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  • Articles  (1,063)
  • Mutation  (593)
  • *Biological Evolution  (495)
  • 2005-2009  (1,063)
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  • Articles  (1,063)
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  • 1
    Publication Date: 2009-12-18
    Description: Avian brood parasites and their hosts provide model systems for investigating links between recognition, learning, and their fitness consequences. One major evolutionary puzzle has continued to capture the attention of naturalists for centuries: why do hosts of brood parasites generally fail to recognize parasitic offspring after they have hatched from the egg, even when the host and parasitic chicks differ to almost comic degrees? One prominent theory to explain this pattern proposes that the costs of mistakenly learning to recognize the wrong offspring make recognition maladaptive. Here we show that American coots, Fulica americana, can recognize and reject parasitic chicks in their brood by using learned cues, despite the fact that the hosts and the brood parasites are of the same species. A series of chick cross-fostering experiments confirm that coots use first-hatched chicks in a brood as referents to learn to recognize their own chicks and then discriminate against later-hatched parasitic chicks in the same brood. When experimentally provided with the wrong reference chicks, coots can be induced to discriminate against their own offspring, confirming that the learning errors proposed by theory can exist. However, learning based on hatching order is reliable in naturally parasitized coot nests because host eggs hatch predictably ahead of parasite eggs. Conversely, a lack of reliable information may help to explain why the evolution of chick recognition is not more common in hosts of most interspecific brood parasites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shizuka, Daizaburo -- Lyon, Bruce E -- England -- Nature. 2010 Jan 14;463(7278):223-6. doi: 10.1038/nature08655. Epub 2009 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA. shizuka@biology.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016486" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds/*parasitology/*physiology ; British Columbia ; Cues ; Discrimination Learning/*physiology ; Feeding Behavior/physiology ; Genetic Fitness ; Nesting Behavior/*physiology ; Ovum/growth & development ; Pattern Recognition, Visual/physiology ; Survival Rate ; Time Factors ; Wetlands
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2009-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kayani, Saheeb Ahmed -- England -- Nature. 2009 Dec 24;462(7276):984. doi: 10.1038/462984b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033020" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; History, 20th Century ; History, 21st Century ; Humans ; Pakistan ; *Religion and Science ; Science/history
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    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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  • 4
    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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  • 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
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    Nature Publishing Group (NPG)
    Publication Date: 2009-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Mar 19;458(7236):259. doi: 10.1038/458259a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295555" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; European Union/organization & administration ; *Federal Government ; Periodicals as Topic/*legislation & jurisprudence ; Politics ; Publishing/*legislation & jurisprudence ; *Religion and Science ; Turkey
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  • 7
    Publication Date: 2009-02-13
    Description: Evolutionary biologists have long sought to understand the relationship between microevolution (adaptation), which can be observed both in nature and in the laboratory, and macroevolution (speciation and the origin of the divisions of the taxonomic hierarchy above the species level, and the development of complex organs), which cannot be witnessed because it occurs over intervals that far exceed the human lifespan. The connection between these processes is also a major source of conflict between science and religious belief. Biologists often forget that Charles Darwin offered a way of resolving this issue, and his proposal is ripe for re-evaluation in the light of recent research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reznick, David N -- Ricklefs, Robert E -- England -- Nature. 2009 Feb 12;457(7231):837-42. doi: 10.1038/nature07894.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California, Riverside, California 92521, USA. gupy@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212402" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Biological Evolution ; Extinction, Biological ; Genetic Speciation
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  • 8
    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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  • 9
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    Nature Publishing Group (NPG)
    Publication Date: 2009-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buchenau, Jurgen -- England -- Nature. 2009 Nov 19;462(7271):284-5. doi: 10.1038/462284a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of History at the University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, USA. jbuchenau@uncc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924194" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Emigration and Immigration ; Europe ; History, 19th Century ; History, 20th Century ; Humans ; Latin America ; Public Policy/history/*trends
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  • 10
    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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  • 11
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    Nature Publishing Group (NPG)
    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Waal, Frans B M -- England -- Nature. 2009 Jul 9;460(7252):175. doi: 10.1038/460175a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Living Links Center, Emory University, 954 N. Gatewood Road, Atlanta, Georgia 30322, USA. dewaal@emory.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587747" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior, Animal/physiology ; *Biological Evolution ; Cognition/*physiology ; Humans ; Laughter ; Phylogeny ; Selection, Genetic
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  • 12
    Publication Date: 2009-02-13
    Description: Why infer evolution when you can watch it happen in real time? This is the basic premise of using populations of fast-replicating microorganisms in test tubes to study evolution. The approach, known as experimental evolution, has provided a way of testing many of the key hypotheses that arose from the modern evolutionary synthesis. However, details of the unnatural histories of microorganisms in test tubes can be extrapolated only so far. Potential future directions for the approach include studying microbial evolution for its own sake under the most natural conditions possible in the test tube, and testing some qualitative theories of genome evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buckling, Angus -- Craig Maclean, R -- Brockhurst, Michael A -- Colegrave, Nick -- England -- Nature. 2009 Feb 12;457(7231):824-9. doi: 10.1038/nature07892.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. angus.buckling@zoo.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212400" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/genetics/growth & development/virology ; Bacterial Physiological Phenomena ; *Biodiversity ; *Biological Evolution ; *Selection, Genetic
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  • 13
    Publication Date: 2009-02-13
