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  • Molecular Sequence Data  (148)
  • Mutation  (135)
  • American Association for the Advancement of Science (AAAS)  (252)
  • National Academy of Sciences
  • 2010-2014  (252)
  • 1980-1984
  • 1925-1929
  • 2013  (106)
  • 2012  (146)
  • 1929
Collection
Keywords
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  • 2010-2014  (252)
  • 1980-1984
  • 1925-1929
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  • 1
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    A high-coverage genome sequence from an archaic Denisovan individual (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-01
    Description: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30x) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617501/" 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/PMC3617501/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, Matthias -- Kircher, Martin -- Gansauge, Marie-Theres -- Li, Heng -- Racimo, Fernando -- Mallick, Swapan -- Schraiber, Joshua G -- Jay, Flora -- Prufer, Kay -- de Filippo, Cesare -- Sudmant, Peter H -- Alkan, Can -- Fu, Qiaomei -- Do, Ron -- Rohland, Nadin -- Tandon, Arti -- Siebauer, Michael -- Green, Richard E -- Bryc, Katarzyna -- Briggs, Adrian W -- Stenzel, Udo -- Dabney, Jesse -- Shendure, Jay -- Kitzman, Jacob -- Hammer, Michael F -- Shunkov, Michael V -- Derevianko, Anatoli P -- Patterson, Nick -- Andres, Aida M -- Eichler, Evan E -- Slatkin, Montgomery -- Reich, David -- Kelso, Janet -- Paabo, Svante -- GM100233/GM/NIGMS NIH HHS/ -- R01 GM040282/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01-GM40282/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. mmeyer@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936568" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Base Sequence ; Fossils ; Gene Flow ; Gene Library ; *Genetic Variation ; Genome, Human/*genetics ; *Heterozygote ; Humans ; Molecular Sequence Data ; Neanderthals/*genetics ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Ancestral developmental potential facilitates parallel evolution in ants (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-10
    Description: Complex worker caste systems have contributed to the evolutionary success of advanced ant societies; however, little is known about the developmental processes underlying their origin and evolution. We combined hormonal manipulation, gene expression, and phylogenetic analyses with field observations to understand how novel worker subcastes evolve. We uncovered an ancestral developmental potential to produce a "supersoldier" subcaste that has been actualized at least two times independently in the hyperdiverse ant genus Pheidole. This potential has been retained and can be environmentally induced throughout the genus. Therefore, the retention and induction of this potential have facilitated the parallel evolution of supersoldiers through a process known as genetic accommodation. The recurrent induction of ancestral developmental potential may facilitate the adaptive and parallel evolution of phenotypes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rajakumar, Rajendhran -- San Mauro, Diego -- Dijkstra, Michiel B -- Huang, Ming H -- Wheeler, Diana E -- Hiou-Tim, Francois -- Khila, Abderrahman -- Cournoyea, Michael -- Abouheif, Ehab -- New York, N.Y. -- Science. 2012 Jan 6;335(6064):79-82. doi: 10.1126/science.1211451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, McGill University, 1205 Avenue Dr. Penfield, Montreal, Quebec, Canada, H3A 1B1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223805" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ants/*genetics/growth & development/physiology ; *Biological Evolution ; Environment ; Female ; Genes, Insect ; Larva/growth & development ; Male ; Methoprene/pharmacology ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Selection, Genetic ; Social Behavior ; Wings, Animal/growth & development
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    MARF1 regulates essential oogenic processes in mice (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-24
    Description: Development of fertilization-competent oocytes depends on integrated processes controlling meiosis, cytoplasmic development, and maintenance of genomic integrity. We show that meiosis arrest female 1 (MARF1) is required for these processes in mammalian oocytes. Mutations of Marf1 cause female infertility characterized by up-regulation of a cohort of transcripts, increased retrotransposon expression, defective cytoplasmic maturation, and meiotic arrest. Up-regulation of protein phosphatase 2 catalytic subunit (PPP2CB) is key to the meiotic arrest phenotype. Moreover, Iap and Line1 retrotransposon messenger RNAs are also up-regulated, and, concomitantly, DNA double-strand breaks are elevated in mutant oocytes. Therefore MARF1, by suppressing levels of specific transcripts, is an essential regulator of important oogenic processes leading to female fertility and the development of healthy offspring.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612990/" 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/PMC3612990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, You-Qiang -- Sugiura, Koji -- Sun, Fengyun -- Pendola, Janice K -- Cox, Gregory A -- Handel, Mary Ann -- Schimenti, John C -- Eppig, John J -- CA34196/CA/NCI NIH HHS/ -- HD42137/HD/NICHD NIH HHS/ -- P01 HD042137/HD/NICHD NIH HHS/ -- P30 CA034196/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 23;335(6075):1496-9. doi: 10.1126/science.1214680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Jackson Laboratory, Bar Harbor, ME 04609, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22442484" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; DNA Breaks, Double-Stranded ; Embryonic Development ; Female ; *Fertility ; Meiosis ; Mice ; Molecular Sequence Data ; Mutation ; Oocytes/*physiology ; *Oogenesis ; Phenotype ; Protein Phosphatase 2/genetics/metabolism ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Retroelements ; Transcription, Genetic ; Transcriptome ; Up-Regulation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    The ancient drug salicylate directly activates AMP-activated protein kinase (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-04-21
    Description: Salicylate, a plant product, has been in medicinal use since ancient times. More recently, it has been replaced by synthetic derivatives such as aspirin and salsalate, both of which are rapidly broken down to salicylate in vivo. At concentrations reached in plasma after administration of salsalate or of aspirin at high doses, salicylate activates adenosine monophosphate-activated protein kinase (AMPK), a central regulator of cell growth and metabolism. Salicylate binds at the same site as the synthetic activator A-769662 to cause allosteric activation and inhibition of dephosphorylation of the activating phosphorylation site, threonine-172. In AMPK knockout mice, effects of salicylate to increase fat utilization and to lower plasma fatty acids in vivo were lost. Our results suggest that AMPK activation could explain some beneficial effects of salsalate and aspirin in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399766/" 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/PMC3399766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hawley, Simon A -- Fullerton, Morgan D -- Ross, Fiona A -- Schertzer, Jonathan D -- Chevtzoff, Cyrille -- Walker, Katherine J -- Peggie, Mark W -- Zibrova, Darya -- Green, Kevin A -- Mustard, Kirsty J -- Kemp, Bruce E -- Sakamoto, Kei -- Steinberg, Gregory R -- Hardie, D Grahame -- 080982/Wellcome Trust/United Kingdom -- 097726/Wellcome Trust/United Kingdom -- MC_U127088492/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 May 18;336(6083):918-22. doi: 10.1126/science.1215327. Epub 2012 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22517326" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/genetics/*metabolism ; Amino Acid Substitution ; Animals ; Aspirin/pharmacology ; Binding Sites ; Carbohydrate Metabolism/drug effects ; Cell Line ; Enzyme Activation ; Enzyme Activators/pharmacology ; HEK293 Cells ; Humans ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism ; Mice ; Mice, Knockout ; Mutation ; Oxygen Consumption/drug effects ; Phosphorylation ; Pyrones/pharmacology ; Rats ; Salicylates/blood/*metabolism/*pharmacology ; Thiophenes/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 5
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    Airborne transmission of influenza A/H5N1 virus between ferrets (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-23
    Description: Highly pathogenic avian influenza A/H5N1 virus can cause morbidity and mortality in humans but thus far has not acquired the ability to be transmitted by aerosol or respiratory droplet ("airborne transmission") between humans. To address the concern that the virus could acquire this ability under natural conditions, we genetically modified A/H5N1 virus by site-directed mutagenesis and subsequent serial passage in ferrets. The genetically modified A/H5N1 virus acquired mutations during passage in ferrets, ultimately becoming airborne transmissible in ferrets. None of the recipient ferrets died after airborne infection with the mutant A/H5N1 viruses. Four amino acid substitutions in the host receptor-binding protein hemagglutinin, and one in the polymerase complex protein basic polymerase 2, were consistently present in airborne-transmitted viruses. The transmissible viruses were sensitive to the antiviral drug oseltamivir and reacted well with antisera raised against H5 influenza vaccine strains. Thus, avian A/H5N1 influenza viruses can acquire the capacity for airborne transmission between mammals without recombination in an intermediate host and therefore constitute a risk for human pandemic influenza.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herfst, Sander -- Schrauwen, Eefje J A -- Linster, Martin -- Chutinimitkul, Salin -- de Wit, Emmie -- Munster, Vincent J -- Sorrell, Erin M -- Bestebroer, Theo M -- Burke, David F -- Smith, Derek J -- Rimmelzwaan, Guus F -- Osterhaus, Albert D M E -- Fouchier, Ron A M -- DP1-OD000490-01/OD/NIH HHS/ -- HHSN266200700010C/PHS HHS/ -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1534-41. doi: 10.1126/science.1213362.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723413" target="_blank"〉PubMed〈/a〉
    Keywords: Air Microbiology ; Amino Acid Substitution ; Animals ; Antiviral Agents/pharmacology ; Containment of Biohazards ; Disease Models, Animal ; Female ; *Ferrets ; Hemagglutinin Glycoproteins, Influenza ; Virus/chemistry/genetics/immunology/metabolism ; Humans ; Immune Sera ; Influenza A Virus, H5N1 Subtype/drug effects/*genetics/*pathogenicity/physiology ; Influenza in Birds/epidemiology/virology ; Influenza, Human/epidemiology/transmission/*virology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutation ; Orthomyxoviridae Infections/transmission/*virology ; Oseltamivir/pharmacology ; Pandemics ; Poultry ; RNA Replicase/chemistry/genetics ; Reassortant Viruses/pathogenicity ; Receptors, Virus/metabolism ; Respiratory System/*virology ; Reverse Genetics ; Serial Passage ; Sialic Acids/metabolism ; Viral Proteins/chemistry/genetics ; Virulence ; Virus Replication ; Virus Shedding
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 6
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    Secreted kinase phosphorylates extracellular proteins that regulate biomineralization (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-15
    Description: Protein phosphorylation is a fundamental mechanism regulating nearly every aspect of cellular life. Several secreted proteins are phosphorylated, but the kinases responsible are unknown. We identified a family of atypical protein kinases that localize within the Golgi apparatus and are secreted. Fam20C appears to be the Golgi casein kinase that phosphorylates secretory pathway proteins within S-x-E motifs. Fam20C phosphorylates the caseins and several secreted proteins implicated in biomineralization, including the small integrin-binding ligand, N-linked glycoproteins (SIBLINGs). Consequently, mutations in Fam20C cause an osteosclerotic bone dysplasia in humans known as Raine syndrome. Fam20C is thus a protein kinase dedicated to the phosphorylation of extracellular proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3754843/" 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/PMC3754843/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tagliabracci, Vincent S -- Engel, James L -- Wen, Jianzhong -- Wiley, Sandra E -- Worby, Carolyn A -- Kinch, Lisa N -- Xiao, Junyu -- Grishin, Nick V -- Dixon, Jack E -- DK018024-37/DK/NIDDK NIH HHS/ -- DK018849-36/DK/NIDDK NIH HHS/ -- GM094575/GM/NIGMS NIH HHS/ -- R01 DK018849/DK/NIDDK NIH HHS/ -- R37 DK018024/DK/NIDDK NIH HHS/ -- T32 CA009523/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1150-3. doi: 10.1126/science.1217817. Epub 2012 May 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0721, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582013" target="_blank"〉PubMed〈/a〉
    Keywords: Abnormalities, Multiple/genetics/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Calcification, Physiologic ; Casein Kinase I ; Casein Kinases/metabolism ; Caseins/*metabolism ; Cattle ; Cell Line, Tumor ; Cleft Palate/genetics/metabolism ; Exophthalmos/genetics/metabolism ; Extracellular Matrix Proteins/chemistry/genetics/*metabolism/secretion ; Glycoproteins/metabolism ; Golgi Apparatus/*enzymology ; HEK293 Cells ; HeLa Cells ; Humans ; Microcephaly/genetics/metabolism ; Milk/enzymology ; Molecular Sequence Data ; Mutation ; Osteopontin ; Osteosclerosis/genetics/metabolism ; Phosphorylation ; Protein Sorting Signals ; Recombinant Fusion Proteins/chemistry/metabolism/secretion ; *Secretory Pathway ; Substrate Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Alzheimer's research. How to talk about Alzheimer's risk (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Greg -- New York, N.Y. -- Science. 2012 Aug 17;337(6096):792. doi: 10.1126/science.337.6096.792.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22903992" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/*diagnosis/*genetics ; Apolipoprotein E4/genetics ; Clinical Trials as Topic ; Genetic Predisposition to Disease ; Humans ; Mutation ; *Patient Selection ; Risk ; Risk Assessment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Mutations in the neverland gene turned Drosophila pachea into an obligate specialist species (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-29
    Description: Most living species exploit a limited range of resources. However, little is known about how tight associations build up during evolution between such specialist species and the hosts they use. We examined the dependence of Drosophila pachea on its single host, the senita cactus. Several amino acid changes in the Neverland oxygenase rendered D. pachea unable to transform cholesterol into 7-dehydrocholesterol (the first reaction in the steroid hormone biosynthetic pathway in insects) and thus made D. pachea dependent on the uncommon sterols of its host plant. The neverland mutations increase survival on the cactus's unusual sterols and are in a genomic region that faced recent positive selection. This study illustrates how relatively few genetic changes in a single gene may restrict the ecological niche of a species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729188/" 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/PMC4729188/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lang, Michael -- Murat, Sophie -- Clark, Andrew G -- Gouppil, Geraldine -- Blais, Catherine -- Matzkin, Luciano M -- Guittard, Emilie -- Yoshiyama-Yanagawa, Takuji -- Kataoka, Hiroshi -- Niwa, Ryusuke -- Lafont, Rene -- Dauphin-Villemant, Chantal -- Orgogozo, Virginie -- AI064950/AI/NIAID NIH HHS/ -- R01 AI064950/AI/NIAID NIH HHS/ -- R01 HG003229/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1658-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR7592, Universite Paris Diderot, Sorbonne Paris Cite, Institut Jacques Monod, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019649" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cactaceae/*metabolism ; Cholesterol/metabolism ; Conserved Sequence ; Dehydrocholesterols/metabolism ; Drosophila/genetics/*physiology ; Drosophila Proteins/chemistry/*genetics/metabolism ; *Food Chain ; Molecular Sequence Data ; *Mutation ; Oxygenases/chemistry/*genetics/metabolism ; Protein Conformation ; RNA Interference ; Selection, Genetic ; Species Specificity
    Print ISSN: 0036-8075
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    Gene loops enhance transcriptional directionality (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-29
    Description: Eukaryotic genomes are extensively transcribed, forming both messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). ncRNAs made by RNA polymerase II often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesize mRNA and ncRNA in opposite directions. We demonstrate that, by adopting a gene-loop conformation, actively transcribed mRNA encoding genes restrict divergent transcription of ncRNAs. Because gene-loop formation depends on a protein factor (Ssu72) that coassociates with both the promoter and the terminator, the inactivation of Ssu72 leads to increased synthesis of promoter-associated divergent ncRNAs, referred to as Ssu72-restricted transcripts (SRTs). Similarly, inactivation of individual gene loops by gene mutation enhances SRT synthesis. We demonstrate that gene-loop conformation enforces transcriptional directionality on otherwise bidirectional promoters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563069/" 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/PMC3563069/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tan-Wong, Sue Mei -- Zaugg, Judith B -- Camblong, Jurgi -- Xu, Zhenyu -- Zhang, David W -- Mischo, Hannah E -- Ansari, Aseem Z -- Luscombe, Nicholas M -- Steinmetz, Lars M -- Proudfoot, Nick J -- 091805/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):671-5. doi: 10.1126/science.1224350. Epub 2012 Sep 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019609" target="_blank"〉PubMed〈/a〉
    Keywords: Exosome Multienzyme Ribonuclease Complex/metabolism ; *Genes, Fungal ; Genome, Fungal ; Mutation ; Nucleic Acid Conformation ; Phosphoprotein Phosphatases/metabolism ; Promoter Regions, Genetic ; RNA Polymerase II/metabolism ; RNA Stability ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/*genetics/metabolism ; RNA, Untranslated/*genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; *Transcription, Genetic ; mRNA Cleavage and Polyadenylation Factors/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Identification and functional expression of the mitochondrial pyruvate carrier (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-26
    Description: The transport of pyruvate, the end product of glycolysis, into mitochondria is an essential process that provides the organelle with a major oxidative fuel. Although the existence of a specific mitochondrial pyruvate carrier (MPC) has been anticipated, its molecular identity remained unknown. We report that MPC is a heterocomplex formed by two members of a family of previously uncharacterized membrane proteins that are conserved from yeast to mammals. Members of the MPC family were found in the inner mitochondrial membrane, and yeast mutants lacking MPC proteins showed severe defects in mitochondrial pyruvate uptake. Coexpression of mouse MPC1 and MPC2 in Lactococcus lactis promoted transport of pyruvate across the membrane. These observations firmly establish these proteins as essential components of the MPC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herzig, Sebastien -- Raemy, Etienne -- Montessuit, Sylvie -- Veuthey, Jean-Luc -- Zamboni, Nicola -- Westermann, Benedikt -- Kunji, Edmund R S -- Martinou, Jean-Claude -- MC_U105663139/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):93-6. doi: 10.1126/science.1218530. Epub 2012 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, University of Geneva, Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628554" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Biological Transport ; Biosynthetic Pathways ; Culture Media ; Lactococcus lactis/genetics/metabolism ; Leucine/metabolism ; Mice ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondrial Membranes/*metabolism ; Molecular Sequence Data ; Proprotein Convertase 1/chemistry/genetics/*metabolism ; Proprotein Convertase 2 ; Pyruvic Acid/*metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/genetics/growth & development/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Thioctic Acid/biosynthesis/metabolism ; Valine/metabolism
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  • 11
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    Highly conserved protective epitopes on influenza B viruses (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-11
    Description: Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538841/" 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/PMC3538841/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dreyfus, Cyrille -- Laursen, Nick S -- Kwaks, Ted -- Zuijdgeest, David -- Khayat, Reza -- Ekiert, Damian C -- Lee, Jeong Hyun -- Metlagel, Zoltan -- Bujny, Miriam V -- Jongeneelen, Mandy -- van der Vlugt, Remko -- Lamrani, Mohammed -- Korse, Hans J W M -- Geelen, Eric -- Sahin, Ozcan -- Sieuwerts, Martijn -- Brakenhoff, Just P J -- Vogels, Ronald -- Li, Olive T W -- Poon, Leo L M -- Peiris, Malik -- Koudstaal, Wouter -- Ward, Andrew B -- Wilson, Ian A -- Goudsmit, Jaap -- Friesen, Robert H E -- GM080209/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- RR017573/RR/NCRR NIH HHS/ -- T32 GM080209/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 14;337(6100):1343-8. doi: 10.1126/science.1222908. Epub 2012 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22878502" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/chemistry/*immunology ; Antibodies, Neutralizing/chemistry/immunology ; Conserved Sequence ; Hemagglutinin Glycoproteins, Influenza Virus/*immunology ; Humans ; Immunodominant Epitopes/chemistry/*immunology ; Influenza B virus/*immunology ; Influenza Vaccines/*immunology ; Mice ; Molecular Sequence Data ; Neutralization Tests ; Orthomyxoviridae Infections/*prevention & control ; Protein Conformation
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  • 12
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    Medicine. The ultimate genetic test (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Drmanac, Radoje -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1110-2. doi: 10.1126/science.1221037.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Complete Genomics, Inc., Mountain View, CA 94043, USA. rdrmanac@completegenomics.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654043" target="_blank"〉PubMed〈/a〉
    Keywords: Genetic Predisposition to Disease ; Genetic Privacy ; *Genetic Testing/economics/methods/standards ; *Genetic Variation ; *Genome, Human ; Humans ; Mutation ; Precision Medicine ; Public Policy ; *Sequence Analysis, DNA/economics/methods/standards
