Sunday, 28 February 2010

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Saturday, 27 February 2010

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Friday, 26 February 2010

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Thursday, 25 February 2010

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PubMed Results
Items 1 -5 of 5

1. Science. 2010 Feb 5;327(5966):682-5.

Flight orientation behaviors promote optimal migration trajectories in high-flying insects.

Chapman JW, Nesbit RL, Burgin LE, Reynolds DR, Smith AD, Middleton DR, Hill JK.

Plant and Invertebrate Ecology Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK. jason.chapman@bbsrc.ac.uk

Many insects undertake long-range seasonal migrations to exploit temporary breeding sites hundreds or thousands of kilometers apart, but the behavioral adaptations that facilitate these movements remain largely unknown. Using entomological radar, we showed that the ability to select seasonally favorable, high-altitude winds is widespread in large day- and night-flying migrants and that insects adopt optimal flight headings that partially correct for crosswind drift, thus maximizing distances traveled. Trajectory analyses show that these behaviors increase migration distances by 40% and decrease the degree of drift from seasonally optimal directions. These flight behaviors match the sophistication of those seen in migrant birds and help explain how high-flying insects migrate successfully between seasonal habitats.

PMID: 20133570 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Research Support, Non-U.S. Gov't

MeSH Terms:

  • Altitude
  • Animal Migration*
  • Animals
  • Butterflies/physiology*
  • Computer Simulation
  • Flight, Animal*
  • Moths/physiology*
  • Orientation
  • Radar
  • Seasons
  • Wind*

Grant Support:

  • Biotechnology and Biological Sciences Research Council/United Kingdom
2. Science. 2010 Feb 5;327(5966):656-61.

Development of monocytes, macrophages, and dendritic cells.

Geissmann F, Manz MG, Jung S, Sieweke MH, Merad M, Ley K.

Centre for Molecular and Cellular Biology of Inflammation, Division of Immunology, Infection, and Inflammatory Diseases, King's College London, Great Maze Pond, London SE1 1UL, UK. frederic.geissmann@kcl.ac.uk

Monocytes and macrophages are critical effectors and regulators of inflammation and the innate immune response, the immediate arm of the immune system. Dendritic cells initiate and regulate the highly pathogen-specific adaptive immune responses and are central to the development of immunologic memory and tolerance. Recent in vivo experimental approaches in the mouse have unveiled new aspects of the developmental and lineage relationships among these cell populations. Despite this, the origin and differentiation cues for many tissue macrophages, monocytes, and dendritic cell subsets in mice, and the corresponding cell populations in humans, remain to be elucidated.

PMID: 20133564 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH Terms:

  • Animals
  • Cell Lineage
  • Cell Proliferation
  • Cytokines/metabolism
  • Dendritic Cells/cytology
  • Dendritic Cells/immunology
  • Dendritic Cells/physiology*
  • Homeostasis
  • Humans
  • Inflammation/immunology
  • Macrophages/cytology
  • Macrophages/immunology
  • Macrophages/physiology*
  • Mice
  • Monocytes/cytology
  • Monocytes/immunology
  • Monocytes/physiology*
  • Myeloid Progenitor Cells/cytology
  • Myeloid Progenitor Cells/physiology
  • Myelopoiesis*
  • Phagocytosis
  • Transcription, Genetic

Substances:

  • Cytokines

Grant Support:

  • G0900867/Medical Research Council/United Kingdom
  • R01 HL058108/HL/NHLBI NIH HHS/United States
3. Nature. 2010 Jan 14;463(7278):237-40.

KAP1 controls endogenous retroviruses in embryonic stem cells.

Rowe HM, Jakobsson J, Mesnard D, Rougemont J, Reynard S, Aktas T, Maillard PV, Layard-Liesching H, Verp S, Marquis J, Spitz F, Constam DB, Trono D.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.

