What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Tuesday, 2014 July 08
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]))

View complete results in PubMed (results may change over time).

Edit saved search settings, or unsubscribe from these e-mail updates.

PubMed Results

Items 1 - 5 of 5

1.	Nature. 2014 May 29;509(7502):S68. doi: 10.1038/509S68a. Perspective: Learning to share. Quackenbush J. Author information: Center for Cancer Computational Biology at the Dana-Farber Cancer Institute in Boston, Massachusetts.
	PMID: 24870827 [PubMed - indexed for MEDLINE]
	Related citations

2.	Nature. 2014 May 29;509(7502):S52-4. doi: 10.1038/509S52a. Therapy: This time it's personal. Gravitz L.
	PMID: 24870820 [PubMed - indexed for MEDLINE]
	Related citations

3.	Nature. 2014 May 29;509(7502):582-7. doi: 10.1038/nature13319. Mass-spectrometry-based draft of the human proteome. Wilhelm M1, Schlegl J2, Hahne H3, Moghaddas Gholami A3, Lieberenz M4, Savitski MM5, Ziegler E4, Butzmann L4, Gessulat S4, Marx H6, Mathieson T5, Lemeer S6, Schnatbaum K7, Reimer U7, Wenschuh H7, Mollenhauer M8, Slotta-Huspenina J8, Boese JH4, Bantscheff M5, Gerstmair A4, Faerber F4, Kuster B9. Author information: 11] Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2] SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany [3]. 21] SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany [2]. 31] Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2]. 4SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany. 5Cellzome GmbH, Meyerhofstraße 1, 69117 Heidelberg, Germany. 6Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany. 7JPT Peptide Technologies GmbH, Volmerstraße 5, 12489 Berlin, Germany. 8Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany. 91] Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2] Center for Integrated Protein Science Munich, Germany. Abstract Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Here we present a mass-spectrometry-based draft of the human proteome and a public, high-performance, in-memory database for real-time analysis of terabytes of big data, called ProteomicsDB. The information assembled from human tissues, cell lines and body fluids enabled estimation of the size of the protein-coding genome, and identified organ-specific proteins and a large number of translated lincRNAs (long intergenic non-coding RNAs). Analysis of messenger RNA and protein-expression profiles of human tissues revealed conserved control of protein abundance, and integration of drug-sensitivity data enabled the identification of proteins predicting resistance or sensitivity. The proteome profiles also hold considerable promise for analysing the composition and stoichiometry of protein complexes. ProteomicsDB thus enables navigation of proteomes, provides biological insight and fosters the development of proteomic technology.
	PMID: 24870543 [PubMed - indexed for MEDLINE]
	Related citations

4.	Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302. A draft map of the human proteome. Kim MS1, Pinto SM2, Getnet D3, Nirujogi RS2, Manda SS2, Chaerkady R1, Madugundu AK2, Kelkar DS2, Isserlin R4, Jain S4, Thomas JK2, Muthusamy B2, Leal-Rojas P5, Kumar P2, Sahasrabuddhe NA2, Balakrishnan L2, Advani J2, George B2, Renuse S2, Selvan LD2, Patil AH2, Nanjappa V2, Radhakrishnan A2, Prasad S6, Subbannayya T2, Raju R2, Kumar M2, Sreenivasamurthy SK2, Marimuthu A2, Sathe GJ2, Chavan S2, Datta KK2, Subbannayya Y2, Sahu A2, Yelamanchi SD2, Jayaram S2, Rajagopalan P2, Sharma J2, Murthy KR2, Syed N2, Goel R2, Khan AA2, Ahmad S2, Dey G2, Mudgal K7, Chatterjee A2, Huang TC6, Zhong J6, Wu X1, Shaw PG6, Freed D6, Zahari MS8, Mukherjee KK9, Shankar S10, Mahadevan A11, Lam H12, Mitchell CJ6, Shankar SK11, Satishchandra P13, Schroeder JT14, Sirdeshmukh R2, Maitra A15, Leach SD16, Drake CG17, Halushka MK18, Prasad TS2, Hruban RH15, Kerr CL19, Bader GD4, Iacobuzio-Donahue CA20, Gowda H2, Pandey A21. Author information: 11] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. 2Institute of Bioinformatics, International Tech Park, Bangalore 560066, India. 31] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana 70130, USA. 4The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. 51] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Pathology, Universidad de La Frontera, Center of Genetic and Immunological Studies-Scientific and Technological Bioresource Nucleus, Temuco 4811230, Chile. 6McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. 7School of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. 8Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. 9Department of Neurosurgery, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India. 10Department of Internal Medicine Armed Forces Medical College, Pune 411040, India. 111] Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India [2] Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore 560029, India. 12Department of Chemical and Biomolecular Engineering and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong. 13Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India. 14Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA. 151] The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [2] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. 161] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. 171] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [2] Departments of Immunology and Urology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. 18The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. 191] Department of Obstetrics and Gynecology, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA [2] Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA. 201] The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [2] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [3] Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA. 211] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [3] Institute of Bioinformatics, International Tech Park, Bangalore 560066, India [4] Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana 70130, USA [5] The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [6] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [7] Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana 70130, USA. Abstract The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames. This large human proteome catalogue (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.
	PMID: 24870542 [PubMed - indexed for MEDLINE]
	Related citations

5.	Nature. 2014 May 29;509(7502):612-6. doi: 10.1038/nature13377. Epub 2014 May 21. Bacterial phylogeny structures soil resistomes across habitats. Forsberg KJ1, Patel S2, Gibson MK3, Lauber CL4, Knight R5, Fierer N6, Dantas G7. Author information: 11] Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA [2]. 21] Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA [3]. 3Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA. 4Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA. 51] Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA [2] Howard Hughes Medical Institute, Boulder, Colorado 80309, USA. 61] Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA [2] Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA. 71] Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA [3] Department of Biomedical Engineering, Washington University, St Louis, Missouri 63130, USA. Comment in Microbiology: Barriers to the spread of resistance. [Nature. 2014] Microbiology: Barriers to the spread of resistance.Sommer MO. Nature. 2014 May 29; 509(7502):567-8. Epub 2014 May 21. Abstract Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny. PMCID: PMC4079543 [Available on 2014/11/29]
	PMID: 24847883 [PubMed - indexed for MEDLINE]
	Related citations