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1. Food inspector scheduling with outcome and daily-schedule effects

Author: Liu, Ming, Tang, Hao, Chu, Feng, Zhu, Zhanguo, Chu, Chengbin, School of Economics & Management, Tongji University, Informatique, BioInformatique, Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay, College of Economics and Management (College of Economics and Management), Nanjing Agricultural University (NAU), Génie des Réseaux de Transport Terrestres et Informatique Avancée (COSYS-GRETTIA ), and Université Gustave Eiffel
Subjects: Inspector scheduling, Outcome effects, Strategy and Management, Inspection bias, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Management Science and Operations Research, Daily-schedule effects, Single-machine scheduling, Industrial and Manufacturing Engineering
Abstract: International audience; Food-safety inspection is regularly executed by the government for quality assessment. Evidence from recent research demonstrates that inspection accuracy and consistency are affected by inspection biases that result from an operational decision: inspector scheduling. More precisely, an inspector's stringency in an inspection is affected by the inspection results at the previous-inspected establishment (outcome effects) and when this inspection occurs within a workday (daily-schedule effects). To our best knowledge, the impact of these effects on scheduling decisions has not been studied in the scheduling literature. In this paper, we study a novel food inspector scheduling problem with these effects, where the inspector should scrutinise establishments with different locations. The problem is viewed as a single-machine scheduling problem with a complex objective function including (i) inspection accuracy, (ii) inspection consistency and (iii) workload of the inspector. To facilitate quantitative analyses of these effects, we model them by sequence-dependent functions and formulate a mixed integer linear programming model. To overcome the computational difficulty in large-scale problems, an efficient Tabu Search algorithm is developed. Experiment results on 135 randomly generated instances with up to 50 establishments and 10 workdays validate the efficiency of the solution method. Besides, managerial insights are drawn.
Published: 2023
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2. Simulation of winter wheat response to variable sowing dates and densities in a high-yielding environment

Author: Dueri, Sibylle, Brown, Hamish, Asseng, Senthold, Ewert, Frank, Webber, Heidi, George, Mike, Craigie, Rob, Guarin, Jose Rafael, Pequeno, Diego N.L., Stella, Tommaso, Ahmed, Mukhtar, Alderman, Phillip D., Basso, Bruno, Berger, Andres G., Mujica, Gennady Bracho, Cammarano, Davide, Chen, Yi, Dumont, Benjamin, Rezaei, Ehsan Eyshi, Fereres, Elias, Ferrise, Roberto, Gaiser, Thomas, Gao, Yujing, Garcia-Vila, Margarita, Gayler, Sebastian, Hochman, Zvi, Hoogenboom, Gerrit, Kersebaum, Kurt C., Nendel, Claas, Olesen, Jørgen E., Padovan, Gloria, Palosuo, Taru, Priesack, Eckart, Pullens, Johannes W.M., Rodríguez, Alfredo, Rötter, Reimund P., Ramos, Margarita Ruiz, Semenov, Mikhail A., Senapati, Nimai, Siebert, Stefan, Srivastava, Amit Kumar, Stöckle, Claudio, Supit, Iwan, Tao, Fulu, Thorburn, Peter, Wang, Enli, Weber, Tobias Karl David, Xiao, Liujun, Zhao, Chuang, Zhao, Jin, Zhao, Zhigan, Zhu, Yan, Martre, Pierre, Rebetzke, Greg, 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), The New Zealand Institute for Plant & Food Research Limited [Auckland] (Plant & Food Research), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Brandenburg University of Technology [Cottbus – Senftenberg] (BTU), Foundation for Arable Research (FAR), University of Florida [Gainesville] (UF), Earth Institute at Columbia University, Columbia University [New York], International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Swedish University of Agricultural Sciences (SLU), Pir Mehr Ali Shah Arid Agriculture University = PMAS-Arid Agriculture University Rawalpindi (AAUR), Oklahoma State University [Stillwater] (OSU), Michigan State University [East Lansing], Michigan State University System, Instituto Nacional de Investigación Agropecuaria (INIA), Georg-August-University = Georg-August-Universität Göttingen, Aarhus University [Aarhus], Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad de Córdoba = University of Córdoba [Córdoba], Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence (UniFI), Institute of Crop Science and Resource Conservation [Bonn] (INRES), University of Hohenheim, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Global Change Research Centre (CzechGlobe), University of Potsdam = Universität Potsdam, Natural Resources Institute Finland (LUKE), Helmholtz Zentrum München = German Research Center for Environmental Health, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Institute of Biochemical Plant Pathology (BIOP), Centro de Estudios e Investigación para la Gestión de Riesgos Agrarios y Medioambientales (CEIGRAM), Universidad Politécnica de Madrid (UPM), Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Washington State University (WSU), Wageningen University and Research [Wageningen] (WUR), Zhejiang University, Nanjing Agricultural University (NAU), China Agricultural University (CAU), Agricultural Model Intercomparison and Improvement Project (AgMIP) Wheat Phase 4 and was supported by the French National Research Institute for Agriculture, Food (INRAE) and the International Maize and Wheat Improvement Center (CIMMYT) through the International Wheat Yield Partnership (IWYP, grant IWYP115)., metaprogram Agriculture and forestry in the face of climate change: adaptation and mitigation (CLIMAE) of INRAE, grant-aided support from the Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat [BB/P016855/1] and Achieving Sustainable Agricultural Systems [NE/N018125/1] jointly funded with NERC, DivCSA project funded by the Academy of Finland (decision no. 316215)., National Natural Science Foundation of China (No. 31761143006), financial support from BARISTA project (031B0811A) through ERA-NET SusCrop under EU-FACCE JPI, German Federal Ministry of Education and Research (BMBF) through the BonaRes project ’’I4S’’ (031B0513I), German Federal Ministry of Education and Research (BMBF) through the BonaRes Project 'Soil3' (FKZ 031B0026A), Ministry of Education, Youth and Sports of Czech Republic through SustES—Adaption strategies for sustainable ecosystem services and food security under adverse environmental conditions (CZ.02.1.01/0.0/0.0/16_019/000797), Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2070 – 390732324', German Research Foundation (DFG, Grant Agreement SFB 1253/1 2017), European Project: 618105,EC:FP7:KBBE,FP7-ERANET-2013-RTD,FACCE ERA NET PLUS(2013), Institut National de la Recherche Agronomique (France), International Maize and Wheat Improvement Center, International Wheat Yield Partnership, National Natural Science Foundation of China, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Education, Youth and Sports (Czech Republic), German Research Foundation, Biotechnology and Biological Sciences Research Council (UK), Natural Environment Research Council (UK), and Academy of Finland
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Physiology, Climate Change, sowing date, Plant Science, CHINA, Multi-model Ensemble, New Zealand, Sowing Date, Sowing Density, Tiller Mortality, Tillering, Wheat, Yield Potential, tillering, wheat, USE EFFICIENCY, sowing density, Life Science, Biomass, ADAPTATION, PLANT-DENSITY, Triticum, METAANALYSIS, Multi-model ensemble, WIMEK, CLIMATE-CHANGE, tiller mortality, PRODUCTIVITY, Temperature, CROP MODELS, yield potential, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ROTATION, GROWTH, Water Systems and Global Change, Seasons
Abstract: Crop multi-model ensembles (MME) have proven to be effective in increasing the accuracy of simulations in modelling experiments. However, the ability of MME to capture crop responses to changes in sowing dates and densities has not yet been investigated. These management interventions are some of the main levers for adapting cropping systems to climate change. Here, we explore the performance of a MME of 29 wheat crop models to predict the effect of changing sowing dates and rates on yield and yield components, on two sites located in a high-yielding environment in New Zealand. The experiment was conducted for 6 years and provided 50 combinations of sowing date, sowing density and growing season. We show that the MME simulates seasonal growth of wheat well under standard sowing conditions, but fails under early sowing and high sowing rates. The comparison between observed and simulated in-season fraction of intercepted photosynthetically active radiation (FIPAR) for early sown wheat shows that the MME does not capture the decrease of crop above ground biomass during winter months due to senescence. Models need to better account for tiller competition for light, nutrients, and water during vegetative growth, and early tiller senescence and tiller mortality, which are exacerbated by early sowing, high sowing densities, and warmer winter temperatures., This study was a part of the Agricultural Model Intercomparison and Improvement Project (AgMIP) Wheat Phase 4 and was supported by the French National Research Institute for Agriculture, Food (INRAE) and the International Maize and Wheat Improvement Center (CIMMYT) through the International Wheat Yield Partnership (IWYP, grant IWYP115). SD and PM acknowledge support from the metaprogram Agriculture and forestry in the face of climate change: adaptation and mitigation (CLIMAE) of INRAE. YC and FT acknowledge support from the National Natural Science Foundation of China (No. 31761143006). RPR and GBM acknowledge financial support from BARISTA project (031B0811A) through ERA-NET SusCrop under EU-FACCE JPI. KCK was funded by the German Federal Ministry of Education and Research (BMBF) through the BonaRes project ’’I4S’’ (031B0513I). AS and TG acknowledge funding by the German Federal Ministry of Education and Research (BMBF) through the BonaRes Project “Soil3” (FKZ 031B0026A). KCK and JEO were supported by the Ministry of Education, Youth and Sports of Czech Republic through SustES—Adaption strategies for sustainable ecosystem services and food security under adverse environmental conditions (CZ.02.1.01/0.0/0.0/16_019/000797). FE acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2070 – 390732324”. TKDW was funded by the German Research Foundation (DFG, Grant Agreement SFB 1253/1 2017). MAS and NS at Rothamsted Research received grant-aided support from the Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat [BB/P016855/1] and Achieving Sustainable Agricultural Systems [NE/N018125/1] jointly funded with NERC. TP and FT are supported by the DivCSA project funded by the Academy of Finland (decision no. 316215).
Published: 2022
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3. Evidence for increasing global wheat yield potential

Author: Jose Rafael Guarin, Pierre Martre, Frank Ewert, Heidi Webber, Sibylle Dueri, Daniel Calderini, Matthew Reynolds, Gemma Molero, Daniel Miralles, Guillermo Garcia, Gustavo Slafer, Francesco Giunta, Diego N L Pequeno, Tommaso Stella, Mukhtar Ahmed, Phillip D Alderman, Bruno Basso, Andres G Berger, Marco Bindi, Gennady Bracho-Mujica, Davide Cammarano, Yi Chen, Benjamin Dumont, Ehsan Eyshi Rezaei, Elias Fereres, Roberto Ferrise, Thomas Gaiser, Yujing Gao, Margarita Garcia-Vila, Sebastian Gayler, Zvi Hochman, Gerrit Hoogenboom, Leslie A Hunt, Kurt C Kersebaum, Claas Nendel, Jørgen E Olesen, Taru Palosuo, Eckart Priesack, Johannes W M Pullens, Alfredo Rodríguez, Reimund P Rötter, Margarita Ruiz Ramos, Mikhail A Semenov, Nimai Senapati, Stefan Siebert, Amit Kumar Srivastava, Claudio Stöckle, Iwan Supit, Fulu Tao, Peter Thorburn, Enli Wang, Tobias Karl David Weber, Liujun Xiao, Zhao Zhang, Chuang Zhao, Jin Zhao, Zhigan Zhao, Yan Zhu, Senthold Asseng, University of Florida [Gainesville] (UF), Center for Climate Systems Research [New York] (CCSR), Columbia University [New York], 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), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Universidad Austral de Chile, International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), KWS Momont SAS, Universitad de Buenos Aires = University of Buenos Aires [Argentina], Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Agronomía [Buenos Aires], Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Universitat de Lleida, Institució Catalana de Recerca i Estudis Avançats (ICREA), Università degli Studi di Sassari = University of Sassari [Sassari] (UNISS), Pir Mehr Ali Shah Arid Agriculture University = PMAS-Arid Agriculture University Rawalpindi (AAUR), Swedish University of Agricultural Sciences (SLU), Oklahoma State University [Stillwater] (OSU), Michigan State University [East Lansing], Michigan State University System, Instituto Nacional de Investigación Agropecuaria (INIA), Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence (UniFI), Georg-August-University = Georg-August-Universität Göttingen, Purdue University [West Lafayette], Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad de Córdoba = University of Córdoba [Córdoba], University of Hohenheim, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Guelph, Global Change Research Centre (CzechGlobe), University of Potsdam = Universität Potsdam, Aarhus University [Aarhus], Natural Resources Institute Finland (LUKE), Helmholtz Zentrum München = German Research Center for Environmental Health, Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), Centro de Estudios e Investigación para la Gestión de Riesgos Agrarios y Medioambientales (CEIGRAM), Universidad Politécnica de Madrid (UPM), Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Washington State University (WSU), Wageningen University and Research [Wageningen] (WUR), Universität Kassel [Kassel], Zhejiang University, Nanjing Agricultural University (NAU), Building artificial Intelligence between trust, Responsibility and Decision (BIRD), Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Beijing Normal University (BNU), China Agricultural University (CAU), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), International Wheat Yield Partnership (IWYP, Grant IWYP115) and the International Maize and Wheat Improvement Center (CIMMYT)., IWYP, CIMMYT (Mexico), and the Chilean Technical and Scientific Research Council (CONICYT) by FONDECYT Project 1141048, National Natural Science Foundation of China (Project Nos. 31761143006 and 41571493), Ministry of Education, Youth and Sports of Czech Republic through SustEs (CZ.02.1.01/0.0/0.0/16_019/000797), Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat (BB/P016855/1) and Achieving Sustainable Agricultural Systems (NE/N018125/1)., International Wheat Yield Partnership, International Maize and Wheat Improvement Center, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), National Natural Science Foundation of China, Ministry of Education, Youth and Sports (Czech Republic), and Biotechnology and Biological Sciences Research Council (UK)
Subjects: Crop Population, Crop Model Ensemble, Global Food Security Supplementary Material For This Article Is Available Online, Radiation Use Efficiency, Wheat Potential Yield, Yield Increase, Climate, Global Food Security, crop model ensemble, Grain Number, global food security Supplementary material for this article is available online, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Photosynthesis, yield increase, General Environmental Science, WIMEK, radiation use efficiency, Renewable Energy, Sustainability and the Environment, Spring Wheat, Public Health, Environmental and Occupational Health, Letter, wheat potential yield, global food security, Food Demand, ddc, Solar-Radiation, Water Systems and Global Change, Biomass Accumulation
Abstract: Wheat is the most widely grown food crop, with 761 Mt produced globally in 2020. To meet the expected grain demand by mid-century, wheat breeding strategies must continue to improve upon yield-advancing physiological traits, regardless of climate change impacts. Here, the best performing doubled haploid (DH) crosses with an increased canopy photosynthesis from wheat field experiments in the literature were extrapolated to the global scale with a multi-model ensemble of process-based wheat crop models to estimate global wheat production. The DH field experiments were also used to determine a quantitative relationship between wheat production and solar radiation to estimate genetic yield potential. The multi-model ensemble projected a global annual wheat production of 1050 ± 145 Mt due to the improved canopy photosynthesis, a 37% increase, without expanding cropping area. Achieving this genetic yield potential would meet the lower estimate of the projected grain demand in 2050, albeit with considerable challenges., This study was a part of the Agricultural Model Intercomparison and Improvement Project (AgMIP) Wheat Phase 4. The study was supported by the International Wheat Yield Partnership (IWYP, Grant IWYP115) and the International Maize and Wheat Improvement Center (CIMMYT). Experiments carried out in Valdivia (Chile) were funded by IWYP, CIMMYT (Mexico), and the Chilean Technical and Scientific Research Council (CONICYT) by FONDECYT Project 1141048. The experimental work conducted at Valdivia by Dr Jaime Herrera (UACh) is appreciated. F T was supported by the National Natural Science Foundation of China (Project Nos. 31761143006 and 41571493). K C K was supported by the Ministry of Education, Youth and Sports of Czech Republic through SustEs (CZ.02.1.01/0.0/0.0/16_019/000797). Rothamsted Research receives support from the Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat (BB/P016855/1) and Achieving Sustainable Agricultural Systems (NE/N018125/1).
Published: 2022
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4. Multiscale modeling of the strain-induced α → β phase transition and piezoelectric activity in semi-crystalline poly(vinylidene fluoride) over a large-strain range

