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

Sent on Thursday, 2010 Mar 04
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 -6 of 6

1.	Nature. 2010 Jan 21;463(7279):374-8. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. Cyclin D1 belongs to the core cell cycle machinery, and it is frequently overexpressed in human cancers. The full repertoire of cyclin D1 functions in normal development and oncogenesis is unclear at present. Here we developed Flag- and haemagglutinin-tagged cyclin D1 knock-in mouse strains that allowed a high-throughput mass spectrometry approach to search for cyclin D1-binding proteins in different mouse organs. In addition to cell cycle partners, we observed several proteins involved in transcription. Genome-wide location analyses (chromatin immunoprecipitation coupled to DNA microarray; ChIP-chip) showed that during mouse development cyclin D1 occupies promoters of abundantly expressed genes. In particular, we found that in developing mouse retinas-an organ that critically requires cyclin D1 function-cyclin D1 binds the upstream regulatory region of the Notch1 gene, where it serves to recruit CREB binding protein (CBP) histone acetyltransferase. Genetic ablation of cyclin D1 resulted in decreased CBP recruitment, decreased histone acetylation of the Notch1 promoter region, and led to decreased levels of the Notch1 transcript and protein in cyclin D1-null (Ccnd1(-/-)) retinas. Transduction of an activated allele of Notch1 into Ccnd1(-/-) retinas increased proliferation of retinal progenitor cells, indicating that upregulation of Notch1 signalling alleviates the phenotype of cyclin D1-deficiency. These studies show that in addition to its well-established cell cycle roles, cyclin D1 has an in vivo transcriptional function in mouse development. Our approach, which we term 'genetic-proteomic', can be used to study the in vivo function of essentially any protein.
	PMID: 20090754 [PubMed - indexed for MEDLINE]
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	Publication Types: Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't MeSH Terms: Alleles Animals CREB-Binding Protein/metabolism Chromatin Immunoprecipitation Cyclin D1/deficiency Cyclin D1/genetics Cyclin D1/metabolism* Gene Expression Regulation, Developmental* Genome/genetics High-Throughput Screening Assays Histone Acetyltransferases/metabolism Mass Spectrometry Mice Oligonucleotide Array Sequence Analysis Promoter Regions, Genetic/genetics Protein Binding Proteomics*/methods Rats Receptor, Notch1/genetics Receptor, Notch1/metabolism Retina/cytology Retina/embryology Retina/metabolism Stem Cells/cytology Stem Cells/metabolism Transcription, Genetic* Substances: Ccnd1 protein, mouse Notch1 protein, mouse Receptor, Notch1 Cyclin D1 CREB-Binding Protein Histone Acetyltransferases Secondary Source ID: GEO/GSE13636 Grant Support: HG004069/HG/NHGRI NIH HHS/United States HG3456/HG/NHGRI NIH HHS/United States P01 CA080111/CA/NCI NIH HHS/United States P01 CA109901/CA/NCI NIH HHS/United States R01 CA108420/CA/NCI NIH HHS/United States R01 EYO9676/PHS HHS/United States Cancer Research UK/United Kingdom

2.	Nature. 2010 Jan 21;463(7279):353-5. Mutational robustness can facilitate adaptation. Draghi JA , Parsons TL, Wagner GP, Plotkin JB. Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. Robustness seems to be the opposite of evolvability. If phenotypes are robust against mutation, we might expect that a population will have difficulty adapting to an environmental change, as several studies have suggested. However, other studies contend that robust organisms are more adaptable. A quantitative understanding of the relationship between robustness and evolvability will help resolve these conflicting reports and will clarify outstanding problems in molecular and experimental evolution, evolutionary developmental biology and protein engineering. Here we demonstrate, using a general population genetics model, that mutational robustness can either impede or facilitate adaptation, depending on the population size, the mutation rate and the structure of the fitness landscape. In particular, neutral diversity in a robust population can accelerate adaptation as long as the number of phenotypes accessible to an individual by mutation is smaller than the total number of phenotypes in the fitness landscape. These results provide a quantitative resolution to a significant ambiguity in evolutionary theory.
	PMID: 20090752 [PubMed - indexed for MEDLINE]
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	Publication Types: Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. MeSH Terms: Adaptation, Physiological/genetics* Evolution* Genetic Fitness/genetics Genetic Variation/genetics Genetics, Population Genotype Models, Genetic Mutagenesis/genetics* Mutation/genetics* Phenotype Population Density Time Factors Grant Support: 2U54AI057168/AI/NIAID NIH HHS/United States