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  • 13
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    Cancer research. Unraveling the obesity-cancer connection (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taubes, Gary -- New York, N.Y. -- Science. 2012 Jan 6;335(6064):28, 30-2. doi: 10.1126/science.335.6064.28.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223787" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Proliferation ; Diabetes Mellitus, Type 2/complications/*metabolism ; Diet ; Glucose/metabolism ; Humans ; Insulin/blood/*metabolism ; Mutation ; Neoplasms/*etiology/genetics/metabolism/pathology ; Obesity/complications/*metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Receptor, Insulin/metabolism ; Receptors, Somatomedin/metabolism ; Signal Transduction ; Somatomedins/*metabolism
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  • 14
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    IBI series winner. A mutant search--Caenorhabditis elegans and gene discovery (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉LaRue, Candace C -- Padilla, Pamela A -- New York, N.Y. -- Science. 2012 Oct 26;338(6106):487-8. doi: 10.1126/science.1215229.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of North Texas, Denton TX 76203, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23112325" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*genetics ; Caenorhabditis elegans Proteins/*genetics ; DNA Mutational Analysis ; *Genetic Association Studies ; Genetic Research ; *Genetic Testing ; Genetics/*education ; Mutation ; Texas ; Universities
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  • 15
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    Identification of small molecule activators of cryptochrome (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-07-17
    Description: Impairment of the circadian clock has been associated with numerous disorders, including metabolic disease. Although small molecules that modulate clock function might offer therapeutic approaches to such diseases, only a few compounds have been identified that selectively target core clock proteins. From an unbiased cell-based circadian phenotypic screen, we identified KL001, a small molecule that specifically interacts with cryptochrome (CRY). KL001 prevented ubiquitin-dependent degradation of CRY, resulting in lengthening of the circadian period. In combination with mathematical modeling, our studies using KL001 revealed that CRY1 and CRY2 share a similar functional role in the period regulation. Furthermore, KL001-mediated CRY stabilization inhibited glucagon-induced gluconeogenesis in primary hepatocytes. KL001 thus provides a tool to study the regulation of CRY-dependent physiology and aid development of clock-based therapeutics of diabetes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589997/" 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/PMC3589997/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hirota, Tsuyoshi -- Lee, Jae Wook -- St John, Peter C -- Sawa, Mariko -- Iwaisako, Keiko -- Noguchi, Takako -- Pongsawakul, Pagkapol Y -- Sonntag, Tim -- Welsh, David K -- Brenner, David A -- Doyle, Francis J 3rd -- Schultz, Peter G -- Kay, Steve A -- GM074868/GM/NIGMS NIH HHS/ -- GM085764/GM/NIGMS NIH HHS/ -- GM096873/GM/NIGMS NIH HHS/ -- MH051573/MH/NIMH NIH HHS/ -- MH082945/MH/NIMH NIH HHS/ -- P50 GM085764/GM/NIGMS NIH HHS/ -- R01 GM041804/GM/NIGMS NIH HHS/ -- R01 GM074868/GM/NIGMS NIH HHS/ -- R01 GM096873/GM/NIGMS NIH HHS/ -- R01 MH051573/MH/NIMH NIH HHS/ -- R01 MH082945/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1094-7. doi: 10.1126/science.1223710. Epub 2012 Jul 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798407" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3 Cells ; Amino Acid Sequence ; Animals ; Carbazoles/chemistry/isolation & purification/*pharmacology ; Cell Line, Tumor ; Circadian Clocks/*drug effects ; Cryptochromes/*agonists/metabolism ; Gluconeogenesis/drug effects/genetics ; Glucose-6-Phosphatase/genetics ; HEK293 Cells ; Hepatocytes/drug effects/metabolism ; Humans ; Liver/cytology/drug effects/metabolism ; Mice ; Molecular Sequence Data ; Phosphoenolpyruvate Carboxykinase (GTP)/genetics ; Protein Stability/drug effects ; Proteolysis/drug effects ; *Small Molecule Libraries ; Sulfonamides/chemistry/isolation & purification/*pharmacology
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  • 16
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    The biology of genomes. Single-cell sequencing tackles basic and biomedical questions (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉New York, N.Y. -- Science. 2012 May 25;336(6084):976-7. doi: 10.1126/science.336.6084.976.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628633" target="_blank"〉PubMed〈/a〉
    Keywords: Breast Neoplasms/genetics ; Cell Line, Tumor ; Female ; Genes, Neoplasm ; *Genome, Human ; Humans ; Lab-On-A-Chip Devices ; Male ; Mutation ; Recombination, Genetic ; Sequence Analysis, DNA/*methods ; *Single-Cell Analysis ; Spermatozoa
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  • 17
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    Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-22
    Description: Symbioses between nitrogen (N)(2)-fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N(2) fixation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thompson, Anne W -- Foster, Rachel A -- Krupke, Andreas -- Carter, Brandon J -- Musat, Niculina -- Vaulot, Daniel -- Kuypers, Marcel M M -- Zehr, Jonathan P -- New York, N.Y. -- Science. 2012 Sep 21;337(6101):1546-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997339" target="_blank"〉PubMed〈/a〉
    Keywords: Calcification, Physiologic ; Carbon/metabolism ; Cyanobacteria/cytology/genetics/isolation & purification/*physiology ; Genes, rRNA ; Genome, Bacterial ; Haptophyta/cytology/genetics/isolation & purification/*physiology ; Molecular Sequence Data ; Nitrogen/metabolism ; *Nitrogen Fixation ; Pacific Ocean ; *Photosynthesis ; Phytoplankton/cytology/genetics/isolation & purification/*physiology ; Seawater/*microbiology ; *Symbiosis
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  • 18
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    Sedlin controls the ER export of procollagen by regulating the Sar1 cycle (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-29
    Description: Newly synthesized proteins exit the endoplasmic reticulum (ER) via coat protein complex II (COPII) vesicles. Procollagen (PC), however, forms prefibrils that are too large to fit into typical COPII vesicles; PC thus needs large transport carriers, which we term megacarriers. TANGO1 assists PC packing, but its role in promoting the growth of megacarriers is not known. We found that TANGO1 recruited Sedlin, a TRAPP component that is defective in spondyloepiphyseal dysplasia tarda (SEDT), and that Sedlin was required for the ER export of PC. Sedlin bound and promoted efficient cycling of Sar1, a guanosine triphosphatase that can constrict membranes, and thus allowed nascent carriers to grow and incorporate PC prefibrils. This joint action of TANGO1 and Sedlin sustained the ER export of PC, and its derangement may explain the defective chondrogenesis underlying SEDT.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471527/" 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/PMC3471527/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venditti, Rossella -- Scanu, Tiziana -- Santoro, Michele -- Di Tullio, Giuseppe -- Spaar, Alexander -- Gaibisso, Renato -- Beznoussenko, Galina V -- Mironov, Alexander A -- Mironov, Alexander Jr -- Zelante, Leopoldo -- Piemontese, Maria Rosaria -- Notarangelo, Angelo -- Malhotra, Vivek -- Vertel, Barbara M -- Wilson, Cathal -- De Matteis, Maria Antonietta -- AR053696/AR/NIAMS NIH HHS/ -- GGP06166/Telethon/Italy -- GGP07075/Telethon/Italy -- GSP08002/Telethon/Italy -- GTF08001/Telethon/Italy -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1668-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Telethon Institute of Genetics and Medicine, Naples, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019651" target="_blank"〉PubMed〈/a〉
    Keywords: Aryl Hydrocarbon Receptor Nuclear Translocator/*metabolism ; COP-Coated Vesicles/metabolism ; Cell Line ; Chondrogenesis/genetics ; Endoplasmic Reticulum/*metabolism ; Golgi Apparatus/metabolism ; Humans ; Membrane Transport Proteins/genetics/*metabolism ; Monomeric GTP-Binding Proteins/*metabolism ; Mutation ; Osteochondrodysplasias/genetics/metabolism ; Procollagen/*metabolism ; Protein Transport ; Transcription Factors/genetics/*metabolism
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  • 19
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    Pigment pattern formation by contact-dependent depolarization (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-02-11
    Description: Although recent experimental studies have suggested that the interactions among the pigment cells play a key role in the skin pattern formation, details of the mechanism remain largely unknown. By using an in vitro cell culture system, we have detected interactions between the two pigment cell types, melanophores and xanthophores, in the zebrafish skin. During primary culture, the melanophore membrane transiently depolarizes when contacted with the dendrites of a xanthophore. This depolarization triggers melanophore migration to avoid further contact with the xanthophores. Cell depolarization and repulsive movement were not observed in pigment cells with the jaguar mutant, which shows defective segregation of melanophores and xanthophores. The depolarization-repulsion of wild-type pigment cells may explain the pigment cell behaviors generating the stripe pattern of zebrafish.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Inaba, Masafumi -- Yamanaka, Hiroaki -- Kondo, Shigeru -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):677. doi: 10.1126/science.1212821.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323812" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Communication ; Cell Movement ; Cells, Cultured ; Chromatophores/*physiology ; Melanophores/*physiology ; Membrane Potentials ; Mutation ; Skin/cytology ; *Skin Pigmentation ; Zebrafish/*anatomy & histology/physiology
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    Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-02-11
    Description: Sodium/calcium (Na(+)/Ca(2+)) exchangers (NCX) are membrane transporters that play an essential role in maintaining the homeostasis of cytosolic Ca(2+) for cell signaling. We demonstrated the Na(+)/Ca(2+)-exchange function of an NCX from Methanococcus jannaschii (NCX_Mj) and report its 1.9 angstrom crystal structure in an outward-facing conformation. Containing 10 transmembrane helices, the two halves of NCX_Mj share a similar structure with opposite orientation. Four ion-binding sites cluster at the center of the protein: one specific for Ca(2+) and three that likely bind Na(+). Two passageways allow for Na(+) and Ca(2+) access to the central ion-binding sites from the extracellular side. Based on the symmetry of NCX_Mj and its ability to catalyze bidirectional ion-exchange reactions, we propose a structure model for the inward-facing NCX_Mj.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Jun -- Li, Hua -- Zeng, Weizhong -- Sauer, David B -- Belmares, Ricardo -- Jiang, Youxing -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):686-90. doi: 10.1126/science.1215759.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323814" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Calcium/*metabolism ; Crystallization ; Crystallography, X-Ray ; Ion Transport ; Ligands ; Methanococcales/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sodium/*metabolism ; Sodium-Calcium Exchanger/*chemistry/*metabolism
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  • 21
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    Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-02-04
    Description: Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iverson, Vaughn -- Morris, Robert M -- Frazar, Christian D -- Berthiaume, Chris T -- Morales, Rhonda L -- Armbrust, E Virginia -- New York, N.Y. -- Science. 2012 Feb 3;335(6068):587-90. doi: 10.1126/science.1212665.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22301318" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/*genetics/metabolism ; Biota ; *Ecosystem ; Enzymes/genetics/metabolism ; Euryarchaeota/classification/*genetics/metabolism/*physiology ; Genes, Archaeal ; *Genome, Archaeal ; Genome, Bacterial ; Heterotrophic Processes ; Lipid Metabolism/genetics ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbial Consortia ; Molecular Sequence Data ; Pacific Ocean ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; Proteins/metabolism ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Seawater/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA
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    Decoding in the absence of a codon by tmRNA and SmpB in the ribosome (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-17
    Description: In bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger RNA (tmRNA), a bifunctional molecule that acts as both a transfer RNA (tRNA) and a messenger RNA (mRNA), and SmpB, a small protein that works in concert with tmRNA. Here, we present the crystal structure of a tmRNA fragment, SmpB and elongation factor Tu bound to the ribosome at 3.2 angstroms resolution. The structure shows how SmpB plays the role of both the anticodon loop of tRNA and portions of mRNA to facilitate decoding in the absence of an mRNA codon in the A site of the ribosome and explains why the tmRNA-SmpB system does not interfere with normal translation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763467/" 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/PMC3763467/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neubauer, Cajetan -- Gillet, Reynald -- Kelley, Ann C -- Ramakrishnan, V -- 082086/Wellcome Trust/United Kingdom -- 096570/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- U105184332/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1366-9. doi: 10.1126/science.1217039.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422985" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/chemistry/metabolism ; Base Sequence ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/*chemistry/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/*chemistry/*metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; RNA-Binding Proteins/*chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism/ultrastructure ; Ribosomes/*chemistry/*metabolism/ultrastructure ; Thermus thermophilus/*chemistry/genetics/metabolism/ultrastructure
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    Crystal structure of the heterodimeric CLOCK:BMAL1 transcriptional activator complex (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-02
    Description: The circadian clock in mammals is driven by an autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete. A key component of this mechanism is a heterodimeric transcriptional activator consisting of two basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain protein subunits, CLOCK and BMAL1. Here, we report the crystal structure of a complex containing the mouse CLOCK:BMAL1 bHLH-PAS domains at 2.3 A resolution. The structure reveals an unusual asymmetric heterodimer with the three domains in each of the two subunits--bHLH, PAS-A, and PAS-B--tightly intertwined and involved in dimerization interactions, resulting in three distinct protein interfaces. Mutations that perturb the observed heterodimer interfaces affect the stability and activity of the CLOCK:BMAL1 complex as well as the periodicity of the circadian oscillator. The structure of the CLOCK:BMAL1 complex is a starting point for understanding at an atomic level the mechanism driving the mammalian circadian clock.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694778/" 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/PMC3694778/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Nian -- Chelliah, Yogarany -- Shan, Yongli -- Taylor, Clinton A -- Yoo, Seung-Hee -- Partch, Carrie -- Green, Carla B -- Zhang, Hong -- Takahashi, Joseph S -- R01 GM081875/GM/NIGMS NIH HHS/ -- R01 GM090247/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):189-94. doi: 10.1126/science.1222804. Epub 2012 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22653727" target="_blank"〉PubMed〈/a〉
    Keywords: ARNTL Transcription Factors/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Animals ; CLOCK Proteins/*chemistry/genetics/metabolism ; Cells, Cultured ; *Circadian Rhythm ; Crystallography, X-Ray ; DNA/metabolism ; HEK293 Cells ; Helix-Loop-Helix Motifs ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; *Transcriptional Activation
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    A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-01-17
    Description: Exocytosis is essential to the lytic cycle of apicomplexan parasites and required for the pathogenesis of toxoplasmosis and malaria. DOC2 proteins recruit the membrane fusion machinery required for exocytosis in a Ca(2+)-dependent fashion. Here, the phenotype of a Toxoplasma gondii conditional mutant impaired in host cell invasion and egress was pinpointed to a defect in secretion of the micronemes, an apicomplexan-specific organelle that contains adhesion proteins. Whole-genome sequencing identified the etiological point mutation in TgDOC2.1. A conditional allele of the orthologous gene engineered into Plasmodium falciparum was also defective in microneme secretion. However, the major effect was on invasion, suggesting that microneme secretion is dispensable for Plasmodium egress.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354045/" 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/PMC3354045/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Farrell, Andrew -- Thirugnanam, Sivasakthivel -- Lorestani, Alexander -- Dvorin, Jeffrey D -- Eidell, Keith P -- Ferguson, David J P -- Anderson-White, Brooke R -- Duraisingh, Manoj T -- Marth, Gabor T -- Gubbels, Marc-Jan -- AI057919/AI/NIAID NIH HHS/ -- AI081220/AI/NIAID NIH HHS/ -- AI087874/AI/NIAID NIH HHS/ -- AI088314/AI/NIAID NIH HHS/ -- HG004719/HG/NHGRI NIH HHS/ -- K08 AI087874/AI/NIAID NIH HHS/ -- K08 AI087874-02/AI/NIAID NIH HHS/ -- R01 AI057919/AI/NIAID NIH HHS/ -- R01 HG004719/HG/NHGRI NIH HHS/ -- R21 AI081220/AI/NIAID NIH HHS/ -- R21 AI088314/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):218-21. doi: 10.1126/science.1210829.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246776" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calcium/*metabolism ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cell Line ; *Exocytosis ; Genes, Protozoan ; Genetic Complementation Test ; Genome, Protozoan ; Humans ; Models, Molecular ; Molecular Sequence Data ; Movement ; Mutagenesis ; Organelles/*metabolism ; Plasmodium falciparum/genetics/growth & development/physiology ; Point Mutation ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Toxoplasma/genetics/growth & development/*physiology/ultrastructure
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    An overlapping protein-coding region in influenza A virus segment 3 modulates the host response (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-30
    Description: Influenza A virus (IAV) infection leads to variable and imperfectly understood pathogenicity. We report that segment 3 of the virus contains a second open reading frame ("X-ORF"), accessed via ribosomal frameshifting. The frameshift product, termed PA-X, comprises the endonuclease domain of the viral PA protein with a C-terminal domain encoded by the X-ORF and functions to repress cellular gene expression. PA-X also modulates IAV virulence in a mouse infection model, acting to decrease pathogenicity. Loss of PA-X expression leads to changes in the kinetics of the global host response, which notably includes increases in inflammatory, apoptotic, and T lymphocyte-signaling pathways. Thus, we have identified a previously unknown IAV protein that modulates the host response to infection, a finding with important implications for understanding IAV pathogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552242/" 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/PMC3552242/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jagger, B W -- Wise, H M -- Kash, J C -- Walters, K-A -- Wills, N M -- Xiao, Y-L -- Dunfee, R L -- Schwartzman, L M -- Ozinsky, A -- Bell, G L -- Dalton, R M -- Lo, A -- Efstathiou, S -- Atkins, J F -- Firth, A E -- Taubenberger, J K -- Digard, P -- 073126/Wellcome Trust/United Kingdom -- 088789/Wellcome Trust/United Kingdom -- G0700815/Medical Research Council/United Kingdom -- G0700815(82260)/Medical Research Council/United Kingdom -- G9800943/Medical Research Council/United Kingdom -- MR/J002232/1/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):199-204. doi: 10.1126/science.1222213. Epub 2012 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22745253" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Codon ; Conserved Sequence ; Female ; *Frameshifting, Ribosomal ; Gene Expression Regulation ; Genome, Viral ; HEK293 Cells ; Humans ; Influenza A Virus, H1N1 Subtype/*genetics/growth & development/pathogenicity ; Influenza A virus/*genetics/metabolism ; Lung/pathology/virology ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Mutation ; *Open Reading Frames ; Orthomyxoviridae Infections/genetics/immunology/pathology/*virology ; Protein Interaction Domains and Motifs ; Proteome ; RNA Replicase/chemistry/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Viral/genetics/metabolism ; Reassortant Viruses/genetics ; Repressor Proteins/chemistry/*genetics/*metabolism ; Viral Nonstructural Proteins/chemistry/*genetics/*metabolism ; Viral Proteins/biosynthesis/chemistry/*genetics/*metabolism ; Virus Replication
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    Benefits and risks of influenza research: lessons learned (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-23
    Description: Given the yearly challenge of seasonal influenza and the potential catastrophic consequences of future pandemics, the need for intensive basic and clinical influenza research is unquestionable. Although the fruits of decades of research have enabled dramatic improvements in our ability to prevent and treat influenza, many fundamental questions remain, including those related to the complex factors associated with host switching and transmission of influenza viruses. Recent public concern over two H5N1 influenza manuscripts that studied the transmissibility of influenza viruses has triggered intense discussion on dual-use research and the way forward.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fauci, Anthony S -- Collins, Francis S -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1522-3. doi: 10.1126/science.1224305.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institutes of Health, Bethesda, MD 20892, USA. afauci@niaid.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723407" target="_blank"〉PubMed〈/a〉