Author: Yan, Zhu, Zaïri, Fahmi, Zaoui, Ali, Nanjing Agricultural University (NAU), Laboratoire de Génie Civil et Géo-Environnement (LGCgE) - ULR 4515 (LGCgE), Université d'Artois (UA)-Université de Lille-Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-JUNIA (JUNIA), and Université catholique de Lille (UCL)-Université catholique de Lille (UCL)
Subjects: [PHYS]Physics [physics], Mechanics of Materials, General Materials Science, Instrumentation
Published: 2023
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5. Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions

Author: Li, Mei, Pommier, Thomas, Yin, Yue, Cao, Wenhui, Zhang, Xiaohui, Hu, Jie, Hautier, Yann, Yang, Tianjie, Xu, Yangchun, Shen, Qirong, Kowalchuk, George A, Jousset, Alexandre, Wei, Zhong, Ecology and Biodiversity, Sub Ecology and Biodiversity, Nanjing Agricultural University (NAU), Utrecht University [Utrecht], Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Ecology and Biodiversity, and Sub Ecology and Biodiversity
Subjects: Taverne, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microbiology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here we use Resource Availability (RA) as model parameter altering resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability.
Published: 2022
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6. Polymyxin causes cell envelope remodelling and stress responses in mcr-1-harbouring Escherichia coli

Author: Sue C. Nang, Mengyao Li, Marina Harper, Eric Mandela, Phillip J. Bergen, Jean-Marc Rolain, Yan Zhu, Tony Velkov, Jian Li, Faculty of Medicine, Nursing and Health Sciences - Monash university [Victoria], Monash university, Jinan University [Guangzhou], Faculty of Pharmacy and Pharmaceutical Sciences - Monash University [Parkville], Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Nanjing Agricultural University (NAU), Faculty of Medicine, Dentistry and Health Sciences [Melbourne], and University of Melbourne
Subjects: Microbiology (medical), [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Colistin, Escherichia coli Proteins, Membrane Proteins, General Medicine, Microbial Sensitivity Tests, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Bacterial, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Escherichia coli, Pharmacology (medical), [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Polymyxins, ComputingMilieux_MISCELLANEOUS, Plasmids
Abstract: Polymyxins remain important last-line antibiotics against multidrug-resistant Gram-negative bacteria. Unfortunately, polymyxin resistance is emerging and the mobile polymyxin resistance gene, mcr, is contributing to the wide dissemination of polymyxin resistance, especially among Escherichia coli, with mcr-1 being the most commonly found variant. The objective of this study was to provide mechanistic insights into concentration-dependent transcriptomic responses of mcr-harbouring E. coli following polymyxin treatment. An mcr-1-carrying clinical isolate of E. coli (LH30) was treated with polymyxin B at 2 and 8 mg/L. Bacterial cultures were collected before and 1 h following treatment for viable counting and transcriptomic analysis. Growth of E. coli LH30 was unaffected by 2 mg/L polymyxin B, whereas killing of approximately 2 log
Published: 2022
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7. Stable Isotope Fractionation of Metals and Metalloids in Plants: A Review

Author: 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)
Subjects: 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
Published: 2022
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8. Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants

Author: Marine Biget, Tingting Wang, Cendrine Mony, Qicheng Xu, Lucie Lecoq, Véronique Chable, Kevin R. Theis, Ning Ling, Philippe Vandenkoornhuyse, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Nanjing Agricultural University (NAU), Domaine expérimental de la Motte au Vicomte (MOTTE AU VICOMTE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-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), Wayne State University School of Medicine, and Watermelon-Bottlegourd-This work was supported by a grant from the National Nature Science Foundation of China (31772398). We deeply acknowledge Dr. Dongsheng Wang from Nanjing Institution of Vegetable Science (China) for chimeric watermelon production. Grapevine- This work was supported by a grant from the CNRS-EC2CO program (HOLOBIONT project), CNRS-IRP program (M-AGRI project) and by the \'Agence Nationale de la Recherche et de la Technologie' (ANRT) through an industrial CIFRE agreement between Château Palmer, Château Latour, Sovivins, Pépinière deSalettes and the University of Rennes 1 (Agreement N° 2017/1579).
Subjects: Multidisciplinary, Bioinformatics, Interaction of plants with organisms, Microbiome, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.
Published: 2023
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9. The influence of shearable and nonshearable precipitates on the Portevin-Le Chatelier behavior in precipitation hardening AlMgScZr alloys

Author: Zhe Chen, Haowei Wang, Han Chen, Shengyi Zhong, Gang Ji, András Borbély, Yves Bréchet, Yubin Ke, Nanjing Agricultural University, University of California [Santa Barbara] (UCSB), University of California, Unité Matériaux et Transformations - UMR 8207 (UMET), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centrale Lille Institut (CLIL), Shanghai Jiao Tong University [Shanghai], Laboratoire Georges Friedel (LGF-ENSMSE), École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Dongguan University of Technology, Science et Ingénierie des Matériaux et Procédés (SIMaP), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Nanjing Agricultural University (NAU), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), and Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 010302 applied physics, Shearing (physics), Materials science, Strain (chemistry), Aluminium alloy, Mechanical Engineering, Dislocations, 02 engineering and technology, Strain rate, 021001 nanoscience & nanotechnology, 01 natural sciences, Precipitates, Serration, [SPI]Engineering Sciences [physics], Precipitation hardening, Mechanics of Materials, Motion Mode, 0103 physical sciences, General Materials Science, Portevin-Le Chatelier effect, Dislocation, Composite material, Strengthening mechanism, 0210 nano-technology, Strengthening mechanisms of materials
Abstract: The well-known mechanisms of interaction between precipitates and dislocations are shearing (for shearable precipitates) and bypassing mechanisms (for nonshearable precipitates). The transition from shearable to nonshearable precipitates in precipitation hardening alloys leads to changes of dislocation motion mode and dislocation multiplication behavior, which inevitably causes different PLC behaviors. In this study, we systematically investigate the influence of shearable and nonshearable Al3(Sc, Zr) precipitates on PLC behaviors by experimental characterization for precipitation hardening AlMgScZr alloys. We analyze the onset strain, critical strain-rate range, serration amplitude, and propagation behavior of PLC bands in detail for AlMgScZr alloys with shearable and nonshearable precipitates, respectively. We find that the transition from shearable to nonshearable precipitates changes the PLC band propagation behavior, decreases the magnitude of serration amplitude, expands the strain-rate range as well as decreases the critical strain rate between normal behavior (the critical strain increases with the increase of strain rate) and inverse behavior (the critical strain decreases with the increase of strain rate) regimes due to the different dislocation-precipitate interactions. Besides, the transition from shearable to nonshearable precipitates increases the onset strain at normal behavior while decreases the onset strain at inverse behavior depending on the different roles of precipitates in the solute-dislocation interaction. Finally, we reveal the nature of influence of different dislocation-precipitate interactions on PLC behavior considering different strengthening mechanisms based on quantitative characterization on precipitates and dislocation density.
Published: 2021
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10. Microbial generalists and specialists differently contribute to the community diversity in farmland soils

Author: Qicheng Xu, Philippe Vandenkoornhuyse, Ling Li, Junjie Guo, Chen Zhu, Shiwei Guo, Ning Ling, Qirong Shen, Nanjing Agricultural University (NAU), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA28030302), the National Natural Science Foundation of China (41977080, 31902114), the Natural Science Foundation of Jiangsu Province (BK20190543), the China Postdoctoral Science Foundation (2019M651861), the Young Elite Scientists Sponsorship Program by CAST (2019QNRC001), and a grant from the CNRS (EC2CO).
Subjects: Soil, Multidisciplinary, Farms, Community diversity, Niche breadth, Bacteria, Community assembly, Biogeographical pattern, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Species interaction, Ecosystem, Soil Microbiology
Abstract: International audience; INTRODUCTION: Microbial generalists and specialists are thought to have distinct impacts on community dynamics, while there have been limited efforts to estimate their contribution to microbial diversity. OBJECTIVES: We aimed to resolve this research gap in microbial ecology to strengthen our understanding of the biogeography of microbial diversity, with implications for global-scale biodiversity mapping. METHODS: Herein, we identified the ecological characteristics of microbial generalists and specialists across over 3,000 farmland soil samples from eleven countries that encompassed seven climate types. RESULTS: Considering the distinct distributions of generalists and specialists in degree of connexions, betweenness and as key species in network topology, both generalists and specialists contributed to species interactions, though through different modalities. A stronger signature of deterministic processes in specialists indicated their lower tolerance to environment fluctuations. Generalists, in contrast, were more characterized by stochastic processes with higher diversification and transition rates that suggested more important roles in maintaining community stability when exposed to environmental disturbances. The relationship between latitude and diversity combining with distance-decay effects showed that generalists dampened microbial biogeographical patterns, with contrasting impacts by specialists. CONCLUSION: By demonstrating the ecological characteristics of microbial generalists and specialists, this study deepens our understanding of microbial diversity and highlights the need to impart systematic distinctions among different categories of species when modelling and predicting the fate of ecosystems in the face of global climate change, rather than assuming that species are functionally equivalent.
Published: 2021
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11. pr2-primers: an 18S rRNA primer database for protists

Author: David Bass, Frédéric Mahé, Daniel Vaulot, Stefan Geisen, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Nanyang Technological University [Singapour], Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Wageningen University and Research [Wageningen] (WUR), Nanjing Agricultural University, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Nanjing Agricultural University (NAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), and Terrestrial Ecology (TE)
Subjects: 0106 biological sciences, In silico, Biology, computer.software_genre, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, 18S ribosomal RNA, 03 medical and health sciences, metabrcoding, Genetics, RNA, Ribosomal, 18S, medicine, primers, Laboratorium voor Nematologie, Ecology, Evolution, Behavior and Systematics, database, 030304 developmental biology, protists, 0303 health sciences, Database, shiny, Eukaryota, Protist, Plan_S-Compliant_NO, PE&RC, Amplicon Size, 18S rRNA, PCR, international, metabarcoding, [SDE]Environmental Sciences, Primer (molecular biology), Laboratory of Nematology, computer, Biotechnology
Abstract: Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost uniquely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, a wise primer choice is needed as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few on-line resources available to list existing primers. We built a database listing 179 primers and 76 primer pairs that have been used for eukaryotic 18S rRNA metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 for eukaryotes and a subset of Silva for prokaryotes. This allowed to determine the taxonomic specificity of primer pairs, the location of mismatches as well as amplicon size. We developed a R-based web application that allows to browse the database, visualize the taxonomic distribution of the amplified sequences with the number of mismatches, and to test any user-defined primer set (https://app.pr2-primers.org). This tool will provide the basis for guided primer choices that will help a wide range of ecologists to implement protists as part of their investigations.
Published: 2021
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12. Importance of the description of light interception in crop growth models

