ALBERT

Description: Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however, no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this correlation does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology of this emerging virus in the Americas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faria, Nuno Rodrigues -- Azevedo, Raimunda do Socorro da Silva -- Kraemer, Moritz U G -- Souza, Renato -- Cunha, Mariana Sequetin -- Hill, Sarah C -- Theze, Julien -- Bonsall, Michael B -- Bowden, Thomas A -- Rissanen, Ilona -- Rocco, Iray Maria -- Nogueira, Juliana Silva -- Maeda, Adriana Yurika -- Vasami, Fernanda Giseli da Silva -- Macedo, Fernando Luiz de Lima -- Suzuki, Akemi -- Rodrigues, Sueli Guerreiro -- Cruz, Ana Cecilia Ribeiro -- Nunes, Bruno Tardeli -- Medeiros, Daniele Barbosa de Almeida -- Rodrigues, Daniela Sueli Guerreiro -- Nunes Queiroz, Alice Louize -- da Silva, Eliana Vieira Pinto -- Henriques, Daniele Freitas -- Travassos da Rosa, Elisabeth Salbe -- de Oliveira, Consuelo Silva -- Martins, Livia Caricio -- Vasconcelos, Helena Baldez -- Casseb, Livia Medeiros Neves -- Simith, Darlene de Brito -- Messina, Jane P -- Abade, Leandro -- Lourenco, Jose -- Carlos Junior Alcantara, Luiz -- de Lima, Maricelia Maia -- Giovanetti, Marta -- Hay, Simon I -- de Oliveira, Rodrigo Santos -- Lemos, Poliana da Silva -- de Oliveira, Layanna Freitas -- de Lima, Clayton Pereira Silva -- da Silva, Sandro Patroca -- de Vasconcelos, Janaina Mota -- Franco, Luciano -- Cardoso, Jedson Ferreira -- Vianez-Junior, Joao Lidio da Silva Goncalves -- Mir, Daiana -- Bello, Gonzalo -- Delatorre, Edson -- Khan, Kamran -- Creatore, Marisa -- Coelho, Giovanini Evelim -- de Oliveira, Wanderson Kleber -- Tesh, Robert -- Pybus, Oliver G -- Nunes, Marcio R T -- Vasconcelos, Pedro F C -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 095066/Wellcome Trust/United Kingdom -- 102427/Wellcome Trust/United Kingdom -- MR/L009528/1/Medical Research Council/United Kingdom -- R24 AT 120942/AT/NCCIH NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 15;352(6283):345-9. doi: 10.1126/science.aaf5036. Epub 2016 Mar 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA 67030-000, Brazil. Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. ; Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para State, Brazil. ; Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. ; Instituto Adolfo Lutz, University of Sao Paulo, Sao Paulo, Brazil. ; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. ; Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. Metabiota, San Francisco, CA 94104, USA. ; Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil. ; Centre of Post Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil. ; Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA 98121, USA. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. ; Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA 67030-000, Brazil. ; Laboratorio de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil. ; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada. Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada. ; Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada. ; Brazilian Ministry of Health, Brasilia, Brazil. ; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA. ; Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. Metabiota, San Francisco, CA 94104, USA. oliver.pybus@zoo.ox.ac.uk marcionunesbrasil@yahoo.com.br pedrovasconcelos@iec.pa.gov.br. ; Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA 67030-000, Brazil. Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA. oliver.pybus@zoo.ox.ac.uk marcionunesbrasil@yahoo.com.br pedrovasconcelos@iec.pa.gov.br. ; Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para State, Brazil. oliver.pybus@zoo.ox.ac.uk marcionunesbrasil@yahoo.com.br pedrovasconcelos@iec.pa.gov.br.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27013429" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nepstad, Daniel -- Soares-Filho, Britaldo S -- Merry, Frank -- Lima, Andre -- Moutinho, Paulo -- Carter, John -- Bowman, Maria -- Cattaneo, Andrea -- Rodrigues, Hermann -- Schwartzman, Stephan -- McGrath, David G -- Stickler, Claudia M -- Lubowski, Ruben -- Piris-Cabezas, Pedro -- Rivero, Sergio -- Alencar, Ane -- Almeida, Oriana -- Stella, Osvaldo -- New York, N.Y. -- Science. 2009 Dec 4;326(5958):1350-1. doi: 10.1126/science.1182108.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Woods Hole Research Center, Falmouth, MA 02540, USA. dnepstad@whrc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965742" target="_blank"〉PubMed〈/a〉

