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  • Animals  (56)
  • American Association for the Advancement of Science (AAAS)  (56)
  • 2015-2019  (56)
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  • 1
    Publication Date: 2015-05-23
    Description: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, 〉0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Vargas, Colomban -- Audic, Stephane -- Henry, Nicolas -- Decelle, Johan -- Mahe, Frederic -- Logares, Ramiro -- Lara, Enrique -- Berney, Cedric -- Le Bescot, Noan -- Probert, Ian -- Carmichael, Margaux -- Poulain, Julie -- Romac, Sarah -- Colin, Sebastien -- Aury, Jean-Marc -- Bittner, Lucie -- Chaffron, Samuel -- Dunthorn, Micah -- Engelen, Stefan -- Flegontova, Olga -- Guidi, Lionel -- Horak, Ales -- Jaillon, Olivier -- Lima-Mendez, Gipsi -- Lukes, Julius -- Malviya, Shruti -- Morard, Raphael -- Mulot, Matthieu -- Scalco, Eleonora -- Siano, Raffaele -- Vincent, Flora -- Zingone, Adriana -- Dimier, Celine -- Picheral, Marc -- Searson, Sarah -- Kandels-Lewis, Stefanie -- Tara Oceans Coordinators -- Acinas, Silvia G -- Bork, Peer -- Bowler, Chris -- Gorsky, Gabriel -- Grimsley, Nigel -- Hingamp, Pascal -- Iudicone, Daniele -- Not, Fabrice -- Ogata, Hiroyuki -- Pesant, Stephane -- Raes, Jeroen -- Sieracki, Michael E -- Speich, Sabrina -- Stemmann, Lars -- Sunagawa, Shinichi -- Weissenbach, Jean -- Wincker, Patrick -- Karsenti, Eric -- New York, N.Y. -- Science. 2015 May 22;348(6237):1261605. doi: 10.1126/science.1261605.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. vargas@sb-roscoff.fr pwincker@genoscope.cns.fr karsenti@embl.de. ; CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, 67663 Kaiserslautern, Germany. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Department of Marine Biology and Oceanography, Institute of Marine Science (ICM)-Consejo Superior de Investigaciones Cientificas (CSIC), Passeig Maritim de la Barceloneta 37-49, Barcelona E08003, Spain. ; Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, 2000 Neuchatel, Switzerland. ; CNRS, FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, UPMC Paris 06, FR 2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. ; Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91000 Evry, France. ; CNRS FR3631, Institut de Biologie Paris-Seine, F-75005, Paris, France. Sorbonne Universites, UPMC Paris 06, Institut de Biologie Paris-Seine, F-75005, Paris, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, 67663 Kaiserslautern, Germany. ; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. ; CNRS, UMR 7093, Laboratoire d'Oceanographie de Villefranche-sur-Mer (LOV), Observatoire Oceanologique, F-06230, Villefranche-sur-Mer, France. Sorbonne Universites, UPMC Paris 06, UMR 7093, LOV, Observatoire Oceanologique, F-06230, Villefranche-sur-Mer, France. ; Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91000 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. ; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic. Canadian Institute for Advanced Research, 180 Dundas Street West, Suite 1400, Toronto, Ontario M5G 1Z8, Canada. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. ; MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy. ; Ifremer, Centre de Brest, DYNECO/Pelagos CS 10070, 29280 Plouzane, France. ; Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. ; Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbruck-Centre for Molecular Medicine, 13092 Berlin, Germany. ; CNRS UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Avenue du Fontaule, 66650 Banyuls-sur-Mer, France. Sorbonne Universites Paris 06, Observatoire Oceanologique de Banyuls (OOB) UPMC, Avenue du Fontaule, 66650 Banyuls-sur-Mer, France. ; Aix Marseille Universite, CNRS IGS UMR 7256, 13288 Marseille, France. ; Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan. ; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany. ; Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA. National Science Foundation, Arlington, VA 22230, USA. ; Department of Geosciences, Laboratoire de Meteorologie Dynamique (LMD), Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Oceans, Universite de Bretagne Occidentale (UBO)-Institut Universitaire Europeen de la Mer (IUEM), Place Copernic, 29820 Plouzane, France. ; Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Genomique, GENOSCOPE, 2 rue Gaston Cremieux, 91000 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. vargas@sb-roscoff.fr pwincker@genoscope.cns.fr karsenti@embl.de. ; Directors' Research, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005 France. vargas@sb-roscoff.fr pwincker@genoscope.cns.fr karsenti@embl.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25999516" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/genetics ; Eukaryota/*classification/genetics ; Oceans and Seas ; Phylogeny ; Plankton/*classification/genetics ; Ribosomes/genetics ; Sequence Analysis, DNA ; Sunlight
