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2. Development and analysis of the Soil Water Infiltration Global database
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M. Rahmati, L. Weihermüller, J. Vanderborght, Y. A. Pachepsky, L. Mao, S. H. Sadeghi, N. Moosavi, H. Kheirfam, C. Montzka, K. Van Looy, B. Toth, Z. Hazbavi, W. Al Yamani, A. A. Albalasmeh, M. Z. Alghzawi, R. Angulo-Jaramillo, A. C. D. Antonino, G. Arampatzis, R. A. Armindo, H. Asadi, Y. Bamutaze, J. Batlle-Aguilar, B. Béchet, F. Becker, G. Blöschl, K. Bohne, I. Braud, C. Castellano, A. Cerdà, M. Chalhoub, R. Cichota, M. Císlerová, B. Clothier, Y. Coquet, W. Cornelis, C. Corradini, A. P. Coutinho, M. B. de Oliveira, J. R. de Macedo, M. F. Durães, H. Emami, I. Eskandari, A. Farajnia, A. Flammini, N. Fodor, M. Gharaibeh, M. H. Ghavimipanah, T. A. Ghezzehei, S. Giertz, E. G. Hatzigiannakis, R. Horn, J. J. Jiménez, D. Jacques, S. D. Keesstra, H. Kelishadi, M. Kiani-Harchegani, M. Kouselou, M. Kumar Jha, L. Lassabatere, X. Li, M. A. Liebig, L. Lichner, M. V. López, D. Machiwal, D. Mallants, M. S. Mallmann, J. D. de Oliveira Marques, M. R. Marshall, J. Mertens, F. Meunier, M. H. Mohammadi, B. P. Mohanty, M. Pulido-Moncada, S. Montenegro, R. Morbidelli, D. Moret-Fernández, A. A. Moosavi, M. R. Mosaddeghi, S. B. Mousavi, H. Mozaffari, K. Nabiollahi, M. R. Neyshabouri, M. V. Ottoni, T. B. Ottoni Filho, M. R. Pahlavan-Rad, A. Panagopoulos, S. Peth, P.-E. Peyneau, T. Picciafuoco, J. Poesen, M. Pulido, D. J. Reinert, S. Reinsch, M. Rezaei, F. P. Roberts, D. Robinson, J. Rodrigo-Comino, O. C. Rotunno Filho, T. Saito, H. Suganuma, C. Saltalippi, R. Sándor, B. Schütt, M. Seeger, N. Sepehrnia, E. Sharifi Moghaddam, M. Shukla, S. Shutaro, R. Sorando, A. A. Stanley, P. Strauss, Z. Su, R. Taghizadeh-Mehrjardi, E. Taguas, W. G. Teixeira, A. R. Vaezi, M. Vafakhah, T. Vogel, I. Vogeler, J. Votrubova, S. Werner, T. Winarski, D. Yilmaz, M. H. Young, S. Zacharias, Y. Zeng, Y. Zhao, H. Zhao, H. Vereecken, Institute of Bio- and Geosciences [Jülich] (IBG), Forschungszentrum Jülich GmbH, Department of Soil Science and Engineering, Faculty of Agriculture, University of Maragheh, ISMC International Soil Modeling Consortium, Institute of Bio and Geosciences Forschungszentrum Jülich, USDA-ARS : Agricultural Research Service, Chinese Academy of Agricultural Sciences (CAAS), Tarbiat Modares University [Tehran], Urmia University, Hungarian Academy of Sciences (MTA), University of Pannonia, UAE University, Jordan University of Science and Technology [Irbid, Jordan], Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centro Acadêmico do Agreste (CAA), Universidade Federal de Pernambuco [Recife] (UFPE), Hellenic Agricultural Organization, Soil and Water Resources Institute, Department of Physics (DFI), Federal University of Lavras (UFLA), University of Tehran, Makerere University (MAK), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Innovative Groundwater Solutions, Interactions et dynamique des environnements de surface (IDES), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Eau et Environnement (IFSTTAR/GERS/EE), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-PRES Université Nantes Angers Le Mans (UNAM), Department of Earth Sciences, Institute of Geographical Sciences, Freie Universität Berlin, Centre for Water Resource Systems, Institute of Hydraulic Engineering and Water Resources Management, University of Technology, University of Rostock [Germany], Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Pyrenean Institute of Ecology (CSIC), Universitat de València (UV), Mount Albert Research Station, New Zealand Institute for Plant and Food Research Limited, Czech Technical University in Prague (CTU), The New Zealand Institute for Plant & Food Research (NEW ZEALAND), Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Biogéosystèmes Continentaux - UMR7327, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Ghent University [Belgium] (UGENT), Department of Civil and Environmental Engineering of the University of Perugia, Italy, Università degli Studi di Perugia (UNIPG), UniRedentor University Center, Embrapa Solos, Ministério da Agricultura, Department of Soil Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Agricultural Research, Education and Extension Organization Maragheh, Dryland Agricultural Research Institute, East Azerbaijan Agricultural and Natural Resources Research and Education center, Scientific Member of Soil and Water Research Department, Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Centre for Agricultural Research [Budapest] (ATK), Department of Natural Resources and Environment, Faculty of Agriculture, Jordan University of Science and Technology, Department of Watershed Management Engineering, Faculty of Natural Resources, Life and Environmental Sciences, University of California, Geographisches Institut, Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Plant Nutrition and Soil Science, Christian-Albrechts-Universität zu Kiel (CAU), ARAID Researcher, Spanish National Research Council (IPE-CSIC), Instituto Pirenaico de Ecología-CSIC (IPE-CSIC), Enginereed and Geosystems Analysis Unit, Belgian Nuclear Research Centre, Soil, Water and Land Use Team, Wageningen Environmental Researc, Civil, Surveying and Environmental Engineering, University of Newcastle [Australia] (UoN), Department of Soil Science, College of Agriculture, Isfahan University of Technology, Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur (IIT Kharagpur), State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Research Soil Scientist, United States Department of Agriculture - Agricultural Research Service, Slovak Academy of Sciences, Slovak Academy of Science [Bratislava] (SAS), Departamento de Suelo y Agua, Consejo Superior de Investigaciones Científicas (CSIC), Pomology Department, Estación Experimental de Aula Dei, Regional Research Station, ICAR-Central Arid Zone Research Institute, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Soil Science Graduate Program (ufsm.br/ppgcs), Federal University of Santa Maria, Science and Technology of the Amazonas – IFAM, Federal Institute of Education, Environment Centre Wales, Bangor University, ENGIE, Earth and Life Institute - Environmental Sciences (ELIE), Université Catholique de Louvain (UCL), Department of Environmental Sciences, Urmia Lake Research Institute, Department of Biological and Agricultural Engineering, 2117 TAMU, College Station, Texas A&M University System, Department of Agroecology, Research Centre Foulum, Aarhus University, Shiraz University (Shiraz University ), University of Kurdistan, University of Tabriz, Department of Hydrology, Geological Survey of Brazil (CPRM), Department of Water Resources and Environment, Soil and Water Research Department, Agricultural Research, Education and Extension Organization (AREEO), Sistan Agricultural and Natural Resources Research and Education Center, Department of Soil Science, University of Saskatchewan, Department of Earth and Environmental Sciences [Leuven-Heverlee], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), GeoEnvironmental Research Group, Faculty of Philosophy and Letters, University of Extremadura, Soil Science Department, University of Panonia, Department of Soil Management, UNESCO Chair on Eremology, Ghent University, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran, Soil and Water Research Institute, Instituto de Geomorfología y Suelos, Department of Geography, Universidad de Málaga [Málaga], Department of Physical Geography, Trier University, Civil Engineering Program, Alberto Luiz Coimbra Institute for Postgraduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro, Faculty of Agriculture, United Graduate School of Agricultural Science, Department of Materials and Life Science, Seikei University, Plant and Environmental Sciences, University of Gothenburg (GU), Rural Development Division, Japan International Research Center for Agricultural Sciences (JIRCAS), RiverLy (UR Riverly), Department of Agricultural and Bio-Resources Engineering, Faculty of Engineering, Ahmadu Bello University Zaria, Federal Agency for Water Management, Institute for land and water management research, Department of Water Resources, ITC Faculty of Geo-Information Science and Earth Observation, Twente University, Faculty of Agriculture and Natural Resources, Ardakan University, Department of Rural Engineering, University of Córdoba, Soil Physics, Embrapa Soils, Department of Soil Science, Agriculture Faculty, University of Zanja, Faculty of Civil Engineering, Department of Geography, Escuela Militar de Ingeniería (EMI), Engineering Faculty, Civil Engineering Department, Munzur University, Bureau of Economic Geology, John A. and Katherine G. Jackson School of Geosciences, University Station, University of Texas at Austin [Austin], Monitoring and Exploration Technologies, Helmholtz Centre for Environmental Research (UFZ), College of Resources and Environmental Engineering, Ludong University, ANR-11-BS56-0027,FLOODSCALE,Observation et modélisation multi-échelles pour la compréhension et la simulation des crues éclair(2011), ANR-07-VULN-0001,AVUPUR,Assessing the Vulnerability of Peri-Urban-Rivers.(2007), MEHDI RAHMATI, University of Maragheh, Maragheh, Iran/Institute of Bio- and Geosciences: Agrosphere (IBG-3), Jülich, Germany, LUTZ WEIHERMÜLLER, Institute of Bio- and Geosciences: Agrosphere (IBG-3), Jülich, Germany, SEYED HAMIDREZA SADEGHI, Tarbiat Modares University, Iran, LILI MAO, Chinese Academy of Agricultural Sciences, Beijing, YAKOV A. PACHEPSKY, USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, JAN VANDERBORGHT, Institute of Bio- and Geosciences: Agrosphere (IBG-3), Jülich, Germany, NILOOFAR MOOSAVI, Institute of Bio- and Geosciences: Agrosphere (IBG-3), Jülich, Germany, HOSSEIN KHEIRFAM, Urmia University, Urmia, Iran, CARSTEN MONTZKA, Institute of Bio- and Geosciences: Agrosphere (IBG-3), Jülich, Germany, KRIS VAN LOOY, Institute of Bio- and Geosciences: Agrosphere (IBG-3), Jülich, Germany, ZEINAB HAZBAVI, Tarbiat Modares University, Iran, BRIGITTA TOTH, Hungarian Academy of Sciences, Budapest, Hungary/University of Pannonia, Keszthely, Hungary, WAFA AL YAMANI, Environment Agency, Abu Dhabi, UAE, AMMAR A. ALBALASMEH, Jordan University of Science and Technology, RAFAEL ANGULO-JARAMILLO, Univ Lyon, Université Claude Bernard Lyon, ANTÔNIO CELSO DANTAS ANTONINO, UFPE, GEORGE ARAMPATZIS, Hellenic Agricultural Organization, Soil and Water Resources Institute, Greece, ROBSON ANDRÉ ARMINDO, UFLA, HOSSEIN ASADI, University of Tehran, Karaj, Iran, YAZIDHI BAMUTAZE, Makerere University, Kampala, Uganda, JORDI BATLLE-AGUILAR, INRA, AgroParisTech Thiverval-Grignon, France/IDES CNRS/Université Paris-Sud, Orsay CEDEX/Innovative Groundwater Solutions (IGS), South Australia, Australia, BÉATRICE BÉCHET, IFSTTAR, GERS, France, MA'IN Z. ALGHZAWI, Jordan University of Science and Technology, FABIAN BECKER, Freie Universität Berlin, BRENT CLOTHIER, Plant and Food Research, Palmerston North, New Zealand, WIM CORNELIS, Ghent University, Ghent, Belgium, CORRADO CORRADINI, University of Perugia, Perugia, Italy, ARTUR PAIVA COUTINHO, UFPE, MURIEL BASTISTA DE OLIVEIRA, UniRedentor, Itaperuna, JOSE RONALDO DE MACEDO, CNPS, MATHEUS FONSECA DURÃES, UFLA, NÁNDOR FODOR, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, GÜNTER BLÖSCHL, Centre for Water Resource Systems, TU Wien, Karlsplatz/Institute of Hydraulic Engineering and Water Resources Management, ALESSIA FLAMMINI, Ghent University, Ghent, Belgium, ASGHAR FARAJNIA, East Azerbaijan Agricultural and Natural Resources Research and Education Center, Iran, IRAJ ESKANDARI, Dryland Agricultural Research Institute, Agricultural Research, Education and Extension Organization Maragheh, East Azerbaijan, Iran, HOJAT EMAMI, Ferdowsi University of Mashhad, Mashhad, Iran, KLAUS BOHNE, University of Rostock, Germany, ISABELLE BRAUD, Irstea, UE RiverLy, Lyon-Villeurbanne Center, France, CLARA CASTELLANO, Pyrenean Institute of Ecology-CSIC, ARTEMI CERDÀ, University of Valencia, Spain, MAHA CHALHOUB, INRA AgroParisTech Functional Ecology and Ecotoxicology of Agroecosystems, ROGERIO CICHOTA, Plant and Food Research, Mount Albert Research Station, Auckland, New Zealand, MILENA CÍSLEROVÁ, Czech Technical University in Prague, Faculty of Civil Engineering, YVES COQUET, INRA AgroParisTech Functional Ecology and Ecotoxicology of Agroecosystems/Université d'Orléans, CNRS, Orléans, France, HAMID KELISHADI, Isfahan University of Technology, Iran, RAINER HORN, Christian-Albrechts-Universität zu Kiel, Germany, EVANGELOS G. HATZIGIANNAKIS, Hellenic Agricultural Organization, Soil and Water Resources Institute, Greece, SIMONE GIERTZ, Universität Bonn, Bonn, Germany, TEAMRAT A. GHEZZEHEI, University of California, Merced, USA, MOHAMAD HOSSEIN GHAVIMIPANAH, Tarbiat Modares University, Iran, MAMOUN GHARAIBEH, Jordan University of Science and Technology, JUAN JOSÉ JIMÉNEZ, ARAID Researcher, Instituto Pirenaico de Ecología, Spanish National Research Council, SASKIA DEBORAH KEESSTRA, Soil, Water and Land Use Team, Wageningen Environmental Research/the University of Newcastle, Australia, DIEDERIK JACQUES, Enginereed and Geosystems Analysis Unit, Belgian Nuclear Research Centre, Mol, Belgium, MAHBOOBEH KIANI-HARCHEGANI, Faculty of Natural Resources, Tarbiat Modares University, Iran, MEHDI KOUSELOU, Faculty of Agriculture, University of Maragheh, Maragheh, Iran, MADAN KUMAR JHA, Indian Institute of Technology Kharagpur, India, LAURENT LASSABATERE, Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Vaulx-en-Velin, France, XIAOYAN LI, Beijing Normal University, Beijing, China, MARK A. LIEBIG, USDA Agricultural Research Service, Mandan, ND, USA, DENIZ YILMAZ, Munzur University, Tunceli, Turkey, MICHAEL H. YOUNG, University of Texas at Austin, University Station, USA, HONG ZHAO, University of Twente, Enschede, the Netherlands, HARRY VEREECKEN, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences: Agrosphere (IBG-3), Jülich, Germany/ISMC International Soil Modeling Consortium, Institute of Bio and Geosciences Forschungszentrum, Germany., MARÍA VICTORIA LÓPEZ, Departamento de Suelo y Agua, Estación Experimental de Aula Dei (EEAD), Consejo Superior de Investigaciones Científicas, Spain, DEEPESH MACHIWAL, ICAR-Central Arid Zone Research Institute, Regional Research Station, Gujarat, India, DIRK MALLANTS, CSIRO Land and Water, Glen Osmond, South Australia, Australia, MICAEL STOLBEN MALLMANN, UFSM, JEAN DALMO DE OLIVEIRA MARQUES, IFAM, MILES R. MARSHALL, Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, UK, JAN MERTENS, ENGIE Research and Technologies, Brussels, Belgium, FÉLICIEN MEUNIER, Université catholique de Louvain, Earth and Life Institute-Environmental Sciences, Louvain-la Neuve, Belgium, MOHAMMAD HOSSEIN MOHAMMADI, University of Tehran, Karaj, Iran, BINAYAK P. MOHANTY, Department of Biological and Agricultural Engineering, Texas A&M Univ., College Station, USA, MANSONIA PULIDO-MONCADA, Aarhus University, Department of Agroecology, Research Centre Foulum, Tjele, Denmark, SUZANA MONTENEGRO, UFPE, RENATO MORBIDELLI, University of Perugia, Perugia, Italy, DAVID MORET-FERNÁNDEZ, Departamento de Suelo y Agua, Estación Experimental de Aula Dei (EEAD), Consejo Superior de Investigaciones Científicas (CSIC), Spain, ALI AKBAR MOOSAVI, Department of Soil Science, College of Agriculture, Shiraz University, Shiraz, Iran, MOHAMMAD REZA MOSADDEGHI, Department of Soil Science, College of Agriculture, Isfahan University of Technology, Iran, SEYED BAHMAN MOUSAVI, Department of Soil Science and Engineering, Faculty of Agriculture, University of Maragheh, Maragheh, Iran, HASAN MOZAFFARI, Department of Soil Science, College of Agriculture, Shiraz University, Shiraz, Iran, KAMAL NABIOLLAHI, Department of Soil Science and Engineering, Faculty of Agriculture, University of Kurdistan, Iran, MOHAMMAD REZA NEYSHABOURI, Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran, MARTA VASCONCELOS OTTONI, CPRM, THEOPHILO BENEDICTO OTTONI FILHO, UFRJ, MOHAMMAD REZA PAHLAVAN-RAD, Soil and Water Research Department, Sistan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Zabol, Iran, ANDREAS PANAGOPOULOS, Hellenic Agricultural Organization, Soil and Water Resources Institute, Greece, STEPHAN PETH, Department of Soil Science, University of Kassel, Germany, PIERRE-EMMANUEL PEYNEAU, IFSTTAR, Bouguenais, France, TOMMASO PICCIAFUOCO, Centre for Water Resource Systems, Vienna, Austria/University of Perugia, Perugia, Italy, JEAN POESEN, Catholic University of Leuven, Geo-Institute, Belgium, MANUEL PULIDO, GeoEnvironmental Research Group, University of Extremadura, Cáceres, Spain, DALVAN JOSÉ REINERT, UFSM, SABINE REINSCH, Centre for Ecology & Hydrology, Environment Centre Wales, UK, MEISAM REZAEI, Department of Soil Management, UNESCO Chair on Eremology, Ghent University, Ghent, Belgium/Soil and Water Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran, FRANCIS PARRY ROBERTS, Centre for Ecology & Hydrology, Environment Centre Wales, UK, DAVID ROBINSON, Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, UK, JESÚS RODRIGO-COMINO, University of Málaga, Spain/Trier University, Trier, Germany, OTTO CORRÊA ROTUNNO FILHO, UFRJ, TADAOMI SAITO, Faculty of Agriculture, Tottori University, Japan, HIDEKI SUGANUMA, Seikei University, Tokyo, Japan, CARLA SALTALIPPI, Department of Civil and Environmental Engineering, University of Perugia, Perugia, Italy, RENÁTA SÁNDOR, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungary, BRIGITTA SCHÜTT, Freie Universität Berlin, Department of Earth Sciences, Institute of Geographical Sciences, Berlin, Germany, MANUEL SEEGER, Department of Physical Geography, Trier University, Germany, NASROLLAH SEPEHRNIA, Department of Soil Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran, EHSAN SHARIFI MOGHADDAM, Department of Watershed Management Engineering, Faculty of Natural Resources, Tarbiat Modares University, Iran, MANOJ SHUKLA, Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA, SHIRAKI SHUTARO, Japan International Research Center for Agricultural Science, Rural Development Division, Tsukuba, Japan, RICARDO SORANDO, Irstea, UE RiverLy, Lyon-Villeurbanne Center, France, AJAYI ASISHANA STANLEY, Ahmadu Bello University Zaria, Nigeria, PETER STRAUSS, Institute for Land and Water Management Research, Federal Agency for Water Management, Austria, ZHONGBO SU, University of Twente, Enschede, the Netherlands, RUHOLLAH TAGHIZADEH-MEHRJARDI, Ardakan University, Ardakan, Yazd Province, Iran, ENCARNACIÓN TAGUAS, University of Córdoba, Spain, WENCESLAU GERALDES TEIXEIRA, CNPS, ALI REZA VAEZI, University of Zanjan, Zanjan, Iran, MEHDI VAFAKHAH, Tarbiat Modares University, Iran, YING ZHAO, Ludong University, China, YIJIAN ZENG, University of Twente, Enschede, the Netherlands, STEFFEN ZACHARIAS, UFZ Helmholtz Centre for Environment Research, Monitoring and Exploration Technologies, Leipzig, Germany, LUBOMÍR LICHNER, Institute of Hydrology, Slovak Academy of Sciences, Bratislava, Slovakia, TOMAS VOGEL, Czech Technical University in Prague, Faculty of Civil Engineering, Czech Republic, IRIS VOGELER, Plant and Food Research, Mount Albert Research Station, Auckland, New Zealand, JANA VOTRUBOVA, Czech Technical University in Prague, Faculty of Civil Engineering, Czech Republic, STEFFEN WERNER, Department of Geography, Ruhr University Bochum, Germany, THIERRY WINARSKI, Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Vaulx-en-Velin, France, Jülich Research Centre, European Commission, Ministerio de Economía y Competitividad (España), Czech Science Foundation, Slovak Research and Development Agency, Rahmati, Mehdi, López Sánchez, María Victoria, Moret-Fernández, David, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL)-PSL Research University (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Rahmati, Mehdi [0000-0001-5547-6442], López Sánchez, María Victoria [0000-0003-4113-0381], Moret-Fernández, David [0000-0002-6674-0453], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Université Claude Bernard Lyon 1 (UCBL), Hellenic Agricultural Organization Demeter (HAO Demeter), Makerere University [Kampala, Ouganda] (MAK), University of Rostock, Plant & Food Research, Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Universiteit Gent = Ghent University [Belgium] (UGENT), Virginia Polytechnic Institute and State University [Blacksburg], Beijing Normal University (BNU), Slovak Academy of Sciences (SAS), Université Catholique de Louvain = Catholic University of Louvain (UCL), Aarhus University [Aarhus], Universidad de Málaga [Málaga] = University of Málaga [Málaga], Programa de Engenharia Civil (COC/COPPE-UFRJ), Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia (COPPE-UFRJ), Universidade Federal do Rio de Janeiro (UFRJ)-Universidade Federal do Rio de Janeiro (UFRJ), Ahmadu Bello University, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), College of Resources and Environmental Engineering [Yantai], Department of Water Resources, UT-I-ITC-WCC, and Faculty of Geo-Information Science and Earth Observation
