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  • Articles  (1,251)
  • *Ecosystem  (661)
  • Mutation  (593)
  • 2005-2009  (1,251)
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  • 1
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    Nature Publishing Group (NPG)
    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 16;458(7240):808. doi: 10.1038/458808a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369979" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; *Ecosystem ; International Cooperation/*legislation & jurisprudence ; Travel/*legislation & jurisprudence
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2009-07-25
    Description: MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of gene expression, involved in diverse physiological and pathological processes. Although miRNAs can function as both tumour suppressors and oncogenes in tumour development, a widespread downregulation of miRNAs is commonly observed in human cancers and promotes cellular transformation and tumorigenesis. This indicates an inherent significance of small RNAs in tumour suppression. However, the connection between tumour suppressor networks and miRNA biogenesis machineries has not been investigated in depth. Here we show that a central tumour suppressor, p53, enhances the post-transcriptional maturation of several miRNAs with growth-suppressive function, including miR-16-1, miR-143 and miR-145, in response to DNA damage. In HCT116 cells and human diploid fibroblasts, p53 interacts with the Drosha processing complex through the association with DEAD-box RNA helicase p68 (also known as DDX5) and facilitates the processing of primary miRNAs to precursor miRNAs. We also found that transcriptionally inactive p53 mutants interfere with a functional assembly between Drosha complex and p68, leading to attenuation of miRNA processing activity. These findings suggest that transcription-independent modulation of miRNA biogenesis is intrinsically embedded in a tumour suppressive program governed by p53. Our study reveals a previously unrecognized function of p53 in miRNA processing, which may underlie key aspects of cancer biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suzuki, Hiroshi I -- Yamagata, Kaoru -- Sugimoto, Koichi -- Iwamoto, Takashi -- Kato, Shigeaki -- Miyazono, Kohei -- England -- Nature. 2009 Jul 23;460(7254):529-33. doi: 10.1038/nature08199.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pathology, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626115" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; DNA Damage/physiology ; Gene Expression Regulation ; HCT116 Cells ; Humans ; MicroRNAs/*metabolism ; Mutation ; *RNA Processing, Post-Transcriptional ; Ribonuclease III/metabolism ; Tumor Suppressor Protein p53/genetics/*metabolism
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2009-06-12
    Description: Cells undergoing developmental processes are characterized by persistent non-genetic alterations in chromatin, termed epigenetic changes, represented by distinct patterns of DNA methylation and histone post-translational modifications. Sirtuins, a group of conserved NAD(+)-dependent deacetylases or ADP-ribosyltransferases, promote longevity in diverse organisms; however, their molecular mechanisms in ageing regulation remain poorly understood. Yeast Sir2, the first member of the family to be found, establishes and maintains chromatin silencing by removing histone H4 lysine 16 acetylation and bringing in other silencing proteins. Here we report an age-associated decrease in Sir2 protein abundance accompanied by an increase in H4 lysine 16 acetylation and loss of histones at specific subtelomeric regions in replicatively old yeast cells, which results in compromised transcriptional silencing at these loci. Antagonizing activities of Sir2 and Sas2, a histone acetyltransferase, regulate the replicative lifespan through histone H4 lysine 16 at subtelomeric regions. This pathway, distinct from existing ageing models for yeast, may represent an evolutionarily conserved function of sirtuins in regulation of replicative ageing by maintenance of intact telomeric chromatin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702157/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702157/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dang, Weiwei -- Steffen, Kristan K -- Perry, Rocco -- Dorsey, Jean A -- Johnson, F Brad -- Shilatifard, Ali -- Kaeberlein, Matt -- Kennedy, Brian K -- Berger, Shelley L -- R01 AG025549/AG/NIA NIH HHS/ -- R01 AG025549-01A2/AG/NIA NIH HHS/ -- R01 AG025549-03/AG/NIA NIH HHS/ -- R01 CA089455/CA/NCI NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):802-7. doi: 10.1038/nature08085.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Expression and Regulation Program, The Wistar Institute Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516333" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/metabolism ; Cell Division ; Chromatin/genetics/metabolism ; Epistasis, Genetic ; Gene Expression Regulation, Fungal ; Gene Silencing ; Histone Acetyltransferases ; Histone Deacetylase Inhibitors ; Histone Deacetylases/deficiency/metabolism ; Histones/*chemistry/genetics/*metabolism ; Lysine/*metabolism ; Mutant Proteins/genetics/metabolism ; Mutation ; Saccharomyces cerevisiae/*cytology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/antagonists & ; inhibitors/deficiency/metabolism ; Sirtuin 2 ; Sirtuins/antagonists & inhibitors/deficiency/metabolism ; Telomere/genetics/metabolism ; Transcription, Genetic
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  • 4
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    Nature Publishing Group (NPG)
    Publication Date: 2009-03-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Feb 26;457(7233):1067. doi: 10.1038/4571067b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19256081" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; Carbon Dioxide/*analysis ; *Ecosystem ; Environmental Monitoring/*instrumentation ; Japan ; *Spacecraft ; United States ; United States National Aeronautics and Space Administration
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2009-08-28
    Description: Mitochondria are found in all eukaryotic cells and contain their own genome (mitochondrial DNA or mtDNA). Unlike the nuclear genome, which is derived from both the egg and sperm at fertilization, the mtDNA in the embryo is derived almost exclusively from the egg; that is, it is of maternal origin. Mutations in mtDNA contribute to a diverse range of currently incurable human diseases and disorders. To establish preclinical models for new therapeutic approaches, we demonstrate here that the mitochondrial genome can be efficiently replaced in mature non-human primate oocytes (Macaca mulatta) by spindle-chromosomal complex transfer from one egg to an enucleated, mitochondrial-replete egg. The reconstructed oocytes with the mitochondrial replacement were capable of supporting normal fertilization, embryo development and produced healthy offspring. Genetic analysis confirmed that nuclear DNA in the three infants born so far originated from the spindle donors whereas mtDNA came from the cytoplast donors. No contribution of spindle donor mtDNA was detected in offspring. Spindle replacement is shown here as an efficient protocol replacing the full complement of mitochondria in newly generated embryonic stem cell lines. This approach may offer a reproductive option to prevent mtDNA disease transmission in affected families.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774772/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774772/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tachibana, Masahito -- Sparman, Michelle -- Sritanaudomchai, Hathaitip -- Ma, Hong -- Clepper, Lisa -- Woodward, Joy -- Li, Ying -- Ramsey, Cathy -- Kolotushkina, Olena -- Mitalipov, Shoukhrat -- P01 HD047675/HD/NICHD NIH HHS/ -- P01 HD047675-01A17045/HD/NICHD NIH HHS/ -- P01 HD047675-04/HD/NICHD NIH HHS/ -- P51 RR000163/RR/NCRR NIH HHS/ -- P51 RR000163-486766/RR/NCRR NIH HHS/ -- P51 RR000163-486775/RR/NCRR NIH HHS/ -- P51 RR000163-486819/RR/NCRR NIH HHS/ -- P51 RR000163-496038/RR/NCRR NIH HHS/ -- P51 RR000163-496045/RR/NCRR NIH HHS/ -- P51 RR000163-496074/RR/NCRR NIH HHS/ -- P51 RR000163-496133/RR/NCRR NIH HHS/ -- P51 RR000163-496134/RR/NCRR NIH HHS/ -- P51 RR000163-496136/RR/NCRR NIH HHS/ -- P51 RR000163-496137/RR/NCRR NIH HHS/ -- R01 HD057121/HD/NICHD NIH HHS/ -- R01 HD057121-01A2/HD/NICHD NIH HHS/ -- R01 NS044330/NS/NINDS NIH HHS/ -- R01 NS044330-05/NS/NINDS NIH HHS/ -- R24 RR013632/RR/NCRR NIH HHS/ -- R24 RR013632-10/RR/NCRR NIH HHS/ -- England -- Nature. 2009 Sep 17;461(7262):367-72. doi: 10.1038/nature08368. Epub 2009 Aug 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Oregon National Primate Research Center, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19710649" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/analysis/*genetics ; Embryo Transfer ; Embryonic Stem Cells/*cytology/*metabolism/transplantation ; Female ; Fertilization in Vitro ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Macaca mulatta/embryology/*genetics ; Male ; Meiosis ; Mitochondrial Diseases/genetics/prevention & control ; Mutation ; Oocytes/cytology/metabolism ; Pregnancy ; *Reproductive Techniques, Assisted
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  • 6
    Publication Date: 2009-04-28
    Description: Plant photosynthesis tends to increase with irradiance. However, recent theoretical and observational studies have demonstrated that photosynthesis is also more efficient under diffuse light conditions. Changes in cloud cover or atmospheric aerosol loadings, arising from either volcanic or anthropogenic emissions, alter both the total photosynthetically active radiation reaching the surface and the fraction of this radiation that is diffuse, with uncertain overall effects on global plant productivity and the land carbon sink. Here we estimate the impact of variations in diffuse fraction on the land carbon sink using a global model modified to account for the effects of variations in both direct and diffuse radiation on canopy photosynthesis. We estimate that variations in diffuse fraction, associated largely with the 'global dimming' period, enhanced the land carbon sink by approximately one-quarter between 1960 and 1999. However, under a climate mitigation scenario for the twenty-first century in which sulphate aerosols decline before atmospheric CO(2) is stabilized, this 'diffuse-radiation' fertilization effect declines rapidly to near zero by the end of the twenty-first century.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mercado, Lina M -- Bellouin, Nicolas -- Sitch, Stephen -- Boucher, Olivier -- Huntingford, Chris -- Wild, Martin -- Cox, Peter M -- England -- Nature. 2009 Apr 23;458(7241):1014-7. doi: 10.1038/nature07949.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ecology and Hydrology, Wallingford OX10 8BB, UK. lmme@ceh.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396143" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols/analysis/chemistry ; Atmosphere/*chemistry ; Carbon/*metabolism ; Carbon Dioxide/analysis ; *Darkness ; *Ecosystem ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Photosynthesis/*radiation effects ; Plants/metabolism/*radiation effects ; Sulfates/metabolism ; *Sunlight ; Volcanic Eruptions
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2009-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Michalakis, Yannis -- Renaud, Francois -- England -- Nature. 2009 Nov 19;462(7271):298-300. doi: 10.1038/462298a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924207" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Culicidae/microbiology/parasitology/*physiology ; Fungi/physiology ; Humans ; Insect Control ; Insect Vectors/microbiology/*physiology ; Insecticides ; *Malaria/parasitology/physiopathology/prevention & control/transmission ; Mutation ; Plasmodium/genetics/*physiology
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  • 8
    Publication Date: 2009-05-05
    Description: The proteasome is a protease that controls diverse processes in eukaryotic cells. Its regulatory particle (RP) initiates the degradation of ubiquitin-protein conjugates by unfolding the substrate and translocating it into the proteasome core particle (CP) to be degraded. The RP has 19 subunits, and their pathway of assembly is not understood. Here we show that in the yeast Saccharomyces cerevisiae three proteins are found associated with RP but not with the RP-CP holoenzyme: Nas6, Rpn14 and Hsm3. Mutations in the corresponding genes confer proteasome loss-of-function phenotypes, despite their virtual absence from the holoenzyme. These effects result from deficient RP assembly. Thus, Nas6, Rpn14 and Hsm3 are RP chaperones. The RP contains six ATPases-the Rpt proteins-and each RP chaperone binds to the carboxy-terminal domain of a specific Rpt. We show in an accompanying study that RP assembly is templated through the Rpt C termini, apparently by their insertion into binding pockets in the CP. Thus, RP chaperones may regulate proteasome assembly by directly restricting the accessibility of Rpt C termini to the CP. In addition, competition between the RP chaperones and the CP for Rpt engagement may explain the release of RP chaperones as proteasomes mature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727592/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727592/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roelofs, Jeroen -- Park, Soyeon -- Haas, Wilhelm -- Tian, Geng -- McAllister, Fiona E -- Huo, Ying -- Lee, Byung-Hoon -- Zhang, Fan -- Shi, Yigong -- Gygi, Steven P -- Finley, Daniel -- 5F32GM75737-2/GM/NIGMS NIH HHS/ -- GM043601/GM/NIGMS NIH HHS/ -- GM67945/GM/NIGMS NIH HHS/ -- R37 GM043601/GM/NIGMS NIH HHS/ -- R37 GM043601-19/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):861-5. doi: 10.1038/nature08063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19412159" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/metabolism ; Carrier Proteins/genetics/metabolism ; Conserved Sequence ; Evolution, Molecular ; Holoenzymes/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Chaperones/genetics/*metabolism ; Mutation ; Phenotype ; Proteasome Endopeptidase Complex/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/genetics/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism
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  • 9
    Publication Date: 2009-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rockstrom, Johan -- Steffen, Will -- Noone, Kevin -- Persson, Asa -- Chapin, F Stuart 3rd -- Lambin, Eric F -- Lenton, Timothy M -- Scheffer, Marten -- Folke, Carl -- Schellnhuber, Hans Joachim -- Nykvist, Bjorn -- de Wit, Cynthia A -- Hughes, Terry -- van der Leeuw, Sander -- Rodhe, Henning -- Sorlin, Sverker -- Snyder, Peter K -- Costanza, Robert -- Svedin, Uno -- Falkenmark, Malin -- Karlberg, Louise -- Corell, Robert W -- Fabry, Victoria J -- Hansen, James -- Walker, Brian -- Liverman, Diana -- Richardson, Katherine -- Crutzen, Paul -- Foley, Jonathan A -- England -- Nature. 2009 Sep 24;461(7263):472-5. doi: 10.1038/461472a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stockholm Resilience Centre, Stockholm University, Kraftriket 2B, 10691 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779433" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Civilization ; Conservation of Natural Resources/*methods/trends ; *Earth (Planet) ; Ecology/*methods/*trends ; *Ecosystem ; Extinction, Biological ; Fossils ; Green Chemistry Technology/*methods/trends ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; History, Ancient ; *Human Activities/history ; Humans ; Nitrogen/metabolism ; Phosphorus/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2009-05-16
    Description: Marine viruses affect Bacteria, Archaea and eukaryotic organisms and are major components of the marine food web. Most studies have focused on their role as predators and parasites, but many of the interactions between marine viruses and their hosts are much more complicated. A series of recent studies has shown that viruses have the ability to manipulate the life histories and evolution of their hosts in remarkable ways, challenging our understanding of this almost invisible world.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rohwer, Forest -- Thurber, Rebecca Vega -- England -- Nature. 2009 May 14;459(7244):207-12. doi: 10.1038/nature08060.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, San Diego State University, San Diego, California 92182, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444207" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; *Marine Biology ; Transduction, Genetic ; *Virus Physiological Phenomena ; *Viruses/genetics
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  • 11
    Publication Date: 2009-05-16
    Description: Numerically, microbial species dominate the oceans, yet their population dynamics, metabolic complexity and synergistic interactions remain largely uncharted. A full understanding of life in the ocean requires more than knowledge of marine microbial taxa and their genome sequences. The latest experimental techniques and analytical approaches can provide a fresh perspective on the biological interactions within marine ecosystems, aiding in the construction of predictive models that can interrelate microbial dynamics with the biogeochemical matter and energy fluxes that make up the ocean ecosystem.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLong, Edward F -- England -- Nature. 2009 May 14;459(7244):200-6. doi: 10.1038/nature08059.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. delong@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444206" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; Gene Expression Profiling ; *Genomics ; *Marine Biology ; Oceans and Seas ; Phylogeny ; *Water Microbiology
