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

Sent on Wednesday, 2013 June 26
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 - 9 of 9

1.	Nature. 2013 Jun 6;498(7452):16-7. doi: 10.1038/498017a. Geneticists push for global data-sharing. Hayden EC.
	PMID: 23739403 [PubMed - indexed for MEDLINE]
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2.	Nature. 2013 May 30;497(7451):535. Overtaken by events. [No authors listed]
	PMID: 23724421 [PubMed - indexed for MEDLINE]
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3.	Nature. 2013 May 30;497(7451):565. doi: 10.1038/497565a. Omics: Account for the 'dark matter' of biology. Varki A. Comment on DNA: Celebrate the unknowns. [Nature. 2013] DNA: Celebrate the unknowns.Ball P. Nature. 2013 Apr 25; 496(7446):419-20.
	PMID: 23719451 [PubMed - indexed for MEDLINE]
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4.	Nature. 2013 May 30;497(7451):546-7. doi: 10.1038/497546a. Tepid showing for genomics X prize. Hayden EC.
	PMID: 23719441 [PubMed - indexed for MEDLINE]
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5.	Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22. The Norway spruce genome sequence and conifer genome evolution. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S. Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden. Comment in Genomics: A spruce sequence. [Nature. 2013] Genomics: A spruce sequence.Sederoff R. Nature. 2013 May 30; 497(7451):569-70. Epub 2013 May 22. Abstract Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
	PMID: 23698360 [PubMed - indexed for MEDLINE]
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6.	Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/nature12113. Integrated genomic characterization of endometrial carcinoma. Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Collaborators: Getz G, Gabriel SB, Cibulskis K, Lander E, Sivachenko A, Sougnez C, Lawrence M, Kandoth C, Dooling D, Fulton R, Fulton L, Kalicki-Veizer J, McLellan MD, O'Laughlin M, Schmidt H, Wilson RK, Ye K, Ding L, Mardis ER, Ally A, Balasundaram M, Birol I, Butterfield YS, Carlsen R, Carter C, Chu A, Chuah E, Chuah HJ, Dhalla N, Guin R, Hirst C, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Plettner P, Schein JE, Sipahimalani P, Tam A, Varhol RJ, Robertson A, Cherniack AD, Pashtan I, Saksena G, Onofrio RC, Schumacher SE, Tabak B, Carter SL, Hernandez B, Gentry J, Salvesen HB, Ardlie K, Getz G, Winckler W, Beroukhim R, Gabriel SB, Meyerson M, Hadjipanayis A, Lee S, Mahadeshwar HS, Park P, Protopopov A, Ren X, Seth S, Song X, Tang J, Xi R, Yang L, Zeng D, Kucherlapati R, Chin L, Zhang J, Auman T, Balu S, Bodenheimer T, Buda E, Hayes D, Hoyle AP, Jefferys SR, Jones CD, Meng S, Mieczkowski PA, Mose LE, Parker JS, Perou CM, Roach J, Shi Y, Simons JV, Soloway MG, Tan D, Topal MD, Waring S, Wu J, Hoadley KA, Baylin SB, Bootwalla MS, Lai PH, Triche TJ Jr, Van Den Berg DJ, Weisenberger DJ, Laird PW, Shen H, Chin L, Zhang J, Getz G, Cho J, DiCara D, Frazer S, Heiman D, Jing R, Lin P, Mallard W, Stojanov P, Voet D, Zhang H, Zou L, Noble M, Lawrence M, Reynolds SM, Shmulevich I, Aksoy B, Antipin Y, Ciriello G, Dresdner G, Gao J, Gross B, Jacobsen A, Ladanyi M, Reva B, Sander C, Sinha R, Sumer S, Taylor BS, Cerami E, Weinhold N, Schultz N, Shen R, Benz S, Goldstein T, Haussler D, Ng S, Szeto C, Stuart J, Benz CC, Yau C, Zhang W, Annala M, Broom BM, Casasent TD, Ju Z, Liang H, Liu G, Lu Y, Unruh AK, Wakefield C, Weinstein JN, Zhang N, Liu Y, Broaddus R, Akbani R, Mills GB, Adams C, Barr T, Black AD, Bowen J, Deardurff J, Frick J, Gastier-Foster JM, Grossman T, Harper HA, Hart-Kothari M, Helsel C, Hobensack A, Kuck H, Kneile K, Leraas KM, Lichtenberg TM, McAllister