- Subjects
Condutividade Hidráulica ,[SDV]Life Sciences [q-bio] ,0208 environmental biotechnology ,02 engineering and technology ,Silt ,computer.software_genre ,Soil ,RING INFILTROMETERS ,900 Geschichte und Geografie::910 Geografie, Reisen::910 Geografie, Reisen ,Hydraulic conductivity ,ELECTRICAL-CONDUCTIVITY ,Agricultural land ,ddc:550 ,Meteorology & Atmospheric Sciences ,SATURATED HYDRAULIC CONDUCTIVITY ,Geosciences, Multidisciplinary ,database ,lcsh:Environmental sciences ,2. Zero hunger ,lcsh:GE1-350 ,Database ,IN-SITU ,lcsh:QE1-996.5 ,Geology ,04 agricultural and veterinary sciences ,PE&RC ,Pedo-transfer functions ,6. Clean water ,Infiltration (hydrology) ,HYDROPHYSICAL PARAMETERS ,[SDE]Environmental Sciences ,Physical Sciences ,INFILTRATION GLOBAL DATABASE ,Hidrologia ,PHYSICAL-PROPERTIES ,SANDY SOIL ,TENSION INFILTROMETER ,Ecology and Environment ,Pedotransfer function ,PEDOTRANSFER FUNCTIONS ,Life Science ,SOIL INFILTRATION MEASUREMENTS ,Land surface models ,Soil Water Infiltration Global database ,ANALYSIS OF THE SOIL WATER ,Science & Technology ,Land use ,Infiltration ,15. Life on land ,020801 environmental engineering ,Infiltração ,lcsh:Geology ,Solo ,Infiltration, Land surface models, Land use, Pedo-transfer functions ,SWIG ,Agriculture and Soil Science ,Data quality ,ITC-ISI-JOURNAL-ARTICLE ,Earth and Environmental Sciences ,INFILTROMETER MEASUREMENTS ,Soil water ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,General Earth and Planetary Sciences ,Environmental science ,Hydrology ,ITC-GOLD ,computer - Abstract
27 Pags.- 11 Tabls.- 8 Figs. © Author(s) 2018. This work is distributed under the Creative Commons Attribution 4.0 License., In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements ( ∼ 76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76 % of the experimental sites with agricultural land use as the dominant type (∼ 40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in *.xlsx and *.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it., First author thanks the International and Scientific Cooperation Office of the University of Maragheh, Iran, as well as the research committee and board members of the university for their assistance in conducting the current work. The financial support received from the Forschungszentrum Jülich GmbH is gratefully acknowledged by the first author. Parts of the database were made available through research work carried out in the framework of LIFE+ projects funded by the EC. The support of the Spanish Ministry of Economy through project CGL2014-53017-C2-1-R is acknowledged. The support of the Czech Science Foundation through project no. 16-05665S is acknowledged. The support of the Slovak Research and Development Agency through project no. APVV-15-0160 is acknowledged.
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- 2018
3. Promises and challenges in insect-plant interactions
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David Giron, Marion O. Harris, Todd M. Palmer, Sylvain Pincebourde, Franck Dedeine, Géraldine Dubreuil, Noah K. Whiteman, Jean-Christophe Simon, Atsushi Kawakita, Isgouhi Kaloshian, John S. Terblanche, Aurélien Sallé, Marcel Dicke, Theodora Petanidou, Michael Poulsen, Carlos Lopez-Vaamonde, Lee A. Dyer, Elisabeth Huguet, H. Arthur Woods, Alison E. Bennett, Denis Thiéry, Matthias Erb, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Department of Evolution, Ecology, and Organismal Biology, Ohio State University [Columbus] (OSU), Laboratory of Entomology, Wageningen University and Research [Wageningen] (WUR), University of Nevada, Partenaires INRAE, Institute of Plant Sciences, University of Bern, North Dakota State University (NDSU), Department of Nematology, University of California, Center for Ecological Research, Kyoto University [Kyoto], Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Department of Biology [Gainesville] (UF|Biology), University of Florida [Gainesville] (UF), Research Centre, University of the Aegean, Centre for Social Evolution (CSE), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Institut National de la Recherche Agronomique (INRA)-Université d'Orléans (UO), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), Stellenbosch University, Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Department of Integrative Biology, Division of Biological Sciences [San Diego], University of California [San Diego] (UC San Diego), University of California-University of California, Centre National de la Recherche Scientifique, Université François-Rabelais, Institut National de la Recherche Agronomique, European Cooperation in Science and Technology, WILEY, British Ecological Society, 2014-00094521, Région Centre Val-de-Loire, MIDI network and the Féri Network, Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), School of agriculture, Université de Berne, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-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), Department of Geography, Department for Food Chemistry, National Food Institute, Danish Technical University, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Santé Végétale (SV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB), University of Montana, University of South Carolina, University of South Carolina [Columbia], COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Entomology, Wageningen University, Wageningen University and Research Centre [Wageningen] (WUR), University of Nevada [Las Vegas] (WGU Nevada), UCR - University of California (Riverside), Zoologie Forestière, University of Copenhagenn, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRA Villenave d'Ornon, University of California [Berkeley], Berkeley University of California (UC BERKELEY), This research was partly supported by LE STUDIUM - Institute for Advanced Studies, Loire Valley, Orléans, France, Centre National de la Recherche Scientifique (CNRS), University of Tours, French National Institute for Agricultural Research (INRA), Region Centre-Val de Loire 2014-00094521, European Cooperation in Science & Technology (COST) program, Wiley, MIDI network, Feri Network, University of California (UC), Kyoto University, Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, School of Biological Sciences [Univ California San Diego] (UC San Diego), and University of California (UC)-University of California (UC)
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0301 basic medicine ,Environmental change ,Research areas ,[SDV]Life Sciences [q-bio] ,multitrophic interactions ,Biology ,03 medical and health sciences ,Multitrophic interactions ,Basic research ,forests and agroecosystems ,Thermal ecology ,Community ecology ,ecological networks ,Technical skills ,Laboratory of Entomology ,thermal ecology ,Global change ,Ecology, Evolution, Behavior and Systematics ,ComputingMilieux_MISCELLANEOUS ,global change ,symbionts ,plant response ,Mutualism (biology) ,Evolutionary genomics ,evolutionary genomics ,Technological evolution ,Environmental ethics ,Adaptive response ,Symbionts ,PE&RC ,Laboratorium voor Entomologie ,insect effectors ,Forests and agroecosystems ,Ecological network ,Phylogenetics ,phylogenetics ,Insect effectors ,030104 developmental biology ,13. Climate action ,Insect Science ,Ecological networks ,Plant response ,EPS ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,community ecology - Abstract
International audience; There is tremendous diversity of interactions between plants and other species. These relationships range from antagonism to mutualism. Interactions of plants with members of their ecological community can lead to a profound metabolic reconfiguration of the plants’ physiology. This reconfiguration can favour beneficial organisms and deter antagonists like pathogens or herbivores. Determining the cellular and molecular dialogue between plants, microbes, and insects, and its ecological and evolutionary implications is important for understanding the options for each partner to adopt an adaptive response to its biotic environment. Moving forward, understanding how such ecological interactions are shaped by environmental change and how we potentially mitigate deleterious effects will be increasingly important. The development of integrative multidisciplinary approaches may provide new solutions to the major ecological and societal issues ahead of us. The rapid evolution of technology provides valuable tools and opens up novel ways to test hypotheses that were previously unanswerable, but requires that scientists master these tools, understand potential ethical problems flowing from their implementation, and train new generations of biologists with diverse technical skills. Here, we provide brief perspectives and discuss future promise and challenges for research on insect–plant interactions building on the 16th International Symposium on Insect–Plant interactions (SIP) meeting that was held in Tours, France (2–6 July 2017). Talks, posters, and discussions are distilled into key research areas in insect–plant interactions, highlighting the current state of the field and major challenges, and future directions for both applied and basic research.
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- 2018
4. The dinoflagellate cyst genera Achomosphaera Evitt 1963 and Spiniferites Mantell 1850 in Pliocene to modern sediments: a summary of round table discussions
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Marianne Ellegaard, Kenneth Neil Mertens, Serdar Uzar, Nicolas Van Nieuwenhove, Sofia Ribeiro, Kara Bogus, Manuel Bringué, Vera Pospelova, Stijn De Schepper, Barrie Dale, Sophie Warny, Michael Schreck, Stephen Louwye, Laurent Londeix, Maija Heikkilä, André Rochon, Andrea M. Price, Haifeng Gu, Anne de Vernal, Francesca Sangiorgi, Hilal Aydin, Martin J. Head, Vladimir Torres, Arjen Grothe, Karin A F Zonneveld, Kazumi Matsuoka, Gerard J M Versteegh, Peta J. Mudie, Edwige Masure, Aurélie Penaud, Fabienne Marret, Audrey Limoges, Pieter Gurdebeke, Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Centre de recherche sur la dynamique du système Terre (GEOTOP), Université de Montréal (UdeM)-McGill University = Université McGill [Montréal, Canada]-École Polytechnique de Montréal (EPM)-Concordia University [Montreal]-Université du Québec à Rimouski (UQAR)-Université du Québec à Montréal = University of Québec in Montréal (UQAM)-Université du Québec en Abitibi-Témiscamingue (UQAT), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Marine Palynology and Palaeoceanography, Utrecht University [Utrecht], Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Geography, University of Liverpool, Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire Géosciences Océan (LGO), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Faculty of Geosciences [Utrecht], Louisiana State University (LSU), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Marine palynology and palaeoceanography, Marine Palynology, Ifremer, LER BO, Station de Biologie Marine, Place de la Croix, Concarneau CEDEX, France, Department of Geoscience, Aarhus University, Aarhus, Denmark, Department of Geology, Ghent University, Ghent, Belgium, Biology Department, Faculty of Sciences and Arts, Celal Bayar University, Manisa, Turkey, International Ocean Discovery Program, Texas A&M University, College Station, TX, United States, School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC, United States, School of Earth and Ocean Sciences, University of Victoria, Victoria, BC, Canada, Geosciences Department, University of Oslo, Oslo, Norway, Uni Research Climate, Bjerknes Centre for Climate Research, Bergen, Norway, Département des sciences de la Terre et de l’Atmosphère, Geotop, Université du Québec à Montréal, Montreal, Canada, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark, Marine Palynology and Paleoceanography, Laboratory of Palaeobotany and Palynology, Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands, Third Institute of Oceanography, SOA, Xiamen, China, Department of Earth Sciences, Brock University, St. Catharines, ON, Canada, Environmental Change Research Unit, Department of Environmental Sciences, University of Helsinki, Finland, Department of Glaciology and Climate, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, Denmark, Université de Bordeaux, UMR 5805 EPOC, Pessac CEDEX, France, School of Environmental Sciences, University of Liverpool, Liverpool, United Kingdom, CR2P Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements, UMR7207–CNRS, MNHN, UPMC, Paris, France, Institute for East China Sea Research (ECSER), Nagasaki, Japan, Geological Survey of Canada, Dartmouth, Canada, UMR6538 Domaines Océaniques, IUEM-UBO, Plouzané, France, Department of Geography, McGill University, Montréal, Canada, ISMER-UQAR, 310 allée des Ursulines, Rimouski, QC, Canada, Department of Geology, University of Tromsø–The Arctic University, Tromsø, Langnes, Norway, Biostratigraphy Core Group, ExxonMobil Exploration Company, Spring, TX, United States, Department of Marine Geochemistry, Alfred-Wegener-Institut (AWI), Helmholtz Zentrum für Polar und Meeresforschung, Bremerhaven, Germany, MARUM–Center for Marine Environmental Sciences, Bremen University, Bremen, Germany, Department of Geology and Geophysics and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States, and Department of Earth Sciences, University of New Brunswick, Fredericton, Canada
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DINOFLAGELLATE ,010506 paleontology ,010502 geochemistry & geophysics ,01 natural sciences ,Pterocysta ,Genus ,Rottnestia ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450 ,Hafniasphaera ,[SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology ,NORTHERN BELGIUM ,14. Life underwater ,ASSEMBLAGES ,[SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography ,0105 earth and related environmental sciences ,[SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics ,VDP::Mathematics and natural science: 400::Geosciences: 450 ,LATE QUATERNARY ,biology ,Achomosphaera ,Spiniferites ,Dinoflagellate ,Biology and Life Sciences ,Paleontology ,DINOPHYCEAE ,biology.organism_classification ,Archaeology ,CENOZOIC ,EEMIAN HYDROGRAPHIC CONDITIONS ,Geography ,Baltic sea ,Round table ,Earth and Environmental Sciences ,BALTIC SEA ,SP-NOV ,MORPHOLOGY ,[SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology ,Cenozoic ,PROPOSALS ,Dinophyceae - Abstract
We present a summary of two round-table discussions held during two subsequent workshops in Montreal (Canada) on 16 April 2014 and Ostend (Belgium) on 8 July 2015. Five species of the genus Achomosphaera Evitt 1963 Evitt WR. 1963. A discussion and proposals concerning fossil dinoflagellates, hystrichospheres, and acritarchs, I. National Academy of Sciences, Washington, Proceedings. 49(2):158–164.[Crossref], [PubMed], [Web of Science ®], , [Google Scholar] and 33 of the genus Spiniferites Mantell 1850 emend. Sarjeant 1970 Sarjeant WAS. 1970. The genus Spiniferites Mantell, 1850 (Dinophyceae). Grana. 10(1):74–78.[Taylor & Francis Online], , [Google Scholar] occuring in Pliocene to modern sediments are listed and briefly described along with remarks made by workshop participants. In addition, several holotypes and topotypes are reillustrated. Three species previously assigned to Spiniferites are here considered/accepted as belonging to other genera: Impagidinium inaequalis (Wall and Dale in Wall et al. 1973 Wall D, Dale B, Harada K. 1973. Descriptions of new fossil dinoflagellates from the Late Quaternary of the Black Sea. Micropaleontology. 19(1):18–31.[Crossref], , [Google Scholar]) Londeix et al. 2009 Londeix L, Herreyre Y, Turon J-L, Fletcher W. 2009. Last Glacial to Holocene hydrology of the Marmara Sea inferred from a dinoflagellate cyst record. Rev Palaeobot Palynol. 158(1-2):52–71.[Crossref], [Web of Science ®], , [Google Scholar], Spiniferites? rubinus (Rossignol 1962 Rossignol M. 1962. Analyse pollinique de sédiments marins quaternaires en Israël II. - Sédiments pleistocènes. Pollen et Spores. 4:121–148. [Google Scholar] ex Rossignol 1964 Rossignol M. 1964. Hystrichosphères du Quaternaire en Méditerranée orientale, dans les sédiments Pléistocènes et les boues marines actuelles. Revue de Micropaléontologie. 7:83–99. [Google Scholar]) Sarjeant 1970 Sarjeant WAS. 1970. The genus Spiniferites Mantell, 1850 (Dinophyceae). Grana. 10(1):74–78.[Taylor & Francis Online], , [Google Scholar], and Thalassiphora balcanica Balteş 1971. This summary forms the basis for a set of papers that follows, where points raised during the workshops are explored in greater detail.