    Keywords: Advisory Committees ; Animals ; *Biomedical Research ; Bioterrorism ; Disease Models, Animal ; Evolution, Molecular ; Ferrets ; Humans ; Influenza A Virus, H5N1 Subtype/*genetics/*pathogenicity ; Influenza, Human/mortality/transmission/*virology ; Mutation ; National Institutes of Health (U.S.) ; Orthomyxoviridae Infections/transmission/*virology ; Public Health ; Public Policy ; *Publishing ; Reassortant Viruses/genetics/pathogenicity ; Risk Assessment ; Security Measures ; United States
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    A core metabolic enzyme mediates resistance to phosphine gas (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-11-10
    Description: Phosphine is a small redox-active gas that is used to protect global grain reserves, which are threatened by the emergence of phosphine resistance in pest insects. We find that polymorphisms responsible for genetic resistance cluster around the redox-active catalytic disulfide or the dimerization interface of dihydrolipoamide dehydrogenase (DLD) in insects (Rhyzopertha dominica and Tribolium castaneum) and nematodes (Caenorhabditis elegans). DLD is a core metabolic enzyme representing a new class of resistance factor for a redox-active metabolic toxin. It participates in four key steps of core metabolism, and metabolite profiles indicate that phosphine exposure in mutant and wild-type animals affects these steps differently. Mutation of DLD in C. elegans increases arsenite sensitivity. This specific vulnerability may be exploited to control phosphine-resistant insects and safeguard food security.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schlipalius, David I -- Valmas, Nicholas -- Tuck, Andrew G -- Jagadeesan, Rajeswaran -- Ma, Li -- Kaur, Ramandeep -- Goldinger, Anita -- Anderson, Cameron -- Kuang, Jujiao -- Zuryn, Steven -- Mau, Yosep S -- Cheng, Qiang -- Collins, Patrick J -- Nayak, Manoj K -- Schirra, Horst Joachim -- Hilliard, Massimo A -- Ebert, Paul R -- R01NS060129/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 9;338(6108):807-10. doi: 10.1126/science.1224951.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Agri-Science Queensland, Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, QLD 4001, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23139334" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arsenicals/pharmacology ; Arsenites/pharmacology ; Beetles/drug effects/*enzymology/genetics/metabolism ; Caenorhabditis elegans/drug effects/*enzymology/genetics/metabolism ; Caenorhabditis elegans Proteins/chemistry/genetics/metabolism ; Catalytic Domain ; Dihydrolipoamide Dehydrogenase/chemistry/*genetics/metabolism ; Insect Proteins/chemistry/genetics/metabolism ; Insecticide Resistance/*genetics ; *Insecticides/pharmacology ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Mutation ; Oxidation-Reduction ; Pesticides ; *Phosphines/pharmacology ; Polymorphism, Genetic ; Protein Multimerization ; Tribolium/drug effects/*enzymology/genetics/metabolism
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    Vitamin K2 is a mitochondrial electron carrier that rescues pink1 deficiency (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-05-15
    Description: Human UBIAD1 localizes to mitochondria and converts vitamin K(1) to vitamin K(2). Vitamin K(2) is best known as a cofactor in blood coagulation, but in bacteria it is a membrane-bound electron carrier. Whether vitamin K(2) exerts a similar carrier function in eukaryotic cells is unknown. We identified Drosophila UBIAD1/Heix as a modifier of pink1, a gene mutated in Parkinson's disease that affects mitochondrial function. We found that vitamin K(2) was necessary and sufficient to transfer electrons in Drosophila mitochondria. Heix mutants showed severe mitochondrial defects that were rescued by vitamin K(2), and, similar to ubiquinone, vitamin K(2) transferred electrons in Drosophila mitochondria, resulting in more efficient adenosine triphosphate (ATP) production. Thus, mitochondrial dysfunction was rescued by vitamin K(2) that serves as a mitochondrial electron carrier, helping to maintain normal ATP production.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vos, Melissa -- Esposito, Giovanni -- Edirisinghe, Janaka N -- Vilain, Sven -- Haddad, Dominik M -- Slabbaert, Jan R -- Van Meensel, Stefanie -- Schaap, Onno -- De Strooper, Bart -- Meganathan, R -- Morais, Vanessa A -- Verstreken, Patrik -- New York, N.Y. -- Science. 2012 Jun 8;336(6086):1306-10. doi: 10.1126/science.1218632. Epub 2012 May 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉VIB Center for the Biology of Disease, Leuven, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582012" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Drosophila/genetics/*metabolism ; Drosophila Proteins/deficiency/*genetics/*metabolism ; *Electron Transport ; Escherichia coli/metabolism ; Flight, Animal ; Genes, Insect ; Membrane Potential, Mitochondrial ; Mitochondria/*metabolism/ultrastructure ; Mitochondria, Muscle/metabolism/ultrastructure ; Mutation ; Oxygen Consumption ; Protein-Serine-Threonine Kinases/deficiency/*genetics/*metabolism ; Ubiquinone/metabolism ; Ubiquitin-Protein Ligases/genetics ; Vitamin K 2/*metabolism/pharmacology
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    Structural biology. Versatility from protein disorder (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Babu, M Madan -- Kriwacki, Richard W -- Pappu, Rohit V -- MC_U105185859/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 Sep 21;337(6101):1460-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. madanm@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997313" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Computer Simulation ; Evolution, Molecular ; Mutation ; Protein Binding ; Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/*metabolism
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    Chitin-induced dimerization activates a plant immune receptor (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-02
    Description: Pattern recognition receptors confer plant resistance to pathogen infection by recognizing the conserved pathogen-associated molecular patterns. The cell surface receptor chitin elicitor receptor kinase 1 of Arabidopsis (AtCERK1) directly binds chitin through its lysine motif (LysM)-containing ectodomain (AtCERK1-ECD) to activate immune responses. The crystal structure that we solved of an AtCERK1-ECD complexed with a chitin pentamer reveals that their interaction is primarily mediated by a LysM and three chitin residues. By acting as a bivalent ligand, a chitin octamer induces AtCERK1-ECD dimerization that is inhibited by shorter chitin oligomers. A mutation attenuating chitin-induced AtCERK1-ECD dimerization or formation of nonproductive AtCERK1 dimer by overexpression of AtCERK1-ECD compromises AtCERK1-mediated signaling in plant cells. Together, our data support the notion that chitin-induced AtCERK1 dimerization is critical for its activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Tingting -- Liu, Zixu -- Song, Chuanjun -- Hu, Yunfei -- Han, Zhifu -- She, Ji -- Fan, Fangfang -- Wang, Jiawei -- Jin, Changwen -- Chang, Junbiao -- Zhou, Jian-Min -- Chai, Jijie -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1160-4. doi: 10.1126/science.1218867.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654057" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylglucosamine/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/immunology/*metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Chitin/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphorylation ; Plants, Genetically Modified ; Protein Multimerization ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry/genetics/*metabolism ; Receptors, Pattern Recognition/*chemistry/genetics/*metabolism ; Signal Transduction
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    Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-07-17
    Description: The Paisley Caves in Oregon record the oldest directly dated human remains (DNA) in the Western Hemisphere. More than 100 high-precision radiocarbon dates show that deposits containing artifacts and coprolites ranging in age from 12,450 to 2295 (14)C years ago are well stratified. Western Stemmed projectile points were recovered in deposits dated to 11,070 to 11,340 (14)C years ago, a time contemporaneous with or preceding the Clovis technology. There is no evidence of diagnostic Clovis technology at the site. These two distinct technologies were parallel developments, not the product of a unilinear technological evolution. "Blind testing" analysis of coprolites by an independent laboratory confirms the presence of human DNA in specimens of pre-Clovis age. The colonization of the Americas involved multiple technologically divergent, and possibly genetically divergent, founding groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenkins, Dennis L -- Davis, Loren G -- Stafford, Thomas W Jr -- Campos, Paula F -- Hockett, Bryan -- Jones, George T -- Cummings, Linda Scott -- Yost, Chad -- Connolly, Thomas J -- Yohe, Robert M 2nd -- Gibbons, Summer C -- Raghavan, Maanasa -- Rasmussen, Morten -- Paijmans, Johanna L A -- Hofreiter, Michael -- Kemp, Brian M -- Barta, Jodi Lynn -- Monroe, Cara -- Gilbert, M Thomas P -- Willerslev, Eske -- New York, N.Y. -- Science. 2012 Jul 13;337(6091):223-8. doi: 10.1126/science.1218443.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA. djenkins@uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798611" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Archaeology ; *Caves ; DNA/analysis ; Emigration and Immigration/history ; Feces ; *Fossils ; History, Ancient ; Humans ; Molecular Sequence Data ; North America ; Oregon ; Population Dynamics ; Radiometric Dating ; Rodentia ; Technology/history ; Time
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    Avian influenza. For young scientists, a wild ride (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Enserink, Martin -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1495. doi: 10.1126/science.336.6088.1495.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723388" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cough ; Ferrets ; *Influenza A Virus, H5N1 Subtype/genetics/pathogenicity ; Mutation ; Orthomyxoviridae Infections/transmission/*virology ; Publishing ; *Research Personnel ; Sneezing
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    Evolution of shape by multiple regulatory changes to a growth gene (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-01
    Description: The genetic changes responsible for morphological differences between species are largely unidentified. Such changes can involve modifications of growth that are relevant to understanding evolution, development, and disease. We identified a gene that induces male-specific wing size and shape differences between Nasonia wasp species. Fine-scale mapping and in situ hybridization reveal that changes in at least three regions (two strictly in noncoding sequence) around the gene unpaired-like (upd-like) cause changes in spatial and temporal expression of upd-like in the developing wing and corresponding changes in wing width. Upd-like shows homology to the Drosophila unpaired gene, a well-studied signaling protein that regulates cell proliferation and differentiation. Our results indicate how multiple changes in the regulation of upd-like are involved in microevolution of morphological and sex-specific differences between species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520604/" 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/PMC3520604/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loehlin, David W -- Werren, John H -- 5R01 GM070026-04/GM/NIGMS NIH HHS/ -- 5R24 GM084917-04/GM/NIGMS NIH HHS/ -- R01 GM070026/GM/NIGMS NIH HHS/ -- R24 GM084917/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):943-7. doi: 10.1126/science.1215193.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Rochester, Rochester, NY 14627, USA. loehlin@wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363002" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Cloning, Molecular ; Drosophila/genetics ; Drosophila Proteins/genetics ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genes, Insect ; Insect Proteins/*genetics/metabolism ; Male ; Molecular Sequence Data ; Morphogenesis/genetics ; Organ Size ; Quantitative Trait Loci ; Sex Characteristics ; Species Specificity ; Transcription Factors/genetics ; Wasps/anatomy & histology/*genetics/*growth & development ; Wings, Animal/*anatomy & histology/*growth & development/metabolism
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    The shared antibiotic resistome of soil bacteria and human pathogens (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-01
    Description: Soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. Using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens. We describe multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics (beta-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines) that have perfect nucleotide identity to genes from diverse human pathogens. This identity encompasses noncoding regions as well as multiple mobilization sequences, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070369/" 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/PMC4070369/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forsberg, Kevin J -- Reyes, Alejandro -- Wang, Bin -- Selleck, Elizabeth M -- Sommer, Morten O A -- Dantas, Gautam -- T32 GM007067/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1107-11. doi: 10.1126/science.1220761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936781" target="_blank"〉PubMed〈/a〉
    Keywords: Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics/pathogenicity ; Base Sequence ; Drug Resistance, Multiple, Bacterial/*genetics ; High-Throughput Screening Assays ; Humans ; Metagenome/*drug effects/*genetics ; Metagenomics ; Molecular Sequence Data ; *Soil Microbiology ; Sulfonamides/pharmacology ; Tetracyclines/pharmacology ; beta-Lactams/pharmacology
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    Single-molecule fluorescence experiments determine protein folding transition path times (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-01
    Description: The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs as the free-energy barrier between two states is crossed. It is a single-molecule property that contains all the mechanistic information on how a process occurs. As a step toward observing transition paths in protein folding, we determined the average transition-path time for a fast- and a slow-folding protein from a photon-by-photon analysis of fluorescence trajectories in single-molecule Forster resonance energy transfer experiments. Whereas the folding rate coefficients differ by a factor of 10,000, the transition-path times differ by a factor of less than 5, which shows that a fast- and a slow-folding protein take almost the same time to fold when folding actually happens. A very simple model based on energy landscape theory can explain this result.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878298/" 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/PMC3878298/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- McHale, Kevin -- Louis, John M -- Eaton, William A -- Z99 DK999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):981-4. doi: 10.1126/science.1215768.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD 20892-0520, USA. chunghoi@niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363011" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Carrier Proteins/*chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Photons ; Protein Conformation ; *Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thermodynamics
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    Personalized medicine. New cystic fibrosis drug offers hope, at a price (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaiser, Jocelyn -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):645. doi: 10.1126/science.335.6069.645.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323790" target="_blank"〉PubMed〈/a〉
    Keywords: Aminophenols/economics/*therapeutic use ; Cystic Fibrosis/*drug therapy/*genetics ; Cystic Fibrosis Transmembrane Conductance ; Regulator/chemistry/*genetics/metabolism ; Drug Approval ; Drug Costs ; Humans ; Molecular Targeted Therapy ; Mutation ; Precision Medicine ; Quinolones/economics/*therapeutic use ; Small Molecule Libraries ; United States ; United States Food and Drug Administration
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    The amyloid precursor protein has a flexible transmembrane domain and binds cholesterol (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-02
    Description: C99 is the transmembrane carboxyl-terminal domain of the amyloid precursor protein that is cleaved by gamma-secretase to release the amyloid-beta polypeptides, which are associated with Alzheimer's disease. Nuclear magnetic resonance and electron paramagnetic resonance spectroscopy show that the extracellular amino terminus of C99 includes a surface-embedded "N-helix" followed by a short "N-loop" connecting to the transmembrane domain (TMD). The TMD is a flexibly curved alpha helix, making it well suited for processive cleavage by gamma-secretase. Titration of C99 reveals a binding site for cholesterol, providing mechanistic insight into how cholesterol promotes amyloidogenesis. Membrane-buried GXXXG motifs (G, Gly; X, any amino acid), which have an established role in oligomerization, were also shown to play a key role in cholesterol binding. The structure and cholesterol binding properties of C99 may aid in the design of Alzheimer's therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528355/" 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/PMC3528355/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barrett, Paul J -- Song, Yuanli -- Van Horn, Wade D -- Hustedt, Eric J -- Schafer, Johanna M -- Hadziselimovic, Arina -- Beel, Andrew J -- Sanders, Charles R -- F31 NS077681/NS/NINDS NIH HHS/ -- P01 GM080513/GM/NIGMS NIH HHS/ -- T32 GM008320/GM/NIGMS NIH HHS/ -- T32 GM08320/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1168-71. doi: 10.1126/science.1219988.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654059" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amyloid beta-Protein Precursor/*chemistry/genetics/*metabolism ; Binding Sites ; Cholesterol/*metabolism ; Electron Spin Resonance Spectroscopy ; Humans ; Micelles ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    The transcription factor c-Maf controls touch receptor development and function (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-22
    Description: The sense of touch relies on detection of mechanical stimuli by specialized mechanosensory neurons. The scarcity of molecular data has made it difficult to analyze development of mechanoreceptors and to define the basis of their diversity and function. We show that the transcription factor c-Maf/c-MAF is crucial for mechanosensory function in mice and humans. The development and function of several rapidly adapting mechanoreceptor types are disrupted in c-Maf mutant mice. In particular, Pacinian corpuscles, a type of mechanoreceptor specialized to detect high-frequency vibrations, are severely atrophied. In line with this, sensitivity to high-frequency vibration is reduced in humans carrying a dominant mutation in the c-MAF gene. Thus, our work identifies a key transcription factor specifying development and function of mechanoreceptors and their end organs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wende, Hagen -- Lechner, Stefan G -- Cheret, Cyril -- Bourane, Steeve -- Kolanczyk, Maria E -- Pattyn, Alexandre -- Reuter, Katja -- Munier, Francis L -- Carroll, Patrick -- Lewin, Gary R -- Birchmeier, Carmen -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1373-6. doi: 10.1126/science.1214314. Epub 2012 Feb 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Biology, Max Delbruck Center (MDC) for Molecular Medicine, Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22345400" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ganglia, Spinal/cytology/embryology ; Gene Expression Regulation, Developmental ; Humans ; Maf Transcription Factors, Large/genetics/metabolism ; Mechanoreceptors/*cytology/*physiology ; Mice ; Mutation ; Pacinian Corpuscles/cytology/physiology ; Proto-Oncogene Proteins c-maf/genetics/*metabolism ; Proto-Oncogene Proteins c-ret/genetics/metabolism ; Skin/innervation ; *Touch ; Vibration
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    Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-17
    Description: In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377438/" 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/PMC3377438/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gagnon, Matthieu G -- Seetharaman, Sai V -- Bulkley, David -- Steitz, Thomas A -- GM022778/GM/NIGMS NIH HHS/ -- P01 GM022778/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1370-2. doi: 10.1126/science.1217443.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422986" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carboxylic Ester Hydrolases/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; Protein Structure, Tertiary ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; RNA, Transfer, Met/chemistry/metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry/metabolism/ultrastructure
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    Assembly of an evolutionarily new pathway for alpha-pyrone biosynthesis in Arabidopsis (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-28
    Description: Plants possess arrays of functionally diverse specialized metabolites, many of which are distributed taxonomically. Here, we describe the evolution of a class of substituted alpha-pyrone metabolites in Arabidopsis, which we have named arabidopyrones. The biosynthesis of arabidopyrones requires a cytochrome P450 enzyme (CYP84A4) to generate the catechol-substituted substrate for an extradiol ring-cleavage dioxygenase (AtLigB). Unlike other ring-cleavage-derived plant metabolites made from tyrosine, arabidopyrones are instead derived from phenylalanine through the early steps of phenylpropanoid metabolism. Whereas CYP84A4, an Arabidopsis-specific paralog of the lignin-biosynthetic enzyme CYP84A1, has neofunctionalized relative to its ancestor, AtLigB homologs are widespread among land plants and many bacteria. This study exemplifies the rapid evolution of a biochemical pathway formed by the addition of a new biological activity into an existing metabolic infrastructure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weng, Jing-Ke -- Li, Yi -- Mo, Huaping -- Chapple, Clint -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):960-4. doi: 10.1126/science.1221614.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923580" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/enzymology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Biosynthetic Pathways ; Catalytic Domain ; Cytochrome P-450 Enzyme System/chemistry/genetics/*metabolism ; Dioxygenases/genetics/metabolism ; Evolution, Molecular ; Gene Duplication ; Genome, Plant ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phenylalanine/metabolism ; Phylogeny ; Plant Stems/metabolism ; Plants, Genetically Modified ; Pyrones/chemistry/*metabolism