Description: Climate influences a variety of ecological processes. These effects operate through local weather parameters such as temperature, wind, rain, snow, and ocean currents, as well as interactions among these. In the temperate zone, local variations in weather are often coupled over large geographic areas through the transient behavior of atmospheric planetary-scale waves. These variations drive temporally and spatially averaged exchanges of heat, momentum, and water vapor that ultimately determine growth, recruitment, and migration patterns. Recently, there have been several studies of the impact of large-scale climatic forcing on ecological systems. We review how two of the best-known climate phenomena-the North Atlantic Oscillation and the El Nino-Southern Oscillation-affect ecological patterns and processes in both marine and terrestrial systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stenseth, Nils Chr -- Mysterud, Atle -- Ottersen, Geir -- Hurrell, James W -- Chan, Kung-Sik -- Lima, Mauricio -- New York, N.Y. -- Science. 2002 Aug 23;297(5585):1292-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Division of Zoology, University of Oslo, Post Office Box 1050 Blindern, N-0316 Oslo, Norway. n.c.stenseth@bio.uio.no〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12193777" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665766/" 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/PMC3665766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lima, Christopher D -- Schulman, Brenda A -- R01 GM065872/GM/NIGMS NIH HHS/ -- R01 GM069530/GM/NIGMS NIH HHS/ -- R01 GM077053/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Sep 6;489(7414):43-4. doi: 10.1038/489043a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955611" target="_blank"〉PubMed〈/a〉

Description: Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748/" 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/PMC4529748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉FANTOM Consortium and the RIKEN PMI and CLST (DGT) -- Forrest, Alistair R R -- Kawaji, Hideya -- Rehli, Michael -- Baillie, J Kenneth -- de Hoon, Michiel J L -- Haberle, Vanja -- Lassmann, Timo -- Kulakovskiy, Ivan V -- Lizio, Marina -- Itoh, Masayoshi -- Andersson, Robin -- Mungall, Christopher J -- Meehan, Terrence F -- Schmeier, Sebastian -- Bertin, Nicolas -- Jorgensen, Mette -- Dimont, Emmanuel -- Arner, Erik -- Schmidl, Christian -- Schaefer, Ulf -- Medvedeva, Yulia A -- Plessy, Charles -- Vitezic, Morana -- Severin, Jessica -- Semple, Colin A -- Ishizu, Yuri -- Young, Robert S -- Francescatto, Margherita -- Alam, Intikhab -- Albanese, Davide -- Altschuler, Gabriel M -- Arakawa, Takahiro -- Archer, John A C -- Arner, Peter -- Babina, Magda -- Rennie, Sarah -- Balwierz, Piotr J -- Beckhouse, Anthony G -- Pradhan-Bhatt, Swati -- Blake, Judith A -- Blumenthal, Antje -- Bodega, Beatrice -- Bonetti, Alessandro -- Briggs, James -- Brombacher, Frank -- Burroughs, A Maxwell -- Califano, Andrea -- Cannistraci, Carlo V -- Carbajo, Daniel -- Chen, Yun -- Chierici, Marco -- Ciani, Yari -- Clevers, Hans C -- Dalla, Emiliano -- Davis, Carrie A -- Detmar, Michael -- Diehl, Alexander D -- Dohi, Taeko -- Drablos, Finn -- Edge, Albert S B -- Edinger, Matthias -- Ekwall, Karl -- Endoh, Mitsuhiro -- Enomoto, Hideki -- Fagiolini, Michela -- Fairbairn, Lynsey -- Fang, Hai -- Farach-Carson, Mary C -- Faulkner, Geoffrey J -- Favorov, Alexander V -- Fisher, Malcolm E -- Frith, Martin C -- Fujita, Rie -- Fukuda, Shiro -- Furlanello, Cesare -- Furino, Masaaki -- Furusawa, Jun-ichi -- Geijtenbeek, Teunis B -- Gibson, Andrew P -- Gingeras, Thomas -- Goldowitz, Daniel -- Gough, Julian -- Guhl, Sven -- Guler, Reto -- Gustincich, Stefano -- Ha, Thomas J -- Hamaguchi, Masahide -- Hara, Mitsuko -- Harbers, Matthias -- Harshbarger, Jayson -- Hasegawa, Akira -- Hasegawa, Yuki -- Hashimoto, Takehiro -- Herlyn, Meenhard -- Hitchens, Kelly J -- Ho Sui, Shannan J -- Hofmann, Oliver M -- Hoof, Ilka -- Hori, Furni -- Huminiecki, Lukasz -- Iida, Kei -- Ikawa, Tomokatsu -- Jankovic, Boris R -- Jia, Hui -- Joshi, Anagha -- Jurman, Giuseppe -- Kaczkowski, Bogumil -- Kai, Chieko -- Kaida, Kaoru -- Kaiho, Ai -- Kajiyama, Kazuhiro -- Kanamori-Katayama, Mutsumi -- Kasianov, Artem S -- Kasukawa, Takeya -- Katayama, Shintaro -- Kato, Sachi -- Kawaguchi, Shuji -- Kawamoto, Hiroshi -- Kawamura, Yuki I -- Kawashima, Tsugumi -- Kempfle, Judith S -- Kenna, Tony J -- Kere, Juha -- Khachigian, Levon M -- Kitamura, Toshio -- Klinken, S Peter -- Knox, Alan J -- Kojima, Miki -- Kojima, Soichi -- Kondo, Naoto -- Koseki, Haruhiko -- Koyasu, Shigeo -- Krampitz, Sarah -- Kubosaki, Atsutaka -- Kwon, Andrew T -- Laros, Jeroen F J -- Lee, Weonju -- Lennartsson, Andreas -- Li, Kang -- Lilje, Berit -- Lipovich, Leonard -- Mackay-Sim, Alan -- Manabe, Ri-ichiroh -- Mar, Jessica C -- Marchand, Benoit -- Mathelier, Anthony -- Mejhert, Niklas -- Meynert, Alison -- Mizuno, Yosuke -- de Lima Morais, David A -- Morikawa, Hiromasa -- Morimoto, Mitsuru -- Moro, Kazuyo -- Motakis, Efthymios -- Motohashi, Hozumi -- Mummery, Christine L -- Murata, Mitsuyoshi -- Nagao-Sato, Sayaka -- Nakachi, Yutaka -- Nakahara, Fumio -- Nakamura, Toshiyuki -- Nakamura, Yukio -- Nakazato, Kenichi -- van Nimwegen, Erik -- Ninomiya, Noriko -- Nishiyori, Hiromi -- Noma, Shohei -- Noazaki, Tadasuke -- Ogishima, Soichi -- Ohkura, Naganari -- Ohimiya, Hiroko -- Ohno, Hiroshi -- Ohshima, Mitsuhiro -- Okada-Hatakeyama, Mariko -- Okazaki, Yasushi -- Orlando, Valerio -- Ovchinnikov, Dmitry A -- Pain, Arnab -- Passier, Robert -- Patrikakis, Margaret -- Persson, Helena -- Piazza, Silvano -- Prendergast, James G D -- Rackham, Owen J L -- Ramilowski, Jordan A -- Rashid, Mamoon -- Ravasi, Timothy -- Rizzu, Patrizia -- Roncador, Marco -- Roy, Sugata -- Rye, Morten B -- Saijyo, Eri -- Sajantila, Antti -- Saka, Akiko -- Sakaguchi, Shimon -- Sakai, Mizuho -- Sato, Hiroki -- Savvi, Suzana -- Saxena, Alka -- Schneider, Claudio -- Schultes, Erik A -- Schulze-Tanzil, Gundula G -- Schwegmann, Anita -- Sengstag, Thierry -- Sheng, Guojun -- Shimoji, Hisashi -- Shimoni, Yishai -- Shin, Jay W -- Simon, Christophe -- Sugiyama, Daisuke -- Sugiyama, Takaai -- Suzuki, Masanori -- Suzuki, Naoko -- Swoboda, Rolf K -- 't Hoen, Peter A C -- Tagami, Michihira -- Takahashi, Naoko -- Takai, Jun -- Tanaka, Hiroshi -- Tatsukawa, Hideki -- Tatum, Zuotian -- Thompson, Mark -- Toyodo, Hiroo -- Toyoda, Tetsuro -- Valen, Elvind -- van de Wetering, Marc -- van den Berg, Linda M -- Verado, Roberto -- Vijayan, Dipti -- Vorontsov, Ilya E -- Wasserman, Wyeth W -- Watanabe, Shoko -- Wells, Christine A -- Winteringham, Louise N -- Wolvetang, Ernst -- Wood, Emily J -- Yamaguchi, Yoko -- Yamamoto, Masayuki -- Yoneda, Misako -- Yonekura, Yohei -- Yoshida, Shigehiro -- Zabierowski, Susan E -- Zhang, Peter G -- Zhao, Xiaobei -- Zucchelli, Silvia -- Summers, Kim M -- Suzuki, Harukazu -- Daub, Carsten O -- Kawai, Jun -- Heutink, Peter -- Hide, Winston -- Freeman, Tom C -- Lenhard, Boris -- Bajic, Vladimir B -- Taylor, Martin S -- Makeev, Vsevolod J -- Sandelin, Albin -- Hume, David A -- Carninci, Piero -- Hayashizaki, Yoshihide -- BB/F003722/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G022771/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/I001107/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- MC_PC_U127597124/Medical Research Council/United Kingdom -- MC_UP_1102/1/Medical Research Council/United Kingdom -- R01 DE022969/DE/NIDCR NIH HHS/ -- R01 GM084875/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24670764" target="_blank"〉PubMed〈/a〉