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- 2018
5. Learning in mosquito larvae ( Aedes aegypti ): Habituation to a visual danger signal
- Author
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Hugo Baglan, Claudio R. Lazzari, Fernando J. Guerrieri, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Centre for Social Evolution (CSE), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Department of Biology [Copenhagen], and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen]
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0301 basic medicine ,Physiology ,[SDV]Life Sciences [q-bio] ,Zoology ,Escape response ,Aedes aegypti ,Stimulus (physiology) ,Biology ,03 medical and health sciences ,[SCCO]Cognitive science ,0302 clinical medicine ,Aedes ,Escape Reaction ,Memory ,parasitic diseases ,Aquatic insect ,Bioassay ,Animals ,Learning ,Habituation ,Habituation, Psychophysiologic ,ComputingMilieux_MISCELLANEOUS ,Larva ,[SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior ,Ecology ,[SCCO.NEUR]Cognitive science/Neuroscience ,fungi ,biology.organism_classification ,3. Good health ,030104 developmental biology ,Insect Science ,[SCCO.PSYC]Cognitive science/Psychology ,Instar ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,030217 neurology & neurosurgery ,Photic Stimulation - Abstract
In spite of the mosquito Aedes aegypti being a vector of several infectious diseases, a limited number of studies has been undertaken on learning in this species. Moreover, larval stages have been neglected as model organisms, although they are active, aquatic and perform stereotyped behavioural responses, e.g. the escape response when disturbed. To study the learning abilities of mosquito larvae, we focused on habituation, a form of non-associative learning widely studied in vertebrates and invertebrates. Habituation was defined as the progressive and reversible decrease in response to a reiterative stimulus. We first aimed at confirming habituation of the escape response in mosquito larvae (4th instar). Then, we determined whether a mnesic trace was established. Larvae were individually stimulated with a visual danger stimulus inducing the escape response. We set up a protocol for testing larvae individually, allowing the control of different parameters that are crucial for the study of cognitive abilities. After 15 trials, the escape response of mosquitoes was significantly lower. A disturbance stimulus presented after the 15th trial, induced the escape response and reversed habituation. Retention was confirmed up to 1h after the last habituation trial. This original bioassay can be adapted for studying the physiology of learning and memory in mosquito larvae, for analysing the effects of chemicals in the water, the characterisation of the cognitive abilities related to the life history of different mosquito species across preimaginal stages.
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- 2017
6. Microarray glycan profiling reveals algal fucoidan epitopes in diverse marine metazoans
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Jozef Mravec, Armando A. Salmeán, Cécile Hervé, William G.T. Willats, Bodil Jørgensen, Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (UCPH), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (KU), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
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0106 biological sciences ,0301 basic medicine ,Glycan ,Cliona celata ,lcsh:QH1-199.5 ,Structural polysaccharides ,Ocean Engineering ,Computational biology ,lcsh:General. Including nature conservation, geographical distribution ,Aquatic Science ,Oceanography ,01 natural sciences ,Epitope ,Microbiology ,Cell wall ,03 medical and health sciences ,chemistry.chemical_compound ,marine fauna ,Marine Science ,structural polysaccharides ,lcsh:Science ,immunolocalisation ,sponges ,ComputingMilieux_MISCELLANEOUS ,Water Science and Technology ,Global and Planetary Change ,Anti-glycan antibodies ,biology ,Phylum ,Fucoidan ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,Microarray profiling ,biology.organism_classification ,fucoidans ,Sponge ,030104 developmental biology ,chemistry ,Marine fauna ,Sponges ,biology.protein ,anti-glycan antibodies ,lcsh:Q ,Immunolocalisation ,microarray profiling ,Fucoidans ,Function (biology) ,010606 plant biology & botany - Abstract
Despite the biological importance and pharmacological potential of glycans from marine organisms, there are many unanswered questions regarding their distribution, function, and evolution. Here we describe microarray-based glycan profiling of a diverse selection of marine animals using antibodies raised against fucoidan isolated from a brown alga. We demonstrate the presence of two fucoidan epitopes in six animals belonging to three phyla including Porifera, Molusca, and Chordata. We studied the spatial distribution of these epitopes in Cliona celata ("boring sponge") and identified their restricted localization on the surface of internal chambers. Our results show the potential of high-throughput screening and probes commonly used in plant and algal cell wall biology to study the diversity and distribution of glycan structures in metazoans.
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- 2017
7. Individual Differences in Exploratory Activity Relate to Cognitive Judgement Bias in Carpenter Ants
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Lisa Signorotti, Claudio Carere, Lara Demora, Patrizia d'Ettorre, Pauline Le Quinquis, Dalila Bovet, Centre for Social Evolution (CSE), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Laboratoire d'Ethologie Expérimentale et Comparée (LEEC), Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13), Laboratoire Éthologie Cognition Développement (LECD), Université Paris Nanterre (UPN), Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)
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0106 biological sciences ,cognition ,media_common.quotation_subject ,[SDV]Life Sciences [q-bio] ,Judgement ,Individuality ,Exploratory activity ,[SHS.PSY]Humanities and Social Sciences/Psychology ,Stimulus (physiology) ,Social insects ,010603 evolutionary biology ,01 natural sciences ,Behavioral Neuroscience ,Affective state ,Animals ,Personality ,Learning ,0501 psychology and cognitive sciences ,050102 behavioral science & comparative psychology ,Reinforcement ,media_common ,Behavior, Animal ,Ants ,05 social sciences ,Cognition ,General Medicine ,Cognitive bias ,Exploratory behaviour ,Exploratory Behavior ,Animal Science and Zoology ,Positive bias ,Psychology ,Social psychology ,Cognitive psychology - Abstract
International audience; Emotional state may influence cognitive processes such as attention and decision-making. A cognitive judgement bias is the propensity to anticipate either positive or negative consequences in response to ambiguous information. Recent work, mainly on vertebrates, showed that the response to ambiguous stimuli might change depending on an individual's affective state, which is influenced by e.g. the social and physical environment. However, the response to ambiguous stimuli could also be affected by the individual's behavioural type (personality), a question that has been under-investigated. We studied the link between individual differences in exploratory activity and the response to an ambiguous stimulus in the ant Camponotus aethiops. Exploratory behaviour, quantified with an open-field test, was variable among individuals but consistent over time within individuals. Individual ants learned to associate a spatial position to a reinforcement and another spatial position to a punishment. Once the ants had acquired this discrimination, cognitive judgement bias was tested with the stimulus in an intermediate position. Fast explorers in the open-field took significantly more time to approach the ambiguous stimulus compared to slow explorers, suggesting a negative judgement bias for fast explorers and a positive bias for slow explorers. This previously unknown link between individual difference in exploratory activity and cognitive bias in a social insect may help understanding the evolution and organization of social life.
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- 2017
8. You Know What? I'm Happy. Cognitive Bias Is Not Related to Personality but Is Induced by Pair-Housing in Canaries (Serinus Canaria)
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Mathilde Lalot, Dalila Bovet, Davy Ung, Patrizia d'Ettorre, Franck Péron, Laboratoire Éthologie Cognition Développement (LECD), Université Paris Nanterre (UPN), Centre for Social Evolution (CSE), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Laboratoire d'Ethologie Expérimentale et Comparée (LEEC), Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13), Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)
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0106 biological sciences ,Male ,Canaries ,media_common.quotation_subject ,[SDV]Life Sciences [q-bio] ,Emotions ,[SHS.PSY]Humanities and Social Sciences/Psychology ,010603 evolutionary biology ,01 natural sciences ,Developmental psychology ,animal welfare ,Behavioral Neuroscience ,Cognition ,biology.animal ,medicine ,Personality ,Animals ,0501 psychology and cognitive sciences ,050102 behavioral science & comparative psychology ,Big Five personality traits ,Serinus canaria ,media_common ,Social enrichment ,biology ,Boldness ,05 social sciences ,Neophobia ,Social environment ,General Medicine ,medicine.disease ,Housing, Animal ,Cognitive bias ,Individual differences ,Animal Science and Zoology ,Female ,Psychology ,Social psychology - Abstract
International audience; Recent studies suggest that cognitive bias could constitute a novel and valid measure of animal welfare. Although interest for a link between personality and cognition is growing, no study to date investigated whether a cognitive bias might be related to the personality of the individuals. We trained 43 domestic canaries (Serinus canaria) to discriminate between two sides of a test cage, each side being associated with a different value (attractive or aversive food in a dish). During the test phase, the dish was placed at intermediate locations, representing ambiguous information. Results show evidence of an "optimistic" bias (flying faster to the dish at the ambiguous location) in birds housed in pairs, compared to birds housed singly, suggesting an influence of social context (living conditions) on canaries' emotions when tested individually. We also studied six traits of individuals' personality and found that aggressiveness, neophobia, one sociability index and obstinacy were repeatable across social context and/or day-light schedule, whereas the other sociability index, boldness and locomotion were not. No correlation between the birds' optimism and any of their personality traits was found, suggesting that cognitive bias may be a matter of social context rather than of individual personality.
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- 2017
9. The role of the glucose-sensing transcription factor carbohydrate-responsive element-binding protein pathway in termite queen fertility
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Maryline Favier, Robert Hanus, Virginie Roy, Michael Poulsen, David Sillam-Dussès, Mireille Vasseur-Cognet, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ethologie Expérimentale et Comparée (LEEC), Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13), Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB / CAS), Czech Academy of Sciences [Prague] (CAS), Department for Food Chemistry, National Food Institute, Danish Technical University, Centre for Social Evolution (CSE), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by a maturation grant from the Institute of Research for Development (IRD) received by D.S.D. and M.V.C. (RVO: 61388963), Czech Science Foundation (14-12774S) to R.H. and a Villum Kann Rasmussen Foundation Young Investigator Fellowship (VKR10101) to M.P., Institut d'écologie et des sciences de l'environnement de Paris ( IEES ), Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Ethologie Expérimentale et Comparée ( LEEC ), Université Paris 13 ( UP13 ) -Université Sorbonne Paris Cité ( USPC ), Institute of Organic Chemistry and Biochemistry [Praha], Czech Academy of Sciences [Prague] ( ASCR ), Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen ( KU ), Institut Cochin ( UM3 (UMR 8104 / U1016) ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC), Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bos, Mireille, Institut d'écologie et des sciences de l'environnement de Paris (IEES), Czech Academy of Sciences [Prague] (ASCR), and Vasseur-Cognet, Mireille
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0301 basic medicine ,Immunology ,education ,Isoptera ,Biology ,phenotypic plasticity ,General Biochemistry, Genetics and Molecular Biology ,reproduction ,03 medical and health sciences ,Downregulation and upregulation ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Animals ,Tissue Distribution ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Protein Interaction Maps ,Carbohydrate-responsive element-binding protein ,lcsh:QH301-705.5 ,Gene ,Transcription factor ,carbohydrate-responsive element-binding protein ,transcription factor ,social insects ,lipogenesis ,[ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Research Articles ,Phylogeny ,General Neuroscience ,Research ,Correction ,Pyruvate carboxylase ,Up-Regulation ,Fatty acid synthase ,030104 developmental biology ,Fertility ,Glucose ,lcsh:Biology (General) ,ChREBP Pathway ,Biochemistry ,Lipogenesis ,biology.protein ,Insect Proteins ,Female ,Signal Transduction ,Transcription Factors - Abstract
Termites are among the few animals that themselves can digest the most abundant organic polymer, cellulose, into glucose. In mice and Drosophila , glucose can activate genes via the transcription factor carbohydrate-responsive element-binding protein (ChREBP) to induce glucose utilization and de novo lipogenesis. Here, we identify a termite orthologue of ChREBP and its downstream lipogenic targets, including acetyl-CoA carboxylase and fatty acid synthase. We show that all of these genes, including ChREBP, are upregulated in mature queens compared with kings, sterile workers and soldiers in eight different termite species. ChREBP is expressed in several tissues, including ovaries and fat bodies, and increases in expression in totipotent workers during their differentiation into neotenic mature queens. We further show that ChREBP is regulated by a carbohydrate diet in termite queens. Suppression of the lipogenic pathway by a pharmacological agent in queens elicits the same behavioural alterations in sterile workers as observed in queenless colonies, supporting that the ChREBP pathway partakes in the biosynthesis of semiochemicals that convey the signal of the presence of a fertile queen. Our results highlight ChREBP as a likely key factor for the regulation and signalling of queen fertility.
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- 2016
10. The role of the glucose-sensing transcription factor carbohydrate-responsive element-binding protein pathway in termite queen fertility (vol 6, 160080, 2016)
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Sillam-Dusses, David, Hanus, Robert, Poulsen, Michael, Roy, Virginie, Favier, Maryline, VASSEUR-COGNET, Mireille, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Czech Academy of Sciences [Prague] (CAS), Centre for Social Evolution (CSE), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Funding Agency and Grant Number : Institute of Research for Development (IRD) [RVO: 61388963], Czech Science Foundation [14-12774S], Villum Kann Rasmussen Foundation [VKR10101], Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ProdInra, Archive Ouverte, Institut d'écologie et des sciences de l'environnement de Paris (IEES), Czech Academy of Sciences [Prague] (ASCR), and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Biology [Copenhagen]
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[SDV] Life Sciences [q-bio] ,reproduction ,social insects ,element-binding protein ,carbohydrate-responsive ,[SDV]Life Sciences [q-bio] ,phenotypic plasticity ,lipogenesis ,transcription factor - Abstract
Correction to "The role of the glucose-sensing transcription factor carbohydrate-responsive element-binding protein pathway in termite queen fertility" DOI :10.1098/rsob.160237 WOS : 000385433600005; Termites are among the few animals that themselves can digest the most abundant organic polymer, cellulose, into glucose. In mice and Drosophila, glucose can activate genes via the transcription factor carbohydrate-responsive element-binding protein (ChREBP) to induce glucose utilization and de novo lipogenesis. Here, we identify a termite orthologue of ChREBP and its downstream lipogenic targets, including acetyl-CoA carboxylase and fatty acid synthase. We show that all of these genes, including ChREBP, are upregulated in mature queens compared with kings, sterile workers and soldiers in eight different termite species. ChREBP is expressed in several tissues, including ovaries and fat bodies, and increases in expression in totipotent workers during their differentiation into neotenic mature queens. We further show that ChREBP is regulated by a carbohydrate diet in termite queens. Suppression of the lipogenic pathway by a pharmacological agent in queens elicits the same behavioural alterations in sterile workers as observed in queenless colonies, supporting that the ChREBP pathway partakes in the biosynthesis of semiochemicals that convey the signal of the presence of a fertile queen. Our results highlight ChREBP as a likely key factor for the regulation and signalling of queen fertility.
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- 2016
11. Paving the way towards future‐proofing our crops
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Alexandra Baekelandt, Vandasue L. R. Saltenis, Philippe Nacry, Aleksandra Malyska, Marc Cornelissen, Amrit Kaur Nanda, Abhishek Nair, Peter Rogowsky, Laurens Pauwels, Bertrand Muller, Jonas Collén, Jonas Blomme, Mathias Pribil, Lars B. Scharff, Jessica Davies, Ralf Wilhelm, Norbert Rolland, Jeremy Harbinson, Wout Boerjan, Erik H. Murchie, Alexandra J. Burgess, Jean‐Pierre Cohan, Philippe Debaeke, Sébastien Thomine, Dirk Inzé, René Klein Lankhorst, Martin A. J. Parry, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), University of Copenhagen = Københavns Universitet (UCPH), Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), European Commission - DG Research and Innovation, BASF Agricultural Solutions Belgium NV, Plants for the Future European Technology Platform, Wageningen University and Research [Wageningen] (WUR), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), University of Nottingham, UK (UON), ARVALIS - Institut du Végétal [Ouzouer le Marché] (ARVALIS), ARVALIS - Institut du végétal [Paris], AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Lancaster Environment Centre, Lancaster University, and European Project: 817690,H2020 CropBooster-P
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Marketing and Consumer Behaviour ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,DIVERSITY ,Biophysics ,IMPROVEMENT ,METABOLISM ,future- proofed crops ,future world scenarios ,future-proofed crops ,plant research ,LIGNIN DEPOSITION ,PLANT ,crop productivity ,Renewable Energy, Sustainability and the Environment ,BioSolar Cells ,Biology and Life Sciences ,Forestry ,crop yield ,PE&RC ,AMARANTH ,[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding ,Biofysica ,DOMESTICATION ,PHOSPHOLIPASE ,Marktkunde en Consumentengedrag ,EPS ,Agronomy and Crop Science ,TRAITS ,RESISTANCE ,Food Science - Abstract
International audience; To meet the increasing global demand for food, feed, fibre and other plant- derivedproducts, a steep increase in crop productivity is a scientifically and technicallychallenging imperative. The CropBooster- P project, a response to the H2020call ‘Future proofing our plants’, is developing a roadmap for plant research toimprove crops critical for the future of European agriculture by increasing cropyield, nutritional quality, value for non- food applications and sustainability.However, if we want to efficiently improve crop production in Europe and pri-oritize methods for crop trait improvement in the coming years, we need to takeinto account future socio- economic, technological and global developments, in-cluding numerous policy and socio- economic challenges and constraints. Basedon a wide range of possible global trends and key uncertainties, we developedfour extreme future learning scenarios that depict complementary future devel-opments. Here, we elaborate on how the scenarios could inform and direct fu-ture plant research, and we aim to highlight the crop improvement approachesthat could be the most promising or appropriate within each of these four futureworld scenarios. Moreover, we discuss some key plant technology options thatwould need to be developed further to meet the needs of multiple future learningscenarios, such as improving methods for breeding and genetic engineering. Inaddition, other diverse platforms of food production may offer unrealized poten-tial, such as underutilized terrestrial and aquatic species as alternative sources ofnutrition and biomass production. We demonstrate that although several meth-ods or traits could facilitate a more efficient crop production system in some ofthe scenarios, others may offer great potential in all four of the future learningscenarios. Altogether, this indicates that depending on which future we are head-ing toward, distinct plant research fields should be given priority if we are to meetour food, feed and non- food biomass production needs in the coming decades.