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  • 2
    Publication Date: 2015-08-01
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692367/" 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/PMC4692367/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Akbari, Omar S -- Bellen, Hugo J -- Bier, Ethan -- Bullock, Simon L -- Burt, Austin -- Church, George M -- Cook, Kevin R -- Duchek, Peter -- Edwards, Owain R -- Esvelt, Kevin M -- Gantz, Valentino M -- Golic, Kent G -- Gratz, Scott J -- Harrison, Melissa M -- Hayes, Keith R -- James, Anthony A -- Kaufman, Thomas C -- Knoblich, Juergen -- Malik, Harmit S -- Matthews, Kathy A -- O'Connor-Giles, Kate M -- Parks, Annette L -- Perrimon, Norbert -- Port, Fillip -- Russell, Steven -- Ueda, Ryu -- Wildonger, Jill -- R01 AI070654/AI/NIAID NIH HHS/ -- R01 AI110713/AI/NIAID NIH HHS/ -- T32 GM007133/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Aug 28;349(6251):927-9. doi: 10.1126/science.aac7932. Epub 2015 Jul 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Entomology, Univ. of California, Riverside, CA 92507, USA. Center for Disease Vector Research, Institute for Integrative Genome Biology, Univ. of California, Riverside, CA 92507, USA. ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA. ; Section of Cell and Developmental Biology, Univ. of California, San Diego, La Jolla, CA 92095, USA. kevin.esvelt@wyss.harvard.edu ebier@ucsd.edu. ; Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ; Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berks SL5 7PY, UK. ; Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. ; Bloomington Drosophila Stock Center, Department of Biology, Indiana Univ., Bloomington, IN 47405, USA. ; Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria. ; CSIRO Centre for Environment and Life Sciences, Underwood Avenue, Floreat, WA 6014, Australia. ; Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA. kevin.esvelt@wyss.harvard.edu ebier@ucsd.edu. ; Section of Cell and Developmental Biology, Univ. of California, San Diego, La Jolla, CA 92095, USA. ; Department of Biology, Univ. of Utah, Salt Lake City, UT 84112, USA. ; Laboratory of Genetics, Univ. of Wisconsin-Madison, Madison, WI 53706, USA. ; Department of Biomolecular Chemistry, Univ. of Wisconsin-Madison, Madison, WI 53706, USA. ; CSIRO Biosecurity Flagship, General Post Of ce Box 1538, Hobart, Tasmania, 7001, Australia. ; Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, Univ. of California at Irvine, Irvine, CA 92697, USA. ; Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. ; Laboratory of Genetics, Univ. of Wisconsin-Madison, Madison, WI 53706, USA. Laboratory of Cell and Molecular Biology, Univ. of Wisconsin-Madison, Madison, WI 53706, USA. ; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. ; Department of Genetics, Univ. of Cambridge, Cambridge, Cambridgeshire CB2 3EH, UK. ; Department of Genetics, Graduate Univ. for Advanced Studies, Mishima, Shizuoka 411-8540, Japan. NIG-Fly Stock Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan. ; Department of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26229113" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Containment of Biohazards ; Endonucleases/metabolism ; *Genetic Engineering ; *Genetic Research ; Genome ; *Organisms, Genetically Modified ; *Safety
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  • 3
    Publication Date: 2015-07-04