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  • 12
    Publication Date: 2009-12-17
    Description: Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly. One checkpoint is the AlaRS editing centre, and the other is from widely distributed AlaXps-free-standing, genome-encoded editing proteins that clear Ser-tRNA(Ala). The paradox of misincorporating both a smaller (glycine) and a larger (serine) amino acid suggests a deep conflict for nature-designed AlaRS. Here we show the chemical basis for this conflict. Nine crystal structures, together with kinetic and mutational analysis, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the alpha-amino group of the bound amino acid by using an acidic residue. This design, dating back more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently because no better architecture for the recognition of alanine could be found, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799227/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799227/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guo, Min -- Chong, Yeeting E -- Shapiro, Ryan -- Beebe, Kirk -- Yang, Xiang-Lei -- Schimmel, Paul -- GM 15539/GM/NIGMS NIH HHS/ -- R01 GM015539/GM/NIGMS NIH HHS/ -- R01 GM015539-43/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 10;462(7274):808-12. doi: 10.1038/nature08612.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010690" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/*metabolism ; Alanine-tRNA Ligase/chemistry/genetics/*metabolism ; Aspartic Acid/genetics/metabolism ; Catalytic Domain ; Crystallization ; Escherichia coli/*enzymology ; Kinetics ; Models, Molecular ; Mutation ; *Protein Biosynthesis ; Protein Conformation ; RNA, Transfer, Ala/metabolism ; Serine/*metabolism ; Structure-Activity Relationship
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  • 13
    Publication Date: 2009-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gurney, Kevin Robert -- England -- Nature. 2009 Apr 23;458(7241):977-9. doi: 10.1038/458977a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396132" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon/analysis/*metabolism ; Carbon Dioxide/analysis/chemistry/metabolism ; China ; *Ecosystem ; *Fossil Fuels ; History, 20th Century ; History, 21st Century ; Soil/analysis ; Trees/metabolism ; United States
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  • 14
    Publication Date: 2009-06-06
    Description: Most protein mutations, and mutations that alter protein functions in particular, undermine stability and are therefore deleterious. Chaperones, or heat-shock proteins, are often implicated in buffering mutations, and could thus facilitate the acquisition of neutral genetic diversity and the rate of adaptation. We examined the ability of the Escherichia coli GroEL/GroES chaperonins to buffer destabilizing and adaptive mutations. Here we show that mutational drifts performed in vitro with four different enzymes indicated that GroEL/GroES overexpression doubled the number of accumulating mutations, and promoted the folding of enzyme variants carrying mutations in the protein core and/or mutations with higher destabilizing effects (destabilization energies of 〉3.5 kcal mol(-)(1), on average, versus approximately 1 kcal mol(-)(1) in the absence of GroEL/GroES). The divergence of modified enzymatic specificity occurred much faster under GroEL/GroES overexpression, in terms of the number of adapted variants (〉or=2-fold) and their improved specificity and activity (〉or=10-fold). These results indicate that protein stability is a major constraint in protein evolution, and buffering mechanisms such as chaperonins are key in alleviating this constraint.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tokuriki, Nobuhiko -- Tawfik, Dan S -- W81XWH-07-2-0020/PHS HHS/ -- England -- Nature. 2009 Jun 4;459(7247):668-73. doi: 10.1038/nature08009.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19494908" target="_blank"〉PubMed〈/a〉
    Keywords: Chaperonin 10/genetics/metabolism ; Chaperonin 60/genetics/metabolism ; Chaperonins/*metabolism ; Escherichia coli/*genetics/*metabolism ; Esterases/metabolism ; *Evolution, Molecular ; *Gene Expression ; *Genetic Variation ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; Humans ; Mutation ; Protein Stability ; Pseudomonas/enzymology ; Substrate Specificity
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  • 15
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    Nature Publishing Group (NPG)
    Publication Date: 2009-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toledo, Franck -- Bardot, Boris -- England -- Nature. 2009 Jul 23;460(7254):466-7. doi: 10.1038/460466a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626103" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Gene Expression Regulation, Neoplastic ; Genes, p53/genetics/*physiology ; Humans ; Mice ; MicroRNAs/*metabolism ; Mutation ; Neoplasms/*metabolism
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  • 16
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    Nature Publishing Group (NPG)
    Publication Date: 2009-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2009 Dec 17;462(7275):834-5. doi: 10.1038/462834a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016566" target="_blank"〉PubMed〈/a〉
    Keywords: *Biomass ; Congresses as Topic ; Conservation of Natural Resources/methods/trends ; Denmark ; *Ecosystem ; Forestry/methods/trends ; Global Warming/prevention & control ; *Internationality ; *Spacecraft ; Trees/*growth & development ; Tropical Climate
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  • 17
    Publication Date: 2009-05-09
    Description: Translation elongation factors facilitate protein synthesis by the ribosome. Previous studies identified two universally conserved translation elongation factors, EF-Tu in bacteria (known as eEF1A in eukaryotes) and EF-G (eEF2), which deliver aminoacyl-tRNAs to the ribosome and promote ribosomal translocation, respectively. The factor eIF5A (encoded by HYP2 and ANB1 in Saccharomyces cerevisiae), the sole protein in eukaryotes and archaea to contain the unusual amino acid hypusine (N(epsilon)-(4-amino-2-hydroxybutyl)lysine), was originally identified based on its ability to stimulate the yield (endpoint) of methionyl-puromycin synthesis-a model assay for first peptide bond synthesis thought to report on certain aspects of translation initiation. Hypusine is required for eIF5A to associate with ribosomes and to stimulate methionyl-puromycin synthesis. Because eIF5A did not stimulate earlier steps of translation initiation, and depletion of eIF5A in yeast only modestly impaired protein synthesis, it was proposed that eIF5A function was limited to stimulating synthesis of the first peptide bond or that eIF5A functioned on only a subset of cellular messenger RNAs. However, the precise cellular role of eIF5A is unknown, and the protein has also been linked to mRNA decay, including the nonsense-mediated mRNA decay pathway, and to nucleocytoplasmic transport. Here we use molecular genetic and biochemical studies to show that eIF5A promotes translation elongation. Depletion or inactivation of eIF5A in the yeast S. cerevisiae resulted in the accumulation of polysomes and an increase in ribosomal transit times. Addition of recombinant eIF5A from yeast, but not a derivative lacking hypusine, enhanced the rate of tripeptide synthesis in vitro. Moreover, inactivation of eIF5A mimicked the effects of the eEF2 inhibitor sordarin, indicating that eIF5A might function together with eEF2 to promote ribosomal translocation. Because eIF5A is a structural homologue of the bacterial protein EF-P, we propose that eIF5A/EF-P is a universally conserved translation elongation factor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140696/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140696/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saini, Preeti -- Eyler, Daniel E -- Green, Rachel -- Dever, Thomas E -- Z01 HD001010-14/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 May 7;459(7243):118-21. doi: 10.1038/nature08034.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19424157" target="_blank"〉PubMed〈/a〉
    Keywords: Indenes/pharmacology ; Lysine/*analogs & derivatives ; Mutation ; Peptide Chain Elongation, Translational/*physiology ; Peptide Elongation Factors/*metabolism ; Peptide Initiation Factors/chemistry/*metabolism ; Polyribosomes/metabolism ; Protein Synthesis Inhibitors/pharmacology ; RNA-Binding Proteins/chemistry/*metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/*genetics/growth & development/*metabolism
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  • 18
    Publication Date: 2009-07-22
    Description: Acquired uniparental disomy (aUPD) is a common feature of cancer genomes, leading to loss of heterozygosity. aUPD is associated not only with loss-of-function mutations of tumour suppressor genes, but also with gain-of-function mutations of proto-oncogenes. Here we show unique gain-of-function mutations of the C-CBL (also known as CBL) tumour suppressor that are tightly associated with aUPD of the 11q arm in myeloid neoplasms showing myeloproliferative features. The C-CBL proto-oncogene, a cellular homologue of v-Cbl, encodes an E3 ubiquitin ligase and negatively regulates signal transduction of tyrosine kinases. Homozygous C-CBL mutations were found in most 11q-aUPD-positive myeloid malignancies. Although the C-CBL mutations were oncogenic in NIH3T3 cells, c-Cbl was shown to functionally and genetically act as a tumour suppressor. C-CBL mutants did not have E3 ubiquitin ligase activity, but inhibited that of wild-type C-CBL and CBL-B (also known as CBLB), leading to prolonged activation of tyrosine kinases after cytokine stimulation. c-Cbl(-/-) haematopoietic stem/progenitor cells (HSPCs) showed enhanced sensitivity to a variety of cytokines compared to c-Cbl(+/+) HSPCs, and transduction of C-CBL mutants into c-Cbl(-/-) HSPCs further augmented their sensitivities to a broader spectrum of cytokines, including stem-cell factor (SCF, also known as KITLG), thrombopoietin (TPO, also known as THPO), IL3 and FLT3 ligand (FLT3LG), indicating the presence of a gain-of-function that could not be attributed to a simple loss-of-function. The gain-of-function effects of C-CBL mutants on cytokine sensitivity of HSPCs largely disappeared in a c-Cbl(+/+) background or by co-transduction of wild-type C-CBL, which suggests the pathogenic importance of loss of wild-type C-CBL alleles found in most cases of C-CBL-mutated myeloid neoplasms. Our findings provide a new insight into a role of gain-of-function mutations of a tumour suppressor associated with aUPD in the pathogenesis of some myeloid cancer subsets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanada, Masashi -- Suzuki, Takahiro -- Shih, Lee-Yung -- Otsu, Makoto -- Kato, Motohiro -- Yamazaki, Satoshi -- Tamura, Azusa -- Honda, Hiroaki -- Sakata-Yanagimoto, Mamiko -- Kumano, Keiki -- Oda, Hideaki -- Yamagata, Tetsuya -- Takita, Junko -- Gotoh, Noriko -- Nakazaki, Kumi -- Kawamata, Norihiko -- Onodera, Masafumi -- Nobuyoshi, Masaharu -- Hayashi, Yasuhide -- Harada, Hiroshi -- Kurokawa, Mineo -- Chiba, Shigeru -- Mori, Hiraku -- Ozawa, Keiya -- Omine, Mitsuhiro -- Hirai, Hisamaru -- Nakauchi, Hiromitsu -- Koeffler, H Phillip -- Ogawa, Seishi -- 2R01CA026038-30/CA/NCI NIH HHS/ -- England -- Nature. 2009 Aug 13;460(7257):904-8. doi: 10.1038/nature08240. Epub 2009 Jul 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genomics Project, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19620960" target="_blank"〉PubMed〈/a〉
    Keywords: Allelic Imbalance ; Amino Acid Sequence ; Animals ; Base Sequence ; Chromosomes, Human, Pair 11/genetics ; Female ; *Genes, Tumor Suppressor ; Humans ; Leukemia, Myeloid/*genetics/metabolism/pathology ; Male ; Mice ; Mice, Knockout ; Mice, Nude ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/*metabolism ; Mutation ; NIH 3T3 Cells ; Neoplasm Transplantation ; Oncogenes/genetics ; Phosphorylation ; Protein Conformation ; Proto-Oncogene Proteins c-cbl/antagonists & ; inhibitors/chemistry/deficiency/*genetics/*metabolism ; Ubiquitination ; Uniparental Disomy/genetics ; ras Proteins/genetics/metabolism
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  • 19
    Publication Date: 2009-06-10
    Description: The plant signalling molecule auxin provides positional information in a variety of developmental processes by means of its differential distribution (gradients) within plant tissues. Thus, cellular auxin levels often determine the developmental output of auxin signalling. Conceptually, transmembrane transport and metabolic processes regulate the steady-state levels of auxin in any given cell. In particular, PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial for generating auxin gradients. Here we show that Arabidopsis thaliana PIN5, an atypical member of the PIN gene family, encodes a functional auxin transporter that is required for auxin-mediated development. PIN5 does not have a direct role in cell-to-cell transport but regulates intracellular auxin homeostasis and metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins, to endoplasmic reticulum (ER), presumably mediating auxin flow from the cytosol to the lumen of the ER. The ER localization of other PIN5-like transporters (including the moss PIN) indicates that the diversification of PIN protein functions in mediating auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane, represent an ancient event during the evolution of land plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mravec, Jozef -- Skupa, Petr -- Bailly, Aurelien -- Hoyerova, Klara -- Krecek, Pavel -- Bielach, Agnieszka -- Petrasek, Jan -- Zhang, Jing -- Gaykova, Vassilena -- Stierhof, York-Dieter -- Dobrev, Petre I -- Schwarzerova, Katerina -- Rolcik, Jakub -- Seifertova, Daniela -- Luschnig, Christian -- Benkova, Eva -- Zazimalova, Eva -- Geisler, Markus -- Friml, Jiri -- P 19585/Austrian Science Fund FWF/Austria -- England -- Nature. 2009 Jun 25;459(7250):1136-40. doi: 10.1038/nature08066. Epub 2009 Jun 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19506555" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/classification/genetics/metabolism/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; Cells, Cultured ; Endoplasmic Reticulum/*metabolism ; Gene Knockout Techniques ; Homeostasis/*physiology ; Indoleacetic Acids/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Mutation ; Phenotype ; Phylogeny ; Plant Growth Regulators/metabolism
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  • 20
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    Nature Publishing Group (NPG)
    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2009 Jul 9;460(7252):161. doi: 10.1038/460161a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587733" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Carbon/metabolism ; Cell Respiration ; *Earth (Planet) ; *Ecosystem ; Fossils ; History, Ancient ; Oceans and Seas ; Oxygen/analysis/*metabolism ; Photosynthesis ; Plants/*metabolism ; Seawater/chemistry
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  • 21
    Publication Date: 2009-03-06
    Description: AMP-activated protein kinase (AMPK) is a metabolic fuel gauge conserved along the evolutionary scale in eukaryotes that senses changes in the intracellular AMP/ATP ratio. Recent evidence indicated an important role for AMPK in the therapeutic benefits of metformin, thiazolidinediones and exercise, which form the cornerstones of the clinical management of type 2 diabetes and associated metabolic disorders. In general, activation of AMPK acts to maintain cellular energy stores, switching on catabolic pathways that produce ATP, mostly by enhancing oxidative metabolism and mitochondrial biogenesis, while switching off anabolic pathways that consume ATP. This regulation can take place acutely, through the regulation of fast post-translational events, but also by transcriptionally reprogramming the cell to meet energetic needs. Here we demonstrate that AMPK controls the expression of genes involved in energy metabolism in mouse skeletal muscle by acting in coordination with another metabolic sensor, the NAD+-dependent type III deacetylase SIRT1. AMPK enhances SIRT1 activity by increasing cellular NAD+ levels, resulting in the deacetylation and modulation of the activity of downstream SIRT1 targets that include the peroxisome proliferator-activated receptor-gamma coactivator 1alpha and the forkhead box O1 (FOXO1) and O3 (FOXO3a) transcription factors. The AMPK-induced SIRT1-mediated deacetylation of these targets explains many of the convergent biological effects of AMPK and SIRT1 on energy metabolism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616311/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616311/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Canto, Carles -- Gerhart-Hines, Zachary -- Feige, Jerome N -- Lagouge, Marie -- Noriega, Lilia -- Milne, Jill C -- Elliott, Peter J -- Puigserver, Pere -- Auwerx, Johan -- 231138/European Research Council/International -- DK069966/DK/NIDDK NIH HHS/ -- DK59820/DK/NIDDK NIH HHS/ -- England -- Nature. 2009 Apr 23;458(7241):1056-60. doi: 10.1038/nature07813.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/ULP, 67404 Illkirch, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19262508" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/*metabolism ; Acetylation ; Aminoimidazole Carboxamide/analogs & derivatives ; Animals ; Cell Line ; *Energy Metabolism/genetics ; Enzyme Activation ; Forkhead Transcription Factors/genetics ; Gene Expression Regulation ; Genes, Mitochondrial/genetics ; Male ; Mice ; Muscle, Skeletal/cytology/enzymology/metabolism ; Mutation ; NAD/*metabolism ; Oxygen Consumption ; Phosphorylation ; Ribonucleotides ; Sirtuin 1 ; Sirtuins/*metabolism ; Trans-Activators/genetics/metabolism ; Transcription Factors ; Transcription, Genetic
