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

Sent on Friday, 2013 January 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. 2013 Jan 11;339(6116):161-6. doi: 10.1126/science.1230719. Leukocyte behavior in atherosclerosis, myocardial infarction, and heart failure. Swirski FK, Nahrendorf M. Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA. fswirski@mgh.harvard.edu Abstract Cardiovascular diseases claim more lives worldwide than any other. Etiologically, the dominant trajectory involves atherosclerosis, a chronic inflammatory process of lipid-rich lesion growth in the vascular wall that can cause life-threatening myocardial infarction (MI). Those who survive MI can develop congestive heart failure, a chronic condition of inadequate pump activity that is frequently fatal. Leukocytes (white blood cells) are important participants at the various stages of cardiovascular disease progression and complication. This Review will discuss leukocyte function in atherosclerosis, MI, and heart failure.
	PMID: 23307733 [PubMed - indexed for MEDLINE]
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2.	Science. 2013 Jan 11;339(6116):147-8. doi: 10.1126/science.1233223. Biomedicine. Improving metabolism by throwing out all the JNK. Ferrante AW Jr. Department of Medicine, Naomi Berrie Diabetes Center, Columbia University, 1150 Saint Nicholas Avenue, New York, NY 10032, USA. awf7@columbia.edu Comment on JNK expression by macrophages promotes obesity-induced insulin resistance and inflammation. [Science. 2013] JNK expression by macrophages promotes obesity-induced insulin resistance and inflammation.Han MS, Jung DY, Morel C, Lakhani SA, Kim JK, Flavell RA, Davis RJ. Science. 2013 Jan 11; 339(6116):218-22. Epub 2012 Dec 6.
	PMID: 23307726 [PubMed - indexed for MEDLINE]
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3.	Science. 2013 Jan 11;339(6116):218-22. doi: 10.1126/science.1227568. Epub 2012 Dec 6. JNK expression by macrophages promotes obesity-induced insulin resistance and inflammation. Han MS, Jung DY, Morel C, Lakhani SA, Kim JK, Flavell RA, Davis RJ. Howard Hughes Medical Institute, Worcester, MA 01605, USA. Comment in Biomedicine. Improving metabolism by throwing out all the JNK. [Science. 2013] Biomedicine. Improving metabolism by throwing out all the JNK.Ferrante AW Jr. Science. 2013 Jan 11; 339(6116):147-8. Abstract The cJun NH(2)-terminal kinase (JNK) signaling pathway contributes to inflammation and plays a key role in the metabolic response to obesity, including insulin resistance. Macrophages are implicated in this process. To test the role of JNK, we established mice with selective JNK deficiency in macrophages. We report that feeding a high-fat diet to control and JNK-deficient mice caused similar obesity, but only mice with JNK-deficient macrophages remained insulin-sensitive. The protection of mice with macrophage-specific JNK deficiency against insulin resistance was associated with reduced tissue infiltration by macrophages. Immunophenotyping demonstrated that JNK was required for pro-inflammatory macrophage polarization. These studies demonstrate that JNK in macrophages is required for the establishment of obesity-induced insulin resistance and inflammation.
	PMID: 23223452 [PubMed - indexed for MEDLINE]
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Sent on Thursday, 2013 January 24
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. 2013 Jan 18;339(6117):321-4. doi: 10.1126/science.1229566. Identifying personal genomes by surname inference. Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Abstract Sharing sequencing data sets without identifiers has become a common practice in genomics. Here, we report that surnames can be recovered from personal genomes by profiling short tandem repeats on the Y chromosome (Y-STRs) and querying recreational genetic genealogy databases. We show that a combination of a surname with other types of metadata, such as age and state, can be used to triangulate the identity of the target. A key feature of this technique is that it entirely relies on free, publicly accessible Internet resources. We quantitatively analyze the probability of identification for U.S. males. We further demonstrate the feasibility of this technique by tracing back with high probability the identities of multiple participants in public sequencing projects.
