Wendl MC, Zhang Q, Durbin RM, Hurles ME, Tyler-Smith C, Albers CA, Ayub Q, Balasubramaniam S, Chen Y, Coffey AJ, Colonna V, Danecek P, Huang N, Jostins L, Keane TM, Li H, McCarthy S, Scally A, Stalker J, Walter K, Xue Y, Zhang Y, Gerstein MB, Abyzov A, Balasubramanian S, Chen J, Clarke D, Fu Y, Habegger L, Harmanci AO, Jin M, Khurana E, Mu XJ, Sisu C, Li Y, Luo R, Zhu H, Lee C, Griffin L, Hsieh CH, Mills RE, Shi X, von Grotthuss M, Zhang C, Marth GT, Garrison EP, Kural D, Lee WP, Ward AN, Wu J, Zhang M, McCarroll SA, Altshuler DM, Banks E, del Angel G, Genovese G, Handsaker RE, Hartl C, Nemesh JC, Shakir K, Yoon SC, Lihm J, Makarov V, Degenhardt J, Flicek P, Clarke L, Smith RE, Zheng-Bradley X, Korbel JO, Rausch T, Stütz AM, Bentley DR, Barnes B, Cheetham R, Eberle M, Humphray S, Kahn S, Murray L, Shaw R, Ye K, Batzer MA, Konkel MK, Walker JA, Lacroute P, Craig DW, Homer N, Church D, Xiao C, Sebat J, Bafna V, Michaelson JJ, Ye K, Devine SE, Liu X, Maroo A, Tallon LJ, Lunter G, Iqbal Z, Witherspoon D, Xing J, Eichler EE, Alkan C , Hajirasouliha I, Hormozdiari F, Ko A, Sudmant PH, Chen K, Chinwalla A, Ding L, McLellan MD, Wallis JW, Hurles ME, Blackburne B, Li H, Lindsay SJ, Ning Z, Scally A, Walter K, Zhang Y, Gerstein MB, Abyzov A, Chen J, Clarke D, Khurana E, Mu XJ, Sisu C, Gibbs RA, Yu F, Bainbridge M, Challis D, Evani US, Kovar C, Lewis L, Lu J, Muzny D, Nagaswamy U, Reid J, Sabo A, Yu J, Guo X, Li Y, Wu R, Marth GT, Garrison EP, Leong WF, Ward AN, del Angel G, DePristo MA, Gabriel SB, Gupta N, Hartl C, Poplin RE, Clark AG, Rodriguez-Flores JL, Flicek P, Clarke L, Smith RE, Zheng-Bradley X, MacArthur DG, Bustamante CD, Gravel S, Craig DW, Christoforides A, Homer N, Izatt T, Sherry ST, Xiao C, Dermitzakis ET, Abecasis GR, Kang HM, McVean GA, Mardis ER, Dooling D, Fulton L, Fulton R, Koboldt DC, Durbin RM, Balasubramaniam S, Keane TM, McCarthy S, Stalker J, Gerstein MB, Balasubramanian S, Habegger L, Garrison EP, Gibbs RA, Bainbridge M, Muzny D, Yu F, Yu J, del Angel G, Handsaker RE, Makarov V, Rodriguez-Flores JL, Jin H, Kim W, Kim KC, Flicek P, Beal K, Clarke L, Cunningham F, Herrero J, McLaren WM, Ritchie GR, Zheng-Bradley X, Tabrizi S, MacArthur DG, Lek M, Bustamante CD, De La Vega FM, Craig DW, Kurdoglu AA, Lappalainen T, Rosenfeld JA, Michelson LP, Awadalla P, Hodgkinson A, McVean GA, Chen K, Tyler-Smith C, Chen Y, Colonna V, Frankish A, Harrow J, Xue Y, Gerstein MB, Abyzov A, Balasubramanian S, Chen J, Clarke D, Fu Y, Harmanci AO, Jin M, Khurana E, Mu XJ, Sisu C, Gibbs RA, Fowler G, Hale W, Kalra D, Kovar C, Muzny D, Reid J, Wang J, Guo X, Li G, Li Y, Zheng X, Altshuler DM, Flicek P, Clarke L, Barker J, Kelman G, Kulesha E, Leinonen R, McLaren WM, Radhakrishnan R, Roa A, Smirnov D, Smith RE, Streeter I, Toneva I, Vaughan B, Zheng-Bradley X, Bentley DR, Cox T, Humphray S, Kahn S, Sudbrak R, Albrecht MW, Lienhard M, Craig DW, Izatt T, Kurdoglu AA, Sherry ST, Ananiev V, Belaia Z, Beloslyudtsev D, Bouk N, Chen C, Church D, Cohen R, Cook C, Garner J, Hefferon T, Kimelman M, Liu C, Lopez J, Meric P, O'Sullivan C, Ostapchuk Y, Phan L, Ponomarov S, Schneider V, Shekhtman E, Sirotkin K, Slotta D, Xiao C, Zhang H, Haussler D, Abecasis GR, McVean GA, Alkan C, Ko A, Dooling D, Durbin RM, Balasubramaniam S, Keane TM, McCarthy S, Stalker J, Chakravarti A, Knoppers BM, Abecasis GR, Barnes KC, Beiswanger C, Burchard EG, Bustamante CD, Cai H, Cao H, Durbin RM, Gharani N, Gibbs RA, Gignoux CR, Gravel S, Henn B, Jones D, Jorde L, Kaye JS, Keinan A, Kent A, Kerasidou A, Li Y, Mathias R, McVean GA, Moreno-Estrada A, Ossorio PN, Parker M, Reich D, Rotimi CN, Royal CD, Sandoval K, Su Y, Sudbrak R, Tian Z, Timmermann B, Tishkoff S, Toji LH, Tyler-Smith C, Via M, Wang Y, Yang H, Yang L, Zhu J, Bodmer W, Bedoya G, Ruiz-Linares A, Ming CZ, Yang G, You CJ, Peltonen L, Garcia-Montero A, Orfao A, Dutil J, Martinez-Cruzado JC, Oleksyk TK, Brooks LD, Felsenfeld AL, McEwen JE, Clemm NC, Duncanson A, Dunn M, Green ED, Guyer MS, Peterson JL. Abstract By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. PMCID: PMC3498066 [Available on 2013/5/1]
	PMID: 23128226 [PubMed - indexed for MEDLINE]
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5.	Nature. 2012 Nov 1;491(7422):27-9. doi: 10.1038/491027a. Genomics: The single life. Owens B.