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  • 22
    Publication Date: 2009-02-06
    Description: For a retrovirus such as HIV to be infectious, a properly formed capsid is needed; however, unusually among viruses, retrovirus capsids are highly variable in structure. According to the fullerene conjecture, they are composed of hexamers and pentamers of capsid protein (CA), with the shape of a capsid varying according to how the twelve pentamers are distributed and its size depending on the number of hexamers. Hexamers have been studied in planar and tubular arrays, but the predicted pentamers have not been observed. Here we report cryo-electron microscopic analyses of two in-vitro-assembled capsids of Rous sarcoma virus. Both are icosahedrally symmetric: one is composed of 12 pentamers, and the other of 12 pentamers and 20 hexamers. Fitting of atomic models of the two CA domains into the reconstructions shows three distinct inter-subunit interactions. These observations substantiate the fullerene conjecture, show how pentamers are accommodated at vertices, support the inference that nucleation is a crucial morphologic determinant, and imply that electrostatic interactions govern the differential assembly of pentamers and hexamers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2721793/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2721793/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cardone, Giovanni -- Purdy, John G -- Cheng, Naiqian -- Craven, Rebecca C -- Steven, Alasdair C -- CA100322/CA/NCI NIH HHS/ -- R01 CA100322/CA/NCI NIH HHS/ -- R01 CA100322-05/CA/NCI NIH HHS/ -- Z01 AR027002-29/Intramural NIH HHS/ -- Z99 AR999999/Intramural NIH HHS/ -- England -- Nature. 2009 Feb 5;457(7230):694-8. doi: 10.1038/nature07724.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Biology, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194444" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/chemistry/*metabolism/*ultrastructure ; Capsid Proteins/chemistry/genetics/metabolism/ultrastructure ; Cryoelectron Microscopy ; HIV/chemistry/genetics/ultrastructure ; Models, Molecular ; Mutant Proteins/chemistry/genetics/metabolism/ultrastructure ; Mutation ; Polymorphism, Genetic ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Subunits/chemistry/metabolism ; Rous sarcoma virus/*chemistry/genetics/*ultrastructure ; Static Electricity ; *Virus Assembly
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  • 23
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    Nature Publishing Group (NPG)
    Publication Date: 2009-07-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwok, Roberta -- England -- Nature. 2009 Jul 2;460(7251):20. doi: 10.1038/460020a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19571850" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Budgets/legislation & jurisprudence/trends ; Conservation of Natural Resources/*economics/trends ; *Ecosystem ; *Greenhouse Effect ; United States ; United States Government Agencies/*economics/legislation & jurisprudence
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  • 24
    Publication Date: 2009-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Caro, Tim -- Sherman, Paul -- England -- Nature. 2009 Dec 24;462(7276):985. doi: 10.1038/462985b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033023" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Wild ; *Conservation of Natural Resources/methods ; *Ecosystem
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  • 25
    Publication Date: 2009-10-02
    Description: Fas ligand (FasL), an apoptosis-inducing member of the TNF cytokine family, and its receptor Fas are critical for the shutdown of chronic immune responses and prevention of autoimmunity. Accordingly, mutations in their genes cause severe lymphadenopathy and autoimmune disease in mice and humans. FasL function is regulated by deposition in the plasma membrane and metalloprotease-mediated shedding. Here we generated gene-targeted mice that selectively lack either secreted FasL (sFasL) or membrane-bound FasL (mFasL) to resolve which of these forms is required for cell killing and to explore their hypothesized non-apoptotic activities. Mice lacking sFasL (FasL(Deltas/Deltas)) appeared normal and their T cells readily killed target cells, whereas T cells lacking mFasL (FasL(Deltam/Deltam)) could not kill cells through Fas activation. FasL(Deltam/Deltam) mice developed lymphadenopathy and hyper-gammaglobulinaemia, similar to FasL(gld/gld) mice, which express a mutant form of FasL that cannot bind Fas, but surprisingly, FasL(Deltam/Deltam) mice (on a C57BL/6 background) succumbed to systemic lupus erythematosus (SLE)-like autoimmune kidney destruction and histiocytic sarcoma, diseases that occur only rarely and much later in FasL(gld/gld) mice. These results demonstrate that mFasL is essential for cytotoxic activity and constitutes the guardian against lymphadenopathy, autoimmunity and cancer, whereas excess sFasL appears to promote autoimmunity and tumorigenesis through non-apoptotic activities.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785124/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785124/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O' Reilly, Lorraine A -- Tai, Lin -- Lee, Lily -- Kruse, Elizabeth A -- Grabow, Stephanie -- Fairlie, W Douglas -- Haynes, Nicole M -- Tarlinton, David M -- Zhang, Jian-Guo -- Belz, Gabrielle T -- Smyth, Mark J -- Bouillet, Philippe -- Robb, Lorraine -- Strasser, Andreas -- CA043540-18/CA/NCI NIH HHS/ -- CA80188-6/CA/NCI NIH HHS/ -- R01 CA043540/CA/NCI NIH HHS/ -- R01 CA043540-18/CA/NCI NIH HHS/ -- R01 CA080188-06/CA/NCI NIH HHS/ -- England -- Nature. 2009 Oct 1;461(7264):659-63. doi: 10.1038/nature08402.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794494" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Antinuclear/immunology ; Antigens, CD95/*metabolism ; *Apoptosis ; Cell Membrane/*metabolism ; Cytidine Deaminase/metabolism ; Cytotoxicity, Immunologic ; Fas Ligand Protein/deficiency/genetics/*metabolism/secretion ; Glomerulonephritis/metabolism ; Histiocytic Sarcoma/metabolism ; Hypergammaglobulinemia/metabolism ; Lupus Erythematosus, Systemic/metabolism ; Lymphatic Diseases/metabolism ; Mice ; Mice, Inbred C57BL ; Mutation ; Splenomegaly/metabolism ; T-Lymphocytes/immunology/metabolism
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  • 26
    Publication Date: 2009-04-03
    Description: Explaining the ecological causes of evolutionary diversification is a major focus of biology, but surprisingly little has been said about the effects of evolutionary diversification on ecosystems. The number of species in an ecosystem and their traits are key predictors of many ecosystem-level processes, such as rates of productivity, biomass sequestration and decomposition. Here we demonstrate short-term ecosystem-level effects of adaptive radiation in the threespine stickleback (Gasterosteus aculeatus) over the past 10,000 years. These fish have undergone recent parallel diversification in several lakes in coastal British Columbia, resulting in the formation of two specialized species (benthic and limnetic) from a generalist ancestor. Using a mesocosm experiment, we demonstrate that this diversification has strong effects on ecosystems, affecting prey community structure, total primary production, and the nature of dissolved organic materials that regulate the spectral properties of light transmission in the system. However, these ecosystem effects do not simply increase in their relative strength with increasing specialization and species richness; instead, they reflect the complex and indirect consequences of ecosystem engineering by sticklebacks. It is well known that ecological factors influence adaptive radiation. We demonstrate that adaptive radiation, even over short timescales, can have profound effects on ecosystems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harmon, Luke J -- Matthews, Blake -- Des Roches, Simone -- Chase, Jonathan M -- Shurin, Jonathan B -- Schluter, Dolph -- England -- Nature. 2009 Apr 30;458(7242):1167-70. doi: 10.1038/nature07974. Epub 2009 Apr 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844-3051, USA. lukeh@uidaho.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19339968" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; Biomass ; British Columbia ; *Ecosystem ; Fishes/*classification/*physiology ; Food Chain ; Fresh Water ; Genetic Speciation ; Models, Biological ; Population Density ; Predatory Behavior
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  • 27
    Publication Date: 2009-09-04
    Description: Complex dynamical systems, ranging from ecosystems to financial markets and the climate, can have tipping points at which a sudden shift to a contrasting dynamical regime may occur. Although predicting such critical points before they are reached is extremely difficult, work in different scientific fields is now suggesting the existence of generic early-warning signals that may indicate for a wide class of systems if a critical threshold is approaching.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheffer, Marten -- Bascompte, Jordi -- Brock, William A -- Brovkin, Victor -- Carpenter, Stephen R -- Dakos, Vasilis -- Held, Hermann -- van Nes, Egbert H -- Rietkerk, Max -- Sugihara, George -- England -- Nature. 2009 Sep 3;461(7260):53-9. doi: 10.1038/nature08227.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Sciences, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands. marten.scheffer@wur.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727193" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Asthma/physiopathology ; Climate ; *Ecosystem ; Eutrophication ; Extinction, Biological ; Humans ; *Models, Biological ; *Models, Economic ; Seizures/physiopathology ; Stochastic Processes
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  • 28
    Publication Date: 2009-06-26
    Description: The integrity of polarized epithelia is critical for development and human health. Many questions remain concerning the full complement and the function of the proteins that regulate cell polarity. Here we report that the Drosophila FERM proteins Yurt (Yrt) and Coracle (Cora) and the membrane proteins Neurexin IV (Nrx-IV) and Na(+),K(+)-ATPase are a new group of functionally cooperating epithelial polarity proteins. This 'Yrt/Cora group' promotes basolateral membrane stability and shows negative regulatory interactions with the apical determinant Crumbs (Crb). Genetic analyses indicate that Nrx-IV and Na(+),K(+)-ATPase act together with Cora in one pathway, whereas Yrt acts in a second redundant pathway. Moreover, we show that the Yrt/Cora group is essential for epithelial polarity during organogenesis but not when epithelial polarity is first established or during terminal differentiation. This property of Yrt/Cora group proteins explains the recovery of polarity in embryos lacking the function of the Lethal giant larvae (Lgl) group of basolateral polarity proteins. We also find that the mammalian Yrt orthologue EPB41L5 (also known as YMO1 and Limulus) is required for lateral membrane formation, indicating a conserved function of Yrt proteins in epithelial polarity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laprise, Patrick -- Lau, Kimberly M -- Harris, Kathryn P -- Silva-Gagliardi, Nancy F -- Paul, Sarah M -- Beronja, Slobodan -- Beitel, Greg J -- McGlade, C Jane -- Tepass, Ulrich -- England -- Nature. 2009 Jun 25;459(7250):1141-5. doi: 10.1038/nature08067.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19553998" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Adhesion Molecules, Neuronal/genetics/*metabolism ; Cell Line ; Cell Polarity ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/*embryology/enzymology/genetics/metabolism ; Epithelium/embryology/*physiology ; Gene Knockdown Techniques ; Membrane Proteins/genetics/*metabolism ; Mutation ; Phenotype ; Sodium-Potassium-Exchanging ATPase/genetics/*metabolism
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  • 29
    Publication Date: 2009-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agrawal, Aneil F -- England -- Nature. 2009 Nov 19;462(7271):294-5. doi: 10.1038/462294a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924202" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Outbred Strains ; *Biological Evolution ; Caenorhabditis elegans/genetics/physiology ; Inbreeding ; Mutation ; Reproduction/*physiology
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  • 30
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    Nature Publishing Group (NPG)
    Publication Date: 2009-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2009 Jan 29;457(7229):520-1. doi: 10.1038/457520b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19177092" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/*chemistry/*isolation & purification ; *Ecosystem ; Germany ; Human Activities ; Iron/*chemistry ; Oceans and Seas ; Reproducibility of Results ; Research/*trends ; Seawater/*chemistry
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  • 31
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Check Hayden, Erika -- England -- Nature. 2009 Feb 12;457(7231):776-9. doi: 10.1038/457776a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212378" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Culture ; Genes/genetics ; Genome, Human ; Humans ; Mutation ; *Selection, Genetic
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  • 32
    Publication Date: 2009-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feagin, Rusty -- England -- Nature. 2009 Sep 17;461(7262):319. doi: 10.1038/461319e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Texas A&M University, College Station, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759583" target="_blank"〉PubMed〈/a〉
    Keywords: Biomass ; Carbon/*metabolism ; *Cyclonic Storms ; Disasters ; *Ecosystem ; Oceans and Seas ; Population Dynamics ; Trees/growth & development/*metabolism ; United States ; Wind
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  • 33
    Publication Date: 2009-05-29
    Description: The AMP-activated protein kinase (AMPK) is characterized by its ability to bind to AMP, which enables it to adjust enzymatic activity by sensing the cellular energy status and maintain the balance between ATP production and consumption in eukaryotic cells. It also has important roles in the regulation of cell growth and proliferation, and in the establishment and maintenance of cell polarity. These important functions have rendered AMPK an important drug target for obesity, type 2 diabetes and cancer treatments. However, the regulatory mechanism of AMPK activity by AMP binding remains unsolved. Here we report the crystal structures of an unphosphorylated fragment of the AMPK alpha-subunit (KD-AID) from Schizosaccharomyces pombe that contains both the catalytic kinase domain and an autoinhibitory domain (AID), and of a phosphorylated kinase domain from Saccharomyces cerevisiae (Snf1-pKD). The AID binds, from the 'backside', to the hinge region of its kinase domain, forming contacts with both amino-terminal and carboxy-terminal lobes. Structural analyses indicate that AID binding might constrain the mobility of helix alphaC, hence resulting in an autoinhibited KD-AID with much lower kinase activity than that of the kinase domain alone. AMP activates AMPK both allosterically and by inhibiting dephosphorylation. Further in vitro kinetic studies demonstrate that disruption of the KD-AID interface reverses the autoinhibition and these AMPK heterotrimeric mutants no longer respond to the change in AMP concentration. The structural and biochemical data have shown the primary mechanism of AMPK autoinhibition and suggest a conformational switch model for AMPK activation by AMP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lei -- Jiao, Zhi-Hao -- Zheng, Li-Sha -- Zhang, Yuan-Yuan -- Xie, Shu-Tao -- Wang, Zhi-Xin -- Wu, Jia-Wei -- England -- Nature. 2009 Jun 25;459(7250):1146-9. doi: 10.1038/nature08075. Epub 2009 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19474788" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/*chemistry/*metabolism ; Adenosine Monophosphate/metabolism ; Amino Acid Sequence ; Animals ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Phosphorylation ; Protein Structure, Tertiary ; Rats ; Saccharomyces cerevisiae/*enzymology ; Schizosaccharomyces/*enzymology ; Sequence Alignment
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  • 34
    Publication Date: 2009-05-16
    Description: Marine diatoms rose to prominence about 100 million years ago and today generate most of the organic matter that serves as food for life in the sea. They exist in a dilute world where compounds essential for growth are recycled and shared, and they greatly influence global climate, atmospheric carbon dioxide concentration and marine ecosystem function. How these essential organisms will respond to the rapidly changing conditions in today's oceans is critical for the health of the environment and is being uncovered by studies of their genomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armbrust, E Virginia -- England -- Nature. 2009 May 14;459(7244):185-92. doi: 10.1038/nature08057.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, Washington 98195, USA. armbrust@ocean.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444204" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Carbon Dioxide/metabolism ; Diatoms/chemistry/classification/genetics/*metabolism ; *Ecosystem ; Food Chain ; Glass ; Humans ; Iron/metabolism ; *Marine Biology