    Description: The past two decades have witnessed profound changes in our understanding of the evolution of arthropods. Many of these insights derive from the adoption of molecular methods by systematists and developmental biologists, prompting a radical reordering of the relationships among extant arthropod classes and their closest non-arthropod relatives, and shedding light on the developmental basis for the origins of key characteristics. A complementary source of data is the discovery of fossils from several spectacular Cambrian faunas. These fossils form well-characterized groupings, making the broad pattern of Cambrian arthropod systematics increasingly consensual.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Budd, Graham E -- Telford, Maximilian J -- England -- Nature. 2009 Feb 12;457(7231):812-7. doi: 10.1038/nature07890.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Uppsala University, Villavagen 16, Uppsala SE-752 36, Sweden. graham.budd@pal.uu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212398" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/anatomy & histology/*classification/*physiology ; *Biological Evolution ; Fossils ; Phylogeny
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  • 14
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Feb 12;457(7231):763-4. doi: 10.1038/457763a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212352" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; History, 19th Century ; *Humanism/history ; Humans
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  • 15
    Publication Date: 2009-06-19
    Description: Natural habitats of some microorganisms may fluctuate erratically, whereas others, which are more predictable, offer the opportunity to prepare in advance for the next environmental change. In analogy to classical Pavlovian conditioning, microorganisms may have evolved to anticipate environmental stimuli by adapting to their temporal order of appearance. Here we present evidence for environmental change anticipation in two model microorganisms, Escherichia coli and Saccharomyces cerevisiae. We show that anticipation is an adaptive trait, because pre-exposure to the stimulus that typically appears early in the ecology improves the organism's fitness when encountered with a second stimulus. Additionally, we observe loss of the conditioned response in E. coli strains that were repeatedly exposed in a laboratory evolution experiment only to the first stimulus. Focusing on the molecular level reveals that the natural temporal order of stimuli is embedded in the wiring of the regulatory network-early stimuli pre-induce genes that would be needed for later ones, yet later stimuli only induce genes needed to cope with them. Our work indicates that environmental anticipation is an adaptive trait that was repeatedly selected for during evolution and thus may be ubiquitous in biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitchell, Amir -- Romano, Gal H -- Groisman, Bella -- Yona, Avihu -- Dekel, Erez -- Kupiec, Martin -- Dahan, Orna -- Pilpel, Yitzhak -- England -- Nature. 2009 Jul 9;460(7252):220-4. doi: 10.1038/nature08112. Epub 2009 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, Weizmann Institute of Science Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536156" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; *Biological Evolution ; Carbohydrate Metabolism ; Carbon/metabolism ; Cell Respiration ; *Environment ; Escherichia coli/genetics/*metabolism ; Fermentation ; Gene Expression Regulation ; Genomics ; Heat-Shock Response/genetics ; Lactose/metabolism ; Maltose/metabolism ; Osmotic Pressure ; Oxidative Stress/genetics ; Saccharomyces cerevisiae/genetics/*metabolism ; Time Factors
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  • 16
    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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  • 17
    Publication Date: 2009-03-20
    Description: Ornithischia is one of the two major groups of dinosaurs, with heterodontosauridae as one of its major clades. Heterodontosauridae is characterized by small, gracile bodies and a problematic phylogenetic position. Recent phylogenetic work indicates that it represents the most basal group of all well-known ornithischians. Previous heterodontosaurid records are mainly from the Early Jurassic period (205-190 million years ago) of Africa. Here we report a new heterodontosaurid, Tianyulong confuciusi gen. et sp. nov., from the Early Cretaceous period (144-99 million years ago) of western Liaoning Province, China. Tianyulong extends the geographical distribution of heterodontosaurids to Asia and confirms the clade's previously questionable temporal range extension into the Early Cretaceous period. More surprisingly, Tianyulong bears long, singular and unbranched filamentous integumentary (outer skin) structures. This represents the first confirmed report, to our knowledge, of filamentous integumentary structures in an ornithischian dinosaur.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zheng, Xiao-Ting -- You, Hai-Lu -- Xu, Xing -- Dong, Zhi-Ming -- England -- Nature. 2009 Mar 19;458(7236):333-6. doi: 10.1038/nature07856.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Shandong Tianyu Museum of Nature, Lianhuashan Road West, Pingyi, Shandong, 273300, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295609" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; China ; Dentition ; Dinosaurs/*anatomy & histology/*classification ; Feathers/anatomy & histology ; Fossils ; History, Ancient ; Integumentary System/*anatomy & histology ; Phylogeny ; Skin/anatomy & histology ; Skull/anatomy & histology
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  • 18
    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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  • 19
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    Nature Publishing Group (NPG)
    Publication Date: 2009-11-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Todes, Daniel -- England -- Nature. 2009 Nov 5;462(7269):36-7. doi: 10.1038/462036a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of the History of Medicine at Johns Hopkins University, 1900 East Monument Street, Baltimore, Maryland 21205, USA. dtodes@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890312" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biological Science Disciplines/*history ; *Competitive Behavior ; Cooperative Behavior ; *Cultural Diversity ; Food Supply ; Great Britain ; History, 19th Century ; History, 20th Century ; Humans ; Literature, Modern/history ; Metaphor ; Models, Biological ; Population Density ; Russia ; Selection, Genetic
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  • 20
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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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  • 21
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    Nature Publishing Group (NPG)
    Publication Date: 2009-01-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Jan 1;457(7225):40. doi: 10.1038/457040a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19122633" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bahamas ; *Biological Evolution ; Fossils ; Geography ; Internet ; Lizards/physiology ; Photography ; *Selection, Genetic
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  • 22
    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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  • 23
    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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  • 24
    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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  • 25
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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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  • 26
    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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  • 27