    Description: The ocean moderates anthropogenic climate change at the cost of profound alterations of its physics, chemistry, ecology, and services. Here, we evaluate and compare the risks of impacts on marine and coastal ecosystems-and the goods and services they provide-for growing cumulative carbon emissions under two contrasting emissions scenarios. The current emissions trajectory would rapidly and significantly alter many ecosystems and the associated services on which humans heavily depend. A reduced emissions scenario-consistent with the Copenhagen Accord's goal of a global temperature increase of less than 2 degrees C-is much more favorable to the ocean but still substantially alters important marine ecosystems and associated goods and services. The management options to address ocean impacts narrow as the ocean warms and acidifies. Consequently, any new climate regime that fails to minimize ocean impacts would be incomplete and inadequate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gattuso, J-P -- Magnan, A -- Bille, R -- Cheung, W W L -- Howes, E L -- Joos, F -- Allemand, D -- Bopp, L -- Cooley, S R -- Eakin, C M -- Hoegh-Guldberg, O -- Kelly, R P -- Portner, H-O -- Rogers, A D -- Baxter, J M -- Laffoley, D -- Osborn, D -- Rankovic, A -- Rochette, J -- Sumaila, U R -- Treyer, S -- Turley, C -- New York, N.Y. -- Science. 2015 Jul 3;349(6243):aac4722. doi: 10.1126/science.aac4722.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire d'Oceanographie de Villefranche, CNRS-Institut National des Sciences de l'Univers, F-06230 Villefranche-sur-mer, France. Sorbonne Universites, Universite Pierre et Marie Curie, Univ Paris 06, Observatoire Oceanologique, F-06230 Villefranche-sur-mer, France. Institute for Sustainable Development and International Relations, Sciences Po, 27 rue Saint Guillaume, F-75007 Paris, France. gattuso@obs-vlfr.fr. ; Institute for Sustainable Development and International Relations, Sciences Po, 27 rue Saint Guillaume, F-75007 Paris, France. ; Secretariat of the Pacific Community, B.P. D5, 98848 Noumea Cedex, New Caledonia. ; Nippon Foundation-UBC Nereus Program, University of British Columbia (UBC), Vancouver, BC V6T 1Z4, Canada. ; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570, Bremenrhaven, Germany. ; Climate and Environmental Physics, Physics Institute and Oeschger Centre for Climate Change Research, University of Bern, Sidlerstrasse 5, CH-3012 Bern, Switzerland. ; Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000 Monaco, Principality of Monaco. Institut Pierre Simon Laplace/Laboratoire des Science du Climat et de l'Environnement, UMR8212, CNRS-Commissariat a l'Energie Atomique et aux Energies Alternatives-Universite de Versailles Saint-Quentin-en-Yvelines, Gif sur Yvette, France. ; Ocean Conservancy, 1300 19th Street NW, 8th Floor, Washington, DC 20036, USA. ; Coral Reef Watch, National Oceanic and Atmospheric Administration, College Park, MD 20740, USA. ; Global Change Institute and Australian Research Council Centre for Excellence in Coral Reef Studies, University of Queensland, Building 20, St Lucia, 4072 Queensland, Australia. ; School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, WA 98105, USA. ; Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. ; Scottish Natural Heritage, 231 Corstorphine Road, Edinburgh EH12 7AT, Scotland. ; IUCN, Rue Mauverney 28, CH-1196 Gland, Switzerland. ; Environment Laboratories, International Atomic Energy Agency, 4a Quai Antoine 1er, MC-98000 Monaco, Principality of Monaco. ; Program on Science, Technology, and Society, John F. Kennedy School of Government, Harvard University, 79 John F. Kennedy Street, Cambridge, MA 02138, USA. ; Institute for Sustainable Development and International Relations, Sciences Po, 27 rue Saint Guillaume, F-75007 Paris, France. Fisheries Economics Research Unit, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. ; Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26138982" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aquaculture ; *Aquatic Organisms ; *Carbon Dioxide ; *Ecosystem ; *Global Warming ; *Greenhouse Effect ; Health ; Humans ; Oceans and Seas ; Risk ; Travel
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  • 4
    Publication Date: 2015-02-14
    Description: Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433/" 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/PMC4681433/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arner, Erik -- Daub, Carsten O -- Vitting-Seerup, Kristoffer -- Andersson, Robin -- Lilje, Berit -- Drablos, Finn -- Lennartsson, Andreas -- Ronnerblad, Michelle -- Hrydziuszko, Olga -- Vitezic, Morana -- Freeman, Tom C -- Alhendi, Ahmad M N -- Arner, Peter -- Axton, Richard -- Baillie, J Kenneth -- Beckhouse, Anthony -- Bodega, Beatrice -- Briggs, James -- Brombacher, Frank -- Davis, Margaret -- Detmar, Michael -- Ehrlund, Anna -- Endoh, Mitsuhiro -- Eslami, Afsaneh -- Fagiolini, Michela -- Fairbairn, Lynsey -- Faulkner, Geoffrey J -- Ferrai, Carmelo -- Fisher, Malcolm E -- Forrester, Lesley -- Goldowitz, Daniel -- Guler, Reto -- Ha, Thomas -- Hara, Mitsuko -- Herlyn, Meenhard -- Ikawa, Tomokatsu -- Kai, Chieko -- Kawamoto, Hiroshi -- Khachigian, Levon M -- Klinken, S Peter -- Kojima, Soichi -- Koseki, Haruhiko -- Klein, Sarah -- Mejhert, Niklas -- Miyaguchi, Ken -- Mizuno, Yosuke -- Morimoto, Mitsuru -- Morris, Kelly J -- Mummery, Christine -- Nakachi, Yutaka -- Ogishima, Soichi -- Okada-Hatakeyama, Mariko -- Okazaki, Yasushi -- Orlando, Valerio -- Ovchinnikov, Dmitry -- Passier, Robert -- Patrikakis, Margaret -- Pombo, Ana -- Qin, Xian-Yang -- Roy, Sugata -- Sato, Hiroki -- Savvi, Suzana -- Saxena, Alka -- Schwegmann, Anita -- Sugiyama, Daisuke -- Swoboda, Rolf -- Tanaka, Hiroshi -- Tomoiu, Andru -- Winteringham, Louise N -- Wolvetang, Ernst -- Yanagi-Mizuochi, Chiyo -- Yoneda, Misako -- Zabierowski, Susan -- Zhang, Peter -- Abugessaisa, Imad -- Bertin, Nicolas -- Diehl, Alexander D -- Fukuda, Shiro -- Furuno, Masaaki -- Harshbarger, Jayson -- Hasegawa, Akira -- Hori, Fumi -- Ishikawa-Kato, Sachi -- Ishizu, Yuri -- Itoh, Masayoshi -- Kawashima, Tsugumi -- Kojima, Miki -- Kondo, Naoto -- Lizio, Marina -- Meehan, Terrence F -- Mungall, Christopher J -- Murata, Mitsuyoshi -- Nishiyori-Sueki, Hiromi -- Sahin, Serkan -- Nagao-Sato, Sayaka -- Severin, Jessica -- de Hoon, Michiel J L -- Kawai, Jun -- Kasukawa, Takeya -- Lassmann, Timo -- Suzuki, Harukazu -- Kawaji, Hideya -- Summers, Kim M -- Wells, Christine -- FANTOM Consortium -- Hume, David A -- Forrest, Alistair R R -- Sandelin, Albin -- Carninci, Piero -- Hayashizaki, Yoshihide -- P30 CA010815/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25678556" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cattle ; Cell Differentiation/*genetics ; Dogs ; *Enhancer Elements, Genetic ; *Gene Expression Regulation, Developmental ; Mice ; RNA, Messenger/genetics/metabolism ; Rats ; Stem Cells/*cytology/metabolism ; Transcription Factors/*metabolism ; *Transcription, Genetic
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  • 5
    Publication Date: 2015-05-16
    Description: The centrosome organizes microtubule arrays within animal cells and comprises two centrioles surrounded by an amorphous protein mass called the pericentriolar material (PCM). Despite the importance of centrosomes as microtubule-organizing centers, the mechanism and regulation of PCM assembly are not well understood. In Caenorhabditis elegans, PCM assembly requires the coiled-coil protein SPD-5. We found that recombinant SPD-5 could polymerize to form micrometer-sized porous networks in vitro. Network assembly was accelerated by two conserved regulators that control PCM assembly in vivo, Polo-like kinase-1 and SPD-2/Cep192. Only the assembled SPD-5 networks, and not unassembled SPD-5 protein, functioned as a scaffold for other PCM proteins. Thus, PCM size and binding capacity emerge from the regulated polymerization of one coiled-coil protein to form a porous network.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Woodruff, Jeffrey B -- Wueseke, Oliver -- Viscardi, Valeria -- Mahamid, Julia -- Ochoa, Stacy D -- Bunkenborg, Jakob -- Widlund, Per O -- Pozniakovsky, Andrei -- Zanin, Esther -- Bahmanyar, Shirin -- Zinke, Andrea -- Hong, Sun Hae -- Decker, Marcus -- Baumeister, Wolfgang -- Andersen, Jens S -- Oegema, Karen -- Hyman, Anthony A -- R01-GM074207/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 May 15;348(6236):808-12. doi: 10.1126/science.aaa3923.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. ; Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA. ; Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany. ; Department of Clinical Biochemistry, Copenhagen University Hospital, Hvidovre 2650, Denmark. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark. ; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark. ; Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA. hyman@mpi-cbg.de koegema@ucsd.edu. ; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. hyman@mpi-cbg.de koegema@ucsd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25977552" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*genetics/*metabolism ; Caenorhabditis elegans Proteins/chemistry/genetics/*metabolism ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; Centrosome/*metabolism/ultrasonography ; Metabolic Networks and Pathways ; Phosphorylation ; Polymerization ; Protein Binding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*metabolism ; Proto-Oncogene Proteins/*metabolism