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  • 35
    Publication Date: 2009-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Henebry, Geoffrey M -- England -- Nature. 2009 Feb 26;457(7233):1089-90. doi: 10.1038/4571089a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242461" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; Carbon/*analysis ; Crops, Agricultural/metabolism ; *Ecosystem ; History, 20th Century ; Poaceae/metabolism ; Republic of Belarus ; Russia ; Soil/*analysis ; Ukraine
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  • 36
    Publication Date: 2009-06-26
    Description: Myogenic potential, survival and expansion of mammalian muscle progenitors depend on the myogenic determinants Pax3 and Pax7 embryonically, and Pax7 alone perinatally. Several in vitro studies support the critical role of Pax7 in these functions of adult muscle stem cells (satellite cells), but a formal demonstration has been lacking in vivo. Here we show, through the application of inducible Cre/loxP lineage tracing and conditional gene inactivation to the tibialis anterior muscle regeneration paradigm, that, unexpectedly, when Pax7 is inactivated in adult mice, mutant satellite cells are not compromised in muscle regeneration, they can proliferate and reoccupy the sublaminal satellite niche, and they are able to support further regenerative processes. Dual adult inactivation of Pax3 and Pax7 also results in normal muscle regeneration. Multiple time points of gene inactivation reveal that Pax7 is only required up to the juvenile period when progenitor cells make the transition into quiescence. Furthermore, we demonstrate a cell-intrinsic difference between neonatal progenitor and adult satellite cells in their Pax7-dependency. Our finding of an age-dependent change in the genetic requirement for muscle stem cells cautions against inferring adult stem-cell biology from embryonic studies, and has direct implications for the use of stem cells from hosts of different ages in transplantation-based therapy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767162/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767162/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lepper, Christoph -- Conway, Simon J -- Fan, Chen-Ming -- R01 HL060714/HL/NHLBI NIH HHS/ -- R01 HL060714-02/HL/NHLBI NIH HHS/ -- R01 HL060714-11/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Jul 30;460(7255):627-31. doi: 10.1038/nature08209.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, Maryland 21218, USA. lepper@ciwemb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19554048" target="_blank"〉PubMed〈/a〉
    Keywords: Aging ; Animals ; Cell Proliferation ; Cells, Cultured ; Gene Expression Regulation, Developmental ; Mice ; Muscle, Skeletal/cytology/growth & development ; Mutation ; PAX7 Transcription Factor/metabolism ; Paired Box Transcription Factors/metabolism ; Regeneration/genetics/*physiology ; Satellite Cells, Skeletal Muscle/*cytology/drug effects/*physiology ; Selective Estrogen Receptor Modulators/pharmacology ; Stem Cells/*cytology/drug effects/*physiology ; Tamoxifen/pharmacology ; Time Factors
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  • 37
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    Nature Publishing Group (NPG)
    Publication Date: 2009-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leveau, Johan -- England -- Nature. 2009 Oct 8;461(7265):741-2. doi: 10.1038/461741a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812663" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/genetics/*isolation & purification/metabolism ; *Ecosystem ; *Genomics ; Plant Leaves/*microbiology ; *Proteomics
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  • 38
    Publication Date: 2009-05-30
    Description: Permafrost soils in boreal and Arctic ecosystems store almost twice as much carbon as is currently present in the atmosphere. Permafrost thaw and the microbial decomposition of previously frozen organic carbon is considered one of the most likely positive climate feedbacks from terrestrial ecosystems to the atmosphere in a warmer world. The rate of carbon release from permafrost soils is highly uncertain, but it is crucial for predicting the strength and timing of this carbon-cycle feedback effect, and thus how important permafrost thaw will be for climate change this century and beyond. Sustained transfers of carbon to the atmosphere that could cause a significant positive feedback to climate change must come from old carbon, which forms the bulk of the permafrost carbon pool that accumulated over thousands of years. Here we measure net ecosystem carbon exchange and the radiocarbon age of ecosystem respiration in a tundra landscape undergoing permafrost thaw to determine the influence of old carbon loss on ecosystem carbon balance. We find that areas that thawed over the past 15 years had 40 per cent more annual losses of old carbon than minimally thawed areas, but had overall net ecosystem carbon uptake as increased plant growth offset these losses. In contrast, areas that thawed decades earlier lost even more old carbon, a 78 per cent increase over minimally thawed areas; this old carbon loss contributed to overall net ecosystem carbon release despite increased plant growth. Our data document significant losses of soil carbon with permafrost thaw that, over decadal timescales, overwhelms increased plant carbon uptake at rates that could make permafrost a large biospheric carbon source in a warmer world.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuur, Edward A G -- Vogel, Jason G -- Crummer, Kathryn G -- Lee, Hanna -- Sickman, James O -- Osterkamp, T E -- England -- Nature. 2009 May 28;459(7246):556-9. doi: 10.1038/nature08031.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Florida, Gainesville, Florida 32611, USA. tschuur@ufl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478781" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Atmosphere/chemistry ; Carbon/*analysis/metabolism ; Carbon Dioxide/analysis/metabolism ; Carbon Radioisotopes ; *Cold Climate ; *Ecosystem ; Feedback ; *Freezing ; *Greenhouse Effect ; Phase Transition ; Soil/*analysis
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  • 39
    Publication Date: 2009-08-14
    Description: Ecological communities characteristically contain a wide diversity of species with important functional, economic and aesthetic value. Ecologists have long questioned how this diversity is maintained. Classic theory shows that stable coexistence requires competitors to differ in their niches; this has motivated numerous investigations of ecological differences presumed to maintain diversity. That niche differences are key to coexistence, however, has recently been challenged by the neutral theory of biodiversity, which explains coexistence with the equivalence of competitors. The ensuing controversy has motivated calls for a better understanding of the collective importance of niche differences for the diversity observed in ecological communities. Here we integrate theory and experimentation to show that niche differences collectively stabilize the dynamics of experimental communities of serpentine annual plants. We used field-parameterized population models to develop a null expectation for community dynamics without the stabilizing effects of niche differences. The population growth rates predicted by this null model varied by several orders of magnitude between species, which is sufficient for rapid competitive exclusion. Moreover, after two generations of community change in the field, Shannon diversity was over 50 per cent greater in communities stabilized by niche differences relative to those exhibiting dynamics predicted by the null model. Finally, in an experiment manipulating species' relative abundances, population growth rates increased when species became rare--the demographic signature of niche differences. Our work thus provides strong evidence that species differences have a critical role in stabilizing species diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levine, Jonathan M -- HilleRisLambers, Janneke -- England -- Nature. 2009 Sep 10;461(7261):254-7. doi: 10.1038/nature08251. Epub 2009 Aug 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA. levine@lifesci.ucsb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19675568" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; California ; *Ecosystem ; Models, Biological ; Plant Development ; *Plant Physiological Phenomena ; Plants/classification ; Population Dynamics ; Seeds/physiology
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  • 40
    Publication Date: 2009-12-04
    Description: A long-standing challenge is to understand at the atomic level how protein dynamics contribute to enzyme catalysis. X-ray crystallography can provide snapshots of conformational substates sampled during enzymatic reactions, while NMR relaxation methods reveal the rates of interconversion between substates and the corresponding relative populations. However, these current methods cannot simultaneously reveal the detailed atomic structures of the rare states and rationalize the finding that intrinsic motions in the free enzyme occur on a timescale similar to the catalytic turnover rate. Here we introduce dual strategies of ambient-temperature X-ray crystallographic data collection and automated electron-density sampling to structurally unravel interconverting substates of the human proline isomerase, cyclophilin A (CYPA, also known as PPIA). A conservative mutation outside the active site was designed to stabilize features of the previously hidden minor conformation. This mutation not only inverts the equilibrium between the substates, but also causes large, parallel reductions in the conformational interconversion rates and the catalytic rate. These studies introduce crystallographic approaches to define functional minor protein conformations and, in combination with NMR analysis of the enzyme dynamics in solution, show how collective motions directly contribute to the catalytic power of an enzyme.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805857/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805857/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fraser, James S -- Clarkson, Michael W -- Degnan, Sheena C -- Erion, Renske -- Kern, Dorothee -- Alber, Tom -- R01 GM048958/GM/NIGMS NIH HHS/ -- R01 GM048958-16/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 3;462(7273):669-73. doi: 10.1038/nature08615.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology/QB3, University of California, Berkeley, California 94720-3220, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956261" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Crystallography, X-Ray/*methods ; Cyclophilin A/*chemistry/genetics ; Humans ; *Models, Molecular ; Mutation ; Protein Structure, Tertiary ; Temperature
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  • 41
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    Nature Publishing Group (NPG)
    Publication Date: 2009-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seastedt, Tim -- England -- Nature. 2009 Jun 11;459(7248):783-4. doi: 10.1038/459783a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516327" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Europe ; Models, Biological ; *Plant Development ; Plants/*microbiology ; Population Growth ; United States
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  • 42
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    Nature Publishing Group (NPG)
    Publication Date: 2009-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seehausen, Ole -- England -- Nature. 2009 Apr 30;458(7242):1122-3. doi: 10.1038/4581122a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19407790" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; British Columbia ; *Ecosystem ; Fishes/*classification/*physiology ; Food Chain ; Fresh Water ; Genetic Speciation ; Models, Biological
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  • 43
    Publication Date: 2009-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cocroft, Rex -- England -- Nature. 2009 Jul 23;460(7254):439. doi: 10.1038/460439e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Missouri, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626069" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Communication ; Animals ; *Biological Evolution ; *Ecosystem ; *Learning ; Predatory Behavior
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  • 44
    Publication Date: 2009-12-25
    Description: Riverine organic matter supports of the order of one-fifth of estuarine metabolism. Coastal ecosystems are therefore sensitive to alteration of both the quantity and lability of terrigenous dissolved organic matter (DOM) delivered by rivers. The lability of DOM is thought to vary with age, with younger, relatively unaltered organic matter being more easily metabolized by aquatic heterotrophs than older, heavily modified material. This view is developed exclusively from work in watersheds where terrestrial plant and soil sources dominate streamwater DOM. Here we characterize streamwater DOM from 11 coastal watersheds on the Gulf of Alaska that vary widely in glacier coverage (0-64 per cent). In contrast to non-glacial rivers, we find that the bioavailability of DOM to marine microorganisms is significantly correlated with increasing (14)C age. Moreover, the most heavily glaciated watersheds are the source of the oldest ( approximately 4 kyr (14)C age) and most labile (66 per cent bioavailable) DOM. These glacial watersheds have extreme runoff rates, in part because they are subject to some of the highest rates of glacier volume loss on Earth. We estimate the cumulative flux of dissolved organic carbon derived from glaciers contributing runoff to the Gulf of Alaska at 0.13 +/- 0.01 Tg yr(-1) (1 Tg = 10(12) g), of which approximately 0.10 Tg is highly labile. This indicates that glacial runoff is a quantitatively important source of labile reduced carbon to marine ecosystems. Moreover, because glaciers and ice sheets represent the second largest reservoir of water in the global hydrologic system, our findings indicate that climatically driven changes in glacier volume could alter the age, quantity and reactivity of DOM entering coastal oceans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hood, Eran -- Fellman, Jason -- Spencer, Robert G M -- Hernes, Peter J -- Edwards, Rick -- D'Amore, David -- Scott, Durelle -- England -- Nature. 2009 Dec 24;462(7276):1044-7. doi: 10.1038/nature08580.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Science and Geography Program, University of Alaska Southeast, Juneau, Alaska 99801, USA. eran.hood@uas.alaska.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033045" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Carbon/analysis ; *Ecosystem ; Fresh Water/*chemistry ; Humic Substances/*analysis ; *Ice Cover/chemistry ; Marine Biology ; Pacific Ocean ; Spectrometry, Fluorescence ; Water Movements
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  • 45
    Publication Date: 2009-10-20
    Description: The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barrick, Jeffrey E -- Yu, Dong Su -- Yoon, Sung Ho -- Jeong, Haeyoung -- Oh, Tae Kwang -- Schneider, Dominique -- Lenski, Richard E -- Kim, Jihyun F -- England -- Nature. 2009 Oct 29;461(7268):1243-7. doi: 10.1038/nature08480. Epub 2009 Oct 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19838166" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; DNA Mutational Analysis ; Escherichia coli/*genetics/growth & development ; *Evolution, Molecular ; Genetic Fitness ; Genome, Bacterial/*genetics ; Models, Genetic ; Mutation ; Selection, Genetic ; Time Factors
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  • 46
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cole, Jonathan J -- England -- Nature. 2009 Jul 23;460(7254):463-4. doi: 10.1038/460463a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626100" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Eutrophication ; *Fresh Water ; Light ; Sweden
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  • 47
    Publication Date: 2009-05-16
    Description: Marine microbial communities are engines of globally important processes, such as the marine carbon, nitrogen and sulphur cycles. Recent data on the structures of these communities show that they adhere to universal biological rules. Co-occurrence patterns can help define species identities, and systems-biology tools are revealing networks of interacting microorganisms. Some microbial systems are found to change predictably, helping us to anticipate how microbial communities and their activities will shift in a changing world.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fuhrman, Jed A -- England -- Nature. 2009 May 14;459(7244):193-9. doi: 10.1038/nature08058.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA. fuhrman@usc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444205" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Genomics/methods/trends ; Greenhouse Effect ; *Marine Biology ; *Water Microbiology
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  • 48
    Publication Date: 2009-11-20