    Publication Date: 2009-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tomescu, Alexandru M F -- England -- Nature. 2009 Feb 19;457(7232):956. doi: 10.1038/457956c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225495" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Plant Physiological Phenomena ; *Selection, Genetic
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  • 28
    Publication Date: 2009-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kutschera, U -- England -- Nature. 2009 Apr 23;458(7241):967. doi: 10.1038/458967c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396120" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Competitive Behavior ; Cooperative Behavior ; History, 19th Century ; Models, Biological ; *Selection, Genetic ; *Translating ; *Translations
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  • 29
    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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  • 30
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2009 Feb 12;457(7231):772-3. doi: 10.1038/457772b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212369" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Biology/education ; Netherlands ; *Personnel Downsizing ; *Universities/economics
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  • 31
    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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  • 32
    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abler, William L -- England -- Nature. 2009 Jan 22;457(7228):379. doi: 10.1038/457379d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158768" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bees/physiology ; *Biological Evolution ; History, 20th Century ; Humans
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  • 33
    Publication Date: 2009-08-21
    Description: Endosymbioses have dramatically altered eukaryotic life, but are thought to have negligibly affected prokaryotic evolution. Here, by analysing the flows of protein families, I present evidence that the double-membrane, gram-negative prokaryotes were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium. The resulting taxon has been extraordinarily successful, and has profoundly altered the evolution of life by providing endosymbionts necessary for the emergence of eukaryotes and by generating Earth's oxygen atmosphere. Their double-membrane architecture and the observed genome flows into them suggest a common evolutionary mechanism for their origin: an endosymbiosis between a clostridium and actinobacterium.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lake, James A -- England -- Nature. 2009 Aug 20;460(7258):967-71. doi: 10.1038/nature08183.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, California 90095, USA. lake@mbi.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693078" target="_blank"〉PubMed〈/a〉
    Keywords: Actinobacteria/*cytology ; *Biological Evolution ; Clostridium/*cytology ; *Endocytosis ; Eukaryotic Cells/cytology ; Gene Flow ; *Models, Biological ; Phylogeny ; Prokaryotic Cells/classification/*cytology ; *Symbiosis
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  • 34
    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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  • 35
    Publication Date: 2009-07-07
    Description: Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fates of individual organisms differently. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve. Here we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an intercompartmental signalling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable 'twin' spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we can systematically tune the penetrance of each mutant fate. Furthermore, signalling and replication perturbations synergize to significantly increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum shows a strong resemblance to twin sporulation in these B. subtilis mutants. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716064/" 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/PMC2716064/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eldar, Avigdor -- Chary, Vasant K -- Xenopoulos, Panagiotis -- Fontes, Michelle E -- Loson, Oliver C -- Dworkin, Jonathan -- Piggot, Patrick J -- Elowitz, Michael B -- GM43577/GM/NIGMS NIH HHS/ -- P50 GM068763/GM/NIGMS NIH HHS/ -- P50 GM068763-060006/GM/NIGMS NIH HHS/ -- R01 GM043577/GM/NIGMS NIH HHS/ -- R01 GM043577-21A2/GM/NIGMS NIH HHS/ -- R01 GM079771/GM/NIGMS NIH HHS/ -- R01 GM079771-03/GM/NIGMS NIH HHS/ -- R01GM079771/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 23;460(7254):510-4. doi: 10.1038/nature08150. Epub 2009 Jul 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Biology and Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19578359" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/genetics/*physiology ; *Biological Evolution ; DNA Replication ; *Gene Expression Regulation, Bacterial ; Spores, Bacterial/growth & development
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  • 36
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    Nature Publishing Group (NPG)
    Publication Date: 2009-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elshakry, Marwa -- England -- Nature. 2009 Oct 29;461(7268):1200-1. doi: 10.1038/4611200a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Columbia University, 611 Fayerweather Hall, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865145" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; History, 19th Century ; Internationality/*history ; Philosophy/*history ; Religion and Science
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  • 37
    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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  • 38
    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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  • 39
    Publication Date: 2009-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahlberg, Per E -- England -- Nature. 2009 Feb 26;457(7233):1094-5. doi: 10.1038/4571094a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242466" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Fertilization/*physiology ; Fishes/anatomy & histology/classification/*embryology/*physiology ; *Fossils ; Viviparity, Nonmammalian/*physiology ; Western Australia
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  • 40
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    Nature Publishing Group (NPG)
    Publication Date: 2009-09-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nicholls, Henry -- England -- Nature. 2009 Sep 10;461(7261):164-6. doi: 10.1038/461164a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741680" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Developmental Biology ; Fossils ; Hagfishes/*anatomy & histology/*classification/embryology/genetics ; Head/anatomy & histology ; Humans ; Lampreys/*anatomy & histology/*classification/embryology/genetics ; MicroRNAs/genetics/metabolism ; Models, Biological ; Phylogeny ; Sharks/anatomy & histology/classification/embryology
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  • 41
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    Nature Publishing Group (NPG)
    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hauser, Marc D -- England -- Nature. 2009 Jul 9;460(7252):190-6. doi: 10.1038/460190a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Psychology, Harvard University, Cambridge, Massachusetts 02138, USA. mdh102559@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587759" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Creativity ; *Culture ; *Developmental Biology ; Finches/anatomy & histology/physiology ; Humans ; Language ; Linguistics ; *Models, Biological ; Music/psychology
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  • 42
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    Nature Publishing Group (NPG)