- Published
- 2023
12. Approaches and determinants to sustainably improve crop production
- Author
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Alain Gojon, Laurent Nussaume, Doan T. Luu, Erik H. Murchie, Alexandra Baekelandt, Vandasue Lily Rodrigues Saltenis, Jean‐Pierre Cohan, Thierry Desnos, Dirk Inzé, John N. Ferguson, Emmanuel Guiderdonni, Anne Krapp, René Klein Lankhorst, Christophe Maurel, Hatem Rouached, Martin A. J. Parry, Mathias Pribil, Lars B. Scharff, Philippe Nacry, Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Plant Environmental Physiology and Stress Signaling (PEPSS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Nottingham, UK (UON), Universiteit Gent = Ghent University (UGENT), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Copenhagen Plant Science Center (CPSC), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), ARVALIS - Institut du végétal [Paris], University of Cambridge [UK] (CAM), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research [Wageningen] (WUR), Lancaster Environment Centre, Lancaster University, European Project: 817690,H2020, Gojon, A [0000-0001-5412-8606], Nussaume, L [0000-0002-9445-2563], Luu, DT [0000-0001-9765-2125], Murchie, EH [0000-0002-7465-845X], Baekelandt, A [0000-0003-0816-7115], Rodrigues Saltenis, VL [0000-0002-1455-7171], Cohan, JP [0000-0003-2117-7027], Desnos, T [0000-0002-6585-1362], Inzé, D [0000-0002-3217-8407], Ferguson, JN [0000-0003-3603-9997], Guiderdonni, E [0000-0003-2760-2864], Krapp, A [0000-0003-2034-5615], Klein Lankhorst, R [0000-0003-1845-8733], Maurel, C [0000-0002-4255-6440], Rouached, H [0000-0002-7751-0477], Parry, MAJ [0000-0002-4477-672X], Pribil, M [0000-0002-9174-9548], Scharff, LB [0000-0003-0210-3428], Nacry, P [0000-0001-7766-4989], and Apollo - University of Cambridge Repository
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0106 biological sciences ,Agriculture and Food Sciences ,PHOSPHORUS-ACQUISITION ,[SDV]Life Sciences [q-bio] ,NITROGEN ASSIMILATION ,drought ,UTILIZATION EFFICIENCY ,SALT TOLERANCE ,01 natural sciences ,nitrogen ,climate change mitigation ,salinity ,heat stress ,03 medical and health sciences ,DROUGHT TOLERANCE ,AFFINITY PHOSPHATE TRANSPORTER ,Life Science ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Renewable Energy ,TRANSCRIPTION FACTOR ,030304 developmental biology ,phosphate ,2. Zero hunger ,0303 health sciences ,Sustainability and the Environment ,Renewable Energy, Sustainability and the Environment ,fungi ,BioSolar Cells ,Biology and Life Sciences ,food and beverages ,Forestry ,15. Life on land ,WATER-USE ,13. Climate action ,ABSCISIC-ACID RECEPTORS ,Agronomy and Crop Science ,010606 plant biology & botany ,Food Science ,HEAT-STRESS - Abstract
International audience; Plant scientists and farmers are facing major challenges in providing food and nutritional security for a growing population, while preserving natural resources and biodiversity. Moreover, this should be done while adapting agriculture to climate change and by reducing its carbon footprint. To address these challenges, there is an urgent need to breed crops that are more resilient to suboptimal environments. Huge progress has recently been made in understanding the physiological, genetic and molecular bases of plant nutrition and environmental responses, paving the way towards a more sustainable agriculture. In this review, we present an overview of these progresses and strategies that could be developed to increase plant nutrient use efficiency and tolerance to abiotic stresses. As illustrated by many examples, they already led to promising achievements and crop improvements. Here, we focus on nitrogen and phosphate uptake and use efficiency and on adaptation to drought, salinity and heat stress. These examples first show the necessity of deepening our physiological and molecular understanding of plant environmental responses. In particular, more attention should be paid to investigate stress combinations and stress recovery and acclimation that have been largely neglected to date. It will be necessary to extend these approaches from model plants to crops, to unravel the relevant molecular targets of biotechnological or genetic strategies directly in these species. Similarly, sustained efforts should be done for further exploring the genetic resources available in these species, as well as in wild species adapted to unfavourable environments. Finally, technological developments will be required to breed crops that are more resilient and efficient. This especially relates to the development of multiscale phenotyping under field conditions and a wide range of environments, and use of modelling and big data management to handle the huge amount of information provided by the new molecular, genetic and phenotyping techniques.
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- 2023
13. Low temperature circulating fluidized bed gasification and co-gasification of municipal sewage sludge. Part 2: Evaluation of ash materials as phosphorus fertilizer
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Müller-Stöver, Dorette [University of Copenhagen, Department of Plant and Environmental Sciences, Plant and Soil Science, Thorvaldsensvej 40, Frederiksberg (Denmark)]
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- 2017
- Full Text
- View/download PDF
14. Assessing age, breeding stage, and mating activity as drivers of variation in the reproductive microbiome of female tree swallows
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Joel W. McGlothlin, Taryn Smith, Catherine Hucul, Jessica Hernandez, Ignacio T. Moore, Emily Reasor, David C. Haak, Lisa K. Belden, Biological Sciences, and School of Plant and Environmental Sciences
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hormone implant ,Ecology ,Host (biology) ,Zoology ,Context (language use) ,Biology ,Brood ,Diversity index ,tree swallows ,mating strategy ,Alpha diversity ,Microbiome ,Species richness ,Mating ,extra‐pair paternity ,reproductive microbiome ,QH540-549.5 ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation ,Original Research - Abstract
Sexually transmitted microbes are hypothesized to influence the evolution of reproductive strategies. Though frequently discussed in this context, our understanding of the reproductive microbiome is quite nascent. Indeed, testing this hypothesis first requires establishing a baseline understanding of the temporal dynamics of the reproductive microbiome and of how individual variation in reproductive behavior and age influence the assembly and maintenance of the reproductive microbiome as a whole. Here, we ask how mating activity, breeding stage, and age influence the reproductive microbiome. We use observational and experimental approaches to explain variation in the cloacal microbiome of free‐living, female tree swallows (Tachycineta bicolor). Using microsatellite‐based parentage analyses, we determined the number of sires per brood (a proxy for female mating activity). We experimentally increased female sexual activity by administering exogenous 17ß‐estradiol. Lastly, we used bacterial 16S rRNA amplicon sequencing to characterize the cloacal microbiome. Neither the number of sires per brood nor the increased sexual activity of females significantly influenced female cloacal microbiome richness or community structure. Female age, however, was positively correlated with cloacal microbiome richness and influenced overall community structure. A hypothesis to explain these patterns is that the effect of sexual activity and the number of mates on variation in the cloacal microbiome manifests over an individual's lifetime. Additionally, we found that cloacal microbiome alpha diversity (Shannon Index, Faith's phylogenetic distance) decreased and community structure shifted between breeding stages. This is one of few studies to document within‐individual changes and age‐related differences in the cloacal microbiome across successive breeding stages. More broadly, our results contribute to our understanding of the role that host life history and behavior play in shaping the cloacal microbiomes of wild birds., In this paper, we ask the question: how do mating activity, breeding stage, and age influence female reproductive microbiomes? We address this question using observational and experimental approaches to explain both between‐ and within‐individual variation in the cloacal microbiome of free‐living, female birds that exhibit differences in extra‐pair paternity rates. We found that female age and breeding stage, but not number of mates or experimentally elevated sexual activity (via 17ß‐estradiol implants), significantly influenced cloacal microbiome alpha diversity and explained variation in bacterial community structure.
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- 2021
15. Learning and perceptual similarity among cuticular hydrocarbons in ants
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Fernando J. Guerrieri, John Nielsen, Charlotte G. Jørgensen, Patrizia d'Ettorre, Stephanie Dreier, Nick Bos, Centre for Social Evolution (CSE), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Medicinal Chemistry, University of Copenhagen = Københavns Universitet (KU), Faculty of Life Science [Copenhagen], Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), 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)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ethologie Expérimentale et Comparée (LEEC), Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC), Department of Plant and Environmental Sciences [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Biology [Copenhagen], Université de Tours-Centre National de la Recherche Scientifique (CNRS), and Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)
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0106 biological sciences ,Sucrose ,0303 health sciences ,Ants ,Physiology ,Ecology ,Ants Camponotus Conditioning Generalisation Learning Nestmate recognition ,Association Learning ,[SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences ,Perceptual similarity ,Biology ,010603 evolutionary biology ,01 natural sciences ,Hydrocarbons ,Social recognition ,03 medical and health sciences ,Chain length ,Generalization, Stimulus ,Evolutionary biology ,Insect Science ,Animals ,Perception ,030304 developmental biology - Abstract
International audience; Nestmate recognition in ants is based on perceived differences in a multi-component blend of hydrocarbons that are present on the insect cuticle. Although supplementation experiments have shown that some classes of hydrocarbons, such as methyl branched alkanes and alkenes, have a salient role in nestmate recognition, there was basically no information available on how ants detect and perceive these molecules. We used a new conditioning procedure to investigate whether individual carpenter ants could associate a given hydrocarbon (linear or methyl-branched alkane) to sugar reward. We then studied perceptual similarity between a hydrocarbon previously associated with sugar and a novel hydrocarbon. Ants learnt all hydrocarbon-reward associations rapidly and with the same efficiency, regardless of the structure of the molecules. Ants could discriminate among a large number of pairs of hydrocarbons, but also generalised. Generalisation depended both on the structure of the molecule and the animal's experience. For linear alkanes, generalisation was observed when the novel molecule was smaller than the conditioned one. Generalisation between pairs of methyl-alkanes was high, while generalisation between hydrocarbons that differed in the presence or absence of a methyl group was low, suggesting that chain length and functional group might be coded independently by the ant olfactory system. Understanding variations in perception of recognition cues in ants is necessary for the general understanding of the mechanisms involved in social recognition processes based on chemical cues.
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- 2012
16. Journal of Integrative Agriculture
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YU Li-li, Yin Man, Gao Hua-wei, Zhang Yong-fang, Zhang Bo, Zhang Chun-yan, Qiu LiJuan, Liu Zhangxiong, LI Fu-heng, GU Yong-zhe, Hong Hui-long, and School of Plant and Environmental Sciences
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Germplasm ,Ecology ,business.industry ,Computer science ,Agriculture (General) ,ComputingMilieux_PERSONALCOMPUTING ,food and beverages ,Plant Science ,germplasm ,Biochemistry ,2-acetyl-1pyrroline ,Biotechnology ,S1-972 ,ComputingMilieux_GENERAL ,Food Animals ,ComputingMilieux_COMPUTERSANDEDUCATION ,Key (cryptography) ,Animal Science and Zoology ,Identification (biology) ,soybean ,GC-MS ,quantification method ,business ,Agronomy and Crop Science ,Food Science - Abstract
In order to screen the aroma characteristics of soybean, a new method was established which can quickly quantify the content of 2-acetyl-1pyrroline (2-AP), an important compound related to soybean aroma, using gas chromatography-mass spectrometry (GC-MS). Based on peak profile, total peak area and retention time as test indexes, an accurate identification method for fragrant soybeans was established. The optimum parameters of the protocol consisted of column temperature 70 degrees C, sample injector temperature 180 degrees C, optimum extraction alcohol content 1 mL, NaCl content 0.1 g, ultrasonication time 10 min, and extraction time 1 h, which were established by using the orthogonal test of single factors and three factors with four levels (L-9(3)(4)). 2-AP content of leaves had significant correlations with seeds, which were easier to measure. The protocol was simple and easy to carry out, consumed only small amounts of reagents, and provided accurate and reliable results with good reproducibility. A total of 101 soybean genotypes from different geographical sources were analyzed using this protocol. The results showed that the average content of 2-AP was 0.29 mg L-1, ranging from 0.094 to 1.816 mg L-1, and the genetic diversity index was 0.54. Among all genotypes-tested, they were classified into three grades, including seven elite genotypes identified as "grade one fragrant soybeans", which were Zhonglong 608, Heinong 88, Ha13-2958, Hongmiandou, Heinong 82, Huangmaodou, and Jiyu 21. These results provide both an identification technique and several elite aroma genotypes for gene discovery and good quality breeding in soybean. National Key R&D Program for Crop Breeding [2016YFD0100201]; Scientific Innovation Program of of the Chinese Academy of Agricultural Sciences (CAAS) Published version This work was supported by the National Key R&D Program for Crop Breeding (2016YFD0100201) and Scientific Innovation Program of of the Chinese Academy of Agricultural Sciences (CAAS) . We thank the Core Facility Platform, Institute of Crop Sciences, CAAS for their assistance with GC-MS analyses.
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- 2021
17. Virulence and resistance in malaria: who drives the outcome of the infection?
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Frédéric Thomas, Thierry Lefèvre, Fleur Ponton, Marta I. Sánchez, David P. Hughes, Génétique et évolution des maladies infectieuses (GEMI), Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre for Social Evolution (CSE), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Biology [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Biology [Copenhagen], and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Department of Plant and Environmental Sciences [Copenhagen]
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0106 biological sciences ,Host effects ,[SDV]Life Sciences [q-bio] ,Virulence ,Biology ,010603 evolutionary biology ,01 natural sciences ,Outcome (game theory) ,Host-Parasite Interactions ,03 medical and health sciences ,Mice ,Genotype ,medicine ,Animals ,Humans ,030304 developmental biology ,Genetics ,0303 health sciences ,Resistance (ecology) ,Host (biology) ,Ecology ,medicine.disease ,Disease control ,3. Good health ,Malaria ,Infectious Diseases ,Plasmodium chabaudi ,Parasitology - Abstract
International audience; Theoretical and experimental studies have established the dynamic nature of virulence and that, like all traits, it has evolved. Understanding parasite evolution offers a conceptual framework for diverse fields and can contribute greatly to decision-making in disease control. Recently, Grech et al. investigated the effects of host genotype-by-parasite genotype interactions on the expression of virulence in an artificial rodent-malaria system. They found that both parasite and host effects explained most of the variance in the virulence, resistance and transmission potential. These findings are a major contribution to the emerging debate on the pros and cons of a coevolutionary approach of virulence evolution; they also hold great potential for more effective control strategies.
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- 2007
18. Evaluation of a Novel Shallow Aggregate Ebb-and-flood Culture System and Transplant Size Effects on Hydroponic Basil Yield
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Michael Evans, Samuel Doty, Ryan W. Dickson, and School of Plant and Environmental Sciences
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Aggregate (composite) ,Flood myth ,Yield (finance) ,deep flow technique ,Horticulture ,soilless culture ,lcsh:Plant culture ,Hydroponics ,Nutrient film technique ,ocimum basilicum ,Agronomy ,Ocimum basilicum ,Environmental science ,nutrient film technique ,lcsh:SB1-1110 - Abstract
Ornamental bedding plant operations transitioning to leafy greens and herb production must decide whether to invest in new hydroponic equipment or modify existing culture systems for edible crops. In addition, common practices used to increase space-use and production efficiencies during bedding plant production may be modified for hydroponic leafy greens and herbs, such as purchasing large seedlings for transplant. The objective of the first experiment was to evaluate plant growth in a modified and novel shallow aggregate ebb-and-flood (SAEF) system intended for bedding plant growers with an emphasis on comparing yield across four basil (Ocimum basilicum) cultivars grown in the SAEF system to those grown using the traditional nutrient film technique (NFT) and deep water culture (DWC) hydroponic systems. The second experiment objective was to evaluate basil seedling size and the time of transplant to NFT hydroponic systems to determine effects on the final yield. ‘Genovese’ basil seedlings were grown in trays with cell counts of 32, 50, 72, 105, and 162 cells with corresponding root volumes per plant of 98.1, 50.2, 38.5, 19.6, and 16.3 cm3, respectively. Seedlings were transplanted to NFT systems at 14, 21, and 28 days after sowing and were harvested at 35 days. In the first experiment, overall basil shoot fresh and dry weights per plant were intermediate in the SAEF system (90.4 and 8.3 g) compared with the DWC (102.6 and 9.1 g) and NFT (75.8 and 6.6 g) hydroponic systems. In the second experiment, final shoot fresh and dry weight per plant increased as seedling root volume increased from 16.3 cm3 [72.8 and 5.5 g (162-cell tray)] to 98.1 cm3 [148.5 and 12.2 g (32-cell tray)]. Transplanting seedlings at later dates decreased yield across tray size and root volume treatments. Differences in yield between culture systems may have resulted from differences in nutrient supply and availability for plant uptake. Transplant of large seedling plugs to hydroponic culture was not shown to increase space-use efficiency after transplant without compromising yield, likely because root zone factors limited growth during seedling production. Further investigation into maximizing plant growth during seedling production and evaluating the effects of seedling size and transplant practices are needed to determine the potential for increasing space-use and production efficiencies.
