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Sender's message: Sepsis or genomics or altitude: JKB_daily1
Sent on Friday, 2015 January 16
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(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]))View complete results in PubMed (results may change over time).
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| 1. | N Engl J Med. 2015 Jan 8;372(2):190. doi: 10.1056/NEJMc1413936#SA3.Pepper DJ. |
| PMID: 25564909 [PubMed - indexed for MEDLINE] |
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| 3. | N Engl J Med. 2015 Jan 8;372(2):189. doi: 10.1056/NEJMc1413936#SA1.Priebe HJ. |
| PMID: 25564907 [PubMed - indexed for MEDLINE] |
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| 5. | Science. 2014 Dec 19;346(6216):1486-92. doi: 10.1126/science.346.6216.1486.Zeng M1, Hu Z2, Shi X2, Li X1, Zhan X1, Li XD3, Wang J3, Choi JH1, Wang KW1, Purrington T1, Tang M1, Fina M1, DeBerardinis RJ2, Moresco EM1, Pedersen G4, McInerney GM4, Hedestam GB4, Chen ZJ3, Beutler B5.AbstractMultivalent molecules with repetitive structures including bacterial capsular polysaccharides and viral capsids elicit antibody responses through B cell receptor (BCR) crosslinking in the absence of T cell help. We report that immunization with these T cell-independent type 2 (TI-2) antigens causes up-regulation of endogenous retrovirus (ERV) RNAs in antigen-specific mouse B cells. These RNAs are detected via a mitochondrial antiviral signaling protein (MAVS)-dependent RNA sensing pathway or reverse-transcribed and detected via the cGAS-cGAMP-STING pathway, triggering a second, sustained wave of signaling that promotes specific immunoglobulin M production. Deficiency of both MAVS and cGAS, or treatment of MAVS-deficient mice with reverse transcriptase inhibitors, dramatically inhibits TI-2 antibody responses. These findings suggest that ERV and two innate sensing pathways that detect them are integral components of the TI-2 B cell signaling apparatus. Copyright © 2014, American Association for the Advancement of Science. |
| PMID: 25525240 [PubMed - indexed for MEDLINE] |
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| 7. | Nat Genet. 2014 Sep;46(9):951-6. doi: 10.1038/ng.3067. Epub 2014 Aug 17.Lorenzo FR1, Huff C2, Myllymäki M3, Olenchock B4, Swierczek S5, Tashi T5, Gordeuk V6, Wuren T7, Ri-Li G7, McClain DA5, Khan TM8, Koul PA9, Guchhait P10, Salama ME11, Xing J12, Semenza GL13, Liberzon E14, Wilson A15, Simonson TS16, Jorde LB17, Kaelin WG Jr14, Koivunen P3, Prchal JT18.AbstractTibetans do not exhibit increased hemoglobin concentration at high altitude. We describe a high-frequency missense mutation in the EGLN1 gene, which encodes prolyl hydroxylase 2 (PHD2), that contributes to this adaptive response. We show that a variant in EGLN1, c.[12C>G; 380G>C], contributes functionally to the Tibetan high-altitude phenotype. PHD2 triggers the degradation of hypoxia-inducible factors (HIFs), which mediate many physiological responses to hypoxia, including erythropoiesis. The PHD2 p.[Asp4Glu; Cys127Ser] variant exhibits a lower K(m) value for oxygen, suggesting that it promotes increased HIF degradation under hypoxic conditions. Whereas hypoxia stimulates the proliferation of wild-type erythroid progenitors, the proliferation of progenitors with the c.[12C>G; 380G>C] mutation in EGLN1 is significantly impaired under hypoxic culture conditions. We show that the c.[12C>G; 380G>C] mutation originated ∼8,000 years ago on the same haplotype previously associated with adaptation to high altitude. The c.[12C>G; 380G>C] mutation abrogates hypoxia-induced and HIF-mediated augmentation of erythropoiesis, which provides a molecular mechanism for the observed protection of Tibetans from polycythemia at high altitude. |
