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2. A Polypill Strategy to Improve Adherence: Results From the FOCUS Project

Author

Castellano, José M., Sanz, Ginés, Peñalvo, José L., Bansilal, Sameer, Fernández-Ortiz, Antonio, Alvarez, Luz, Guzmán, Luis, Linares, Juan Carlos, García, Fernando, D’Aniello, Fabiana, Arnáiz, Joan Albert, Varea, Sara, Martínez, Felipe, Lorenzatti, Alberto, Imaz, Iñaki, Sánchez-Gómez, Luis M., Roncaglioni, Maria Carla, Baviera, Marta, Smith, Sidney C., Jr., Taubert, Kathryn, Pocock, Stuart, Brotons, Carlos, Farkouh, Michael E., and Fuster, Valentin

Published
2014
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3. The effect of component-resolved diagnosis on specific immunotherapy prescription in children with hay fever

Author

Stringari, Giovanna, Tripodi, Salvatore, Caffarelli, Carlo, Dondi, Arianna, Asero, Riccardo, Di Rienzo Businco, Andrea, Bianchi, Annamaria, Candelotti, Paolo, Ricci, Giampaolo, Bellini, Federica, Maiello, Nunzia, Miraglia del Giudice, Michele, Frediani, Tullio, Sodano, Simona, Dello Iacono, Iride, Macrì, Francesco, Peparini, Ilaria, Povesi Dascola, Carlotta, Patria, Maria Francesca, Varin, Elena, Peroni, Diego, Comberiati, Pasquale, Chini, Loredana, Moschese, Viviana, Lucarelli, Sandra, Bernardini, Roberto, Pingitore, Giuseppe, Pelosi, Umberto, Tosca, Mariangela, Cirisano, Anastasia, Faggian, Diego, Travaglini, Alessandro, Plebani, Mario, and Matricardi, Paolo Maria

Published
2014
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8. STS-95における植物研究実験 1998年

Author

Japanese Soc. for Biol. Sci. in Space

Subjects
微小重力, 屈曲, 宇宙輸送システム, Vigna, growth, Cucumis sativus L, Arabidopsis thaliana L, 生長抑制, STS 95, Zea mays, microgravity, growth inhibition, 遮光, 生長, curvature, etiolation, Oryza sativa L, Space Transportation System, 発生, development, cell wall extensibility, Pisum sativum, STS-95, 細胞壁伸展
Abstract

宇宙における微小重力の植物に対する影響に関し、以下の主題について年齢・組織・器官・部位・変種・種による反応の違いを調べ、地上対照実験との比較を論じた。遮光条件下での苗条の生長と発生、細胞壁の伸展性、オーキシン極性移動、電界印加による伸長抑制、負の重力依存形態形成、CS-IAA1の発現様式、細胞および細胞骨格構造変化、屈水反応、細胞壁代謝の変化、自発的形態形成、細胞壁の背腹性、および植物ホルモンの形態形成への影響。, Under microgravity conditions in space, the different responses according to the difference of ages, tissues, organs, regions cultivars and species were examined on the following topics and compared with those on the ground experiments: growth and development of etiolated seedlings, cell walls extensibility, auxin polar transport, inhibition of elongation by an applied electric field, negative gravimorphogenesis, expression patterns of CS-IAA1, changes of cytological and cytoskeletal structure, hydrotropism, changes in cell wall metabolism, automorphogenesis, dorsiventrality of cell wall, and effect of phytohormones for automorphogenesis., 資料番号: AA0003840000, レポート番号: NASDA-TMR-000004E

Published
2000

22. Prognostic Impact of EZH2 and ASXL1 Mutation in Myelofibrosis

Author

Guglielmelli, Paola, Biamonte, Flavia, Score, Johannah, Hidalgo-Curtis, Claire, Cervantes, Francisco, Maffioli, Margherita, Fanelli, Tiziana, Ernst, Thomas, Winkelman, Nils, Jones, Amy V, Zoi, Katerina, Reiter, Andreas, Duncombe, Andrew, Villani, Laura, Paoli, Chiara, Bosi, Alberto, Barosi, Giovanni, Cross, Nicholas C.P., and Vannucchi, Alessandro M.

Published
2011
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26. Microbial characteristics in homes of asthmatic and non-asthmatic adults in the ECRHS cohort

Author

1 ] Natl Inst Hlth & Welf, Living Environm & Hlth Unit, Kuopio, Finland Show more [ 2 ] Univ Eastern Finland, Dept Environm & Biol Sci, Kuopio, Finland Show more [ 3 ] Univ Helsinki, Dept Publ Hlth, Helsinki, Finland Show more [ 4 ] Ctr Res Environm Epidemiol CREAL, ISGlobal, Barcelona, Spain Show more [ 5 ] UPF, Barcelona, Spain Show more [ 6 ] CIBERESP, Barcelona, Spain Show more [ 7 ] Katholieke Univ Leuven, Dept Publ Hlth & Primary Care, Ctr Environm & Hlth, Leuven, Belgium [ 8 ] Res Fdn Flanders FWO, Brussels, Belgium Show more [ 9 ] Swiss Trop & Publ Hlth Inst, Head Dept Epidemiol & Publ Hlth, Basel, Switzerland Show more [ 10 ] Univ Basel, Dept Publ Hlth, Basel, Switzerland Show more [ 11 ] Umea Univ, Dept Publ Hlth & Clin Med, Occupat & Environm Med, Umea, Sweden Show more [ 12 ] Sahlgrens Univ Hosp, Dept Occupat & Environm Med, Gothenburg, Sweden Show more [ 13 ] Uppsala Univ, Dept Med Sci, Uppsala, Sweden Show more [ 14 ] Univ Grenoble Alpes, INSERM, CHU Grenoble Alpes, U 1209, Grenoble, France [ 15 ] Landspitali Univ Hosp E7, Dept Resp Med & Sleep, Reykjavik, Iceland Show more [ 16 ] Univ Iceland, Fac Med, Reykjavik, Iceland Show more [ 17 ] Imperial Coll, Natl Heart & Lung Inst, Populat Hlth & Occupat Dis, London, England Show more [ 18 ] Imperial Coll, MRC PHE Ctr Environm & Hlth, London, England Show more [ 19 ] Ludwig Maximillians Univ Munich, Univ Hosp Munich, Inst & Outpatient Clin Occupat Social & Environm, German Ctr Lung Res DZL, Munich, Germany Show more [ 20 ] German Res Ctr Environm Hlth, Inst Epidemiol 1, Helmholtz Zentrum Munchen, Neuherberg, German, Living Environment and Health Unit; National Institute for Health and Welfare; Kuopio Finland, ISGlobal; Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain, Centre for Environment and Health - Department of Public Health and Primary Care; KU Leuven; Leuven Belgium, Head Department Epidemiology and Public Health; Swiss Tropical and Public Health Institute; Basel Switzerland, Department of Public Health and Clinical Medicine, Occupational and Environmental Medicine; Umeå University; Umeå Sweden, Department of Occupational and Environmental Medicine; Sahlgrenska University Hospital; Gothenburg Sweden, Department of Medical Sciences; Uppsala University; Uppsala Sweden, CHU de Grenoble Alpes; INSERM U 1209; Université Grenoble Alpes; Grenoble France, Department of Respiratory Medicine and Sleep; Landspitali University Hospital (E7); Reykjavik Iceland, Population Health and Occupational Disease; Imperial College; National Heart and Lung Institute; London UK, Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine; University Hospital Munich; Ludwig Maximillians University Munich; Member of German Center for Lung Research (DZL); Munich Germany, Valkonen, M., Täubel, M., Pekkanen, J., Tischer, C., Rintala, H., Zock, J.-P., Casas, L., Probst-Hensch, N., Forsberg, B., Holm, M., Janson, C., Pin, I., Gislason, T., Jarvis, D., Heinrich, J., Hyvärinen, A., 1 ] Natl Inst Hlth & Welf, Living Environm & Hlth Unit, Kuopio, Finland Show more [ 2 ] Univ Eastern Finland, Dept Environm & Biol Sci, Kuopio, Finland Show more [ 3 ] Univ Helsinki, Dept Publ Hlth, Helsinki, Finland Show more [ 4 ] Ctr Res Environm Epidemiol CREAL, ISGlobal, Barcelona, Spain Show more [ 5 ] UPF, Barcelona, Spain Show more [ 6 ] CIBERESP, Barcelona, Spain Show more [ 7 ] Katholieke Univ Leuven, Dept Publ Hlth & Primary Care, Ctr Environm & Hlth, Leuven, Belgium [ 8 ] Res Fdn Flanders FWO, Brussels, Belgium Show more [ 9 ] Swiss Trop & Publ Hlth Inst, Head Dept Epidemiol & Publ Hlth, Basel, Switzerland Show more [ 10 ] Univ Basel, Dept Publ Hlth, Basel, Switzerland Show more [ 11 ] Umea Univ, Dept Publ Hlth & Clin Med, Occupat & Environm Med, Umea, Sweden Show more [ 12 ] Sahlgrens Univ Hosp, Dept Occupat & Environm Med, Gothenburg, Sweden Show more [ 13 ] Uppsala Univ, Dept Med Sci, Uppsala, Sweden Show more [ 14 ] Univ Grenoble Alpes, INSERM, CHU Grenoble Alpes, U 1209, Grenoble, France [ 15 ] Landspitali Univ Hosp E7, Dept Resp Med & Sleep, Reykjavik, Iceland Show more [ 16 ] Univ Iceland, Fac Med, Reykjavik, Iceland Show more [ 17 ] Imperial Coll, Natl Heart & Lung Inst, Populat Hlth & Occupat Dis, London, England Show more [ 18 ] Imperial Coll, MRC PHE Ctr Environm & Hlth, London, England Show more [ 19 ] Ludwig Maximillians Univ Munich, Univ Hosp Munich, Inst & Outpatient Clin Occupat Social & Environm, German Ctr Lung Res DZL, Munich, Germany Show more [ 20 ] German Res Ctr Environm Hlth, Inst Epidemiol 1, Helmholtz Zentrum Munchen, Neuherberg, German, Living Environment and Health Unit; National Institute for Health and Welfare; Kuopio Finland, ISGlobal; Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain, Centre for Environment and Health - Department of Public Health and Primary Care; KU Leuven; Leuven Belgium, Head Department Epidemiology and Public Health; Swiss Tropical and Public Health Institute; Basel Switzerland, Department of Public Health and Clinical Medicine, Occupational and Environmental Medicine; Umeå University; Umeå Sweden, Department of Occupational and Environmental Medicine; Sahlgrenska University Hospital; Gothenburg Sweden, Department of Medical Sciences; Uppsala University; Uppsala Sweden, CHU de Grenoble Alpes; INSERM U 1209; Université Grenoble Alpes; Grenoble France, Department of Respiratory Medicine and Sleep; Landspitali University Hospital (E7); Reykjavik Iceland, Population Health and Occupational Disease; Imperial College; National Heart and Lung Institute; London UK, Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine; University Hospital Munich; Ludwig Maximillians University Munich; Member of German Center for Lung Research (DZL); Munich Germany, Valkonen, M., Täubel, M., Pekkanen, J., Tischer, C., Rintala, H., Zock, J.-P., Casas, L., Probst-Hensch, N., Forsberg, B., Holm, M., Janson, C., Pin, I., Gislason, T., Jarvis, D., Heinrich, J., and Hyvärinen, A.

Abstract

To access publisher's full text version of this article click on the hyperlink below, Microbial exposures in homes of asthmatic adults have been rarely investigated; specificities and implications for respiratory health are not well understood. The objectives of this study were to investigate associations of microbial levels with asthma status, asthma symptoms, bronchial hyperresponsiveness (BHR), and atopy. Mattress dust samples of 199 asthmatics and 198 control subjects from 7 European countries participating in the European Community Respiratory Health Survey II study were analyzed for fungal and bacterial cell wall components and individual taxa. We observed trends for protective associations of higher levels of mostly bacterial markers. Increased levels of muramic acid, a cell wall component predominant in Gram-positive bacteria, tended to be inversely associated with asthma (OR's for different quartiles: II 0.71 [0.39-1.30], III 0.44 [0.23-0.82], and IV 0.60 [0.31-1.18] P for trend .07) and with asthma score (P for trend .06) and with atopy (P for trend .02). These associations were more pronounced in northern Europe. This study among adults across Europe supports a potential protective effect of Gram-positive bacteria in mattress dust and points out that this may be more pronounced in areas where microbial exposure levels are generally lower.

28. Pan-genomic analysis of Corynebacterium amycolatum gives insights into molecular mechanisms underpinning the transition to a pathogenic phenotype

Author

Jesus, Hendor N. R., Rocha, Danilo J. P. G., Ramos, Rommel T. J., Silva, Artur, Brenig, Bertram, Goes-Neto, Aristoteles, Costa, Mateus M., Soares, Siomar C., Azevedo, Vasco, Aguiar, Eric R. G. R., Martinez-Martinez, Luiz, Ocampo, Alain, Alibi, Sana, Dorta, Alexis, Pacheco, Luis G. C., Navas, Jesus, [Jesus, Hendor N. R.] Univ Fed Bahia, Inst Hlth Sci, Multictr Postgrad Program Biochem & Mol Biol PMBq, Salvador, BA, Brazil, [Pacheco, Luis G. C.] Univ Fed Bahia, Inst Hlth Sci, Multictr Postgrad Program Biochem & Mol Biol PMBq, Salvador, BA, Brazil, [Rocha, Danilo J. P. G.] Univ Fed Bahia, Inst Hlth Sci, Postgrad Program Biotechnol, Salvador, BA, Brazil, [Pacheco, Luis G. C.] Univ Fed Bahia, Inst Hlth Sci, Postgrad Program Biotechnol, Salvador, BA, Brazil, [Ramos, Rommel T. J.] Fed Univ Para, Inst Biol Sci, Belem, Para, Brazil, [Silva, Artur] Fed Univ Para, Inst Biol Sci, Belem, Para, Brazil, [Brenig, Bertram] Univ Gottingen, Inst Vet Med, Gottingen, Germany, [Goes-Neto, Aristoteles] Univ Fed Minas Gerais, Inst Biol Sci, Belo Horizonte, MG, Brazil, [Azevedo, Vasco] Univ Fed Minas Gerais, Inst Biol Sci, Belo Horizonte, MG, Brazil, [Costa, Mateus M.] Univ Fed Vale Do Sao Francisco, Lab Microbiol & Imunol Anim LAMIA, Petrolina, PE, Brazil, [Soares, Siomar C.] Fed Univ Triangulo Mineiro UFTM, Inst Biol & Nat Sci, Dept Immunol Microbiol & Parasitol, Uberaba, MG, Brazil, [Aguiar, Eric R. G. R.] State Univ St Cruz, Dept Biol Sci, Ilheus, BA, Brazil, [Martinez-Martinez, Luiz] Hosp Univ Reina Sofia, Unidad Gest Clin, Cordoba, Spain, [Martinez-Martinez, Luiz] Univ Cordoba, Dept Microbiol, Cordoba, Spain, [Martinez-Martinez, Luiz] Inst Maimonides Invest Biomed Cordoba IMIBIC, Cordoba, Spain, [Ocampo, Alain] Univ Hosp Marques de Valdecilla, Microbiol Serv, Santander, Spain, [Ocampo, Alain] Inst Invest Valdecilla IDIVAL, Santander, Spain, [Dorta, Alexis] Inst Invest Valdecilla IDIVAL, Santander, Spain, [Navas, Jesus] Inst Invest Valdecilla IDIVAL, Santander, Spain, [Alibi, Sana] Res Unit Anal & Proc Appl Environm, Rejiche, Tunisia, [Dorta, Alexis] Cantabria Univ, Fac Med, BIOMEDAGE Grp, Santander, Spain, [Navas, Jesus] Cantabria Univ, Fac Med, BIOMEDAGE Grp, Santander, Spain, FAPESB, CNPq, CAPES, and RECOM Network, Brazil

Subjects
Islands, System, Microbiology (medical), Identification, Virulence, Iron, Diphtheriae, virulence factor, Microbiology, Pilus, Mycolic acids, multidrug resistance, Siderophore, Corynebacterium amycolatum, pan-genome, emerging pathogen, Cell-wall
Abstract

Corynebacterium amycolatum is a nonlipophilic coryneform which is increasingly being recognized as a relevant human and animal pathogen showing multidrug resistance to commonly used antibiotics. However, little is known about the molecular mechanisms involved in transition from colonization to the MDR invasive phenotype in clinical isolates. In this study, we performed a comprehensive pan-genomic analysis of C. amycolatum, including 26 isolates from different countries. We obtained the novel genome sequences of 8 of them, which are multidrug resistant clinical isolates from Spain and Tunisia. They were analyzed together with other 18 complete or draft C. amycolatum genomes retrieved from GenBank. The species C. amycolatum presented an open pan-genome (α = 0.854905), with 3,280 gene families, being 1,690 (51.52%) in the core genome, 1,121 related to accessory genes (34.17%), and 469 related to unique genes (14.29%). Although some classic corynebacterial virulence factors are absent in the species C. amycolatum, we did identify genes associated with immune evasion, toxin, and antiphagocytosis among the predicted putative virulence factors. Additionally, we found genomic evidence for extensive acquisition of antimicrobial resistance genes through genomic islands.