Author: Liu, Shouyang, Baret, Frédéric, Abichou, Mariem, Manceau, Loïc, Andrieu, Bruno, Weiss, Marie, Martre, Pierre, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nanjing Agricultural University, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), European Project: 727247,H2020,H2020-SFS-2016-2,SolACE(2017), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), and Nanjing Agricultural University (NAU)
Subjects: Crops, Agricultural, Plant Leaves, Light, [SDE]Environmental Sciences, Models, Theoretical, Edible Grain, Research Articles, Triticum, SolACEWP2
Abstract: Canopy light interception determines the amount of energy captured by a crop, and is thus critical to modeling crop growth and yield, and may substantially contribute to the prediction uncertainty of crop growth models (CGMs). We thus analyzed the canopy light interception models of the 26 wheat (Triticum aestivum) CGMs used by the Agricultural Model Intercomparison and Improvement Project (AgMIP). Twenty-one CGMs assume that the light extinction coefficient (K) is constant, varying from 0.37 to 0.80 depending on the model. The other models take into account the illumination conditions and assume either that all green surfaces in the canopy have the same inclination angle ([Formula: see text]) or that [Formula: see text] distribution follows a spherical distribution. These assumptions have not yet been evaluated due to a lack of experimental data. Therefore, we conducted a field experiment with five cultivars with contrasting leaf stature sown at normal and double row spacing, and analyzed [Formula: see text] distribution in the canopies from three-dimensional canopy reconstructions. In all the canopies, [Formula: see text] distribution was well represented by an ellipsoidal distribution. We thus carried out an intercomparison between the light interception models of the AgMIP–Wheat CGMs ensemble and a physically based K model with ellipsoidal leaf angle distribution and canopy clumping ([Formula: see text]). Results showed that the [Formula: see text] model outperformed current approaches under most illumination conditions and that the uncertainty in simulated wheat growth and final grain yield due to light models could be as high as 45%. Therefore, our results call for an overhaul of light interception models in CGMs.
Published: 2021
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13. Seed-borne, endospheric and rhizospheric core microbiota as predictor for plant functional traits across rice cultivars are dominated by deterministic processes

Author: Junjie Guo, Qirong Shen, Kaisong Li, Shiwei Guo, Huiling Ning, Philippe Vandenkoornhuyse, Yong Li, Ning Ling, Nanjing Agricultural University, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Huazhong Agricultural University, KYT201802, Fundamental Research Funds for the Central Universities, 31902114, National Natural Science Foundation of China, 2019M651861, China Postdoctoral Science Foundation, BK20190543, Natural Science Foundation of Jiangsu Province, Nanjing Agricultural University (NAU), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Huazhong Agricultural University [Wuhan] (HZAU)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Seed habitat, Plant Science, Subspecies, Biology, Generalist and specialist species, Plant Roots, 01 natural sciences, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cultivar, Relative species abundance, Soil Microbiology, 2. Zero hunger, Rhizosphere, Bacteria, Plant-microbiota association, Ecology, Community assembly, Microbiota, fungi, food and beverages, Oryza, 15. Life on land, 030104 developmental biology, Microbial population biology, Seeds, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Root endosphere, 010606 plant biology & botany
Abstract: International audience; A host-plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host-associated microbiota are poorly understood. Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associate with plant phenotypic properties. Plant microhabitat, rather than subspecies type, was the major driver shaping plant-associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root-associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host-plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms. Overall, bacterial microbiota is assembled by host-plant interactions in deterministic-based manner. This study enhances our understanding of driving mechanism and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance.
Published: 2021
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14. Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants

Author: Liam Dolan, Benoît Menand, Houqing Zeng, Hongyu Zhao, Long Wang, Lei Xu, Xianqing Jia, Keke Yi, Yuxin Zhang, Yiyong Zhu, Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences (CAAS), Nanjing Agricultural University (NAU), Luminy Génétique et Biophysique des Plantes (LGBP), 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), College of Life and Environmental Sciences, Hangzhou Normal University, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China, European Project: 787613,DENOVO-P, Nanjing Agricultural University, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, SPX-VTC, [SDV]Life Sciences [q-bio], SPX-SLC, plant evolution, chemistry.chemical_element, Chlamydomonas reinhardtii, Plant Science, Vacuole, Viridiplantae, 01 natural sciences, 03 medical and health sciences, Polyphosphates, Homeostasis, Molecular Biology, Phylogeny, Plant Proteins, biology, Permease, Phosphorus, Chlamydomonas, polyphosphate, biology.organism_classification, Solute carrier family, vacuolar phosphate, 030104 developmental biology, Biochemistry, chemistry, Chaperone (protein), Vacuoles, biology.protein, 010606 plant biology & botany, Molecular Chaperones
Abstract: International audience; Phosphorus is an essential nutrient for plants. It is stored as inorganic phosphate (Pi) in the vacuoles of land plants but as inorganic polyphosphate (polyP) in chlorophyte algae. Although it is recognized that the SPXMajor Facilitator Superfamily (MFS) and VPE proteins are responsible for Pi influx and efflux, respectively, across the tonoplast in land plants, the mechanisms that underlie polyP homeostasis and the transition of phosphorus storage forms during the evolution of green plants remain unclear. In this study, we showed that CrPTC1, encoding a protein with both SPX and SLC (permease solute carrier 13) domains for Pi transport, and CrVTC4, encoding a protein with both SPX and vacuolar transporter chaperone (VTC) domains for polyP synthesis, are required for vacuolar polyP accumulation in the chlorophyte Chlamydomonas reinhardtii. Phylogenetic analysis showed that the SPX-SLC, SPX-VTC, and SPX-MFS proteins were present in the common ancestor of green plants (Viridiplantae). The SPX-SLC and SPX-VTC proteins are conserved among species that store phosphorus as vacuolar polyP and absent from genomes of plants that store phosphorus as vacuolar Pi. By contrast, SPX-MFS genes are present in the genomes of streptophytes that store phosphorus as Pi in the vacuoles. These results suggest that loss of SPX-SLC and SPX-VTC genes and functional conservation of SPX-MFS proteins during the evolution of streptophytes accompanied the change from ancestral polyP storage to Pi storage.
Published: 2020
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15. Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes

Author: Shiwei Guo, Jianyun Ruan, Qicheng Xu, Ning Ling, Junjie Guo, Qirong Shen, Achim Quaiser, Philippe Vandenkoornhuyse, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Nanjing Agricultural University, Chinese Academy of Tropical Agricultural Sciences (CATAS), This work was supported by the National Key Research and Development Program of China (2016YFD0200900)., Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Nanjing Agricultural University (NAU)
Subjects: 0301 basic medicine, Assembly rules, Rare biosphere, China, Tea garden soils, 030106 microbiology, Rare species, Soil Science, Biology, 03 medical and health sciences, Soil, Microbial ecology, Soil functions, Soil pH, Bacterial assembly, Null model framework, Ecology, Evolution, Behavior and Systematics, Soil Microbiology, 2. Zero hunger, Ecology, Bacteria, Null model, 15. Life on land, Stochastic process, 030104 developmental biology, Biological dispersal, Deterministic process, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.
Published: 2020
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16. Long-Term Chemical-Only Fertilization Induces a Diversity Decline and Deep Selection on the Soil Bacteria

Author: Qicheng Xu, Shuangqing Wang, How-Huan Chen, Philippe Vandenkoornhuyse, Ning Ling, Qirong Shen, Yinghua Duan, Nanjing Agricultural University (NAU), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Anhui Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences (CAAS), EC2CO-Microland Project, Centre National de la Recherche Scientifique, 41977080, National Natural Science Foundation of China, Nanjing Agricultural University, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0301 basic medicine, Assembly rules, Physiology, specialist, 030106 microbiology, lcsh:QR1-502, Ecological succession, Biology, Biochemistry, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Human fertilization, Soil retrogression and degradation, Genetics, Ecosystem, generalist, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, business.industry, Ecology, Applied and Environmental Science, deterministic processes, 15. Life on land, QR1-502, Computer Science Applications, 030104 developmental biology, 13. Climate action, Agriculture, fertilization, Modeling and Simulation, Soil water, stochastic processes, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Research Article
Abstract: Chemical-only fertilization is ubiquitous in contemporary conventional agriculture despite the fact that sustainability of this agricultural practice is increasingly being questioned because of the current observed soil degradation. We explored how long-term chemical-only versus organic-only fertilizations impacted the soil microbiota reservoir in terms of both diversity and induced assembly processes. The results showed that long-term chemical-only fertilization resulted in deep selection pressure on the soil microbial community reservoir, with both a higher proportion of specialists and a stronger signature of deterministic processes. The soil microbiota has clearly changed as a consequence of the fertilization regime. The diagnoses of the functional consequences of these ecoevolutionary changes in relation to agricultural practices are key to imagining agriculture in the time ahead and especially regarding future efforts for the conservation, restoration, and management of the soil microbiota reservoir which is key to the fertility of the ecosystem., Fertilization regimes are known to drive succession of the soil microbial community, whereas the assembly rules involved remain elusive. Moreover, the ecological roles of microbial “generalists” and “specialists” in soils with contrasting fertilization regimes have not been characterized. We explored how long-term fertilization regimes (i.e., treatments conducted for at least 30 years) impact the soil bacteria by modifying species richness, diversity, bacterial assembly, and niche breadth. Compared with long-term organic fertilizer input, the soils having undergone chemical-only fertilization contained smaller amounts of carbon resources and had a more acidic environment. This strong environmental constraint lowered the soil bacterial reservoir and resulted in a detectable ecoevolutionary transformation, with both a higher proportion of specialists and a stronger signature of deterministic processes. Overall, this study provided a new comprehensive understanding of the assembly rules of bacterial generalists and specialists under long-term fertilization regimes. This study also highlighted that chemical-only fertilization, a ubiquitous agricultural practice of current conventional agriculture, induced a strong and similar environmental force that transformed the soil microbiota from 28°N to 46°N included in this study. IMPORTANCE Chemical-only fertilization is ubiquitous in contemporary conventional agriculture despite the fact that sustainability of this agricultural practice is increasingly being questioned because of the current observed soil degradation. We explored how long-term chemical-only versus organic-only fertilizations impacted the soil microbiota reservoir in terms of both diversity and induced assembly processes. The results showed that long-term chemical-only fertilization resulted in deep selection pressure on the soil microbial community reservoir, with both a higher proportion of specialists and a stronger signature of deterministic processes. The soil microbiota has clearly changed as a consequence of the fertilization regime. The diagnoses of the functional consequences of these ecoevolutionary changes in relation to agricultural practices are key to imagining agriculture in the time ahead and especially regarding future efforts for the conservation, restoration, and management of the soil microbiota reservoir which is key to the fertility of the ecosystem.
Published: 2020
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17. Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development

Author: Jie Hu, Yangchun Xu, Alexandre Jousset, George A. Kowalchuk, Qirong Shen, Zhong Wei, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Jiangsu Provincial Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University (NAU), Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University [Utrecht], ALW.870.15.050, Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Ecology and Biodiversity, and Sub Ecology and Biodiversity
Subjects: Climax, Plant Development, Biology, Plant Roots, Microbiology, Life history theory, 03 medical and health sciences, Solanum lycopersicum, Microbiome, ComputingMilieux_MISCELLANEOUS, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Rhizosphere, Bacteria, Resistance (ecology), 030306 microbiology, Ecology, Microbiota, 15. Life on land, Trait, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Climax community, Soil microbiology
Abstract: The rhizosphere microbiome is essential for plant growth and health, and numerous studies have attempted to link microbiome functionality to species and trait composition. However, to date little is known about the actual ecological processes shaping community composition, complicating attempts to steer microbiome functionality. Here, we assess the development of microbial life history and community‐level species interaction patterns that emerge during plant development. We use microbial phenotyping to experimentally test the development of niche complementarity and life history traits linked to microbiome performance. We show that the rhizosphere microbiome assembles from pioneer assemblages of species with random resource overlap into high‐density, functionally complementary climax communities at later stages. During plant growth, fast‐growing species were further replaced by antagonistic and stress‐tolerant ones. Using synthetic consortia isolated from different plant growth stages, we demonstrate that the high functional diversity of ‘climax’ microbiomes leads to a better resistance to bacterial pathogen invasion. By demonstrating that different life‐history strategies prevail at different plant growth stages and that community‐level processes may supersede the importance of single species, we provide a new toolbox to understand microbiome assembly and steer its functionality at a community level.
Published: 2020
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18. Glutathione‐dependent denitrosation of GSNOR1 promotes oxidative signalling downstream of H 2 O 2