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- 2020
19. Community-Driven Metadata Standards for Agricultural Microbiome Research
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Posy E. Busby, Jan E. Leach, R. B. Calderon, B. A. Vinatzer, Anjali S. Iyer-Pascuzzi, Linda L. Kinkel, Emiley A. Eloe-Fadrosh, K. A. T. Silverstein, Gwyn A. Beattie, Bharath Prithiviraj, Neelam R. Redekar, Joanne B. Emerson, J. E. Maul, M. Potrykus, J. A. Rojas, A. I. Huerta, D. J. Tomso, Lynn M. Schriml, F. P. Brennan, J. Leonard, Sydney E. Everhart, Kellye Eversole, Jose Pablo Dundore-Arias, Kenneth E. Frost, Sarah C. Castle, A. K. Kalil, Joshua R. Herr, Susannah G. Tringe, and School of Plant and Environmental Sciences
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Agroecosystem ,phytobiome ,microbiome ,Genomics ,Plant Science ,lcsh:Plant culture ,Crop productivity ,lcsh:Microbial ecology ,03 medical and health sciences ,0302 clinical medicine ,genomics ,ontologies ,lcsh:SB1-1110 ,Microbiome ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Pace ,0303 health sciences ,metagenomics ,Ecology ,business.industry ,lcsh:QK900-989 ,Data science ,omics ,Metadata ,meta-analysis ,Geography ,Metagenomics ,Agriculture ,synthetic ,lcsh:Plant ecology ,lcsh:QR100-130 ,Zero Hunger ,business ,Agronomy and Crop Science ,030217 neurology & neurosurgery - Abstract
Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of "required" and "desirable" metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research. National Science FoundationNational Science Foundation (NSF) [1714276] This material was supported in part by the National Science Foundation under grant number 1714276. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. Public domain – authored by a U.S. government employee
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- 2020
20. Critical Assessment of Metagenome Interpretation: the second round of challenges
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Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S. Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard, Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy, Braunschweig Integrated Centre of Systems Biology [Braunschweig] (BRICS), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig]-Helmholtz Centre for Infection Research (HZI), Pennsylvania State University (Penn State), Penn State System, German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), Saint Petersburg State University (SPBU), Department of Information Technology and Electrical Engineering [Zürich] (D-ITET), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Center for Algorithmic Biotechnology [Saint Petersburg], Institute of Translational Biomedicine [Saint-Petersburg], Saint Petersburg University (SPBU)-Saint Petersburg University (SPBU), Centre for Integrative Biology (CIBIO), University of Trento (CIBIO), University of Trento [Trento], Genome Institute of Singapore (GIS), University of Southern California (USC), University of California [Davis] (UC Davis), University of California (UC), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Institut Pasteur [Paris] (IP), National Food Institute [Lyngby] (Forside), Drexel University, Robert Koch Institute [Berlin] (RKI), University of Technology Sydney (UTS), DOE Joint Genome Institute [Walnut Creek], University of California [Los Angeles] (UCLA), Intel Corporation [Santa Clara], Intel Corporation [USA], Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (UCPH), Fudan University [Shanghai], Beijing Genomics Institute [Shenzhen] (BGI), Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université de Genève = University of Geneva (UNIGE), The Arctic University of Norway [Tromsø, Norway] (UiT), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], University of California [San Diego] (UC San Diego), University of Wisconsin-Madison, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Hasso Plattner Institute [Potsdam, Germany], The University of Sydney, Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Amsterdam UMC - Amsterdam University Medical Center, Structural and Computational Biology, European Molecular Biology Laboratory [Heidelberg] (EMBL), DTU Electrical Engineering [Lyngby], National Institutes of Health [Bethesda] (NIH), Department of Biology [ETH Zürich] (D-BIOL), University of Virginia, IT University of Copenhagen (ITU), Freie Universität Berlin, University of Potsdam = Universität Potsdam, Florida International University [Miami] (FIU), National Research Council of Canada (NRC), Phase Genomics [Seattle], Max Planck Institute for Plant Breeding Research (MPIPZ), Helmholtz Centre for Infection Research (HZI), Aarhus University [Aarhus], Center for Biotechnology (CeBiTec), Universität Bielefeld = Bielefeld University, Open access funding provided by Helmholtz-Zentrum für Infektionsforschung GmbH (HZI), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), and Medical Microbiology and Infection Prevention
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06 Biological Sciences, 10 Technology, 11 Medical and Health Sciences ,Reproducibility of Results ,Cell Biology ,DNA ,Sequence Analysis, DNA ,Biochemistry ,Archaea ,Software ,Metagenome ,Metagenomics ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Molecular Biology ,Sequence Analysis ,Biotechnology ,Developmental Biology - Abstract
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses., Nature Methods, 19 (8), ISSN:1548-7105, ISSN:1548-7091
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- 2022
21. A field indicator for rhizosphere effect monitoring in arable soils
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Sébastian Mira, Mathieu Emily, Christophe Mougel, Morgane Ourry, Edith Le Cadre, Sol Agro et hydrosystème Spatialisation (SAS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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 de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut Agro Rennes Angers, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (UCPH), and ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011)
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[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Plant soil feedback ,Intercropping ,Plant diversity ,[MATH.MATH-ST]Mathematics [math]/Statistics [math.ST] ,Microbiota ,Soil Science ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Plant Science ,Holobiont - Abstract
International audience; For the agroecological transition, the rhizosphere is a critical interface for plants to acquire resources and to enhance plant health with limited inputs. In the present study, we developed a new indicator to estimate and monitor the intensity of plant-soil-microbiota interactions under field conditions.A Rhizosphere Effect Indicator (REI) was calculated by comparing individual and aggregated variables of bulk soil to those of the rhizosphere (i.e. soil enzyme activities and nutrient fluxes) every 2 weeks in the fields of three farms along a crop-diversification gradient. The diversity and structure of microbial communities in bulk soil and the rhizosphere in each field were assessed at flowering.The REI revealed statistically distinct dynamics and intensities of rhizosphere functioning among the three farms. Soil enzyme activities contributed more to the rhizosphere effect than nitrate and phosphate fluxes. Molecular analysis distinguished the two soil compartments and all crop-diversification levels. An integrated REI that provided a single value monitored the rhizosphere effect reliably.Methodological limits due to sampling of the rhizosphere under field conditions must be overcome to develop the REI, but the REI can serve as a complementary tool to traditional soil analysis for agroecological cropping system design and evaluation.
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- 2022
22. Stable Isotope Fractionation of Metals and Metalloids in Plants: A Review
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Wiggenhauser, Matthias, Moore, Rebekah E. T., Wang, Peng, Bienert, Gerd Patrick, Laursen, Kristian Holst, Blotevogel, Simon, Hanikenne, M, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Imperial College London, Nanjing Agricultural University (NAU), Technische Universität München = Technical University of Munich (TUM), Copenhagen Plant Science Center (CPSC), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Laboratoire Matériaux et Durabilité des constructions (LMDC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)
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metalloids ,0607 Plant Biology ,food and beverages ,stable isotopes ,translocation ,metals ,Plant Science ,[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics ,fractionation ,plant uptake ,process tracing ,multiple-collector-ICP-MS ,[CHIM.ANAL]Chemical Sciences/Analytical chemistry ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] - Abstract
This work critically reviews stable isotope fractionation of essential (B, Mg, K, Ca, Fe, Ni, Cu, Zn, Mo), beneficial (Si), and non-essential (Cd, Tl) metals and metalloids in plants. The review (i) provides basic principles and methodologies for non-traditional isotope analyses, (ii) compiles isotope fractionation for uptake and translocation for each element and connects them to physiological processes, and (iii) interlinks knowledge from different elements to identify common and contrasting drivers of isotope fractionation. Different biological and physico-chemical processes drive isotope fractionation in plants. During uptake, Ca and Mg fractionate through root apoplast adsorption, Si through diffusion during membrane passage, Fe and Cu through reduction prior to membrane transport in strategy I plants, and Zn, Cu, and Cd through membrane transport. During translocation and utilization, isotopes fractionate through precipitation into insoluble forms, such as phytoliths (Si) or oxalate (Ca), structural binding to cell walls (Ca), and membrane transport and binding to soluble organic ligands (Zn, Cd). These processes can lead to similar (Cu, Fe) and opposing (Ca vs. Mg, Zn vs. Cd) isotope fractionation patterns of chemically similar elements in plants. Isotope fractionation in plants is influenced by biotic factors, such as phenological stages and plant genetics, as well as abiotic factors. Different nutrient supply induced shifts in isotope fractionation patterns for Mg, Cu, and Zn, suggesting that isotope process tracing can be used as a tool to detect and quantify different uptake pathways in response to abiotic stresses. However, the interpretation of isotope fractionation in plants is challenging because many isotope fractionation factors associated with specific processes are unknown and experiments are often exploratory. To overcome these limitations, fundamental geochemical research should expand the database of isotope fractionation factors and disentangle kinetic and equilibrium fractionation. In addition, plant growth studies should further shift toward hypothesis-driven experiments, for example, by integrating contrasting nutrient supplies, using established model plants, genetic approaches, and by combining isotope analyses with complementary speciation techniques. To fully exploit the potential of isotope process tracing in plants, the interdisciplinary expertise of plant and isotope geochemical scientists is required., Frontiers in Plant Science, 13, ISSN:1664-462X
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- 2022
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23. The Science of the Total Environment
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Marcella Biddoccu, Ryan D. Stewart, Vittoria Giannini, Rafael Angulo-Jaramillo, Vittorio Longo, Filippo Giadrossich, Laurent Lassabatere, Antonio D. del Campo, Pier Paolo Roggero, Majdi Abou Najm, Simone Di Prima, Mario Pirastru, Giorgio Capello, Sergio Campus, Thierry Winiarski, Ludmila Ribeiro Roder, Department of Agricultural Sciences, Desertification Research Centre, University of Sassari, Sassari, Italy, Desertification Research Center, University of Sassari, Équipe 5 - Impact des Aménagements et des Polluants sur les HYdrosystèmes (IAPHY), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Department of Architecture, Design and Urban planning (DADU), University of Sassari, Italy, School of Agriculture, São Paulo State University ((UNESP)), Fazenda Experimental Lageado, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University [Blacksburg], Department of Land, Air and Water Resources, University of California [Davis] (UC Davis), University of California-University of California, Department of Chemistry and Pharmacy, Research Group in Forest Science and Technology ((Re-ForeST)), Universitat Politècnica de València (UPV), Institute of Sciences and Technologies for Sustainable Energy and Mobility ( (STEMS)), National Research Council of Italy, UMR5023 LEHNA, Universidade Estadual Paulista (UNESP), Virginia Polytechnic Institute and State University, University of California, and Universitat Politècnica de València
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Environmental Engineering ,GPR ,Flow (psychology) ,0207 environmental engineering ,Soil science ,02 engineering and technology ,Time-Lapse Imaging ,pr ,Trees ,law.invention ,Soil ,Water infiltration ,law ,Water Movements ,Environmental Chemistry ,penetration resistance ,Radar ,Preferential flow ,020701 environmental engineering ,Subsurface flow ,Soil layers ,Waste Management and Disposal ,Stemflow ,gpr ,04 agricultural and veterinary sciences ,Pollution ,Current (stream) ,Infiltration (hydrology) ,Ground-penetrating radar ,water infiltration ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Soil horizon ,Layering ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Environmental Sciences ,Geology ,GPR Water infiltration Soil layers Stemflow Preferential flow - Abstract
Made available in DSpace on 2022-04-28T19:44:52Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-02-01 Consiglio Nazionale delle Ricerche European Regional Development Fund Università degli Studi di Sassari Agence Nationale de la Recherche Ministero dell’Istruzione, dell’Università e della Ricerca Understanding linkages between heterogeneous soil structures and non-uniform flow is fundamental for interpreting infiltration processes and improving hydrological simulations. Here, we utilized ground-penetrating radar (GPR) as a non-invasive technique to investigate those linkages and to complement current traditional methods that are labor-intensive, invasive, and non-repeatable. We combined time-lapse GPR surveys with different types of infiltration experiments to create three-dimensional (3D) diagrams of the wetting dynamics. We carried out the GPR surveys and validated them with in situ observations, independent measurements and field excavations at two experimental sites. Those sites were selected to represent different mechanisms that generate non-uniform flow: (1) preferential water infiltration initiated by tree trunk and root systems; and (2) lateral subsurface flow due to soil layering. Results revealed links between different types of soil heterogeneity and non-uniform flow. The first experimental site provided evidence of root-induced preferential flow paths along coarse roots, emphasizing the important role of coarse roots in facilitating preferential water movement through the subsurface. The second experimental site showed that water infiltrated through the restrictive layer mainly following the plant root system. The presented approach offers a non-invasive, repeatable and accurate way to detect non-uniform flow. Department of Agricultural Sciences University of Sassari, Viale Italia, 39A Desertification Research Center University of Sassari, Viale Italia, 39 Univ Lyon Université Claude Bernard Lyon 1 CNRS ENTPE UMR5023 LEHNA Department of Architecture Design and Urban Planning University of Sassari, Via Piandanna, 4 School of Agriculture São Paulo State University (UNESP) Fazenda Experimental Lageado School of Plant and Environmental Sciences Virginia Polytechnic Institute and State University Department of Land Air and Water Resources University of California Department of Chemistry and Pharmacy University of Sassari, Via Piandanna 4 Research Group in Forest Science and Technology (Re-ForeST) Universitat Politècnica de València, Camí de Vera Institute of Sciences and Technologies for Sustainable Energy and Mobility (STEMS) National Research Council of Italy, Strada delle Cacce, 73 School of Agriculture São Paulo State University (UNESP) Fazenda Experimental Lageado Agence Nationale de la Recherche: ANR-17-CE04-0010 Ministero dell’Istruzione, dell’Università e della Ricerca: J54I18000120001
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- 2022
24. Arginine vasopressin in brains of free ranging striped mouse males following alternative reproductive tactics
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Ivana Schoepf, Wiliam Kenkel, Carsten Schradin, Institute of Evolutionary Biology and Environmental Studies, Universität Zürich [Zürich] = University of Zurich (UZH), School of animal, Plant and Environmental Sciences, University of the Witwatersrand [Johannesburg] (WITS), Indiana University [Bloomington], Indiana University System, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), University of Zurich, and Schoepf, Ivana
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medicine.medical_specialty ,Vasopressin ,Evolution ,Captivity ,Brain mass ,142-005 142-005 ,chemistry.chemical_compound ,Intra-specific variation in social organisation ,Behavior and Systematics ,Corticosterone ,Internal medicine ,medicine ,Testosterone ,Ecology, Evolution, Behavior and Systematics ,biology ,Ecology ,food and beverages ,Social flexibility ,biology.organism_classification ,Endocrinology ,1105 Ecology, Evolution, Behavior and Systematics ,Oxytocin ,chemistry ,Animal ecology ,[SDE]Environmental Sciences ,570 Life sciences ,590 Animals (Zoology) ,Philopatry ,Animal Science and Zoology ,1103 Animal Science and Zoology ,Rhabdomys pumilio ,medicine.drug - Abstract
Oxytocin (OT) and arginine vasopressin (AVP) are produced in the brain. Due to their importance in modulating social behaviour, these two neuropepetides have been extensively studied in captivity, yet few data are available from the field. Here we report the findings from an immunohistochemistry study, where we measured density of OT and AVP in different brain nuclei of wild African striped mice (Rhabdomys pumilio). Striped mice are socially flexible with both sexes being able to follow alternative reproductive tactics. Adult males can remain natally philopatric, or they can disperse and live solitarily as roamers or immigrate into a group and become breeders. Previous studies in captivity found no differences between solitary and group-living striped mice in AVPR1a expression, but solitary males had higher irAVP concentrations in the paraventricular nucleus and BNST. In the present study we tested whether the results obtained from captive studies could be replicated in the wild. We collected brains from 5 breeders, 9 philopatrics, and 3 roamers from a field site in South Africa and transported them to the USA for immunohistochemistry. Our results showed that roamers have higher irAVP concentrations in the BNST than philopatrics, which leads us to predict for future experimental studies that roamers will be able to increase AVP secretion in the brain when becoming group-living.