C, Pyatt RE, Ramirez NC, Tabler TR, Vanhoose N, White P, Wise L, Zmuda E, Barnabas N, Berry-Green C, Blanc V, Boice L, Button M, Farkas A, Green A, MacKenzie J, Nicholson D, Kalloger SE, Gilks CB, Karlan BY, Lester J, Orsulic S, Borowsky M, Cadungog M, Czerwinski C, Huelsenbeck-Dill L, Iacocca M, Petrelli N, Rabeno B, Witkin G, Nemirovich-Danchenko E, Potapova O, Rotin D, Berchuck A, Birrer M, DiSaia P, Monovich L, Curley E, Gardner J, Mallery D, Penny R, Dowdy SC, Winterhoff B, Dao L, Gostout B, Meuter A, Teoman A, Dao F, Olvera N, Bogomolniy F, Garg K, Soslow RA, Levine DA, Abramov M, Bartlett JM, Kodeeswaran S, Parfitt J, Moiseenko F, Clarke BA, Goodman MT, Carney ME, Matsuno RK, Fisher J, Huang M, Rathmell W, Thorne L, Van Le L, Dhir R, Edwards R, Elishaev E, Zorn K, Broaddus R, Goodfellow PJ, Mutch D, Schultz N, Liu Y, Akbani R, Cherniack AD, Cerami E, Weinhold N, Shen H, Hoadley KA, Kahn AB, Bell DW, Pollock PM, Wang C, Wheeler DA, Shinbrot E, Karlan BY, Berchuck A, Dowdy SC, Winterhoff B, Goodman MT, Robertson A, Beroukhim R, Pashtan I, Salvesen HB, Laird PW, Noble M, Stuart J, Ding L, Kandoth C, Gilks C, Soslow RA, Goodfellow PJ, Mutch D, Broaddus R, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA, Ayala B, Chu AL, Jensen MA, Kothiyal P, Pihl TD, Pontius J, Pot DA, Snyder EE, Srinivasan D, Kahn AB, Shaw KR, Sheth M, Davidsen T, Eley G, Ferguson ML, Demchok JA, Yang L, Guyer MS, Ozenberger BA, Sofia HJ. Abstract We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.
	PMID: 23636398 [PubMed - indexed for MEDLINE]
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7.	Nature. 2013 May 2;497(7447):127-31. doi: 10.1038/nature12121. Epub 2013 Apr 24. Extensive transcriptional heterogeneity revealed by isoform profiling. Pelechano V, Wei W, Steinmetz LM. Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Comment in Molecular biology: The ends justify the means. [Nature. 2013] Molecular biology: The ends justify the means.Pugh BF. Nature. 2013 May 2; 497(7447):48-9. Epub 2013 Apr 24. Abstract Transcript function is determined by sequence elements arranged on an individual RNA molecule. Variation in transcripts can affect messenger RNA stability, localization and translation, or produce truncated proteins that differ in localization or function. Given the existence of overlapping, variable transcript isoforms, determining the functional impact of the transcriptome requires identification of full-length transcripts, rather than just the genomic regions that are transcribed. Here, by jointly determining both transcript ends for millions of RNA molecules, we reveal an extensive layer of isoform diversity previously hidden among overlapping RNA molecules. Variation in transcript boundaries seems to be the rule rather than the exception, even within a single population of yeast cells. Over 26 major transcript isoforms per protein-coding gene were expressed in yeast. Hundreds of short coding RNAs and truncated versions of proteins are concomitantly encoded by alternative transcript isoforms, increasing protein diversity. In addition, approximately 70% of genes express alternative isoforms that vary in post-transcriptional regulatory elements, and tandem genes frequently produce overlapping or even bicistronic transcripts. This extensive transcript diversity is generated by a relatively simple eukaryotic genome with limited splicing, and within a genetically homogeneous population of cells. Our findings have implications for genome compaction, evolution and phenotypic diversity between single cells. These data also indicate that isoform diversity as well as RNA abundance should be considered when assessing the functional repertoire of genomes.