3.	Nature. 2010 Jan 21;463(7279):303-4. Genetics: Decoding a national treasure. Worley KC, Gibbs RA. Comment on: Nature. 2010 Jan 21;463(7279):311-7.
	PMID: 20090741 [PubMed - indexed for MEDLINE]
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	Publication Types: Comment News MeSH Terms: Animals Contig Mapping Genetics, Population Genome/genetics* Genomics*/economics Genomics*/trends Humans Sequence Analysis, DNA/economics Sequence Analysis, DNA/trends Ursidae/genetics*

4.	Nature. 2010 Jan 21;463(7279):278. Genomics boosts brain-cancer work. Hayden EC.
	PMID: 20090720 [PubMed - indexed for MEDLINE]
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	Publication Types: News MeSH Terms: Brain Neoplasms/classification Brain Neoplasms/diagnosis* Brain Neoplasms/genetics* Brain Neoplasms/therapy Clinical Trials as Topic/trends Databases, Genetic Gene Expression Profiling Gene Expression Regulation, Neoplastic Genetic Testing/trends Genome, Human Genomics* Glioblastoma/classification Glioblastoma/diagnosis Glioblastoma/genetics Glioblastoma/therapy Humans Pharmacogenetics/trends Prognosis

5.	Nature. 2010 Jan 21;463(7279):E3; discussion E4. Essentiality of FASII pathway for Staphylococcus aureus. Balemans W, Lounis N, Gilissen R, Guillemont J, Simmen K, Andries K, Koul A. Department of Antimicrobial Research, Tibotec BVBA, Johnson & Johnson, Turnhoutseweg 30, B-2340 Beerse, Belgium. Comment on: Nature. 2009 Mar 5;458(7234):83-6. Recently, Brinster et al. suggested that type II fatty-acid biosynthesis (FASII) is not a suitable antibacterial target for Gram-positive pathogens because they use fatty acids directly from host serum rather than de novo synthesis. Their findings, if confirmed, are relevant for further scientific and financial investments in the development of new drugs targeting FASII. We present here in vitro and in vivo data demonstrating that their observations do not hold for Staphylococcus aureus, a major Gram-positive pathogen causing several human infections. The observed differences among Gram-positive pathogens in FASII reflects heterogeneity either in fatty-acid synthesis or in the capacity for fatty-acid uptake from the environment.
	PMID: 20090698 [PubMed - indexed for MEDLINE]
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	Publication Types: Comment MeSH Terms: Animals Anti-Bacterial Agents/pharmacology Anti-Bacterial Agents/therapeutic use Bacteremia/drug therapy Bacteremia/microbiology Bacterial Proteins/antagonists & inhibitors Bacterial Proteins/genetics Bacterial Proteins/metabolism Fatty Acids/biosynthesis* Fatty Acids/metabolism Fatty Acids/pharmacology Host-Pathogen Interactions/drug effects Humans Mice Reproducibility of Results Staphylococcal Infections/drug therapy Staphylococcal Infections/microbiology Staphylococcus aureus/drug effects Staphylococcus aureus/genetics Staphylococcus aureus/metabolism* Staphylococcus aureus/pathogenicity Triclosan/pharmacology Substances: Anti-Bacterial Agents Bacterial Proteins Fatty Acids Triclosan

6.	Nature. 2010 Jan 21;463(7279):311-7. Epub 2009 Dec 13. The sequence and de novo assembly of the giant panda genome. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J. BGI-Shenzhen, Shenzhen 518083, China. Comment in: Nature. 2010 Jan 21;463(7279):303-4. Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.
	PMID: 20010809 [PubMed - indexed for MEDLINE]
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	Publication Types: Research Support, Non-U.S. Gov't MeSH Terms: Algorithms Animals China Conserved Sequence/genetics Contig Mapping Diet/veterinary Dogs Evolution, Molecular Female Fertility/genetics Fertility/physiology Genome/genetics* Genomics* Heterozygote Humans Multigene Family/genetics Polymorphism, Single Nucleotide/genetics Receptors, G-Protein-Coupled/genetics Sequence Alignment Sequence Analysis, DNA Synteny/genetics Ursidae/classification Ursidae/genetics* Ursidae/physiology Substances: Receptors, G-Protein-Coupled taste receptors, type 1