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- 2021
25. Effects of Fertilizer Source and Rate on Zinnia Cut Flower Production in a High Tunnel
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Bi, Guihong, Li, Tongyin, Gu, Mengmeng, Evans, William B., Williams, Mark A., and School of Plant and Environmental Sciences
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fungi ,food and beverages ,complex mixtures - Abstract
Sustainable nutrient management in high tunnel production is critical for optimizing crop yield and quality and improving soil health. In this study, we investigated the influence of different pre-plant composts (composted broiler litter, vemicompost, and cotton gin compost) in combination with different rates of organic or conventional fertilizer on zinnia plant growth, marketable yield of cut flower stems (>30 cm), and soil nutrients in a high tunnel over two years. Results showed that in general, pre-plant compost influenced plant growth, and plants that received composted broiler litter had the highest plant growth index. However, pre-plant compost did not affect the number of marketable cut stems. Fertigation during the growing season influenced the number of marketable cut stems. Comparable rates of nitrogen, from either organic or conventional fertilizer, produced similar numbers of marketable stems, suggesting that the organic fertilizer used in this study can be used as a fertilizer source for the production of zinnia cut flowers. After two years of production under the high tunnel, soil-extractable phosphorus, sodium, zinc, and pH significantly increased, suggesting that salt accumulation should be closely monitored in response to different compost or fertilizer sources with long-term production under high tunnels. Published version
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- 2021
26. Evaluation of Blossom Thinning Spray Timing Strategies in Apple
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Allen, W. Chester, Kon, Tom, Sherif, Sherif M., Alson H. Smith Jr. Agricultural Research and Extension Center, and School of Plant and Environmental Sciences
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fungi - Abstract
In the eastern USA and several other apple-growing regions, apple blossom thinning using lime sulfur is a relatively new crop load management strategy. This study sought to evaluate how application timing of lime sulfur + stylet oil blossom thinning sprays would influence thinning efficacy and crop safety of ‘Gala’ apples. This project occurred at two locations in the USA, Winchester, Virginia, and Mills River, North Carolina, during the 2019 growing season. Two main timing strategies were assessed: (1) model-guided sprays with the pollen tube growth model (PTGM), (2) fixed spray intervals with the first spray applied at a specified percentage of open bloom (20% vs. 80%), and the second spray applied at a reapplication interval (48 h vs. 72 h). Model-guided and 20% open bloom + 48-h treatments reduced fruit set and increased fruit weight, diameter, and length at both sites. Treatments with a delayed first spray at 80% open bloom or a more extended second reapplication of 72 h were generally ineffective. There was no conclusive evidence that lime sulfur + stylet oil blossom thinning spray timing influenced russet incidence/severity or leaf phytotoxicity. This study demonstrated that effective and safe blossom thinning can be obtained from applying two sprays at 20% open bloom and 48 h thereafter or using the PTGM. Published version
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- 2021
27. Sound Splits as Influenced by Seed Size for Runner and Virginia Market Type Peanut Shelled on a Reciprocating Sheller
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Jeffrey C. Dunne, Nino Brown, Maria Balota, Daniel J. Anco, and School of Plant and Environmental Sciences
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geography ,geography.geographical_feature_category ,Agriculture ,kernel geometry ,Reciprocating motion ,Animal science ,Arachis hypogaea L ,extra-large kernels ,farmer stock ,deduction ,Kernel size ,Agronomy and Crop Science ,Sound (geography) ,Mathematics - Abstract
The objective of this study was to examine peanut (Arachis hypogaea L.) kernel percent sound splits as a function of sound mature kernel seed size when shelled on a reciprocating sheller. Data were compiled from a total of 139 field experiments conducted in the Virginia-Carolina region and Georgia from 2005 to 2020. Runner and Virginia peanut market types were graded according to United States Department of Agriculture (USDA) standards using standard sheller screens with upper grid sizes corresponding to the red pan from the pre-sizer of 10.3 × 19.1 mm (26/64 × 3/4 ″) and 13.5 × 25.4 mm (34/64 × 1 ″) with minimum bar grid clearances of 8.7 (11/32 ″) and 12.7 mm (1/2 ″), respectively. A subset of runner market type samples was graded using the Virginia sheller screen. Grade data per market type and sheller screen was analyzed separately. Among runner market types shelled with the standard runner-type screen, percent sound splits increased linearly with increasing seed size at the logit rate of 1.16 per sound mature kernel g (p < 0.001). Sound splits for Virginia and runner market types shelled on the standard Virginia-type screen did not significantly vary by kernel size (p = 0.939 and 0.687, respectively). Extra-large kernels (proportion) for Virginia types linearly increased with seed size at 1.91 per sound mature kernel g (logit scale) (p < 0.001). Runner market types sized 75 to 91 g/100 sound mature kernels (605 to 500 seed/lb) were estimated to have a 50% probability of a 2.3 to 4.5% or greater increase in sound splits when shelled with the standard runner-type screen compared to runner-type seed sized 55 g/100 sound mature kernels (820 seed/lb), respectively, equivalent to a potential deduction increase of 1.8 to 4.4 USD /1000 kg. For both Virginia and runner market types, seed weight linearly increased with pod weight at 0.169 and 0.195 g/g (p < 0.001), respectively. Results from this study may be used as a reference to suggest runner-type seed sizes above which larger reciprocating sheller screen utilization in line with USDA grading practices is warranted to reduce mechanically induced sound splits during grading and subsequent economic deduction penalties for corresponding farmer stock peanut. Published version
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- 2021
28. Comparison of nitrogen monoxide emissions from several African tropical ecosystems and influence of season and fire
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Robert J. Delmas, X. Le Roux, R. Lensi, O. Ronce, D. A. B. Parsons, L. Labroue, Dominique Serça, M. C. Scholes, Luc Abbadie, UMR Physiologie Intégrée de l'Arbre Fruitier et Forestier, Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire d'aérologie (LA), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Équipe Troposphère, Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Groupe d'étude de l'atmosphère météorologique (CNRM-GAME), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS)-Centre national de recherches météorologiques (CNRM), Météo France-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Animal, Plant and Environmental Sciences (CSIR), University of the Witwatersrand [Johannesburg] (WITS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'aérologie - LA ( LA ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Animal, Plant and Environmental Sciences ( CSIR ), University of the Witwaterstrand, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Institut des Sciences de l'Evolution de Montpellier ( ISEM ), Université de Montpellier ( UM ) -Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'aérologie (LAERO), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Groupe d'étude de l'atmosphère météorologique (CNRM-GAME), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
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Wet season ,Atmospheric Science ,Denitrification ,food.ingredient ,010504 meteorology & atmospheric sciences ,BIOGENIC EMISSIONS ,Soil biology ,MID-PACIFIC TROPOSPHERE ,Atmospheric sciences ,01 natural sciences ,Grassland ,food ,NITRIC-OXIDE EMISSIONS ,Dry season ,Forest ecology ,Environmental Chemistry ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[ SDE.MCG.ECO ] Environmental Sciences/Global Changes/domain_sde.mcg.eco ,Ecosystem ,SAVANNA SOILS ,Hyperthelia ,COSTA-RICA ,ComputingMilieux_MISCELLANEOUS ,0105 earth and related environmental sciences ,General Environmental Science ,Hydrology ,Global and Planetary Change ,geography ,geography.geographical_feature_category ,04 agricultural and veterinary sciences ,15. Life on land ,NOX EMISSIONS ,FOREST ,SOUTH-AFRICA ,FIELD-MEASUREMENTS ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,[SDU]Sciences of the Universe [physics] ,13. Climate action ,GLOBAL INVENTORY ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Environmental science ,[SDE.MCG.ECO]Environmental Sciences/Global Changes/domain_sde.mcg.eco - Abstract
International audience; NO emission rates from soils were measured for twelve major African ecosystems in four countries (Congo, Niger, Ivory Coast, and South Africa) and within four major phytogeographic domains: the Guineo-Congolese, Guinean, Sahelian, and Zambezian domains. Measurements were performed during wet and/or dry seasons. All the measurements were made with the same dynamic chamber device, which allowed true comparisons to be made. This study showed that emission rates strongly differed between ecosystems and exhibited a marked temporal variability. Ecosystem effect was highly significant during both the dry and wet seasons. Emission rates were low (7 ng NO-N m(-2) s(-1)) in a seasonally wetted grassland (site 2) and in particular sites subjected to various disturbances, for example soil fauna activity (termite mounds) or past human disturbance (Acacia patches-settlement site). Microbial activity potentials (i.e., carbon mineralization, nitrification, denitrification, and total net N mineralization) were determined for most of the soils where NO fluxes were measured. In some sites, these potential activities were useful to identify the major processes controlling NO emission rates. Denitrification potential was very low and could not explain substantial NO fluxes from broad-and fine-leafed savannas and Hyperthelia savannas of the Zambezian domain. Very low potentials of both nitrification and denitrification could be related to the low NO fluxes for the three Guinean savanna sites studied. NO fluxes were significantly higher during the wet season than the dry season in both savanna and forest ecosystems. Emission rates in savanna ecosystems were significantly increased within a few hours after fire. The measurements presented here provide a unique, consistent database which can be used to further analyze the processes involved in the spatial and temporal variations of NO emissions.
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- 1998
29. Endogenous Regulation and Pharmacological Modulation of Sepsis-Induced HMGB1 Release and Action: An Updated Review
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Jianhua Li, Wei Wang, Cassie Shu Zhu, Weiqiang Chen, Haichao Wang, Xiqian Lan, Xiaoling Qiang, and School of Plant and Environmental Sciences
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Lipopolysaccharides ,hemichannel ,QH301-705.5 ,Review ,HMGB1 ,Sepsis ,sepsis ,inflammasome ,Intensive care ,medicine ,Animals ,Humans ,antibodies ,Biology (General) ,HMGB1 Protein ,innate immune cells ,Innate immune system ,biology ,business.industry ,pyroptosis ,Acute-phase protein ,Pyroptosis ,Inflammasome ,General Medicine ,medicine.disease ,Immunology ,herbal medicine ,acute-phase proteins ,biology.protein ,Cytokines ,Tumor necrosis factor alpha ,business ,medicine.drug - Abstract
Sepsis remains a common cause of death in intensive care units, accounting for approximately 20% of total deaths worldwide. Its pathogenesis is partly attributable to dysregulated inflammatory responses to bacterial endotoxins (such as lipopolysaccharide, LPS), which stimulate innate immune cells to sequentially release early cytokines (such as tumor necrosis factor (TNF) and interferons (IFNs)) and late mediators (such as high-mobility group box 1, HMGB1). Despite difficulties in translating mechanistic insights into effective therapies, an improved understanding of the complex mechanisms underlying the pathogenesis of sepsis is still urgently needed. Here, we review recent progress in elucidating the intricate mechanisms underlying the regulation of HMGB1 release and action, and propose a few potential therapeutic candidates for future clinical investigations. Published version
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- 2021
30. Protoplast Regeneration and Its Use in New Plant Breeding Technologies
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Reed, Kelsey M., Bargmann, Bastiaan O. R., and School of Plant and Environmental Sciences
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fungi ,food and beverages - Abstract
The development of gene-editing technology holds tremendous potential for accelerating crop trait improvement to help us address the need to feed a growing global population. However, the delivery and access of gene-editing tools to the host genome and subsequent recovery of successfully edited plants form significant bottlenecks in the application of new plant breeding technologies. Moreover, the methods most suited to achieve a desired outcome vary substantially, depending on species' genotype and the targeted genetic changes. Hence, it is of importance to develop and improve multiple strategies for delivery and regeneration in order to be able to approach each application from various angles. The use of transient transformation and regeneration of plant protoplasts is one such strategy that carries unique advantages and challenges. Here, we will discuss the use of protoplast regeneration in the application of new plant breeding technologies and review pertinent literature on successful protoplast regeneration. Accepted version
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- 2021
31. Rootstocks Overexpressing StNPR1 and StDREB1 Improve Osmotic Stress Tolerance of Wild-Type Scion in Transgrafted Tobacco Plants
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Hezema, Yasmine S., Shukla, Mukund R., Goel, Alok, Ayyanath, Murali M., Sherif, Sherif M., Saxena, Praveen K., Alson H. Smith Jr. Agricultural Research and Extension Center, and School of Plant and Environmental Sciences
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mRNA transport ,StDREB1 ,ABA ,fungi ,food and beverages ,ROS ,osmotic stress ,transgrafting ,StNPR1 ,ORGs - Abstract
In grafted plants, the movement of long-distance signals from rootstocks can modulate the development and function of the scion. To understand the mechanisms by which tolerant rootstocks improve scion responses to osmotic stress (OS) conditions, mRNA transport of osmotic responsive genes (ORGs) was evaluated in a tomato/potato heterograft system. In this system, Solanum tuberosum was used as a rootstock and Solanum lycopersicum as a scion. We detected changes in the gene expression levels of 13 out of the 21 ORGs tested in the osmotically stressed plants; of these, only NPR1 transcripts were transported across the graft union under both normal and OS conditions. Importantly, OS increased the abundance of StNPR1 transcripts in the tomato scion. To examine mRNA mobility in transgrafted plants, StNPR1 and StDREB1 genes representing the mobile and non-mobile transcripts, respectively, were overexpressed in tobacco (Nicotiana tabacum). The evaluation of transgenic tobacco plants indicated that overexpression of these genes enhanced the growth and improved the physiological status of transgenic plants growing under OS conditions induced by NaCl, mannitol and polyethylene glycol (PEG). We also found that transgenic tobacco rootstocks increased the OS tolerance of the WT-scion. Indeed, WT scions on transgenic rootstocks had higher ORGs transcript levels than their counterparts on non-transgenic rootstocks. However, neither StNPR1 nor StDREB1 transcripts were transported from the transgenic rootstock to the wild-type (WT) tobacco scion, suggesting that other long-distance signals downstream these transgenes could have moved across the graft union leading to OS tolerance. Overall, our results signify the importance of StNPR1 and StDREB1 as two anticipated candidates for the development of stress-resilient crops through transgrafting technology. Published version
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- 2021
32. International Journal of Molecular Science
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Sherif M. Sherif, Yasmine S. Hezema, Praveen K. Saxena, Mukund R. Shukla, Murali M. Ayyanath, Alson H. Smith Jr. Agricultural Research and Extension Center, and School of Plant and Environmental Sciences
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0106 biological sciences ,0301 basic medicine ,Stomatal conductance ,Osmotic shock ,water use efficiency ,QH301-705.5 ,Plant Roots ,01 natural sciences ,Article ,Catalysis ,Inorganic Chemistry ,abscisic acid ,03 medical and health sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Osmotic Pressure ,PEG ratio ,Biology (General) ,Physical and Theoretical Chemistry ,Water-use efficiency ,QD1-999 ,Molecular Biology ,Abscisic acid ,Water content ,Spectroscopy ,Plant Proteins ,Transpiration ,relative water content ,Organic Chemistry ,General Medicine ,Computer Science Applications ,apple rootstocks ,Chemistry ,Horticulture ,030104 developmental biology ,chemistry ,Malus ,osmotic responsive genes ,osmotic stress ,Rootstock ,010606 plant biology & botany - Abstract
The growth and productivity of several apple rootstocks have been evaluated in various previous studies. However, limited information is available on their tolerance to osmotic stress. In the present study, the physiological and molecular responses as well as abscisic acid (ABA) levels were assessed in six apple rootstocks (M26, V3, G41, G935, B9 and B118) osmotically stressed with polyethylene glycol (PEG, 30%) application under greenhouse conditions. Our results showed that V3, G41, G935 and B9 had higher relative water content (RWC), and lower electrolyte leakage (EL) under stress conditions compared to M26 and B118. Additionally, water use efficiency (WUE) was higher in V3, G41 and B9 than M26, which might be partially due to the lower transpiration rate in these tolerant rootstocks. V3, G41 and B9 rootstocks also displayed high endogenous ABA levels which was combined with a reduction in stomatal conductance and decreased water loss. At the transcriptional level, genes involved in ABA-dependent and ABA-independent pathways, e.g., SnRK, DREB, ERD and MYC2, showed higher expression in V3, G41, G935 and B9 rootstocks compared to M26 in response to stress. In contrast, WRKY29 was down-regulated in response to stress in the tolerant rootstocks, and its expression was negatively correlated with ABA content and stomatal closure. Overall, the findings of this study showed that B9, V3 and G41 displayed better osmotic stress tolerance followed by G935 then M26 and B118 rootstocks. Published version
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- 2021
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33. Remote Sensing
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Hillary L. Mehl, David B. Langston, Xing Wei, Song Li, Marcela A. Johnson, School of Plant and Environmental Sciences, and Virginia Agricultural Experiment Station
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0106 biological sciences ,Athelia rolfsii ,spectroscopy ,Computer science ,Science ,Sclerotium rolfsii ,Feature selection ,Machine learning ,computer.software_genre ,01 natural sciences ,03 medical and health sciences ,feature selection ,recursive feature elimination ,support vector machine ,030304 developmental biology ,0303 health sciences ,Spectral signature ,biology ,business.industry ,Hyperspectral imaging ,biology.organism_classification ,Plant disease ,hyperspectral band selection ,soilborne diseases ,Support vector machine ,Feature (computer vision) ,General Earth and Planetary Sciences ,Artificial intelligence ,Stem rot ,business ,computer ,peanut stem rot ,random forest ,010606 plant biology & botany - Abstract
Hyperspectral sensors combined with machine learning are increasingly utilized in agricultural crop systems for diverse applications, including plant disease detection. This study was designed to identify the most important wavelengths to discriminate between healthy and diseased peanut (Arachis hypogaea L.) plants infected with Athelia rolfsii, the causal agent of peanut stem rot, using in-situ spectroscopy and machine learning. In greenhouse experiments, daily measurements were conducted to inspect disease symptoms visually and to collect spectral reflectance of peanut leaves on lateral stems of plants mock-inoculated and inoculated with A. rolfsii. Spectrum files were categorized into five classes based on foliar wilting symptoms. Five feature selection methods were compared to select the top 10 ranked wavelengths with and without a custom minimum distance of 20 nm. Recursive feature elimination methods outperformed the chi-square and SelectFromModel methods. Adding the minimum distance of 20 nm into the top selected wavelengths improved classification performance. Wavelengths of 501–505, 690–694, 763 and 884 nm were repeatedly selected by two or more feature selection methods. These selected wavelengths can be applied in designing optical sensors for automated stem rot detection in peanut fields. The machine-learning-based methodology can be adapted to identify spectral signatures of disease in other plant-pathogen systems. Published version
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- 2021
34. Molecular Biology and Evolution
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Matthew W. Hahn, Meng Wu, David C. Haak, Gregory J. Anderson, Leonie C. Moyle, Rafael F. Guerrero, and School of Plant and Environmental Sciences
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0106 biological sciences ,Dioecy ,Sequence assembly ,Biology ,AcademicSubjects/SCI01180 ,Solanum ,01 natural sciences ,Genome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Sex-determination system ,Genetics ,sex chromosome ,Clade ,Gene ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,Foundation (engineering) ,AcademicSubjects/SCI01130 ,Sex Determination Processes ,biology.organism_classification ,Biological Evolution ,dioecy ,Evolutionary biology ,Multigene Family ,genome assembly ,Pectins ,sex evolution ,Heterogametic sex ,Genome, Plant ,010606 plant biology & botany - Abstract
Dissecting the genetic mechanisms underlying dioecy (i.e., separate female and male individuals) is critical for understanding the evolution of this pervasive reproductive strategy. Nonetheless, the genetic basis of sex determination remains unclear in many cases, especially in systems where dioecy has arisen recently. Within the economically important plant genus Solanum (similar to 2,000 species), dioecy is thought to have evolved independently at least 4 times across roughly 20 species. Here, we generate the first genome sequence of a dioecious Solanum and use it to ascertain the genetic basis of sex determination in this species. We de novo assembled and annotated the genome of Solanum appendiculatum (assembly size: similar to 750 Mb scaffold N50: 0.92 Mb; similar to 35,000 genes), identified sex-specific sequences and their locations in the genome, and inferred that males in this species are the heterogametic sex. We also analyzed gene expression patterns in floral tissues of males and females, finding approximately 100 genes that are differentially expressed between the sexes. These analyses, together with observed patterns of gene-family evolution specific to S. appendiculatum, consistently implicate a suite of genes from the regulatory network controlling pectin degradation and modification in the expression of sex. Furthermore, the genome of a species with a relatively young sex-determination system provides the foundational resources for future studies on the independent evolution of dioecy in this Glade. National Science Foundation (USA NSF)National Science Foundation (NSF) [IOS-1127059]; Department of Biology at Indiana University Published version We are grateful to J.L. Kostyun for help in the laboratory and greenhouse, and to the editor and anonymous reviewer for helpful comments. This work was done with support from National Science Foundation (USA NSF Grant No. IOS-1127059) and the Department of Biology at Indiana University. Previous support from NSF, and the University of Connecticut, supported the field collections and greenhouse experiments with Solanum appendiculatum.