Author: Bo Wei, Lingling Fan, Wei Xuan, Mingyue Ma, Wei Zhang, Shengchun Li, Tao Chen, Tianru Zhang, Graham Noctor, Yi Han, Linlin Zhang, School of Food and Biological Engineering, University of Science and Technology of China [Hefei] (USTC), Engineering Research Center of Bio-process, Ministry of Education, University of Science and Technology of China [Hefei] (USTC)-University of Science and Technology of China [Hefei] (USTC), State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University-Hubei University, State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University (NAU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Nanjing Agricultural University, and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Programmed cell death, Physiology, H2O2, salicylic acid, [SDV]Life Sciences [q-bio], Mutant, Plant Science, Oxidative phosphorylation, Reductase, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Arabidopsis, Gene expression, oxidative stress, glutathione, denitrosation, GSNOR1, biology, Glutathione, biology.organism_classification, Cell biology, 030104 developmental biology, chemistry, Intracellular, 010606 plant biology & botany
Abstract: Photorespiratory hydrogen peroxide (H2 O2 ) plays key roles in pathogenesis responses by triggering the salicylic acid (SA) pathway in Arabidopsis. However, factors linking intracellular H2 O2 to activation of the SA pathway remain elusive. In this work, the catalase-deficient Arabidopsis mutant, cat2, was exploited to elucidate the impact of S-nitrosoglutathione reductase 1 (GSNOR1) on H2 O2 -dependent signalling pathways. Introducing the gsnor1-3 mutation into the cat2 background increased S-nitrosothiol levels and abolished cat2-triggered cell death, SA accumulation, and associated gene expression but had little additional effect on the major components of the ascorbate-glutathione system or glycolate oxidase activities. Differential transcriptome profiles between gsnor1-3 and cat2 gsnor1-3 together with damped ROS-triggered gene expression in cat2 gsnor1-3 further indicated that GSNOR1 acts to mediate the SA pathway downstream of H2 O2 . Up-regulation of GSNOR activity was compromised in cat2 cad2 and cat2 pad2 mutants in which glutathione accumulation was genetically prevented. Experiments with purified recombinant GSNOR revealed that the enzyme is posttranslationally regulated by direct denitrosation in a glutathione-dependent manner. Together, our findings identify GSNOR1-controlled nitrosation as a key factor in activation of the SA pathway by H2 O2 and reveal that glutathione is required to maintain this biological function.
Published: 2020
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19. Belowground impacts of alpine woody encroachment are determined by plant traits, local climate, and soil conditions

Author: Hui Guo, Concepción L. Alados, Nuttapon Pombubpa, Chatrina Caviezel, Marko J. Spasojevic, Jana Müllerová, Oriol Grau, Nikolas J. Kuhn, Jason E. Stajich, Gaku Kudo, Nicoletta Cannone, Hannah Shulman, Courtney G. Collins, Frédérique Reverchon, Juan C. Benavides, Michala L. Phillips, Sören E. Weber, Alexia Stokes, Jeffrey M. Diez, Emma L. Aronson, Institute of Arctic Alpine Research [University of Colorado Boulder] (INSTAAR), University of Colorado [Boulder], University of California [Riverside] (UC Riverside), University of California (UC), Instituto Pirenaico de Ecologìa = Pyrenean Institute of Ecology [Zaragoza] (IPE - CSIC), Pontificia Universidad Javeriana (PUJ), Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), University of Basel (Unibas), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nanjing Agricultural University (NAU), Hokkaido University [Sapporo, Japan], Instituto de Ecologia (INECOL), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-16-CE03-0009,ECOPICS,Services écosystémiques souterrains produits par les communautés végétales le long de gradients altitudinaux en France et au Mexique(2016), Institute of Arctic and Alpine Research (INSTAAR), University of California [Riverside] (UCR), University of California, Instituto Pirenaico de Ecología-CSIC (IPE-CSIC), Universitá degli Studi dell’Insubria, Nanjing Agricultural University, University of Zurich, and Collins, Courtney G
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Nitrogen, Climate, 2306 Global and Planetary Change, Soil microbes, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, 2300 General Environmental Science, 10127 Institute of Evolutionary Biology and Environmental Studies, Soil, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Soil pH, Environmental Chemistry, Land use, land-use change and forestry, Plant–soil interactions, Woody encroachment, Global change, Ecosystem, 0105 earth and related environmental sciences, General Environmental Science, 2. Zero hunger, Abiotic component, Global and Planetary Change, Ecology, 15. Life on land, Herbaceous plant, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Alpine, Arid, 13. Climate action, 2304 Environmental Chemistry, Soil water, Leaf traits, Environmental science, 570 Life sciences, biology, 590 Animals (Zoology), alpine, global change, leaf traits, plant–soil interactions, soil microbes, woody encroachment, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 2303 Ecology, Woody plant
Abstract: International audience; Global climate and land use change are causing woody plant encroachment in arctic, alpine, and arid/semi-arid ecosystems around the world, yet our understanding of the belowground impacts of this phenomenon is limited. We conducted a globally distributed field study of 13 alpine sites across four continents undergoing woody plant encroachment and sampled soils from both woody encroached and nearby herbaceous plant community types. We found that woody plant encroachment influenced soil microbial richness and community composition across sites based on multiple factors including woody plant traits, site level climate, and abiotic soil conditions. In particular, root symbiont type was a key determinant of belowground effects, as Nitrogen-fixing woody plants had higher soil fungal richness, while Ecto/Ericoid mycorrhizal species had higher soil bacterial richness and symbiont types had distinct soil microbial community composition. Woody plant leaf traits indirectly influenced soil microbes through their impact on soil abiotic conditions, primarily soil pH and C:N ratios. Finally, site-level climate affected the overall magnitude and direction of woody plant influence, as soil fungal and bacterial richness were either higher or lower in woody encroached versus herbaceous soils depending on mean annual temperature and precipitation. All together, these results document global impacts of woody plant encroachment on soil microbial communities, but highlight that multiple biotic and abiotic pathways must be considered to scale up globally from site- and species-level patterns. Considering both the aboveground and belowground effects of woody encroachment will be critical to predict future changes in alpine ecosystem structure and function and subsequent feedbacks to the global climate system. © 2020 John Wiley & Sons Ltd
Published: 2020
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20. Rejoinder to Comments on Minasny et al., 2017 Soil carbon 4 per mille Geoderma 292, 59–86

Author: Manuel Martin, Inakwu O. A. Odeh, Vera Leatitia Mulder, Brendan P. Malone, Carolyn Hedley, Vladimir Stolbovoy, Vincent Chaplot, Anne C. Richer-de-Forges, Bhabani S. Das, Yiyi Sulaeman, Chun Chih Tsui, Igor Savin, Bas van Wesemael, Ben P. Marchant, Suk Young Hong, Tor-Gunnar Vågen, Dominique Arrouays, Alex B. McBratney, Sharon M. O’Rourke, Genxing Pan, Damien J. Field, Alessandro Gimona, Biswapati Mandal, José Padarian, Laura Poggio, Budiman Minasny, Adam Chambers, Kun Cheng, Denis A. Angers, Keith Paustian, Leigh A. Winowiecki, B. G. McConkey, Zueng-Sang Chen, Uta Stockmann, The University of Sydney, InfoSol (InfoSol), Institut National de la Recherche Agronomique (INRA), Agriculture and Agri-Food [Ottawa] (AAFC), USDA Agricultural Research Service [Maricopa, AZ] (USDA), United States Department of Agriculture (USDA), Biogéochimie-Traceurs-Paléoclimat (BTP), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Xi'an Jiaotong University (Xjtu), Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, The James Hutton Institute, Manaaki Whenua – Landcare Research [Lincoln], Bidhan Chandra Krishi Viswavidyalaya, British Geological Survey (BGS), University of Sydney, Dep. of Environmental Sciences, Department of Soil and Crop Sciences, Natural Resource Ecology Laboratory, Colorado State University [Fort Collins] (CSU), People's Friendship University of Russia [Moscow], Indonesian Agency for Agricultural Research and Development Ministry of Agriculture, World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Département de Géographie (UCL GEO), Université Catholique de Louvain = Catholic University of Louvain (UCL), Unité INFOSOL (ORLEANS INFOSOL), United States Department of Agriculture - USDA (USA), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Landcare Research [Lincoln], World Agroforestry Centre (ICRAF), Université Catholique de Louvain (UCL), Agriculture and Agri-Food (AAFC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Nanjing Agricultural University (NAU), Indonesian Agency for Agricultural Research and Development (IAARD), and UCL - SST/ELI/ELIC - Earth & Climate
Subjects: 010504 meteorology & atmospheric sciences, organic-carbon, Soil Science, Climate change, chemistry.chemical_element, challenges, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], 01 natural sciences, 7. Clean energy, nitrogen, 12. Responsible consumption, mitigation, 11. Sustainability, Life Science, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, 2. Zero hunger, Total organic carbon, Food security, sequestration, food security, dynamics, 04 agricultural and veterinary sciences, Soil carbon, 15. Life on land, PE&RC, Nitrogen, losses, Tillage, Bodemgeografie en Landschap, Agronomy, chemistry, 13. Climate action, climate-change, tillage, 040103 agronomy & agriculture, Soil Geography and Landscape, 0401 agriculture, forestry, and fisheries, Environmental science, Per mille
Abstract: We thank the authors for their thought-provoking comments on our paper. Most of the commentators agree that soil organic carbon (SOC) sequestration is important for improving the quality of soil, however they argue that we have overstated the potential of soil carbon sequestration. We welcome the comments and appreciate that the issue of SOC sequestration has always been somewhat factious (Schlesinger, 2000). We shall address the significance of the quantity “4 per mille”, reported sequestration rates, the limitation of carbon sequestration with time, and nutrient requirements. We clarify that our paper (Minasny et al., 2017) mainly deals with potentials for the 20 countries and regions, where SOC sequestration can also be seen as a way to improving the resilience of the soil to future climate change, that is, improving adaptation rather than mitigation. We believe that in some parts of the world where food security is threatened, the benefit of soil carbon management for adaptation should be stressed more than for mitigation. This is the reason why the 4 per mille initiative explicitly includes food security (Chabbi et al., 2017; Soussana et al., 2015). We need to add that the “4 per mille Soils for Food Security and Climate” initiative is just one of many national and global initiatives on SOC sequestration for mitigating climate change. The Intergovernmental Technical Panel on Soils (ITPS) of the Global Soil Partnership (GSP) discussed incorporating the topic of SOC in the IPCC Assessment Report (ARs), from AR6 onwards. The IPCC has also put a focus on soil in their upcoming special report “Climate Change and Land” (http://www.ipcc.ch/report/sr2/). The recent FAO Global Symposium (GSOC17) assembled experts engaged in FAO, GSP and its ITPS, IPCC, UNCCD-SPI and WMO activities to work together for the common goal of appropriate SOC management as part of overall sustainable soil management within the climate change mitigation and adaptation, sustainable development, Land Degradation Neutrality (LDN) and food security agendas (http://www.fao.org/about/meetings/soil-organic-carbon-symposium/en/). The Global Research Alliance on Agricultural Greenhouse Gases (GRA) focused on opportunities to reduce agricultural greenhouse gas emissions and increase soil carbon sequestration while still helping to meet food security objectives (http://globalresearchalliance.org/about/). The Common Agriculture Policy in the EU is currently being revised to include the potential use of SOC as an indicator. The 4 per mille initiative was launched at COP21, where the Paris Agreement was adopted, and one of the main aims of the Paris Agreement is to stop the planet from warming an additional two Celsius degrees. The two-degree target, although suggested by scientists through modelling work, was chosen more for political and pragmatic reasons whereby countries could agree on a target that they could work towards (Tollefson, 2015). And of course, there are many scientific critiques of this target (Knutti et al., 2016). Similarly, the 4 per mille initiative comes from a politically-driven aspiration, and our paper (Minasny et al., 2017) is a response to such an aspiration, to seek and outline possibilities based on current knowledge. The important concept is that soil and agriculture are part of the solution, and it is an interim and evidence-based solution that we can implement. Now we shall respond to each of the commentaries.
Published: 2018
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21. Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes

Author: Lisheng Liu, Min Wang, Ling Li, Junjie Guo, Zhaojie Chen, Shiwei Guo, Chao Xue, Qirong Shen, Ning Ling, Jianyun Ruan, Limin Gao, Philippe Vandenkoornhuyse, Nanjing Agricultural University, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Chinese Academy of Agricultural Sciences (CAAS), Tea Research Institute, National Key Research and Development Program of China. Grant Number: 2016YFD0200900, Innovative Research Team Development Plan of the Ministry of Education of China. Grant Number: IRT_17R56, Fundamental Research Funds for the Central Universities. Grant Number: KYT201802, Nanjing Agricultural University (NAU), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, China, Soil test, Physiology, media_common.quotation_subject, Niche, Distribution (economics), Fertility, Plant Science, Biology, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Soil fertility, 01 natural sciences, 03 medical and health sciences, Soil, Ecological processes, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ecosystem, Fungal functional guilds, Fungal ecology, Relative species abundance, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Soil Microbiology, media_common, Ecology, business.industry, Community assembly, Fungi, 15. Life on land, 030104 developmental biology, Soil water, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany
Abstract: International audience; In the processes controlling ecosystem fertility, fungi are increasingly acknowledged as key drivers. However, our understanding of the rules behind fungal community assembly regarding the effect of soil fertility level remains limited. Using soil samples from typical tea plantations spanning c. 2167 km north-east to south-west across China, we investigated the assemblage complexity and assembly processes of 140 fungal communities along a soil fertility gradient. The community dissimilarities of total fungi and fungal functional guilds increased with increasing soil fertility index dissimilarity. The symbiotrophs were more sensitive to variations in soil fertility compared with pathotrophs and saprotrophs. Fungal networks were larger and showed higher connectivity as well as greater potential for inter-module connection in more fertile soils. Environmental factors had a slightly greater influence on fungal community composition than spatial factors. Species abundance fitted the Zipf-Mandelbrot distribution (niche-based mechanisms), which provided evidence for deterministic-based processes. Overall, the soil fungal communities in tea plantations responded in a deterministic manner to soil fertility, with high fertility correlated with complex fungal community assemblages. This study provides new insights that might contribute to predictions of fungal community complexity.
Published: 2019
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22. Soil carbon mineralization in response to nitrogen enrichment in surface and subsurface layers in two land use types

Author: Nazia Perveen, Ming Xu, Muhammad Rashid Siddiq, Muhammad Sohail Memon, Mariam Ayub, Hamid Saeed, Sébastien Barot, Tanvir Shahzad, Henan University, Forman Christian College, Government College University of Faisalabad (GCUF), Technishe Universität Bergakademie Freiberg (TU Bergakademie Freiberg), Nanjing Agricultural University (NAU), Sindh Agriculture University, 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), Higher Education Commission of Pakistan21-613/SRGP/RD/HEC/2015, National Key Research and Development Program of China 2017YFA06043002018YFA0606500, Henan University, Kaifeng, Nanjing Agricultural University, 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), Institute of Soil Science, University of Faisalabad, Institut d'écologie et des sciences de l'environnement de Paris (IEES), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Conditions Extrêmes et Matériaux : Haute Température et Irradiation (CEMHTI), and Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Environmental Impacts, 010504 meteorology & atmospheric sciences, chemistry.chemical_element, Soil Science, lcsh:Medicine, 01 natural sciences, Microbiology, complex mixtures, General Biochemistry, Genetics and Molecular Biology, Environmental Impacts Keywords Soil c mineralization, Subjects Agricultural Science, Environmental Impacts Soil c mineralization, C sequestration, Water holding capacity, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Agricultural Science, 0105 earth and related environmental sciences, 2. Zero hunger, General Neuroscience, lcsh:R, Lawn, 04 agricultural and veterinary sciences, General Medicine, Soil carbon, 15. Life on land, Nitrogen, Biomass carbon, Subsurface soil C, chemistry, Environmental chemistry, [SDE]Environmental Sciences, Soil water, Land use types, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Soil horizon, Nitrogen enrichment, General Agricultural and Biological Sciences, Soil c mineralization
Abstract: Atmospheric nitrogen (N) deposition increases N availability in soils, with consequences affecting the decomposition of soil carbon (C). The impacts of increasing N availability on surface soil C dynamics are well studied. However, subsurface soils have been paid less attention although more than 50% soil C stock is present below this depth (below 20 cm). This study was designed to investigate the response of surface (0–20 cm) and subsurface (20–40 cm and 40–60 cm) C dynamics to 0 (0 kg N ha−1), low (70 kg N ha−1) and high (120 kg N ha−1) levels of N enrichment. The soils were sampled from a cropland and a grass lawn and incubated at 25 °C and 60% water holding capacity for 45 days. Results showed that N enrichment significantly decreased soil C mineralization (Rs) in all the three soil layers in the two studied sites (p
Published: 2019
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23. An efficient three-level heuristic for the large-scaled multi-product production routing problem with outsourcing

Author: Chengbin Chu, Yantong Li, Zhanguo Zhu, Feng Chu, Informatique, BioInformatique, Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), School of Economics and Management, Fuzhou University, Tongji University, ESIEE Paris, College of Economics and Management, Nanjing Agricultural University, and Nanjing Agricultural University (NAU)
Subjects: Mathematical optimization, Information Systems and Management, General Computer Science, Linear programming, Computer science, Heuristic (computer science), Iterative method, 0211 other engineering and technologies, 02 engineering and technology, Management Science and Operations Research, Industrial and Manufacturing Engineering, Outsourcing, 0502 economics and business, Three-level matheuristic, Multi-product, Supply chain management, 050210 logistics & transportation, 021103 operations research, Heuristic, business.industry, 05 social sciences, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Production routing, Modeling and Simulation, Benchmark (computing), Routing (electronic design automation), business, Integer (computer science)
Abstract: International audience; A classic production routing problem (PRP), in which a plant produces and distributes a single product to a set of customers over a finite time horizon, consists of planning simultaneously the production, inventory and routing activities to minimize the total cost. The last few decades have witnessed the increasing efforts made to solve such a complex problem. In this paper, we investigate a generalized PRP by considering multiple products and outsourcing (MPRP-OS). The newly studied problem is first formulated into a mixed integer linear program. Then a three-level mathematical-programming-based heuristic called TLH is developed to solve it. TLH combines a two-phase iterative method, a repairing strategy and a fix-and-optimize procedure to find near-optimal solutions. In addition, it is adaptable to solve the classic PRP. Computational experiments on 225 newly generated MPRP-OS instances with up to 200 customers, 20 vehicles, 6 periods and 12 products show the effectiveness and efficiency of the proposed heuristic. The performance of TLH is further demonstrated by testing 1530 classic PRP benchmark instances with up to 200 customers, 13 vehicles and 20 periods. Experimental results indicate that TLH is able to solve large-sized MPRP-OS instances and generally outperforms the state-of-the-art heuristics for the classic PRP. In addition, TLH provides new best solutions for 364 out of 1530 benchmark instances. Particularly, it finds 88 new best solutions for 90 very large-sized benchmark instances.
Published: 2019
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24. RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation

Author: Lalaouna, David, Baude, Jessica, Wu, Zongfu, Tomasini, Arnaud, Chicher, Johana, Marzi, Stefano, Vandenesch, François, Romby, Pascale, Caldelari, Isabelle, Moreau, Karen, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Nanjing Agricultural University, Plateforme Protéomique Strasbourg Esplanade, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, MATHELIN, Sandra, Nanjing Agricultural University (NAU), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE11-0007,RIBOSTAPH,La traduction et son contrôle chez Staphylococcus aureus: conséquences sur la virulence et la réponse aux stress(2016), and ANR-17-EURE-0023,IMCBio,Integrative Molecular and Cellular Biology(2017)
Subjects: Manganese, Staphylococcus aureus, Superoxide Dismutase, Gene Expression Regulation, Bacterial, Staphylococcal Infections, Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Sciences du Vivant [q-bio]/Génétique, Oxidative Stress, Bacterial Proteins, Starvation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA and RNA-protein complexes, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Homeostasis, Humans, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Oxidation-Reduction
Abstract: International audience; The human opportunistic pathogen Staphylococcus aureus produces numerous small regulatory RNAs (sRNAs) for which functions are still poorly understood. Here, we focused on an atypical and large sRNA called RsaC. Its length varies between different isolates due to the presence of repeated sequences at the 5′ end while its 3′ part is structurally independent and highly conserved. Using MS2-affinity purification coupled with RNA sequencing (MAPS) and quantitative differential proteomics, sodA mRNA was identified as a primary target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. Remarkably, rsaC gene is co-transcribed with the major manganese ABC transporter MntABC and, consequently, RsaC is mainly produced in response to Mn starvation. This 3′UTR-derived sRNA is released from mntABC-RsaC precursor after cleavage by RNase III. The mature and stable form of RsaC inhibits the synthesis of the Mn-containing enzyme SodA synthesis and favors the oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. In addition, other putative targets of RsaC are involved in oxidative stress (ROS and NOS) and metal homeostasis (Fe and Zn). Consequently, RsaC may balance two interconnected defensive responses, i.e. oxidative stress and metal-dependent nutritional immunity.
Published: 2019
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25. Evolution and comparative genomics of the most common Trichoderma species

Author: Sabrina Sarrocco, Eva M. Kubicek, Andrei Stecca Steindorff, Igor V. Grigoriev, Bernard Henrissat, Qirong Shen, Alan Kuo, Alexey G. Kopchinskiy, Feng Cai, Giovanni Vannacci, Eliane Ferreira Noronha, Gelsomina Manganiello, Christian P. Kubicek, Jian Zhang, Komal Chenthamara, Irina S. Druzhinina, Riccardo Baroncelli, Vienna University of Technology, United States Department of Energy, Universidade de Brasília (UnB), Seconda Università degli Studi di Napoli = Second University of Naples, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, King Abdulaziz University, Nanjing Agricultural University (NAU), Universidad de Salamanca, Department of Agriculture, Food and Environment, University of California [Berkeley] (UC Berkeley), University of California (UC), 2017YFD 0200806, Austrian Science Foundation (FWF) 25613-B20 I-1249, CAPES foundation 99999.001745/2014-00, CNPq 482697/2011-3, 141180/2012-9, Office of Science of the U.S. Department of Energy DE-AC02-05CH11231, Seconda Università degli studi di Napoli, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Nanjing Agricultural University, University of California [Berkeley], University of California, Kubicek, C. P., Steindorff, A. S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., Cai, F., Kopchinskiy, A. G., Kubicek, E. M., Kuo, A., Baroncelli, R., Sarrocco, S., Noronha, E. F., Vannacci, G., Shen, Q., Grigoriev, I. V., Druzhinina, I. S., Kubicek C.P., Steindorff A.S., Chenthamara K., Manganiello G., Henrissat B., Zhang J., Cai F., Kopchinskiy A.G., Kubicek E.M., Kuo A., Baroncelli R., Sarrocco S., Noronha E.F., Vannacci G., Shen Q., Grigoriev I.V., and Druzhinina I.S.
Subjects: hypocréales, 0106 biological sciences, enzyme cellulolytique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Gene loss, Medical and Health Sciences, 01 natural sciences, Genome, Orphan, Biopolymers, Clade, Gene gain, Environmental opportunism, 2. Zero hunger, Trichoderma, 0303 health sciences, biology, Ascomycota, Orphans, Hydrolysis, Reproduction, Gene lo, food and beverages, Genomics, Biological Sciences, Ankyrin domains, CAZymes, Core genome, SSCPs, Fungal, CAZyme, Biotechnology, Research Article, Genome evolution, lcsh:QH426-470, Evolution, Bioinformatics, lcsh:Biotechnology, Hypocreales, Genes, Fungal, Biotechnologies, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, lcsh:TP248.13-248.65, Information and Computing Sciences, Genetics, analyse génomique, Gene, 030304 developmental biology, Comparative genomics, Human Genome, Molecular, diversité fongique, biology.organism_classification, Carbon, lcsh:Genetics, Genes, Evolutionary biology, Ankyrin domain, Extracellular Space, 010606 plant biology & botany
Abstract: Background The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. Results We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist. Electronic supplementary material The online version of this article (10.1186/s12864-019-5680-7) contains supplementary material, which is available to authorized users.
Published: 2019
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26. What is cost-efficient phenotyping? Optimizing costs for different scenarios

Author: Mehdi Khafif, François Tardieu, Ji Zhou, Aakash Chawade, Francesco Cellini, Koji Noshita, Daniel Reynolds, Mark Mueller-Linow, Joshua Ball, Aaron Bostrom, Argelia Lorence, Claude Welcker, Frédéric Baret, Biotechnology and Biological Sciences Research Council, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), 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), Agenzia Lucana di Sviluppo di Innovazione in Agricoltura, Partenaires INRAE, Arkansas State University, Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), The University of Tokyo (UTokyo), Japan Science and Technology Agency (JST), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Nanjing Agricultural University, ANR-PIA project PHENOME FPPN (ANR-11-INBS-0012), Biotechnology and Biological Sciences Research Council (BBSRC), Core Strategic Programme Grant (BB/CSP17270/1), BBSRC’s Designing Future Wheat Strategic Programme (BB/P016855/1), (BBS/E/T/000PR9785), EPPN2020 (UE H2020 grant agreement No 731013), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), European Project: 731013 ,EPPN2020(2017), Biotechnology and Biological Sciences Research Council (BBSRC), and Nanjing Agricultural University (NAU)
Subjects: 0106 biological sciences, 0301 basic medicine, Total cost, Cost, Cost-Benefit Analysis, media_common.quotation_subject, Context (language use), Plant Science, Biology, analyse d'image, Affordable, 01 natural sciences, Information system, Imaging, 03 medical and health sciences, phénotypage, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Quality (business), Phenomics, media_common, Vegetal Biology, Cost efficiency, General Medicine, Plants, Investment (macroeconomics), Pipeline (software), Reliability engineering, photographie aérienne, Pipeline transport, Phenotype, 030104 developmental biology, Phenotyping, Agronomy and Crop Science, Biologie végétale, Information Systems, 010606 plant biology & botany, analyse des coûts
Abstract: International audience; Progress in remote sensing and robotic technologies decreases the hardware costs of phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, and present a trade-off between investment and manpower costs. We then discuss the structure of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) major costs arise from plant handling and manpower; (ii) the total costs per pot/microplot are similar in robotized platform or field experiments with drones, hand-held or robotized ground vehicles; (iii) the cost of vehicles carrying sensors represents only 5-26% of the total costs. These conclusions depend on the context, in particular for labor cost, the quantitative demand of phenotyping and the number of days available for phenotypic measurements due to climatic constraints. Data analysis represents 10-20% of total cost if pipelines have already been developed. A trade-off exists between the initial high cost of pipeline development and labor cost of manual operations. Overall, depending on the context and objectives, “cost-effective” phenotyping may involve either low investment (“affordable phenotyping”), or initial high investments in sensors, vehicles and pipelines that result in higher quality and lower operational costs.
Published: 2019
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27. Experimental and modelling assessment of ductility in a precipitation hardening AlMgScZr alloy