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〉

Description: Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lima-Mendez, Gipsi -- Faust, Karoline -- Henry, Nicolas -- Decelle, Johan -- Colin, Sebastien -- Carcillo, Fabrizio -- Chaffron, Samuel -- Ignacio-Espinosa, J Cesar -- Roux, Simon -- Vincent, Flora -- Bittner, Lucie -- Darzi, Youssef -- Wang, Jun -- Audic, Stephane -- Berline, Leo -- Bontempi, Gianluca -- Cabello, Ana M -- Coppola, Laurent -- Cornejo-Castillo, Francisco M -- d'Ovidio, Francesco -- De Meester, Luc -- Ferrera, Isabel -- Garet-Delmas, Marie-Jose -- Guidi, Lionel -- Lara, Elena -- Pesant, Stephane -- Royo-Llonch, Marta -- Salazar, Guillem -- Sanchez, Pablo -- Sebastian, Marta -- Souffreau, Caroline -- Dimier, Celine -- Picheral, Marc -- Searson, Sarah -- Kandels-Lewis, Stefanie -- Tara Oceans coordinators -- Gorsky, Gabriel -- Not, Fabrice -- Ogata, Hiroyuki -- Speich, Sabrina -- Stemmann, Lars -- Weissenbach, Jean -- Wincker, Patrick -- Acinas, Silvia G -- Sunagawa, Shinichi -- Bork, Peer -- Sullivan, Matthew B -- Karsenti, Eric -- Bowler, Chris -- de Vargas, Colomban -- Raes, Jeroen -- New York, N.Y. -- Science. 2015 May 22;348(6237):1262073. doi: 10.1126/science.1262073.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. ; Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Universite Libre de Bruxelles (ULB), Brussels, Belgium. ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. ; VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Institut de Biologie Paris-Seine, CNRS FR3631, F-75005, Paris, France. ; VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. ; Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. ; CNRS, UMR 7093, Laboratoire d'Oceanographie de Villefranche (LOV), Observatoire Oceanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universites, UPMC Paris 06, UMR 7093, Laboratoire d'Oceanographie de Villefranche (LOV), Observatoire Oceanologique, F-06230 Villefranche-sur-mer, France. ; Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Universite Libre de Bruxelles (ULB), Brussels, Belgium. ; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Cientificas (CSIC), Pg. Maritim de la Barceloneta, 37-49, Barcelona E08003, Spain. ; Sorbonne Universites, UPMC, Universite Paris 06, CNRS-Institut pour la Recherche et le Developpement-Museum National d'Histoire Naturelle, Laboratoire d'Oceanographie et du Climat: Experimentations et Approches Numeriques (LOCEAN) Laboratory, 4 Place Jussieu, 75005, Paris, France. ; KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Charles Deberiotstraat 32, 3000 Leuven. ; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Hochschulring 18, 28359 Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Hochschulring 18, 28359 Bremen, Germany. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany. ; Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011 Kyoto, Japan. ; Department of Geosciences, Laboratoire de Meteorologie Dynamique (LMD), Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Ocean, Universite de Bretagne Occidentale (UBO)-Institut Universaire Europeen de la Mer (IUEM), Palce Copernic, 29820 Polouzane, France. ; Commissariat a l'Energie Atomique (CEA), Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France. CNRS, UMR 8030, 2 rue Gaston Cremieux, 91000 Evry, France. Universite d'Evry, UMR 8030, CP5706 Evry, France. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbruck-Centre for Molecular Medicine, 13092 Berlin, Germany. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de. ; Ecole Normale Superieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de. ; Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universites, Universite Pierre et Marie Curie (UPMC) Universite Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de. ; Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. jeroen.raes@vib-kuleuven.be vargas@sb-roscoff.fr cbowler@biologie.ens.fr karsenti@embl.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25999517" target="_blank"〉PubMed〈/a〉