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- 2021
35. Ice Nucleation Activity of Alpine Bioaerosol Emitted in Vicinity of a Birch Forest
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Teresa M. Seifried, Paul Bieber, Anna T. Kunert, David G. Schmale, Karin Whitmore, Janine Fröhlich-Nowoisky, Hinrich Grothe, and School of Plant and Environmental Sciences
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birch ,Meteorology. Climatology ,alpine vegetation ,QC851-999 ,bioaerosol ,ice nucleation ,fluorescence microscopy ,scanning electron microscopy - Abstract
In alpine environments, many plants, bacteria, and fungi contain ice nuclei (IN) that control freezing events, providing survival benefits. Once airborne, IN could trigger ice nucleation in cloud droplets, influencing the radiation budget and the hydrological cycle. To estimate the atmospheric relevance of alpine IN, investigations near emission sources are inevitable. In this study, we collected 14 aerosol samples over three days in August 2019 at a single site in the Austrian Alps, close to a forest of silver birches, which are known to release IN from their surface. Samples were taken during and after rainfall, as possible trigger of aerosol emission by an impactor and impinger at the ground level. In addition, we collected aerosol samples above the canopy using a rotary wing drone. Samples were analyzed for ice nucleation activity, and bioaerosols were characterized based on morphology and auto-fluorescence using microscopic techniques. We found high concentrations of IN below the canopy, with a freezing behavior similar to birch extracts. Sampled particles showed auto-fluorescent characteristics and the morphology strongly suggested the presence of cellular material. Moreover, some particles appeared to be coated with an organic film. To our knowledge, this is the first investigation of aerosol emission sources in alpine vegetation with a focus on birches. Published version
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- 2021
36. Untargeted Metabolomics and Antioxidant Capacities of Muscadine Grape Genotypes during Berry Development
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Islam El-Sharkawy, Mehboob B. Sheikh, Ahmed Gomaa Gomaa Darwish, Ahmed Ismail, Pranavkumar Gajjar, Protiva Rani Das, Violeta Tsolova, Sherif M. Sherif, Subramani Paranthaman Balasubramani, Alson H. Smith Jr. Agricultural Research and Extension Center, and School of Plant and Environmental Sciences
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0301 basic medicine ,Antioxidant ,Physiology ,DPPH ,medicine.medical_treatment ,Clinical Biochemistry ,nutritional biomarkers ,RM1-950 ,Berry ,developmental stages ,Biology ,01 natural sciences ,Biochemistry ,Article ,Veraison ,03 medical and health sciences ,chemistry.chemical_compound ,Metabolome ,medicine ,Gallic acid ,Food science ,Molecular Biology ,010401 analytical chemistry ,Catechin ,Cell Biology ,metabolomics ,0104 chemical sciences ,030104 developmental biology ,chemistry ,muscadine genotypes ,Therapeutics. Pharmacology ,Malic acid - Abstract
Three muscadine grape genotypes (Muscadinia rotundifolia (Michx.) Small) were evaluated for their metabolite profiling and antioxidant activities at different berry developmental stages. A total of 329 metabolites were identified using UPLC-TOF-MS analysis (Ultimate 3000LC combined with Q Exactive MS and screened with ESI-MS) in muscadine genotypes throughout different developmental stages. Untargeted metabolomics study revealed the dominant chemical groups as amino acids, organic acids, sugars, and phenolics. Principal component analysis indicated that developmental stages rather than genotypes could explain the variations among the metabolic profiles of muscadine berries. For instance, catechin, epicatechin-3-gallate, and gallic acid were more accumulated in ripening seeds (RIP-S). However, tartaric acid and malonic acid were more abundant during the fruit-set (FS) stage, and malic acid was more abundant in the veraison (V) stage. The variable importance in the projection (VIP >, 0.5) in partial least-squares–discriminant analysis described 27 biomarker compounds, representing the muscadine berry metabolome profiles. A heatmap of Pearson’s correlation analysis between the 27 biomarker compounds and antioxidant activities was able to identify nine antioxidant determinants, among them, gallic acid, 4-acetamidobutanoic acid, trehalose, catechine, and epicatechin-3-gallate displayed the highest correlations with different types of antioxidant activities. For instance, DPPH and FRAP conferred a similar antioxidant activity pattern and were highly correlated with gallic acid and 4-acetamidobutanoic acid. This comprehensive study of the metabolomics and antioxidant activities of muscadine berries at different developmental stages is of great reference value for the plant, food, pharmaceutical, and nutraceutical sectors.
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- 2021
37. Dataset of biomass and chemical quality of crop residues from European areas
- Author
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Lars Stoumann Jensen, Pascal Thiébeau, Sylvie Recous, Fabien Ferchaud, Fractionnement des AgroRessources et Environnement (FARE), Université de Reims Champagne-Ardenne (URCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Copenhagen = Københavns Universitet (UCPH), Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), ResidueGas (ERA-GAS), Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark, Transfrontalière BioEcoAgro (Transfrontalière BioEcoAgro), and Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
Crop residue ,Science (General) ,Crop residues ,[SDE.MCG]Environmental Sciences/Global Changes ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Biomass ,Forage ,7. Clean energy ,C:N ratio ,Q1-390 ,Green manure ,Chemical characteristics ,N ratio [N content, C] ,N content ,Cover crop ,N content, C:N ratio ,Data Article ,2. Zero hunger ,Multidisciplinary ,0402 animal and dairy science ,04 agricultural and veterinary sciences ,15. Life on land ,040201 dairy & animal science ,Energy crop ,Agronomy ,Literature survey ,13. Climate action ,Greenhouse gas ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Environmental science ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
International audience; This dataset presents the chemical characteristics of plant biomass and crop residues from agrosystems in European areas (carbon and nitrogen contents and biochemical composition). These data have been collected from the scientific literature. The specific data and their origins are presented. The mean values from these data are also provided by major production type (main crops, forage and pasture crops, green manure and cover crops, vegetable crops and energy crops), species and litter type. These data were collected as part of the framework of the European project ResidueGas (ERA-GAS, 2017-2021), which aims to improve the estimation of greenhouse gas emissions associated with crop residues.
- Published
- 2021
38. Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
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Bradley S. Bushman, Wengang Xie, Aureliano Bombarely, Haidong Yan, Zhongren Zhang, Guangyan Feng, Zhongfu Yang, Peilin Chen, Xinxin Zhao, Lei Xu, Jianping Wang, Gang Nie, Xinquan Zhang, Linkai Huang, Wenkai Jiang, Mingzhou Li, and School of Plant and Environmental Sciences
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,Genome evolution ,transposon ,Sequence assembly ,Plant Science ,Flowers ,01 natural sciences ,Genome ,Evolution, Molecular ,03 medical and health sciences ,long‐read sequencing ,Gene Regulatory Networks ,Triticeae ,Dactylis ,Gene ,Research Articles ,reference genome ,Phylogeny ,biology ,Phylogenetic tree ,food and beverages ,flowering time ,biology.organism_classification ,030104 developmental biology ,Phenotype ,Evolutionary biology ,long-read sequencing ,Agronomy and Crop Science ,Dactylis glomerata ,010606 plant biology & botany ,Biotechnology ,Reference genome ,Research Article ,Microsatellite Repeats - Abstract
Orchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an similar to 1.84-Gb chromosome-scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super-scaffold N50 of 252.52 Mb, which is the first chromosome-scale assembled genome of a cool-season forage grass. The genome includes 40 088 protein-coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the 'Silk Road' or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome-scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses. National Basic Research Program (973 Program) in ChinaNational Basic Research Program of China [2014CB138705]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [NSFC 31872997]; Earmarked Fund for Modern Agro-industry Technology Research System [CARS-34]; National Project on Sci-Tec Foundation Resources Survey [2017FY100602] This research work was funded by the National Basic Research Program (973 Program) in China (No. 2014CB138705), the National Natural Science Foundation of China (NSFC 31872997), the Earmarked Fund for Modern Agro-industry Technology Research System (No. CARS-34) and the National Project on Sci-Tec Foundation Resources Survey (2017FY100602). Public domain – authored by a U.S. government employee
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- 2019
39. Comparing time series transcriptome data between plants using a network module finding algorithm
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Jiyoung Lee, Ruth Grene, Lenwood S. Heath, Song Li, Computer Science, Fralin Life Sciences Institute, and School of Plant and Environmental Sciences
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0106 biological sciences ,0301 basic medicine ,Computer science ,Comparative transcriptome analysis ,Arabidopsis ,Network ,Plant Science ,lcsh:Plant culture ,computer.software_genre ,Embryo development ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,Software ,Gene expression ,Genetics ,lcsh:SB1-1110 ,Gene ,Protocol (object-oriented programming) ,lcsh:QH301-705.5 ,biology ,business.industry ,Embryogenesis ,Methodology ,Expression (computer science) ,biology.organism_classification ,Pipeline (software) ,030104 developmental biology ,lcsh:Biology (General) ,Scripting language ,Simulated annealing ,Sequence homology ,business ,Soybean ,computer ,Algorithm ,010606 plant biology & botany ,Biotechnology - Abstract
Background Comparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic studies in plants have been performed in model species, including Arabidopsis and rice, comparative transcriptome analysis is particularly important for functional annotation of genes in diverse plant species. Many biological processes, such as embryo development, are highly conserved between different plant species. The challenge is to establish one-to-one mapping of the developmental stages between two species. Results In this manuscript, we solve this problem by converting the gene expression patterns into co-expression networks and then apply network module finding algorithms to the cross-species co-expression network. We describe how such analyses are carried out using bash scripts for preliminary data processing followed by using the R programming language for module finding with a simulated annealing method. We also provide instructions on how to visualize the resulting co-expression networks across species. Conclusions We provide a comprehensive pipeline from installing software and downloading raw transcriptome data to predicting homologous genes and finding orthologous co-expression networks. From the example provided, we demonstrate the application of our method to reveal functional conservation and divergence of genes in two plant species. Published version
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- 2019
40. Climate change impact and adaptation for wheat protein
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Mohamed Jabloun, Pierre Martre, Garry O'Leary, Dominique Ripoche, Bruno Basso, Pramod K. Aggarwal, Daniel Wallach, Matthew P. Reynolds, Marijn van der Velde, John R. Porter, Heidi Webber, Enli Wang, Frank Ewert, Joost Wolf, Christian Klein, Belay T. Kassie, Christian Biernath, Margarita Garcia-Vila, M. Ali Babar, Pierre Stratonovitch, Yujing Gao, Glenn J. Fitzgerald, Davide Cammarano, Bing Liu, Peter J. Thorburn, Fulu Tao, Andrew J. Challinor, Reimund P. Rötter, Christine Girousse, Zhigan Zhao, Christoph Müller, Ann-Kristin Koehler, Jørgen E. Olesen, Elias Fereres, Iwan Supit, Andrea Maiorano, Marco Bindi, Sebastian Gayler, Kurt Christian Kersebaum, Giacomo De Sanctis, Alex C. Ruane, Rosella Motzo, Juraj Balkovic, Manuel Montesino San Martin, Roberto Ferrise, Mikhail A. Semenov, Claudio O. Stöckle, Soora Naresh Kumar, Gerrit Hoogenboom, Benjamin Dumont, Ehsan Eyshi Rezaei, Mukhtar Ahmed, Senthold Asseng, Thilo Streck, Yan Zhu, R. Cesar Izaurralde, Katharina Waha, Ahmed M. S. Kheir, Taru Palosuo, Liujun Xiao, Sara Minoli, Eckart Priesack, Heidi Horan, Curtis D. Jones, Francesco Giunta, Zhao Zhang, Claas Nendel, International Food Policy Research Institute (US), CGIAR (France), European Commission, Institut National de la Recherche Agronomique (France), National Natural Science Foundation of China, Federal Ministry of Food and Agriculture (Germany), Biotechnology and Biological Sciences Research Council (UK), Innovation Fund Denmark, China Scholarship Council, Ministero delle Politiche Agricole Alimentari e Forestali, Academy of Finland, Finnish Ministry of Agriculture and Forestry, Federal Ministry of Education and Research (Germany), Department of Agriculture and Water Resources (Australia), University of Melbourne, Grains Research and Development Corporation (Australia), National Institute of Food and Agriculture (US), German Research Foundation, Gorgan University, Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), European Food Safety Authority = Autorité européenne de sécurité des aliments, Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), Georg-August-University = Georg-August-Universität Göttingen, Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Department of Economic Drt and Resources, Grains Innovation Park, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, Faculty of Veterinary and Agricultural Science [Melbourne], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Department of Agricultural Sciences, University of Naples Federico II = Università degli studi di Napoli Federico II, World Food Crops Breeding, Department of Agronomy, IFAS, University of Florida [Gainesville] (UF), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Soils, Water and Environment Research Institute, Agricultural Research Center (ARC), Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), International Maize and Wheat Improvement Centre [Inde] (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Biological Systems Engineering, University of Wisconsin-Madison, Department of Agronomy, University of El-Tarf, Ecosystem Services and Management Program, International Institute for Applied Systems Analysis (IIASA), Department of Soil Science, Faculty of Natural Sciences, Comenius University in Bratislava, W. K. Kellogg Biological Station (KBS), Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Department of Earth and Environmental Sciences [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Institute of Biochemical Plant Pathology, Research Center for Environmental Health, Helmholtz Zentrum München = German Research Center for Environmental Health, Department of Agri‐food Production and Environmental Sciences (DISPAA), Università degli Studi di Firenze = University of Florence (UniFI), The James Hutton Institute, Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, Collaborative Research Program from CGIAR and Future Earth on Climate Change, Agriculture and Food Security (CCAFS), International Center for Tropical Agriculture, GMO Unit, European Food Safety Authority, Department Terra & AgroBioChem, Gembloux Agro‐Bio Tech, Université de Liège, Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Department of Crop Sciences, Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Soil Science and Land Evaluation, University of Hohenheim, Food Systems Institute [Gainesville] (UF|IFAS), Department of Geographical Sciences, College Park, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institute of Biochemical Plant Pathology [Neuherberg], German Research Center for Environmental Health - Helmholtz Center München (GmbH), National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricutural University, Member of the Leibniz Association, Potsdam Institute for Climate Impact Research (PIK), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Centre for Environment Science and Climate Resilient Agriculture [New Delhi], Indian Agricultural Research Institute (IARI), Natural Resources Institute Finland (LUKE), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), 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)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Lincoln, Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Water & Food and Water Systems & Global Change Group, Wageningen University and Research [Wageningen] (WUR), Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Joint Research Centre (IPTS), Commission Européenne, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), CSIRO Agriculture and Food (CSIRO), Plant Production Systems, State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University (BNU), Department of Agronomy and Biotechnology, China Agricultural University (CAU), National Research Foundation for the Doctoral Program of Higher Education of China, Grant/Award Number: 20120097110042, International Food Policy, European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Georg-August-University [Göttingen], Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen - Georg-August-Universität Göttingen, University of Naples Federico II, Helmholtz-Zentrum München (HZM), Universtiy of Florence, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Natural Resources Institute Finland, 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), Wageningen University, Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agricultural & Biological Engineering Department, University of Florida [Gainesville], Georg-August-Universität Göttingen, University of Goettingen, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Research Program on Climate Change, Agriculture and Food Security, BISA‐CIMMYT, Consultative Group on International Agricultural Research (CGIAR), Comenius University [Bratislava], Helmholtz Zentrum München, Institute of Crop Science and Resource Conservation INRES, University of Bonn, IAS‐CSIC, Universidad de Cordoba, Institute for Sustainable Food Systems, Texas A&M AgriLife Research and Extension Center, Aarhus University, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UE Agroclim (UE AGROCLIM), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Wageningen University and Research Center (WUR), Beijing Normal University, and China Agricultural University
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[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,0106 biological sciences ,010504 meteorology & atmospheric sciences ,Water en Voedsel ,01 natural sciences ,grain protein ,adaptation au milieu ,climate change adaptation ,climate change impact ,food security ,wheat ,Co2 concentration ,adaptation to the environment ,Triticum ,General Environmental Science ,2. Zero hunger ,changement climatique ,Global and Planetary Change ,Food security ,Ecology ,Temperature ,food and beverages ,Adaptation, Physiological ,Droughts ,Nitrogen ,Climate Change ,Climate change ,010603 evolutionary biology ,blé ,Crop production ,Food Quality ,Grain quality ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Environmental Chemistry ,Grain Proteins ,global change ,0105 earth and related environmental sciences ,WIMEK ,Water and Food ,Global change ,Carbon Dioxide ,Models, Theoretical ,15. Life on land ,Agronomy ,13. Climate action ,Grain yield ,Environmental science ,Water Systems and Global Change ,Protein concentration - Abstract
Wheat grain protein concentration is an important determinant of wheat quality for human nutrition that is often overlooked in efforts to improve crop production. We tested and applied a 32‐multi‐model ensemble to simulate global wheat yield and quality in a changing climate. Potential benefits of elevated atmospheric CO2 concentration by 2050 on global wheat grain and protein yield are likely to be negated by impacts from rising temperature and changes in rainfall, but with considerable disparities between regions. Grain and protein yields are expected to be lower and more variable in most low‐rainfall regions, with nitrogen availability limiting growth stimulus from elevated CO2. Introducing genotypes adapted to warmer temperatures (and also considering changes in CO2 and rainfall) could boost global wheat yield by 7% and protein yield by 2%, but grain protein concentration would be reduced by −1.1 percentage points, representing a relative change of −8.6%. Climate change adaptations that benefit grain yield are not always positive for grain quality, putting additional pressure on global wheat production., B.L received support from the International Food Policy Research Institute (IFPRI) through the Global Futures and Strategic Foresight project, the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS) and the CGIAR Research Program on Wheat. A.M. received support from the EU Marie Curie FP7 COFUND People Programme, through an AgreenSkills fellowship under grant agreement no. PCOFUND‐GA‐2010‐267196. PM, A.M., D.R., and D.W. acknowledge support from the FACCE JPI MACSUR project (031A103B) through the metaprogram Adaptation of Agriculture and Forests to Climate Change (AAFCC) of the French National Institute for Agricultural Research (INRA). L.X. and Y.Z. were supported by the National High‐Tech Research and Development Program of China (2013AA100404), the National Natural Science Foundation of China (31271616), the National Research Foundation for the Doctoral Program of Higher Education of China (20120097110042), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). F.T. and Z.Z. were supported by the National Natural Science Foundation of China (41571088, 41571493 and 31561143003). R.R. received support from the German Ministry for Research and Education (BMBF) through project SPACES‐LLL. Rothamsted Research receives support from the Biotechnology and Biological Sciences Research Council (BBSRC) Designing Future Wheat programme [BB/P016855/1]. M.J. and J.E.O. were supported by Innovation Fund Denmark through the MACSUR project. L.X. and Y.G. acknowledge support from the China Scholarship Council. M.B and R.F. were funded by JPI FACCE MACSUR2 through the Italian Ministry for Agricultural, Food and Forestry Policies and thank A. Soltani from Gorgan Univ. of Agric. Sci. & Natur. Resour. for his support. R.P.R., T.P., and F.T. received financial support from the FACCE MACSUR project funded through the Finnish Ministry of Agriculture and Forestry (MMM) and from the Academy of Finland through the projects NORFASYS (decision nos. 268277 and 292944) and PLUMES (decision nos. 277403 and 292836). K.C.K. and C.N. received support from the German Ministry for Research and Education (BMBF) within the FACCE JPI MACSUR project. S.M. and C.M. acknowledge financial support from the MACMIT project (01LN1317A) funded through BMBF. G.J.O. and G.J.F. acknowledge support from the Victorian Department of Economic Development, Jobs, Transport and Resources, the Australian Department of Agriculture and Water Resources, The University of Melbourne and the Grains Research Development Corporation, Australia. P.K.A.'s work was implemented as part of the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), which is carried out with support from the CGIAR Trust Fund and through bilateral funding agreements. For details please visit https://ccafs.cgiar.org/donors. The views expressed in this document cannot be taken to reflect the official opinions of these organizations.. B.B. received financial support from USDA NIFA‐Water Cap Award 2015‐68007‐23133. F.E. acknowledges support from the FACCE JPI MACSUR project through the German Federal Ministry of Food and Agriculture (2815ERA01J) and from the German Science Foundation (project EW 119/5‐1).