Published
2022

30. Diversity and carbon storage across the tropical forest biome

Author

Connie J. Clark, Kofi Affum-Baffoe, Lan Qie, Timothy R. Baker, Abel Monteagudo-Mendoza, Lise Zemagho, Yadvinder Malhi, Javier Silva Espejo, Patricia Alvarez-Loayza, Lindsay F. Banin, Jefferson S. Hall, Ima Célia Guimarães Vieira, H. Priyadi, Jérôme Chave, Fernando Cornejo Valverde, Peter M. Umunay, J. W. Ferry Slik, Martin Gilpin, Ana Andrade, Andrew R. Marshall, Alvaro Cogollo Pacheco, Bonaventure Sonké, Rodrigo Sierra, Jan Bogaert, Emanuel Gloor, Christopher Baraloto, Guido Pardo, Nicholas J. Berry, Simon L. Lewis, Georgia Pickavance, Axel Dalberg Poulsen, Ismayadi Samsoedin, Vincent A. Vos, Carlos Cerón, Jean-Louis Doucet, Peter S. Ashton, William F. Laurance, Wannes Hubau, Thomas E. Lovejoy, Eric Chezeaux, Zorayda Restrepo, Aida Cuni-Sanchez, Kanehiro Kitayama, Everton Cristo de Almeida, Luiz E. O. C. Aragão, Sophie Fauset, Nadir Pallqui Camacho, Jan Reitsma, Corneille E. N. Ewango, Percy Núñez Vargas, Hans ter Steege, John Terborgh, Roel J. W. Brienen, Jean-François Bastin, Kamariah Abu Salim, Jon C. Lovett, Beatriz Schwantes Marimon, Simon Willcock, Marisol Toledo, Ben Hur Marimon Junior, Serge K. Begne, Greta C. Dargie, Carlos A. Quesada, Terese B. Hart, Martin J. P. Sullivan, Terry Sunderland, Ted R. Feldpausch, Eurídice N. Honorio Coronado, Stuart J. Davies, Lera Miles, Sean C. Thomas, Lip Khoon Kho, Lisa Steel, Jaques Mukinzi, Marie Noel Djuikouo K., Rafael de Paiva Salomão, Terry L. Erwin, Ervan Rutishauser, Edmar Almeida de Oliveira, Rafael Herrera, Shin-ichiro Aiba, Faustin Mpanya Lukasu, Damien Bonal, Sylvester Tan, Esteban Alvarez Dávila, Marielos Peña-Claros, José Luís Camargo, Lee J. T. White, James A. Comiskey, Hermann Taedoumg, Maxime Réjou-Méchain, Pascal Petronelli, Jean-Remy Makana, Ophelia Wang, Richard B. Primack, Gerardo A. Aymard C, Charles De Cannière, Luis Valenzuela Gamarra, Gabriela Lopez-Gonzalez, Leandro Maracahipes, Kuswata Kartawinata, Michael Balinga, Victor Chama Moscoso, Susan G. Laurance, Marcos Silveira, David Harris, Miguel E. Leal, Paulo S. Morandi, John Tshibamba Mukendi, Frans Bongers, Joey Talbot, Douglas Sheil, Reuben Nilus, John R. Poulsen, Oliver L. Phillips, Sch Geog, University of Nottingham, Dept Geog, University College of London [London] (UCL), Plant Systemat & Ecol Lab, Université de Yaoundé, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Instituto Nacional de Pesquisas da Amazônia (INPA), United Nations Environment Programme World Conservation Monitoring Centre, Missouri Botanical Garden (USA), Universidad Nacional San Antonio Abad del Cusco, Center for International Forestry Research (CIFOR), Coll Marine & Environm Sci, James Cook University, Leiden University, Agence Nationale des Parcs Nationaux du Gabon, Ecole de Terrain en Ecologie Tropicale (ECOTROP), Mensurat Unit, Forestry Research Institute of Ghana, Grad Sch Sci & Engn, Kagoshima University, Inst Biodiversidade & Floresta, Universidade Federal do Oeste do Pará, Universidade Federal do Mato Grosso (UFMT), Ctr Trop Conservat, Duke University [Durham], Universidad Nacional de Colombia, Coll Life & Environm Sci, University of Exeter, Dept Organism & Evolutionary Biol, Harvard University [Cambridge], Programa Ciencias Agro & Mar, Herbario Universitario PORT, Ctr Ecol & Hydrol, Dept Biol Sci, Int Ctr Trop Bot, Florida International University (FIU), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (Cirad-Es-UPR 105 BSEF), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Sch Geosci, University of Edinburgh, Biodivers & Landscape Unit, Université de Liège, Gembloux Agro-Bio Tech [Gembloux], Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Forest Ecol & Forest Management Grp, Wageningen University and Research Centre [Wageningen] (WUR), Projeto Dinam Biol Fragmentos Florestais, Herbario Alfredo Paredes, Universidad Agraria del Ecuador, Rougier Gabon, Nicholas Sch Environm, Duke University, Jardín Botánico de Medellín, Inventory & Monitoring Program, National Park Service, Smithsonian Institution, Andes to Amazon Biodiversity Program, Instituto de Investigaciones de la Amazonía Peruana, Smithsonian Tropical Research Institute, Landscape Ecol & Vegetal Prod Syst Unit, Université Libre de Bruxelles [Bruxelles] (ULB), Dept Bot & Plant Physiol, Fac Sci, University of Buea, Wildlife Conservation Society, Centre de Formation et de Recherche en Conservation Forestière (CEFRECOF), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Ctr Ecol, Instituto Venezolano de Investigaciones Cientificas (IVIC), Inst Geog & Reg Forsch, University of Vienna, Royal Botanic Garden Edinburgh, Lukuru Wildlife Res Fdn, Div Vertebrate Zool, National Museum of Natural History, Herbarium Bogoriense, Indonesian Institute of Sciences, Integrat Res Ctr, Field Museum of Natural History [Chicago, USA], Trop Peat Res Inst, Biol Res Div, Malaysian Palm Oil Board, Kyoto University, Ctr Trop Environm & Sustainabil Sci, Coll Sci & Engn, Dept Environm Sci & Policy, George Mason University, Fac Sci Agron, University of Kisangani, Sch Geog & Environm, University of Oxford, Universidade Federal de Goiás [Goiânia] (UFG), Flamingo Land LTD, Dept Environm, CIRCLE, University of York, Salonga Natl Pk, sabah Parks, Universidad Autonoma del Beni, Inst Boliviano Invest Forestal, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Natural History Museum [Oslo], University of Oslo (UiO), Southern Swedish Forest Res Ctr, Swedish University of Agricultural Sciences (SLU), Bur Waarderburg, Fundación Con-Vida, CarboForExpert, Fac Sci, Environm & Life Sci, University of Brunei Darussalam (Biology Department), Museu Paraense Emílio Goeldi, Forestry Research and Development Agency (FORDA), Norwegian University of Life Sciences (NMBU), Geoinformática y Sistemas , Cia. Ltda (GeoIS), Museu Univ, Universidade Federal do Acre (UFAC), World Wide Fund for Nature, CTFS AA Asia Program, Fac Forestry, University Stefan cel Mare of Suceava (USU), Sch Forestry & Environm Studies, Yale University [New Haven], Centro de Investigación y Promoción del Campesinado Norte Amazónico, Sch Earth Sci & Environm Sustainabil, Northern Arizona University [Flagstaff], Biol Sci, Liverpool John Moore University (ljmu), Sch Environm Nat Resources & Geog, Bangor University, European Research Council (ERC), Gordon and Betty Moore Foundation, David and Lucile Packard Foundation, European Union's Seventh Framework Programme 283080, 282664, Natural Environment Research Council (NERC) Urgency Grants, NERC Consortium Grant 'AMAZONICA' NE/F005806/1, NERC Consortium Grant 'TROBIT' NE/D005590/1, NERC Consortium Grant 'BIO-RED' NE/N012542/1, NERC New Investigators Grant, Royal Society, Centre for International Forestry (CIFOR), Gabon's National Parks Agency (ANPN), NERC PhD Studentship, UNEP-WCMC, NERC research fellowship NE/I021160/1, Royal Society University Research Fellowship ERC Advanced Grant (T-FORCES), Phillip Leverhulme Prize, Royal Society Wolfson Research Merit Award, NERC studentship, RGS-IBG Henrietta Hutton Grant, National Council for Science and Technology Development of Brazil (CNPq) PELD/403725/2012-7, CNPq/PPBio/457602/2012-0, National Council for Science and Technology Development of Brazil (CNPq) Productivity Grant, Leverhulme Trust under the Valuing the Arc project, Missouri Botanical Garden, Sullivan, Martin J. P., Université de Yaoundé I, Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Florida International University [Miami] (FIU), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (UPR BSEF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Wageningen University and Research [Wageningen] (WUR), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Université libre de Bruxelles (ULB), University of Vienna [Vienna], Indonesian Institute of Sciences (LIPI), University of Oxford [Oxford], Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Southern Swedish Forest Research Centre, Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Université de Toulouse (UT), James Cook University (JCU), Universiteit Leiden, Agence Nationale des Parcs Nationaux du Gabon (ANPN), Harvard University, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Royal Botanic Garden [Edinburgh]

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, INCREASES, ALPHA-DIVERSITY, [SDV]Life Sciences [q-bio], Biome, Biodiversity, COMPLEMENTARITY, forêt tropicale, Forests, 01 natural sciences, AMAZONIAN FORESTS, Tropic Climate, biodiversité, biomasse aérienne des arbres, conservation des forêts, Tropical climate, stockage du carbone, Biomass (ecology), Multidisciplinary, PRODUCTIVITY, Agroforestry, Ecology, Plants, PE&RC, Classification, Tropical ecology, Chemistry, séquestration du carbone, biome, diversité variétale, protection de la forêt, P01 - Conservation de la nature et ressources foncières, ABOVEGROUND BIOMASS, tropical forest, Asia, F60 - Physiologie et biochimie végétale, TREE ALPHA-DIVERSITY, forêt amazonienne, CONSERVATION, 010603 evolutionary biology, Article, Ecology and Environment, Phénomènes atmosphériques, Forest ecology, Life Science, Bosecologie en Bosbeheer, Forest, AFRICAN RAIN-FORESTS, WOOD PRODUCTION, BIODIVERSITY, CLIMATE, K70 - Dégâts causés aux forêts et leur protection, atténuation des effets du changement climatique, 0105 earth and related environmental sciences, Tropical Climate, Western Hemisphere, TREE SPECIES RICHNESS, Tropics, Plant, 15. Life on land, Forest Ecology and Forest Management, Carbon, biodiversité forestière, DOMINANCE, 13. Climate action, Earth and Environmental Sciences, Africa, Alpha diversity, Americas, structure de la canopée
Abstract

Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-Tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity., 0, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2017

31. Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of five new species from the Afrotropics

Author

Rose Ndemah, Gael J. Kergoat, Bruno Le Ru, Boaz K. Musyoka, Beatrice Pallangyo, George Ong’amo, Gilson Chipabika, Mohamedi Njaku, Grégoire Bani, Richard Molo, Onésime Mubenga, Claire Capdevielle-Dulac, Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), UMR 247, Institut de Recherche pour le Développement (IRD [France-Ouest]), Biocontrol Programme, Faculté des Sciences agronomiques, Université du Burundi, International Institute of Tropical Agriculture (IITA-DRC), International Institute of Tropical Agriculture [Nigeria] (IITA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre de recherches agronomiques de Loudima (CRAL), Namulonge Agricultural and Animal Production Research Institute (NAARI), Sch. Biol. Sci. Coll. Phys. & Biol. Sci., University of Nairobi, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), UMR Lab Evolut. Genomes Speciat., Centre National de la Recherche Scientifique (CNRS), Université Paris Sud (Paris 11), and International Institute of Tropical Agriculture (IITA)

Subjects
0106 biological sciences, Systematics, Species complex, Acrapex, [SDV]Life Sciences [q-bio], 010607 zoology, Sesamiina, Apameini, 01 natural sciences, Afrotropical Region, Genus, Botany, Cymbopogon schoenanthus, Ecology, Evolution, Behavior and Systematics, Chrysopogon, biology, biology.organism_classification, Noctuinae, 010602 entomology, QL1-991, QK1-989, Noctuidae, Taxonomy (biology), Zoology
Abstract

Ten morphologically similar species of Acrapex Hampson, 1891 (Lepidoptera, Noctuidae, Noctuinae, Apameini) from Central and Eastern Africa are reviewed, including five new species: Acrapex kafula le Ru sp. nov., A. kavumba le Ru sp. nov., A. kiakouama le Ru sp. nov., A. miscantha le Ru sp. nov. and A. simillima le Ru sp. nov. Evidence is provided to transfer the monotypic genus Poecopa Bowden, 1956 to the genus Acrapex . Host plants of five species are recorded, some of them for the first time. Acrapex kavumba sp. nov., A. miscantha sp. nov. and A. simillima sp. nov. were found on one host plant each. Acrapex mediopuncta , previously reported in West Africa from Pennisetum purpureum Schumach. , Rottboellia compressa L., Setaria megaphylla (Steud) Dur. & Schinz. and Sorghum arundinaceum (Desv.) Stapf, was only found from S. megaphylla in Central Africa. Larvae of Acrapex unicolora were collected on Andropogon gayanus Kunth, Chrysopogon zizanoides (L.) Roberty, Cymbopogon schoenanthus subsp. proximus (Hochst. ex A.Rich.) Maire & Weller, Cymbopogon pospischiilii (K.Schum.) C.E.Hubb. , Hyparrhenia diplandra (Hack.) Stapf and Setaria sphacelata (Schumach.) Moss. We also conducted molecular phylogenetic analyses (using maximum likelihood) and molecular species delimitation analyses on a comprehensive sample of 61 specimens belonging to eight of the studied species. Molecular phylogenetic analyses provided additional evidence of the synonymy of Acrapex and Poecopa , whereas molecular species delimitation analyses support the validity of the five newly described species and unravel another potential new species, only collected in the larval stage.