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    Tricking the guard: exploiting plant defense for disease susceptibility (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-10-23
    Description: Typically, pathogens deploy virulence effectors to disable defense. Plants defeat effectors with resistance proteins that guard effector targets. We found that a pathogen exploits a resistance protein by activating it to confer susceptibility in Arabidopsis. The guard mechanism of plant defense is recapitulated by interactions among victorin (an effector produced by the necrotrophic fungus Cochliobolus victoriae), TRX-h5 (a defense-associated thioredoxin), and LOV1 (an Arabidopsis susceptibility protein). In LOV1's absence, victorin inhibits TRX-h5, resulting in compromised defense but not disease by C. victoriae. In LOV1's presence, victorin binding to TRX-h5 activates LOV1 and elicits a resistance-like response that confers disease susceptibility. We propose that victorin is, or mimics, a conventional pathogen virulence effector that was defeated by LOV1 and confers virulence to C. victoriae solely because it incites defense.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125361/" 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/PMC4125361/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lorang, J -- Kidarsa, T -- Bradford, C S -- Gilbert, B -- Curtis, M -- Tzeng, S-C -- Maier, C S -- Wolpert, T J -- BB/D016541/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H008039/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- P30 ES000210/ES/NIEHS NIH HHS/ -- P30ES200210/ES/NIEHS NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):659-62. doi: 10.1126/science.1226743. Epub 2012 Oct 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23087001" target="_blank"〉PubMed〈/a〉
    Keywords: *Arabidopsis/immunology/metabolism/microbiology ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Ascomycota/metabolism/*pathogenicity ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Disease Susceptibility ; Fungal Proteins/*metabolism ; Mutation ; Mycotoxins/*metabolism ; Oxidation-Reduction ; *Plant Diseases/immunology/microbiology ; *Plant Immunity ; Protein Binding ; Protein Interaction Domains and Motifs ; Thioredoxins/genetics/*metabolism ; Tobacco/genetics/metabolism ; Virulence Factors/*metabolism
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    Structural basis for prereceptor modulation of plant hormones by GH3 proteins (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-26
    Description: Acyl acid amido synthetases of the GH3 family act as critical prereceptor modulators of plant hormone action; however, the molecular basis for their hormone selectivity is unclear. Here, we report the crystal structures of benzoate-specific Arabidopsis thaliana AtGH3.12/PBS3 and jasmonic acid-specific AtGH3.11/JAR1. These structures, combined with biochemical analysis, define features for the conjugation of amino acids to diverse acyl acid substrates and highlight the importance of conformational changes in the carboxyl-terminal domain for catalysis. We also identify residues forming the acyl acid binding site across the GH3 family and residues critical for amino acid recognition. Our results demonstrate how a highly adaptable three-dimensional scaffold is used for the evolution of promiscuous activity across an enzyme family for modulation of plant signaling molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westfall, Corey S -- Zubieta, Chloe -- Herrmann, Jonathan -- Kapp, Ulrike -- Nanao, Max H -- Jez, Joseph M -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1708-11. doi: 10.1126/science.1221863. Epub 2012 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Washington University, St. Louis, MO 63130, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628555" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Arabidopsis ; Arabidopsis Proteins/*chemistry/metabolism ; Benzoates/chemistry ; Binding Sites ; Crystallography, X-Ray ; Cyclopentanes/chemistry ; Indoleacetic Acids/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleotidyltransferases/*chemistry/metabolism ; Oxylipins/chemistry ; Plant Growth Regulators/chemistry/metabolism ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Substrate Specificity
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    Population genomics of early events in the ecological differentiation of bacteria (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-04-12
    Description: Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337212/" 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/PMC3337212/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, B Jesse -- Friedman, Jonathan -- Cordero, Otto X -- Preheim, Sarah P -- Timberlake, Sonia C -- Szabo, Gitta -- Polz, Martin F -- Alm, Eric J -- U54 GM088558/GM/NIGMS NIH HHS/ -- U54 GM088558-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Apr 6;336(6077):48-51. doi: 10.1126/science.1218198.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22491847" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Bacterial/genetics ; *Ecosystem ; *Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Oceans and Seas ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Seawater/*microbiology ; *Selection, Genetic ; Vibrio/classification/*genetics
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    Neuroscience. All eyes on RNA (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-12-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garber, Ken -- New York, N.Y. -- Science. 2012 Dec 7;338(6112):1282-3. doi: 10.1126/science.338.6112.1282.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23224536" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis/*genetics/metabolism ; Chromosomes, Human, Pair 9/genetics ; DNA-Binding Proteins/genetics/metabolism ; Dementia/genetics/metabolism ; Humans ; Motor Neurons/metabolism/pathology ; Mutation ; Proteins/genetics ; RNA/*metabolism ; RNA-Binding Protein FUS/genetics/metabolism ; RNA-Binding Proteins/*genetics/metabolism
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    Cytoplasmic ATP hydrolysis powers transport of lipopolysaccharide across the periplasm in E. coli (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-11-10
    Description: Millions of molecules of lipopolysaccharide (LPS) must be assembled on the Escherichia coli cell surface each time the cell divides. The biogenesis of LPS requires seven essential lipopolysaccharide transport (Lpt) proteins to move LPS from the inner membrane through the periplasm to the cell surface. However, no intermediate transport states have been observed. We developed methods to observe intermediate LPS molecules bound to Lpt proteins in the process of being transported in vivo. Movement of individual LPS molecules along these binding sites required multiple rounds of adenosine triphosphate (ATP) hydrolysis in vitro, which suggests that ATP is used to push a continuous stream of LPS through a transenvelope bridge in discrete steps against a concentration gradient.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552488/" 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/PMC3552488/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Okuda, Suguru -- Freinkman, Elizaveta -- Kahne, Daniel -- AI081059/AI/NIAID NIH HHS/ -- GM066174/GM/NIGMS NIH HHS/ -- R01 AI081059/AI/NIAID NIH HHS/ -- R01 GM066174/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1214-7. doi: 10.1126/science.1228984. Epub 2012 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23138981" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/chemistry/metabolism ; Adenosine Triphosphate/*metabolism ; Bacterial Proteins/chemistry/metabolism ; Biological Transport ; Carrier Proteins/chemistry/genetics/metabolism ; Cytoplasm/*metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Hydrolysis ; Lipopolysaccharides/*metabolism ; Membrane Proteins/chemistry/genetics/metabolism ; Mutation ; Periplasm/*metabolism ; Protein Conformation
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    Glacial survival of boreal trees in northern Scandinavia (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-03
    Description: It is commonly believed that trees were absent in Scandinavia during the last glaciation and first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 years ago. Here, we show the presence of a rare mitochondrial DNA haplotype of spruce that appears unique to Scandinavia and with its highest frequency to the west-an area believed to sustain ice-free refugia during most of the last ice age. We further show the survival of DNA from this haplotype in lake sediments and pollen of Trondelag in central Norway dating back ~10,300 years and chloroplast DNA of pine and spruce in lake sediments adjacent to the ice-free Andoya refugium in northwestern Norway as early as ~22,000 and 17,700 years ago, respectively. Our findings imply that conifer trees survived in ice-free refugia of Scandinavia during the last glaciation, challenging current views on survival and spread of trees as a response to climate changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parducci, Laura -- Jorgensen, Tina -- Tollefsrud, Mari Mette -- Elverland, Ellen -- Alm, Torbjorn -- Fontana, Sonia L -- Bennett, K D -- Haile, James -- Matetovici, Irina -- Suyama, Yoshihisa -- Edwards, Mary E -- Andersen, Kenneth -- Rasmussen, Morten -- Boessenkool, Sanne -- Coissac, Eric -- Brochmann, Christian -- Taberlet, Pierre -- Houmark-Nielsen, Michael -- Larsen, Nicolaj Krog -- Orlando, Ludovic -- Gilbert, M Thomas P -- Kjaer, Kurt H -- Alsos, Inger Greve -- Willerslev, Eske -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1083-6. doi: 10.1126/science.1216043.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383845" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Europe ; *Fossils ; Geologic Sediments ; Haplotypes ; *Ice Cover ; Molecular Sequence Data ; Mutation ; Norway ; *Picea/genetics ; *Pinus/genetics ; Scandinavian and Nordic Countries ; Time
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    The crystal structure of TAL effector PthXo1 bound to its DNA target (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-01-10
    Description: DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427646/" 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/PMC3427646/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mak, Amanda Nga-Sze -- Bradley, Philip -- Cernadas, Raul A -- Bogdanove, Adam J -- Stoddard, Barry L -- R01 GM049857/GM/NIGMS NIH HHS/ -- R01 GM088277/GM/NIGMS NIH HHS/ -- R01 GM098861/GM/NIGMS NIH HHS/ -- R01GM098861/GM/NIGMS NIH HHS/ -- RL1 0CA833133/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):716-9. doi: 10.1126/science.1216211. Epub 2012 Jan 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025 Seattle, WA 98019, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223736" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; DNA, Plant/*chemistry/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; High-Throughput Screening Assays ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Processes ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repetitive Sequences, Amino Acid ; Virulence Factors/*chemistry/*metabolism ; Xanthomonas/*chemistry/pathogenicity
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    Imaginal discs secrete insulin-like peptide 8 to mediate plasticity of growth and maturation (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-05-05
    Description: Developing animals frequently adjust their growth programs and/or their maturation or metamorphosis to compensate for growth disturbances (such as injury or tumor) and ensure normal adult size. Such plasticity entails tissue and organ communication to preserve their proportions and symmetry. Here, we show that imaginal discs autonomously activate DILP8, a Drosophila insulin-like peptide, to communicate abnormal growth and postpone maturation. DILP8 delays metamorphosis by inhibiting ecdysone biosynthesis, slowing growth in the imaginal discs, and generating normal-sized animals. Loss of dilp8 yields asymmetric individuals with an unusually large variation in size and a more varied time of maturation. Thus, DILP8 is a fundamental element of the hitherto ill-defined machinery governing the plasticity that ensures developmental stability and robustness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garelli, Andres -- Gontijo, Alisson M -- Miguela, Veronica -- Caparros, Esther -- Dominguez, Maria -- New York, N.Y. -- Science. 2012 May 4;336(6081):579-82. doi: 10.1126/science.1216735.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas-Universidad Miguel Hernandez de Elche, Sant Joan d'Alacant, 03550 Alicante, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556250" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apoptosis ; Drosophila Proteins/chemistry/*genetics/*metabolism ; Drosophila melanogaster/*genetics/*growth & development/metabolism ; Ecdysone/biosynthesis ; Ethyl Methanesulfonate/pharmacology ; Gene Expression Regulation, Developmental ; Genes, Insect ; Imaginal Discs/growth & development/*physiology ; Intercellular Signaling Peptides and Proteins/chemistry/*genetics/metabolism ; Intracellular Signaling Peptides and Proteins/genetics/metabolism ; Larva/growth & development ; *Metamorphosis, Biological/genetics ; Molecular Sequence Data ; Neoplasms, Experimental/genetics/metabolism/pathology ; Peptide Initiation Factors/genetics/metabolism ; Pupa/growth & development ; Regeneration
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    Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-18
    Description: It is held as a paradigm that ribosomally synthesized peptides and proteins contain only l-amino acids. We demonstrate a ribosomal origin of the marine sponge-derived polytheonamides, exceptionally potent, giant natural-product toxins. Isolation of the biosynthetic genes from the sponge metagenome revealed a bacterial gene architecture. Only six candidate enzymes were identified for 48 posttranslational modifications, including 18 epimerizations and 17 methylations of nonactivated carbon centers. Three enzymes were functionally validated, which showed that a radical S-adenosylmethionine enzyme is responsible for the unidirectional epimerization of multiple and different amino acids. Collectively, these complex alterations create toxins that function as unimolecular minimalistic ion channels with near-femtomolar activity. This study broadens the biosynthetic scope of ribosomal systems and creates new opportunities for peptide and protein bioengineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freeman, Michael F -- Gurgui, Cristian -- Helf, Maximilian J -- Morinaka, Brandon I -- Uria, Agustinus R -- Oldham, Neil J -- Sahl, Hans-Georg -- Matsunaga, Shigeki -- Piel, Jorn -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):387-90. doi: 10.1126/science.1226121. Epub 2012 Sep 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22983711" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Ion Channels/biosynthesis/*metabolism ; Marine Toxins/biosynthesis/*metabolism ; *Metagenome ; Methylation ; Molecular Sequence Data ; Protein Biosynthesis ; *Protein Processing, Post-Translational ; Proteins/*metabolism ; Ribosomes/metabolism ; S-Adenosylmethionine/metabolism ; Theonella/*microbiology
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    Direct observation of cotranscriptional folding in an adenine riboswitch (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-10-23
    Description: Growing RNA chains fold cotranscriptionally as they are synthesized by RNA polymerase. Riboswitches, which regulate gene expression by adopting alternative RNA folds, are sensitive to cotranscriptional events. We developed an optical-trapping assay to follow the cotranscriptional folding of a nascent RNA and used it to monitor individual transcripts of the pbuE adenine riboswitch, visualizing distinct folding transitions. We report a particular folding signature for the riboswitch aptamer whose presence directs the gene-regulatory transcription outcome, and we measured the termination frequency as a function of adenine level and tension applied to the RNA. Our results demonstrate that the outcome is kinetically controlled. These experiments furnish a means to observe conformational switching in real time and enable the precise mapping of events during cotranscriptional folding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496414/" 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/PMC3496414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frieda, Kirsten L -- Block, Steven M -- R37 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):397-400. doi: 10.1126/science.1225722.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23087247" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*chemistry/metabolism ; Bacillus subtilis/genetics ; Base Sequence ; Kinetics ; Molecular Sequence Data ; *Optical Tweezers ; *RNA Folding ; Riboswitch/*genetics ; *Transcription, Genetic
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    RNA editing underlies temperature adaptation in K+ channels from polar octopuses (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-10
    Description: To operate in the extreme cold, ion channels from psychrophiles must have evolved structural changes to compensate for their thermal environment. A reasonable assumption would be that the underlying adaptations lie within the encoding genes. Here, we show that delayed rectifier K(+) channel genes from an Antarctic and a tropical octopus encode channels that differ at only four positions and display very similar behavior when expressed in Xenopus oocytes. However, the transcribed messenger RNAs are extensively edited, creating functional diversity. One editing site, which recodes an isoleucine to a valine in the channel's pore, greatly accelerates gating kinetics by destabilizing the open state. This site is extensively edited in both Antarctic and Arctic species, but mostly unedited in tropical species. Thus adenosine-to-inosine RNA editing can respond to the physical environment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4219319/" 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/PMC4219319/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garrett, Sandra -- Rosenthal, Joshua J C -- 2 U54 NS039405-06/NS/NINDS NIH HHS/ -- FNS064774A/PHS HHS/ -- G12 RR 03051/RR/NCRR NIH HHS/ -- R01 NS064259/NS/NINDS NIH HHS/ -- U54 NS039405/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 17;335(6070):848-51. doi: 10.1126/science.1212795. Epub 2012 Jan 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Neurobiology, University of Puerto Rico-Medical Sciences Campus, San Juan 00901, PR.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223739" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/*genetics ; Adenosine/metabolism ; Animals ; Antarctic Regions ; Inosine/metabolism ; Molecular Sequence Data ; Octopodiformes/genetics/*physiology ; *RNA Editing ; Recombinant Proteins ; Shaker Superfamily of Potassium Channels/genetics/*physiology ; Species Specificity ; Xenopus laevis
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    Cell biology. The unusual case of Porcupine (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-28
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4314091/" 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/PMC4314091/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lum, Lawrence -- Clevers, Hans -- R21 HD061303/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):922-3. doi: 10.1126/science.1228179.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. lawrence.lum@utsouthwestern.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923569" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/pharmacology/*therapeutic use ; Clinical Trials, Phase I as Topic ; DNA-Binding Proteins/genetics ; Drug Discovery ; Enzyme Inhibitors/pharmacology/*therapeutic use ; Humans ; Membrane Proteins/*antagonists & inhibitors/genetics/*metabolism ; Molecular Targeted Therapy ; Mutation ; Neoplasms/*drug therapy/genetics/metabolism ; Oncogene Proteins/genetics ; Palmitic Acid/metabolism ; Protein-Serine-Threonine Kinases/genetics ; Wnt Proteins/*metabolism ; Wnt Signaling Pathway/*drug effects
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    IBI* series winner. Adapting to osmotic stress and the process of science (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gasper, Brittany J -- Minchella, Dennis J -- Weaver, Gabriela C -- Csonka, Laszlo N -- Gardner, Stephanie M -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Mar 30;335(6076):1590-1. doi: 10.1126/science.1215582.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22461603" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Awards and Prizes ; Bacterial Proteins/genetics/metabolism ; Genetics, Microbial/*education ; Mutation ; Osmotic Pressure ; Research/*education ; Salmonella typhimurium/*genetics/physiology ; *Stress, Physiological ; Symporters/genetics/metabolism ; Universities
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    dSarm/Sarm1 is required for activation of an injury-induced axon death pathway (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-09
    Description: Axonal and synaptic degeneration is a hallmark of peripheral neuropathy, brain injury, and neurodegenerative disease. Axonal degeneration has been proposed to be mediated by an active autodestruction program, akin to apoptotic cell death; however, loss-of-function mutations capable of potently blocking axon self-destruction have not been described. Here, we show that loss of the Drosophila Toll receptor adaptor dSarm (sterile alpha/Armadillo/Toll-Interleukin receptor homology domain protein) cell-autonomously suppresses Wallerian degeneration for weeks after axotomy. Severed mouse Sarm1 null axons exhibit remarkable long-term survival both in vivo and in vitro, indicating that Sarm1 prodegenerative signaling is conserved in mammals. Our results provide direct evidence that axons actively promote their own destruction after injury and identify dSarm/Sarm1 as a member of an ancient axon death signaling pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Osterloh, Jeannette M -- Yang, Jing -- Rooney, Timothy M -- Fox, A Nicole -- Adalbert, Robert -- Powell, Eric H -- Sheehan, Amy E -- Avery, Michelle A -- Hackett, Rachel -- Logan, Mary A -- MacDonald, Jennifer M -- Ziegenfuss, Jennifer S -- Milde, Stefan -- Hou, Ying-Ju -- Nathan, Carl -- Ding, Aihao -- Brown, Robert H Jr -- Conforti, Laura -- Coleman, Michael -- Tessier-Lavigne, Marc -- Zuchner, Stephan -- Freeman, Marc R -- 5R01-NS050557-05/NS/NINDS NIH HHS/ -- AI030165/AI/NIAID NIH HHS/ -- R01NS059991/NS/NINDS NIH HHS/ -- R01NS072248/NS/NINDS NIH HHS/ -- RC2-NS070-342/NS/NINDS NIH HHS/ -- U54NS065712/NS/NINDS NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jul 27;337(6093):481-4. doi: 10.1126/science.1223899. Epub 2012 Jun 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22678360" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Apoptosis ; Armadillo Domain Proteins/analysis/*genetics/*physiology ; Axons/*physiology/ultrastructure ; Axotomy ; Cell Survival ; Cells, Cultured ; Cytoskeletal Proteins/analysis/*genetics/*physiology ; Denervation ; Drosophila/embryology/genetics/physiology ; Drosophila Proteins/analysis/*genetics/*physiology ; Mice ; Mutation ; Neurons/*physiology ; Sciatic Nerve/injuries/physiology ; Signal Transduction ; Superior Cervical Ganglion/cytology ; Tissue Culture Techniques ; *Wallerian Degeneration
