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 Friday, 2010 May 21
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]))
Click here to view complete results in PubMed. (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Items 1 - 11 of 11

1.	Nature. 2010 Apr 1;464(7289):757-62. The genome of a songbird. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK. The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. wwarren@watson.wustl.edu Abstract The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
	PMID: 20360741 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Comparative Study Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't MeSH Terms: 3' Untranslated Regions/genetics Animals Auditory Perception/genetics Brain/physiology Chickens/genetics Evolution, Molecular Female Finches/genetics* Finches/physiology Gene Duplication Gene Regulatory Networks/genetics Genome/genetics* Male MicroRNAs/genetics Models, Animal Multigene Family/genetics Retroelements/genetics Sex Chromosomes/genetics Terminal Repeat Sequences/genetics Transcription, Genetic/genetics Vocalization, Animal/physiology Substances: 3' Untranslated Regions MicroRNAs Retroelements Grant Support: BBE0175091/Biotechnology and Biological Sciences Research Council/United Kingdom R01 DC007218/DC/NIDCD NIH HHS/United States R01 GM59290/GM/NIGMS NIH HHS/United States R01 NS045264/NS/NINDS NIH HHS/United States R01NS051820/NS/NINDS NIH HHS/United States Howard Hughes Medical Institute/United States

2.	Nature. 2010 Apr 1;464(7289):679. Counterpoint: Data first. Golub T. Cancer Program at the Broad Institute, Cambridge, Massachusetts 02142, USA. golub@broadinstitute.org Comment on: Nature. 2010 Apr 1;464(7289):678.
	PMID: 20360719 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Comment MeSH Terms: Antineoplastic Agents/pharmacology Antineoplastic Agents/therapeutic use Drug Discovery/methods Drug Discovery/trends* Fusion Proteins, bcr-abl/antagonists & inhibitors Fusion Proteins, bcr-abl/genetics Fusion Proteins, bcr-abl/metabolism Genome, Human/genetics* Genomics/trends Humans Individualized Medicine/trends Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics Neoplasms/drug therapy* Neoplasms/genetics* Piperazines/pharmacology Piperazines/therapeutic use Pyrimidines/pharmacology Pyrimidines/therapeutic use Substances: Antineoplastic Agents Fusion Proteins, bcr-abl Piperazines Pyrimidines imatinib

3.	Nature. 2010 Apr 1;464(7289):678. Point: Hypotheses first. Weinberg R. Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA. weinberg@wi.mit.edu Comment in: Nature. 2010 Apr 1;464(7289):679.
	PMID: 20360718 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Historical Article MeSH Terms: Genome, Human/genetics Genomics/economics Genomics/trends History, 20th Century History, 21st Century Human Genome Project/economics Humans Models, Biological* Neoplasms/diagnosis Neoplasms/drug therapy Neoplasms/genetics* Neoplasms/pathology Signal Transduction Systems Biology/economics Systems Biology/trends*

4.	Nature. 2010 Apr 1;464(7289):676-7. Multiple personal genomes await. Venter JC. J. Craig Venter Institute, La Jolla, California 92121, USA. jcventer@jcvi.org
	PMID: 20360717 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Historical Article MeSH Terms: Animals Continental Population Groups/genetics Diploidy Female Genetic Predisposition to Disease/genetics Genetic Variation/genetics Genetics, Medical/trends* Genome, Human/genetics* Genomics/economics Genomics/history Genomics/trends* Haploidy Haplotypes/genetics History, 20th Century History, 21st Century Human Genome Project/economics Human Genome Project/history Humans Individualized Medicine/trends* Male Phenotype Sequence Analysis, DNA/economics Sequence Analysis, DNA/history Sequence Analysis, DNA/instrumentation Sequence Analysis, DNA/methods