    Publication Date: 2009-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erwin, Douglas -- England -- Nature. 2009 Nov 19;462(7271):282-3. doi: 10.1038/462282a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Paleobiology, National Museum of Natural History, Washington DC, USA. erwind@si.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924193" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; Fossils ; *Models, Biological ; Paleontology/*methods
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  • 43
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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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  • 44
    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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  • 45
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-03-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hendry, Andrew P -- England -- Nature. 2009 Mar 12;458(7235):162-4. doi: 10.1038/458162a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19279629" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Biological Evolution ; *Genetic Speciation ; Humans ; Hybridization, Genetic ; Species Specificity ; Terminology as Topic
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  • 46
    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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  • 47
    Publication Date: 2009-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flannery, David -- England -- Nature. 2009 Dec 24;462(7276):984. doi: 10.1038/462984c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033018" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; China ; *Terminology as Topic ; *Translating
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  • 48
    Publication Date: 2009-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Attenborough, David -- England -- Nature. 2009 Feb 19;457(7232):967. doi: 10.1038/457967a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225509" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biology/history ; Greenhouse Effect ; History, 19th Century ; History, 20th Century ; Human Activities ; *Television
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  • 49
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    Nature Publishing Group (NPG)
    Publication Date: 2009-03-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoag, Hannah -- England -- Nature. 2009 Mar 26;458(7237):393. doi: 10.1038/458393a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325594" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Canada ; History, 21st Century ; Religion and Science ; Science/*organization & administration
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  • 50
    Publication Date: 2009-09-18
    Description: Adaptive radiations often follow the evolution of key traits, such as the origin of the amniotic egg and the subsequent radiation of terrestrial vertebrates. The mechanism by which a species determines the sex of its offspring has been linked to critical ecological and life-history traits but not to major adaptive radiations, in part because sex-determining mechanisms do not fossilize. Here we establish a previously unknown coevolutionary relationship in 94 amniote species between sex-determining mechanism and whether a species bears live young or lays eggs. We use that relationship to predict the sex-determining mechanism in three independent lineages of extinct Mesozoic marine reptiles (mosasaurs, sauropterygians and ichthyosaurs), each of which is known from fossils to have evolved live birth. Our results indicate that each lineage evolved genotypic sex determination before acquiring live birth. This enabled their pelagic radiations, where the relatively stable temperatures of the open ocean constrain temperature-dependent sex determination in amniote species. Freed from the need to move and nest on land, extreme physical adaptations to a pelagic lifestyle evolved in each group, such as the fluked tails, dorsal fins and wing-shaped limbs of ichthyosaurs. With the inclusion of ichthyosaurs, mosasaurs and sauropterygians, genotypic sex determination is present in all known fully pelagic amniote groups (sea snakes, sirenians and cetaceans), suggesting that this mode of sex determination and the subsequent evolution of live birth are key traits required for marine adaptive radiations in amniote lineages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Organ, Chris L -- Janes, Daniel E -- Meade, Andrew -- Pagel, Mark -- 1 F32 GM075490-01/GM/NIGMS NIH HHS/ -- 5 F32 GM072494/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Sep 17;461(7262):389-92. doi: 10.1038/nature08350.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA. corgan@oeb.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759619" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/genetics/physiology ; Algorithms ; Animals ; Bayes Theorem ; *Biological Evolution ; *Extinction, Biological ; Female ; Fossils ; Genotype ; History, Ancient ; Male ; Marine Biology ; Markov Chains ; Monte Carlo Method ; Oviposition/genetics/physiology ; Phylogeny ; Reptiles/classification/*genetics/*physiology ; Sex Chromosomes/*genetics ; *Sex Determination Processes ; Sex Ratio ; Temperature ; Viviparity, Nonmammalian/genetics/*physiology
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  • 51
    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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  • 52
    Publication Date: 2009-05-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lieberman, Daniel E -- England -- Nature. 2009 May 7;459(7243):41-2. doi: 10.1038/459041a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19424142" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthropology ; *Biological Evolution ; *Fossils ; Geography ; Hominidae/*anatomy & histology/*classification ; Humans ; Indonesia ; Paleontology ; Species Specificity
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  • 53
    facet.materialart.
    Unknown
    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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  • 54
    Publication Date: 2009-10-23
    Description: Adapiform or 'adapoid' primates first appear in the fossil record in the earliest Eocene epoch ( approximately 55 million years (Myr) ago), and were common components of Palaeogene primate communities in Europe, Asia and North America. Adapiforms are commonly referred to as the 'lemur-like' primates of the Eocene epoch, and recent phylogenetic analyses have placed adapiforms as stem members of Strepsirrhini, a primate suborder whose crown clade includes lemurs, lorises and galagos. An alternative view is that adapiforms are stem anthropoids. This debate has recently been rekindled by the description of a largely complete skeleton of the adapiform Darwinius, from the middle Eocene of Europe, which has been widely publicised as an important 'link' in the early evolution of Anthropoidea. Here we describe the complete dentition and jaw of a large-bodied adapiform (Afradapis gen. nov.) from the earliest late Eocene of Egypt ( approximately 37 Myr ago) that exhibits a striking series of derived dental and gnathic features that also occur in younger anthropoid primates-notably the earliest catarrhine ancestors of Old World monkeys and apes. Phylogenetic analysis of 360 morphological features scored across 117 living and extinct primates (including all candidate stem anthropoids) does not place adapiforms as haplorhines (that is, members of a Tarsius-Anthropoidea clade) or as stem anthropoids, but rather as sister taxa of crown Strepsirrhini; Afradapis and Darwinius are placed in a geographically widespread clade of caenopithecine adapiforms that left no known descendants. The specialized morphological features that these adapiforms share with anthropoids are therefore most parsimoniously interpreted as evolutionary convergences. As the largest non-anthropoid primate ever documented in Afro-Arabia, Afradapis nevertheless provides surprising new evidence for prosimian diversity in the Eocene of Africa, and raises the possibility that ecological competition between adapiforms and higher primates might have played an important role during the early evolution of stem and crown Anthropoidea in Afro-Arabia.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seiffert, Erik R -- Perry, Jonathan M G -- Simons, Elwyn L -- Boyer, Doug M -- England -- Nature. 2009 Oct 22;461(7267):1118-21. doi: 10.1038/nature08429.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomical Sciences, Stony Brook University, Stony Brook, New York 11794-8081, USA. erik.seiffert@stonybrook.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847263" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Biological Evolution ; Dentition ; Egypt ; Mandible/anatomy & histology ; Phylogeny ; Primates/*anatomy & histology/*classification ; Tooth/anatomy & histology