    Description: The phytohormone abscisic acid (ABA) regulates the expression of many genes in plants; it has critical functions in stress resistance and in growth and development. Several proteins have been reported to function as ABA receptors, and many more are known to be involved in ABA signalling. However, the identities of ABA receptors remain controversial and the mechanism of signalling from perception to downstream gene expression is unclear. Here we show that by combining the recently identified ABA receptor PYR1 with the type 2C protein phosphatase (PP2C) ABI1, the serine/threonine protein kinase SnRK2.6/OST1 and the transcription factor ABF2/AREB1, we can reconstitute ABA-triggered phosphorylation of the transcription factor in vitro. Introduction of these four components into plant protoplasts results in ABA-responsive gene expression. Protoplast and test-tube reconstitution assays were used to test the function of various members of the receptor, protein phosphatase and kinase families. Our results suggest that the default state of the SnRK2 kinases is an autophosphorylated, active state and that the SnRK2 kinases are kept inactive by the PP2Cs through physical interaction and dephosphorylation. We found that in the presence of ABA, the PYR/PYL (pyrabactin resistance 1/PYR1-like) receptor proteins can disrupt the interaction between the SnRK2s and PP2Cs, thus preventing the PP2C-mediated dephosphorylation of the SnRK2s and resulting in the activation of the SnRK2 kinases. Our results reveal new insights into ABA signalling mechanisms and define a minimal set of core components of a complete major ABA signalling pathway.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803041/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803041/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fujii, Hiroaki -- Chinnusamy, Viswanathan -- Rodrigues, Americo -- Rubio, Silvia -- Antoni, Regina -- Park, Sang-Youl -- Cutler, Sean R -- Sheen, Jen -- Rodriguez, Pedro L -- Zhu, Jian-Kang -- R01 GM059138/GM/NIGMS NIH HHS/ -- R01 GM059138-12/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 3;462(7273):660-4. doi: 10.1038/nature08599. Epub 2009 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany and Plant Sciences, University of California at Riverside, Riverside, California 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924127" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/*physiology ; Arabidopsis/enzymology/*physiology ; Arabidopsis Proteins/genetics/metabolism/*physiology ; *Gene Expression Regulation, Plant ; Mutation ; Phenotype ; Phosphorylation ; Protoplasts/physiology ; *Signal Transduction ; Stress, Physiological/*physiology
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  • 49
    Publication Date: 2009-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baumann, Peter -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 3;462(7273):547. doi: 10.1038/462547e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, Missouri, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956219" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture ; Crops, Agricultural/*genetics ; Genome, Plant/genetics ; Germ Cells, Plant/cytology ; Meiosis/genetics ; Mutation ; Seeds/genetics/physiology
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  • 50
    Publication Date: 2009-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Louys, Julien -- Bishop, Laura C -- Wilkinson, David M -- England -- Nature. 2009 Dec 17;462(7275):847. doi: 10.1038/462847b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016575" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Ecology/*trends ; *Ecosystem ; Fossils ; Paleontology/*trends ; Research/*trends
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  • 51
    Publication Date: 2009-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shindell, Drew -- England -- Nature. 2009 May 21;459(7245):321. doi: 10.1038/459321b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19458692" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/economics/*prevention & control ; Conservation of Natural Resources/*economics/*methods ; *Ecosystem ; Green Chemistry Technology/economics/methods
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  • 52
    Publication Date: 2009-04-17
    Description: Annual plants complete their life cycle in one year and initiate flowering only once, whereas perennials live for many years and flower repeatedly. How perennials undergo repeated cycles of vegetative growth and flowering that are synchronized to the changing seasons has not been extensively studied. Flowering is best understood in annual Arabidopsis thaliana, but many closely related species, such as Arabis alpina, are perennials. We identified the A. alpina mutant perpetual flowering 1 (pep1), and showed that PEP1 contributes to three perennial traits. It limits the duration of flowering, facilitating a return to vegetative development, prevents some branches from undergoing the floral transition allowing polycarpic growth habit, and confers a flowering response to winter temperatures that restricts flowering to spring. Here we show that PEP1 is the orthologue of the A. thaliana gene FLOWERING LOCUS C (FLC). The FLC transcription factor inhibits flowering until A. thaliana is exposed to winter temperatures, which trigger chromatin modifications that stably repress FLC transcription. In contrast, PEP1 is only transiently repressed by low temperatures, causing repeated seasonal cycles of repression and activation of PEP1 transcription that allow it to carry out functions characteristic of the cyclical life history of perennials. The patterns of chromatin modifications at FLC and PEP1 differ correlating with their distinct expression patterns. Thus we describe a critical mechanism by which flowering regulation differs between related perennial and annual species, and propose that differences in chromatin regulation contribute to this variation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Renhou -- Farrona, Sara -- Vincent, Coral -- Joecker, Anika -- Schoof, Heiko -- Turck, Franziska -- Alonso-Blanco, Carlos -- Coupland, George -- Albani, Maria C -- England -- Nature. 2009 May 21;459(7245):423-7. doi: 10.1038/nature07988. Epub 2009 Apr 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829 Cologne, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369938" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Arabis/anatomy & histology/genetics/*growth & development ; Chromatin/genetics ; Flowers/genetics/*growth & development ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Histones/metabolism ; MADS Domain Proteins/genetics ; Methylation ; Molecular Sequence Data ; Mutation ; *Periodicity ; Plant Proteins/genetics/*metabolism
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  • 53
    Publication Date: 2009-11-27
    Description: Light is necessary for photosynthesis, but its absorption by pigment molecules such as chlorophyll can cause severe oxidative damage and result in cell death. The excess absorption of light energy by photosynthetic pigments has led to the evolution of protective mechanisms that operate on the timescale of seconds to minutes and involve feedback-regulated de-excitation of chlorophyll molecules in photosystem II (qE). Despite the significant contribution of eukaryotic algae to global primary production, little is known about their qE mechanism, in contrast to that in flowering plants. Here we show that a qE-deficient mutant of the unicellular green alga Chlamydomonas reinhardtii, npq4, lacks two of the three genes encoding LHCSR (formerly called LI818). This protein is an ancient member of the light-harvesting complex superfamily, and orthologues are found throughout photosynthetic eukaryote taxa, except in red algae and vascular plants. The qE capacity of Chlamydomonas is dependent on environmental conditions and is inducible by growth under high light conditions. We show that the fitness of the npq4 mutant in a shifting light environment is reduced compared to wild-type cells, demonstrating that LHCSR is required for survival in a dynamic light environment. Thus, these data indicate that plants and algae use different proteins to dissipate harmful excess light energy and protect the photosynthetic apparatus from damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peers, Graham -- Truong, Thuy B -- Ostendorf, Elisabeth -- Busch, Andreas -- Elrad, Dafna -- Grossman, Arthur R -- Hippler, Michael -- Niyogi, Krishna K -- England -- Nature. 2009 Nov 26;462(7272):518-21. doi: 10.1038/nature08587.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940928" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/radiation effects ; Algal Proteins/genetics/*metabolism ; Cell Survival/radiation effects ; Chlamydomonas reinhardtii/cytology/genetics/*metabolism/radiation effects ; Chlorophyll/metabolism ; Fluorescence ; Genetic Complementation Test ; Light-Harvesting Protein Complexes/genetics/*metabolism ; Mutation ; *Photosynthesis/radiation effects ; RNA, Messenger/genetics/metabolism ; Time Factors
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  • 54
    Publication Date: 2009-11-27
    Description: FocA is a representative member of the formate-nitrite transporter family, which transports short-chain acids in bacteria, archaea, fungi, algae and parasites. The structure and transport mechanism of the formate-nitrite transporter family remain unknown. Here we report the crystal structure of Escherichia coli FocA at 2.25 A resolution. FocA forms a symmetric pentamer, with each protomer consisting of six transmembrane segments. Despite a lack of sequence homology, the overall structure of the FocA protomer closely resembles that of aquaporin and strongly argues that FocA is a channel, rather than a transporter. Structural analysis identifies potentially important channel residues, defines the channel path and reveals two constriction sites. Unlike aquaporin, FocA is impermeable to water but allows the passage of formate. A structural and biochemical investigation provides mechanistic insights into the channel activity of FocA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Yi -- Huang, Yongjian -- Wang, Jiawei -- Cheng, Chao -- Huang, Weijiao -- Lu, Peilong -- Xu, Ya-Nan -- Wang, Pengye -- Yan, Nieng -- Shi, Yigong -- England -- Nature. 2009 Nov 26;462(7272):467-72. doi: 10.1038/nature08610.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940917" target="_blank"〉PubMed〈/a〉
    Keywords: Aquaporins/*chemistry/metabolism ; Crystallography, X-Ray ; Escherichia coli/chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Formates/metabolism ; Liposomes/chemistry/metabolism ; Membrane Transport Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Mimicry ; Mutation ; Permeability ; Protein Structure, Quaternary ; Structure-Activity Relationship ; Water/analysis/metabolism
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  • 55
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lubick, Naomi -- England -- Nature. 2009 Feb 5;457(7230):640-1. doi: 10.1038/457640a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194411" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Animals ; *Drug Industry ; *Ecosystem ; Humans ; India ; Industrial Waste/*adverse effects/*analysis ; Larva/drug effects ; Rivers/chemistry ; Sweden ; *Waste Disposal, Fluid ; Water Pollutants/*adverse effects/*analysis ; Water Supply/analysis ; Zebrafish/embryology
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  • 56
    Publication Date: 2009-03-03
    Description: Clostridium difficile is the leading cause of infectious diarrhoea in hospitals worldwide, because of its virulence, spore-forming ability and persistence. C. difficile-associated diseases are induced by antibiotic treatment or disruption of the normal gastrointestinal flora. Recently, morbidity and mortality resulting from C. difficile-associated diseases have increased significantly due to changes in the virulence of the causative strains and antibiotic usage patterns. Since 2002, epidemic toxinotype III NAP1/027 strains, which produce high levels of the major virulence factors, toxin A and toxin B, have emerged. These toxins have 63% amino acid sequence similarity and are members of the large clostridial glucosylating toxin family, which are monoglucosyltransferases that are pro-inflammatory, cytotoxic and enterotoxic in the human colon. Inside host cells, both toxins catalyse the transfer of glucose onto the Rho family of GTPases, leading to cell death. However, the role of these toxins in the context of a C. difficile infection is unknown. Here we describe the construction of isogenic tcdA and tcdB (encoding toxin A and B, respectively) mutants of a virulent C. difficile strain and their use in the hamster disease model to show that toxin B is a key virulence determinant. Previous studies showed that purified toxin A alone can induce most of the pathology observed after infection of hamsters with C. difficile and that toxin B is not toxic in animals unless it is co-administered with toxin A, suggesting that the toxins act synergistically. Our work provides evidence that toxin B, not toxin A, is essential for virulence. Furthermore, it is clear that the importance of these toxins in the context of infection cannot be predicted exclusively from studies using purified toxins, reinforcing the importance of using the natural infection process to dissect the role of toxins in disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679968/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679968/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyras, Dena -- O'Connor, Jennifer R -- Howarth, Pauline M -- Sambol, Susan P -- Carter, Glen P -- Phumoonna, Tongted -- Poon, Rachael -- Adams, Vicki -- Vedantam, Gayatri -- Johnson, Stuart -- Gerding, Dale N -- Rood, Julian I -- AI057637/AI/NIAID NIH HHS/ -- R01 AI057637/AI/NIAID NIH HHS/ -- R01 AI057637-01A1/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Apr 30;458(7242):1176-9. doi: 10.1038/nature07822. Epub 2009 Mar 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Victoria 3800, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19252482" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Adhesion ; Bacterial Proteins/biosynthesis/genetics/*metabolism/pharmacology ; Bacterial Toxins/biosynthesis/genetics/*metabolism/pharmacology ; Cell Line ; Clostridium difficile/genetics/*pathogenicity ; Cricetinae ; Disease Models, Animal ; Enterotoxins/genetics/metabolism ; Humans ; Mutation ; Virulence
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  • 57
    Publication Date: 2009-02-17
    Description: How and why organisms are distributed as they are has long intrigued evolutionary biologists. The tendency for species to retain their ancestral ecology has been demonstrated in distributions on local and regional scales, but the extent of ecological conservatism over tens of millions of years and across continents has not been assessed. Here we show that biome stasis at speciation has outweighed biome shifts by a ratio of more than 25:1, by inferring ancestral biomes for an ecologically diverse sample of more than 11,000 plant species from around the Southern Hemisphere. Stasis was also prevalent in transocean colonizations. Availability of a suitable biome could have substantially influenced which lineages establish on more than one landmass, in addition to the influence of the rarity of the dispersal events themselves. Conversely, the taxonomic composition of biomes has probably been strongly influenced by the rarity of species' transitions between biomes. This study has implications for the future because if clades have inherently limited capacity to shift biomes, then their evolutionary potential could be strongly compromised by biome contraction as climate changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crisp, Michael D -- Arroyo, Mary T K -- Cook, Lyn G -- Gandolfo, Maria A -- Jordan, Gregory J -- McGlone, Matt S -- Weston, Peter H -- Westoby, Mark -- Wilf, Peter -- Linder, H Peter -- England -- Nature. 2009 Apr 9;458(7239):754-6. doi: 10.1038/nature07764. Epub 2009 Feb 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Botany and Zoology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia. mike.crisp@anu.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19219025" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; Conservation of Natural Resources ; Demography ; *Ecosystem ; Geography ; Phylogeny ; *Plant Physiological Phenomena ; Time Factors
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  • 58
    Publication Date: 2009-12-17
    Description: Biota can be described in terms of elemental composition, expressed as an atomic ratio of carbon:nitrogen:phosphorus (refs 1-3). The elemental stoichiometry of microoorganisms is fundamental for understanding the production dynamics and biogeochemical cycles of ecosystems because microbial biomass is the trophic base of detrital food webs. Here we show that heterotrophic microbial communities of diverse composition from terrestrial soils and freshwater sediments share a common functional stoichiometry in relation to organic nutrient acquisition. The activities of four enzymes that catalyse the hydrolysis of assimilable products from the principal environmental sources of C, N and P show similar scaling relationships over several orders of magnitude, with a mean ratio for C:N:P activities near 1:1:1 in all habitats. We suggest that these ecoenzymatic ratios reflect the equilibria between the elemental composition of microbial biomass and detrital organic matter and the efficiencies of microbial nutrient assimilation and growth. Because ecoenzymatic activities intersect the stoichiometric and metabolic theories of ecology, they provide a functional measure of the threshold at which control of community metabolism shifts from nutrient to energy flow.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sinsabaugh, Robert L -- Hill, Brian H -- Follstad Shah, Jennifer J -- England -- Nature. 2009 Dec 10;462(7274):795-8. doi: 10.1038/nature08632.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, University of New Mexico, Albuquerque, New Mexico 871312, USA. rlsinsab@unm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010687" target="_blank"〉PubMed〈/a〉