Published
2017

32. Warm temperatures induce transgenerational epigenetic release of RNA silencing by inhibiting siRNA biogenesis in Arabidopsis

Author

Junzhong Liu, Joanne Chory, Zuhua He, Yijun Qi, Zhi-Yong Wang, Sihui Zhong, Xiao-Ya Chen, Qun Li, Hua Jin, Ying Chen, Jianming Li, Yuexing Yuan, Hai Huang, Hervé Vaucheret, Lin Lin, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Natl Key Lab Plant Mol Genet, Chinese Academy of Sciences [Beijing] (CAS), Dept Mol Cellular & Dev Biol, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Howard Hughes Med Inst, The Salk Institute for Biological Studies, Natl Inst Biol Sci, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, National Research Program of China [2011CB100700], National Natural Science Foundation of China [91117018, 30730064], Chinese Academy of Sciences, and National Science Foundation [IOS1121496]

Subjects
0106 biological sciences, Small interfering RNA, TRANSCRIPTION FACTOR PIF4, FLOWERING TIME, STRESS, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Trans-acting siRNA, Arabidopsis, Biology, Real-Time Polymerase Chain Reaction, INHERITANCE, 01 natural sciences, Epigenesis, Genetic, 03 medical and health sciences, Gene Expression Regulation, Plant, RNA interference, Gene silencing, PLANTS, RNA, Small Interfering, 030304 developmental biology, SUPPRESSION, 2. Zero hunger, Regulation of gene expression, 0303 health sciences, Multidisciplinary, Base Sequence, RECEPTOR, Arabidopsis Proteins, Temperature, High-Throughput Nucleotide Sequencing, RNA, PATHWAYS, Sequence Analysis, DNA, Biological Sciences, VIRUS-RESISTANCE, GENE, Plants, Genetically Modified, Molecular biology, RNA silencing, 13. Climate action, RNA Interference, Protein Kinases, Biogenesis, 010606 plant biology & botany
Abstract

Owing to their sessile nature, plants have evolved sophisticated genetic and epigenetic regulatory systems to respond quickly and reversibly to daily and seasonal temperature changes. However, our knowledge of how plants sense and respond to warming ambient temperatures is rather limited. Here we show that an increase in growth temperature from 22 °C to 30 °C effectively inhibited transgene-induced posttranscriptional gene silencing (PTGS) in Arabidopsis . Interestingly, warmth-induced PTGS release exhibited transgenerational epigenetic inheritance. We discovered that the warmth-induced PTGS release occurred during a critical step that leads to the formation of double-stranded RNA (dsRNA) for producing small interfering RNAs (siRNAs). Deep sequencing of small RNAs and RNA blot analysis indicated that the 22–30 °C increase resulted in a significant reduction in the abundance of many trans -acting siRNAs that require dsRNA for biogenesis. We discovered that the temperature increase reduced the protein abundance of SUPPRESSOR OF GENE SILENCING 3, as a consequence, attenuating the formation of stable dsRNAs required for siRNA biogenesis. Importantly, SUPPRESSOR OF GENE SILENCING 3 overexpression released the warmth-triggered inhibition of siRNA biogenesis and reduced the transgenerational epigenetic memory. Thus, our study reveals a previously undescribed association between warming temperatures, an epigenetic system, and siRNA biogenesis.

Published
2013

33. The Amborella Genome and the Evolution of Flowering Plants

Author

Albert, Va, Barbazuk, Wb, Depamphilis, Cw, Der, Jp, Leebens Mack, J, Ma, H, Palmer, Jd, Rounsley, S, Sankoff, D, Schuster, Sc, Soltis, De, Soltis, Ps, Wessler, Sr, Wing, Ra, Ammiraju, Js, Chamala, S, Chanderbali, As, Determann, R, Ralph, P, Talag, J, Tomsho, L, Walts, B, Wanke, S, Chang, Th, Lan, T, Arikit, S, Axtell, Mj, Ayyampalayam, S, Burnette JM 3rd, DE PAOLI, Emanuele, Estill, Jc, Farrell, Np, Harkess, A, Jiao, Y, Liu, K, Mei, W, Meyers, Bc, Shahid, S, Wafula, E, Zhai, J, Zhang, X, Carretero Paulet, L, Lyons, E, Tang, H, Zheng, C, Altman, Ns, Chen, F, Chen, Jq, Chiang, V, De Paoli, E, Fogliani, B, Guo, C, Harholt, J, Job, C, Job, D, Kim, S, Kong, H, Li, G, Li, L, Liu, J, Park, J, Qi, X, Rajjou, L, Burtet Sarramegna, V, Sederoff, R, Sun, Yh, Ulvskov, P, Villegente, M, Xue, Jy, Yeh, Tf, Yu, X, Acosta, Jj, Bruenn, Ra, de Kochko, A, Herrera Estrella LR, Ibarra Laclette, E, Kirst, M, Pissis, Sp, Poncet, V, Tomsho, L., Department of Biological Sciences, University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY)-State University of New York (SUNY), Department of Biology, University of Florida [Gainesville], University of Florida Genetics Institute, Huck Institutes of the Life Sciences [University Park], Intercollege Plant Biology Graduate Program, Pennsylvania State University (Penn State), Penn State System-Penn State System, Center for Comparative Genomics and Bioinformatics, Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA, Université Paris Diderot - Paris 7 (UPD7), Department of Plant Biology [Athens], University of Georgia [USA], Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA, Penn State Univ, Dept Biol, University Pk, PA 16802 USA, Fudan Univ, Sch Life Sci, State Key Lab Genet Engn, Shanghai 200433, Peoples R China, Fudan Univ, Inst Genet, Inst Plant Biol, Ctr Evolutionary Biol,Inst Biomed Sci, Shanghai 200433, Peoples R China, Indiana Univ, Dept Biol, Bloomington, IN 47405 USA, Univ Arizona, Inst Collaborat Res BIO5, Tucson, AZ 85721 USA, Dow AgroSci, Indianapolis, IN 46268 USA, Univ Arizona, Sch Biol Sci, Tucson, AZ 85721 USA, Department of Mathematics and Statistics, University of Ottawa [Ottawa] (uOttawa), Singapore Ctr Environm Life Sci Engn, Singapore, Singapore, Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA, Florida Museum of Natural History, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UCR), University of California-University of California, Univ Arizona, Arizona Genom Inst, Tucson, AZ 85721 USA, Atlanta Bot Garden, Atlanta, GA 30309 USA, Univ Florida, Dept Biol, Gainesville, FL 32611 USA, Tech Univ Dresden, Inst Bot, D-01062 Dresden, Germany, SUNY Buffalo, Dept Biol Sci, Buffalo, NY 14260 USA, Chongqing Univ Sci & Technol, Dept Biol, Chongqing 4000042, Peoples R China, Univ Delaware, Delaware Biotechnol Inst, Newark, DE 19711 USA, Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA, Univ Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine, Italy, Penn State Univ, Intercoll Plant Biol Grad Program, University Pk, PA 16802 USA, Univ Arizona, iPlant Collaborat, Tucson, AZ 85721 USA, J Craig Venter Inst, Rockville, MD 20850 USA, Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada, Penn State Univ, Dept Stat, University Pk, PA 16802 USA, Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA, Nanjing Univ, Sch Life Sci, Nanjing 210093, Jiangsu, Peoples R China, N Carolina State Univ, Dept Forestry & Environm Resources, Raleigh, NC 27695 USA, Institut Agronomique Néo-Calédonien (IAC), Univ New Caledonia, Lab Insulaire Vivant & Environm, Noumea 98851, New Caledonia, Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China, Univ Copenhagen, Dept Plant & Environm Sci, DK-1871 Frederiksberg C, Denmark, Univ Claude Bernard Lyon, Inst Natl Sci Appl Bayer CropSci Joint Lab UMR524, CNRS, Bayer CropSci, F-69263 Lyon 9, France, Sungshin Womens Univ, Basic Sci Res Inst, Seoul 142732, South Korea, Sungshin Womens Univ, Sch Biol Sci & Chem, Seoul 142732, South Korea, Zhejiang Univ, Coll Life Sci, Lab Systemat & Evolutionary Bot & Biodivers, Hangzhou 310058, Zhejiang, Peoples R China, Zhejiang Univ, Coll Life Sci, Key Lab Conservat Biol Endangered Wildlife, Minist Educ, Hangzhou 310058, Zhejiang, Peoples R China, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Natl Chung Hsing Univ, Dept Forestry, Taichung 40227, Taiwan, Natl Taiwan Univ, Sch Forestry & Resource Conservat, Taipei 10617, Taiwan, Univ Florida, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA, Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Lab Nacl Genom Biodiversidad, Irapuato 36821, Mexico, Univ Florida, Genet Inst, Gainesville, FL 32610 USA, Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA, Heidelberg Inst Theoret Studies, Sci Comp Grp, D-69118 Heidelberg, Germany, NSF Plant Genome Research Program [0922742], NSF, University of Florida [Gainesville] (UF), University of Florida Genetics Institute (UFGI), Center for Comparative Genomics and Bioinformatics (CCBB), Department of Biology [PennState], State Key Laboratory of Genetic Engineering, Fudan University [Shanghai], Institute of Plant Biology [Shanghai], Department of Biology [Bloomington], Indiana University [Bloomington], Indiana University System-Indiana University System, BIO5 - Institute for Collaborative Bioresearch, University of Arizona, Dow AgroSciences LLC, School of Plant Sciences [Tucson], Department of Mathematics and Statistics [Ottawa], University of Ottawa [Ottawa], Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], Department of Biochemistry and Molecular Biology [PennState], Arizona Genomics Institute [Tucson], Atlanta Botanical Garden, Department of Biology [Gainesville] (UF|Biology), Institut für Botanik [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Department of Biological Sciences [Buffalo], Department of Biology [Chongqing], Chongqing University of Science & Technology, Plant Genome Mapping Laboratory (PGML), Dipartimento di Scienze Agrarie e Ambientali (DiSA), Università degli Studi di Udine - University of Udine [Italie], iPlant Collaborative, J. Craig Venter Institute, Department of Statistics [PennState], Department of Plant Sciences [Knoxville], The University of Tennessee [Knoxville], School of Life Sciences [Nanjing] (SLiS), Nanjing University (NJU), Department of Forestry and Environmental Resources [Raleigh] (FER), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Université de la Nouvelle-Calédonie (UNC), State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany [Beijing] (IB-CAS), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (KU), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Génomique fonctionnelle des champignons pathogènes des plantes (FungiPath), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Basic Science Research Institute [Seoul], Sungshin Women's University, School of Biological Sciences and Chemistry [Seoul], Laboratory of Systematic & Evolutionary Botany and Biodiversity, Zhejiang University, Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Department of Forestry [Taichung], National Chung Hsing University (NCHU), School of Forestry and Resource Conservation [Taiwan], National Taïwan University (NTU), School of Forest Resources and Conservation [Gainesville] (UF|IFAS|FFGS), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley], Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Florida Museum of Natural History [Gainesville], Heidelberg Institute for Theoretical Studies (HITS ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
0106 biological sciences, Most recent common ancestor, Genetics, Transposable element, 0303 health sciences, education.field_of_study, Multidisciplinary, Lineage (evolution), [SDV]Life Sciences [q-bio], Population, fungi, food and beverages, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Gene duplication, Gene family, education, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract

Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.

Published
2013

34. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

Author

Edgar Huitema, Pedro M. Coutinho, Susan I. Fuerstenberg, H. Brouwer, Frank N. Martin, John P. Hamilton, Liliana M. Cano, Stephan Wawra, Francine Govers, Jason E. Stajich, Gregg P. Robideau, C. André Lévesque, Sucheta Tripathy, Marco Thines, Dana A. Busam, Elodie Gaulin, Neil R. Horner, Laura J. Grenville-Briggs, Justin Johnson, Theerapong Krajaejun, Jyoti Shetty, Haining Lin, Jessica B. Hostetler, Sophien Kamoun, Harold J. G. Meijer, Paul Morris, Gordon W. Beakes, Brett R Whitty, Jeffrey L. Boore, Pieter van West, Rays H. Y. Jiang, Bernard Henrissat, Joe Win, Carson Holt, Steve Ferriera, Barry Moore, Marcelo M. Zerillo, Sylvain Raffaele, Bernard Dumas, C. Robin Buell, Ronald P. de Vries, Paul Thomas, Ned Tisserat, Claire M. M. Gachon, Daniela Puiu, Brett M. Tyler, Vipaporn Phuntmart, Mark Yandell, Agriculture and Agri-Food [Ottawa] (AAFC), Department of Biology, Northern Arizona University [Flagstaff], John Innes Centre, The Sainsbury Laboratory [Norwich] (TSL), CBS-KNAW Fungal Biodiversity Centre, Department Plant Biology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Eccles Institute Human Genetic, Utah State University (USU), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Dept Biol Sci, Inst Ecol Evolut & Divers, Goethe-Universität Frankfurt am Main, Dept Bioagr Sci & Pest Management, Colorado State University [Fort Collins] (CSU), School Biolology, Newcastle University, Genome Project Solutions, J. Craig Venter Institute [La Jolla, USA] (JCVI), Interactions Microbiennes dans la Rhizosphère et les Racines, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Scottish Association for Marine Sciences, Phytopathology Laboratory, Wageningen University and Research [Wageningen] (WUR), Centre for Biosystems Genomics, Departmentt Biology Science, Bowling Green State University, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Dept Pathol, Fac Med, Ramathibodi Hosp, Mahidol University [Bangkok], Dept Biol Sci, University of South Alabama, Dept Plant Pathol & Microbiol, University of California [Riverside] (UCR), University of California-University of California, Virginia Tech [Blacksburg], Architecture et fonction des Macromolécules Biologiques - UMR 6098 (AFMB), Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), USDA-ARS : Agricultural Research Service, SRI International, Evolutionary System Biolology, US Department of Agriculture (USDA) National Institute of Food and Agriculture : 2007-35600-17774, 2007-35600-18886, NIH/NHGRI : 5R01HG004694, National Research Initiative of the USDA CSREES : 2007-35600-18530, National Science Foundation : MCB-0731969 NSERC, European Commission : MIEF-CT-2006-022837, PERG03-GA-2008-230865, Dutch Ministry of Agriculture, Nature and Food Quality, Max-Planck Society, German Science Foundation (DFG), Landesstiftung Baden-Wurttemberg, Hesse's Ministry of Higher Education, Research, and the Arts : National Institutes of Health : NCRR 1 S10 RR17214-01, Agriculture and Agri-Food (AAFC), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of California [Riverside] (UC Riverside), and University of California (UC)-University of California (UC)

Subjects
Antifungal Agents, Genome, Gene Order, Arabidopsis thaliana, Pathogen, Phylogeny, 2. Zero hunger, Oomycete, Genetics, Gene Rearrangement, 0303 health sciences, Vegetal Biology, biology, Effector, EPS-2, food and beverages, Genomics, Plants, Cadherins, Pythium ultimum, Multigene Family, Host-Pathogen Interactions, gene family, Carbohydrate Metabolism, Pythium, arabidopsis-thaliana, Synteny, 03 medical and health sciences, cadherin superfamily, pleiotropic drug, ddc:570, Humans, pythium ultimum, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, oomycete phytophthora-infestans, potato famine pathogen, protein families, genome, 030304 developmental biology, Repetitive Sequences, Nucleic Acid, microbe interactions, Base Sequence, 030306 microbiology, molecular evolution, génome, Research, fungi, Proteins, Gene rearrangement, Sequence Analysis, DNA, biology.organism_classification, Laboratorium voor Phytopathologie, mitochondrial genome, Genome, Mitochondrial, Laboratory of Phytopathology, Sequence Alignment, Biologie végétale
Abstract

Background Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans. Conclusions Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.