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2016-02-27
    Description: Defects in the mitochondrial respiratory chain (RC) underlie a spectrum of human conditions, ranging from devastating inborn errors of metabolism to aging. We performed a genome-wide Cas9-mediated screen to identify factors that are protective during RC inhibition. Our results highlight the hypoxia response, an endogenous program evolved to adapt to limited oxygen availability. Genetic or small-molecule activation of the hypoxia response is protective against mitochondrial toxicity in cultured cells and zebrafish models. Chronic hypoxia leads to a marked improvement in survival, body weight, body temperature, behavior, neuropathology, and disease biomarkers in a genetic mouse model of Leigh syndrome, the most common pediatric manifestation of mitochondrial disease. Further preclinical studies are required to assess whether hypoxic exposure can be developed into a safe and effective treatment for human diseases associated with mitochondrial dysfunction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860742/" 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/PMC4860742/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jain, Isha H -- Zazzeron, Luca -- Goli, Rahul -- Alexa, Kristen -- Schatzman-Bone, Stephanie -- Dhillon, Harveen -- Goldberger, Olga -- Peng, Jun -- Shalem, Ophir -- Sanjana, Neville E -- Zhang, Feng -- Goessling, Wolfram -- Zapol, Warren M -- Mootha, Vamsi K -- 1R01-MH110049/MH/NIMH NIH HHS/ -- 5DP1-MH100706/DP/NCCDPHP CDC HHS/ -- 5R01DK097768-03/DK/NIDDK NIH HHS/ -- DP1 MH100706/MH/NIMH NIH HHS/ -- K99 HG008171/HG/NHGRI NIH HHS/ -- K99-HG008171/HG/NHGRI NIH HHS/ -- R01 DK090311/DK/NIDDK NIH HHS/ -- R01 DK097768/DK/NIDDK NIH HHS/ -- R01 MH110049/MH/NIMH NIH HHS/ -- R01DK090311/DK/NIDDK NIH HHS/ -- R24 OD017870/OD/NIH HHS/ -- R24OD017870/OD/NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2016 Apr 1;352(6281):54-61. doi: 10.1126/science.aad9642. Epub 2016 Feb 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA. Department of Systems Biology, Harvard Medical School, Boston, MA, USA. Broad Institute of Harvard and MIT, Cambridge, MA, USA. ; Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA. ; Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. ; Broad Institute of Harvard and MIT, Cambridge, MA, USA. McGovern Institute for Brain Research, Cambridge, MA, USA. Department of Brain and Cognitive Sciences and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. ; Broad Institute of Harvard and MIT, Cambridge, MA, USA. Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA. Harvard Stem Cell Institute, Cambridge, MA, USA. ; Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA. Department of Systems Biology, Harvard Medical School, Boston, MA, USA. Broad Institute of Harvard and MIT, Cambridge, MA, USA. vamsi@hms.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26917594" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Animals ; Antimycin A/analogs & derivatives/pharmacology ; Bacterial Proteins ; Biomarkers/blood ; Body Temperature ; Body Weight ; Disease Models, Animal ; Electron Transport/drug effects ; Electron Transport Complex I/genetics ; Endonucleases ; Energy Metabolism/drug effects/genetics ; Gene Knockout Techniques ; Genome-Wide Association Study ; Glycine/analogs & derivatives/pharmacology/therapeutic use ; Humans ; Hypoxia-Inducible Factor 1/metabolism ; Isoquinolines/pharmacology/therapeutic use ; K562 Cells ; Leigh Disease/*genetics/pathology/*therapy ; Mice ; Mice, Knockout ; Mitochondria/drug effects/*metabolism ; Oxygen/*metabolism ; Respiration ; Suppression, Genetic ; Von Hippel-Lindau Tumor Suppressor Protein/antagonists & inhibitors/*genetics ; Zebrafish
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2015-08-22