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  • 55
    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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  • 56
    Publication Date: 2009-09-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Friedman, William E -- England -- Nature. 2009 Sep 10;461(7261):167. doi: 10.1038/461167b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741683" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anniversaries and Special Events ; *Biological Evolution ; Biological Science Disciplines/*history ; History, 18th Century ; History, 19th Century ; Selection, Genetic
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  • 57
    Publication Date: 2009-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Friedman, Matt -- England -- Nature. 2009 Nov 19;462(7271):255. doi: 10.1038/462255e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924171" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Biological Evolution ; Models, Statistical ; Paleontology/methods ; Vertebrates/*classification
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  • 58
    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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  • 59
    Publication Date: 2009-06-12
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689211/" 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/PMC3689211/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Litman, Gary W -- Cannon, John P -- R01 AI023338/AI/NIAID NIH HHS/ -- R01 AI023338-24/AI/NIAID NIH HHS/ -- R01 AI057559/AI/NIAID NIH HHS/ -- R01 AI057559-05/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):784-6. doi: 10.1038/459784a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516328" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/immunology ; *Biological Evolution ; Humans ; Lampreys/*immunology/metabolism ; Lymphocytes/cytology/*immunology/metabolism ; Receptors, Immunologic/*immunology ; T-Lymphocytes/immunology
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  • 60
    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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  • 61
    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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  • 62
    Publication Date: 2009-11-06
    Description: Bet hedging-stochastic switching between phenotypic states-is a canonical example of an evolutionary adaptation that facilitates persistence in the face of fluctuating environmental conditions. Although bet hedging is found in organisms ranging from bacteria to humans, direct evidence for an adaptive origin of this behaviour is lacking. Here we report the de novo evolution of bet hedging in experimental bacterial populations. Bacteria were subjected to an environment that continually favoured new phenotypic states. Initially, our regime drove the successive evolution of novel phenotypes by mutation and selection; however, in two (of 12) replicates this trend was broken by the evolution of bet-hedging genotypes that persisted because of rapid stochastic phenotype switching. Genome re-sequencing of one of these switching types revealed nine mutations that distinguished it from the ancestor. The final mutation was both necessary and sufficient for rapid phenotype switching; nonetheless, the evolution of bet hedging was contingent upon earlier mutations that altered the relative fitness effect of the final mutation. These findings capture the adaptive evolution of bet hedging in the simplest of organisms, and suggest that risk-spreading strategies may have been among the earliest evolutionary solutions to life in fluctuating environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beaumont, Hubertus J E -- Gallie, Jenna -- Kost, Christian -- Ferguson, Gayle C -- Rainey, Paul B -- England -- Nature. 2009 Nov 5;462(7269):90-3. doi: 10.1038/nature08504.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉New Zealand Institute for Advanced Study and Allan Wilson Centre for Molecular Ecology & Evolution, Massey University, Private Bag 102904, North Shore Mail Centre, North Shore City 0745, Auckland, New Zealand. h.j.e.beaumont@biology.leidenuniv.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890329" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/genetics/*physiology ; *Biological Evolution ; Cell Shape ; Colony Count, Microbial ; *Environment ; Genes, Bacterial/genetics ; Genetic Fitness ; Genotype ; Models, Biological ; Phenotype ; Pseudomonas fluorescens/cytology/*genetics/growth & development/*physiology ; Selection, Genetic ; Stochastic Processes
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  • 63
    Publication Date: 2009-10-02
    Description: The early evolution of the major groups of derived non-avialan theropods is still not well understood, mainly because of their poor fossil record in the Jurassic. A well-known result of this problem is the 'temporal paradox' argument that is sometimes made against the theropod hypothesis of avian origins. Here we report on an exceptionally well-preserved small theropod specimen collected from the earliest Late Jurassic Tiaojishan Formation of western Liaoning, China. The specimen is referable to the Troodontidae, which are among the theropods most closely related to birds. This new find refutes the 'temporal paradox'1 and provides significant information on the temporal framework of theropod divergence. Furthermore, the extensive feathering of this specimen, particularly the attachment of long pennaceous feathers to the pes, sheds new light on the early evolution of feathers and demonstrates the complex distribution of skeletal and integumentary features close to the dinosaur-bird transition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Dongyu -- Hou, Lianhai -- Zhang, Lijun -- Xu, Xing -- England -- Nature. 2009 Oct 1;461(7264):640-3. doi: 10.1038/nature08322.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Paleontological Institute, Shenyang Normal University, 253 North Huanghe Street, Shenyang 110034, China. hudongyu@synu.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794491" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Birds/anatomy & histology/classification ; Calibration ; China ; Dinosaurs/*anatomy & histology/*classification ; Feathers/*anatomy & histology ; Flight, Animal ; Foot/anatomy & histology ; *Fossils ; Metatarsus/*anatomy & histology ; Phylogeny
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  • 64
    Publication Date: 2009-02-27