    Keywords: Biomass ; Carbon/*metabolism ; *Ecosystem ; Enzyme Assays ; Enzymes/*metabolism ; Food Chain ; Geologic Sediments/*chemistry/microbiology ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; Plants/metabolism ; Rivers ; *Soil Microbiology ; United States ; Wetlands
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  • 59
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    Nature Publishing Group (NPG)
    Publication Date: 2009-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Sep 24;461(7263):447-8. doi: 10.1038/461447b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779405" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/analysis ; *Earth (Planet) ; Ecology/*methods ; *Ecosystem ; Greenhouse Effect ; *Human Activities ; Humans ; Hydrogen-Ion Concentration ; Nitrogen/metabolism ; Seawater/chemistry
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  • 60
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    Nature Publishing Group (NPG)
    Publication Date: 2009-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jayaraman, Killugudi -- England -- Nature. 2009 Sep 24;461(7263):459. doi: 10.1038/461459a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779423" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; Elephants ; Facility Design and Construction/economics/trends ; India ; *Laboratories/economics/trends ; *Physics/economics ; Tigers ; Trees
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  • 61
    Publication Date: 2009-04-28
    Description: Global terrestrial ecosystems absorbed carbon at a rate of 1-4 Pg yr(-1) during the 1980s and 1990s, offsetting 10-60 per cent of the fossil-fuel emissions. The regional patterns and causes of terrestrial carbon sources and sinks, however, remain uncertain. With increasing scientific and political interest in regional aspects of the global carbon cycle, there is a strong impetus to better understand the carbon balance of China. This is not only because China is the world's most populous country and the largest emitter of fossil-fuel CO(2) into the atmosphere, but also because it has experienced regionally distinct land-use histories and climate trends, which together control the carbon budget of its ecosystems. Here we analyse the current terrestrial carbon balance of China and its driving mechanisms during the 1980s and 1990s using three different methods: biomass and soil carbon inventories extrapolated by satellite greenness measurements, ecosystem models and atmospheric inversions. The three methods produce similar estimates of a net carbon sink in the range of 0.19-0.26 Pg carbon (PgC) per year, which is smaller than that in the conterminous United States but comparable to that in geographic Europe. We find that northeast China is a net source of CO(2) to the atmosphere owing to overharvesting and degradation of forests. By contrast, southern China accounts for more than 65 per cent of the carbon sink, which can be attributed to regional climate change, large-scale plantation programmes active since the 1980s and shrub recovery. Shrub recovery is identified as the most uncertain factor contributing to the carbon sink. Our data and model results together indicate that China's terrestrial ecosystems absorbed 28-37 per cent of its cumulated fossil carbon emissions during the 1980s and 1990s.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Piao, Shilong -- Fang, Jingyun -- Ciais, Philippe -- Peylin, Philippe -- Huang, Yao -- Sitch, Stephen -- Wang, Tao -- England -- Nature. 2009 Apr 23;458(7241):1009-13. doi: 10.1038/nature07944.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, College of Urban and Environmental Science, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China. slpiao@pku.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396142" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Biomass ; Carbon/analysis/*metabolism ; Carbon Dioxide/analysis/chemistry/metabolism ; China ; *Ecosystem ; Forestry/history ; Fossil Fuels/*history ; History, 20th Century ; Soil/analysis ; Trees/metabolism
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  • 62
    Publication Date: 2009-04-08
    Description: Innate social behaviours emerge from neuronal circuits that interpret sensory information on the basis of an individual's own genotype, sex and experience. The regulated aggregation behaviour of the nematode Caenorhabditis elegans, a simple animal with only 302 neurons, is an attractive system to analyse these circuits. Wild social strains of C. elegans aggregate in the presence of specific sensory cues, but solitary strains do not. Here we identify the RMG inter/motor neuron as the hub of a regulated circuit that controls aggregation and related behaviours. RMG is the central site of action of the neuropeptide receptor gene npr-1, which distinguishes solitary strains (high npr-1 activity) from wild social strains (low npr-1 activity); high RMG activity is essential for all aspects of social behaviour. Anatomical gap junctions connect RMG to several classes of sensory neurons known to promote aggregation, and to ASK sensory neurons, which are implicated in male attraction to hermaphrodite pheromones. We find that ASK neurons respond directly to pheromones, and that high RMG activity enhances ASK responses in social strains, causing hermaphrodite attraction to pheromones at concentrations that repel solitary hermaphrodites. The coordination of social behaviours by RMG suggests an anatomical hub-and-spoke model for sensory integration in aggregation, and points to functions for related circuit motifs in the C. elegans wiring diagram.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760495/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macosko, Evan Z -- Pokala, Navin -- Feinberg, Evan H -- Chalasani, Sreekanth H -- Butcher, Rebecca A -- Clardy, Jon -- Bargmann, Cornelia I -- CA24487/CA/NCI NIH HHS/ -- F32 GM077943/GM/NIGMS NIH HHS/ -- F32 GM077943-03/GM/NIGMS NIH HHS/ -- GM07739/GM/NIGMS NIH HHS/ -- GM077943/GM/NIGMS NIH HHS/ -- R01 CA024487/CA/NCI NIH HHS/ -- R01 CA024487-30/CA/NCI NIH HHS/ -- T32 GM007739/GM/NIGMS NIH HHS/ -- T32 GM007739-30/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Apr 30;458(7242):1171-5. doi: 10.1038/nature07886. Epub 2009 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Laboratory of Neural Circuits and Behavior, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19349961" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/cytology/drug effects/*physiology ; Caenorhabditis elegans Proteins/genetics/metabolism ; Disorders of Sex Development ; Feeding Behavior/drug effects/physiology ; Male ; Models, Neurological ; Mutation ; Neural Pathways/drug effects/*physiology ; Neurons/drug effects/physiology ; Pheromones/pharmacology/*physiology ; Receptors, Neuropeptide Y/genetics/metabolism ; *Social Behavior
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  • 63
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    Nature Publishing Group (NPG)
    Publication Date: 2009-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jayaraman, K S -- England -- Nature. 2009 Nov 26;462(7272):397. doi: 10.1038/462397b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940886" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; Elephants ; India ; *Laboratories/economics ; *Physics/economics ; Tigers
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  • 64
    Publication Date: 2009-05-16
    Description: Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean's response to climate change, improving the predictive power of climate models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowler, Chris -- Karl, David M -- Colwell, Rita R -- 1R01A139129-01/PHS HHS/ -- England -- Nature. 2009 May 14;459(7244):180-4. doi: 10.1038/nature08056.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR8186, Department of Biology, Ecole Normale Superieure, 46 rue d'Ulm, Paris, France. cbowler@biologie.ens.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444203" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Gene Expression Profiling/trends ; Genomics/trends ; Greenhouse Effect ; Human Activities ; Humans ; *Marine Biology/trends ; *Oceanography ; Oceans and Seas ; Plankton/genetics/isolation & purification/metabolism ; Seawater/*microbiology/virology ; Vibrio cholerae/isolation & purification/metabolism ; *Water Microbiology ; Water Pollution/adverse effects
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  • 65
    Publication Date: 2009-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pysek, Petr -- Hulme, Philip E -- England -- Nature. 2009 Jul 16;460(7253):324. doi: 10.1038/460324b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19606125" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Conservation of Natural Resources ; Ecology/*trends ; *Ecosystem ; Population Dynamics
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  • 66
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    Nature Publishing Group (NPG)
    Publication Date: 2009-11-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marris, Emma -- England -- Nature. 2009 Nov 5;462(7269):30-2. doi: 10.1038/462030a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890304" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Conservation of Natural Resources/*methods ; *Ecosystem ; Internationality ; Netherlands ; *Wilderness
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  • 67
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    Nature Publishing Group (NPG)
    Publication Date: 2009-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marris, Emma -- England -- Nature. 2009 Jul 23;460(7254):450-3. doi: 10.1038/460450a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626087" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Ecology/methods ; *Ecosystem ; Hawaii ; Humans ; Trees
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  • 68
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    Nature Publishing Group (NPG)
    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marris, Emma -- England -- Nature. 2009 Jun 18;459(7249):906-8. doi: 10.1038/459906a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536238" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological/*physiology ; British Columbia ; Conservation of Natural Resources/*methods ; *Ecosystem ; Forestry/*methods ; *Greenhouse Effect ; Time Factors ; Trees/*physiology
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  • 69
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    Nature Publishing Group (NPG)
    Publication Date: 2009-09-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- England -- Nature. 2009 Sep 3;461(7260):34-6. doi: 10.1038/461034a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727180" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Animals ; Arctic Regions ; Atmosphere/chemistry ; Carbon/*analysis/metabolism ; Carbon Dioxide/analysis/metabolism ; *Ecosystem ; *Fires ; Freezing ; Fresh Water/chemistry ; Geologic Sediments/chemistry ; Greenhouse Effect ; Photosynthesis ; Soil/analysis
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  • 70
    Publication Date: 2009-11-06
    Description: Redox processes are at the heart of numerous functions in chemistry and biology, from long-range electron transfer in photosynthesis and respiration to catalysis in industrial and fuel cell research. These functions are accomplished in nature by only a limited number of redox-active agents. A long-standing issue in these fields is how redox potentials are fine-tuned over a broad range with little change to the redox-active site or electron-transfer properties. Resolving this issue will not only advance our fundamental understanding of the roles of long-range, non-covalent interactions in redox processes, but also allow for design of redox-active proteins having tailor-made redox potentials for applications such as artificial photosynthetic centres or fuel cell catalysts for energy conversion. Here we show that two important secondary coordination sphere interactions, hydrophobicity and hydrogen-bonding, are capable of tuning the reduction potential of the cupredoxin azurin over a 700 mV range, surpassing the highest and lowest reduction potentials reported for any mononuclear cupredoxin, without perturbing the metal binding site beyond what is typical for the cupredoxin family of proteins. We also demonstrate that the effects of individual structural features are additive and that redox potential tuning of azurin is now predictable across the full range of cupredoxin potentials.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149807/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149807/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marshall, Nicholas M -- Garner, Dewain K -- Wilson, Tiffany D -- Gao, Yi-Gui -- Robinson, Howard -- Nilges, Mark J -- Lu, Yi -- 5 T32 GM070421/GM/NIGMS NIH HHS/ -- T32 GM070421/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Nov 5;462(7269):113-6. doi: 10.1038/nature08551.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890331" target="_blank"〉PubMed〈/a〉
    Keywords: Azurin/*chemistry/genetics/*metabolism ; Binding Sites ; Copper/metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation ; Oxidation-Reduction ; Protein Conformation
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  • 71
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    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- England -- Nature. 2009 Jan 15;457(7227):246-7. doi: 10.1038/457246a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148066" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture ; China ; *Conservation of Natural Resources ; *Ecosystem ; Hevea/*growth & development/metabolism ; Poverty/prevention & control ; Rain ; Rubber/economics ; Trees/growth & development/metabolism
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  • 72
    Publication Date: 2009-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rainey, Paul B -- England -- Nature. 2009 Oct 29;461(7268):1219-21. doi: 10.1038/4611219a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865158" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; DNA Mutational Analysis ; Escherichia coli/*genetics/growth & development ; *Evolution, Molecular ; Genetic Fitness ; Genome, Bacterial/*genetics ; Mutation ; Selection, Genetic ; Time Factors
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  • 73
    Publication Date: 2009-02-06
    Description: The 5'--〉3' exoribonucleases (XRNs) comprise a large family of conserved enzymes in eukaryotes with crucial functions in RNA metabolism and RNA interference. XRN2, or Rat1 in yeast, functions primarily in the nucleus and also has an important role in transcription termination by RNA polymerase II (refs 7-14). Rat1 exoribonuclease activity is stimulated by the protein Rai1 (refs 15, 16). Here we report the crystal structure at 2.2 A resolution of Schizosaccharomyces pombe Rat1 in complex with Rai1, as well as the structures of Rai1 and its murine homologue Dom3Z alone at 2.0 A resolution. The structures reveal the molecular mechanism for the activation of Rat1 by Rai1 and for the exclusive exoribonuclease activity of Rat1. Biochemical studies confirm these observations, and show that Rai1 allows Rat1 to degrade RNAs with stable secondary structure more effectively. There are large differences in the active site landscape of Rat1 compared to related and PIN (PilT N terminus) domain-containing nucleases. Unexpectedly, we identified a large pocket in Rai1 and Dom3Z that contains highly conserved residues, including three acidic side chains that coordinate a divalent cation. Mutagenesis and biochemical studies demonstrate that Rai1 possesses pyrophosphohydrolase activity towards 5' triphosphorylated RNA. Such an activity is important for messenger RNA degradation in bacteria, but this is, to our knowledge, the first demonstration of this activity in eukaryotes and suggests that Rai1/Dom3Z may have additional important functions in RNA metabolism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739979/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739979/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiang, Song -- Cooper-Morgan, Amalene -- Jiao, Xinfu -- Kiledjian, Megerditch -- Manley, James L -- Tong, Liang -- GM077175/GM/NIGMS NIH HHS/ -- GM28983/GM/NIGMS NIH HHS/ -- GM67005/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM067005/GM/NIGMS NIH HHS/ -- R01 GM067005-01A2/GM/NIGMS NIH HHS/ -- R01 GM077175/GM/NIGMS NIH HHS/ -- R01 GM077175-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Apr 9;458(7239):784-8. doi: 10.1038/nature07731. Epub 2009 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194460" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Exoribonucleases/*chemistry/genetics/*metabolism ; Mice ; *Models, Molecular ; Mutation ; *Nuclear Proteins/chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; *Schizosaccharomyces/chemistry/enzymology/genetics ; Schizosaccharomyces pombe Proteins/*chemistry/genetics/*metabolism
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  • 74
    Publication Date: 2009-07-25