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    An exon splice enhancer primes IGF2:IGF2R binding site structure and function evolution (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-01
    Description: Placental development and genomic imprinting coevolved with parental conflict over resource distribution to mammalian offspring. The imprinted genes IGF2 and IGF2R code for the growth promoter insulin-like growth factor 2 (IGF2) and its inhibitor, mannose 6-phosphate (M6P)/IGF2 receptor (IGF2R), respectively. M6P/IGF2R of birds and fish do not recognize IGF2. In monotremes, which lack imprinting, IGF2 specifically bound M6P/IGF2R via a hydrophobic CD loop. We show that the DNA coding the CD loop in monotremes functions as an exon splice enhancer (ESE) and that structural evolution of binding site loops (AB, HI, FG) improved therian IGF2 affinity. We propose that ESE evolution led to the fortuitous acquisition of IGF2 binding by M6P/IGF2R that drew IGF2R into parental conflict; subsequent imprinting may then have accelerated affinity maturation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658703/" 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/PMC4658703/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Christopher -- Hoppe, Hans-Jurgen -- Rezgui, Dellel -- Strickland, Madeleine -- Forbes, Briony E -- Grutzner, Frank -- Frago, Susana -- Ellis, Rosamund Z -- Wattana-Amorn, Pakorn -- Prince, Stuart N -- Zaccheo, Oliver J -- Nolan, Catherine M -- Mungall, Andrew J -- Jones, E Yvonne -- Crump, Matthew P -- Hassan, A Bassim -- 082352/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 9891/Cancer Research UK/United Kingdom -- A13295/Cancer Research UK/United Kingdom -- A9891/Cancer Research UK/United Kingdom -- C375/Cancer Research UK/United Kingdom -- C429/Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1209-13. doi: 10.1126/science.1228633.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organic and Biological Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197533" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Animals ; Binding Sites/genetics ; Conserved Sequence ; Enhancer Elements, Genetic/*genetics ; *Evolution, Molecular ; *Exons ; Genomic Imprinting ; Humans ; Insulin-Like Growth Factor II/*chemistry/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Receptor, IGF Type 2/*chemistry/classification/genetics ; Species Specificity
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    Recent explosive human population growth has resulted in an excess of rare genetic variants (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-05-15
    Description: Human populations have experienced recent explosive growth, expanding by at least three orders of magnitude over the past 400 generations. This departure from equilibrium skews patterns of genetic variation and distorts basic principles of population genetics. We characterized the empirical signatures of explosive growth on the site frequency spectrum and found that the discrepancy in rare variant abundance across demographic modeling studies is mostly due to differences in sample size. Rapid recent growth increases the load of rare variants and is likely to play a role in the individual genetic burden of complex disease risk. Hence, the extreme recent human population growth needs to be taken into consideration in studying the genetics of complex diseases and traits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586590/" 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/PMC3586590/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keinan, Alon -- Clark, Andrew G -- GM065509/GM/NIGMS NIH HHS/ -- HL102419/HL/NHLBI NIH HHS/ -- R01 HG003229/HG/NHGRI NIH HHS/ -- RC2 HL102419/HL/NHLBI NIH HHS/ -- U01 HG005715/HG/NHGRI NIH HHS/ -- U01-HG005715/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2012 May 11;336(6082):740-3. doi: 10.1126/science.1217283.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA. ak735@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22582263" target="_blank"〉PubMed〈/a〉
    Keywords: Asian Continental Ancestry Group/genetics ; European Continental Ancestry Group/genetics ; Gene Frequency ; Genetic Association Studies ; Genetic Predisposition to Disease ; *Genetic Variation ; Genetics, Population/methods ; Genome, Human ; Haplotypes ; Heterozygote ; Humans ; Models, Genetic ; Mutation ; Polymorphism, Single Nucleotide ; *Population Density ; *Population Growth ; Sample Size ; Sequence Analysis, DNA
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    Vasopressin/oxytocin-related signaling regulates gustatory associative learning in C. elegans (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-01
    Description: Vasopressin- and oxytocin-related neuropeptides are key regulators of animal physiology, including water balance and reproduction. Although these neuropeptides also modulate social behavior and cognition in mammals, the mechanism for influencing behavioral plasticity and the evolutionary origin of these effects are not well understood. Here, we present a functional vasopressin- and oxytocin-like signaling system in the nematode Caenorhabditis elegans. Through activation of its receptor NTR-1, a vasopressin/oxytocin-related neuropeptide, designated nematocin, facilitates the experience-driven modulation of salt chemotaxis, a type of gustatory associative learning in C. elegans. Our study suggests that vasopressin and oxytocin neuropeptides have ancient roles in modulating sensory processing in neural circuits that underlie behavioral plasticity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beets, Isabel -- Janssen, Tom -- Meelkop, Ellen -- Temmerman, Liesbet -- Suetens, Nick -- Rademakers, Suzanne -- Jansen, Gert -- Schoofs, Liliane -- New York, N.Y. -- Science. 2012 Oct 26;338(6106):543-5. doi: 10.1126/science.1226860.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Functional Genomics and Proteomics Unit, KU Leuven, 3000 Leuven, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23112336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biological Evolution ; Caenorhabditis elegans/genetics/*physiology ; Caenorhabditis elegans ; Proteins/agonists/chemistry/genetics/metabolism/pharmacology/*physiology ; Learning/drug effects/*physiology ; Male ; Molecular Sequence Data ; Neuropeptides/chemistry/genetics/pharmacology/*physiology ; Oxytocin/chemistry/genetics/pharmacology/*physiology ; Receptors, G-Protein-Coupled/agonists/genetics/metabolism/*physiology ; Signal Transduction ; Taste/drug effects/*physiology ; Vasopressins/chemistry/genetics/pharmacology/*physiology
    Print ISSN: 0036-8075
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    Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-10
    Description: We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 base pairs long, are derived from unique nonrepetitive sequence, and are enriched in the 5'-untranslated regions of genes, exons, and CpG islands. Chromosomal loci that are enriched sources of microDNA in the adult brain are somatically mosaic for microdeletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the "Thousand Genomes" project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a previously unknown DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703515/" 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/PMC3703515/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shibata, Yoshiyuki -- Kumar, Pankaj -- Layer, Ryan -- Willcox, Smaranda -- Gagan, Jeffrey R -- Griffith, Jack D -- Dutta, Anindya -- ES013773/ES/NIEHS NIH HHS/ -- GM31819/GM/NIGMS NIH HHS/ -- GM84465/GM/NIGMS NIH HHS/ -- P30 CA016086/CA/NCI NIH HHS/ -- R01 CA060499/CA/NCI NIH HHS/ -- R01 CA060499-18/CA/NCI NIH HHS/ -- R01 CA60499/CA/NCI NIH HHS/ -- R01 ES013773/ES/NIEHS NIH HHS/ -- R01 GM031819/GM/NIGMS NIH HHS/ -- R01 GM084465/GM/NIGMS NIH HHS/ -- R01 GM084465-04/GM/NIGMS NIH HHS/ -- T32 GM008136/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Apr 6;336(6077):82-6. doi: 10.1126/science.1213307. Epub 2012 Mar 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22403181" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Animals ; Base Pairing ; Base Sequence ; Brain/*embryology ; Brain Chemistry ; Cell Line ; Cell Line, Tumor ; *Chromosome Deletion ; Chromosomes, Human/*genetics ; Chromosomes, Mammalian/*genetics ; CpG Islands ; DNA Replication ; *DNA, Circular/analysis/chemistry/isolation & purification/metabolism ; Exons ; Germ Cells/chemistry ; Heart/embryology ; Humans ; Liver/chemistry/embryology ; Mice ; Mice, Inbred C57BL ; Microscopy, Electron ; Molecular Sequence Data ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid
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    The structure and catalytic cycle of a sodium-pumping pyrophosphatase (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-07-28
    Description: Membrane-integral pyrophosphatases (M-PPases) are crucial for the survival of plants, bacteria, and protozoan parasites. They couple pyrophosphate hydrolysis or synthesis to Na(+) or H(+) pumping. The 2.6-angstrom structure of Thermotoga maritima M-PPase in the resting state reveals a previously unknown solution for ion pumping. The hydrolytic center, 20 angstroms above the membrane, is coupled to the gate formed by the conserved Asp(243), Glu(246), and Lys(707) by an unusual "coupling funnel" of six alpha helices. Comparison with our 4.0-angstrom resolution structure of the product complex suggests that helix 12 slides down upon substrate binding to open the gate by a simple binding-change mechanism. Below the gate, four helices form the exit channel. Superimposing helices 3 to 6, 9 to 12, and 13 to 16 suggests that M-PPases arose through gene triplication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kellosalo, Juho -- Kajander, Tommi -- Kogan, Konstantin -- Pokharel, Kisun -- Goldman, Adrian -- New York, N.Y. -- Science. 2012 Jul 27;337(6093):473-6. doi: 10.1126/science.1222505.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology and Biophysics Program, Institute of Biotechnology, Post Office Box 65, University of Helsinki, FIN-00014, Finland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22837527" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/metabolism ; Biocatalysis ; Calcium/chemistry ; Catalytic Domain ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Diphosphates/*metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Pyrophosphatases/*chemistry/genetics/*metabolism ; Sodium/*metabolism ; Sodium-Potassium-Exchanging ATPase/*chemistry/genetics/metabolism ; Thermotoga maritima/*enzymology
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    Natural variation in a chloride channel subunit confers avermectin resistance in C. elegans (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-04
    Description: Resistance of nematodes to anthelmintics such as avermectins has emerged as a major global health and agricultural problem, but genes conferring natural resistance to avermectins are unknown. We show that a naturally occurring four-amino-acid deletion in the ligand-binding domain of GLC-1, the alpha-subunit of a glutamate-gated chloride channel, confers resistance to avermectins in the model nematode Caenorhabditis elegans. We also find that the same variant confers resistance to the avermectin-producing bacterium Streptomyces avermitilis. Population-genetic analyses identified two highly divergent haplotypes at the glc-1 locus that have been maintained at intermediate frequencies by long-term balancing selection. These results implicate variation in glutamate-gated chloride channels in avermectin resistance and provide a mechanism by which such resistance can be maintained.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273849/" 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/PMC3273849/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghosh, Rajarshi -- Andersen, Erik C -- Shapiro, Joshua A -- Gerke, Justin P -- Kruglyak, Leonid -- P50-GM071508/GM/NIGMS NIH HHS/ -- R01 HG004321/HG/NHGRI NIH HHS/ -- R01 HG004321-03/HG/NHGRI NIH HHS/ -- R01-HG004321/HG/NHGRI NIH HHS/ -- R37- MH59520/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 3;335(6068):574-8. doi: 10.1126/science.1214318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lewis-Sigler Institute for Integrative Genomics, Department of Ecology and Evolutionary Biology, and Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22301316" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Antinematodal Agents/*pharmacology ; Caenorhabditis elegans/*drug effects/*genetics/physiology ; Caenorhabditis elegans Proteins/chemistry/*genetics/metabolism ; Chloride Channels/chemistry/*genetics/metabolism ; Crosses, Genetic ; Drug Resistance/genetics ; Genes, Helminth ; Genome-Wide Association Study ; Ivermectin/*analogs & derivatives/*pharmacology ; Ligands ; Molecular Sequence Data ; Mutation ; Polymorphism, Single Nucleotide ; Protein Structure, Tertiary ; Quantitative Trait Loci ; Selection, Genetic ; Streptomyces/physiology
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    A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-06-02
    Description: Noscapine is an antitumor alkaloid from opium poppy that binds tubulin, arrests metaphase, and induces apoptosis in dividing human cells. Elucidation of the biosynthetic pathway will enable improvement in the commercial production of noscapine and related bioactive molecules. Transcriptomic analysis revealed the exclusive expression of 10 genes encoding five distinct enzyme classes in a high noscapine-producing poppy variety, HN1. Analysis of an F(2) mapping population indicated that these genes are tightly linked in HN1, and bacterial artificial chromosome sequencing confirmed that they exist as a complex gene cluster for plant alkaloids. Virus-induced gene silencing resulted in accumulation of pathway intermediates, allowing gene function to be linked to noscapine synthesis and a novel biosynthetic pathway to be proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Winzer, Thilo -- Gazda, Valeria -- He, Zhesi -- Kaminski, Filip -- Kern, Marcelo -- Larson, Tony R -- Li, Yi -- Meade, Fergus -- Teodor, Roxana -- Vaistij, Fabian E -- Walker, Carol -- Bowser, Tim A -- Graham, Ian A -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1704-8. doi: 10.1126/science.1220757. Epub 2012 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22653730" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents, Phytogenic/*biosynthesis ; *Genes, Plant ; Molecular Sequence Data ; *Multigene Family ; Noscapine/*metabolism ; Papaver/enzymology/*genetics/metabolism
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    Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-10-16
    Description: The rhg1-b allele of soybean is widely used for resistance against soybean cyst nematode (SCN), the most economically damaging pathogen of soybeans in the United States. Gene silencing showed that genes in a 31-kilobase segment at rhg1-b, encoding an amino acid transporter, an alpha-SNAP protein, and a WI12 (wound-inducible domain) protein, each contribute to resistance. There is one copy of the 31-kilobase segment per haploid genome in susceptible varieties, but 10 tandem copies are present in an rhg1-b haplotype. Overexpression of the individual genes in roots was ineffective, but overexpression of the genes together conferred enhanced SCN resistance. Hence, SCN resistance mediated by the soybean quantitative trait locus Rhg1 is conferred by copy number variation that increases the expression of a set of dissimilar genes in a repeated multigene segment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cook, David E -- Lee, Tong Geon -- Guo, Xiaoli -- Melito, Sara -- Wang, Kai -- Bayless, Adam M -- Wang, Jianping -- Hughes, Teresa J -- Willis, David K -- Clemente, Thomas E -- Diers, Brian W -- Jiang, Jiming -- Hudson, Matthew E -- Bent, Andrew F -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1206-9. doi: 10.1126/science.1228746. Epub 2012 Oct 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23065905" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Animals ; *Gene Dosage ; Gene Expression Regulation, Plant ; *Genetic Loci ; Genetic Variation ; Haplotypes ; Male ; Molecular Sequence Data ; Plant Diseases/*genetics/*parasitology ; Plant Proteins/*genetics ; Plant Roots/genetics/parasitology ; Protein Structure, Tertiary/genetics ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins/genetics ; Soybeans/*genetics/*parasitology ; *Tylenchoidea
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    ER cargo properties specify a requirement for COPII coat rigidity mediated by Sec13p (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-02-04
    Description: Eukaryotic secretory proteins exit the endoplasmic reticulum (ER) via transport vesicles generated by the essential coat protein complex II (COPII) proteins. The outer coat complex, Sec13-Sec31, forms a scaffold that is thought to enforce curvature. By exploiting yeast bypass-of-sec-thirteen (bst) mutants, where Sec13p is dispensable, we probed the relationship between a compromised COPII coat and the cellular context in which it could still function. Genetic and biochemical analyses suggested that Sec13p was required to generate vesicles from membranes that contained asymmetrically distributed cargoes that were likely to confer opposing curvature. Thus, Sec13p may rigidify the COPII cage and increase its membrane-bending capacity; this function could be bypassed when a bst mutation renders the membrane more deformable.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306526/" 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/PMC3306526/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Copic, Alenka -- Latham, Catherine F -- Horlbeck, Max A -- D'Arcangelo, Jennifer G -- Miller, Elizabeth A -- GM078186/GM/NIGMS NIH HHS/ -- GM085089/GM/NIGMS NIH HHS/ -- R01 GM078186/GM/NIGMS NIH HHS/ -- R01 GM078186-05/GM/NIGMS NIH HHS/ -- R01 GM085089/GM/NIGMS NIH HHS/ -- R01 GM085089-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1359-62. doi: 10.1126/science.1215909. Epub 2012 Feb 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22300850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; COP-Coated Vesicles/*chemistry/metabolism/ultrastructure ; Endoplasmic Reticulum/*metabolism ; Genes, Fungal ; Models, Biological ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; Mutation ; Nuclear Pore Complex Proteins/chemistry/genetics/*metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Protein Transport ; Saccharomyces cerevisiae/genetics/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Vesicular Transport Proteins/chemistry/metabolism
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    iRhom2 regulation of TACE controls TNF-mediated protection against Listeria and responses to LPS (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-17
    Description: Innate immune responses are vital for pathogen defense but can result in septic shock when excessive. A key mediator of septic shock is tumor necrosis factor-alpha (TNFalpha), which is shed from the plasma membrane after cleavage by the TNFalpha convertase (TACE). We report that the rhomboid family member iRhom2 interacted with TACE and regulated TNFalpha shedding. iRhom2 was critical for TACE maturation and trafficking to the cell surface in hematopoietic cells. Gene-targeted iRhom2-deficient mice showed reduced serum TNFalpha in response to lipopolysaccharide (LPS) and could survive a lethal LPS dose. Furthermore, iRhom2-deficient mice failed to control the replication of Listeria monocytogenes. Our study has identified iRhom2 as a regulator of innate immunity that may be an important target for modulating sepsis and pathogen defense.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250273/" 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/PMC4250273/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McIlwain, David R -- Lang, Philipp A -- Maretzky, Thorsten -- Hamada, Koichi -- Ohishi, Kazuhito -- Maney, Sathish Kumar -- Berger, Thorsten -- Murthy, Aditya -- Duncan, Gordon -- Xu, Haifeng C -- Lang, Karl S -- Haussinger, Dieter -- Wakeham, Andrew -- Itie-Youten, Annick -- Khokha, Rama -- Ohashi, Pamela S -- Blobel, Carl P -- Mak, Tak W -- GM64750/GM/NIGMS NIH HHS/ -- R01 GM064750/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):229-32. doi: 10.1126/science.1214448.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Campell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network (UHN), 620 University Avenue, Toronto, Ontario M5G 2C1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22246778" target="_blank"〉PubMed〈/a〉
    Keywords: ADAM Proteins/genetics/*metabolism ; Amino Acid Sequence ; Animals ; B-Lymphocytes/immunology/metabolism ; Base Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cell Membrane/metabolism ; Gene Deletion ; *Immunity, Innate ; Lipopolysaccharides/*immunology ; Listeria monocytogenes/immunology/physiology ; Listeriosis/*immunology/metabolism/microbiology/pathology ; Macrophages/immunology/metabolism ; Macrophages, Peritoneal/immunology/metabolism/microbiology ; Mice ; Molecular Sequence Data ; Protein Transport ; Shock, Septic/*immunology/metabolism ; Spleen/cytology ; Tumor Necrosis Factor-alpha/blood/genetics/*metabolism
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    Mitochondrial fission, fusion, and stress (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-01
    Description: Mitochondrial fission and fusion play critical roles in maintaining functional mitochondria when cells experience metabolic or environmental stresses. Fusion helps mitigate stress by mixing the contents of partially damaged mitochondria as a form of complementation. Fission is needed to create new mitochondria, but it also contributes to quality control by enabling the removal of damaged mitochondria and can facilitate apoptosis during high levels of cellular stress. Disruptions in these processes affect normal development, and they have been implicated in neurodegenerative diseases, such as Parkinson's.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762028/" 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/PMC4762028/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Youle, Richard J -- van der Bliek, Alexander M -- GM051866/GM/NIGMS NIH HHS/ -- Z99 NS999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 31;337(6098):1062-5. doi: 10.1126/science.1219855.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA. youler@ninds.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936770" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autophagy ; DNA, Mitochondrial/genetics ; Humans ; *Membrane Fusion ; Mice ; Mitochondria/genetics/*physiology ; Mitochondrial Diseases/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; Neurodegenerative Diseases/metabolism ; Parkinson Disease/metabolism ; *Stress, Physiological