    Description: Evidence of reproductive biology is extremely rare in the fossil record. Recently the first known embryos were discovered within the Placodermi, an extinct class of armoured fish, indicating a viviparous mode of reproduction in a vertebrate group outside the crown-group Gnathostomata (Chondrichthyes and Osteichthyes). These embryos were found in ptyctodontids, a small group of placoderms phylogenetically basal to the largest group, the Arthrodira. Here we report the discovery of embryos in the Arthrodira inside specimens of Incisoscutum ritchiei from the Upper Devonian Gogo Formation of Western Australia (approximately 380 million years ago), providing the first evidence, to our knowledge, for reproduction using internal fertilization in this diverse group. We show that Incisoscutum and some phyllolepid arthrodires possessed pelvic girdles with long basipterygia that articulated distally with an additional cartilaginous element or series, as in chondrichthyans, indicating that the pelvic fin was used in copulation. As homology between similar pelvic girdle skeletal structures in ptyctodontids, arthrodires and chondrichthyans is difficult to reconcile in the light of current phylogenies of lower gnathostomes, we explain these similarities as being most likely due to convergence (homoplasy). These new finds confirm that reproduction by internal fertilization and viviparity was much more widespread in the earliest gnathostomes than had been previously appreciated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, John A -- Trinajstic, Kate -- Johanson, Zerina -- England -- Nature. 2009 Feb 26;457(7233):1124-7. doi: 10.1038/nature07732.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum Victoria, PO Box 666, Melbourne 3001, Victoria, Australia. jlong@museum.vic.gov.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242474" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Fertilization/*physiology ; Fishes/anatomy & histology/classification/*embryology/*physiology ; *Fossils ; Pelvis/anatomy & histology ; Phylogeny ; Sharks/anatomy & histology/classification/embryology ; Viviparity, Nonmammalian/physiology ; Western Australia
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  • 65
    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shettleworth, Sara J -- England -- Nature. 2009 May 28;459(7246):506. doi: 10.1038/459506b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478765" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cognition/*physiology ; Human Characteristics ; Humans ; *Models, Biological
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  • 66
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huber, Matthew -- England -- Nature. 2009 Feb 5;457(7230):669-71. doi: 10.1038/457669a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Body Size ; Body Temperature Regulation ; Boidae/*anatomy & histology/metabolism ; Colombia ; *Fossils ; Greenhouse Effect ; History, Ancient ; *Temperature ; *Tropical Climate
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  • 67
    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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  • 68
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hui, Jerome H L -- England -- Nature. 2009 Apr 2;458(7238):571. doi: 10.1038/458571b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19340060" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Biology/*education/*standards ; Hong Kong ; *Religion and Science
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  • 69
    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, Tim F -- England -- Nature. 2009 Jul 9;460(7252):181. doi: 10.1038/460181a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587752" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; *Biological Evolution ; Conditioning, Classical ; Escherichia coli/*metabolism ; Ethanol/metabolism ; Fermentation ; Heat-Shock Response ; Lactose/metabolism ; Maltose/metabolism ; Oxidative Stress ; Saccharomyces cerevisiae/*metabolism ; Selection, Genetic ; Time Factors
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  • 70
    Publication Date: 2009-02-06
    Description: The Neoproterozoic era (1,000-542 Myr ago) was an era of climatic extremes and biological evolutionary developments culminating in the emergence of animals (Metazoa) and new ecosystems. Here we show that abundant sedimentary 24-isopropylcholestanes, the hydrocarbon remains of C(30) sterols produced by marine demosponges, record the presence of Metazoa in the geological record before the end of the Marinoan glaciation ( approximately 635 Myr ago). These sterane biomarkers are abundant in all formations of the Huqf Supergroup, South Oman Salt Basin, and, based on a new high-precision geochronology, constitute a continuous 100-Myr-long chemical fossil record of demosponges through the terminal Neoproterozoic and into the Early Cambrian epoch. The demosponge steranes occur in strata that underlie the Marinoan cap carbonate (〉635 Myr ago). They currently represent the oldest evidence for animals in the fossil record, and are evidence for animals pre-dating the termination of the Marinoan glaciation. This suggests that shallow shelf waters in some late Cryogenian ocean basins (〉635 Myr ago) contained dissolved oxygen in concentrations sufficient to support basal metazoan life at least 100 Myr before the rapid diversification of bilaterians during the Cambrian explosion. Biomarker analysis has yet to reveal any convincing evidence for ancient sponges pre-dating the first globally extensive Neoproterozoic glacial episode (the Sturtian, approximately 713 Myr ago in Oman).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Love, Gordon D -- Grosjean, Emmanuelle -- Stalvies, Charlotte -- Fike, David A -- Grotzinger, John P -- Bradley, Alexander S -- Kelly, Amy E -- Bhatia, Maya -- Meredith, William -- Snape, Colin E -- Bowring, Samuel A -- Condon, Daniel J -- Summons, Roger E -- England -- Nature. 2009 Feb 5;457(7230):718-21. doi: 10.1038/nature07673.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of California, Riverside, California 92521, USA. glove@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194449" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabia ; *Biological Evolution ; Biomarkers/analysis/chemistry ; Cholestanes/*analysis/*chemistry/isolation & purification ; *Fossils ; Gas Chromatography-Mass Spectrometry ; Geologic Sediments/*chemistry ; History, Ancient ; Hydrocarbons/analysis/chemistry ; Ice Cover ; Oceans and Seas ; Oxygen/analysis ; Porifera/*physiology ; Seawater/chemistry
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  • 71
    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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  • 72
    Publication Date: 2009-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berry, R J -- England -- Nature. 2009 Nov 26;462(7272):411. doi: 10.1038/462411b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940898" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Cultural Diversity ; Great Britain ; History, 19th Century ; History, 20th Century ; *Religion and Science
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  • 73
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    Nature Publishing Group (NPG)
    Publication Date: 2009-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Oct 29;461(7268):1173-4. doi: 10.1038/4611173b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865116" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; China ; *Culture ; History, 19th Century ; History, 20th Century ; Internationality ; Public Opinion/*history ; *Religion and Science ; Russia
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  • 74
    Publication Date: 2009-02-13
    Description: Do new anatomical structures arise de novo, or do they evolve from pre-existing structures? Advances in developmental genetics, palaeontology and evolutionary developmental biology have recently shed light on the origins of some of the structures that most intrigued Charles Darwin, including animal eyes, tetrapod limbs and giant beetle horns. In each case, structures arose by the modification of pre-existing genetic regulatory circuits established in early metazoans. The deep homology of generative processes and cell-type specification mechanisms in animal development has provided the foundation for the independent evolution of a great variety of structures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shubin, Neil -- Tabin, Cliff -- Carroll, Sean -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Feb 12;457(7231):818-23. doi: 10.1038/nature07891.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismal Biology and Anatomy, University of Chicago, 1027 East 57th Street, Chicago, Illinois 60637, USA. nshubin@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212399" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Beetles/anatomy & histology ; *Biological Evolution ; Extremities/anatomy & histology/*physiology ; Eye/anatomy & histology ; Gene Expression Regulation ; Horns/anatomy & histology/*physiology ; *Ocular Physiological Phenomena ; Transcription Factors/physiology