Published
2010

35. Population structure and geographical subdivision of the Leishmania major vector Phlebotomus papatasi as revealed by microsatellite variation

Author

Omar Hamarsheh, Gabriele Schönian, M. L. Das, Amer Al-Jawabreh, M. Hassan, Y. Hashiguchi, Ramesh C. Dhiman, Ahmad Amro, Ahmad Al-Lahem, Wolfgang Presber, J. Ghrab, N. Seridi, Samir S. Sawalha, Souad Guernaoui, Mohammad Reza Yaghoobi-Ershadi, Dept Biol Sci, Al-Quds University, Dept Parasitol, Charite, Inst Microbiol & Hyg, University of Tehran, Dept Med Entomol & Vector Control, Tehran University, Leishmaniasis Res Lab, Leishmania Res Unit, Jericho, Dept Primary Hlth Care, Minist Hlth, Dept Zool, University of Aleppo [Aleppo], Dept Microbiol, BP Koirala Inst Hlth Sci, Lab Ecol Anim Terrestre, Faculté des Sciences Semlalia, Genet Lab, USTHB, Fac Biol Sci, Natl Inst Malaria Res ICMR, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Natl Res Ctr, Res Inst Trop Med, and Kochi Univ, Kochi Med Sch

Subjects
sandflies, Genotype, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Population, Population Dynamics, Population genetics, India, microsatellites, 03 medical and health sciences, Middle East, 0302 clinical medicine, Nepal, Animals, Psychodidae, education, Phlebotomus papatasi, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Leishmania major, Genetics, 0303 health sciences, education.field_of_study, General Veterinary, biology, population structure, biology.organism_classification, Sandfly, Insect Vectors, F-statistics, Evolutionary biology, Insect Science, Phlebotomus, Genetic structure, Africa, Microsatellite, Biological dispersal, Parasitology
Abstract

International audience; Multi-locus microsatellite typing (MLMT) has been employed to infer the population structure of Phlebotomus papatasi (Scopoli) (Diptera: Psychodidae) sandflies and assign individuals to populations. Phlebotomus papatasi sandflies were collected from 35 sites in 15 countries. A total of 188 P. papatasi individuals were typed using five microsatellite loci, resulting in 113 different genotypes. Unique microsatellite signatures were observed for some of the populations analysed. Comparable results were obtained when the data were analysed with Bayesian model and distance-based methods. Bayesian statistic-based analyses split the dataset into two distinct genetic clusters, A and B, with further substructuring within each. Population A consisted of five subpopulations representing large numbers of alleles that were correlated with the geographical origins of the sandflies. Cluster B comprised individuals collected in the Middle East and the northern Mediterranean area. The subpopulations B1 and B2 did not, however, show any further correlation to geographical origin. The genetic differentiation between subpopulations was supported by F statistics showing statistically significant (Bonferroni-corrected P < 0.005) values of 0.221 between B2 and B1 and 0.816 between A5 and A4. Identification of the genetic structure of P. papatasi populations is important for understanding the patterns of dispersal of this species and to developing strategies for sandfly control.

Published
2009

36. Manipulating plant community composition to steer efficient N-cycling in intensively managed grasslands

Author

David Bru, Laurent Philippot, Callum Clark, Ignacio Mariscal-Sancho, Gerlinde B. De Deyn, Barbora Oudová, Ioannis Pantelis, Andrea Fiorini, Diego Abalos, Natalie J. Oram, Jan Willem van Groenigen, Wageningen Univ, Soil Biol Grp, Wageningen, Netherlands., Aarhus University [Aarhus], Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Univ East Anglia, Sch Biol Sci, Norwich, Norfolk, England., Univ Cattolica Sacro Cuore, Dept Sustainable Crop Prod, Piacenza, Italy., and Univ Politecn Madrid, ETS Ingn Agron Alimentaria & Biosistemas, Dept Prod Agr, Madrid, Spain

Subjects
0106 biological sciences, Agroecosystem, DECOMPOSITION, N2O emissions, DIVERSITY, COMPLEMENTARITY, nitrogen losses, 010603 evolutionary biology, 01 natural sciences, nitrogen cycling, Abundance (ecology), functional traits, plant and soil interactions, Nitrogen cycle, Legume, Bodembiologie, 2. Zero hunger, Biomass (ecology), Ecology, biology, grass legume mixtures, 010604 marine biology & hydrobiology, SPECIES RICHNESS, Earthworm, fungi, MIXTURES, food and beverages, Plant community, Soil Biology, 15. Life on land, biology.organism_classification, PE&RC, SOIL, Agronomy, FUNCTIONAL TRAITS, NO emissions, 13. Climate action, [SDE]Environmental Sciences, BIODIVERSITY, plant mixtures, plant species identity, Monoculture, ELEVATED CO2
Abstract

Minimizing nitrogen (N) losses and increasing plant N uptake in agroecosystems is a major global challenge. Ecological concepts from (semi)natural grasslands suggest that manipulating plant community composition using plant species with different traits may represent a promising opportunity to face this challenge. Here, we translate these trait-based concepts to agricultural systems in a field experiment, aiming to reveal the main determinants of how plant community composition regulates N-cycling in intensively managed grasslands.We focused on key N pools (plant N from soil and from biological N-fixation, soil mineral N and N2O emissions) as well as on biological drivers of N-cycling in soil (abundance of N-cycling microbial communities, earthworm populations and arbuscular mycorrhizal fungi), using three common grass and one legume species in monoculture, two- and four-species mixtures. We hypothesized that: (a) plant species mixtures increase plant N uptake, reduce soil mineral N concentrations and N2O emissions and promote the abundance of biological N-cyclers; (b) legume presence stimulates N pools, fluxes and biological N-cycling activity, (c) but in combination with a grass with acquisitive traits, more N is retained in the plant community, while N2O emissions are reduced.We found that mixtures increased plant N and lowered the soil mineral N pool compared to monocultures. However, plant species identity played an overarching role: Legume presence increased N2O emissions, plant N pools, soil mineral N and the abundance of N-cycling microbes and earthworms. Combining the legume with a grass with low leaf dry matter content and high root length density (and with high root biomass) reduced the higher soil mineral N and N2O emissions induced by the legume, while harnessing positive effects on plant N pools and biological N-fixation.Synthesis and applications. Our results show the potential of plant community composition to steer N-cycling in fertilized agroecosystems, paving the way for a more biologically based agriculture. Legumes will play a crucial role, but selecting an optimum companion species is key for the sustainability of the agroecosystem.

Published
2021

37. Phaeocedus is a new genus of ground spider (Araneae, Gnaphosidae) in Turkey

Author

Seyyar, Osman, Demir, Hakan, Topcu, Aydin, Tasdemir, Abdulkadir, [Seyyar, Osman -- Tasdemir, Abdulkadir] Erciyes Univ, Dept Biol, Sci & Art Fac, TR-38039 Kayseri, Turkey -- [Demir, Hakan -- Topcu, Aydin] Nigde Univ, Dept Biol, Sci & Art Fac, TR-51200 Nigde, Turkey, and 0-Belirlenecek

Subjects
Turkey and new record, Gnaphosidae, Phaeocedus
Abstract

WOS: 000204015000006, The spider genus Phaeocedus belonging to family of Gnaphosidae is recorded from Turkey for the first time. The characteristic features are described and illustrated, and data on distribution are given.

Published
2006

38. Squalene attenuates the oxidative stress and activates AKT/mTOR pathway against cisplatin-induced kidney damage in mice

Author

Mehmet Ozansoy, Rumeyza Kazancioglu, Ulkan Kilic, Arzu Şakul, Yasemin Yozgat, Şule Ayla, Kazim Sahin, Birsen Elibol, Mehmet Yalçın Günal, Huveyda Basaga, ALKÜ, 0-belirlenecek, ELİBOL, BİRSEN, Sakul, Arzu Istanbul Medipol Univ, Sch Med, Dept Med Pharmacol, Istanbul, Turkey, Ozansoy, Mehmet Istanbul Medipol Univ, Sch Med, Dept Physiol, Istanbul, Turkey, Elibol, Birsen Bezmialem Vakif Univ, Fac Med, Dept Med Biol, Istanbul, Turkey, Ayla, Sule Istanbul Medipol Univ, Sch Med, Dept Histol & Embryol, Istanbul, Turkey, Gunal, Mehmet Yalcin Alanya Alaaddin Keykubat Univ, Dept Physiol, Sch Med, Antalya, Turkey, Yozgat, Yasemin Istanbul Medipol Univ, Regenerat & Restorat Med Res Ctr REMER, Istanbul, Turkey, Basaga, Huveyda Sabanci Univ, Fac Engn & Nat Sci, Biol Sci & Bioengn Program, Istanbul, Turkey, Sahin, Kazim Firat Univ, Fac Vet Med, Dept Anim Nutr, Elazig, Turkey, Kazancioglu, Rumeyza Bezmialem Vakif Univ, Fac Med, Dept Nephrol, Istanbul, Turkey, Kilic, Ulkan Univ Hlth Sci, Fac Med, Dept Med Biol, Istanbul, Turkey, gunal, mehmet yalcin -- 0000-0001-7702-2441, and Sahin, Kazim -- 0000-0001-9542-5244

Subjects
cisplatin-induced nephrotoxicity, mice, Physiology, 0206 medical engineering, 02 engineering and technology, Biology, Pharmacology, squalene, medicine.disease_cause, Microbiology, Article, Nephrotoxicity, Proinflammatory cytokine, 03 medical and health sciences, Squalene, chemistry.chemical_compound, 0302 clinical medicine, Genetics, medicine, oxidative-stress, Molecular Biology, Protein kinase B, PI3K/AKT/mTOR pathway, Cisplatin, Kidney, AKT, Cell Biology, Sakul A., Ozansoy M., ELİBOL B., Ayla S., Gunal M. Y. , Yozgat Y., Basaga H., Sahin K., KAZANCIOĞLU R., Kilic U., -Squalene attenuates the oxidative stress and activates AKT/mTOR pathway against cisplatin-induced kidney damage in mice-, TURKISH JOURNAL OF BIOLOGY, cilt.43, ss.179-188, 2019, 020601 biomedical engineering, medicine.anatomical_structure, chemistry, 030220 oncology & carcinogenesis, mTOR, General Agricultural and Biological Sciences, Oxidative stress, Biyoloji, medicine.drug
Abstract

WOS: 000471268100003 The clinical use of cisplatin, which is a first-line anticancer agent, is highly restricted due to its adverse effects on kidneys that lead to nephrotoxicity. Therefore, some potential reno-protective substances have been used in combination with cisplatin to cope with nephrotoxicity. Due to its high antitumor activity and oxygen-carrying capacity, we investigated the molecular effects of squalene against cisplatin-induced oxidative stress and kidney damage in mice. Single dose of cisplatin (7 mg/kg) was given to male Balb/c mice. Squalene (100 mg/kg/day) was administered orogastrically to mice for 10 days. Following sacrification, molecular alterations were investigated as analysis of the levels of oxidative stress index (OSI), inflammatory cytokines and cell survival-related proteins in addition to histopathological examinations in mice kidney tissue. The level OSI and Interferon-gamma (IFN-gamma) decreased in the cisplatin and squalene cotreated mice compared to cisplatin-treated mice. Squalene treatment also increased the activation of protein kinase B (AKT). Furthermore, cisplatin-induced inactivation of mammalian target of rapamycin (mTOR) and histopathological damages were reversed by squalene. It may be suggested that squalene ameliorated the cisplatin-induced histopathological damages in the kidney through activation of AKT/mTOR signaling pathway by regulating the balance of the redox system due to its antioxidative effect.

Published
2019

39. Genome-wide association study identified candidate genes for seed size and seed composition improvement in M. truncatula

Author

Yi-Min She, Yun Kang, Vanessa Lancon-Verdier, Christine Le Signor, Zhijuan Chen, Jerome Verdier, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Groupe de Recherche en Agroalimentaire sur les Produits et les Procédés (GRAPPE), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Chinese Acad Sci, Shanghai Inst Biol Sci, CAS MPG Partner Inst Computat Biol, CAS Key Lab Computat Biol, Shanghai, Peoples R China, Partenaires INRAE, Ottawa Health Research Institute, Region Pays de la Loire, European Commission, and China Scholarship Council (CSC) from the Ministry of Education of P.R. China: 01704910863.

Subjects
Agricultural genetics, 0106 biological sciences, 0301 basic medicine, Plant genetics, Science, Quantitative Trait Loci, Population, Quantitative trait locus, Biology, Genes, Plant, 01 natural sciences, Article, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Quantitative Trait, Heritable, Medicago truncatula, Botany, Storage protein, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Legume, 2. Zero hunger, chemistry.chemical_classification, education.field_of_study, Genetic diversity, Multidisciplinary, Medicago, Geography, Computational Biology, food and beverages, 15. Life on land, biology.organism_classification, Gene Ontology, Phenotype, 030104 developmental biology, chemistry, Plant protein, Seeds, Medicine, Edible Grain, Algorithms, Genome, Plant, Genome-Wide Association Study, 010606 plant biology & botany
Abstract

Grain legumes are highly valuable plant species, as they produce seeds with high protein content. Increasing seed protein production and improving seed nutritional quality represent an agronomical challenge in order to promote plant protein consumption of a growing population. In this study, we used the genetic diversity, naturally present in Medicago truncatula, a model plant for legumes, to identify genes/loci regulating seed traits. Indeed, using sequencing data of 162 accessions from the Medicago HAPMAP collection, we performed genome-wide association study for 32 seed traits related to seed size and seed composition such as seed protein content/concentration, sulfur content/concentration. Using different GWAS and postGWAS methods, we identified 79 quantitative trait nucleotides (QTNs) as regulating seed size, 41 QTNs for seed composition related to nitrogen (i.e. storage protein) and sulfur (i.e. sulfur-containing amino acid) concentrations/contents. Furthermore, a strong positive correlation between seed size and protein content was revealed within the selected Medicago HAPMAP collection. In addition, several QTNs showed highly significant associations in different seed phenotypes for further functional validation studies, including one near an RNA-Binding Domain protein, which represents a valuable candidate as central regulator determining both seed size and composition. Finally, our findings in M. truncatula represent valuable resources to be exploitable in many legume crop species such as pea, common bean, and soybean due to its high synteny, which enable rapid transfer of these results into breeding programs and eventually help the improvement of legume grain production.