    Description: Productivity denotes the rate of biomass synthesis in ecosystems and is a fundamental characteristic that frames ecosystem function and management. Limitation of productivity by nutrient availability is an established paradigm for lake ecosystems. Here, we assess the relevance of this paradigm for a majority of the world's small, nutrient-poor lakes, with different concentrations of coloured organic matter. By comparing small unproductive lakes along a water colour gradient, we show that coloured terrestrial organic matter controls the key process for new biomass synthesis (the benthic primary production) through its effects on light attenuation. We also show that this translates into effects on production and biomass of higher trophic levels (benthic invertebrates and fish). These results are inconsistent with the idea that nutrient supply primarily controls lake productivity, and we propose that a large share of the world's unproductive lakes, within natural variations of organic carbon and nutrient input, are limited by light and not by nutrients. We anticipate that our result will have implications for understanding lake ecosystem function and responses to environmental change. Catchment export of coloured organic matter is sensitive to short-term natural variability and long-term, large-scale changes, driven by climate and different anthropogenic influences. Consequently, changes in terrestrial carbon cycling will have pronounced effects on most lake ecosystems by mediating changes in light climate and productivity of lakes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karlsson, Jan -- Bystrom, Par -- Ask, Jenny -- Ask, Per -- Persson, Lennart -- Jansson, Mats -- England -- Nature. 2009 Jul 23;460(7254):506-9. doi: 10.1038/nature08179.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Climate Impacts Research Centre, Department of Ecology and Environmental Science, Umea University, Box 62, SE-981 07 Abisko, Sweden. Jan.Karlsson@emg.umu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626113" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomass ; Carbon/analysis/metabolism ; *Ecosystem ; Eukaryota/physiology ; Fishes/physiology ; Fresh Water/*chemistry ; *Light ; Nitrogen/analysis ; Phosphorus/analysis ; Sweden
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  • 75
    Publication Date: 2009-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strong, Aaron -- Chisholm, Sallie -- Miller, Charles -- Cullen, John -- England -- Nature. 2009 Sep 17;461(7262):347-8. doi: 10.1038/461347a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology in Cambridge, Massachusetts, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759603" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbon Dioxide/metabolism ; Ecology/*methods ; *Ecosystem ; *Greenhouse Effect ; Iron/*metabolism ; Oxygen/metabolism ; Phytoplankton/metabolism ; Reproducibility of Results ; Seawater/*chemistry/parasitology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 76
    Publication Date: 2009-08-29
    Description: Coat color and type are essential characteristics of domestic dog breeds. Although the genetic basis of coat color has been well characterized, relatively little is known about the genes influencing coat growth pattern, length, and curl. We performed genome-wide association studies of more than 1000 dogs from 80 domestic breeds to identify genes associated with canine fur phenotypes. Taking advantage of both inter- and intrabreed variability, we identified distinct mutations in three genes, RSPO2, FGF5, and KRT71 (encoding R-spondin-2, fibroblast growth factor-5, and keratin-71, respectively), that together account for most coat phenotypes in purebred dogs in the United States. Thus, an array of varied and seemingly complex phenotypes can be reduced to the combinatorial effects of only a few genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897713/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897713/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cadieu, Edouard -- Neff, Mark W -- Quignon, Pascale -- Walsh, Kari -- Chase, Kevin -- Parker, Heidi G -- Vonholdt, Bridgett M -- Rhue, Alison -- Boyko, Adam -- Byers, Alexandra -- Wong, Aaron -- Mosher, Dana S -- Elkahloun, Abdel G -- Spady, Tyrone C -- Andre, Catherine -- Lark, K Gordon -- Cargill, Michelle -- Bustamante, Carlos D -- Wayne, Robert K -- Ostrander, Elaine A -- 1R01GM83606/GM/NIGMS NIH HHS/ -- GM063056/GM/NIGMS NIH HHS/ -- R01 GM063056/GM/NIGMS NIH HHS/ -- R01 GM063056-09/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2009 Oct 2;326(5949):150-3. doi: 10.1126/science.1177808. Epub 2009 Aug 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19713490" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Dogs/*genetics ; Fibroblast Growth Factor 5/*genetics ; Genome-Wide Association Study ; *Hair/anatomy & histology/growth & development ; Haplotypes ; Keratins, Hair-Specific/*genetics ; Lod Score ; Molecular Sequence Data ; Mutation ; Oligonucleotide Array Sequence Analysis ; Phenotype ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Thrombospondins/*genetics ; United States
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  • 77
    Publication Date: 2009-09-12
    Description: RNA interference (RNAi), a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast Saccharomyces cerevisiae. Here, we show that RNAi is present in other budding yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate small interfering RNAs, which mostly correspond to transposable elements and Y' subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess Y' messenger RNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a previously unknown class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786161/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786161/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Drinnenberg, Ines A -- Weinberg, David E -- Xie, Kathleen T -- Mower, Jeffrey P -- Wolfe, Kenneth H -- Fink, Gerald R -- Bartel, David P -- GM0305010/GM/NIGMS NIH HHS/ -- GM040266/GM/NIGMS NIH HHS/ -- GM067031/GM/NIGMS NIH HHS/ -- R01 GM067031/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Oct 23;326(5952):544-50. doi: 10.1126/science.1176945. Epub 2009 Sep 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19745116" target="_blank"〉PubMed〈/a〉
    Keywords: Fungal Proteins/genetics/metabolism ; Gene Expression Profiling ; Genes, Fungal ; Genetic Loci ; Mutation ; Open Reading Frames ; *RNA Interference ; RNA, Double-Stranded/genetics/metabolism ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Small Interfering/genetics/*metabolism ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Ribonuclease III/genetics/metabolism ; Saccharomyces/*genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Saccharomycetales/*genetics/metabolism ; Sequence Analysis, RNA ; Transcription, Genetic ; Transformation, Genetic
    Print ISSN: 0036-8075
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  • 78
    Publication Date: 2009-02-07
    Description: Prabhakar et al. (Reports, 5 September 2008, p. 1346) argued that the conserved noncoding sequence HACNS1 has undergone positive selection and contributed to human adaptation. However, the pattern of substitution in HACNS1 is more consistent with the neutral process of biased gene conversion (BGC). The reported human-specific gain of function is likely due to the accumulation of deleterious mutations driven by BGC, not positive selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duret, Laurent -- Galtier, Nicolas -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):714; author reply 714. doi: 10.1126/science.1165848.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite de Lyon, Universite Lyon 1, CNRS, UMR5558, Laboratoire de Biometrie et Biologie Evolutive, F-69622, Villeurbanne, France. duret@biomserv.univ-lyon1.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197042" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conserved Sequence ; *Enhancer Elements, Genetic ; Evolution, Molecular ; *Gene Conversion ; Humans ; Mutation ; Recombination, Genetic ; Selection, Genetic
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  • 79
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-05-09
    Description: Understanding of plant-pathogen coevolution in natural systems continues to develop as new theories at the population and species level are increasingly informed by studies unraveling the molecular basis of interactions between individual plants and their pathogens. The next challenge lies in further integration of these approaches to develop a comprehensive picture of how life history traits of both players interact with the environment to shape evolutionary trajectories.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689373/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689373/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burdon, Jeremy J -- Thrall, Peter H -- R01 GM074265-01A2/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 May 8;324(5928):755-6. doi: 10.1126/science.1171663.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commonwealth Scientific and Industrial Research Organization (CSIRO)-Plant Industry, Post Office Box 1600, Canberra, ACT 2601, Australia. Jeremy.Burdon@csiro.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19423818" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; *Ecosystem ; Fungal Proteins/genetics/metabolism ; Fungi/genetics/*pathogenicity/physiology ; *Host-Pathogen Interactions ; Immunity, Innate ; Plant Diseases/immunology/*microbiology ; Plant Proteins/genetics/metabolism ; Plants/genetics/immunology/metabolism/*microbiology
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 80
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-08-01
    Description: Microorganisms have critical roles in the functioning of soil in nutrient cycling, structural formation, and plant interactions, both positive and negative. These roles are important in reestablishing function and biodiversity in ecosystem restoration. Measurement of the community indicates the status of the system in relation to restoration targets and the effectiveness of management interventions, and manipulation of the community shows promise in the enhancement of the rate of recovery of degraded systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harris, Jim -- New York, N.Y. -- Science. 2009 Jul 31;325(5940):573-4. doi: 10.1126/science.1172975.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Natural Resources, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19644111" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Physiological Phenomena ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Fungi/*physiology ; Mycorrhizae/*physiology ; Plant Physiological Phenomena ; *Soil Microbiology ; Symbiosis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 81
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-08-01
    Description: Ecological restoration is an activity that ideally results in the return of an ecosystem to an undisturbed state. Ecosystem services are the benefits humans derive from ecosystems. The two have been joined to support growing environmental markets with the goal of creating restoration-based credits that can be bought and sold. However, the allure of these markets may be overshadowing shortcomings in the science and practice of ecological restoration. Before making risky investments, we must understand why and when restoration efforts fall short of recovering the full suite of ecosystem services, what can be done to improve restoration success, and why direct measurement of the biophysical processes that support ecosystem services is the only way to guarantee the future success of these markets. Without new science and an oversight framework to protect the ecosystem service assets which people depend, markets could actually accelerate environmental degradation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmer, Margaret A -- Filoso, Solange -- New York, N.Y. -- Science. 2009 Jul 31;325(5940):575-6. doi: 10.1126/science.1172976.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD 20688, USA. mpalmer@umd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19644112" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; Biophysical Processes ; *Conservation of Natural Resources ; *Ecosystem ; *Environment ; Humans ; Wetlands
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  • 82
    Publication Date: 2009-02-21
    Description: Thin layers of phytoplankton are important hotspots of ecological activity that are found in the coastal ocean, meters beneath the surface, and contain cell concentrations up to two orders of magnitude above ambient concentrations. Current interpretations of their formation favor abiotic processes, yet many phytoplankton species found in these layers are motile. We demonstrated that layers formed when the vertical migration of phytoplankton was disrupted by hydrodynamic shear. This mechanism, which we call gyrotactic trapping, can be responsible for the thin layers of phytoplankton commonly observed in the ocean. These results reveal that the coupling between active microorganism motility and ambient fluid motion can shape the macroscopic features of the marine ecological landscape.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Durham, William M -- Kessler, John O -- Stocker, Roman -- New York, N.Y. -- Science. 2009 Feb 20;323(5917):1067-70. doi: 10.1126/science.1167334.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19229037" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomechanical Phenomena ; Cell Shape ; Chlamydomonas/cytology/*physiology ; *Ecosystem ; Flagella ; Gravitation ; Movement ; Phytoplankton/cytology/*physiology ; *Water ; *Water Movements
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  • 83
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-09-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alberts, Bruce -- New York, N.Y. -- Science. 2009 Sep 11;325(5946):1319. doi: 10.1126/science.1181224.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19745119" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; *Biomedical Research ; DNA Repair ; Drug Discovery ; Humans ; Mutation ; *Neoplasms/drug therapy/genetics
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  • 84
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Patterson, David J -- New York, N.Y. -- Science. 2009 Sep 18;325(5947):1506-7. doi: 10.1126/science.1179690.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Encyclopedia of Life, Biodiversity Informatics, Marine Biological Laboratory, Woods Hole, MA 02543, USA. dpatterson@eol.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19762632" target="_blank"〉PubMed〈/a〉
    Keywords: Arctic Regions ; *Bacteria/classification ; Bacterial Physiological Phenomena ; Biodiversity ; *Diatoms ; *Ecosystem ; Geologic Sediments/*microbiology ; Seawater/*microbiology
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  • 85
    Publication Date: 2009-05-09
    Description: Climate change could lead to mismatches between the reproductive cycles of marine organisms and their planktonic food. We tested this hypothesis by comparing shrimp (Pandalus borealis) egg hatching times and satellite-derived phytoplankton bloom dynamics throughout the North Atlantic. At large spatial and long temporal (10 years or longer) scales, hatching was correlated with the timing of the spring phytoplankton bloom. Annual egg development and hatching times were determined locally by bottom water temperature. We conclude that different populations of P. borealis have adapted to local temperatures and bloom timing, matching egg hatching to food availability under average conditions. This strategy is vulnerable to interannual oceanographic variability and long-term climatic changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koeller, P -- Fuentes-Yaco, C -- Platt, T -- Sathyendranath, S -- Richards, A -- Ouellet, P -- Orr, D -- Skuladottir, U -- Wieland, K -- Savard, L -- Aschan, M -- New York, N.Y. -- Science. 2009 May 8;324(5928):791-3. doi: 10.1126/science.1170987.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Fisheries and Oceans, Bedford Institute of Oceanography, Post Office Box 1006, Dartmouth, B2Y 4A2 Nova Scotia, Canada. koellerp@mar.dfo-mpo.gc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19423827" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atlantic Ocean ; Climate ; *Cold Temperature ; *Ecosystem ; Female ; Ovum/growth & development/physiology ; Pandalidae/*physiology ; Phytoplankton/*physiology ; Population Dynamics ; Reproduction ; Seasons ; *Seawater
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  • 86
    Publication Date: 2009-06-13
    Description: Photosynthesis and respiration occur widely on Earth's surface, and the 18O/16O ratio of the oxygen produced and consumed varies with climatic conditions. As a consequence, the history of climate is reflected in the deviation of the 18O/16O of air (delta18Oatm) from seawater delta18O (known as the Dole effect). We report variations in delta18Oatm over the past 60,000 years related to Heinrich and Dansgaard-Oeschger events, two modes of abrupt climate change observed during the last ice age. Correlations with cave records support the hypothesis that the Dole effect is primarily governed by the strength of the Asian and North African monsoons and confirm that widespread changes in low-latitude terrestrial rainfall accompanied abrupt climate change. The rapid delta18Oatm changes can also be used to synchronize ice records by providing global time markers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Severinghaus, Jeffrey P -- Beaudette, Ross -- Headly, Melissa A -- Taylor, Kendrick -- Brook, Edward J -- New York, N.Y. -- Science. 2009 Jun 12;324(5933):1431-4. doi: 10.1126/science.1169473.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Institution of Oceanography, University of California, San Diego, CA 92093-0244, USA. jseveringhaus@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19520957" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; Atmosphere/*chemistry ; *Climatic Processes ; *Ecosystem ; Ice Cover/*chemistry ; Oxygen/*analysis ; Oxygen Isotopes/*analysis ; Photosynthesis ; Rain ; Seawater/chemistry ; Time