5.	Nature. 2010 Apr 1;464(7289):674-5. Has the revolution arrived? Collins F. National Institutes of Health, Bethesda, Maryland 20892, USA. francis.collins@nih.gov
	PMID: 20360716 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Historical Article MeSH Terms: Access to Information Genetic Predisposition to Disease/genetics Genetics, Medical/trends* Genome, Human/genetics* Genome-Wide Association Study Genomics/economics Genomics/history Genomics/trends* Haplotypes/genetics History, 20th Century History, 21st Century Humans Individualized Medicine/trends* Sequence Analysis, DNA/economics Sequence Analysis, DNA/history Sequence Analysis, DNA/trends

6.	Nature. 2010 Apr 1;464(7289):670-1. Human genome at ten: The sequence explosion. [No authors listed]
	PMID: 20360711 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Historical Article News MeSH Terms: Archives Databases, Genetic/history Databases, Genetic/statistics & numerical data* Databases, Genetic/trends Female Genome, Human/genetics* Genomics/economics Genomics/history Genomics/methods Genomics/trends* History, 20th Century History, 21st Century Human Genome Project/economics Human Genome Project/history Humans Male Sequence Analysis, DNA/economics Sequence Analysis, DNA/history Sequence Analysis, DNA/methods

7.	Nature. 2010 Apr 1;464(7289):668-9. Human genome at ten: The human race. Abbott A.
	PMID: 20360710 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Historical Article News MeSH Terms: Animals Computational Biology/economics Computational Biology/history Computational Biology/trends Epigenesis, Genetic Genome, Human/genetics* Genomics/history* Genomics/standards Genomics/trends History, 20th Century History, 21st Century Human Genome Project/history* Humans Metagenome Patents as Topic/history RNA Interference

8.	Nature. 2010 Apr 1;464(7289):664-7. Human genome at ten: Life is complicated. Check Hayden E.
	PMID: 20360709 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Historical Article News MeSH Terms: Animals Data Mining Gene Expression Regulation Genes/genetics Genome, Human/genetics* Genomics/history Genomics/trends History, 20th Century History, 21st Century Human Genome Project/history Humans Models, Biological* Molecular Biology/history* Neoplasms/genetics Neoplasms/therapy RNA, Untranslated/genetics RNA, Untranslated/metabolism Sea Urchins/embryology Sea Urchins/genetics Systems Biology/trends* Tumor Suppressor Protein p53/chemistry Tumor Suppressor Protein p53/genetics Tumor Suppressor Protein p53/metabolism Uncertainty* Substances: RNA, Untranslated Tumor Suppressor Protein p53

9.	Nature. 2010 Apr 1;464(7289):649-50. The human genome at ten. [No authors listed]
	PMID: 20360688 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Editorial Historical Article MeSH Terms: Data Collection Genetic Testing/trends Genetics, Medical/trends* Genome, Human/genetics* Genomics/economics Genomics/history* Genomics/trends Haplotypes/genetics History, 20th Century History, 21st Century Human Genome Project/history* Humans Time Factors

