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

Sent on Wednesday, 2013 November 20
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 Oct;45(10):1105-7. doi: 10.1038/ng.2775. Genomics informs glioblastoma biology. Schonberg DL, Bao S, Rich JN. Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA. Comment on The integrated landscape of driver genomic alterations in glioblastoma. [Nat Genet. 2013] The integrated landscape of driver genomic alterations in glioblastoma.Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, et al. Nat Genet. 2013 Oct; 45(10):1141-9. Epub 2013 Aug 5. Abstract Identifying genomic alterations in cancer does not guarantee therapeutic benefit. A new study combining DNA and RNA sequencing with functional validation uncovers new genetic driver alterations in glioblastoma with potential for clinical translation.
	PMID: 24071842 [PubMed - indexed for MEDLINE]
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2.	Nat Genet. 2013 Oct;45(10):1141-9. doi: 10.1038/ng.2734. Epub 2013 Aug 5. The integrated landscape of driver genomic alterations in glioblastoma. Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Privé GG, Bigner DD, Lasorella A, Rabadan R, Iavarone A. 1] Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA. [2]. Comment in Genomics informs glioblastoma biology. [Nat Genet. 2013] Genomics informs glioblastoma biology.Schonberg DL, Bao S, Rich JN. Nat Genet. 2013 Oct; 45(10):1105-7. Genetics: Glioblastoma landscape revealed. [Nat Rev Clin Oncol. 2013] Genetics: Glioblastoma landscape revealed.Kirk R. Nat Rev Clin Oncol. 2013 Oct; 10(10):547. Epub 2013 Aug 20. Abstract Glioblastoma is one of the most challenging forms of cancer to treat. Here we describe a computational platform that integrates the analysis of copy number variations and somatic mutations and unravels the landscape of in-frame gene fusions in glioblastoma. We found mutations with loss of heterozygosity in LZTR1, encoding an adaptor of CUL3-containing E3 ligase complexes. Mutations and deletions disrupt LZTR1 function, which restrains the self renewal and growth of glioma spheres that retain stem cell features. Loss-of-function mutations in CTNND2 target a neural-specific gene and are associated with the transformation of glioma cells along the very aggressive mesenchymal phenotype. We also report recurrent translocations that fuse the coding sequence of EGFR to several partners, with EGFR-SEPT14 being the most frequent functional gene fusion in human glioblastoma. EGFR-SEPT14 fusions activate STAT3 signaling and confer mitogen independence and sensitivity to EGFR inhibition. These results provide insights into the pathogenesis of glioblastoma and highlight new targets for therapeutic intervention. PMCID: PMC3799953 [Available on 2014/4/1]
	PMID: 23917401 [PubMed - indexed for MEDLINE]
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What's new for 'JKB_daily1' in PubMed

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

Sent on Saturday, 2013 November 16
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 Nov 1;342(6158):621-4. doi: 10.1126/science.1243768. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Comment in Ecology. Dust unto dust. [Science. 2013] Ecology. Dust unto dust.Scholes MC, Scholes RJ. Science. 2013 Nov 1; 342(6158):565-6. Abstract Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.
	PMID: 24179225 [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, 2013 November 13
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. 2013 Nov 7;369(19):1828-35. doi: 10.1056/NEJMoa1302976. Epub 2013 Oct 23. 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. From the Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore (D.P., C.Z., Y.H.C.), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick (M.P.), and the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda (T.-W.C.) - all in Maryland; the Department of Pediatrics, University of Mississippi Medical Center, Jackson (H.G.); the University of California San Diego, La Jolla, and the Veterans Affairs San Diego Healthcare System, San Diego (M.S., D.R.); and the Department of Pediatrics, Program in Molecular Medicine, and Center for Clinical and Translational Science, University of Massachusetts Medical School, Worcester (K.L.). Comment in Baby steps on the road to HIV eradication. [N Engl J Med. 2013] Baby steps on the road to HIV eradication.Hammer SM. N Engl J Med. 2013 Nov 7; 369(19):1855-7. Epub 2013 Oct 23. Abstract An infant born to a woman with human immunodeficiency virus type 1 (HIV-1) infection began receiving antiretroviral therapy (ART) 30 hours after birth owing to high-risk exposure. ART was continued when detection of HIV-1 DNA and RNA on repeat testing met the standard diagnostic criteria for infection. After therapy was discontinued (when the child was 18 months of age), levels of plasma HIV-1 RNA, proviral DNA in peripheral-blood mononuclear cells, and HIV-1 antibodies, as assessed by means of clinical assays, remained undetectable in the child through 30 months of age. This case suggests that very early ART in infants may alter the establishment and long-term persistence of HIV-1 infection. Free Article
	PMID: 24152233 [PubMed - indexed for MEDLINE]
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2.	N Engl J Med. 2013 Nov 7;369(19):1855-7. doi: 10.1056/NEJMe1309006. Epub 2013 Oct 23. Baby steps on the road to HIV eradication. Hammer SM. From the Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York. 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. Free Article
	PMID: 24152231 [PubMed - indexed for MEDLINE]
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What's new for 'JKB_daily1' in PubMed