    Description: Plasma membrane depolarization can trigger cell proliferation, but how membrane potential influences mitogenic signaling is uncertain. Here, we show that plasma membrane depolarization induces nanoscale reorganization of phosphatidylserine and phosphatidylinositol 4,5-bisphosphate but not other anionic phospholipids. K-Ras, which is targeted to the plasma membrane by electrostatic interactions with phosphatidylserine, in turn undergoes enhanced nanoclustering. Depolarization-induced changes in phosphatidylserine and K-Ras plasma membrane organization occur in fibroblasts, excitable neuroblastoma cells, and Drosophila neurons in vivo and robustly amplify K-Ras-dependent mitogen-activated protein kinase (MAPK) signaling. Conversely, plasma membrane repolarization disrupts K-Ras nanoclustering and inhibits MAPK signaling. By responding to voltage-induced changes in phosphatidylserine spatiotemporal dynamics, K-Ras nanoclusters set up the plasma membrane as a biological field-effect transistor, allowing membrane potential to control the gain in mitogenic signaling circuits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687752/" 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/PMC4687752/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Yong -- Wong, Ching-On -- Cho, Kwang-jin -- van der Hoeven, Dharini -- Liang, Hong -- Thakur, Dhananiay P -- Luo, Jialie -- Babic, Milos -- Zinsmaier, Konrad E -- Zhu, Michael X -- Hu, Hongzhen -- Venkatachalam, Kartik -- Hancock, John F -- R01 NS081301/NS/NINDS NIH HHS/ -- R01NS081301/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2015 Aug 21;349(6250):873-6. doi: 10.1126/science.aaa5619.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Biology and Pharmacology, Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA. ; Department of Diagnostic and Biomedical Sciences, Dental School, University of Texas Health Science Center at Houston, Houston, TX 77054, USA. ; Department of Neuroscience, University of Arizona, Tucson, AZ 85721, USA. ; Department of Integrative Biology and Pharmacology, Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Program in Cell and Regulatory Biology, University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA. ; Department of Integrative Biology and Pharmacology, Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Program in Cell and Regulatory Biology, University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA. john.f.hancock@uth.tmc.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26293964" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Cell Membrane/metabolism/*physiology ; Cricetinae ; Drosophila melanogaster ; Fibroblasts ; *Membrane Potentials ; Mice ; Neurons ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphatidylserines/*metabolism ; Signal Transduction ; ras Proteins/*metabolism
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  • 8
    Publication Date: 2015-09-12
    Description: The function of neural circuits depends on the generation of specific classes of neurons. Neural identity is typically established near the time when neurons exit the cell cycle to become postmitotic cells, and it is generally accepted that, once the identity of a neuron has been established, its fate is maintained throughout life. Here, we show that network activity dynamically modulates the properties of fast-spiking (FS) interneurons through the postmitotic expression of the transcriptional regulator Er81. In the adult cortex, Er81 protein levels define a spectrum of FS basket cells with different properties, whose relative proportions are, however, continuously adjusted in response to neuronal activity. Our findings therefore suggest that interneuron properties are malleable in the adult cortex, at least to a certain extent.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702376/" 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/PMC4702376/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dehorter, Nathalie -- Ciceri, Gabriele -- Bartolini, Giorgia -- Lim, Lynette -- del Pino, Isabel -- Marin, Oscar -- 103714MA/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2015 Sep 11;349(6253):1216-20. doi: 10.1126/science.aab3415.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Centre for Developmental Neurobiology, Medical Research Council, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK. Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernandez, 03550 Sant Joan d'Alacant, Spain. ; Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernandez, 03550 Sant Joan d'Alacant, Spain. ; MRC Centre for Developmental Neurobiology, Medical Research Council, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK. Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernandez, 03550 Sant Joan d'Alacant, Spain. oscar.marin@kcl.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26359400" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cerebral Cortex/cytology/metabolism/*physiology ; DNA-Binding Proteins/genetics/*metabolism ; Interneurons/cytology/metabolism/*physiology ; Mice ; Mice, Mutant Strains ; Mitosis ; Mutation ; Nerve Net/cytology/metabolism/*physiology ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic
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  • 9
    Publication Date: 2015-03-15
    Description: Human occupation of tropical rainforest habitats is thought to be a mainly Holocene phenomenon. Although archaeological and paleoenvironmental data have hinted at pre-Holocene rainforest foraging, earlier human reliance on rainforest resources has not been shown directly. We applied stable carbon and oxygen isotope analysis to human and faunal tooth enamel from four late Pleistocene-to-Holocene archaeological sites in Sri Lanka. The results show that human foragers relied primarily on rainforest resources from at least ~20,000 years ago, with a distinct preference for semi-open rainforest and rain forest edges. Homo sapiens' relationship with the tropical rainforests of South Asia is therefore long-standing, a conclusion that indicates the time-depth of anthropogenic reliance and influence on these habitats.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roberts, Patrick -- Perera, Nimal -- Wedage, Oshan -- Deraniyagala, Siran -- Perera, Jude -- Eregama, Saman -- Gledhill, Andrew -- Petraglia, Michael D -- Lee-Thorp, Julia A -- New York, N.Y. -- Science. 2015 Mar 13;347(6227):1246-9. doi: 10.1126/science.aaa1230.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Archaeology, Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, University of Oxford, South Parks Road, Oxford OX1 3QY, UK. patrick.roberts@rlaha.ox.ac.uk. ; Postgraduate Institute of Archaeology, 407 Bauddhaloka Mawatha, Colombo 00700, Sri Lanka. ; Department of Archaeology, Sir Marcus Fernando Mawatha, Colombo, Sri Lanka. ; Division of Geographic, Archaeological and Environmental Sciences, University of Bradford, Bradford BD7 1DP, UK. ; School of Archaeology, Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, University of Oxford, South Parks Road, Oxford OX1 3QY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25766234" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeology ; Carbon Isotopes/analysis ; Dental Enamel/chemistry ; Diet ; *Fossils ; History, Ancient ; Humans ; Oxygen Isotopes/analysis ; Paleodontology ; Plants ; *Rainforest ; Sri Lanka ; Time ; Trees
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  • 10
    Publication Date: 2015-06-06
    Description: Warming of the oceans and consequent loss of dissolved oxygen (O2) will alter marine ecosystems, but a mechanistic framework to predict the impact of multiple stressors on viable habitat is lacking. Here, we integrate physiological, climatic, and biogeographic data to calibrate and then map a key metabolic index-the ratio of O2 supply to resting metabolic O2 demand-across geographic ranges of several marine ectotherms. These species differ in thermal and hypoxic tolerances, but their contemporary distributions are all bounded at the equatorward edge by a minimum metabolic index of ~2 to 5, indicative of a critical energetic requirement for organismal activity. The combined effects of warming and O2 loss this century are projected to reduce the upper ocean's metabolic index by ~20% globally and by ~50% in northern high-latitude regions, forcing poleward and vertical contraction of metabolically viable habitats and species ranges.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deutsch, Curtis -- Ferrel, Aaron -- Seibel, Brad -- Portner, Hans-Otto -- Huey, Raymond B -- New York, N.Y. -- Science. 2015 Jun 5;348(6239):1132-5. doi: 10.1126/science.aaa1605.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA. cdeutsch@uw.edu. ; Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, CA 90095, USA. ; Biological Sciences Department, University of Rhode Island, Kingston, RI 02881, USA. ; Alfred Wegener Institute, D-27570 Bremerhaven, Germany. ; Department of Biology, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26045435" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Animals ; Aquatic Organisms/*metabolism ; Brachyura/metabolism ; *Climate Change ; Ecosystem ; Gadus morhua/metabolism ; Oceans and Seas ; Oxygen/*metabolism ; Perciformes/metabolism ; Sea Bream/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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