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- 2019
41. Crop Diversification for Improved Weed Management: A Review
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Swati Shrestha, Te-Ming Tseng, Kunwar Sudip, Gourav Sharma, and School of Plant and Environmental Sciences
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0106 biological sciences ,Agriculture (General) ,Climate change ,Plant Science ,Diversification (marketing strategy) ,01 natural sciences ,S1-972 ,crop rotation ,crop diversification ,herbicide resistance ,Herbicide resistance ,weeds ,biochemistry ,Cropping system ,Cover crop ,biology ,Agricultural diversification ,Agroforestry ,Intercropping ,04 agricultural and veterinary sciences ,Crop rotation ,biology.organism_classification ,Weed control ,climate change ,Agronomy ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Business ,cover crops ,sustainable ,Weed ,Agronomy and Crop Science ,intercropping ,010606 plant biology & botany ,Food Science - Abstract
Weeds are among the major constraints to any crop production system, reducing productivity and profitability. Herbicides are among the most effective methods to control weeds, and reliance on herbicides for weed control has increased significantly with the advent of herbicide-resistant crops. Unfortunately, over-reliance on herbicides leads to environmental-health issues and herbicide-resistant weeds, causing human-health and ecological concerns. Crop diversification can help manage weeds sustainably in major crop production systems. It acts as an organizing principle under which technological innovations and ecological insights can be combined to manage weeds sustainably. Diversified cropping can be defined as the conscious inclusion of functional biodiversity at temporal and/or spatial levels to improve the productivity and stability of ecosystem services. Crop diversification helps to reduce weed density by negatively impacting weed seed germination and weed growth. Additionally, diversified farming systems are more resilient to climate change than monoculture systems and provide better crop yield. However, there are a few challenges to adopting a diversified cropping system, which ranges from technology innovations, government policies, farm-level decisions, climate change, and market conditions. In this review, we discuss how crop diversification supports sustainable weed management, the challenges associated with it, and the future of weed management with respect to the diversification concept.
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- 2021
42. Identification of Quantitative Disease Resistance Loci Toward Four Pythium Species in Soybean
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Clevinger, Elizabeth M., Biyashev, Ruslan M., Lerch-Olson, Elizabeth, Yu, Haipeng, Quigley, Charles, Song, Qijian, Dorrance, Anne E., Robertson, Alison E., Saghai-Maroof, Mohammad A., and School of Plant and Environmental Sciences
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resistance ,recombinant inbred line population ,Plant Sciences ,quantitative disease resistant loci ,0607 Plant Biology ,food and beverages ,Pythium ,soybean ,Life Sciences & Biomedicine - Abstract
In this study, four recombinant inbred line (RIL) soybean populations were screened for their response to infection by Pythium sylvaticum, Pythium irregulare, Pythium oopapillum, and Pythium torulosum. The parents, PI 424237A, PI 424237B, PI 408097, and PI 408029, had higher levels of resistance to these species in a preliminary screening and were crossed with “Williams,” a susceptible cultivar. A modified seed rot assay was used to evaluate RIL populations for their response to specific Pythium species selected for a particular population based on preliminary screenings. Over 2500 single-nucleotide polymorphism (SNP) markers were used to construct chromosomal maps to identify regions associated with resistance to Pythium species. Several minor and large effect quantitative disease resistance loci (QDRL) were identified including one large effect QDRL on chromosome 8 in the population of PI 408097 × Williams. It was identified by two different disease reaction traits in P. sylvaticum, P. irregulare, and P. torulosum. Another large effect QDRL was identified on chromosome 6 in the population of PI 408029 × Williams, and conferred resistance to P. sylvaticum and P. irregulare. These large effect QDRL will contribute toward the development of improved soybean cultivars with higher levels of resistance to these common soil-borne pathogens. Published version
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- 2021
43. K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology
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Ziarsolo, Peio, Hasing, Tomas, Hilario, Rebeca, Garcia-Carpintero, Victor, Blanca, Jose, Bombarely, Aureliano, Cañizares, Joaquin, and School of Plant and Environmental Sciences
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genetic processes ,food and beverages ,natural sciences - Abstract
Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies. Published version
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- 2021
44. What is the impact of human wastewater biosolids (sewage sludge) application on long-term soil carbon sequestration rates? A systematic review protocol
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Kathryn Haering, W. Lee Daniels, Mike J. Badzmierowski, Gregory K. Evanylo, and School of Plant and Environmental Sciences
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Biosolids ,Land management ,Amendment ,Agricultural engineering ,010501 environmental sciences ,Management, Monitoring, Policy and Law ,01 natural sciences ,Carbon credit ,Sewage sludge ,lcsh:Environmental sciences ,Stock (geology) ,Land application ,0105 earth and related environmental sciences ,lcsh:GE1-350 ,Soil organic matter ,Ecology ,Soil organic carbon ,business.industry ,04 agricultural and veterinary sciences ,Soil carbon ,Pollution ,Meta-analysis ,Agriculture ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Environmental science ,business - Abstract
Background Human wastewater biosolids, hereafter referred to as biosolids, are produced in significant quantities around the world and often applied to an extensive land mass including agricultural fields, forests, mine lands, and urban areas. Land-application of biosolids has been reported in peer-reviewed and non-peer-reviewed work to change soil organic carbon stocks in varying amounts. Determining the potential of soil organic carbon (SOC) stock change and sequestration from biosolids land application is critical for biosolids producers and users to gain access to carbon credit markets. Our review question is, "what is the impact of biosolids application on long-term soil carbon sequestration rates?” We look to explore this main question with the follow-up, "does biosolids processing methods and characteristics, application method, soil properties, land management and other modifiers affect rates of carbon accumulation from land-applied biosolids?" Methods Searches will be conducted using online databases (i.e., Web of Science Core Collection, CAB Abstracts, Scopus, ProQuest Dissertations & Theses Global), search engines (Google Scholar and Microsoft Academic), and specialist websites to find primary field studies and grey literature of biosolids land-application effects on soil organic carbon stocks. We will use English search terms and predefined inclusion criteria of: (1) a field study of at least 24 months that reports soil organic carbon/matter (SOC/SOM) concentrations/stocks; (2) has two types of treatments: (i) a control (non-intervention AND/OR synthetic fertilizer) AND (ii) a biosolids-based amendment; and (3) information of amendment properties and application dates and rates to estimate the relative contribution of the applied materials to SOC changes. We will screen results in two stages: (1) title and abstract and (2) full text. A 10% subset will be screened by two reviewers for inclusion at the title and abstract level and use a kappa analysis to ensure agreement of at least 0.61. All results in the full text stage will be dual screened. Data will be extracted by one person and reviewed by a second person. Critical appraisal will be used to assess studies’ potential bias and done by two reviewers. A meta-analysis using random effects models will be conducted if sufficient data of high enough quality are extracted.
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- 2021
45. Strain, Soil-Type, Irrigation Regimen, and Poultry Litter Influence Salmonella Survival and Die-off in Agricultural Soils
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Bardsley, Cameron, Weller, Daniel L., Ingram, David T., Chen, Yuhuan, Oryang, David O., Rideout, Steven L., Strawn, Laura K., Food Science and Technology, School of Plant and Environmental Sciences, and Virginia Agricultural Experiment Station
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Salmonella ,strain variability ,biological soil amendments of animal origin ,poultry litter ,time to harvest interval ,complex mixtures ,survival ,die-off rate ,irrigation - Abstract
The use of untreated biological soil amendments of animal origin (BSAAO) have been identified as one potential mechanism for the dissemination and persistence of Salmonella in the produce growing environment. Data on factors influencing Salmonella concentration in amended soils are therefore needed. The objectives here were to (i) compare die-off between 12 Salmonella strains following inoculation in amended soil and (ii) characterize any significant effects associated with soil-type, irrigation regimen, and amendment on Salmonella survival and die-off. Three greenhouse trials were performed using a randomized complete block design. Each strain (similar to 4 log CFU/g) was homogenized with amended or non-amended sandy-loam or clay-loam soil. Salmonella levels were enumerated In 25 g samples 0, 0.167 (4 h), 1,2, 4, 7, 10, 14, 21,28, 56, 84, 112, 168, 210, 252, and 336 days post-inoculation (dpi), or until two consecutive samples were enrichment negative. Regression analysis was performed between strain, soil-type, Irrigation, and (i) time to last detect (survival) and (li) concentration at each time-point (die-off rate). Similar effects of strain, irrigation, soil-type, and amendment were identified using the survival and die-off models. Strain explained up to 18% of the variance in survival, and up to 19% of variance In die-off rate. On average Salmonella survived for 129 days in amended soils, however, Salmonella survived, on average, 30 days longer In clay-loam soils than sandy-loam soils [95% Confidence interval (Cl) = 45, 15], with survival time ranging from 84 to 210 days for the individual strains during dally irrigation. When strain- specific associations were investigated using regression trees, S. Javiana and S. Saintpaul were found to survive longer In sandy-loam soil, whereas most of the other strains survived longer In clay-loam soil. Salmonella also survived, on average, 128 days longer when irrigated weekly, compared to daily (Cl = 101, 154), and 89 days longer in amended soils, than non-amended soils (Cl = 61,116). Overall, this study provides insight into Salmonella survival following contamination of field soils by BSAAO. Specifically, Salmonella survival may be strain- specific as affected by both soil characteristics and management practices. These data can assist in risk assessment and strain selection for use in challenge and validation studies. Food and Drug Administration (FDA)United States Department of Health & Human Services; Specialty Crop Block Grant Program at the United States Department of Agriculture (USDA)through the Virginia Department of Agriculture and Consumer Services (VDACS); Virginia Agricultural Experiment Station; Hatch Program of the National Institute of Food and Agriculture, USDA; National Institute of Environmental Health Sciences of the National Institutes of Health (NIH)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Environmental Health Sciences (NIEHS) [T32ES007271] This project was funded, in part, by the Food and Drug Administration (FDA), and by the Specialty Crop Block Grant Program at the United States Department of Agriculture (USDA) through the Virginia Department of Agriculture and Consumer Services (VDACS). Funding for this work was also provided by the Virginia Agricultural Experiment Station and the Hatch Program of the National Institute of Food and Agriculture, USDA. Manuscript preparation and data analyses were supported by the National Institute of Environmental Health Sciences of the National Institutes of Health (NIH) under award number T32ES007271. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the FDA, USDA, NIH, and VDACS.
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- 2021
46. Development of Breeder-Friendly KASP Markers for Low Concentration of Kunitz Trypsin Inhibitor in Soybean Seeds
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Rosso, M. Luciana, Shang, Chao, Song, Qijian, Escamilla, Diana M., Gillenwater, Jay, Zhang, Bo, and School of Plant and Environmental Sciences
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anti-nutritional factor ,single nucleotide polymorphism ,quantitative trait loci ,food and beverages ,KASP ,soybean ,Kunitz trypsin inhibitor - Abstract
Trypsin inhibitors (TI), a common anti-nutritional factor in soybean, prevent animals’ protein digestibility reducing animal growth performance. No commercial soybean cultivars with low or null concentration of TI are available. The availability of a high throughput genotyping assay will be beneficial to incorporate the low TI trait into elite breeding lines. The aim of this study is to develop and validate a breeder friendly Kompetitive Allele Specific PCR (KASP) assay linked to low Kunitz trypsin inhibitor (KTI) in soybean seeds. A total of 200 F3:5 lines derived from PI 547656 (low KTI) X Glenn (normal KTI) were genotyped using the BARCSoySNP6K_v2 Beadchip. F3:4 and F3:5 lines were grown in Blacksburg and Orange, Virginia in three years, respectively, and were measured for KTI content using a quantitative HPLC method. We identified three SNP markers tightly linked to the major QTL associated to low KTI in the mapping population. Based on these SNPs, we developed and validated the KASP assays in a set of 93 diverse germplasm accessions. The marker Gm08_44814503 has 86% selection efficiency for the accessions with low KTI and could be used in marker assisted breeding to facilitate the incorporation of low KTI content in soybean seeds. Published version
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- 2021
47. Analysis of Shoot Architecture Traits in Edamame Reveals Potential Strategies to Improve Harvest Efficiency
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Dhakal, Kshitiz, Zhu, Qian, Zhang, Bo, Li, Mao, Li, Song, and School of Plant and Environmental Sciences
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phenotyping ,edamame ,breeding ,food and beverages ,shoot architecture ,persistent homology - Abstract
Edamame is a type of green, vegetable soybean and improving shoot architecture traits for edamame is important for breeding of high-yield varieties by decreasing potential loss due to harvesting. In this study, we use digital imaging technology and computer vision algorithms to characterize major traits of shoot architecture for edamame. Using a population of edamame PIs, we seek to identify underlying genetic control of different shoot architecture traits. We found significant variations in the shoot architecture of the edamame lines including long-skinny and candle stick-like structures. To quantify the similarity and differences of branching patterns between these edamame varieties, we applied a topological measurement called persistent homology. Persistent homology uses algebraic geometry algorithms to measure the structural similarities between complex shapes. We found intriguing relationships between the topological features of branching networks and pod numbers in our plant population, suggesting combination of multiple topological features contribute to the overall pod numbers on a plant. We also identified potential candidate genes including a lateral organ boundary gene family protein and a MADS-box gene that are associated with the pod numbers. This research provides insight into the genetic regulation of shoot architecture traits and can be used to further develop edamame varieties that are better adapted to mechanical harvesting.
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- 2021
48. AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
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Amy Pruden, Ishi Keenum, Kyle Akers, Lenwood S. Heath, Kang Xia, Lauren Wind, Liqing Zhang, Suraj Gupta, Chaoqi Chen, Xiao Liang, Katharine F. Knowlton, Reem Aldaihani, Computer Science, Civil and Environmental Engineering, Biological Systems Engineering, Dairy Science, and School of Plant and Environmental Sciences
- Subjects
Web server ,Computer science ,Antibiotic resistance ,Context (language use) ,Space (commercial competition) ,computer.software_genre ,lcsh:Computer applications to medicine. Medical informatics ,Biochemistry ,Data science ,03 medical and health sciences ,Structural Biology ,Environmental Microbiology ,Computational analysis ,Molecular Biology ,lcsh:QH301-705.5 ,Ecosystem ,030304 developmental biology ,0303 health sciences ,Metadata ,Internet ,Point (typography) ,030306 microbiology ,Applied Mathematics ,Drug Resistance, Microbial ,Computer Science Applications ,Data sharing ,lcsh:Biology (General) ,Metagenomics ,Genes, Bacterial ,lcsh:R858-859.7 ,Metagenome ,computer ,Software - Abstract
Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/.
- Published
- 2021
49. LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes
- Author
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Boris A. Vinatzer, Reza Mazloom, Long Tian, Lenwood S. Heath, School of Plant and Environmental Sciences, and Computer Science
- Subjects
Computer science ,Bioinformatics ,Pipeline (computing) ,lcsh:Medicine ,Computational biology ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Set (abstract data type) ,03 medical and health sciences ,0302 clinical medicine ,Similarity (network science) ,Genomic similarity ,Phylogenomics ,Prokaryotes ,030304 developmental biology ,Taxonomy ,Comparative genomics ,0303 health sciences ,General Neuroscience ,lcsh:R ,Computational Biology ,General Medicine ,Genomics ,Genome-based taxonomy ,Average nucleotide identity ,Identification (information) ,Pairwise comparison ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery - Abstract
Background: Computing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods. Methods: Here we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools. Results: LINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset. National Science FoundationNational Science Foundation (NSF) [IOS-1354215]; College of Agriculture and Life Sciences at Virginia Polytechnic Institute and State University; Virginia Agricultural Experiment Station; Hatch Program of the National Institute of Food and Agriculture, US Department of Agriculture This study was supported by the National Science Foundation (IOS-1354215) and the College of Agriculture and Life Sciences at Virginia Polytechnic Institute and State University. Funding to Boris A. Vinatzer was also provided in part by the Virginia Agricultural Experiment Station and the Hatch Program of the National Institute of Food and Agriculture, US Department of Agriculture. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- Published
- 2021
50. Multiple microscopic approaches demonstrate linkage between chromoplast architecture and carotenoid composition in diverse Capsicum annuum fruit
- Author
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O'Connell, Mary [Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces NM 88003 USA]
- Published
- 2013
- Full Text
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