Published
2021

40. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

Author

Sook Jung, Bryon Sosinski, Vladimir Shulaev, Alessandro Cestaro, Kevin M. Folta, Riccardo Velasco, Jean-Marc Celton, Il-Hyung Cho, Albert G. Abbott, Ping Zheng, Ignazio Verde, Michele Morgante, Michela Troggio, Daniel S. Rokhsar, Pere Arús, Dorrie Main, Daniel J. Sargent, Dept Hort & Landscape Architecture, Washington State University (WSU), Istituto Agrario di San Michele all' Adige, Univ Ctr, University Ctr, Saginaw Valley State Univ, Dept Hort Sci, University of Florida [Gainesville] (UF), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Dept Biochem & Genet, Clemson University, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Ctr Recerca Agrigenom, IRTA Barcelona, Spanish National Research Council (CSIC), Dept Biol Sci, University of North Texas (UNT), CRA Fruit Tree Res Ctr, Applied Genomics Institute (IGA), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), USDA NIFA SCRI [2010-2010-03255], and University of Florida [Gainesville]

Subjects
0106 biological sciences, CHROMOSOME, Rosaceae, [SDV]Life Sciences [q-bio], SEQUENCE DATA, 01 natural sciences, Genome, Prunus, MARKERS, Conserved Sequence, Phylogeny, 0303 health sciences, biology, ORIGIN, Genomics, PROVIDE, Fragaria, Settore AGR/07 - GENETICA AGRARIA, Malus, Algorithms, Genome, Plant, Research Article, Biotechnology, lcsh:QH426-470, Evolution, lcsh:Biotechnology, Chromosomes, Plant, LINKAGE MAP, Evolution, Molecular, 03 medical and health sciences, Sequence Homology, Nucleic Acid, lcsh:TP248.13-248.65, Botany, Genetics, 030304 developmental biology, Synteny, Comparative genomics, ARABIDOPSIS-THALIANA, SYNTENY, 15. Life on land, biology.organism_classification, lcsh:Genetics, Rosacea, 010606 plant biology & botany
Abstract

Background Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. Results Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. Conclusion Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae., This project has been supported by the USDA NIFA SCRI grant # 2010-2010-03255. We acknowledge International Peach Genome Initiative for the permission to use the peach genome in this study

Published
2021

41. Siesta : recent developments and applications

Author

Rafi Ullah, Georg Huhs, Emanuele Bosoni, Volker Blum, Alberto García, Pablo Ordejón, Emilio Artacho, Andrei Postnikov, Irina V. Lebedeva, Fabiano Corsetti, Richard Korytár, Miguel Pruneda, Ramón Cuadrado, Vladimir Dikan, Roberto Robles, Pablo García-Fernández, Jaime Ferrer, Mads Brandbyge, Javier Junquera, Jorge Cerdá, José M. Soler, Pedro Brandimarte, Nick Rübner Papior, Lin Lin, Victor Yu, Stephan Mohr, Sandra García, Sergio Illera, Peter Koval, Víctor M. García-Suárez, Arsalan Akhtar, Yann Pouillon, Pablo López-Tarifa, Sara G. Mayo, Julian D. Gale, Daniel Sánchez-Portal, Barcelona Supercomputing Center, Facultad de Ciencias y Tecnologías Químicas de Ciudad Real (UCLM), Institut Català de Nanociència i Nanotecnologia (ICN2), Universitat Autònoma de Barcelona (UAB), Catalan Institute of Nanoscience and Nanotechnology (ICN2), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Barcelona Institute of Science and Technology (BIST), Department of Earth Sciences [Cambridge, UK], University of Cambridge [UK] (CAM), Duke University [Durham], Institut de Ciència de Materials de Barcelona (ICMAB), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Donostia International Physics Center (DIPC), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Center for Nanostructured Graphene, Instituto Ciencias del Mar, CICNanoGUNE, University of Oviedo, Nanochemistry Research Institute, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Universidad de Cantabria [Santander], Universidad de Oviedo [Oviedo], Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Department of Applied Mathematics and Institute of Theoretical Computer Science (Charles University), Charles University [Prague] (CU), CIC NanoGUNE BRTA, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Natl Key Lab Plant Mol Genet, Chinese Academy of Sciences [Beijing] (CAS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Universidad Autonoma de Madrid (UAM), University of Basel (Unibas), Laboratoire de Chimie et Physique - Approche Multi-échelle des Milieux Complexes (LCP-A2MC), Université de Lorraine (UL), ICN2 - Institut Catala de Nanociencia i Nanotecnologia (ICN2), Centro Mixto CSIC-UPV/EHU, Donostia International Physics Center - DIPC (SPAIN), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU)-University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Departamento de Ciencias de la Tierra y Fisica de la Materia Condensada, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, European Commission, Universidad del País Vasco, Eusko Jaurlaritza, National Science Foundation (US), Universidad de Cantabria, and Simune Atomistics

Subjects
Scheme (programming language), Interface (Java), Computer science, Wannier functions, [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph], Interoperability, FOS: Physical sciences, General Physics and Astronomy, Molecular dynamics, 010402 general chemistry, computer.software_genre, 01 natural sciences, Electronic Structure Software, Computational science, Informàtica::Aplicacions de la informàtica [Àrees temàtiques de la UPC], Ab initio electronic structure calculations, Matrix analytic methods, 0103 physical sciences, Spin-orbit interactions, Plug-in, Dinàmica molecular, Multiscale methods, Charge density, Density functional theory (DFT)+U, Physical and Theoretical Chemistry, SIESTA (computer program), Electronic Structure Library, computer.programming_language, Ballistic electron transport, Condensed Matter - Materials Science, Mathematical models, 010304 chemical physics, SIESTA, Electron transport, Hybrid density functional calculations, Materials Science (cond-mat.mtrl-sci), Models matemàtics, Computational Physics (physics.comp-ph), Grid, Supercomputer, Pseudopotential method, PSeudopotential Markup Language, 0104 chemical sciences, Time dependent density functional theory, Workflow, Density functional theory, High performance computing, Physics - Computational Physics, computer
Abstract

This article is part of the JCP Special Topic on Electronic Structure Software., A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-1990s, SIESTA’s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a realspace grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin–orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as WANNIER90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various post-processing utilities. SIESTA has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments., Siesta development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Center of Excellence Program [Grant Nos. SEV-2015-0496 (ICMAB) and SEV-2017-0706 (ICN2)], the GenCat (Grant No. 2017SGR1506), and the European Union MaX Center of Excellence (EU-H2020 Grant No. 824143). P.G.-F. acknowledges support from Ramón y Cajal (Grant No. RyC-2013-12515). J.I.C. acknowledges Grant No. RTI2018-097895-B-C41. R.C. acknowledges the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodoswka-Curie Grant Agreement No. 665919. D.S.P, P.K., and P.B. acknowledge Grant No. MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant No. IT1246-19. V. W. Yu was supported by a MolSSI Fellowship (U.S. NSF Award No. 1547580), and V.B. and V.W.Y. were supported by the ELSI Development by the NSF (Award No. 1450280).

Published
2021

42. The essentials of marine biotechnology

Author

Ana Rotter, Michéle Barbier, Francesco Bertoni, Atle M. Bones, M. Leonor Cancela, Jens Carlsson, Maria F. Carvalho, Marta Cegłowska, Jerónimo Chirivella-Martorell, Meltem Conk Dalay, Mercedes Cueto, Thanos Dailianis, Irem Deniz, Ana R. Díaz-Marrero, Dragana Drakulovic, Arita Dubnika, Christine Edwards, Hjörleifur Einarsson, Ayşegül Erdoǧan, Orhan Tufan Eroldoǧan, David Ezra, Stefano Fazi, Richard J. FitzGerald, Laura M. Gargan, Susana P. Gaudêncio, Marija Gligora Udovič, Nadica Ivošević DeNardis, Rósa Jónsdóttir, Marija Kataržytė, Katja Klun, Jonne Kotta, Leila Ktari, Zrinka Ljubešić, Lada Lukić Bilela, Manolis Mandalakis, Alexia Massa-Gallucci, Inga Matijošytė, Hanna Mazur-Marzec, Mohamed Mehiri, Søren Laurentius Nielsen, Lucie Novoveská, Donata Overlingė, Giuseppe Perale, Praveen Ramasamy, Céline Rebours, Thorsten Reinsch, Fernando Reyes, Baruch Rinkevich, Johan Robbens, Eric Röttinger, Vita Rudovica, Jerica Sabotič, Ivo Safarik, Siret Talve, Deniz Tasdemir, Xenia Theodotou Schneider, Olivier P. Thomas, Anna Toruńska-Sitarz, Giovanna Cristina Varese, Marlen I. Vasquez, Slovenian Research Agency, Research Council of Norway, European Maritime and Fisheries Fund, European Commission, Ministerio de Ciencia e Innovación (España), Interreg MAC, Cabildo de Tenerife, Universidad de La Laguna, Fundação para a Ciência e a Tecnologia (Portugal), National Science Centre (Poland), Department of Agriculture, Food and Marine (Ireland), European Cooperation in Science and Technology, [Rotter, Ana] Natl Inst Biol, Marine Biol Stn Piran, Piran, Slovenia, [Klun, Katja] Natl Inst Biol, Marine Biol Stn Piran, Piran, Slovenia, [Barbier, Michele] Inst Sci & Eth, Nice, France, [Bertoni, Francesco] Univ Svizzera Italiana, Inst Oncol Res, Fac Biomed Sci, Bellinzona, Switzerland, [Mehiri, Mohamed] Univ Svizzera Italiana, Inst Oncol Res, Fac Biomed Sci, Bellinzona, Switzerland, [Bertoni, Francesco] Oncol Inst Southern Switzerland, Bellinzona, Switzerland, [Bones, Atle M.] Norwegian Univ Sci & Technol, Cell Mol Biol & Genom Grp, Dept Biol, Trondheim, Norway, [Cancela, M. Leonor] Univ Algarve, Ctr Marine Sci CCMAR, Faro, Portugal, [Cancela, M. Leonor] Univ Algarve, Fac Med & Biomed Sci, Algarve Biomed Ctr, Faro, Portugal, [Carlsson, Jens] Univ Coll Dublin, Sch Biol & Environm Sci, Area Res Grp 52, Earth Inst, Dublin, Ireland, [Gargan, Laura M.] Univ Coll Dublin, Sch Biol & Environm Sci, Area Res Grp 52, Earth Inst, Dublin, Ireland, [Carvalho, Maria F.] Univ Porto, CIIMAR Interdisciplinary Ctr Marine & Environm Re, Porto, Portugal, [Ceglowska, Marta] Polish Acad Sci, Inst Oceanol, Marine Biochem Lab, Sopot, Poland, [Chirivella-Martorell, Jeronimo] IMEDMAR Catholic Univ Valencia, Valencia, Spain, [Dalay, Meltem Conk] Ege Univ, Fac Engn, Dept Bioengn, Izmir, Turkey, [Cueto, Mercedes] Inst Prod Nat & Agrobiol IPNA CSIC, San Cristobal la Laguna, Spain, [Dailianis, Thanos] Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture, Iraklion, Greece, [Mandalakis, Manolis] Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture, Iraklion, Greece, [Deniz, Irem] Manisa Celal Bayar Univ, Fac Engn, Dept Bioengn, Manisa, Turkey, [Diaz-Marrero, Ana R.] Univ La Laguna, Inst Univ Bioorgan Antonio Gonzailez, Tenerife, Spain, [Drakulovic, Dragana] Univ Montenegro, Inst Marine Biol, Kotor, Montenegro, [Dubnika, Arita] Riga Tech Univ, Fac Mat Sci & Appl Chem, Rudolfs Cimdins Riga Biomat Innovat & Dev Ctr, Inst Gen Chem Engn, Riga, Latvia, [Edwards, Christine] Robert Gordon Univ, Sch Pharm & Life Sci, Aberdeen, Scotland, [Einarsson, Hjoerleifur] Univ Akureyri, Fac Nat Resource Sci, Akureyri, Iceland, [Erdogan, Aysegul] Ege Univ, Applicat & Res Ctr Testing & Anal EGE MATAL, Izmir, Turkey, [Eroldogan, Orhan Tufan] Cukurova Univ, Fac Fisheries, Dept Aquaculture, Adana, Turkey, [Ezra, David] Agr Res Org, Volcani Ctr, Rishon Leziyyon, Israel, [Fazi, Stefano] CNR, Water Res Inst, Monterotondo, Italy, [FitzGerald, Richard J.] Univ Limerick, Dept Biol Sci, Limerick, Ireland, [Gaudencio, Susana P.] NOVA Univ Lisbon, Fac Sci & Technol, Dept Chem, UCIBIO Appl Mol Biosci Unit, Caparica, Portugal, [Udovic, Marija Gligora] Univ Zagreb, Fac Sci, Dept Biol, Zagreb, Croatia, [Ljubesic, Zrinka] Univ Zagreb, Fac Sci, Dept Biol, Zagreb, Croatia, [DeNardis, Nadica Ivosevic] Rudjer Boskovic Inst, Zagreb, Croatia, [Jonsdottir, Rosa] Matis Ohf, Reykjavik, Iceland, [Katarzyte, Marija] Klaipeda Univ, Marine Res Inst, Klaipeda, Lithuania, [Overlinge, Donata] Klaipeda Univ, Marine Res Inst, Klaipeda, Lithuania, [Kotta, Jonne] Univ Tartu, Estonian Marine Inst, Tallinn, Estonia, [Ktari, Leila] Carthage Univ, Natl Inst Marine Sci & Technol, B3Aqua Lab, Tunis, Tunisia, [Bilela, Lada Lukic] Univ Sarajevo, Fac Sci, Dept Biol, Sarajevo, Bosnia & Herceg, [Massa-Gallucci, Alexia] AquaBioTech Grp, Dept Fisheries Res & Dev, Mosta, Malta, [Matijosyte, Inga] Vilnius Univ, Life Sci Ctr, Inst Biotechnol, Vilnius, Lithuania, [Mazur-Marzec, Hanna] Univ Gdansk, Fac Oceanog & Geog, Div Marine Biotechnol, Gdynia, Poland, [Torunska-Sitarz, Anna] Univ Gdansk, Fac Oceanog & Geog, Div Marine Biotechnol, Gdynia, Poland, [Mehiri, Mohamed] Univ Cote dAzur, UMR CNRS, Marine Nat Prod Team, Inst Chem Nice, Nice, France, [Roettinger, Eric] Univ Cote dAzur, Federat Res Inst Marine Resources IFR MARRES, Nice, France, [Nielsen, Soren Laurentius] Roskilde Univ, Dept Sci & Environm, Roskilde, Denmark, [Ramasamy, Praveen] Roskilde Univ, Dept Sci & Environm, Roskilde, Denmark, [Novoveska, Lucie] Scottish Assoc Marine Sci, Oban, Argyll, Scotland, [Perale, Giuseppe] Univ Svizzera Italiana, Fac Biomed Sci, Lugano, Switzerland, [Perale, Giuseppe] Ludwig Boltzmann Inst Expt & Clin Traumatol, Vienna, Austria, [Perale, Giuseppe] Ind Biomed Insubri SA, Mezzovico Vira, Switzerland, [Rebours, Celine] Moreforsking AS, Alesund, Norway, [Reinsch, Thorsten] Christian Albrechts Univ Kiel, Inst Crop Sci & Plant Breeding, Kiel, Germany, [Reyes, Fernando] Fdn MEDINA, Granada, Spain, [Rinkevich, Baruch] Natl Inst Oceanog, Israel Oceanog & Limnol Res, Haifa, Israel, [Robbens, Johan] Flanders Res Inst Agr Fisheries & Food, Oostende, Belgium, [Roettinger, Eric] Univ Cote dAzur, Inst Res Canc & Aging Nice IRCAN, INSERM, CNRS, Nice, France, [Rudovica, Vita] Univ Latvia, Dept Analyt Chem, Riga, Latvia, [Sabotid, Jerica] Jozef Stefan Inst, Dept Biotechnol, Ljubljana, Slovenia, [Safarik, Ivo] CAS, Dept Nanobiotechnol, ISB, Biol Ctr, Ceske Budejovice, Czech Republic, [Safarik, Ivo] Palacky Univ, Reg Ctr Adv Technol & Mat, Olomouc, Czech Republic, [Talve, Siret] Minist Rural Affairs, Dept Res & Dev, Tallinn, Estonia, [Tasdemir, Deniz] GEOMAR Helmholtz Ctr Ocean Res, GEOMAR Ctr Marine Biotechnol, Res Unit Marine Nat Prod Chem, Kiel, Germany, [Tasdemir, Deniz] Univ Kiel, Fac Math & Nat Sci, Kiel, Germany, [Schneider, Xenia Theodotou] XPRO Consulting Ltd, Nicosia, Cyprus, [Thomas, Olivier P.] Natl Univ Ireland, Sch Chem, Marine Biodiscovery, Galway, Ireland, [Thomas, Olivier P.] Natl Univ Ireland, Ryan Inst, Galway, Ireland, [Varese, Giovanna Cristina] Univ Torino, Mycotheca Univ Taurinensis, Dept Life Sci & Syst Biol, Turin, Italy, [Vasquez, Marlen, I] Cyprus Univ Technol, Dept Chem Engn, Limassol, Cyprus, COST (European Cooperation in Science and Technology) program, Institut de Chimie de Nice (ICN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Université Côte d'Azur (UCA), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)