	PMID: 23128208 [PubMed - indexed for MEDLINE]
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6.	Nature. 2012 Nov 1;491(7422):129-33. doi: 10.1038/nature11443. Epub 2012 Sep 30. Vaccine-induced CD8+ T cells control AIDS virus replication. Mudd PA, Martins MA, Ericsen AJ, Tully DC, Power KA, Bean AT, Piaskowski SM, Duan L, Seese A, Gladden AD, Weisgrau KL, Furlott JR, Kim YI, Veloso de Santana MG, Rakasz E, Capuano S 3rd, Wilson NA, Bonaldo MC, Galler R, Allison DB, Piatak M Jr, Haase AT, Lifson JD, Allen TM, Watkins DI. Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53711, USA. Abstract Developing a vaccine for human immunodeficiency virus (HIV) may be aided by a complete understanding of those rare cases in which some HIV-infected individuals control replication of the virus. Most of these elite controllers express the histocompatibility alleles HLA-B*57 or HLA-B*27 (ref. 3). These alleles remain by far the most robust associations with low concentrations of plasma virus, yet the mechanism of control in these individuals is not entirely clear. Here we vaccinate Indian rhesus macaques that express Mamu-B*08, an animal model for HLA-B*27-mediated elite control, with three Mamu-B*08-restricted CD8(+) T-cell epitopes, and demonstrate that these vaccinated animals control replication of the highly pathogenic clonal simian immunodeficiency virus (SIV) mac239 virus. High frequencies of CD8(+) T cells against these Vif and Nef epitopes in the blood, lymph nodes and colon were associated with viral control. Moreover, the frequency of the CD8(+) T-cell response against the Nef RL10 epitope (Nef amino acids 137-146) correlated significantly with reduced acute phase viraemia. Finally, two of the eight vaccinees lost control of viral replication in the chronic phase, concomitant with escape in all three targeted epitopes, further implicating these three CD8(+) T-cell responses in the control of viral replication. Our findings indicate that narrowly targeted vaccine-induced virus-specific CD8(+) T-cell responses can control replication of the AIDS virus.
	PMID: 23023123 [PubMed - indexed for MEDLINE]
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7.	Nature. 2012 Nov 1;491(7422):114-8. doi: 10.1038/nature11537. Epub 2012 Sep 23. In vivo genome editing using a high-efficiency TALEN system. Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG 2nd, Tan W, Penheiter SG, Ma AC, Leung AY, Fahrenkrug SC, Carlson DF, Voytas DF, Clark KJ, Essner JJ, Ekker SC. Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA. Abstract The zebrafish (Danio rerio) is increasingly being used to study basic vertebrate biology and human disease with a rich array of in vivo genetic and molecular tools. However, the inability to readily modify the genome in a targeted fashion has been a bottleneck in the field. Here we show that improvements in artificial transcription activator-like effector nucleases (TALENs) provide a powerful new approach for targeted zebrafish genome editing and functional genomic applications. Using the GoldyTALEN modified scaffold and zebrafish delivery system, we show that this enhanced TALEN toolkit has a high efficiency in inducing locus-specific DNA breaks in somatic and germline tissues. At some loci, this efficacy approaches 100%, including biallelic conversion in somatic tissues that mimics phenotypes seen using morpholino-based targeted gene knockdowns. With this updated TALEN system, we successfully used single-stranded DNA oligonucleotides to precisely modify sequences at predefined locations in the zebrafish genome through homology-directed repair, including the introduction of a custom-designed EcoRV site and a modified loxP (mloxP) sequence into somatic tissue in vivo. We further show successful germline transmission of both EcoRV and mloxP engineered chromosomes. This combined approach offers the potential to model genetic variation as well as to generate targeted conditional alleles. PMCID: PMC3491146 [Available on 2013/5/1]
	PMID: 23000899 [PubMed - indexed for MEDLINE]
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