More than forty per cent of the mammalian genome is derived from retroelements, of which about one-quarter are endogenous retroviruses (ERVs). Some are still active, notably in mice the highly polymorphic early transposon (ETn)/MusD and intracisternal A-type particles (IAP). ERVs are transcriptionally silenced during early embryogenesis by histone and DNA methylation (and reviewed in ref. 7), although the initiators of this process, which is essential to protect genome integrity, remain largely unknown. KAP1 (KRAB-associated protein 1, also known as tripartite motif-containing protein 28, TRIM28) represses genes by recruiting the histone methyltransferase SETDB1, heterochromatin protein 1 (HP1) and the NuRD histone deacetylase complex, but few of its physiological targets are known. Two lines of evidence suggest that KAP1-mediated repression could contribute to the control of ERVs: first, KAP1 can trigger permanent gene silencing during early embryogenesis, and second, a KAP1 complex silences the retrovirus murine leukaemia virus in embryonic cells. Consistent with this hypothesis, here we show that KAP1 deletion leads to a marked upregulation of a range of ERVs, in particular IAP elements, in mouse embryonic stem (ES) cells and in early embryos. We further demonstrate that KAP1 acts synergistically with DNA methylation to silence IAP elements, and that it is enriched at the 5' untranslated region (5'UTR) of IAP genomes, where KAP1 deletion leads to the loss of histone 3 lysine 9 trimethylation (H3K9me3), a hallmark of KAP1-mediated repression. Correspondingly, IAP 5'UTR sequences can impose in cis KAP1-dependent repression on a heterologous promoter in ES cells. Our results establish that KAP1 controls endogenous retroelements during early embryonic development.

PMID: 20075919 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Research Support, Non-U.S. Gov't

MeSH Terms:

  • 5' Untranslated Regions/genetics
  • Acetylation
  • Animals
  • DNA Methylation
  • Embryo, Mammalian/metabolism
  • Embryo, Mammalian/virology
  • Embryonic Stem Cells/metabolism*
  • Embryonic Stem Cells/virology
  • Endogenous Retroviruses/genetics*
  • Fibroblasts
  • Gene Silencing*
  • Genes, Intracisternal A-Particle/genetics*
  • Genes, Reporter
  • Green Fluorescent Proteins/genetics
  • Green Fluorescent Proteins/metabolism
  • Histones/metabolism
  • Leukemia Virus, Murine/genetics
  • Leukemia Virus, Murine/physiology
  • Lysine/metabolism
  • Methylation
  • Mice
  • Nuclear Proteins/deficiency
  • Nuclear Proteins/genetics
  • Nuclear Proteins/metabolism*
  • Promoter Regions, Genetic/genetics
  • Repressor Proteins/deficiency
  • Repressor Proteins/genetics
  • Repressor Proteins/metabolism*

Substances:

  • 5' Untranslated Regions
  • Histones
  • Nuclear Proteins
  • Repressor Proteins
  • Trim28 protein, mouse
  • Green Fluorescent Proteins
  • Lysine
4. Nature. 2010 Jan 14;463(7278):178-83.

Genome sequence of the palaeopolyploid soybean.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA.

HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA.

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

PMID: 20075913 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH Terms:

  • Arabidopsis/genetics
  • Breeding
  • Chromosomes, Plant/genetics
  • Evolution, Molecular
  • Gene Duplication
  • Genes, Duplicate/genetics
  • Genes, Plant/genetics
  • Genome, Plant/genetics*
  • Genomics*
  • Molecular Sequence Data
  • Multigene Family/genetics
  • Phylogeny
  • Plant Root Nodulation/genetics
  • Polyploidy*
  • Quantitative Trait Loci/genetics
  • Recombination, Genetic
  • Repetitive Sequences, Nucleic Acid/genetics
  • Soybean Oil/biosynthesis
  • Soybeans/genetics*
  • Synteny/genetics
  • Transcription Factors/genetics

Substances:

  • Transcription Factors
  • Soybean Oil

Secondary Source ID:

  • GENBANK/ACUP00000000
  • GENBANK/ACUP01000000
5. Nature. 2010 Jan 14;463(7278):157.

Spanish cuts could do lasting damage to biomedical research.

Albar JP.