Author: Gang Ji, Haowei Wang, Shengyi Zhong, Yubin Ke, Zhe Chen, András Borbély, Yves Bréchet, Han Chen, Nanjing Agricultural University, University of California [Santa Barbara] (UCSB), University of California, Unité Matériaux et Transformations - UMR 8207 (UMET), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centrale Lille Institut (CLIL), Shanghai Jiao Tong University [Shanghai], Laboratoire Georges Friedel (LGF-ENSMSE), École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Dongguan University of Technology, Science et Ingénierie des Matériaux et Procédés (SIMaP), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centrale Lille Institut (CLIL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Nanjing Agricultural University (NAU), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), and Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Materials science, Alloy, chemistry.chemical_element, 02 engineering and technology, engineering.material, 01 natural sciences, modelling, [SPI]Engineering Sciences [physics], a dislocation-based approach, Precipitation hardening, Aluminium, 0103 physical sciences, General Materials Science, Ductility, 010302 applied physics, Structural material, Precipitation (chemistry), Mechanical Engineering, Metallurgy, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, [CHIM.POLY]Chemical Sciences/Polymers, chemistry, 13. Climate action, Mechanics of Materials, engineering, precipitates, Dislocation, Deformation (engineering), 0210 nano-technology, dislocations
Abstract: International audience; Precipitation hardening is the most effective strategy to enhance the mechanical properties of metals. Dislocation mechanisms to control strengthening during precipitation have been demonstrated extensively. However, owing to the complexity of different precipitates in alloys, variations in ductility caused by precipitation are complex and have not been clarified so far. In this study, the effects of precipitation on ductility in precipitation hardening aluminium alloys are investigated based on a modified dislocation-based approach and experimental characterisation. The AlMgScZr alloy with spherical Al3(Sc, Zr) precipitates is used as a model alloy system to understand the effects of precipitation on ductility. Via heat treatment, shearable and nonshearable Al3(Sc, Zr) precipitates are introduced in the AlMg matrix. The results show that the ductility of AlMgScZr alloy decreases when shearable precipitates occur, while it increases with shearable precipitates being replaced by nonshearable precipitates. The variation in ductility of AlMgScZr alloy is mainly controlled by the dynamic recovery rate of the dislocations. Finally, by analysing the different precipitate-dislocation interactions and evaluating the dislocation density evolution during deformation, the dislocation mechanisms of 2 ductility during precipitation for AlMgScZr alloy are demonstrated. This study reveals the dislocation mechanism for controlling ductility during precipitation for AlMgScZr alloy which can provide a theoretical foundation for the design of high-performance structural materials.
Published: 2021
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28. Leaf Eh and pH: A Novel Indicator of Plant Stress. Spatial, Temporal and Genotypic Variability in Rice (Oryza sativa L.)

Author: Alain Audebert, Olivier Husson, Stéphane Boulakia, Philippe Menozzi, Brigitte Soglonou, Jean-Pierre Sarthou, Stephen Joseph, Ibnou Dieng, Lydia Bousset, Jaroslav Benada, Firmin Tano, Koichi Futakuchi, Africa Rice Center [Côte d'Ivoire] (AfricaRice), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre Etude Regional pour l'Amelioration de l'Adaptation à la Sécheresse, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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), School of Materials Science and Engineering, University of New South Wales [Sydney] (UNSW), Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University (NAU), University of Newcastle (UoN), CIRAD (UPR AIDA), CIRAD (CRESI action), Africa Rice Center, 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Nanjing Agricultural University
Subjects: 0106 biological sciences, 0301 basic medicine, F08 - Systèmes et modes de culture, agroécologie, 01 natural sciences, F30 - Génétique et amélioration des plantes, redox potential, Maladie des plantes, Genotype, Expression des gènes, oxidative stress, 2. Zero hunger, Vegetal Biology, pH, indicator, Potentiel redox, Plant level, Physiologie végétale, Horticulture, agroecological crop protection, method, Génotype, F60 - Physiologie et biochimie végétale, Oryza sativa, Crop cultivation, Biology, lcsh:Agriculture, 03 medical and health sciences, Variation génétique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Stress oxydatif, lcsh:S, Crop protection, 030104 developmental biology, Hydric soil, measurement, plant health, H50 - Troubles divers des plantes, Agronomy and Crop Science, Biologie végétale, 010606 plant biology & botany
Abstract: AGAP; International audience; A wealth of knowledge has been published in the last decade on redox regulations in plants. However, these works remained largely at cellular and organelle levels. Simple indicators of oxidative stress at the plant level are still missing. We developed a method for direct measurement of leaf Eh and pH, which revealed spatial, temporal, and genotypic variations in rice. Eh (redox potential) and Eh@pH7 (redox potential corrected to pH 7) of the last fully expanded leaf decreased after sunrise. Leaf Eh was high in the youngest leaf and in the oldest leaves, and minimum for the last fully expanded leaf. Leaf pH decreased from youngest to oldest leaves. The same gradients in Eh-pH were measured for various varieties, hydric conditions, and cropping seasons. Rice varieties differed in Eh, pH, and/or Eh@pH7. Leaf Eh increases and leaf pH decreases with plant age. These patterns and dynamics in leaf Eh-pH are in accordance with the pattern and dynamics of disease infections. Leaf Eh-pH can bring new insight on redox processes at plant level and is proposed as a novel indicator of plant stress/health. It could be used by agronomists, breeders, and pathologists to accelerate the development of crop cultivation methods leading to agroecological crop protection.
Published: 2018
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29. Recent advances and opportunities in sustainable food supply chain: a model-oriented review

Author: Selwyn Piramuthu, Zhanguo Zhu, Wei Zhou, Feng Chu, Chengbin Chu, Alexandre Dolgui, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), College of Economics and Management, Nanjing Agricultural University, Management Engineering Research Center, Xihua University, Département Automatique, Productique et Informatique (IMT Atlantique - DAPI), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Systèmes Logistiques et de Production (SLP ), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Laboratoire Génie Industriel - EA 2606 (LGI), CentraleSupélec, School of Management, Northwestern Polytechnical University, Department of Information Operations management, Ecole Supérieure de Commerce de Paris (ESCP Europe), University of Florida [Gainesville] (UF), Nanjing Agricultural University (NAU), IMT Atlantique (IMT Atlantique), Systèmes Logistiques et de Production (LS2N - équipe SLP ), and Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)
Subjects: Food industry, Natural resource economics, Strategy and Management, Supply chain, Population, 0211 other engineering and technologies, 02 engineering and technology, Review, Management Science and Operations Research, Operations research, Industrial and Manufacturing Engineering, Models, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, 0502 economics and business, Sustainable agriculture, education, 2. Zero hunger, education.field_of_study, 021103 operations research, business.industry, Sustainable supply chain, 05 social sciences, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Sustainability, business, 050203 business & management
Abstract: International audience; Faced with the challenges associated with sustainably feeding the world’s growing population, the food industry is increasingly relying on operations research (OR) techniques to achieve economic, environmental and social sustainability. It is therefore important to understand the context-specific model-oriented applications of OR techniques in the sustainable food supply chain (SFSC) domain. While existing food supply chain reviews provide an excellent basis for this process, the explicit consideration of sustainability from a model-oriented perspective along with a structured outline of relevant SFSC research techniques are missing in extant literature. We attempt to fill this gap by reviewing 83 related scientific journal publications that utilise mathematical modelling techniques to address issues in SFSC. To this end, we first identify the salient dimensions that include economic, environmental and social issues in SFSC. We then review the models and methods that use these dimensions to solve issues that arise in SFSC. We identify some of the main challenges in analytical modelling of SFSC as well as future research directions.
Published: 2018
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30. Exploring the genetic variability of peach skin phenolics and triterpenoids as natural defenses against brown rot

Author: Bénédicte Quilot-Turion, Silvia Scariotto, Marie Noëlle Corre, Leandro de Oliveira-Lino, Véronique Signoret, Maximiliano Dini Vinoly, Lorraine Latchoumane, Maria Do Carmo Raseira, Jean-Luc Poëssel, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, ID 1503003 _ ANR10LABX000101, and Nanjing Agricultural University (NAU). Nanjing, CHN.
Subjects: résistance aux maladies, Prunus persica, Disease resistance, Vegetal Biology, pourriture brune, QTL, variabilité génétique, food and beverages, GWAS, Monilinia spp, monilinia, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, pêche, phénols, triterpénoïde, Biologie végétale
Abstract: Brown rot caused by Monilinia spp. provokes dramatic losses of peach in all production regions. In this context, the general objective of our work is to develop sustainable ways to fight against this damaging disease. This study explored phenolic and triterpenoid diversity of fruit skin together with brown rot resistance. A Brazilian peach collection and an interspecific cross between P. davidiana and P. persica, each of 120 genotyped individuals, have been screened for 3 years, for susceptibility to M. fructicola and to M. laxa respectively. Some genotypes of the two populations showed low or null infection the 3 years. Secondary compounds of fruit skin of all genotypes were analyzed two years by HPLC-DAD. Depending on the genotypes, 30 to 40 compounds including triterpenoids, hydroxycinnamic derivatives and flavonoids, were quantified and around 20 were identified by mass spectrometry. Among these, phenolic esters of triterpenoids were identified for the first time in peach fruit. The correlation of quantitative data between years showed their robustness. A large diversity in contents of the compounds was observed. The association and QTL analyses proved to be complementary and led to assumptions about the co-locations of loci controlling different traits, especially for compounds with differential levels in the skin of peaches and nectarines. These analyses will help deciphering the genetic control of fruit skin phenolics and triterpenoids and pave the way to the identification of the underlying genes. Detection of loci related to resistance will provide tools for the implementation of marker assisted selection. Correlations between compounds and infection traits led us to hypothesize that some compounds from peach skin could play a role in the brown rot control. The fungicide activity of these compounds is being tested in vitro.
Published: 2018

31. Modeling trophic dependencies and exchanges among insects’ bacterial symbionts in a host-simulated environment

Author: Laurence Mouton, Einat Zchori-Fein, Itai Opatovsky, Jiandong Jiang, Zhepu Ruan, Shany Ofaim, Valeria Barbe, Diego Santos-Garcia, Tamar Lahav, Shiri Freilich, Newe Ya’ar Research Center, Agricultural Research Organization, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València (UV), Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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 de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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), Nanjing Agricultural University (NAU), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Nanjing Agricultural University
Subjects: 0301 basic medicine, lcsh:QH426-470, lcsh:Biotechnology, 030106 microbiology, Genomics, Biology, Environment, Genome, Bemisia tabaci, Models, Biological, Hemiptera, 03 medical and health sciences, lcsh:TP248.13-248.65, Genetics, Animals, Symbiosis, Metabolic interactions, Trophic level, Facultative, Bacteria, Host (biology), Community structure, biology.organism_classification, Symbionts, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, lcsh:Genetics, 030104 developmental biology, Evolutionary biology, Wolbachia, Network analysis, Genome, Bacterial, Metabolic Networks and Pathways, Biotechnology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, Research Article
Abstract: Background Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. In phloem-feeding insects such metabolic interactions with bacteria enable complementation of their deprived nutrition. The phloem-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. This well-defined bacterial community in B. tabaci serves here as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented occurrences of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts genera (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species’ combinations, and (3) dependencies of each species on different media components. Results The predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggests several previously un-reported routes for complementary interactions and estimated the dependency of each symbiont in specific host metabolites. No clear association was detected between metabolic co-dependencies and co-occurrence patterns. Conclusions The analysis generated predictions for testable hypotheses of metabolic exchanges and co-dependencies in bacterial communities and by crossing them with co-occurrence profiles, contextualized interaction patterns into a wider ecological perspective. Electronic supplementary material The online version of this article (10.1186/s12864-018-4786-7) contains supplementary material, which is available to authorized users.
Published: 2018
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32. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