	PMID: 23615609 [PubMed - indexed for MEDLINE]
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8.	Nature. 2013 May 2;497(7447):108-12. doi: 10.1038/nature12065. Epub 2013 Apr 7. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas C, Rosenfeld N. Cancer Research UK Cambridge Institute and University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK. Abstract Cancers acquire resistance to systemic treatment as a result of clonal evolution and selection. Repeat biopsies to study genomic evolution as a result of therapy are difficult, invasive and may be confounded by intra-tumour heterogeneity. Recent studies have shown that genomic alterations in solid cancers can be characterized by massively parallel sequencing of circulating cell-free tumour DNA released from cancer cells into plasma, representing a non-invasive liquid biopsy. Here we report sequencing of cancer exomes in serial plasma samples to track genomic evolution of metastatic cancers in response to therapy. Six patients with advanced breast, ovarian and lung cancers were followed over 1-2 years. For each case, exome sequencing was performed on 2-5 plasma samples (19 in total) spanning multiple courses of treatment, at selected time points when the allele fraction of tumour mutations in plasma was high, allowing improved sensitivity. For two cases, synchronous biopsies were also analysed, confirming genome-wide representation of the tumour genome in plasma. Quantification of allele fractions in plasma identified increased representation of mutant alleles in association with emergence of therapy resistance. These included an activating mutation in PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) following treatment with paclitaxel; a truncating mutation in RB1 (retinoblastoma 1) following treatment with cisplatin; a truncating mutation in MED1 (mediator complex subunit 1) following treatment with tamoxifen and trastuzumab, and following subsequent treatment with lapatinib, a splicing mutation in GAS6 (growth arrest-specific 6) in the same patient; and a resistance-conferring mutation in EGFR (epidermal growth factor receptor; T790M) following treatment with gefitinib. These results establish proof of principle that exome-wide analysis of circulating tumour DNA could complement current invasive biopsy approaches to identify mutations associated with acquired drug resistance in advanced cancers. Serial analysis of cancer genomes in plasma constitutes a new paradigm for the study of clonal evolution in human cancers.
	PMID: 23563269 [PubMed - indexed for MEDLINE]
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9.	Nature. 2013 May 2;497(7447):122-6. doi: 10.1038/nature12052. Epub 2013 Apr 7. Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX. Ko M, An J, Bandukwala HS, Chavez L, Aijö T, Pastor WA, Segal MF, Li H, Koh KP, Lähdesmäki H, Hogan PG, Aravind L, Rao A. Division of Signaling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, California 92037, USA. Abstract TET (ten-eleven-translocation) proteins are Fe(ii)- and α-ketoglutarate-dependent dioxygenases that modify the methylation status of DNA by successively oxidizing 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, potential intermediates in the active erasure of DNA-methylation marks. Here we show that IDAX (also known as CXXC4), a reported inhibitor of Wnt signalling that has been implicated in malignant renal cell carcinoma and colonic villous adenoma, regulates TET2 protein expression. IDAX was originally encoded within an ancestral TET2 gene that underwent a chromosomal gene inversion during evolution, thus separating the TET2 CXXC domain from the catalytic domain. The IDAX CXXC domain binds DNA sequences containing unmethylated CpG dinucleotides, localizes to promoters and CpG islands in genomic DNA and interacts directly with the catalytic domain of TET2. Unexpectedly, IDAX expression results in caspase activation and TET2 protein downregulation, in a manner that depends on DNA binding through the IDAX CXXC domain, suggesting that IDAX recruits TET2 to DNA before degradation. IDAX depletion prevents TET2 downregulation in differentiating mouse embryonic stem cells, and short hairpin RNA against IDAX increases TET2 protein expression in the human monocytic cell line U937. Notably, we find that the expression and activity of TET3 is also regulated through its CXXC domain. Taken together, these results establish the separate and linked CXXC domains of TET2 and TET3, respectively, as previously unknown regulators of caspase activation and TET enzymatic activity. PMCID: PMC3643997 [Available on 2014/5/2]
	PMID: 23563267 [PubMed - indexed for MEDLINE]
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