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    Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-08
    Description: In animals and plants, social structure can reduce conflict within populations and bias aggression toward competing populations; however, for bacteria in the wild it remains unknown whether such population-level organization exists. Here, we show that environmental bacteria are organized into socially cohesive units in which antagonism occurs between rather than within ecologically defined populations. By screening approximately 35,000 possible mutual interactions among Vibrionaceae isolates from the ocean, we show that genotypic clusters known to have cohesive habitat association also act as units in terms of antibiotic production and resistance. Genetic analyses show that within populations, broad-range antibiotics are produced by few genotypes, whereas all others are resistant, suggesting cooperation between conspecifics. Natural antibiotics may thus mediate competition between populations rather than solely increase the success of individuals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cordero, Otto X -- Wildschutte, Hans -- Kirkup, Benjamin -- Proehl, Sarah -- Ngo, Lynn -- Hussain, Fatima -- Le Roux, Frederique -- Mincer, Tracy -- Polz, Martin F -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1228-31. doi: 10.1126/science.1219385.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955834" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*biosynthesis ; *Antibiosis ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; *Ecosystem ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genotype ; *Microbial Interactions ; Molecular Sequence Data ; Oceans and Seas ; Polyketide Synthases/genetics ; Seawater/*microbiology ; Vibrio/*drug effects/genetics/metabolism/*physiology
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    An early-branching microbialite cyanobacterium forms intracellular carbonates (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-04-28
    Description: Cyanobacteria have affected major geochemical cycles (carbon, nitrogen, and oxygen) on Earth for billions of years. In particular, they have played a major role in the formation of calcium carbonates (i.e., calcification), which has been considered to be an extracellular process. We identified a cyanobacterium in modern microbialites in Lake Alchichica (Mexico) that forms intracellular amorphous calcium-magnesium-strontium-barium carbonate inclusions about 270 nanometers in average diameter, revealing an unexplored pathway for calcification. Phylogenetic analyses place this cyanobacterium within the deeply divergent order Gloeobacterales. The chemical composition and structure of the intracellular precipitates suggest some level of cellular control on the biomineralization process. This discovery expands the diversity of organisms capable of forming amorphous calcium carbonates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couradeau, Estelle -- Benzerara, Karim -- Gerard, Emmanuelle -- Moreira, David -- Bernard, Sylvain -- Brown, Gordon E Jr -- Lopez-Garcia, Purificacion -- New York, N.Y. -- Science. 2012 Apr 27;336(6080):459-62. doi: 10.1126/science.1216171.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Mineralogie et de Physique de la Matiere Condensee, CNRS UMR 7590, Universite Pierre et Marie Curie, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539718" target="_blank"〉PubMed〈/a〉
    Keywords: Barium/analysis ; Base Sequence ; *Biofilms ; Calcification, Physiologic ; Calcium/analysis ; Calcium Carbonate/*analysis ; Carbonates/*analysis/metabolism ; Chemical Precipitation ; Cyanobacteria/classification/*isolation & purification/*physiology/ultrastructure ; Genes, Bacterial ; Genes, rRNA ; Inclusion Bodies/*chemistry/*ultrastructure ; Lakes/*microbiology ; Magnesium/analysis ; Mexico ; Molecular Sequence Data ; Phylogeny ; Strontium/analysis
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    Catalysis and sulfa drug resistance in dihydropteroate synthase (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-03
    Description: The sulfonamide antibiotics inhibit dihydropteroate synthase (DHPS), a key enzyme in the folate pathway of bacteria and primitive eukaryotes. However, resistance mutations have severely compromised the usefulness of these drugs. We report structural, computational, and mutagenesis studies on the catalytic and resistance mechanisms of DHPS. By performing the enzyme-catalyzed reaction in crystalline DHPS, we have structurally characterized key intermediates along the reaction pathway. Results support an S(N)1 reaction mechanism via formation of a novel cationic pterin intermediate. We also show that two conserved loops generate a substructure during catalysis that creates a specific binding pocket for p-aminobenzoic acid, one of the two DHPS substrates. This substructure, together with the pterin-binding pocket, explains the roles of the conserved active-site residues and reveals how sulfonamide resistance arises.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531234/" 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/PMC3531234/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yun, Mi-Kyung -- Wu, Yinan -- Li, Zhenmei -- Zhao, Ying -- Waddell, M Brett -- Ferreira, Antonio M -- Lee, Richard E -- Bashford, Donald -- White, Stephen W -- AI070721/AI/NIAID NIH HHS/ -- CA21765/CA/NCI NIH HHS/ -- P30 CA021765/CA/NCI NIH HHS/ -- R01 AI070721/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1110-4. doi: 10.1126/science.1214641.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383850" target="_blank"〉PubMed〈/a〉
    Keywords: 4-Aminobenzoic Acid/chemistry/metabolism ; Amino Acid Sequence ; Anti-Bacterial Agents/chemistry/metabolism/*pharmacology ; Bacillus anthracis/drug effects/enzymology ; Biocatalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Dihydropteroate Synthase/*chemistry/genetics/*metabolism ; Diphosphates/chemistry/metabolism ; *Drug Resistance, Bacterial ; Magnesium/chemistry ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Parabens/chemistry/metabolism ; Protein Conformation ; Sulfamethoxazole/chemistry/metabolism/*pharmacology ; Sulfathiazoles/chemistry/metabolism/*pharmacology ; Yersinia pestis/drug effects/enzymology
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    Neuroscience. The emerging biology of autism spectrum disorders (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-18
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657753/" 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/PMC3657753/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉State, Matthew W -- Sestan, Nenad -- P50MH081756/MH/NIMH NIH HHS/ -- R01 NS054273/NS/NINDS NIH HHS/ -- R01MH081754/MH/NIMH NIH HHS/ -- R01NS054273/NS/NINDS NIH HHS/ -- RC2MH089956/MH/NIMH NIH HHS/ -- U01 MH081896/MH/NIMH NIH HHS/ -- U01MH081896/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 14;337(6100):1301-3. doi: 10.1126/science.1224989.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06510, USA. matthew.state@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22984058" target="_blank"〉PubMed〈/a〉
    Keywords: Child Development Disorders, Pervasive/*genetics ; Child, Preschool ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genetic Loci ; Humans ; Mutation ; Neocortex/*growth & development/metabolism
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    A mutation in EGF repeat-8 of Notch discriminates between Serrate/Jagged and Delta family ligands (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-12-01
    Description: Notch signaling affects many developmental and cellular processes and has been implicated in congenital disorders, stroke, and numerous cancers. The Notch receptor binds its ligands Delta and Serrate and is able to discriminate between them in different contexts. However, the specific domains in Notch responsible for this selectivity are poorly defined. Through genetic screens in Drosophila, we isolated a mutation, Notch(jigsaw), that affects Serrate- but not Delta-dependent signaling. Notch(jigsaw) carries a missense mutation in epidermal growth factor repeat-8 (EGFr-8) and is defective in Serrate binding. A homologous point mutation in mammalian Notch2 also exhibits defects in signaling of a mammalian Serrate homolog, Jagged1. Hence, an evolutionarily conserved valine in EGFr-8 is essential for ligand selectivity and provides a molecular handle to study numerous Notch-dependent signaling events.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663443/" 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/PMC3663443/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamamoto, Shinya -- Charng, Wu-Lin -- Rana, Nadia A -- Kakuda, Shinako -- Jaiswal, Manish -- Bayat, Vafa -- Xiong, Bo -- Zhang, Ke -- Sandoval, Hector -- David, Gabriela -- Wang, Hao -- Haltiwanger, Robert S -- Bellen, Hugo J -- 1RC4GM096355-01/GM/NIGMS NIH HHS/ -- 5K12GM084897/GM/NIGMS NIH HHS/ -- 5P30HD024064/HD/NICHD NIH HHS/ -- 5R01GM061126-12/GM/NIGMS NIH HHS/ -- 5R01GM067858/GM/NIGMS NIH HHS/ -- 5T32-HD055200/HD/NICHD NIH HHS/ -- K12 GM084897/GM/NIGMS NIH HHS/ -- P30 HD024064/HD/NICHD NIH HHS/ -- R01 GM061126/GM/NIGMS NIH HHS/ -- R01 GM067858/GM/NIGMS NIH HHS/ -- RC4 GM096355/GM/NIGMS NIH HHS/ -- T32 HD055200/HD/NICHD NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Nov 30;338(6111):1229-32. doi: 10.1126/science.1228745.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23197537" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Calcium-Binding Proteins/*metabolism ; Cells, Cultured ; DNA Mutational Analysis ; Drosophila Proteins/*genetics/*metabolism ; Drosophila melanogaster/genetics/*metabolism ; Epidermal Growth Factor/genetics ; Evolution, Molecular ; Humans ; Intercellular Signaling Peptides and Proteins/*metabolism ; Intracellular Signaling Peptides and Proteins/*metabolism ; Ligands ; Male ; Membrane Proteins/*metabolism ; Methionine/genetics ; Molecular Sequence Data ; Mutation ; Receptor, Notch2/genetics/metabolism ; Receptors, Notch/*genetics/*metabolism ; Tandem Repeat Sequences/genetics ; Valine/genetics ; X Chromosome/genetics
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    Bacterial quorum sensing and metabolic incentives to cooperate (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-10-16
    Description: The opportunistic pathogen Pseudomonas aeruginosa uses a cell-cell communication system termed "quorum sensing" to control production of public goods, extracellular products that can be used by any community member. Not all individuals respond to quorum-sensing signals and synthesize public goods. Such social cheaters enjoy the benefits of the products secreted by cooperators. There are some P. aeruginosa cellular enzymes controlled by quorum sensing, and we show that quorum sensing-controlled expression of such private goods can put a metabolic constraint on social cheating and prevent a tragedy of the commons. Metabolic constraint of social cheating provides an explanation for private-goods regulation by a cooperative system and has general implications for population biology, infection control, and stabilization of quorum-sensing circuits in synthetic biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587168/" 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/PMC3587168/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dandekar, Ajai A -- Chugani, Sudha -- Greenberg, E Peter -- GM-59026/GM/NIGMS NIH HHS/ -- P30 DK 89507/DK/NIDDK NIH HHS/ -- P30 DK089507/DK/NIDDK NIH HHS/ -- R01 GM059026/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Oct 12;338(6104):264-6. doi: 10.1126/science.1227289.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Pulmonary and Critical Care Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23066081" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl-Butyrolactones/metabolism ; Adenosine/*metabolism ; Bacterial Proteins/genetics/metabolism ; Caseins/metabolism ; Culture Media/metabolism ; Microarray Analysis ; Mutation ; Pseudomonas aeruginosa/genetics/*growth & development/*metabolism ; Quorum Sensing/genetics/*physiology ; Signal Transduction ; Social Behavior ; Trans-Activators/genetics/metabolism
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    Botulinum neurotoxin is shielded by NTNHA in an interlocked complex (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-01
    Description: Botulinum neurotoxins (BoNTs) are highly poisonous substances that are also effective medicines. Accidental BoNT poisoning often occurs through ingestion of Clostridium botulinum-contaminated food. Here, we present the crystal structure of a BoNT in complex with a clostridial nontoxic nonhemagglutinin (NTNHA) protein at 2.7 angstroms. Biochemical and functional studies show that NTNHA provides large and multivalent binding interfaces to protect BoNT from gastrointestinal degradation. Moreover, the structure highlights key residues in BoNT that regulate complex assembly in a pH-dependent manner. Collectively, our findings define the molecular mechanisms by which NTNHA shields BoNT in the hostile gastrointestinal environment and releases it upon entry into the circulation. These results will assist in the design of small molecules for inhibiting oral BoNT intoxication and of delivery vehicles for oral administration of biologics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545708/" 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/PMC3545708/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Shenyan -- Rumpel, Sophie -- Zhou, Jie -- Strotmeier, Jasmin -- Bigalke, Hans -- Perry, Kay -- Shoemaker, Charles B -- Rummel, Andreas -- Jin, Rongsheng -- R01 AI091823/AI/NIAID NIH HHS/ -- U54 AI057159/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):977-81. doi: 10.1126/science.1214270.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neuroscience, Aging and Stem Cell Research, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363010" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Botulinum Toxins, Type A/*chemistry/metabolism ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Multiprotein Complexes/chemistry/metabolism ; Mutagenesis ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary
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    Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-11-23
    Description: Oxamniquine resistance evolved in the human blood fluke (Schistosoma mansoni) in Brazil in the 1970s. We crossed parental parasites differing ~500-fold in drug response, determined drug sensitivity and marker segregation in clonally derived second-generation progeny, and identified a single quantitative trait locus (logarithm of odds = 31) on chromosome 6. A sulfotransferase was identified as the causative gene by using RNA interference knockdown and biochemical complementation assays, and we subsequently demonstrated independent origins of loss-of-function mutations in field-derived and laboratory-selected resistant parasites. These results demonstrate the utility of linkage mapping in a human helminth parasite, while crystallographic analyses of protein-drug interactions illuminate the mode of drug action and provide a framework for rational design of oxamniquine derivatives that kill both S. mansoni and S. haematobium, the two species responsible for 〉99% of schistosomiasis cases worldwide.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136436/" 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/PMC4136436/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valentim, Claudia L L -- Cioli, Donato -- Chevalier, Frederic D -- Cao, Xiaohang -- Taylor, Alexander B -- Holloway, Stephen P -- Pica-Mattoccia, Livia -- Guidi, Alessandra -- Basso, Annalisa -- Tsai, Isheng J -- Berriman, Matthew -- Carvalho-Queiroz, Claudia -- Almeida, Marcio -- Aguilar, Hector -- Frantz, Doug E -- Hart, P John -- LoVerde, Philip T -- Anderson, Timothy J C -- 098051/Wellcome Trust/United Kingdom -- 5R21-AI072704/AI/NIAID NIH HHS/ -- 5R21-AI096277/AI/NIAID NIH HHS/ -- C06 RR013556/RR/NCRR NIH HHS/ -- HHSN272201000005I/PHS HHS/ -- R01 AI097576/AI/NIAID NIH HHS/ -- R01-AI097576/AI/NIAID NIH HHS/ -- R21 AI072704/AI/NIAID NIH HHS/ -- R21 AI096277/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1385-9. doi: 10.1126/science.1243106. Epub 2013 Nov 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Biochemistry and Pathology, University of Texas Health Science Center, San Antonio, TX 78229, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24263136" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Drug Resistance/*genetics ; Gene Knockdown Techniques ; Genetic Linkage ; Helminth Proteins/*genetics ; Humans ; Molecular Sequence Data ; Mutation ; Oxamniquine/*pharmacology ; Phylogeny ; Protein Conformation ; Quantitative Trait Loci ; RNA Interference ; Schistosoma mansoni/*drug effects/*genetics ; Schistosomicides/*pharmacology ; Sulfotransferases/chemistry/classification/*genetics
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    Stepwise evolution of essential centromere function in a Drosophila neogene (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-06-08
    Description: Evolutionarily young genes that serve essential functions represent a paradox; they must perform a function that either was not required until after their birth or was redundant with another gene. How young genes rapidly acquire essential function is largely unknown. We traced the evolutionary steps by which the Drosophila gene Umbrea acquired an essential role in chromosome segregation in D. melanogaster since the gene's origin less than 15 million years ago. Umbrea neofunctionalization occurred via loss of an ancestral heterochromatin-localizing domain, followed by alterations that rewired its protein interaction network and led to species-specific centromere localization. Our evolutionary cell biology approach provides temporal and mechanistic detail about how young genes gain essential function. Such innovations may constantly alter the repertoire of centromeric proteins in eukaryotes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119826/" 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/PMC4119826/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ross, Benjamin D -- Rosin, Leah -- Thomae, Andreas W -- Hiatt, Mary Alice -- Vermaak, Danielle -- de la Cruz, Aida Flor A -- Imhof, Axel -- Mellone, Barbara G -- Malik, Harmit S -- R01 GM074108/GM/NIGMS NIH HHS/ -- R01GM074108/GM/NIGMS NIH HHS/ -- T32HG000035/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1211-4. doi: 10.1126/science.1234393.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744945" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Centromere/genetics/*physiology ; Chromosomal Proteins, Non-Histone/*genetics ; Drosophila/*genetics ; Drosophila Proteins/*genetics ; *Evolution, Molecular ; Gene Duplication ; Genes, Insect/*physiology ; Molecular Sequence Data
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    Unraveling the mechanism of protein disaggregation through a ClpB-DnaK interaction (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-02-09
    Description: HSP-100 protein machines, such as ClpB, play an essential role in reactivating protein aggregates that can otherwise be lethal to cells. Although the players involved are known, including the DnaK/DnaJ/GrpE chaperone system in bacteria, details of the molecular interactions are not well understood. Using methyl-transverse relaxation-optimized nuclear magnetic resonance spectroscopy, we present an atomic-resolution model for the ClpB-DnaK complex, which we verified by mutagenesis and functional assays. ClpB and GrpE compete for binding to the DnaK nucleotide binding domain, with GrpE binding inhibiting disaggregation. DnaK, in turn, plays a dual role in both disaggregation and subsequent refolding of polypeptide chains as they emerge from the aggregate. On the basis of a combined structural-biochemical analysis, we propose a model for the mechanism of protein aggregate reactivation by ClpB.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenzweig, Rina -- Moradi, Shoeib -- Zarrine-Afsar, Arash -- Glover, John R -- Kay, Lewis E -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Mar 1;339(6123):1080-3. doi: 10.1126/science.1233066. Epub 2013 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. rina.rosenzweig@utoronto.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393091" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/genetics ; Adenosine Triphosphate/chemistry/metabolism ; Bacterial Proteins/chemistry ; Heat-Shock Proteins/*chemistry/genetics ; Hydrolysis ; *Models, Chemical ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Interaction Domains and Motifs ; Protein Interaction Maps ; Protein Multimerization ; *Protein Refolding ; Protein Structure, Tertiary ; Protein Transport ; Thermus thermophilus
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    FtsZ protofilaments use a hinge-opening mechanism for constrictive force generation (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-07-28
    Description: The essential bacterial protein FtsZ is a guanosine triphosphatase that self-assembles into a structure at the division site termed the "Z ring". During cytokinesis, the Z ring exerts a constrictive force on the membrane by using the chemical energy of guanosine triphosphate hydrolysis. However, the structural basis of this constriction remains unresolved. Here, we present the crystal structure of a guanosine diphosphate-bound Mycobacterium tuberculosis FtsZ protofilament, which exhibits a curved conformational state. The structure reveals a longitudinal interface that is important for function. The protofilament curvature highlights a hydrolysis-dependent conformational switch at the T3 loop that leads to longitudinal bending between subunits, which could generate sufficient force to drive cytokinesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816583/" 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/PMC3816583/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Ying -- Hsin, Jen -- Zhao, Lingyun -- Cheng, Yiwen -- Shang, Weina -- Huang, Kerwyn Casey -- Wang, Hong-Wei -- Ye, Sheng -- 1F32GM100677-01A1/GM/NIGMS NIH HHS/ -- DP2 OD006466/OD/NIH HHS/ -- DP2OD006466/OD/NIH HHS/ -- F32 GM100677/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jul 26;341(6144):392-5. doi: 10.1126/science.1239248.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang, P.R. China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23888039" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/physiology ; Crystallography, X-Ray ; *Cytokinesis ; Cytoskeletal Proteins/*chemistry/genetics/*metabolism ; Escherichia coli/chemistry ; Guanosine Diphosphate/chemistry/metabolism ; Guanosine Triphosphate/metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Mycobacterium tuberculosis/*chemistry/physiology ; Point Mutation ; Protein Conformation ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Staphylococcus aureus/chemistry
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    Voltage-gated sodium channel in grasshopper mice defends against bark scorpion toxin (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-10-26