Subjects
0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, lcsh:QH1-199.5, Stakeholder engagement, Oceanography, Responsible research and innovation (RRI), challanges, Natural-products, Responsible research and innovation, 0302 clinical medicine, Marine bioeconomy, In-silico prediction, lcsh:Science, valorization, Marine biodiversity, Water Science and Technology, biodiversity, Heavy-metal detoxification, Bioprospecting, Global and Planetary Change, Lead-like molecules, conservation, Biological Sciences, Sustainability, Marine natural products, [SDE]Environmental Sciences, Solid-phase microextraction, Deep-sea sediments, Natural Sciences, marine biotechnology, marine bioeconomy, Marine conservation, marine biotechnology, valorization, biodiversity, conservation, challanges, Ocean Engineering, Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, Bioactive compounds, Blue growth, Waste-water treatment, 03 medical and health sciences, bioprospecting, blue growth, marine biodiversity, marine natural products, sustainability, ethics, responsible research and innovation (RRI), 14. Life underwater, Recreation, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Ethics, Responsible Research and Innovation, business.industry, Secondary metabolites, Particulate organic-carbon, Biotechnology, 030104 developmental biology, 13. Climate action, Agriculture, Marine Biodiversity, marine natural product, Responsible research & innovation, lcsh:Q, business, 030217 neurology & neurosurgery, Tourism
Abstract

Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well as tried to support new economic endeavors (ocean energy, desalination for water supply, and seabed mining). Modern societies and lifestyle resulted in an increased demand for dietary diversity, better health and well-being, new biomedicines, natural cosmeceuticals, environmental conservation, and sustainable energy sources. These societal needs stimulated the interest of researchers on the diverse and underexplored marine environments as promising and sustainable sources of biomolecules and biomass, and they are addressed by the emerging field of marine (blue) biotechnology. Blue biotechnology provides opportunities for a wide range of initiatives of commercial interest for the pharmaceutical, biomedical, cosmetic, nutraceutical, food, feed, agricultural, and related industries. This article synthesizes the essence, opportunities, responsibilities, and challenges encountered in marine biotechnology and outlines the attainment and valorization of directly derived or bio-inspired products from marine organisms. First, the concept of bioeconomy is introduced. Then, the diversity of marine bioresources including an overview of the most prominent marine organisms and their potential for biotechnological uses are described. This is followed by introducing methodologies for exploration of these resources and the main use case scenarios in energy, food and feed, agronomy, bioremediation and climate change, cosmeceuticals, bio-inspired materials, healthcare, and well-being sectors. The key aspects in the fields of legislation and funding are provided, with the emphasis on the importance of communication and stakeholder engagement at all levels of biotechnology development. Finally, vital overarching concepts, such as the quadruple helix and Responsible Research and Innovation principle are highlighted as important to follow within the marine biotechnology field. The authors of this review are collaborating under the European Commission-funded Cooperation in Science and Technology (COST) Action Ocean4Biotech – European transdisciplinary networking platform for marine biotechnology and focus the study on the European state of affairs., This publication is based upon work from COST Action CA18238 (Ocean4Biotech), supported by COST (European Cooperation in Science and Technology) program.AR, KK, and TR: the publication is part of a project that has received funding from the European Union Horizon 2020 Research and Innovation Programme under grant agreement no. 774499 – GoJelly project. AR and KK: this research was funded by the Slovenian Research Agency (research core funding P1-0245 and P1-0237). AR: this publication has been produced with financial assistance of the Interreg MED Programme, co-financed by the European Regional Development Fund (Project No. 7032, internal ref. 8MED20_4.1_SP_001) – B-Blue project. AB: acknowledges the support from the Research Council of Norway through the grant 267474 from the HAVBRUK2 program. MLC: acknowledges the Portuguese Foundation for Science and Technology (UIDB/04326/2020), the European Maritime and Fisheries Fund (MAR2020 OSTEOMAR/16-02-01-FMP-0057 and ALGASOLE/16.02.01-FMP-0058), the European Regional Development Fund (Atlantic Area BLUEHUMAN/EAPA/151/2016 and INTERREG V-A Spain-Portugal ALGARED+), and the European Commision (H2020-MSCA-ITN BIOMEDAQU/766347). MFC: wishes to acknowledge the funding from CEEC program supported by FCT/MCTES (CEECIND/02968/2017); ACTINODEEPSEA project (POCI-01-0145-FEDER-031045) co-financed by COMPETE 2020, Portugal 2020, ERDF and FCT; Strategic Funding UIDB/04423/2020 and UIDP/04423/2020 through national funds provided by FCT and ERDF. MC: financial support from the Programme of the Institute of Oceanology, PAS (grant no. II.3) and National Science Centre in Poland (project number NCN 2016/21/B/NZ9/02304). MCu: acknowledges the funding from the Ministerio de Ciencia e Innovación of Spain (SAF2009-0839 and RTA 2015-00010-C03-02) and INTERREG-MAC2/1.1b/279 (AHIDAGRO). AD-M: acknowledge financial support from INTERREG-MAC/1.1b/042 (BIOTRANSFER2) and Agustín de Betancourt Programme (Cabildo de Tenerife and Universidad de La Laguna). AD: work has been supported by the ERDF Activity 1.1.1.2 “Post-doctoral Research Aid” of the Specific Aid Objective 1.1.1, Operational Programme “Growth and Employment” (No. 1.1.1.2/VIAA/1/16/048). RJF: funding for this research was provided under the Marine Research Programme 2014–2020, through the Marine Institute of Ireland under grant PBA/MB/16/01 “A National Marine Biodiscovery Laboratory of Ireland (NMBLI)” and through the Food Institutional Research Measure, administered by the Department of Agriculture, Food, and the Marine, Ireland under grant issue 17/F/260 (MaraBioActive). SG: this work was supported by the Applied Molecular Biosciences Unit-UCIBIO which is financed by national funds from FCT/MCTES (UID/Multi/04378/2019). SG thanks financial support provided by FCT/MCTES through grant IF/00700/2014 and OceanTresaures project PTDC/QUIQUI/119116/2010. NID: wishes to acknowledge the funding from the Croatian Science Foundation Project CELLSTRESS (IP-2018-01-5840). MMa and TD: we wish to acknowledge funding from the General Secretariat for Research and Technology (GSRT) and the Hellenic Foundation for Research and Innovation (HFRI) under grant no. 239 (SPINAQUA project). AM-G: acknowledges the financial contribution from the project BYTHOS funded by the European Union’s Interreg V-A Italia-Malta Programme under project code C1-1.1-9. HM-M: financial support from National Science Centre in Poland 2016/21/B/NZ9/02304 and 2017/25/B/NZ9/00202. MMe: this work has been supported by the French Government, through the UCAJEDI Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-15-IDEX-01. MMe: thanks the Canceropôle Provence-Alpes-Côte d’Azur, and the Provence-Alpes-Côte d’Azur Region for the financial support provided to the MetaboCell project. DO: supported by the Doctorate Study program in Ecology and Environmental Sciences, Marine Research Institute, Klaipėda University, Lithuania. CR: we gratefully acknowledge the Research Council of Norway, the Møre and Romsdal County Council and Møreforsking AS for their financial contributions through the PROMAC (244244; www.promac.no), the Norwegian Seaweed Biorefinery Platform (294946; http://seaweedplatform.no/), and the Blå-Grønn (55031) projects. ER: this work benefited from financial support from the PACA Canceropôle, the National Cancer Institute, the PACA Regional Council and the French Government, managed by the National Research Agency as part of the Université Côte d’AzurJEDI Investissement d’Avenir project (ANR-15-IDEX-01). JS: work was supported by the Slovenian Research Agency (P4-0127 and J4-1771). IS: financial support from Ministry of Education, Youth and Sports of the Czech Republic (project CZ.02.1.01/0.0/0.0/17_048/0007323). XT: the tool “RRI Roadmap” was developed as part of the European Horizon 2020 project MARINA “Marine Knowledge Sharing Platform for Federating Responsible Research and Innovation Communities” under the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 710566 (2016–2019). OT: his contribution is carried out with the support of the Marine Institute and is funded under the Marine Research Programme by the Irish Government (Grant-Aid Agreement No. PBA/MB/16/01).

Published
2021

43. Putative adverse outcome pathways for female reproductive disorders to improve testing and regulation of chemicals

Author

Andres Salumets, Agne Velthut-Meikas, Pauline Lelandais, Séverine Mazaud-Guittot, Marijke de Cock, Panagiotis Filis, Lisa Connolly, Pauliina Damdimopoulou, Julie Boberg, Sofie Christiansen, Majorie B.M. van Duursen, Paul Fowler, Magdalena Wagner, Anne-Simone Parent, Delphine Franssen, Terje Svingen, Hanna Katarina Lilith Johansson, Monica Kam Draskau, Yuling Xie, Kersti Jääger, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Karolinska Inst, Dept Clinique Sci Intervent and Technology, Div Obstet and Gynecol, Sweden, Karolinska Institutet [Stockholm], Vrije Universiteit Amsterdam [Amsterdam] (VU), GIGA [Université Liège], Université de Liège, Tallinn University of Technology (TTÜ), Queens University Belfast, Sch Biol Sci, Inst Global Food Secur, Belfast BT9 5DL, North Ireland, Queen's University [Belfast] (QUB), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), University of Tartu, University of Aberdeen, Centre Hospitalier Universitaire de Liège (CHU-Liège), EU Horizon 2020 project FREIA [825100], HUS Gynecology and Obstetrics, Clinicum, Department of Obstetrics and Gynecology, University of Helsinki, Helsinki University Hospital Area, Technical University of Denmark [Lyngby] (DTU), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Jonchère, Laurent

Subjects
0301 basic medicine, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], ENDOCRINE DISRUPTING CHEMICALS, LESS CONFUSING TERMINOLOGY, Review Article, Safeguarding, Toxicology, Mice, ODS, 0302 clinical medicine, 3123 Gynaecology and paediatrics, Pregnancy, Regulation of chemicals, Adverse Outcome Pathway, Medicine, Ovarian Diseases, Continuous exposure, GENE-EXPRESSION, Reproductive health, Ovarian dysgenesis syndrome, 030219 obstetrics & reproductive medicine, SDG 5 - Gender Equality, BISPHENOL-A EXPOSURE, Reproduction, General Medicine, Chemical Safety, POLYCYSTIC-OVARY-SYNDROME, 3. Good health, [SDV] Life Sciences [q-bio], Reproductive Health, Maternal Exposure, Female, ANTI-MULLERIAN HORMONE, Endocrine System Diseases, Female reproductive disorders, Risk Assessment, Letter to the Editor, News and Views, Birth rate, 03 medical and health sciences, Adverse outcome pathway, SDG 3 - Good Health and Well-being, Environmental health, PRIMORDIAL FOLLICLE, Toxicity Tests, Animals, Humans, AOP, ORGANOCHLORINE PESTICIDES, Endocrine-disrupting chemicals, Adverse Outcome Pathways, business.industry, Ovary, Review article, GERM-CELL, 030104 developmental biology, IN-UTERO EXPOSURE, 3111 Biomedicine, business, EDC
Abstract

Modern living challenges female reproductive health. We are witnessing a rise in reproductive disorders and drop in birth rates across the world. The reasons for these manifestations are multifaceted and most likely include continuous exposure to an ever-increasing number of chemicals. The cause–effect relationships between chemical exposure and female reproductive disorders, however, have proven problematic to determine. This has made it difficult to assess the risks chemical exposures pose to a woman’s reproductive development and function. To address this challenge, this review uses the adverse outcome pathway (AOP) concept to summarize current knowledge about how chemical exposure can affect female reproductive health. We have a special focus on effects on the ovaries, since they are essential for lifelong reproductive health in women, being the source of both oocytes and several reproductive hormones, including sex steroids. The AOP framework is widely accepted as a new tool for toxicological safety assessment that enables better use of mechanistic knowledge for regulatory purposes. AOPs equip assessors and regulators with a pragmatic network of linear cause–effect relationships, enabling the use of a wider range of test method data in chemical risk assessment and regulation. Based on current knowledge, we propose ten putative AOPs relevant for female reproductive disorders that can be further elaborated and potentially be included in the AOPwiki. This effort is an important step towards better safeguarding the reproductive health of all girls and women.