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  • 87
    Publication Date: 2009-12-08
    Description: Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edwards, Marcus J -- Flatman, Ruth H -- Mitchenall, Lesley A -- Stevenson, Clare E M -- Le, Tung B K -- Clarke, Thomas A -- McKay, Adam R -- Fiedler, Hans-Peter -- Buttner, Mark J -- Lawson, David M -- Maxwell, Anthony -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2009 Dec 4;326(5958):1415-8. doi: 10.1126/science.1179123.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965760" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/chemistry/metabolism/pharmacology ; Binding Sites ; Coumarins/chemistry/metabolism/pharmacology ; Crystallography, X-Ray ; DNA Gyrase/*chemistry/genetics/*metabolism ; DNA, Bacterial/metabolism ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*enzymology/genetics ; Glycosides/chemistry/metabolism/pharmacology ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis, Site-Directed ; Mutation ; Protein Multimerization ; Protein Structure, Tertiary ; Topoisomerase II Inhibitors
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  • 88
    Publication Date: 2009-02-07
    Description: Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carnaval, Ana Carolina -- Hickerson, Michael J -- Haddad, Celio F B -- Rodrigues, Miguel T -- Moritz, Craig -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):785-9. doi: 10.1126/science.1166955.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA. carnaval@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197066" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anura/classification/*genetics ; Bayes Theorem ; *Biodiversity ; Brazil ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Demography ; *Ecosystem ; Geography ; Molecular Sequence Data ; Mutation ; Phylogeny ; Population Dynamics ; Time ; *Trees ; *Tropical Climate
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  • 89
    Publication Date: 2009-11-11
    Description: Rapid antigenic evolution in the influenza A virus hemagglutinin precludes effective vaccination with existing vaccines. To understand this phenomenon, we passaged virus in mice immunized with influenza vaccine. Neutralizing antibodies selected mutants with single-amino acid hemagglutinin substitutions that increased virus binding to cell surface glycan receptors. Passaging these high-avidity binding mutants in naive mice, but not immune mice, selected for additional hemagglutinin substitutions that decreased cellular receptor binding avidity. Analyzing a panel of monoclonal antibody hemagglutinin escape mutants revealed a positive correlation between receptor binding avidity and escape from polyclonal antibodies. We propose that in response to variation in neutralizing antibody pressure between individuals, influenza A virus evolves by adjusting receptor binding avidity via amino acid substitutions throughout the hemagglutinin globular domain, many of which simultaneously alter antigenicity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784927/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784927/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hensley, Scott E -- Das, Suman R -- Bailey, Adam L -- Schmidt, Loren M -- Hickman, Heather D -- Jayaraman, Akila -- Viswanathan, Karthik -- Raman, Rahul -- Sasisekharan, Ram -- Bennink, Jack R -- Yewdell, Jonathan W -- GM 57073/GM/NIGMS NIH HHS/ -- U54 GM62116/GM/NIGMS NIH HHS/ -- Z01 AI001014-01/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2009 Oct 30;326(5953):734-6. doi: 10.1126/science.1178258.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19900932" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; Antigenic Variation/genetics/*immunology ; Cell Line ; Hemagglutinin Glycoproteins, Influenza Virus/genetics/immunology/*metabolism ; Influenza A Virus, H1N1 Subtype/genetics/*immunology ; Influenza Vaccines/immunology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Models, Immunological ; Mutation ; Receptors, Virus/*metabolism ; Serial Passage
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  • 90
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koenig, Robert -- New York, N.Y. -- Science. 2009 Jul 31;325(5940):562-3. doi: 10.1126/science.325_562.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19644106" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Conservation of Natural Resources/economics/methods ; *Ecosystem ; Insects ; Plant Development ; *Plants ; South Africa ; Water Supply
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  • 91
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weis, Virginia M -- Allemand, Denis -- New York, N.Y. -- Science. 2009 May 29;324(5931):1153-5. doi: 10.1126/science.1172540.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, Oregon State University, Corvallis, OR 97331, USA. weisv@science.oregonstate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478172" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/genetics/*physiology ; *Calcification, Physiologic ; Dinoflagellida/physiology ; *Ecosystem ; Hydrogen-Ion Concentration ; Oceans and Seas ; Seawater/chemistry ; Stress, Physiological ; *Symbiosis
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  • 92
    Publication Date: 2009-06-13
    Description: Rotavirus outer-layer protein VP7 is a principal target of protective antibodies. Removal of free calcium ions (Ca2+) dissociates VP7 trimers into monomers, releasing VP7 from the virion, and initiates penetration-inducing conformational changes in the other outer-layer protein, VP4. We report the crystal structure at 3.4 angstrom resolution of VP7 bound with the Fab fragment of a neutralizing monoclonal antibody. The Fab binds across the outer surface of the intersubunit contact, which contains two Ca2+ sites. Mutations that escape neutralization by other antibodies suggest that the same region bears the epitopes of most neutralizing antibodies. The monovalent Fab is sufficient to neutralize infectivity. We propose that neutralizing antibodies against VP7 act by stabilizing the trimer, thereby inhibiting the uncoating trigger for VP4 rearrangement. A disulfide-linked trimer is a potential subunit immunogen.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995306/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995306/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aoki, Scott T -- Settembre, Ethan C -- Trask, Shane D -- Greenberg, Harry B -- Harrison, Stephen C -- Dormitzer, Philip R -- AI-21362/AI/NIAID NIH HHS/ -- CA-13202/CA/NCI NIH HHS/ -- DK-56339/DK/NIDDK NIH HHS/ -- R37 CA013202/CA/NCI NIH HHS/ -- R37 CA013202-38/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Jun 12;324(5933):1444-7. doi: 10.1126/science.1170481.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19520960" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology/metabolism ; Antibodies, Viral/chemistry/*immunology/metabolism ; Antigens, Viral/*chemistry/genetics/*immunology/metabolism ; Binding Sites ; Binding Sites, Antibody ; Calcium/metabolism ; Capsid Proteins/*chemistry/genetics/*immunology/metabolism ; Crystallography, X-Ray ; Epitopes/immunology ; Immunoglobulin Fab Fragments/chemistry/*immunology/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neutralization Tests ; Protein Folding ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Subunits ; Recombinant Proteins/chemistry ; Rotavirus/*chemistry/immunology ; Serotyping
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  • 93
    Publication Date: 2009-07-04
    Description: Of fundamental interest in conservation ecology are the regulatory mechanisms that maintain communities. We document a mechanism that maintains forests in the Serengeti ecosystem, Tanzania, and the destabilization when disturbance opens forest canopy. Forest birds, by consuming seeds, protected them from beetle attack. Consumption increased the germination rate and the density of seedlings and recruits, which was sufficient to maintain the forest. Opening of the canopy resulted in loss of birds, increased beetle attack, and loss of germination. Thus, frugivorous birds are necessary for the maintenance of forests. Their absence could have resulted in the observed forest decline since 1966.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharam, Gregory J -- Sinclair, A R E -- Turkington, Roy -- New York, N.Y. -- Science. 2009 Jul 3;325(5936):51. doi: 10.1126/science.1173805.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biodiversity Research Center, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19574381" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Beetles ; *Birds ; *Ecosystem ; Feeding Behavior ; Germination ; Population Dynamics ; *Seeds/growth & development ; Tanzania ; *Trees/growth & development
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  • 94
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-12-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2009 Dec 18;326(5960):1612. doi: 10.1126/science.326.5960.1612.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20019263" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Biological Evolution ; DNA-Binding Proteins/genetics/physiology ; Drosophila Proteins/genetics/physiology ; Drosophila melanogaster/*genetics/growth & development/physiology ; *Enhancer Elements, Genetic ; *Gene Expression Regulation, Developmental ; Mutation ; Paired Box Transcription Factors/genetics ; Pigmentation/genetics ; Regulatory Sequences, Nucleic Acid ; Smegmamorpha/anatomy & histology/*genetics/growth & development
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  • 95
    Publication Date: 2009-04-18
    Description: Genes are not simply turned on or off, but instead their expression is fine-tuned to meet the needs of a cell. How genes are modulated so precisely is not well understood. The glucocorticoid receptor (GR) regulates target genes by associating with specific DNA binding sites, the sequences of which differ between genes. Traditionally, these binding sites have been viewed only as docking sites. Using structural, biochemical, and cell-based assays, we show that GR binding sequences, differing by as little as a single base pair, differentially affect GR conformation and regulatory activity. We therefore propose that DNA is a sequence-specific allosteric ligand of GR that tailors the activity of the receptor toward specific target genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777810/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777810/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meijsing, Sebastiaan H -- Pufall, Miles A -- So, Alex Y -- Bates, Darren L -- Chen, Lin -- Yamamoto, Keith R -- GM08537/GM/NIGMS NIH HHS/ -- R01 CA020535/CA/NCI NIH HHS/ -- R01 CA020535-31/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 17;324(5925):407-10. doi: 10.1126/science.1164265.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19372434" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Cell Line, Tumor ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; Humans ; Ligands ; Models, Molecular ; Mutation ; Protein Conformation ; Protein Isoforms/chemistry/metabolism ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rats ; Receptors, Glucocorticoid/chemistry/genetics/*metabolism ; Transcriptional Activation
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  • 96
    Publication Date: 2009-11-07
    Description: Human activities have more than doubled the amount of nitrogen (N) circulating in the biosphere. One major pathway of this anthropogenic N input into ecosystems has been increased regional deposition from the atmosphere. Here we show that atmospheric N deposition increased the stoichiometric ratio of N and phosphorus (P) in lakes in Norway, Sweden, and Colorado, United States, and, as a result, patterns of ecological nutrient limitation were shifted. Under low N deposition, phytoplankton growth is generally N-limited; however, in high-N deposition lakes, phytoplankton growth is consistently P-limited. Continued anthropogenic amplification of the global N cycle will further alter ecological processes, such as biogeochemical cycling, trophic dynamics, and biological diversity, in the world's lakes, even in lakes far from direct human disturbance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elser, James J -- Andersen, Tom -- Baron, Jill S -- Bergstrom, Ann-Kristin -- Jansson, Mats -- Kyle, Marcia -- Nydick, Koren R -- Steger, Laura -- Hessen, Dag O -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):835-7. doi: 10.1126/science.1176199.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA. j.elser@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892979" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; Biodiversity ; Biomass ; Colorado ; *Ecosystem ; Food Chain ; Fresh Water/*chemistry ; Human Activities ; Humans ; Nitrates/analysis ; Nitrogen/*analysis ; Norway ; Phosphorus/*analysis ; Phytoplankton/growth & development/*physiology ; Sweden ; Trees
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  • 97
    Publication Date: 2009-04-11
    Description: Synonymous mutations do not alter the encoded protein, but they can influence gene expression. To investigate how, we engineered a synthetic library of 154 genes that varied randomly at synonymous sites, but all encoded the same green fluorescent protein (GFP). When expressed in Escherichia coli, GFP protein levels varied 250-fold across the library. GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression. Rather, the stability of mRNA folding near the ribosomal binding site explained more than half the variation in protein levels. In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902468/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902468/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kudla, Grzegorz -- Murray, Andrew W -- Tollervey, David -- Plotkin, Joshua B -- BB/D019621/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/DO19621/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/DO19621/1/Wellcome Trust/United Kingdom -- P50 GM068763/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 10;324(5924):255-8. doi: 10.1126/science.1170160.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19359587" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Base Composition ; Cloning, Molecular ; *Codon ; Escherichia coli/*genetics/growth & development/metabolism ; *Gene Expression ; Gene Library ; Genes, Synthetic ; Green Fluorescent Proteins/*genetics/metabolism ; Mutation ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA Stability ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Messenger/chemistry/*genetics/metabolism ; Spectrometry, Fluorescence
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  • 98
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-01-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2009 Jan 2;323(5910):27. doi: 10.1126/science.323.5910.27.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19119193" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/growth & development/*physiology ; Australia ; *Calcification, Physiologic ; Calcium Carbonate/analysis ; Carbon Dioxide ; *Ecosystem ; Hydrogen-Ion Concentration ; Oceans and Seas ; Seawater/*chemistry ; Temperature
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  • 99
    Publication Date: 2009-05-23
    Description: Reconstructing ancient communities depends on how accurately fossil assemblages retain information about living populations. We report a high level of fidelity between modern bone assemblages and living populations based on a 40-year study of the Amboseli ecosystem in southern Kenya. Relative abundance of 15 herbivorous species recorded in the bone assemblage accurately tracks the living populations through major changes in community composition and habitat over intervals as short as 5 years. The aggregated bone sample provides an accurate record of community structure time-averaged over four decades. These results lay the groundwork for integrating paleobiological and contemporary ecological studies across evolutionary and ecological time scales. Bone surveys also provide a useful method of assessing population changes and community structure for modern vertebrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Western, David -- Behrensmeyer, Anna K -- New York, N.Y. -- Science. 2009 May 22;324(5930):1061-4. doi: 10.1126/science.1171155.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉African Conservation Center, Box 62844, Nairobi, Kenya. dwestern@africaonline.co.ke〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19461002" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Body Size ; *Bone and Bones ; *Ecosystem ; Fossils ; Kenya ; Population Dynamics ; Regression Analysis ; Statistics, Nonparametric ; *Vertebrates
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  • 100
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Penuelas, Josep -- Rutishauser, This -- Filella, Iolanda -- New York, N.Y. -- Science. 2009 May 15;324(5929):887-8. doi: 10.1126/science.1173004.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Global Ecology Unit, Center for Ecological Research and Forestry Applications (CREAF-CEAB-CSIC), Universitat Autonoma de Barcelona, 08193 Bellaterra (Barcelona), Spain. josep.penuelas@uab.cat〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19443770" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Biophysical Phenomena ; Carbon Dioxide/analysis/metabolism ; *Climate ; *Ecosystem ; *Greenhouse Effect ; Organic Chemicals/analysis/metabolism ; *Plant Development ; Plant Leaves/*growth & development/metabolism ; Plants/metabolism ; *Seasons ; Temperature
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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