    Description: Painful venoms are used to deter predators. Pain itself, however, can signal damage and thus serves an important adaptive function. Evolution to reduce general pain responses, although valuable for preying on venomous species, is rare, likely because it comes with the risk of reduced response to tissue damage. Bark scorpions capitalize on the protective pain pathway of predators by inflicting intensely painful stings. However, grasshopper mice regularly attack and consume bark scorpions, grooming only briefly when stung. Bark scorpion venom induces pain in many mammals (house mice, rats, humans) by activating the voltage-gated Na(+) channel Nav1.7, but has no effect on Nav1.8. Grasshopper mice Nav1.8 has amino acid variants that bind bark scorpion toxins and inhibit Na(+) currents, blocking action potential propagation and inducing analgesia. Thus, grasshopper mice have solved the predator-pain problem by using a toxin bound to a nontarget channel to block transmission of the pain signals the venom itself is initiating.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172297/" 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/PMC4172297/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rowe, Ashlee H -- Xiao, Yucheng -- Rowe, Matthew P -- Cummins, Theodore R -- Zakon, Harold H -- NS 053422/NS/NINDS NIH HHS/ -- R01 NS053422/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 25;342(6157):441-6. doi: 10.1126/science.1236451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Neurobiology, The University of Texas at Austin, Austin, TX 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24159039" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials/drug effects/physiology ; Amino Acid Sequence ; Animals ; Arvicolinae/*metabolism ; *Food Chain ; Formaldehyde/pharmacology ; Mice ; Molecular Sequence Data ; NAV1.7 Voltage-Gated Sodium Channel/chemistry/genetics/*metabolism ; NAV1.8 Voltage-Gated Sodium Channel/chemistry/genetics/*metabolism ; Pain/chemically induced/*metabolism ; *Predatory Behavior ; Protein Structure, Tertiary ; Scorpion Venoms
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    Structure and allostery of the PKA RIIbeta tetrameric holoenzyme (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-02-11
    Description: In its physiological state, cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is a tetramer that contains a regulatory (R) subunit dimer and two catalytic (C) subunits. We describe here the 2.3 angstrom structure of full-length tetrameric RIIbeta(2):C(2) holoenzyme. This structure showing a dimer of dimers provides a mechanistic understanding of allosteric activation by cAMP. The heterodimers are anchored together by an interface created by the beta4-beta5 loop in the RIIbeta subunit, which docks onto the carboxyl-terminal tail of the adjacent C subunit, thereby forcing the C subunit into a fully closed conformation in the absence of nucleotide. Diffusion of magnesium adenosine triphosphate (ATP) into these crystals trapped not ATP, but the reaction products, adenosine diphosphate and the phosphorylated RIIbeta subunit. This complex has implications for the dissociation-reassociation cycling of PKA. The quaternary structure of the RIIbeta tetramer differs appreciably from our model of the RIalpha tetramer, confirming the small-angle x-ray scattering prediction that the structures of each PKA tetramer are different.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985767/" 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/PMC3985767/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Ping -- Smith-Nguyen, Eric V -- Keshwani, Malik M -- Deal, Michael S -- Kornev, Alexandr P -- Taylor, Susan S -- GM34921/GM/NIGMS NIH HHS/ -- R01 GM034921/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):712-6. doi: 10.1126/science.1213979.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093-0654, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323819" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Allosteric Site ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/metabolism ; Cyclic AMP-Dependent Protein Kinase Catalytic Subunits/*chemistry/*metabolism ; Cyclic AMP-Dependent Protein Kinase RIIbeta Subunit/*chemistry/*metabolism ; Holoenzymes/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Folding ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Rats
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    Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-03-23
    Description: Glycosylated alpha-dystroglycan (alpha-DG) serves as cellular entry receptor for multiple pathogens, and defects in its glycosylation cause hereditary Walker-Warburg syndrome (WWS). At least eight proteins are critical to glycosylate alpha-DG, but many genes mutated in WWS remain unknown. To identify modifiers of alpha-DG, we performed a haploid screen for Lassa virus entry, a hemorrhagic fever virus causing thousands of deaths annually that hijacks glycosylated alpha-DG to enter cells. In complementary screens, we profiled cells for absence of alpha-DG carbohydrate chains or biochemically related glycans. This revealed virus host factors and a suite of glycosylation units, including all known Walker-Warburg genes and five additional factors critical for the modification of alpha-DG. Our findings accentuate the complexity of this posttranslational feature and point out genes defective in dystroglycanopathies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919138/" 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/PMC3919138/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jae, Lucas T -- Raaben, Matthijs -- Riemersma, Moniek -- van Beusekom, Ellen -- Blomen, Vincent A -- Velds, Arno -- Kerkhoven, Ron M -- Carette, Jan E -- Topaloglu, Haluk -- Meinecke, Peter -- Wessels, Marja W -- Lefeber, Dirk J -- Whelan, Sean P -- van Bokhoven, Hans -- Brummelkamp, Thijn R -- AI057159/AI/NIAID NIH HHS/ -- AI081842/AI/NIAID NIH HHS/ -- R01 AI081842/AI/NIAID NIH HHS/ -- U54 AI057159/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 26;340(6131):479-83. doi: 10.1126/science.1233675. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519211" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Line ; Dystroglycans/*metabolism ; Female ; Glycosylation ; Haploidy ; Host-Pathogen Interactions/*genetics ; Humans ; Infant ; Lassa Fever/*genetics/virology ; Lassa virus/*physiology ; Male ; Membrane Proteins/*genetics ; Molecular Sequence Data ; Mutation ; Pedigree ; Proteome/*metabolism ; *Virus Internalization ; Walker-Warburg Syndrome/*genetics
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    ATAXIN-2 activates PERIOD translation to sustain circadian rhythms in Drosophila (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-05-21
    Description: Evidence for transcriptional feedback in circadian timekeeping is abundant, yet little is known about the mechanisms underlying translational control. We found that ATAXIN-2 (ATX2), an RNA-associated protein involved in neurodegenerative disease, is a translational activator of the rate-limiting clock component PERIOD (PER) in Drosophila. ATX2 specifically interacted with TWENTY-FOUR (TYF), an activator of PER translation. RNA interference-mediated depletion of Atx2 or the expression of a mutant ATX2 protein that does not associate with polyadenylate-binding protein (PABP) suppressed behavioral rhythms and decreased abundance of PER. Although ATX2 can repress translation, depletion of Atx2 from Drosophila S2 cells inhibited translational activation by RNA-tethered TYF and disrupted the association between TYF and PABP. Thus, ATX2 coordinates an active translation complex important for PER expression and circadian rhythms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lim, Chunghun -- Allada, Ravi -- R01NS059042/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 17;340(6134):875-9. doi: 10.1126/science.1234785.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23687047" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ataxins ; Cell Line ; *Circadian Rhythm ; Drosophila Proteins/*biosynthesis/genetics/metabolism ; Drosophila melanogaster/metabolism/*physiology ; Mutation ; Nerve Tissue Proteins/genetics/*metabolism ; Period Circadian Proteins/*biosynthesis ; Poly(A)-Binding Proteins/metabolism ; Protein Biosynthesis ; RNA Interference
    Print ISSN: 0036-8075
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    Microbiology. Eliminating malaria (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-07-03
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361224/" 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/PMC4361224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fidock, David A -- R01 AI050234/AI/NIAID NIH HHS/ -- R01 AI079709/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1531-3. doi: 10.1126/science.1240539.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology and Division of Infectious Diseases, Columbia University Medical Center, New York, NY 10032, USA. df2260@columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812705" target="_blank"〉PubMed〈/a〉
    Keywords: Antimalarials/*administration & dosage ; Artemisinins/*administration & dosage ; Child ; DNA Mismatch Repair/*genetics ; Disease Eradication/*methods ; Drug Resistance/*genetics ; Humans ; Malaria, Falciparum/parasitology/*prevention & control ; Mutation ; Plasmodium falciparum/drug effects/*genetics
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    Epistasis among adaptive mutations in deer mouse hemoglobin (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-06-15
    Description: Epistatic interactions between mutant sites in the same protein can exert a strong influence on pathways of molecular evolution. We performed protein engineering experiments that revealed pervasive epistasis among segregating amino acid variants that contribute to adaptive functional variation in deer mouse hemoglobin (Hb). Amino acid mutations increased or decreased Hb-O2 affinity depending on the allelic state of other sites. Structural analysis revealed that epistasis for Hb-O2 affinity and allosteric regulatory control is attributable to indirect interactions between structurally remote sites. The prevalence of sign epistasis for fitness-related biochemical phenotypes has important implications for the evolutionary dynamics of protein polymorphism in natural populations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409680/" 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/PMC4409680/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Natarajan, Chandrasekhar -- Inoguchi, Noriko -- Weber, Roy E -- Fago, Angela -- Moriyama, Hideaki -- Storz, Jay F -- HL087216-S1/HL/NHLBI NIH HHS/ -- R01 HL087216/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 14;340(6138):1324-7. doi: 10.1126/science.1236862.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23766324" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological/*genetics ; Alleles ; Animals ; *Epistasis, Genetic ; *Evolution, Molecular ; Exons ; Genetic Variation ; Hemoglobins/*chemistry/*genetics ; Hydrogen Bonding ; Mutation ; Oxygen/chemistry ; Peromyscus/genetics/*physiology ; Polymorphism, Genetic ; Protein Structure, Secondary ; alpha-Globins/chemistry/genetics ; beta-Globins/genetics
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    Parallel molecular evolution in an herbivore community (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-09-29
    Description: Numerous insects have independently evolved the ability to feed on plants that produce toxic secondary compounds called cardenolides and can sequester these compounds for use in their defense. We surveyed the protein target for cardenolides, the alpha subunit of the sodium pump, Na(+),K(+)-ATPase (ATPalpha), in 14 species that feed on cardenolide-producing plants and 15 outgroups spanning three insect orders. Despite the large number of potential targets for modulating cardenolide sensitivity, amino acid substitutions associated with host-plant specialization are highly clustered, with many parallel substitutions. Additionally, we document four independent duplications of ATPalpha with convergent tissue-specific expression patterns. We find that unique substitutions are disproportionately associated with recent duplications relative to parallel substitutions. Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3770729/" 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/PMC3770729/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhen, Ying -- Aardema, Matthew L -- Medina, Edgar M -- Schumer, Molly -- Andolfatto, Peter -- R01 GM083228/GM/NIGMS NIH HHS/ -- R01-GM083228/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1634-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019645" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological/*genetics ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Apocynaceae/*metabolism/parasitology ; Cardenolides/*metabolism ; *Evolution, Molecular ; Genetic Pleiotropy ; Herbivory/*genetics ; Host-Parasite Interactions/*genetics ; Insects/enzymology/*genetics/physiology ; Molecular Sequence Data ; Organ Specificity ; Sodium-Potassium-Exchanging ATPase/chemistry/*genetics/metabolism
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    Sex-specific adaptation drives early sex chromosome evolution in Drosophila (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-07-24
    Description: Most species' sex chromosomes are derived from ancient autosomes and show few signatures of their origins. We studied the sex chromosomes of Drosophila miranda, where a neo-Y chromosome originated only approximately 1 million years ago. Whole-genome and transcriptome analysis reveals massive degeneration of the neo-Y, that male-beneficial genes on the neo-Y are more likely to undergo accelerated protein evolution, and that neo-Y genes evolve biased expression toward male-specific tissues--the shrinking gene content of the neo-Y becomes masculinized. In contrast, although older X chromosomes show a paucity of genes expressed in male tissues, neo-X genes highly expressed in male-specific tissues undergo increased rates of protein evolution if haploid in males. Thus, the response to sex-specific selection can shift at different stages of X differentiation, resulting in masculinization or demasculinization of the X-chromosomal gene content.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107656/" 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/PMC4107656/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Qi -- Bachtrog, Doris -- R01 GM076007/GM/NIGMS NIH HHS/ -- R01 GM093182/GM/NIGMS NIH HHS/ -- R01GM076007/GM/NIGMS NIH HHS/ -- R01GM093182/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jul 20;337(6092):341-5. doi: 10.1126/science.1225385.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22822149" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Animals ; Drosophila/genetics/*physiology ; *Evolution, Molecular ; Female ; Gene Expression Regulation ; *Genes, Insect ; Genome-Wide Association Study ; Male ; Mutation ; Open Reading Frames ; Sex Factors ; Testis ; X Chromosome/*genetics ; Y Chromosome/*genetics
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    The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-12-18
    Description: An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920664/" 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/PMC3920664/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ryan, Joseph F -- Pang, Kevin -- Schnitzler, Christine E -- Nguyen, Anh-Dao -- Moreland, R Travis -- Simmons, David K -- Koch, Bernard J -- Francis, Warren R -- Havlak, Paul -- NISC Comparative Sequencing Program -- Smith, Stephen A -- Putnam, Nicholas H -- Haddock, Steven H D -- Dunn, Casey W -- Wolfsberg, Tyra G -- Mullikin, James C -- Martindale, Mark Q -- Baxevanis, Andreas D -- ZIA HG000140-13/Intramural NIH HHS/ -- ZIA HG000140-14/Intramural NIH HHS/ -- ZIA HG000140-15/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1242592. doi: 10.1126/science.1242592.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Technology Branch, Division of Intramural Research, 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/24337300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; *Biological Evolution ; Cell Lineage/*genetics ; Ctenophora/classification/*cytology/*genetics ; *Genome ; Mesoderm/cytology ; Molecular Sequence Data ; Muscle Development/genetics ; Neurogenesis/genetics ; Phylogeny
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    Defining stem cell dynamics in models of intestinal tumor initiation (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-11-23
    Description: Cancer is a disease in which cells accumulate genetic aberrations that are believed to confer a clonal advantage over cells in the surrounding tissue. However, the quantitative benefit of frequently occurring mutations during tumor development remains unknown. We quantified the competitive advantage of Apc loss, Kras activation, and P53 mutations in the mouse intestine. Our findings indicate that the fate conferred by these mutations is not deterministic, and many mutated stem cells are replaced by wild-type stem cells after biased, but still stochastic events. Furthermore, P53 mutations display a condition-dependent advantage, and especially in colitis-affected intestines, clones harboring mutations in this gene are favored. Our work confirms the previously theoretical notion that the tissue architecture of the intestine suppresses the accumulation of mutated lineages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vermeulen, Louis -- Morrissey, Edward -- van der Heijden, Maartje -- Nicholson, Anna M -- Sottoriva, Andrea -- Buczacki, Simon -- Kemp, Richard -- Tavare, Simon -- Winton, Douglas J -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2013 Nov 22;342(6161):995-8. doi: 10.1126/science.1243148.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK, Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24264992" target="_blank"〉PubMed〈/a〉
    Keywords: Adenomatous Polyposis Coli Protein/genetics ; Animals ; Cell Transformation, Neoplastic/*genetics/*pathology ; *Gene Expression Regulation, Neoplastic ; Intestinal Neoplasms/*genetics/*pathology ; Mice ; Mice, Mutant Strains ; Models, Biological ; Mutation ; Neoplastic Stem Cells/metabolism/*pathology ; Proto-Oncogene Proteins p21(ras)/genetics ; Transcriptional Activation ; Tumor Suppressor Protein p53/genetics
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    Allele-specific silencing of mutant Myh6 transcripts in mice suppresses hypertrophic cardiomyopathy (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-10-05
    Description: Dominant mutations in sarcomere proteins such as the myosin heavy chains (MHC) are the leading genetic causes of human hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy. We found that expression of the HCM-causing cardiac MHC gene (Myh6) R403Q mutation in mice can be selectively silenced by an RNA interference (RNAi) cassette delivered by an adeno-associated virus vector. RNAi-transduced MHC(403/+) mice developed neither hypertrophy nor myocardial fibrosis, the pathologic manifestations of HCM, for at least 6 months. Because inhibition of HCM was achieved by only a 25% reduction in the levels of the mutant transcripts, we suggest that the variable clinical phenotype in HCM patients reflects allele-specific expression and that partial silencing of mutant transcripts may have therapeutic benefit.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100553/" 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/PMC4100553/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Jianming -- Wakimoto, Hiroko -- Seidman, J G -- Seidman, Christine E -- R01 HL084553/HL/NHLBI NIH HHS/ -- R01HL084553/HL/NHLBI NIH HHS/ -- U01 HL066582/HL/NHLBI NIH HHS/ -- U01 HL098166/HL/NHLBI NIH HHS/ -- U01HL098166/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):111-4. doi: 10.1126/science.1236921.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092743" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Cardiomyopathy, Hypertrophic/*diagnosis/genetics/pathology ; Dependovirus ; Fibrosis ; Gene Silencing ; *Genetic Therapy ; HEK293 Cells ; Humans ; Mice ; Mutation ; Myosin Heavy Chains/*genetics ; *RNA Interference
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    Adaptive evolution of multiple traits through multiple mutations at a single gene (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-16
    Description: The identification of precise mutations is required for a complete understanding of the underlying molecular and evolutionary mechanisms driving adaptive phenotypic change. Using plasticine models in the field, we show that the light coat color of deer mice that recently colonized the light-colored soil of the Nebraska Sand Hills provides a strong selective advantage against visually hunting predators. Color variation in an admixed population suggests that this light Sand Hills phenotype is composed of multiple traits. We identified distinct regions within the Agouti locus associated with each color trait and found that only haplotypes associated with light trait values have evidence of selection. Thus, local adaptation is the result of independent selection on many mutations within a single locus, each with a specific effect on an adaptive phenotype, thereby minimizing pleiotropic consequences.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836219/" 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/PMC3836219/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Linnen, Catherine R -- Poh, Yu-Ping -- Peterson, Brant K -- Barrett, Rowan D H -- Larson, Joanna G -- Jensen, Jeffrey D -- Hoekstra, Hopi E -- 308796/European Research Council/International -- New York, N.Y. -- Science. 2013 Mar 15;339(6125):1312-6. doi: 10.1126/science.1233213.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Kentucky, Lexington, KY 40506, USA. catherine.linnen@uky.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23493712" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Agouti Signaling Protein/genetics ; Animals ; *Biological Evolution ; Color ; Food Chain ; *Multifactorial Inheritance ; Mutation ; Organic Chemicals ; Peromyscus/genetics/*physiology ; Pigmentation/*genetics ; Selection, Genetic
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    Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-03
    Description: Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating disease that can cause severe yield losses. A previously uncharacterized Pgt race, designated Ug99, has overcome most of the widely used resistance genes and is threatening major wheat production areas. Here, we demonstrate that the Sr35 gene from Triticum monococcum is a coiled-coil, nucleotide-binding, leucine-rich repeat gene that confers near immunity to Ug99 and related races. This gene is absent in the A-genome diploid donor and in polyploid wheat but is effective when transferred from T. monococcum to polyploid wheat. The cloning of Sr35 opens the door to the use of biotechnological approaches to control this devastating disease and to analyses of the molecular interactions that define the wheat-rust pathosystem.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748951/" 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/PMC4748951/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saintenac, Cyrille -- Zhang, Wenjun -- Salcedo, Andres -- Rouse, Matthew N -- Trick, Harold N -- Akhunov, Eduard -- Dubcovsky, Jorge -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Aug 16;341(6147):783-6. doi: 10.1126/science.1239022. Epub 2013 Jun 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23811222" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; *Basidiomycota/pathogenicity ; Cloning, Molecular ; Disease Resistance/genetics ; *Genes, Plant ; Haplotypes ; Molecular Sequence Annotation ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Diseases/genetics/*immunology/microbiology ; Plant Proteins/chemistry/genetics ; Plant Stems/microbiology ; Plants, Genetically Modified ; Polymorphism, Single Nucleotide ; Polyploidy ; Sequence Analysis, DNA ; Triticum/*genetics/immunology/microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Influence of HLA-C expression level on HIV control (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-04-06