Comment on:

PMID: 20075897 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Comment
  • Letter

MeSH Terms:

  • Biomedical Research/economics*
  • Biomedical Research/trends
  • Budgets*
  • Federal Government
  • Genomics/economics
  • Spain
  • Technology Transfer

Wednesday, 24 February 2010

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Tuesday, 23 February 2010

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Monday, 22 February 2010

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Sunday, 21 February 2010

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Saturday, 20 February 2010

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Friday, 19 February 2010

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PubMed Results
Item 1 of 1

1. Lancet. 2010 Jan 30;375(9712):396-407. Epub 2010 Jan 12.

Switch to a raltegravir-based regimen versus continuation of a lopinavir-ritonavir-based regimen in stable HIV-infected patients with suppressed viraemia (SWITCHMRK 1 and 2): two multicentre, double-blind, randomised controlled trials.

Eron JJ, Young B, Cooper DA, Youle M, Dejesus E, Andrade-Villanueva J, Workman C, Zajdenverg R, Fätkenheuer G, Berger DS, Kumar PN, Rodgers AJ, Shaughnessy MA, Walker ML, Barnard RJ, Miller MD, Dinubile MJ, Nguyen BY, Leavitt R, Xu X, Sklar P; SWITCHMRK 1 and 2 investigators.

Collaborators: Workman C, Lalonde R, Rachlis A, Graham HR, Walmsley S, Gerstoft J, Mathiesen L, Arasteh K, Faetkenheuer G, Jaeger H, van Lunzen J, Antinori A, Lazzarin A, Mazzotta F, Rizzardini G, Antunes F, Branco T, Maltez F, Marques R, Sarmento R, Teofilo E, Ibarguren KA, Garcia JG, Hernandez-Quero J, Aldegue JL, Fisher M, Johnson MA, Nelson M, Orkin C, Bellos N, Berger D, Church LW, DeJesus E, de la Garza G, Gottlieb M, Hannon J, Liporace RL, Mills A, Myers RA, Pierone G, Poretz DM, Redfield RR, Rieg G, Ruane P, Saag MS, Scarsella A, Slim J, Squires K, Young B, Cooper D, Gold J, Workman C, Leite OM, Souza TN, Zajdenverg R, Alvarez CA, Arango AI, Velez JD, Patel AK, Saple DG, Andrade J, Torres I, Valdovinos S, Levia PL, Urbina FM, Fernandez JS, Andrews SM, Baraldi E, Johnson DW, Miller S, Anekthananon T, Kiertiburanakul S, Sungkanuparph S, Campbell T, Currier J, Frank I, Garcia-Diaz J, Gathe J, Kumar PN, Parenti D, Perez G, Ruane PJ, Santiago S, Schrader SR, Smith KY, Swaminathan S, Thompson MA, Wohl D, Wright DP.

University of North Carolina School of Medicine, Chapel Hill, NC, USA.

Comment in:

BACKGROUND: To reduce lipid abnormalities and other side-effects associated with antiretroviral regimens containing lopinavir-ritonavir, patients might want to switch one or more components of their regimen. We compared substitution of raltegravir for lopinavir-ritonavir with continuation of lopinavir-ritonavir in HIV-infected patients with stable viral suppression on lopinavir-ritonavir-based combination therapy. METHODS: The SWITCHMRK 1 and 2 studies were multicentre, double-blind, double-dummy, phase 3, randomised controlled trials. HIV-infected patients aged 18 years or older were eligible if they had documented viral RNA (vRNA) concentration below the limit of assay quantification for at least 3 months while on a lopinavir-ritonavir-based regimen. 707 eligible patients were randomly allocated by interactive voice response system in a 1:1 ratio to switch from lopinavir-ritonavir to raltegravir (400 mg twice daily; n=353) or to remain on lopinavir-ritonavir (two 200 mg/50 mg tablets twice daily; n=354), while continuing background therapy consisting of at least two nucleoside or nucleotide reverse transcriptase inhibitors. Primary endpoints were the mean percentage change in serum lipid concentrations from baseline to week 12; the proportion of patients with vRNA concentration less than 50 copies per mL at week 24 (with all treated patients who did not complete the study counted as failures) with a prespecified non-inferiority margin of -12% for each study; and the frequency of adverse events up to 24 weeks. Analyses were done according to protocol. These trials are registered with ClinicalTrials.gov, numbers NCT00443703 and NCT00443729. FINDINGS: 702 patients received at least one dose of study drug and were included in the efficacy and safety analyses for the combined trials (raltegravir, n=350; lopinavir-ritonavir, n=352). Percentage changes in lipid concentrations from baseline to week 12 were significantly greater (p<0.0001) in the raltegravir group than in the lopinavir-ritonavir group in each study, yielding combined results for total cholesterol -12.6%vs 1.0%, non-HDL cholesterol -15.0%vs 2.6%, and triglycerides -42.2%vs 6.2%. At week 24, 293 (84.4%, 95% CI 80.2-88.1) of 347 patients in the raltegravir group had vRNA concentration less than 50 copies per mL compared with 319 (90.6%, 87.1-93.5) of 352 patients in the lopinavir-ritonavir group (treatment difference -6.2%, -11.2 to -1.3). Clinical and laboratory adverse events occurred at similar frequencies in the treatment groups. There were no serious drug-related adverse events or deaths. The only drug-related clinical adverse event of moderate to severe intensity reported in 1% or more of either treatment group was diarrhoea, which occurred in ten patients in the lopinavir-ritonavir group (3%) and no patients in the raltegravir group. The studies were terminated at week 24 because of lower than expected virological efficacy in the raltegravir group compared with the lopinavir-ritonavir group. INTERPRETATION: Although switching to raltegravir was associated with greater reductions in serum lipid concentrations than was continuation of lopinavir-ritonavir, efficacy results did not establish non-inferiority of raltegravir to lopinavir-ritonavir. FUNDING: Merck. Copyright 2010 Elsevier Ltd. All rights reserved.

PMID: 20074791 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Comparative Study
  • Multicenter Study
  • Randomized Controlled Trial
  • Research Support, Non-U.S. Gov't

MeSH Terms:

  • Adult
  • Anti-HIV Agents/adverse effects
  • Anti-HIV Agents/therapeutic use*
  • Cholesterol, LDL/blood
  • Cholesterol, LDL/drug effects
  • Double-Blind Method
  • Drug Administration Schedule
  • Drug Therapy, Combination
  • Female
  • HIV Infections/blood
  • HIV Infections/drug therapy*
  • HIV Infections/virology
  • HIV-1/drug effects*
  • HIV-1/genetics
  • Humans
  • Male
  • Middle Aged
  • Pyrimidinones/adverse effects
  • Pyrimidinones/therapeutic use*
  • Pyrrolidinones/adverse effects
  • Pyrrolidinones/therapeutic use*
  • RNA, Viral/blood
  • RNA, Viral/drug effects
  • Ritonavir/adverse effects
  • Ritonavir/therapeutic use*
  • Treatment Outcome
  • Viremia/physiopathology
  • Viremia/virology

Substances:

  • Anti-HIV Agents
  • Cholesterol, LDL
  • MK 0518
  • Pyrimidinones
  • Pyrrolidinones
  • RNA, Viral
  • Ritonavir
  • lopinavir

Secondary Source ID:

  • ClinicalTrials.gov/NCT00443703
  • ClinicalTrials.gov/NCT00443729

Thursday, 18 February 2010

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PubMed Results
Items 1 -5 of 5

1. Nature. 2010 Jan 28;463(7280):425.

Mind the gap: social sciences can reveal community needs.

Morris C.

Comment on:

PMID: 20110970 [PubMed - indexed for MEDLINE]
Related articles
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Publication Types:

  • Comment
  • Letter

MeSH Terms:

  • Molecular Biology*/methods
  • Molecular Biology*/trends
  • Residence Characteristics
  • Social Sciences*/trends
  • Software Design
2. Science. 2010 Jan 29;327(5965):538-9.