| PMID: 25129147 [PubMed - indexed for MEDLINE] |
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| 8. | Nat Genet. 2014 Sep;46(9):944-50. doi: 10.1038/ng.3050. Epub 2014 Aug 3.Samocha KE1, Robinson EB2, Sanders SJ3, Stevens C4, Sabo A5, McGrath LM6, Kosmicki JA7, Rehnström K8, Mallick S9, Kirby A10, Wall DP11, MacArthur DG10, Gabriel SB12, DePristo M13, Purcell SM14, Palotie A15, Boerwinkle E16, Buxbaum JD17, Cook EH Jr18, Gibbs RA5, Schellenberg GD19, Sutcliffe JS20, Devlin B21, Roeder K22, Neale BM2, Daly MJ2.AbstractSpontaneously arising (de novo) mutations have an important role in medical genetics. For diseases with extensive locus heterogeneity, such as autism spectrum disorders (ASDs), the signal from de novo mutations is distributed across many genes, making it difficult to distinguish disease-relevant mutations from background variation. Here we provide a statistical framework for the analysis of excesses in de novo mutation per gene and gene set by calibrating a model of de novo mutation. We applied this framework to de novo mutations collected from 1,078 ASD family trios, and, whereas we affirmed a significant role for loss-of-function mutations, we found no excess of de novo loss-of-function mutations in cases with IQ above 100, suggesting that the role of de novo mutations in ASDs might reside in fundamental neurodevelopmental processes. We also used our model to identify ∼1,000 genes that are significantly lacking in functional coding variation in non-ASD samples and are enriched for de novo loss-of-function mutations identified in ASD cases. |
| PMID: 25086666 [PubMed - indexed for MEDLINE] |
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| 9. | Nat Genet. 2014 Sep;46(9):939-43. doi: 10.1038/ng.3051. Epub 2014 Aug 3.Gross AM1, Orosco RK2, Shen JP3, Egloff AM4, Carter H3, Hofree M5, Choueiri M3, Coffey CS2, Lippman SM6, Hayes DN7, Cohen EE8, Grandis JR4, Nguyen QT9, Ideker T10.AbstractHead and neck squamous cell carcinoma (HNSCC) is characterized by aggressive behavior with a propensity for metastasis and recurrence. Here we report a comprehensive analysis of the molecular and clinical features of HNSCC that govern patient survival. We find that TP53 mutation is frequently accompanied by loss of chromosome 3p and that the combination of these events is associated with a surprising decrease in survival time (1.9 years versus >5 years for TP53 mutation alone). The TP53-3p interaction is specific to chromosome 3p and validates in HNSCC and pan-cancer cohorts. In human papillomavirus (HPV)-positive tumors, in which HPV inactivates TP53, 3p deletion is also common and is associated with poor outcomes. The TP53-3p event is modified by mir-548k expression, which decreases survival further, and is mutually exclusive with mutations affecting RAS signaling. Together, the identified markers underscore the molecular heterogeneity of HNSCC and enable a new multi-tiered classification of this disease. |
| PMID: 25086664 [PubMed - indexed for MEDLINE] |
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| 10. | Nat Genet. 2014 Sep;46(9):982-8. doi: 10.1038/ng.3044. Epub 2014 Jul 27.Wang M1, Yu Y1, Haberer G2, Marri PR3, Fan C4, Goicoechea JL5, Zuccolo A6, Song X5, Kudrna D5, Ammiraju JS7, Cossu RM8, Maldonado C5, Chen J9, Lee S5, Sisneros N5, de Baynast K5, Golser W5, Wissotski M5, Kim W5, Sanchez P10, Ndjiondjop MN11, Sanni K11, Long M12, Carney J13, Panaud O14, Wicker T15, Machado CA16, Chen M9, Mayer KF17, Rounsley S18, Wing RA5.AbstractThe cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes. |
| PMID: 25064006 [PubMed - indexed for MEDLINE] |
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