    Description: A variant upstream of human leukocyte antigen C (HLA-C) shows the most significant genome-wide effect on HIV control in European Americans and is also associated with the level of HLA-C expression. We characterized the differential cell surface expression levels of all common HLA-C allotypes and tested directly for effects of HLA-C expression on outcomes of HIV infection in 5243 individuals. Increasing HLA-C expression was associated with protection against multiple outcomes independently of individual HLA allelic effects in both African and European Americans, regardless of their distinct HLA-C frequencies and linkage relationships with HLA-B and HLA-A. Higher HLA-C expression was correlated with increased likelihood of cytotoxic T lymphocyte responses and frequency of viral escape mutation. In contrast, high HLA-C expression had a deleterious effect in Crohn's disease, suggesting a broader influence of HLA expression levels in human disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784322/" 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/PMC3784322/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Apps, Richard -- Qi, Ying -- Carlson, Jonathan M -- Chen, Haoyan -- Gao, Xiaojiang -- Thomas, Rasmi -- Yuki, Yuko -- Del Prete, Greg Q -- Goulder, Philip -- Brumme, Zabrina L -- Brumme, Chanson J -- John, Mina -- Mallal, Simon -- Nelson, George -- Bosch, Ronald -- Heckerman, David -- Stein, Judy L -- Soderberg, Kelly A -- Moody, M Anthony -- Denny, Thomas N -- Zeng, Xue -- Fang, Jingyuan -- Moffett, Ashley -- Lifson, Jeffrey D -- Goedert, James J -- Buchbinder, Susan -- Kirk, Gregory D -- Fellay, Jacques -- McLaren, Paul -- Deeks, Steven G -- Pereyra, Florencia -- Walker, Bruce -- Michael, Nelson L -- Weintrob, Amy -- Wolinsky, Steven -- Liao, Wilson -- Carrington, Mary -- 5-M01-RR-00722/RR/NCRR NIH HHS/ -- HHSN261200800001E/CA/NCI NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- K08 AR057763/AR/NIAMS NIH HHS/ -- K08AR057763/AR/NIAMS NIH HHS/ -- K24 AI069994/AI/NIAID NIH HHS/ -- K24AI069994/AI/NIAID NIH HHS/ -- N02-CP-55504/CP/NCI NIH HHS/ -- P30 AI027763/AI/NIAID NIH HHS/ -- P30 AI027767/AI/NIAID NIH HHS/ -- P30 AI027767-24/AI/NIAID NIH HHS/ -- P30 MH62246/MH/NIMH NIH HHS/ -- PG/09/077/27964/British Heart Foundation/United Kingdom -- R01 AI046995/AI/NIAID NIH HHS/ -- R01 AI060460/AI/NIAID NIH HHS/ -- R01 AI087145/AI/NIAID NIH HHS/ -- R01 AR065174/AR/NIAMS NIH HHS/ -- R01-AI046995/AI/NIAID NIH HHS/ -- R01-AI060460/AI/NIAID NIH HHS/ -- R01-DA-04334/DA/NIDA NIH HHS/ -- R01-DA-12568/DA/NIDA NIH HHS/ -- R01-DA04334/DA/NIDA NIH HHS/ -- R01-DA12568/DA/NIDA NIH HHS/ -- R24 AI067039/AI/NIAID NIH HHS/ -- U01-AI-067854/AI/NIAID NIH HHS/ -- U01-AI-35039/AI/NIAID NIH HHS/ -- U01-AI-35040/AI/NIAID NIH HHS/ -- U01-AI-35041/AI/NIAID NIH HHS/ -- U01-AI-35042/AI/NIAID NIH HHS/ -- U01-AI-35043/AI/NIAID NIH HHS/ -- U01-AI-37613/AI/NIAID NIH HHS/ -- U01-AI-37984/AI/NIAID NIH HHS/ -- UL1 RR024131/RR/NCRR NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):87-91. doi: 10.1126/science.1232685.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23559252" target="_blank"〉PubMed〈/a〉
    Keywords: African Americans/genetics ; Alleles ; Amino Acid Sequence ; Anti-Retroviral Agents/therapeutic use ; Crohn Disease/genetics/immunology ; *Gene Expression Regulation ; HIV/genetics/*immunology ; HIV Infections/drug therapy/*genetics/*immunology ; HLA-C Antigens/*genetics ; Humans ; Immunodominant Epitopes/genetics ; Molecular Sequence Data ; Mutation ; Peptide Fragments/immunology ; Polymorphism, Single Nucleotide ; T-Lymphocytes, Cytotoxic/*immunology ; Viral Load/genetics
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    Mechanism of eukaryotic RNA polymerase III transcription termination (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-03
    Description: Gene expression in organisms involves many factors and is tightly controlled. Although much is known about the initial phase of transcription by RNA polymerase III (Pol III), the enzyme that synthesizes the majority of RNA molecules in eukaryotic cells, termination is poorly understood. Here, we show that the extensive structure of Pol III-synthesized transcripts dictates the release of elongation complexes at the end of genes. The poly-T termination signal, which does not cause termination in itself, causes catalytic inactivation and backtracking of Pol III, thus committing the enzyme to termination and transporting it to the nearest RNA secondary structure, which facilitates Pol III release. Similarity between termination mechanisms of Pol III and bacterial RNA polymerase suggests that hairpin-dependent termination may date back to the common ancestor of multisubunit RNA polymerases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760304/" 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/PMC3760304/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nielsen, Soren -- Yuzenkova, Yulia -- Zenkin, Nikolay -- 202994/European Research Council/International -- BB/F013558/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/J006378/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1577-80. doi: 10.1126/science.1237934.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812715" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Molecular Sequence Data ; Nucleic Acid Conformation ; Poly T/metabolism ; Poly U/metabolism ; RNA Polymerase III/*metabolism ; RNA, Ribosomal, 5S/chemistry/genetics ; RNA, Transfer, Tyr/chemistry/genetics ; Saccharomyces cerevisiae/*enzymology/genetics ; *Transcription Termination, Genetic
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    Cancer. Potential of the synthetic lethality principle (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-11-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nijman, Sebastian M B -- Friend, Stephen H -- New York, N.Y. -- Science. 2013 Nov 15;342(6160):809-11. doi: 10.1126/science.1244669.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24233712" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila melanogaster/genetics ; Gene Targeting ; *Genes, Lethal ; *Genes, Modifier ; Genetic Therapy/*methods ; Humans ; Immunotherapy ; Molecular Targeted Therapy ; Mutation ; Neoplasms/*genetics/*therapy ; Saccharomyces cerevisiae/genetics ; Tumor Suppressor Proteins/genetics
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    Genomic diversity and evolution of the head crest in the rock pigeon (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-02-02
    Description: The geographic origins of breeds and the genetic basis of variation within the widely distributed and phenotypically diverse domestic rock pigeon (Columba livia) remain largely unknown. We generated a rock pigeon reference genome and additional genome sequences representing domestic and feral populations. We found evidence for the origins of major breed groups in the Middle East and contributions from a racing breed to North American feral populations. We identified the gene EphB2 as a strong candidate for the derived head crest phenotype shared by numerous breeds, an important trait in mate selection in many avian species. We also found evidence that this trait evolved just once and spread throughout the species, and that the crest originates early in development by the localized molecular reversal of feather bud polarity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778192/" 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/PMC3778192/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, Michael D -- Kronenberg, Zev -- Li, Cai -- Domyan, Eric T -- Pan, Hailin -- Campbell, Michael -- Tan, Hao -- Huff, Chad D -- Hu, Haofu -- Vickrey, Anna I -- Nielsen, Sandra C A -- Stringham, Sydney A -- Hu, Hao -- Willerslev, Eske -- Gilbert, M Thomas P -- Yandell, Mark -- Zhang, Guojie -- Wang, Jun -- GO RC2HG005619/HG/NHGRI NIH HHS/ -- R01 GM104390/GM/NIGMS NIH HHS/ -- R01 HG004694/HG/NHGRI NIH HHS/ -- R01HG004694/HG/NHGRI NIH HHS/ -- R44 HG006579/HG/NHGRI NIH HHS/ -- RC2 HG005619/HG/NHGRI NIH HHS/ -- T32 GM007464/GM/NIGMS NIH HHS/ -- T32 HD007491/HD/NICHD NIH HHS/ -- T32GM007464/GM/NIGMS NIH HHS/ -- T32HD07491/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2013 Mar 1;339(6123):1063-7. doi: 10.1126/science.1230422. Epub 2013 Jan 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Utah, Salt Lake City, UT 84112, USA. mike.shapiro@utah.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23371554" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Domestic/anatomy & histology/classification/genetics ; Animals, Wild/anatomy & histology/classification/genetics ; Breeding ; Columbidae/anatomy & histology/*classification/*genetics ; *Evolution, Molecular ; Feathers/anatomy & histology ; *Genetic Variation ; Genome ; Head/*anatomy & histology ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide ; *Quantitative Trait, Heritable ; Receptor, EphB2/genetics ; Sequence Analysis, DNA
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    Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-10-05
    Description: Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argonaute 1 (AGO1) and selectively silencing host immunity genes. The Arabidopsis ago1 mutant exhibits reduced susceptibility to B. cinerea, and the B. cinerea dcl1 dcl2 double mutant that can no longer produce these Bc-sRNAs displays reduced pathogenicity on Arabidopsis and tomato. Thus, this fungal pathogen transfers "virulent" sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096153/" 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/PMC4096153/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiberg, Arne -- Wang, Ming -- Lin, Feng-Mao -- Zhao, Hongwei -- Zhang, Zhihong -- Kaloshian, Isgouhi -- Huang, Hsien-Da -- Jin, Hailing -- R01 GM093008/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):118-23. doi: 10.1126/science.1239705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092744" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*immunology/microbiology ; Arabidopsis Proteins/genetics ; Argonaute Proteins/genetics ; Botrytis/genetics/*pathogenicity ; Gene Expression Regulation, Plant ; Host-Pathogen Interactions/genetics/*immunology ; Lycopersicon esculentum/genetics/immunology/microbiology ; Mutation ; Plant Diseases/genetics/immunology/*microbiology ; *RNA Interference ; RNA, Fungal/*genetics ; RNA, Small Interfering/*genetics ; Virulence/genetics
    Print ISSN: 0036-8075
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    Identification of a colonial chordate histocompatibility gene (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-28
    Description: Histocompatibility is the basis by which multicellular organisms of the same species distinguish self from nonself. Relatively little is known about the mechanisms underlying histocompatibility reactions in lower organisms. Botryllus schlosseri is a colonial urochordate, a sister group of vertebrates, that exhibits a genetically determined natural transplantation reaction, whereby self-recognition between colonies leads to formation of parabionts with a common vasculature, whereas rejection occurs between incompatible colonies. Using genetically defined lines, whole-transcriptome sequencing, and genomics, we identified a single gene that encodes self-nonself and determines "graft" outcomes in this organism. This gene is significantly up-regulated in colonies poised to undergo fusion and/or rejection, is highly expressed in the vasculature, and is functionally linked to histocompatibility outcomes. These findings establish a platform for advancing the science of allorecognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810301/" 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/PMC3810301/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Voskoboynik, Ayelet -- Newman, Aaron M -- Corey, Daniel M -- Sahoo, Debashis -- Pushkarev, Dmitry -- Neff, Norma F -- Passarelli, Benedetto -- Koh, Winston -- Ishizuka, Katherine J -- Palmeri, Karla J -- Dimov, Ivan K -- Keasar, Chen -- Fan, H Christina -- Mantalas, Gary L -- Sinha, Rahul -- Penland, Lolita -- Quake, Stephen R -- Weissman, Irving L -- 1R01AG037968/AG/NIA NIH HHS/ -- 1R56AI089968/AI/NIAID NIH HHS/ -- K12 HL087746/HL/NHLBI NIH HHS/ -- K99 CA151673/CA/NCI NIH HHS/ -- K99CA151673-01A1/CA/NCI NIH HHS/ -- R01 AG037968/AG/NIA NIH HHS/ -- R01 GM100315/GM/NIGMS NIH HHS/ -- R01GM100315/GM/NIGMS NIH HHS/ -- R56 AI089968/AI/NIAID NIH HHS/ -- T32 CA009302/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Jul 26;341(6144):384-7. doi: 10.1126/science.1238036.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. ayeletv@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23888037" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; *Genes ; Genome ; Genotype ; Histocompatibility/*genetics ; Immune Tolerance ; Molecular Sequence Data ; Sequence Analysis, DNA ; Transcriptome ; Up-Regulation ; Urochordata/*genetics/*immunology/physiology
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    PINK1-phosphorylated mitofusin 2 is a Parkin receptor for culling damaged mitochondria (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-04-27
    Description: Senescent and damaged mitochondria undergo selective mitophagic elimination through mechanisms requiring two Parkinson's disease factors, the mitochondrial kinase PINK1 (PTEN-induced putative kinase protein 1; PTEN is phosphatase and tensin homolog) and the cytosolic ubiquitin ligase Parkin. The nature of the PINK-Parkin interaction and the identity of key factors directing Parkin to damaged mitochondria are unknown. We show that the mitochondrial outer membrane guanosine triphosphatase mitofusin (Mfn) 2 mediates Parkin recruitment to damaged mitochondria. Parkin bound to Mfn2 in a PINK1-dependent manner; PINK1 phosphorylated Mfn2 and promoted its Parkin-mediated ubiqitination. Ablation of Mfn2 in mouse cardiac myocytes prevented depolarization-induced translocation of Parkin to the mitochondria and suppressed mitophagy. Accumulation of morphologically and functionally abnormal mitochondria induced respiratory dysfunction in Mfn2-deficient mouse embryonic fibroblasts and cardiomyocytes and in Parkin-deficient Drosophila heart tubes, causing dilated cardiomyopathy. Thus, Mfn2 functions as a mitochondrial receptor for Parkin and is required for quality control of cardiac mitochondria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774525/" 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/PMC3774525/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Yun -- Dorn, Gerald W 2nd -- R01 HL059888/HL/NHLBI NIH HHS/ -- R21 HL107276/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 26;340(6131):471-5. doi: 10.1126/science.1231031.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Pharmacogenomics, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23620051" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Autophagy ; Cardiomyopathies/enzymology ; Drosophila melanogaster ; Fibroblasts/ultrastructure ; GTP Phosphohydrolases/genetics/*metabolism ; HEK293 Cells ; Humans ; Mice ; Mice, Mutant Strains ; Mitochondria/enzymology ; Mitochondria, Heart/*enzymology ; Molecular Sequence Data ; Myocytes, Cardiac/*enzymology/ultrastructure ; Phosphorylation ; Protein Kinases/*metabolism ; Ubiquitin-Protein Ligases/*metabolism ; Ubiquitination
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
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    Following gene duplication, paralog interference constrains transcriptional circuit evolution (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-10-05
    Description: Most models of gene duplication assume that the ancestral functions of the preduplication gene are independent and can therefore be neatly partitioned between descendant paralogs. However, many gene products, such as transcriptional regulators, are components within cooperative assemblies; here, we show that a natural consequence of duplication and divergence of such proteins can be competitive interference between the paralogs. Our example is based on the duplication of the essential MADS-box transcriptional regulator Mcm1, which is found in all fungi and regulates a large set of genes. We show that a set of historical amino acid sequence substitutions minimized paralog interference in contemporary species and, in doing so, increased the molecular complexity of this gene regulatory network. We propose that paralog interference is a common constraint on gene duplicate evolution, and its resolution, which can generate additional regulatory complexity, is needed to stabilize duplicated genes in the genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911913/" 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/PMC3911913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Christopher R -- Hanson-Smith, Victor -- Johnson, Alexander D -- F32 GM108299/GM/NIGMS NIH HHS/ -- R01 GM037049/GM/NIGMS NIH HHS/ -- R01 GM057049/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):104-8. doi: 10.1126/science.1240810.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbiology, University of California, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092741" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/genetics ; Candida albicans/genetics ; *Evolution, Molecular ; *Gene Duplication ; *Gene Regulatory Networks ; Kluyveromyces/genetics ; Minichromosome Maintenance 1 Protein/*genetics ; Molecular Sequence Data ; Saccharomyces cerevisiae/genetics ; Sequence Deletion ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
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    Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-21
    Description: The Na(+), K(+)-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na(+) and K(+) across the plasma membrane--a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K(+)-bound or ouabain-blocked forms. We present the crystal structure of a Na(+)-bound Na(+), K(+)-ATPase as determined at 4.3 A resolution. Compared with the K(+)-bound form, large conformational changes are observed in the alpha subunit whereas the beta and gamma subunit structures are maintained. The locations of the three Na(+) sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na(+) from IIIb through IIIa, followed by exchange of Na(+) for K(+) at sites I and II, is suggested.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nyblom, Maria -- Poulsen, Hanne -- Gourdon, Pontus -- Reinhard, Linda -- Andersson, Magnus -- Lindahl, Erik -- Fedosova, Natalya -- Nissen, Poul -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):123-7. doi: 10.1126/science.1243352. Epub 2013 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Membrane Pumps in Cells and Disease-PUMPkin, Danish National Research Foundation, DK-8000 Aarhus, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24051246" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Membrane/enzymology ; Crystallography, X-Ray ; *Models, Molecular ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium/*chemistry ; Sodium-Potassium-Exchanging ATPase/*chemistry/genetics ; Swine
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
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    Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-07
    Description: Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057101/" 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/PMC4057101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walker, Mark C -- Thuronyi, Benjamin W -- Charkoudian, Louise K -- Lowry, Brian -- Khosla, Chaitan -- Chang, Michelle C Y -- 1 DP2 OD008696/OD/NIH HHS/ -- 1 T32 GMO66698/PHS HHS/ -- 1S10RR023679-01/RR/NCRR NIH HHS/ -- F32 CA137994/CA/NCI NIH HHS/ -- R01 GM087934/GM/NIGMS NIH HHS/ -- S10 RR16634-01/RR/NCRR NIH HHS/ -- T32 GM066698/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Sep 6;341(6150):1089-94. doi: 10.1126/science.1242345.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24009388" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/metabolism ; Base Sequence ; Biological Products/chemistry/*metabolism ; Burkholderia/enzymology ; Coenzyme A Ligases/chemistry/genetics/metabolism ; Escherichia coli ; Fluoroacetates/chemistry/*metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Polyketide Synthases/chemistry/genetics/*metabolism ; Polyketides/chemistry/*metabolism ; Protein Engineering ; Protein Structure, Tertiary ; Streptomyces coelicolor/enzymology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
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    Uncovering the protein translocon at the chloroplast inner envelope membrane (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-02-02
    Description: Chloroplasts require protein translocons at the outer and inner envelope membranes, termed TOC and TIC, respectively, to import thousands of cytoplasmically synthesized preproteins. However, the molecular identity of the TIC translocon remains controversial. Tic20 forms a 1-megadalton complex at the inner membrane and directly interacts with translocating preproteins. We purified the 1-megadalton complex from Arabidopsis, comprising Tic20 and three other essential components, one of which is encoded by the enigmatic open reading frame ycf1 in the chloroplast genome. All four components, together with well-known TOC components, were found stoichiometrically associated with different translocating preproteins. When reconstituted into planar lipid bilayers, the purified complex formed a preprotein-sensitive channel. Thus, this complex constitutes a general TIC translocon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kikuchi, Shingo -- Bedard, Jocelyn -- Hirano, Minako -- Hirabayashi, Yoshino -- Oishi, Maya -- Imai, Midori -- Takase, Mai -- Ide, Toru -- Nakai, Masato -- New York, N.Y. -- Science. 2013 Feb 1;339(6119):571-4. doi: 10.1126/science.1229262.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Regulation of Biological Reactions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23372012" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*metabolism ; Arabidopsis Proteins/genetics/isolation & purification/*metabolism ; Cell Membrane/*metabolism ; Chloroplasts/*metabolism ; Evolution, Molecular ; Gene Knockout Techniques ; Lipid Bilayers/metabolism ; Membrane Transport Proteins/genetics/isolation & purification/*metabolism ; Mutation ; Open Reading Frames ; Protein Transport
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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