Winner of Science Prize fo r Online Resources in Education. Making genetics easy to understand.

Stark LA, Pompei K.

Genetic Science Learning Center, University of Utah, Salt Lake City, UT 84112, USA. louisa.stark@utah.edu

PMID: 20110495 [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:

  • Awards and Prizes
  • Computer-Assisted Instruction*
  • Curriculum
  • Education
  • Genetics/education*
  • Genomics/education*
  • Internet*
  • Online Systems*
  • Teaching
  • Teaching Materials

Grant Support:

  • Howard Hughes Medical Institute/United States
3. Science. 2010 Jan 29;327(5965):504.

Science education web sites.

Alberts B.
PMID: 20110470 [PubMed - indexed for MEDLINE]
Related articles Free article
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Publication Types:

  • Editorial

MeSH Terms:

  • Awards and Prizes*
  • Computer-Assisted Instruction*
  • Genetics/education*
  • Internet*
  • Online Systems*
  • Science/education*
  • Teaching
4. Lancet. 2010 Jan 16;375(9710):224-30. Epub 2009 Dec 10.

Accurate and rapid identification of bacterial species from positive blood cultures with a DNA-based microarray platform: an observational study.Tissari P, Zumla A, Tarkka E, Mero S, Savolainen L, Vaara M, Aittakorpi A, Laakso S, Lindfors M, Piiparinen H, Mäki M, Carder C, Huggett J, Gant V.

Division of Clinical Microbiology, Helsinki University Hospital Laboratory, Helsinki, Finland.

Comment in:

BACKGROUND: New DNA-based microarray platforms enable rapid detection and species identification of many pathogens, including bacteria. We assessed the sensitivity, specificity, and turnaround time of a new molecular sepsis assay. METHODS: 2107 positive blood-culture samples of 3318 blood samples from patients with clinically suspected sepsis were investigated for bacterial species by both conventional culture and Prove-it sepsis assay (Mobidiag, Helsinki, Finland) in two centres (UK and Finland). The assay is a novel PCR and microarray method that is based on amplification and detection of gyrB, parE, and mecA genes of 50 bacterial species. Operators of the test assay were not aware of culture results. We calculated sensitivity, specificity, and turnaround time according to Clinical and Laboratory Standards Institute recommendations. FINDINGS: 1807 of 2107 (86%) positive blood-culture samples included a pathogen covered by the assay. The assay had a clinical sensitivity of 94.7% (95% CI 93.6-95.7) and a specificity of 98.8% (98.1-99.2), and 100% for both measures for meticillin-resistant Staphylococcus aureus bacteraemia. The assay was a mean 18 h faster than was the conventional culture-based method, which takes an additional 1-2 working days. 34 of 3284 (1.0%) samples were excluded because of technical and operator errors. INTERPRETATION: Definitive identification of bacterial species with this microarray platform was highly sensitive, specific, and faster than was the gold-standard culture-based method. This assay could enable fast and earlier evidence-based management for clinical sepsis. Copyright 2010 Elsevier Ltd. All rights reserved.

PMID: 20004964 [PubMed - indexed for MEDLINE]
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MeSH Terms:

  • Bacteremia/microbiology*
  • Bacteria/isolation & purification*
  • Bacterial Proteins/analysis
  • Bacteriological Techniques
  • DNA Gyrase/analysis
  • DNA Topoisomerase IV/analysis
  • DNA, Bacterial/analysis*
  • Drug Resistance, Bacterial/genetics
  • Genes, Bacterial
  • Humans
  • Nucleic Acid Amplification Techniques
  • Oligonucleotide Array Sequence Analysis*
  • Polymerase Chain Reaction*
  • Sensitivity and Specificity

Substances:

  • Bacterial Proteins
  • DNA, Bacterial
  • mecA protein, Staphylococcus aureus
  • DNA Gyrase
  • DNA Topoisomerase IV
5. Lancet. 2010 Jan 16;375(9710):178-9. Epub 2009 Dec 10.

Molecular methods for pathogen detection in blood.

Lin S, Yang S.

Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Comment on:

PMID: 20004963 [PubMed - indexed for MEDLINE]
Related articles
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Publication Types:

  • Comment

MeSH Terms:

  • Bacteremia/microbiology*
  • Bacteria/isolation & purification*
  • Bacteriological Techniques
  • DNA, Bacterial/analysis*
  • Humans
  • Nucleic Acid Amplification Techniques
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • Sensitivity and Specificity

Substances:

  • DNA, Bacterial

Wednesday, 17 February 2010

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Items 1 -4 of 4

1. Nature. 2010 Jan 7;463(7277):25.

Icelandic genetic database not at risk from bankruptcy.

Stefánsson K.

Comment on:

PMID: 20054376 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Comment
  • Letter

MeSH Terms:

  • Databases, Genetic/economics*
  • Databases, Genetic/trends*
  • Genetics, Medical
  • Genome, Human
  • Genomics/economics*
  • Genomics/trends*
  • Humans
  • Iceland
2. Nature. 2010 Jan 7;463(7277):12-3.

New year, new science.

Van Noorden R.
PMID: 20054366 [PubMed - indexed for MEDLINE]
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Publication Types:

  • News

MeSH Terms:

  • Animals
  • Astronomy
  • Climate
  • Conservation of Natural Resources
  • Embryonic Stem Cells/transplantation
  • Genomics
  • HIV Infections/prevention & control
  • Humans
  • Lasers
  • Nuclear Reprogramming
  • Physics
  • Science/trends*
  • Space Flight
  • Systems Biology
3. Nat Genet. 2010 Jan;42(1):13-4.

Exome sequencing makes medical genomics a reality.

Biesecker LG.

Comment on:

Massively parallel sequencing of the exomes of four individuals with Miller syndrome, combined with filtering to exclude benign and unrelated variants, has identified causative mutations in DHODH. This approach will accelerate discovery of the genetic bases of hundreds of other rare mendelian disorders.

PMID: 20037612 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Comment
  • News

MeSH Terms:

  • Abnormalities, Multiple/genetics
  • Abnormalities, Multiple/pathology
  • Exons/genetics*
  • Genetic Predisposition to Disease
  • Genetics, Medical/methods*
  • Genomics/methods*
  • Humans
  • Mandibulofacial Dysostosis/pathology
  • Mutation
  • Open Reading Frames/genetics
  • Oxidoreductases Acting on CH-CH Group Donors/genetics
  • Sequence Analysis, DNA/methods*
  • Syndrome

Substances:

  • Oxidoreductases Acting on CH-CH Group Donors
  • dihydroorotate dehydrogenase
4. Nat Genet. 2010 Jan;42(1):62-7. Epub 2009 Dec 6.

Geographical genomics of human leukocyte gene expression variation in southern Morocco.

Idaghdour Y, Czika W, Shianna KV, Lee SH, Visscher PM, Martin HC, Miclaus K, Jadallah SJ, Goldstein DB, Wolfinger RD, Gibson G.

Department of Genetics, North Carolina State University, Raleigh, North Carolina, USA.

Studies of the genetics of gene expression can identify expression SNPs (eSNPs) that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment of transcripts involved in ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples: cis eSNPs (P < 10(-08)) were identified for 346 genes, and trans eSNPs (P < 10(-11)) for 10 genes. All of these associations were consistent both across the three sample locations and after controlling for ancestry and relatedness. No evidence of large-effect trans-acting mediators of the pervasive environmental influence was found; instead, genetic and environmental factors acted in a largely additive manner.

PMCID: PMC2798927 [Available on 2010/7/1]

PMID: 19966804 [PubMed - indexed for MEDLINE]
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Publication Types:

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH Terms:

  • Arabs/genetics
  • Gene Expression Profiling/methods*
  • Genetic Predisposition to Disease
  • Genetic Variation*
  • Genetics, Population
  • Genome-Wide Association Study
  • Genomics/methods*
  • Geography
  • Humans
  • Leukocytes/metabolism*
  • Morocco
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis

Secondary Source ID:

  • GEO/GSE17065