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  • 75
    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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  • 76
    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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  • 77
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gee, Henry -- Howlett, Rory -- England -- Nature. 2009 Feb 12;457(7231):807. doi: 10.1038/457807a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212396" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Selection, Genetic
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  • 78
    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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  • 79
    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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  • 80
    Publication Date: 2009-06-12
    Description: The cause of the most marked changes in the evolution of life, which define the first-order stratigraphic boundary between the Precambrian and the Phanerozoic eon, remains enigmatic and a highly topical subject of debate. A global ocean anoxic event, triggered by large-scale hydrogen sulphide (H(2)S) release to surface waters, has been suggested by Wille et al., on the basis of two data sets from South China and Oman, to explain the fundamental biological changes across the Precambrian/Cambrian (PC/C) boundary. Here we report a new precise SHRIMP U-Pb zircon age of 532.3 +/- 0.7 million years (Myr) ago (Fig. 1) for a volcanic ash bed in the critical unit that reflects the ocean anoxic event, the lowermost black shale sequence of the Niutitang Formation in the Guizhou Province, South China. This age is significantly younger than the precise PC/C boundary age of 542.0 +/- 0.3 Myr ago, approximately 10 Myr younger than the extinction of the Ediacaran fauna, and thus challenging the view of a major ocean anoxic event having been responsible for the major changes in the direction of evolution at the PC/C boundary.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Shao-Yong -- Pi, Dao-Hui -- Heubeck, Christoph -- Frimmel, Hartwig -- Liu, Yu-Ping -- Deng, Hai-Lin -- Ling, Hong-Fei -- Yang, Jing-Hong -- England -- Nature. 2009 Jun 11;459(7248):E5-6; discussion E6. doi: 10.1038/nature08048.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory for Mineral Deposits Research, Department of Earth Sciences, Nanjing University, Nanjing 210093, China. shyjiang@nju.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516284" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; China ; History, Ancient ; Oceans and Seas ; Oxygen/*analysis/*metabolism ; Seawater/*chemistry ; Volcanic Eruptions
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  • 81
    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bolhuis, Johan J -- Wynne, Clive D L -- England -- Nature. 2009 Apr 16;458(7240):832-3. doi: 10.1038/458832a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Helmholtz Institute, Utrecht University, the Netherlands. j.j.bolhuis@uu.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19370014" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds/physiology ; Brain/*physiology ; Cognition/*physiology ; Humans ; Primates/physiology ; Reward ; Selection, Genetic
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  • 82
    Publication Date: 2009-05-29
    Description: Adaptation is conventionally regarded as occurring at the level of the individual organism, where it functions to maximize the individual's inclusive fitness. However, it has recently been argued that empirical studies on the evolution of parasite virulence in spatial populations show otherwise. In particular, it has been claimed that the evolution of lower virulence in response to limited parasite dispersal provides proof of Wynne-Edwards's idea of adaptation at the group level. Although previous theoretical work has shown that limited dispersal can favour lower virulence, it has not clarified why, with five different suggestions having been given. Here we show that the effect of dispersal on parasite virulence can be understood entirely within the framework of inclusive fitness theory. Limited parasite dispersal favours lower parasite growth rates and, hence, reduced virulence because it (1) decreases the direct benefit of producing offspring (dispersers are worth more than non-dispersers, because they can go to patches with no or fewer parasites), and (2) increases the competition for hosts experienced by both the focal individual ('self-shading') and their relatives ('kin shading'). This demonstrates that reduced virulence can be understood as an individual-level adaptation by the parasite to maximize its inclusive fitness, and clarifies the links with virulence theory more generally.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wild, Geoff -- Gardner, Andy -- West, Stuart A -- England -- Nature. 2009 Jun 18;459(7249):983-6. doi: 10.1038/nature08071. Epub 2009 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Mathematics, University of Western Ontario, London, Ontario N6A 5B7, Canada. gwild@uwo.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19474791" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Animals ; *Biological Evolution ; Geography ; *Models, Biological ; Parasites/*pathogenicity ; Selection, Genetic ; Virulence
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  • 83
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    Nature Publishing Group (NPG)
    Publication Date: 2009-08-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marks, Jonathan -- England -- Nature. 2009 Aug 13;460(7257):796. doi: 10.1038/460796a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19675625" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*physiology ; Animals ; Behavior ; Behavior, Animal ; *Biological Evolution ; Hominidae/*physiology ; Humans ; Pan troglodytes/physiology
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  • 84
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2009 Feb 26;457(7233):1067. doi: 10.1038/4571067a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242439" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; Biology/*education ; Curriculum/*standards/trends ; Guidelines as Topic ; Hong Kong ; Origin of Life ; Teaching/*standards/trends
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  • 85
    Publication Date: 2009-10-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Witmer, Lawrence M -- England -- Nature. 2009 Oct 1;461(7264):601-2. doi: 10.1038/461601a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794481" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Birds/anatomy & histology/classification/physiology ; China ; Dinosaurs/*anatomy & histology/classification/physiology ; Feathers/*anatomy & histology/physiology ; Flight, Animal ; Foot/anatomy & histology/physiology ; *Fossils ; History, Ancient ; Phylogeny
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  • 86
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    Nature Publishing Group (NPG)
    Publication Date: 2009-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pusey, James -- England -- Nature. 2009 Nov 12;462(7270):162-3. doi: 10.1038/462162a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bucknell University, 701 Moore Avenue, Lewisburg, Pennsylvania 17837, USA. pusey@bucknell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19907478" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; China ; Communism/history ; Europe ; History, 19th Century ; History, 20th Century ; *Models, Biological ; Political Systems/*history ; Politics ; Religious Philosophies ; Warfare