Author: Igor V. Grigoriev, Youzhi Miao, Alexey G. Kopchinskiy, Irina S. Druzhinina, Kurt LaButti, Shadi Pourmehdi, Asaf Salamov, Kamariah Abu Salim, Kerrie Barry, Jian Zhang, Lea Atanasova, Mohammad Javad Rahimi, Bernard Henrissat, Hope Hundley, Qirong Shen, Alan Kuo, Anna Lipzen, Komal Chenthamara, Feng Cai, Christian P. Kubicek, Marica Grujic, Andrea Aerts, Carina Pretzer, Dongqing Yang, Mei Wang, Research Area Biotechnology and Microbiology, Technical University of Vienna [Vienna] (TU WIEN)-Institute of Chemical Engineering, Technische Universität Wien (TU Wien), Laboratoire de Linguistique Formelle (LLF UMR7110), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Nanjing Agricultural University, Fac Sci, Environm & Life Sci, University of Brunei Darussalam (Biology Department), Universiti Brunei Darussalam, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), Dept Energy Great Lakes Bioenergy Res Ctr, Joint Genome institute, United States Department of Energy, Joint Genome Institute, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), ANR-17-CE34-0002,EMBRASE,Environnement MicroBiologique et Risque Allergique, Suivi des Enfants à 5 ans(2017), Vienna University of Technology (TU Wien)-Institute of Chemical Engineering, Vienna University of Technology (TU Wien), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Nanjing Agricultural University (NAU), U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), Austrian Science Fund (FWF) [P 25613 B20], Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], National Natural Science Foundation of China [31330069], Chinese Ministry of Science and Technology (973 Program) [2015CB150500], IDEX Aix-Marseille (Grant Microbio-E), Kuala Belalong Field Studies Centre [WWTF-LS13-048], Martin, Francis, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Druzhinina, Irina S., and Shen, Qirong
Subjects: 0301 basic medicine, Cancer Research, Gene Transfer, genome sequence, phylogenetic analysis, transplant recipient, multiple alignments, dna polymorphism, pythium-ultimum, life-style, web server, evolution, reesei, Fungal genetics, Cell Wall, Scanning, Fungal genomics, Genetics (clinical), Phylogeny, Data Management, 2. Zero hunger, Trichoderma, Fungal protein, Microscopy, Phylogenetic analysis, biology, Ascomycota, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Eukaryota, food and beverages, Basidiomycota, Genomics, Plants, Phylogenetics, Parasite evolution, Host-Pathogen Interactions, Hypocreales, Biotechnology, Research Article, Computer and Information Sciences, Hypha, lcsh:QH426-470, Gene Transfer, Horizontal, Glycoside Hydrolases, Hyphae, Fungus, Mycology, Electron, complex mixtures, Horizontal, Fungal Proteins, 03 medical and health sciences, Botany, Genetics, Evolutionary Systematics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Taxonomy, Evolutionary Biology, fungi, Organisms, technology, industry, and agriculture, Fungi, Biology and Life Sciences, 15. Life on land, biology.organism_classification, Ascomycetes, lcsh:Genetics, 030104 developmental biology, Microscopy, Electron, Scanning, Parasitology, Fungal evolution, Developmental Biology
Abstract: Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass., Author summary Individual fungi rely on particular host organisms or substrates for their nutrition. Therefore, the genomes of fungi feeding on plant biomass necessarily contain genes encoding plant cell wall-degrading enzymes, while animal parasites may depend on proteolytic activity. Molds in the genus Trichoderma (Ascomycota) display a unique nutritional versatility. They can feed on other fungi, attack animals, and degrade plant debris. The later property is so efficient that one species (T. reesei) is commercially used for the production of cellulolytic enzymes required for making biofuels and other industry. In this work, we have investigated the evolution of proteins required for plant cell wall degradation in nine Trichoderma genomes and found an unprecedented number of lateral gene transfer (LGT) events for genes encoding these enzymes. Interestingly, the transfers specifically occurred from Ascomycota molds that feed on plants. We detected no cases of LGT from other fungi (e.g., mushrooms or wood-rotting fungi from Basidiomycota) that are frequent hosts of Trichoderma. Therefore, we propose that LGT may be linked to the ability of Trichoderma to parasitize on related organisms. This is a characteristic ecological trait that distinguishes Trichoderma from other mycoparasitic fungi. In this report, we demonstrate that the lateral transfer of genes may result in a profound nutritional expansion and contribute to the emergence of a generalist capable of feeding on organic matter of any origin.
Published: 2018
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33. The improved assembly of the European Pear

Author: Linsmith, Gareth, Bianco, Luca, Liu, C, Rombauts, S, Celton, Jean-Marc, Montanari, Sara, Schijlen, Elio, Bakker, L, Deng, C, Durel, Charles-Eric, Laurens, Francois, Chagne, D, Velasco, Riccardo, Neale, D, Van De Peer, Yves, Troggio, Michela, Universiteit Gent = Ghent University [Belgium] (UGENT), Centro Ricerca e Innovazione, Fondazione Edmund Mach, Instituto Agrario S. Michele all' Adige, Center for Plant Molecular Biology, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of Plant Sciences, University of California [Davis] (UC Davis), University of California-University of California, Wageningen University and Research Centre (WUR), Plant & Food Research, Nanjing Agricultural University (NAU). CHN., Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California, and Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: malus domestica, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Vegetal Biology, génomique comparative, pyrus communis, [SDV]Life Sciences [q-bio], assemblage bioinformatique, pommier, gène hic1, Agricultural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, séquençage du génome, nanobiotechnologie, poirier, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biologie végétale, Sciences agricoles, ComputingMilieux_MISCELLANEOUS, Autre (Sciences du Vivant)
Abstract: Apple and Pear diverged from each other between 5.4 and 21.5 MYA and are believed to share a common genome duplication event between 35 and 50 MYA (Velasco et al. 2010, Wu et al. 2012). Size differences have been observed between the Apple and Pear genomes which are estimated at 527Mb (Pyrus x Bretschneideri Rehd) and 700Mb (Malus x Domestica Borkh) respectively (Wu et al. 2013, Li et al. 2016). The difference in genome size has been accounted for primarily by the proliferation of transposable elements, with the gene space thought to be fairly similar between the two species (Wu et al. 2012). Comparative genomics of the lineage has however, been hampered by the fragmented nature of the reference assemblies. A new chromosome scale assembly was recently produced (Daccord et al. 2017) and now also a chromosome scale assmble of the European Pear (this study), which shows strong collinearity with Apple, greatly facilitating the comparative study of these genomes.
Published: 2018

34. Multimodel ensembles improve predictions of crop–environment–management interactions

Author: Giacomo De Sanctis, Taru Palosuo, Davide Cammarano, Frank Ewert, Soora Naresh Kumar, Roberto C. Izaurralde, Gerrit Hoogenboom, Elias Fereres, Bing Liu, Thilo Streck, Mikhail A. Semenov, Ehsan Eyshi Rezaei, Peter J. Thorburn, Claudio O. Stöckle, Benjamin Dumont, Andrea Maiorano, Eckart Priesack, Iwan Supit, Heidi Horan, Kurt Christian Kersebaum, Pierre Martre, Margarita Garcia-Vila, Dominique Ripoche, Pierre Stratonovitch, Yujing Gao, Zhao Zhang, Ann-Kristin Koehler, Curtis D Jones, Fulu Tao, Claas Nendel, Christoph Müller, Andrew J. Challinor, Reimund P. Rötter, Mukhtar Ahmed, Senthold Asseng, Christine Girousse, Bruno Basso, Christian Klein, Pramod K. Aggarwal, Joost Wolf, Glenn J. Fitzgerald, Martin K. van Ittersum, Garry O'Leary, Belay T. Kassie, Christian Biernath, Sebastian Gayler, Daniel Wallach, Sara Minoli, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Nanjing Agricultural 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), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Plant Production Systems Group, Wageningen University and Research [Wageningen] (WUR), Agriculture and Food Security (CCAFS), Biological Systems Engineering, Washington State University (WSU), Department of Agronomy, University of El-Tarf, Department of Earth and Environmental Sciences [East Lansing], Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Plant Pathology, The James Hutton Institute, University of Leeds, Consultative Group on International Agricultural Research (CGIAR), GMO Unit, European Food Safety Authority = Autorité européenne de sécurité des aliments, Department Terra & AgroBioChem, Gembloux Agro‐Bio Tech, Université de Liège, Center for Development Research, University of Córdoba, Agriculture Victoria Research, University of Melbourne, Institute of Soil Science and Land Evaluation, University of Hohenheim, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of Florida [Gainesville] (UF), Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Institute of landscape systems analysis, School of Earth and Environment, European Food Safety Authority (EFSA), Potsdam Institute for Climate Impact Research (PIK), Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Natural Resources Institute Finland (LUKE), Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), University Medical Center Göttingen (UMG), Computational and Systems Biology Department, Rothamsted Research, Water & Food and Water Systems & Global Change Group, Wageningen University, Institute of geographical sciences and natural resources research, Chinese Academy of Sciences [Changchun Branch] (CAS), Plant Production Systems, State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University (BNU), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Université de Toulouse (UT)-Université de Toulouse (UT), 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), Nanjing Agricultural University (NAU), Universidad de Córdoba = University of Córdoba [Córdoba], Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Institute of geographical sciences and natural resources research [CAS] (IGSNRR), and Chinese Academy of Sciences [Beijing] (CAS)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 010504 meteorology & atmospheric sciences, Mean squared error, Climate Change, [SDE.MCG]Environmental Sciences/Global Changes, Inverse, Water en Voedsel, Monotonic function, multi-model ensemble, Environment, High skill, 01 natural sciences, crop models, ensemble mean, Statistics, Environmental Chemistry, Triticum, 0105 earth and related environmental sciences, General Environmental Science, Mathematics, 2. Zero hunger, ensemble median, Global and Planetary Change, WIMEK, Water and Food, Ecology, Ensemble average, Simulation modeling, Agriculture, 04 agricultural and veterinary sciences, Variance (accounting), prediction, Models, Theoretical, PE&RC, Plant Production Systems, multimodel ensemble, 13. Climate action, Plantaardige Productiesystemen, climate change impact, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Water Systems and Global Change, Environment management
Abstract: International audience; A recent innovation in assessment of climate change impact on agricultural production has been to use crop multi model ensembles (MMEs). These studies usually find large variability between individual models but that the ensemble mean (e‐mean) and median (e‐median) often seem to predict quite well. However few studies have specifically been concerned with the predictive quality of those ensemble predictors. We ask what is the predictive quality of e‐mean and e‐median, and how does that depend on the ensemble characteristics. Our empirical results are based on five MME studies applied to wheat, using different data sets but the same 25 crop models. We show that the ensemble predictors have quite high skill and are better than most and sometimes all individual models for most groups of environments and most response variables. Mean squared error of e‐mean decreases monotonically with the size of the ensemble if models are added at random, but has a minimum at usually 2‐6 models if best‐fit models are added first. Our theoretical results describe the ensemble using four parameters; average bias, model effect variance, environment effect variance and interaction variance. We show analytically that mean squared error of prediction (MSEP) of e‐mean will always be smaller than MSEP averaged over models, and will be less than MSEP of the best model if squared bias is less than the interaction variance. If models are added to the ensemble at random, MSEP of e‐mean will decrease as the inverse of ensemble size, with a minimum equal to squared bias plus interaction variance. This minimum value is not necessarily small, and so it is important to evaluate the predictive quality of e‐mean for each target population of environments. These results provide new information on the advantages of ensemble predictors, but also show their limitations.
Published: 2018
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35. Scheduling on a two-machine permutation flow shop under time-of-use electricity tariffs

Author: Shijin Wang, Kan Fang, Zhanguo Zhu, Chengbin Chu, Feng Chu, Department of Management Science and Engineering, Tongji University, College of Economics and Management, Nanjing Agricultural University, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), ESIEE Paris, and Nanjing Agricultural University (NAU)
Subjects: 0209 industrial biotechnology, Mathematical optimization, electricity cost, Computer science, Iterated local search, Strategy and Management, 0211 other engineering and technologies, 02 engineering and technology, Management Science and Operations Research, Industrial and Manufacturing Engineering, Scheduling (computing), 020901 industrial engineering & automation, Electricity cost, scheduling, Integer programming, dynamic programming, 021103 operations research, business.industry, Flow shop scheduling, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], iterated local search, flow shop, Dynamic programming, Electricity, business, Time of use
Abstract: International audience; We consider a two-machine permutation flow shop scheduling problem to minimise the total electricity cost of processing jobs under time-of-use electricity tariffs. We formulate the problem as a mixed integer linear programming, then we design two heuristic algorithms based on Johnson’s rule and dynamic programming method, respectively. In particular, we show how to find an optimal schedule using dynamic programming when the processing sequence is fixed. In addition, we propose an iterated local search algorithm to solve the problem with problem-tailored procedures and move operators, and test the computational performance of these methods on randomly generated instances.
Published: 2018
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36. Organic vs. Non-Organic Food Products: Credence and Price Competition