10.	J Leukoc Biol. 2010 May;87(5):815-22. Epub 2010 Feb 1. A conserved distal segment of the mouse CSF-1 receptor promoter is required for maximal expression of a reporter gene in macrophages and osteoclasts of transgenic mice. Ovchinnikov DA, DeBats CE, Sester DP, Sweet MJ, Hume DA. Institute for Molecular Bioscience, University of Queensland, Australia. Abstract Csf1r mRNA in adult mice is expressed in cells of the macrophage lineage, and during development, it is also expressed from a separate promoter in placental trophoblast cells. This mouse trophoblast promoter sequence is conserved across species, but human trophoblasts actually initiate transcription from a separate promoter 20 kb upstream, which is not conserved in rodents. A 7.2-kb fragment of the mouse Csf1r genomic DNA, including the 3.5-kb promoter, the first coding exon and downstream intron, is sufficient to direct reproducible position- and copy number-independent expression of an EGFP reporter in vitro and in vivo. In this study, we have examined the consequence of removal of the 150-bp fragment encompassing the conserved trophoblast promoter region in the context of the 7.2-kb promoter on reporter gene expression in transgenic mice. The deletion ablated expression in the placenta but also abolished expression in multinucleated OCL and reduced expression in macrophages. RT-PCR analyses of Csf1r mRNA revealed that mouse OCL use another promoter within this region, distinct from that used in placental trophoblasts, to generate an alternative 5'UTR.
	PMID: 20123678 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Research Support, Non-U.S. Gov't MeSH Terms: 5' Untranslated Regions/genetics Amino Acid Sequence Animals Base Sequence Cell Differentiation/genetics Cell Separation Conserved Sequence Female Flow Cytometry Gene Expression Gene Expression Regulation* Genes, Reporter Humans Macrophages/cytology Macrophages/immunology* Macrophages/metabolism Mice Mice, Transgenic Molecular Sequence Data Osteoclasts/cytology Osteoclasts/immunology* Osteoclasts/metabolism Pregnancy Promoter Regions, Genetic/genetics* RNA, Messenger/analysis Receptor, Macrophage Colony-Stimulating Factor/genetics* Reverse Transcriptase Polymerase Chain Reaction Transfection Trophoblasts/metabolism Substances: 5' Untranslated Regions RNA, Messenger Receptor, Macrophage Colony-Stimulating Factor Grant Support: Biotechnology and Biological Sciences Research Council/United Kingdom

11.	J Leukoc Biol. 2010 May;87(5):753-64. Epub 2010 Jan 5. Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products. Garceau V, Smith J, Paton IR, Davey M, Fares MA, Sester DP, Burt DW, Hume DA. The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, United Kingdom. Comment in: J Leukoc Biol. 2010 May;87(5):745-7. Abstract Macrophages are involved in many aspects of development, host defense, pathology, and homeostasis. Their normal differentiation, proliferation, and survival are controlled by CSF-1 via the activation of the CSF1R. A recently discovered cytokine, IL-34, was shown to bind the same receptor in humans. Chicken is a widely used model organism in developmental biology, but the factors that control avian myelopoiesis have not been identified previously. The CSF-1, IL-34, and CSF1R genes in chicken and zebra finch were identified from respective genomic/cDNA sequence resources. Comparative analysis of the avian CSF1R loci revealed likely orthologs of mammalian macrophage-specific promoters and enhancers, and the CSF1R gene is expressed in the developing chick embryo in a pattern consistent with macrophage-specific expression. Chicken CSF-1 and IL-34 were expressed in HEK293 cells and shown to elicit macrophage growth from chicken BM cells in culture. Comparative sequence and co-evolution analysis across all vertebrates suggests that the two ligands interact with distinct regions of the CSF1R. These studies demonstrate that there are two separate ligands for a functional CSF1R across all vertebrates.
	PMID: 20051473 [PubMed - indexed for MEDLINE]
	Related citations
	Publication Types: Research Support, Non-U.S. Gov't MeSH Terms: Amino Acid Sequence Animals Birds Chick Embryo Chickens Conserved Sequence Evolution Finches Gene Expression Humans In Situ Hybridization Interleukins/chemistry Interleukins/genetics* Interleukins/metabolism Macrophage Colony-Stimulating Factor/chemistry Macrophage Colony-Stimulating Factor/genetics* Macrophage Colony-Stimulating Factor/metabolism Macrophages/metabolism* Molecular Sequence Data Phylogeny Protein Structure, Quaternary Receptor, Macrophage Colony-Stimulating Factor/chemistry Receptor, Macrophage Colony-Stimulating Factor/genetics* Receptor, Macrophage Colony-Stimulating Factor/metabolism Sequence Homology, Amino Acid Structural Homology, Protein Substances: Interleukins interleukin-34, human Macrophage Colony-Stimulating Factor Receptor, Macrophage Colony-Stimulating Factor Grant Support: BB/D010705/1/Biotechnology and Biological Sciences Research Council/United Kingdom