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  • 87
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Witmer, Lawrence M -- England -- Nature. 2009 Mar 19;458(7236):293-5. doi: 10.1038/458293a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295598" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; China ; Dinosaurs/*anatomy & histology/classification ; Feathers/*anatomy & histology ; Fossils ; History, Ancient ; Phylogeny ; Skin/*anatomy & histology
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  • 88
    Publication Date: 2009-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brocks, Jochen J -- Butterfield, Nicholas J -- England -- Nature. 2009 Feb 5;457(7230):672-3. doi: 10.1038/457672a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194441" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biomarkers/analysis/chemistry ; Cholestanes/*analysis/*chemistry/isolation & purification ; *Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; Porifera/*physiology
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  • 89
    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolpert, Lewis -- England -- Nature. 2009 May 28;459(7246):506. doi: 10.1038/459506a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478764" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cognition/*physiology ; Human Characteristics ; Humans ; Models, Biological
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  • 90
    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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  • 91
    Publication Date: 2009-02-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stenseth, Nils Chr -- Dunlop, Erin S -- England -- Nature. 2009 Feb 12;457(7231):803-4. doi: 10.1038/457803a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212394" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Conservation of Natural Resources ; Ecosystem ; *Fisheries ; Humans ; *Predatory Behavior
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  • 92
    Publication Date: 2009-01-09
    Description: Diatoms are the dominant group of phytoplankton in the modern ocean. They account for approximately 40% of oceanic primary productivity and over 50% of organic carbon burial in marine sediments. Owing to their role as a biological carbon pump and effects on atmospheric CO(2) levels, there is great interest in elucidating factors that influenced the rapid rise in diatom diversity during the past 40 million years. Two biotic controls on diversification have been proposed to explain this diversity increase: (1) geochemical coupling between terrestrial grasslands and marine ecosystems through the global silicon cycle; and (2) competitive displacement of other phytoplankton lineages. However, these hypotheses have not been tested using sampling-standardized fossil data. Here we show that reconstructions of species diversity in marine phytoplankton reject these proposed controls and suggest a new pattern for oceanic diatom diversity across the Cenozoic. Peak species diversity in marine planktonic diatoms occurred at the Eocene-Oligocene boundary and was followed by a pronounced decline, from which diversity has not recovered. Although the roles of abiotic and biotic drivers of diversification remain unclear, major features of oceanic diatom evolution are decoupled from both grassland expansion and competition among phytoplankton groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rabosky, Daniel L -- Sorhannus, Ulf -- England -- Nature. 2009 Jan 8;457(7226):183-6. doi: 10.1038/nature07435.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA. DLR32@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19129846" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; *Biological Evolution ; Databases, Factual ; Diatoms/classification/*physiology ; Fossils ; History, Ancient ; Phytoplankton/classification/*physiology ; Poaceae ; Time Factors
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  • 93
    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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  • 94
    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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  • 95
    Publication Date: 2009-06-19
    Description: Theropods have traditionally been assumed to have lost manual digits from the lateral side inward, which differs from the bilateral reduction pattern seen in other tetrapod groups. This unusual reduction pattern is clearly present in basal theropods, and has also been inferred in non-avian tetanurans based on identification of their three digits as the medial ones of the hand (I-II-III). This contradicts the many developmental studies indicating II-III-IV identities for the three manual digits of the only extant tetanurans, the birds. Here we report a new basal ceratosaur from the Oxfordian stage of the Jurassic period of China (156-161 million years ago), representing the first known Asian ceratosaur and the only known beaked, herbivorous Jurassic theropod. Most significantly, this taxon possesses a strongly reduced manual digit I, documenting a complex pattern of digital reduction within the Theropoda. Comparisons among theropod hands show that the three manual digits of basal tetanurans are similar in many metacarpal features to digits II-III-IV, but in phalangeal features to digits I-II-III, of more basal theropods. Given II-III-IV identities in avians, the simplest interpretation is that these identities were shared by all tetanurans. The transition to tetanurans involved complex changes in the hand including a shift in digit identities, with ceratosaurs displaying an intermediate condition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Xing -- Clark, James M -- Mo, Jinyou -- Choiniere, Jonah -- Forster, Catherine A -- Erickson, Gregory M -- Hone, David W E -- Sullivan, Corwin -- Eberth, David A -- Nesbitt, Sterling -- Zhao, Qi -- Hernandez, Rene -- Jia, Cheng-kai -- Han, Feng-lu -- Guo, Yu -- England -- Nature. 2009 Jun 18;459(7249):940-4. doi: 10.1038/nature08124.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Vertebrate Paleontology and Paleoanthropology, Beijing 100044, China. xingxu@vip.sina.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536256" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds/*anatomy & histology ; China ; Dinosaurs/*anatomy & histology ; Extremities/*anatomy & histology ; *Fossils ; Phylogeny
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  • 96
    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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  • 97
    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
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  • 98
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-09-26
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847887/" 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/PMC2847887/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hedrick, Stephen M -- R01 AI021372/AI/NIAID NIH HHS/ -- R01 AI021372-26/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2009 Sep 25;325(5948):1623-4. doi: 10.1126/science.325_1623a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA. shedrick@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779174" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Immune System/*physiology ; *Immunity ; Immunity, Innate ; Invertebrates/*immunology ; Selection, Genetic ; Vertebrates/*immunology
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  • 99
    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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  • 100
    facet.materialart.
    Unknown
    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
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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