Published
2020

44. Safeguarding female reproductive health against endocrine disrupting chemicals—The FREIA project

Author

van Duursen, Majorie B.M., Boberg, Julie, Christiansen, Sofie, Connolly, Lisa, Damdimopoulou, Pauliina, Filis, Panagiotis, Fowler, Paul A., Gadella, Bart M., Holte, Jan, Jääger, Kersti, Johansson, Hanna K.L., Li, Tianyi, Mazaud-Guittot, Séverine, Parent, Anne Simone, Salumets, Andres, Soto, Ana M., Svingen, Terje, Velthut-Meikas, Agne, Wedebye, Eva Bay, Xie, Yuling, van den Berg, Martin, One Health Toxicologie, FAH klinische reproductie, Veterinaire biochemie, dB&C FR-RMSC FR, dES/dFAH FR, IRAS OH Toxicology, dIRAS RA-1, One Health Toxicologie, FAH klinische reproductie, Veterinaire biochemie, dB&C FR-RMSC FR, dES/dFAH FR, IRAS OH Toxicology, dIRAS RA-1, E&H: Environmental Health and Toxicology, AIMMS, Vrije Universiteit Amsterdam [Amsterdam] (VU), Tech University Denmark, National Food Inst, Denmark, Technical University of Denmark [Lyngby] (DTU), Queens University Belfast, Sch Biol Sci, Inst Global Food Secur, Belfast BT9 5DL, North Ireland, Queen's University [Belfast] (QUB), Karolinska Inst, Dept Clinique Sci Intervent and Technology, Div Obstet and Gynecol, Sweden, CHU Stockholm, Karolinska Institutet [Stockholm], Inst Med Sci, Sch Med Med Sci and Nutr, Foresterhill, Scotland, University of Aberdeen, UniversiteitUtrecht, Fac Vet Med, Dept Populat Hlth Sci, Yalelaan 2, Netherlands, Utrecht University [Utrecht], Carl von Linne Clinique, Uppsala Sci Pk, Sweden, Competence Centre Hlth Technology, Teaduspargi 13, Estonia, University of Tartu, Institut de recherche en santé, environnement et travail (Irset), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), University Liege, [GIGA] Inst, Neuroendocrinol Unit, Ave Hôpital, Belgium, GIGA [Université Liège], Université de Liège, Tufts University [Medford], Tallinn University of Technology (TTÜ), European UnionEuropean Union (EU) [825100], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Jonchère, Laurent

Subjects
0301 basic medicine, Oocyte, [SDV]Life Sciences [q-bio], Endocrine Disruptors, Female reproductive system, Safeguarding, Female reproductive health, lcsh:Chemistry, 0302 clinical medicine, Risk Factors, Adrenal, Endocrine disrupting chemicals, lcsh:QH301-705.5, Spectroscopy, media_common, Reproductive health, Risk assessment, fertility, 030219 obstetrics & reproductive medicine, SDG 5 - Gender Equality, Reproduction, risk assessment, General Medicine, 3. Good health, Computer Science Applications, [SDV] Life Sciences [q-bio], Reproductive Health, medicine.anatomical_structure, Environmental Pollutants, Female, Bioassay, Test methods, Project Report, media_common.quotation_subject, Mammary gland, Endocrine System, Fertility, Ovary, test methods, Catalysis, Inorganic Chemistry, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Environmental health, medicine, Animals, Humans, Endocrine system, Physical and Theoretical Chemistry, Molecular Biology, business.industry, Puberty, Organic Chemistry, Environmental Exposure, endocrine disrupting chemicals, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, Steroidogenesis, Chemical regulation, ovary, business, female reproductive health
Abstract

International audience; Currently available test methods are not well-suited for the identification of chemicals that disturb hormonal processes involved in female reproductive development and function. This renders women's reproductive health at increasing risk globally, which, coupled with increasing incidence rates of reproductive disorders, is of great concern. A woman's reproductive health is largely established during embryonic and fetal development and subsequently matures during puberty. The endocrine system influences development, maturation, and function of the female reproductive system, thereby making appropriate hormone levels imperative for correct functioning of reproductive processes. It is concerning that the effects of human-made chemicals on the endocrine system and female reproductive health are poorly addressed in regulatory chemical safety assessment, partly because adequate test methods are lacking. Our EU-funded project FREIA aims to address this need by increasing understanding of how endocrine disrupting chemicals (EDCs) can impact female reproductive health. We will use this information to provide better test methods that enable fit-for-purpose chemical regulation and then share our knowledge, promote a sustainable society, and improve the reproductive health of women globally.

Published
2020

45. Long-term thermal sensitivity of Earth's tropical forests

Author

Bruno Herault, Peter J. Van Der Meer, Jean-François Bastin, Aurora Levesley, Michael D. Swaine, Rodolfo Vásquez Martínez, Martin Dančák, Matt Bradford, Frans Bongers, Stuart J. Davies, Reuben Nilus, Adriano José Nogueira Lima, Lip Khoon Kho, Edmar Almeida de Oliveira, Joey Talbot, Richard F. Preziosi, Jagoba Malumbres-Olarte, James A. Comiskey, Thalès de Haulleville, José Luís Camargo, Terese B. Hart, Juliana Schietti, Peter S. Ashton, Thomas E. Lovejoy, Ophelia Wang, Kanehiro Kitayama, Francis Q. Brearley, Peter van der Hout, Amy C. Bennett, Janvier Lisingo, Luis Valenzuela Gamarra, Lily Rodriguez Bayona, Zorayda Restrepo Correa, Jérôme Chave, Connie J. Clark, Christopher Baraloto, Gerardo Aymard, Serge K. Begne, Kofi Affum-Baffoe, Abel Monteagudo-Mendoza, Geertje M. F. van der Heijden, Fernanda Coelho de Souza, Timothy R. Baker, Rahayu Sukmaria Sukri, Julie Peacock, Hermann Taedoumg, Simon L. Lewis, Yahn Carlos Soto Shareva, Greta C. Dargie, Murielle Simo-Droissart, David Harris, Faizah Metali, Hans ter Steege, Richard Lowe, Géraldine Derroire, Benoit Burban, Camila Silva Valeria, Martin Svátek, Wannes Hubau, Sarah A. Batterman, Vincent A. Vos, Elizabeth Kearsley, Peter M. Umunay, Martin J. P. Sullivan, Flávia R. C. Costa, Hans Verbeeck, Maria Cristina Peñuela Mora, John R. Poulsen, Simon Willcock, Simone Aparecida Vieira, Jean-Louis Doucet, Foster Brown, Yadvinder Malhi, Luisa Fernanda Duque, Ronald Vernimmen, Miguel E. Leal, Alan Hamilton, Martin Gilpin, Colin R. Maycock, Carlos Cerón, Radim Hédl, Oliver L. Phillips, Walter Huaraca Huasco, Jon C. Lovett, Beatriz Schwantes Marimon, Roderick Zagt, Ted R. Feldpausch, Gabriela Lopez-Gonzalez, Ima Célia Guimarães Vieira, Pascal Boeckx, Roel J. W. Brienen, Marcelo F. Simon, Keith C. Hamer, Alberto Vicentini, Corneille E. N. Ewango, Clément Stahl, Javier Silva Espejo, Ana Andrade, Anand Roopsind, Erika Berenguer, Pieter A. Zuidema, Vianet Mihindou, Murray Collins, Simone Matias Reis, Emilio Vilanova Torre, Kathryn J. Jeffery, Marie Noël Kamdem Djuikouo, Terry Brncic, Percy Núñez Vargas, John Terborgh, Paulo S. Morandi, Bonaventure Sonké, Jan Bogaert, William E. Magnusson, Lilian Blanc, Terry L. Erwin, Ervan Rutishauser, Anthony Di Fiore, Isau Huamantupa-Chuquimaco, Edward T. A. Mitchard, Massiel Corrales Medina, Nicholas J. Berry, Juliana Stropp, Maureen Playfair, Luzmila Arroyo, Douglas Sheil, Armando Torres-Lezama, David A. Neill, Sean C. Thomas, Eric Arets, Ernest G. Foli, Lola da Costa, Ricardo Keichi Umetsu, Lan Qie, James Singh, Lise Zemagho, Agustín Rudas, Richard B. Primack, Jan Reitsma, Annette Hladik, Alexander K. Koch, Colin A. Pendry, Walter A. Palacios, Sabina Cerruto Ribeiro, Nicolas Labrière, Fernando Elias, Eric Chezeaux, William Milliken, Manuel Gloor, Romeo Ekoungoulou, Jefferson S. Hall, Henrique E. M. Nascimento, Susan G. Laurance, Axel Dalberg Poulsen, Marcos Silveira, Carolina V. Castilho, Plínio Barbosa de Camargo, Eurídice N. Honorio Coronado, Kamariah Abu Salim, Joeri A. Zwerts, Marcelo Brilhante de Medeiros, Jos Barlow, Georgia Pickavance, Joice Ferreira, Mark van Nieuwstadt, Jorcely Barroso, Andrew R. Marshall, Miguel Alexiades, Lindsay F. Banin, Terry Sunderland, Lourens Poorter, Alejandro Araujo-Murakami, Varun Swamy, Rafael Herrera, Hans Beeckman, Gerardo Flores Llampazo, Shin-ichiro Aiba, Adriane Esquivel-Muelbert, Michelle Kalamandeen, Adriana Prieto, Ben Hur Marimon, Casimiro Mendoza, Victor Chama Moscoso, Eliana Jimenez-Rojas, Hirma Ramírez-Angulo, Maxime Réjou-Méchain, Vincent Droissart, Nigel C. A. Pitman, Hannah L. Mossman, Everton Cristo de Almeida, Fernando Cornejo Valverde, Ângelo Gilberto Manzatto, Aurélie Dourdain, Luiz E. O. C. Aragão, Raquel Thomas, David W. Galbraith, Kenneth R. Young, Nallaret Davila Cardozo, Timothy J. Killeen, Rafael de Paiva Salomão, Bente B. Klitgaard, James Taplin, Damien Bonal, Karina Melgaço, William F. Laurance, Jason Vleminckx, Esteban Alvarez Dávila, Verginia Wortel, Richarlly da Costa Silva, Thaiane Rodrigues de Sousa, Sophie Fauset, Nadir Pallqui Camacho, Wendeson Castro, Toby R. Marthews, Fabricio Beggiato Baccaro, John T. Woods, David Taylor, Patricia Alvarez Loayza, Andrew Ford, Niro Higuchi, Aida Cuni Sanchez, Aline Pontes Lopes, Laszlo Nagy, John Pipoly, Lee J. T. White, Jhon del Aguila Pasquel, European Research Council, European Commission, Royal Society (UK), Leverhulme Trust, Gordon and Betty Moore Foundation, David and Lucile Packard Foundation, Fundação de Amparo à Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Agence Nationale de la Recherche (France), Missouri Botanical Garden, Smithsonian Institution, Wildlife Conservation Society, National Geographic Society, Centre for International Forestry Research, Agence Nationale Des Parcs Nationaux (Gabon), University of Leeds, Mensurat Unit, Forestry Research Institute of Ghana, Centro de Pesquisa Agroflorestal de Roraima, Brazilian Agricultural Research Corporation (Embrapa), Sch Geog, University of Nottingham, Department of Biology, Higher Teachers Training College (HTTC), Université deYaoundé I, School of Geography [Leeds], University of Edinburgh, School of Geography and the Environment, Environmental Change Institute, University of Oxford [Oxford], Grad Sch Sci & Engn, Kagoshima University, University of Kent [Canterbury], Universidade Federal do Mato Grosso (UFMT), Universidad Nacional de Colombia, Duke University [Durham], Instituto Nacional de Pesquisas da Amazônia (INPA), University of Campinas [Campinas] (UNICAMP), National Institute for Space Research [Sao José dos Campos] (INPE), Universidad Autonoma Gabriel René Moreno (UAGRM), Wageningen University and Research [Wageningen] (WUR), Dept Organism & Evolutionary Biol, Harvard University [Cambridge], Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Universidade de São Paulo (USP), Universidade Federal do Acre (UFAC), Research Unit of Landscape Ecology and Plant Production Systems, Université libre de Bruxelles (ULB), School of Engineering and Science, Jacobs University [Bremen], Lancaster Environment Centre, Lancaster University, Sch Geosci, Laboratory of Applied Physical Chemistry, Universiteit Gent = Ghent University [Belgium] (UGENT), Biodiversité et Paysage, Université de Liège - Gembloux, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Forest Ecol & Forest Management Grp, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Woods Hole Research Center, Partenaires INRAE, Herbario Alfredo Paredes, Universidad Agraria del Ecuador, Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Rougier Gabon, Andes to Amazon Biodiversity Program, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Smithsonian Tropical Research Institute, Universidad Nacional de la Amazonía Peruana [Loreto, Perou] (UNAP), AgroParisTech, University of Texas at Austin [Austin], Université de Liège, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Milieux Désordonnés et Hétérogènes (LMDH), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Commonwealth Scientific & Industrial Research Organisation (CSIRO), Royal Botanic Gardens, Czech Academy of Sciences [Prague] (CAS), Commissariat général du Plan (CGP), Premier ministre, Instituto Nacional de Pequisas da Amazônia, Instituto National de Pequisas da Amazonia Brazil, Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale des Parcs Nationaux, Agence Nationale des Parcs Nationaux, BP 30 379 Libreville, Gabon, Malaysian Palm Oil Board, Kyoto University, Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], James Cook University (JCU), Laboratoire d'Etude de l'Apprentissage et du Développement [Dijon] (LEAD), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB), Coordenac Bao de Pesquisas em Ecologia, Universidade do Estado de Mato Grosso (UNEMAT), University of Mary Washington, Chercheur indépendant, Royal Botanic Garden , Kew, Department of Biochemistry and Molecular Biology, Medical and Health Science Center, Instituto Superior Técnico, Universidade Técnica de Lisboa (IST), Universidad Estatal Amazonica, Forest Research Centre (FRC), Forest Ecology and Forest Management Group, Natural History Museum [Oslo], University of Oslo (UiO), Bur Waarderburg, Iwokrama International Centre for Rainforest Conservation and Development, CarboForExpert, Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Center for International Forestry Research (CIFOR), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Yaoundé [Cameroun], JRC Institute for Environment and Sustainability (IES), European Commission - Joint Research Centre [Ispra] (JRC), Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Plant Systemat & Ecol Lab, Université de Yaoundé I, Department of Neurology, Great Ormond Street Hospital for Children [London] (GOSH), Naturalis Biodiversity Center [Leiden], Division of Marine Science and Conservation, Nicholas School of the Environment, Instituto de Investigaciones para el Desarrollo Forestal, Universidad de los Andes [Bogota] (UNIANDES), University of Wisconsin - Milwaukee, Van der Hout Forestry Consulting, University Medical Center Groningen [Groningen] (UMCG), Computational & Applied Vegetation Ecology (CAVElab), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Sch Earth Sci & Environm Sustainabil, Northern Arizona University [Flagstaff], University of Stirling, Biol Sci, Liverpool John Moore University (ljmu), Biodiversity Department, Center for Agricultural Research in Suriname (CELOS), Sub Ecology and Biodiversity, Sub Animal Ecology, Ecology and Biodiversity, Animal Ecology, and Systems Ecology

Subjects
0106 biological sciences, Tropical trees, Hot Temperature, 010504 meteorology & atmospheric sciences, Earth, Planet, Climate, Acclimatization, Tropical forest carbon stocks, Bos- en Landschapsecologie, Growth, Forests, Atmospheric sciences, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Trees, Tropical climate, SDG 13 - Climate Action, Forest and Landscape Ecology, Biomass, Photosynthesis, Hectare, Productivity, Biomass (ecology), Multidisciplinary, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, PE&RC, Wood, Productivity (ecology), Vegetatie, Bos- en Landschapsecologie, C180 Ecology, Tree, Leaf Respiration, Carbon-Cycle Feedbacks, Climate Change, Climate change and forestry, Climate change, 010603 evolutionary biology, Carbon cycle, Carbon Cycle, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Life Science, Bosecologie en Bosbeheer, Vegetatie, 0105 earth and related environmental sciences, Tropical Climate, Vegetation, Global warming, Tropics, 15. Life on land, Forest Ecology and Forest Management, Carbon, CO₂ Fertilization, 13. Climate action, Environmental science, Vegetation, Forest and Landscape Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Acclimation
Abstract

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate., Our plot monitoring networks havebeen supported by multiple grants from a large number of funding bodies: European Research Council; Natural Environment Research Council; European Union’s Fifth, Sixth, and Seventh Framework Programme; Royal Society, Leverhulme Trust; Gordon and Betty Moore Foundation; David and Lucile Packard Foundation; State of São Paulo Research Foundation (FAPESP); National Council for Science and Technology Development of Brazil (CNPq); Agence Nationale de la Recherche; Conservation International; Missouri Botanical Garden; Smithsonian Institution; Wildlife Conservation Society; National Geographic Society; Centre for International Forestry; and Gabon’s National Park Agency.