	PMID: 23329047 [PubMed - indexed for MEDLINE]
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2.	Science. 2013 Jan 18;339(6117):275-6. doi: 10.1126/science.1234593. Research ethics. The complexities of genomic identifiability. Rodriguez LL, Brooks LD, Greenberg JH, Green ED. National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
	PMID: 23329035 [PubMed - indexed for MEDLINE]
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Sent on Thursday, 2013 January 17
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.	Nature. 2012 Nov 29;491(7426):705-10. doi: 10.1038/nature11650. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N. Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK. Comment in Genomics: Decoding our daily bread. [Nature. 2012] Genomics: Decoding our daily bread.Langridge P. Nature. 2012 Nov 29; 491(7426):678-80. Abstract Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop. PMCID: PMC3510651 [Available on 2013/5/29]
	PMID: 23192148 [PubMed - indexed for MEDLINE]
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2.	Nature. 2012 Nov 29;491(7426):692-7. doi: 10.1038/nature11579. The mystery of recent stratospheric temperature trends. Thompson DW, Seidel DJ, Randel WJ, Zou CZ, Butler AH, Mears C, Osso A, Long C, Lin R. Department of Atmospheric Science, Colorado State University, Fort Collins, Colorado 80523, USA. davet@atmos.colostate.edu Abstract A new data set of middle- and upper-stratospheric temperatures based on reprocessing of satellite radiances provides a view of stratospheric climate change during the period 1979-2005 that is strikingly different from that provided by earlier data sets. The new data call into question our understanding of observed stratospheric temperature trends and our ability to test simulations of the stratospheric response to emissions of greenhouse gases and ozone-depleting substances. Here we highlight the important issues raised by the new data and suggest how the climate science community can resolve them.
	PMID: 23192146 [PubMed - indexed for MEDLINE]
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3.	Nature. 2012 Nov 29;491(7426):756-60. doi: 10.1038/nature11584. Epub 2012 Oct 24. The genomic landscape of species divergence in Ficedula flycatchers. Ellegren H, Smeds L, Burri R, Olason PI, Backström N, Kawakami T, Künstner A, Mäkinen H, Nadachowska-Brzyska K, Qvarnström A, Uebbing S, Wolf JB. Dept of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden. Abstract Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.
	PMID: 23103876 [PubMed - indexed for MEDLINE]
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4.	Nature. 2012 Nov 29;491(7426):774-8. doi: 10.1038/nature11599. Epub 2012 Oct 24. Resurrection of endogenous retroviruses in antibody-deficient mice. Young GR, Eksmond U, Salcedo R, Alexopoulou L, Stoye JP , Kassiotis G. Division of Immunoregulation, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK. Comment in Antiviral immunity: Immune control of endogenous retroviruses. [Nat Rev Immunol. 2012] Antiviral immunity: Immune control of endogenous retroviruses.Leavy O. Nat Rev Immunol. 2012 Dec; 12(12):805. Abstract The mammalian host has developed a long-standing symbiotic relationship with a considerable number of microbial species. These include the microbiota on environmental surfaces, such as the respiratory and gastrointestinal tracts, and also endogenous retroviruses (ERVs), comprising a substantial fraction of the mammalian genome. The long-term consequences for the host of interactions with these microbial species can range from mutualism to parasitism and are not always completely understood. The potential effect of one microbial symbiont on another is even less clear. Here we study the control of ERVs in the commonly used C57BL/6 (B6) mouse strain, which lacks endogenous murine leukaemia viruses (MLVs) able to replicate in murine cells. We demonstrate the spontaneous emergence of fully infectious ecotropic MLV in B6 mice with a range of distinct immune deficiencies affecting antibody production. These recombinant retroviruses establish infection of immunodeficient mouse colonies, and ultimately result in retrovirus-induced lymphomas. Notably, ERV activation in immunodeficient mice is prevented in husbandry conditions associated with reduced or absent intestinal microbiota. Our results shed light onto a previously unappreciated role for immunity in the control of ERVs and provide a potential mechanistic link between immune activation by microbial triggers and a range of pathologies associated with ERVs, including cancer. PMCID: PMC3511586 [Available on 2013/5/29]
	PMID: 23103862 [PubMed - indexed for MEDLINE]