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

Sent on Monday, 2013 November 11
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. 2013 Oct 3;502(7469):5-6. Dangerous work. [No authors listed]
	PMID: 24137647 [PubMed - indexed for MEDLINE]
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2.	Nature. 2013 Oct 3;502(7469):26-8. doi: 10.1038/502026a. Ethics: Taboo genetics. Hayden EC.
	PMID: 24091964 [PubMed - indexed for MEDLINE]
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What's new for 'JKB_daily1' in PubMed

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Sent on Thursday, 2013 November 07
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. 2013 Sep 26;501(7468):512-6. doi: 10.1038/nature12566. Epub 2013 Sep 4. The ubiquitin ligase parkin mediates resistance to intracellular pathogens. Manzanillo PS, Ayres JS, Watson RO, Collins AC, Souza G, Rae CS, Schneider DS, Nakamura K, Shiloh MU, Cox JS. Department of Microbiology and Immunology Program in Microbial Pathogenesis and Host Defense, University of California, San Francisco, San Francisco, California 94158, USA. Comment in Cell biology: A table for two. [Nature. 2013] Cell biology: A table for two.Behr MA, Schurr E. Nature. 2013 Sep 26; 501(7468):498-9. Epub 2013 Sep 4. Abstract Ubiquitin-mediated targeting of intracellular bacteria to the autophagy pathway is a key innate defence mechanism against invading microbes, including the important human pathogen Mycobacterium tuberculosis. However, the ubiquitin ligases responsible for catalysing ubiquitin chains that surround intracellular bacteria are poorly understood. The parkin protein is a ubiquitin ligase with a well-established role in mitophagy, and mutations in the parkin gene (PARK2) lead to increased susceptibility to Parkinson's disease. Surprisingly, genetic polymorphisms in the PARK2 regulatory region are also associated with increased susceptibility to intracellular bacterial pathogens in humans, including Mycobacterium leprae and Salmonella enterica serovar Typhi, but the function of parkin in immunity has remained unexplored. Here we show that parkin has a role in ubiquitin-mediated autophagy of M. tuberculosis. Both parkin-deficient mice and flies are sensitive to various intracellular bacterial infections, indicating parkin has a conserved role in metazoan innate defence. Moreover, our work reveals an unexpected functional link between mitophagy and infectious disease.
	PMID: 24005326 [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, 2013 November 06
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. 2013 Sep 19;501(7467):300-2. doi: 10.1038/501300a. Climate science: Rising tide. Jones N.
	PMID: 24048051 [PubMed - indexed for MEDLINE]
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2.	Nature. 2013 Sep 19;501(7467):283. doi: 10.1038/501283a. The Himalayas must be protected. Pandit MK. Department of Environmental Studies, University of Delhi, India. rajkpandit@gmail.com
	PMID: 24048033 [PubMed - indexed for MEDLINE]
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What's new for 'JKB_daily1' in PubMed

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Sent on Saturday, 2013 November 02
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 Med. 2013 Aug;19(8):955. doi: 10.1038/nm0813-955. Straight talk with...Sir John Chisholm. Interview by Elie Dolgin. Chisholm J.
	PMID: 23921732 [PubMed - indexed for MEDLINE]