Published
2020

46. Accelerated increase in plant species richness on mountain summits is linked to warming

Author

Jonathan Lenoir, Sara Palacio, Anna Delimat, Ingolf Kühn, Blazena Sedlakova, Gerald Jurasinski, Robert Kanka, Sarah J. Woodin, Stefan Dullinger, Sonja Wipf, Daniel Gómez-García, Olatz Fernández-Arberas, Umberto Morra di Cella, Manuel J. Steinbauer, Jens-Christian Svenning, Magalì Matteodo, Veronika Piscová, Vivian A. Felde, Christian Rixen, Siri V. Haugum, Hanne Henriksen, Veronika Stöckli, María J. Herreros, Manfred Bardy-Durchhalter, Signe Normand, Arvid Odland, Martina Petey, Harald Pauli, Niklaus E. Zimmermann, Andrea Lamprecht, Brigitta Erschbamer, Frank T. Breiner, Aino Kulonen, John-Arvid Grytnes, Bogdan Jaroszewicz, Anne D. Bjorkman, Elena Barni, Siri Lie Olsen, Klaus Steinbauer, Jutta Kapfer, Francesca Jaroszynska, Kari Klanderud, Pascal Vittoz, Melissa A. Dawes, Jean-Paul Theurillat, Erlend T. Grindrud, Guido Teppa, Manuela Winkler, Kjetil F. Fossheim, Sylvia Haider, Sarah Burg, Patryk Czortek, Damien Georges, BayCEER, Bayreuth Center of Ecology and Environmental Research, Dept Biol, University of Bergen (UiB), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), University of Vienna [Vienna], WSL Institute for Snow and Avalanche Research SLF, Department of Biological Sciences [Bergen] (BIO / UiB), Instituto Pirenaico de Ecologia (IPE), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Warsaw (UW), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Institut des Dynamiques de la Surface Terrestre [Lausanne] (IDYST), Université de Lausanne (UNIL), Dept Biol Sci, Ecoinformat & Biodivers Grp, Aarhus University [Aarhus], Centre alpien de Phytogéographie, Fondation J.-M. Aubert, Département d'écologie et évolution, Université de Lausanne (UNIL)-Université de Lausanne (UNIL), Institut Fédéral de Recherches sur la Forêt, la Neige et le Paysage (WSL), and Institut Fédéral de Recherches [Suisse]

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, RANGE SHIFTS, [SDE.MCG]Environmental Sciences/Global Changes, CLIMATE CHANGE, Species distribution, DIVERSITY, Biodiversity, Geographic Mapping, Climate change, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Global Warming, History, 21st Century, 010603 evolutionary biology, 01 natural sciences, Ecosystem, ELEVATION, Macroecology, 0105 earth and related environmental sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, CLIMATE-CHANGE, NITROGEN DEPOSITION, Multidisciplinary, CLIMATE CHANGE, ALPINE PLANTS, NITROGEN DEPOSITION, RANGE SHIFTS, MODEL, DIVERSITY, ELEVATION, Ecology, Altitude, Global warming, Temperature, ALPINE PLANTS, Global change, History, 20th Century, Plants, 15. Life on land, Europe, MODEL, Geography, 13. Climate action, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Globally accelerating trends in societal development and human environmental impacts since the mid-twentieth century 1–7 are known as the Great Acceleration and have been discussed as a key indicator of the onset of the Anthropocene epoch 6 . While reports on ecological responses (for example, changes in species range or local extinctions) to the Great Acceleration are multiplying 8, 9 , it is unknown whether such biotic responses are undergoing a similar acceleration over time. This knowledge gap stems from the limited availability of time series data on biodiversity changes across large temporal and geographical extents. Here we use a dataset of repeated plant surveys from 302 mountain summits across Europe, spanning 145 years of observation, to assess the temporal trajectory of mountain biodiversity changes as a globally coherent imprint of the Anthropocene. We find a continent-wide acceleration in the rate of increase in plant species richness, with five times as much species enrichment between 2007 and 2016 as fifty years ago, between 1957 and 1966. This acceleration is strikingly synchronized with accelerated global warming and is not linked to alternative global change drivers. The accelerating increases in species richness on mountain summits across this broad spatial extent demonstrate that acceleration in climate-induced biotic change is occurring even in remote places on Earth, with potentially far-ranging consequences not only for biodiversity, but also for ecosystem functioning and services.

Published
2018

47. Direct detection of phenol using a new bacterial strain-based conductometric biosensor

Author

Mohamed Braiek, Seyed Omid Ranaei-Siadat, Nicole Jaffrezic-Renault, Florence Lagarde, Gholamhossein Ebrahimipour, Narjes Kolahchi, Dept Microbiol, Shahid Beheshti Univ, Fac Biol Sci, Interfaces & biosensors - Interfaces & biocapteurs, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Dept Biotechnol, Shahid Beheshti Univ, Fac Energy Engn & New Technol, and This work was partially supported by the ministry of Science, Research and Technology, Islamic Republic of Iran-Department of Scholarships and Overseas Students' Affairs and was carried out in the University of Lyon, institute of Analytical Sciences, UMR-CNRS 5280, France.

Subjects
Pseudomonas sp. (GSN23), Interdigitated microelectrodes, 0211 other engineering and technologies, 02 engineering and technology, 01 natural sciences, chemistry.chemical_compound, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Chemical Engineering (miscellaneous), Phenol, Phenols, Whole cell biosensor, Waste Management and Disposal, Detection limit, 021110 strategic, defence & security studies, Chromatography, biology, Process Chemistry and Technology, 010401 analytical chemistry, Pseudomonas, biology.organism_classification, Pollution, Bacterial strain, 0104 chemical sciences, Microelectrode, chemistry, 13. Climate action, Biosensor, Bacteria
Abstract

The authors thank Science et Surface company (Lyon-France) for SEM micrographs. Carole Chaix is thanked for fruitful discussions, Carole Farre for SEM observations, Gaetan Raimondi and Colin Minini for preparation and characterization of AuNPs.; International audience; During the last two decades, phenolic compounds have become the subject of intense research in the environmental preservation field. Phenols are included on the lists of priority pollutants in many countries and their determination is required. In this work, a fast, sensitive miniaturized whole cell conductometric biosensor was developed for the determination of phenol. The biosensor assembly was prepared by immobilizing Pseudomonas sp. (GSN23) bacteria, from oil refinery contaminated soils, on the surface of gold interdigitated microelectrodes. The results obtained with conductometric measurement allowed sensitive detection of phenol from 1 to 300 mg L-1 (10-3187 mu M), with a detection limit (LOD) of 0.2 mg L-1 (2 mu M). Furthermore, the bacterial biosensor was successfully applied to the determination of phenol in spiked river samples.Capsule abstract: A conductometric bacterial biosensor based on Pseudomonas sp. (GSN23) bacteria, from oil refinery contaminated soils has been developed. The detection limit for phenol is 2 mu M.

Published
2018

48. CuS Decorated Functionalized Reduced Graphene Oxide: A Dual Responsive Nanozyme for Selective Detection and Photoreduction of Cr(VI) in an Aqueous Medium

Author

Priyakshree Borthakur, Rabah Boukherroub, Manash R. Das, Sabine Szunerits, Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), CSIR North East Inst Sci & Technol, Biol Sci & Technol Div, Jorhat 785006, Assam, India, Partenaires INRAE, Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), NanoBioInterfaces - IEMN (NBI - IEMN), and Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)

Subjects
General Chemical Engineering, Oxide, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, law.invention, Nanomaterials, chemistry.chemical_compound, law, Environmental Chemistry, [CHIM]Chemical Sciences, ComputingMilieux_MISCELLANEOUS, biology, Aqueous medium, Renewable Energy, Sustainability and the Environment, Graphene, General Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, chemistry, biology.protein, 0210 nano-technology, Biosensor, Peroxidase
Abstract

Design of functional nanomaterials as peroxidase mimics has attracted great attention due to promising applications in numerous fields, including biosensing, cancer diagnostics, immunoassays, envir...

Published
2019

49. Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Author

Balamuralikrishna Jayaprakash, Kurt V. Fagerstedt, Jorma Vahala, Saijaliisa Kangasjärvi, Courtney A. Hollender, Moona Rahikainen, Peter J. Gollan, Tiina Blomster, Ville Pennanen, Alexey Shapiguzov, Matti Rousi, Adrien Gauthier, Sirpa Kärenlampi, Raili Ruonala, Timo Sipilä, Mikael Brosché, Leila Kauppinen, Juan de Dios Barajas-López, Tuula Puhakainen, Kirk Overmyer, Airi Lamminmäki, Omid Safronov, Ari Pekka Mähönen, Kean-Jin Lim, Annikki Welling, Ykä Helariutta, Martin Lascoux, Colin T. Kelleher, Ali Amiryousefi, Katriina Mouhu, Fred O. Asiegbu, Johanna Leppälä, Ülo Niinemets, Pezhman Safdari, Pauliina Halimaa, Sari Kontunen-Soppela, Gugan Eswaran, Pekka Heino, Juan Antonio Alonso Serra, Fuqiang Cui, Juha Mikola, Jarkko Salojärvi, Lidia Vetchinnikova, Sacha Escamez, Hiroaki Fujii, Daniel Blande, Juha Immanen, Péter Poczai, Viivi Ahonen, Alan H. Schulman, Pasi Rastas, Chris Dardick, Matleena Punkkinen, Kristiina Himanen, Jaakko Tanskanen, Christiaan van der Schoot, Sanna Ehonen, Elina Oksanen, Anna Kärkönen, Victor A. Albert, Suvi Sutela, Olli-Pekka Smolander, Lee Macpherson, Michael Wrzaczek, E. Tapio Palva, Maija Sierla, Boy J.H.M. Possen, Juhana Kammonen, Sitaram Rajaraman, Paula Elomaa, Tianying Lan, Enjun Xu, Olga Blokhina, Suvi K. Broholm, Kaisa Nieminen, J. Patrik Koskinen, Jaakko Kangasjärvi, Risto Hagqvist, Lars Paulin, Arja Tervahauta, Aleksia Vaattovaara, Andriy Kovalchuk, Leila Pazouki, Petri Auvinen, Teemu H. Teeri, Department of Plant Molecular Biology, Université de Lausanne (UNIL), SUNY Buffalo, Dept Biol Sci, Buffalo, NY 14260 USA, Université Paris Diderot - Paris 7 (UPD7), Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Division of Plant Physiology, University of Helsinki, Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Molecular Plant Biology, University of Turku, University of Turku, University of Eastern Finland, Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], University of Helsinki-University of Helsinki, Estonian University of Life Sciences, Viikki Plant Science Centre (ViPS), Faculty of Biological and Environmental Sciences [Helsinki], Natural Resources Institute Finland, University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Department of Biological Sciences [Buffalo], University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY)-State University of New York (SUNY), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Estonian University of Life Sciences (EMU), and Natural resources institute Finland

Subjects
Mutation rate, Fitness landscape, Population, Adaptation, Biological, Mistake, Computational biology, Biology, Polymorphism, Single Nucleotide, DNA sequencing, Interpretation (model theory), [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, 0302 clinical medicine, Gene Duplication, Genetics, Author Correction, education, Betula, Finland, Phylogeny, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 030304 developmental biology, Population Density, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Notice, Published Erratum, Genetics, Population, Genome, Plant, 030217 neurology & neurosurgery
Abstract

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

Published
2019

50. Evaluation of resistivity anisotropy parameters in the Eastern Mitidja basin, Algeria, using azimuthal electrical resistivity tomography

Author

Sid‐Ali Messaoudi, Abdallah Bounif, Roza Aissaoui, Hermann Zeyen, University of Sciences and Technology Houari Boumediene [Alger] (USTHB), Mouloud Mammeri Univ Tizi Ouzou, Fac Biol Sci & Agron Sci, Dept Geol Sci, Tizi Ouzou, Algeria, Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB), Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), and Université Hassiba Ben Bouali de Chlef (UHBC)

Subjects
Regional geology, Hydrogeology, 010504 meteorology & atmospheric sciences, Groundwater flow, Water flow, Hydrogeophysics, Mineralogy, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010502 geochemistry & geophysics, 01 natural sciences, 6. Clean water, Geophysics, Electrical resistivity and conductivity, [SDU]Sciences of the Universe [physics], Electrical resistivity tomography, Anisotropy, Geology, 0105 earth and related environmental sciences
Abstract

International audience; We study electrical anisotropy using azimuthal electrical resistivity tomography (A-ERT) for identifying geological layers and determining the preferential aquifer flow direction. The work presented in this paper aims at calculating the anisotropy coefficient from the inverted resistivity measurements, relating the geophysical results to the site geology and water flow direction, and comparing the results with those obtained from prior studies using hydrogeological approaches. The study area is located in the Eastern Mitidja basin, about 15 km east of Algiers. The work carried out includes three measurement points, totalling 24 ERT profiles. For each point, eight A-ERT profiles, using Wenner-Schlumberger array configuration, were performed every 22.5 degrees around a fixed central point. The data processing includes two-dimensional inversion of each profile, representation of the inverted resistivities at the central points as a function of the azimuth in polar diagrams, and implementation of an inversion program to determine the best fitting azimuthal anisotropy parameters. The origin of electrical anisotropy is probably due to grain alignment, which is often observed in fine-grained sediments such as clays and some sands. This alignment creates a higher electrical resistivity perpendicular to the alignment than parallel to it, which is an indicator for higher hydraulic permeability in the minimum resistivity direction, which corresponds to the preferential groundwater flow direction.

Published
2019

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