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5.	Nature. 2012 Nov 29;491(7426):711-6. doi: 10.1038/nature11543. Epub 2012 Oct 17. A physical, genetic and functional sequence assembly of the barley genome. International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N. Collaborators: Mayer KF, Waugh R, Langridge P, Close TJ, Wise RP, Graner A, Matsumoto T, Sato K, Schulman A, Muehlbauer GJ, Stein N, Ariyadasa R, Schulte D, Poursarebani N, Zhou R, Steuernagel B, Mascher M, Scholz U, Shi B, Langridge P, Madishetty K, Svensson JT, Bhat P, Moscou M, Resnik J, Close TJ, Muehlbauer GJ, Hedley P, Liu H, Morris J, Waugh R, Frenkel Z, Korol A, Bergès H, Graner A, Stein N, Steuernagel B, Scholz U, Taudien S, Felder M, Groth M, Platzer M, Stein N, Steuernagel B, Scholz U, Himmelbach A, Taudien S, Felder M, Platzer M, Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Ciardo G, Ma Y, Wanamaker S, Close TJ, Stein N, Cattonaro F, Vendramin V, Scalabrin S, Radovic S, Wing R, Schulte D, Steuernagel B, Morgante M, Stein N, Waugh R, Nussbaumer T, Gundlach H, Martis M, Ariyadasa R, Poursarebani N, Steuernagel B, Scholz U, Wise RP, Poland J, Stein N, Mayer KF, Spannagl M, Pfeifer M, Gundlach H, Mayer KF, Gundlach H, Moisy C, Tanskanen J, Scalabrin S, Zuccolo A, Vendramin V, Morgante M, Schulman A, Pfeifer M, Spannagl M, Hedley P, Morris J, Russell J, Druka A, Marshall D, Bayer M, Swarbreck D, Sampath D, Ayling S, Febrer M, Caccamo M, Matsumoto T, Tanaka T, Sato K, Wise RP, Close TJ, Wannamaker S, Muehlbauer GJ, Stein N, Waugh R, Steuernagel B, Schmutzer T, Mascher M, Scholz U, Taudien S, Platzer M, Sato K, Marshall D, Bayer M, Waugh R, Stein N. Abstract Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
	PMID: 23075845 [PubMed - indexed for MEDLINE]
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Sent on Wednesday, 2013 January 16
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1.	Nature. 2012 Nov 22;491(7425):S55. Perspective: Finding cancer's first principles. Gatenby R. Departments of Radiology andIntegrated Mathematical Oncology at the H. Lee Moffitt CancerCenter in Tampa, Florida, USA.robert.gatenby@moffitt.org
	PMID: 23320287 [PubMed - indexed for MEDLINE]

2.	Nature. 2012 Nov 22;491(7425):S52-4. Megadata: The odd couple. Vance E.
	PMID: 23320285 [PubMed - indexed for MEDLINE]

3.	Science. 2013 Jan 4;339(6115):25-7. doi: 10.1126/science.339.6115.25. Cell biology. The immune system's compact genomic counterpart. Leslie M.
	PMID: 23288523 [PubMed - indexed for MEDLINE]
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4.	Science. 2013 Jan 4;339(6115):74-8. doi: 10.1126/science.1228282. Epub 2012 Dec 20. An update of Wallace's zoogeographic regions of the world. Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB , Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark. Abstract Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
	PMID: 23258408 [PubMed - indexed for MEDLINE]
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Sent on Friday, 2013 January 11
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1.	Nature. 2012 Nov 8;491(7423):183-5. doi: 10.1038/491183a. Autoimmunity: The worm returns. Weinstock JV. Tufts Medical Center, Boston, Massachusetts 02111, USA. jweinstock2@tuftsmedicalcenter.org Comment in Autoimmune disease: Patients self-treat with parasitic worms. [Nature. 2013] Autoimmune disease: Patients self-treat with parasitic worms.Flowers S, Hopkins M. Nature. 2013 Jan 10; 493(7431):163.
	PMID: 23135449 [PubMed - indexed for MEDLINE]
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2.	Nature. 2012 Nov 8;491(7423):180-2. doi: 10.1038/491180a. Melting in the Andes: Goodbye glaciers. Fraser B.
	PMID: 23135448 [PubMed - indexed for MEDLINE]
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3.	Nature. 2012 Nov 8;491(7423):171. doi: 10.1038/491171a. One-stop shop for disease genes. Baker M.
	PMID: 23135443 [PubMed - indexed for MEDLINE]
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1.	Nat Med. 2012 Oct;18(10):1499-502. doi: 10.1038/nm.2931. On the road from classical to modern molecular biology. Maniatis T. Department of Biochemistry & Biophysics, Columbia University, New York, New York, USA. tm2472@columbia.edu
	PMID: 23042362 [PubMed - indexed for MEDLINE]
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2.	Nat Med. 2012 Oct;18(10):1496-8. doi: 10.1038/nm.2929. Developmental biology using purified genes. Brown DD. Department of Embryology, Carnegie Institute for Science, Baltimore, Maryland, USA. brown@ciwemb.edu
	PMID: 23042361 [PubMed - indexed for MEDLINE]
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1.	Science. 2012 Dec 21;338(6114):1532. doi: 10.1126/science.338.6114.1532. Breakthrough of the year. Scorecard: rating last year's areas to watch. [No authors listed]
	PMID: 23258868 [PubMed - indexed for MEDLINE]
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2.	Science. 2012 Dec 21;338(6114):1525-32. doi: 10.1126/science.338.6114.1525. Breakthrough of the year. The runners-up. [No authors listed]
	PMID: 23258865 [PubMed - indexed for MEDLINE]
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1.	Lancet. 2012 Nov 3;380(9853):1546. Grants aim to boost African genomic research. McCall B.
	PMID: 23130361 [PubMed - indexed for MEDLINE]