Author: Feng Chu, Zhanguo Zhu, Yi Wang, School of Management, Hangzhou Dianzi University (HDU), College of Economics and Management, Nanjing Agricultural University, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), Management Engineering Research Center, Xihua University, and Nanjing Agricultural University (NAU)
Subjects: Organic product, Credence, Geography, Planning and Development, TJ807-830, Context (language use), Management, Monitoring, Policy and Law, TD194-195, Renewable energy sources, Competition (economics), Willingness to pay, 0502 economics and business, Production (economics), GE1-350, Organic food products, 2. Zero hunger, Environmental effects of industries and plants, Competition, Renewable Energy, Sustainability and the Environment, 05 social sciences, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Investment (macroeconomics), Product type, Environmental sciences, Commerce, Sustainability, 050211 marketing, 050202 agricultural economics & policy, Business, organic food products, sustainability, credence, competition
Abstract: International audience; We analyze the organic and non-organic production choices of two firms by considering customers' trust in organic food products. In the context of customers' possible willingness to pay a premium price and their mistrust in organic food products, two firms first make choices on offering organic and non-organic food products. If offering organic products, a firm can further invest in the credence system to increase customers' trust in their organic products. At the final stage, two firms determine prices. We provide serval insights. First, we characterize the market conditions in which only one firm, both firms or neither firm will choose to offer organic food products. We find that the higher the production costs or credence investment costs for organic food products are, the more likely firms are to choose to produce non-organic food products. Second, if it is expensive enough to invest in organic credence, offering organic food products may still be uncompetitive, even if organic production cost appears to have no disadvantage compared to non-organic food products. Third, we highlight how the prices of organic food products in equilibrium are affected by market parameters. We show that when only one firm offers organic food products, this firm tends to offer a relatively low price if organic credence investment is expensive. Fourth, we highlight how one firm's credence investment decision in equilibrium can be affected by the product type choice of the other firm. We find that the investment in organic credence is lower when both firms offer organic food products compared with the case when only one firm offers organic food products.
Published: 2017
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37. 4 per 1000 soil carbon sequestration

Author: Minasny, Budiman, Mcbratney, Alex B., Malone, Brendan P., Angers, Denis, Arrouays, Dominique, Chambers, Adam, Chaplot, Vincent, Chen, Zueng-Sang, Cheng, Kun, Das, Bhabani S., Field, Damien J., Gimona, Alessandro, Hedley, Carolyn B., Hong, Suk Young, Mandal, Biswapati, Marchant, Ben, Martin, Manuel, Mcconkey, Brian G., Mulder, Vera Leatitia, O Rourke, Sharon, Anne Richer-de-Forges, Odeh, Inakwu, Padarian, José, Paustian, Keith, Pan, Genxing, Poggio, Laura, Savin, Igor, Stolbovoy, Vladimir, Stockmann, Uta, Sulaeman, Yiyi, Tsui, Chun-Chih, Vågen, Tor-Gunnar, Wesemael, Bas, Winowiecki, Leigh A., Sydney Institute of Agriculture, The University of Sydney, Agriculture and Agri-Food (AAFC), InfoSol (InfoSol), Institut National de la Recherche Agronomique (INRA), United states, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Agricultural Chemistry, National Taiwan University [Taiwan] (NTU), Nanjing Agricultural University (NAU), Indian Institute of Technology Kharagpur (IIT Kharagpur), The James Hutton Institute, Manaaki Whenua – Landcare Research [Lincoln], Rural Development Administration, Bidhan Chandra Krishi Viswavidyalaya, British Geological Survey (BGS), Université libre de Bruxelles (ULB), University College Dublin (UCD), Colorado State University [Fort Collins] (CSU), People's Friendship University of Russia, Dokuchaev Soil Science Institute (SSI), Russian Academy of Agricultural Sciences, Indonesian Agency for Agricultural Research and Development (IAARD), World Agroforestry Centre, Université Catholique de Louvain = Catholic University of Louvain (UCL), Food and Agriculture Organization (FAO). ITA., Agriculture and Agri-Food [Ottawa] (AAFC), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Nanjing Agricultural University, and Indonesian Agency for Agricultural Research and Development Ministry of Agriculture
Subjects: sciences du sol, changement climatique, sécurité alimentaire, carte des sols, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, carbone organique du sol, gaz à effet de serre, cartographie numérique du sol, ComputingMilieux_MISCELLANEOUS, carte pédologique, matière organique du sol
Abstract: Budiman Minasny, Alex. B. McBratney, Brendan P. Malone, Denis A. Angers, Dominique Arrouays, Adam Chambers, Vincent Chaplot, Zueng-Sang Chen, Kun Cheng, Bhabani S. Das, Damien J. Field, Alessandro Gimona, Carolyn Hedley, Suk Young Hong, Biswapati Mandal, Ben P. Marchant, Manuel Martin, Brian G. McConkey, Vera Leatitia Mulder, Sharon O’Rourke, Anne C. Richer-de-Forges, Inakwu Odeh, José Padarian, Keith Paustian,Genxing Pan, Laura Poggio, Igor Savin, Vladimir Stolbovoy, Uta Stockmann, Yiyi Sulaeman, Chun-Chih Tsui, Tor-Gunnar Vågen, Bas van Wesemael, Leigh Winowiecki 2017. 4 per 1000 soil carbon sequestration. Proceedings of the Global Symposium on Soil Organic Carbon 2017. 21-23 March 2017. Rome, Italy. FAO.; International audience
Published: 2017

38. Changing Structure and Sustainable Development for China’s Hog Sector

Author: Feng Chu, Xiaoheng Zhang, Yingheng Zhou, Xu Tian, Jinyang Yang, Xianhui Geng, Xiaohua Yu, College of Economics and Management (College of Economics and Management), Nanjing Agricultural University (NAU), Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), Management Engineering Research Center, Xihua University, Courant Research Centre Poverty, Inequity and Growth, Georg-August-University = Georg-August-Universität Göttingen, Department of Health Policy and Management, Yale University [New Haven], Nanjing Agricultural University, and Georg-August-University [Göttingen]
Subjects: China, Natural resource economics, Geography, Planning and Development, TJ807-830, Economic shortage, Management, Monitoring, Policy and Law, TD194-195, Hog production, Renewable energy sources, Market economy, 0502 economics and business, Production (economics), GE1-350, 050207 economics, Productivity, 2. Zero hunger, Sustainable development, Environmental effects of industries and plants, Renewable Energy, Sustainability and the Environment, Production cost, 05 social sciences, Metafrontier, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Environmental sciences, 13. Climate action, productivity, metafrontier, production cost, hog production, 050202 agricultural economics & policy, Business, Allocative efficiency, Inefficiency
Abstract: International audience; Supply shortages and competitive disadvantages are the main problems faced by China's hog sector. The non-essential import of pork products, triggered by competitive disadvantages, poses great challenges to hog farms. Structural changes are an important policy concern in China and elsewhere. Previous literature has ignored whether the ongoing structural changes from backyard to large farms can contribute to sustainable development. This study adopts the micro-level data of hog farms collected from Jiangsu Province, and uses a two-step metafrontier model and a primal system approach. The empirical results reveal that the ongoing structural changes are capable of boosting the growth in output in China's hog sector, since the stronger increase in comparable technical efficiency compensates for the inappropriate technology. Furthermore, the ongoing structural changes are also beneficial in the reduction of production costs and in improving competitiveness in China's hog sector. The decline in technical and allocative inefficiency costs, particularly for technical inefficiency costs, contributes to the cost advantage with the increasing farm size.
Published: 2017
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39. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species

Author: Peter M. Campbell, David F. Clarke, H-J. Zhang, Christopher W. Coppin, Brian P. Walenz, L. B. Han, Irene Horne, Stephen L. Pearce, Philip G. Board, Peter D. East, Annette McGrath, Heiko Vogel, René Feyereisen, Sharon Downes, G. Duan, Trent Perry, S. Li, Rahul V. Rane, Z. Zou, Emmanuelle Jacquin-Joly, Owain R. Edwards, Klas Hatje, Tom Walsh, Daniel S.T. Hughes, Samia Elfekih, Omaththage P. Perera, N-Y. Liu, Steven E. Scherer, Granger G. Sutton, Richard A. Gibbs, Suyog S. Kuwar, David G. Heckel, Shalini N. Jhangiani, John G. Oakeshott, Thomas Chertemps, Nicolas Montagné, Alisha Anderson, Y. P. Huang, John T. Christeller, Martin Kollmar, Angela McGaughran, Craig Anderson, William James, Karl H.J. Gordon, Robert T. Good, A. Papanikolaou, Wei Xu, Stephen Richards, Anne Bretschneider, Lars S. Jermiin, Claire A. Farnsworth, Charles Robin, Jiaxin Qu, Y. C. Han, S. V. Song, Martine Maïbèche, Yidong Wu, Sassan Asgari, Wee Tek Tay, Kim C. Worley, Philip J. Batterham, Jason R. Miller, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Melbourne, Research School of Biology, Australian National University (ANU), USDA-ARS : Agricultural Research Service, Human Genome Sequencing Center, Baylor College of Medicine (BCM), Baylor University-Baylor University, Biological and Environmental Sciences, University of Stirling, School of Biological Sciences, University of Queensland [Brisbane], John Curtin School of Medical Research, Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, 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), Plant & Food Research, School Biology Science, Royal Holloway [University of London] (RHUL), State key laboratory of Integrated Management of pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences [Changchun Branch] (CAS), Nanjing Agricultural University (NAU), Max Planck Institute for Biophysical Chemistry (MPI-BPC), Chinese Academy of Sciences (CAS), Southwest Forestry University (SWFU), J. Craig Venter Institute [La Jolla, USA] (JCVI), Université Pierre et Marie Curie - Paris 6 (UPMC), School of Veterinary and Life Sciences, Murdoch University, Chongqing Medical University, University of Copenhagen = Københavns Universitet (UCPH), CSIRO Transformational Biology Program University of Melbourne Max-Planck-Gesellschaft Agricultural Research Service, US Department of Agriculture NIH (USA) 2 R01 GM0//11/-04A1 National Natural Science Foundation of China 31530060 New Zealand Government Public Good Science Fund FRST C06X0804 Chinese Scholarship Council, 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), Nanjing Agricultural University, and University of Copenhagen = Københavns Universitet (KU)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, ARMIGERA HUBNER LEPIDOPTERA, HELIOTHIS-VIRESCENS LEPIDOPTERA, MAXIMUM-LIKELIHOOD PHYLOGENIES, DNA-SEQUENCING DATA, WILD HOST PLANTS, RNA-SEQ DATA, INSECTICIDE RESISTANCE, BACILLUS-THURINGIENSIS, ZEA LEPIDOPTERA, COTTON BOLLWORM, [SDV]Life Sciences [q-bio], Genomics, Plant Science, Helicoverpa armigera, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Structural Biology, Botany, Journal Article, Gene family, Gene, Helicoverpa, lcsh:QH301-705.5, Ecology, Evolution, Behavior and Systematics, Genetics, Comparative genomics, biology, fungi, Cell Biology, biology.organism_classification, 010602 entomology, 030104 developmental biology, lcsh:Biology (General), [SDE]Environmental Sciences, Helicoverpa zea, General Agricultural and Biological Sciences, Developmental Biology, Biotechnology
Abstract: International audience; Background: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. Results: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. Conclusions: The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.
Published: 2017
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40. Impact of fat mass and distribution on lipid turnover in human adipose tissue

Author: Lena Appelsved, Henrik Druid, Mikael Rydén, Peter Arner, Keng-Yeh Fu, Anders Thorell, Göran Possnert, Mehran Salehpour, Kanar Alkass, Kirsty L. Spalding, Samuel Bernard, Erik Näslund, Department of Cell and Molecular Biology [Stockholm], Karolinska Institutet [Stockholm], Multi-scale modelling of cell dynamics : application to hematopoiesis (DRACULA), Institut Camille Jordan [Villeurbanne] (ICJ), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Modélisation mathématique, calcul scientifique (MMCS), Division of Surgery, Department of Clinical Sciences, Karolinska Institutet [Stockholm]-Danderyd Hospital, Department of Physics and Astronomy [Uppsala], Uppsala University, Nanjing Agricultural University, Jiangsu Academy of Agricultural Sciences, Department of Forensic Medicine [Stockholm], Department of Clinical Sciences, Danderyd Hospital, Department of medicine [Stockholm], Karolinska Institutet [Stockholm]-Karolinska University Hospital [Stockholm], Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Camille Jordan (ICJ), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut Camille Jordan (ICJ), Karolinska Institutet [Stockholm]-Danderyds sjukhus = Danderyd University Hospital, Nanjing Agricultural University (NAU), and Danderyds sjukhus = Danderyd University Hospital
Subjects: 0301 basic medicine, Adult, medicine.medical_specialty, Science, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], General Physics and Astronomy, Adipose tissue, Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy), 030209 endocrinology & metabolism, White adipose tissue, Overweight, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Body Mass Index, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Waist–hip ratio, Internal medicine, medicine, Adipocytes, Humans, Carbon Radioisotopes, Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci), Triglycerides, Adiposity, Cell Size, Multidisciplinary, Triglyceride, Anthropometry, Waist-Hip Ratio, Radiometric Dating, Lipid metabolism, General Chemistry, medicine.disease, Lipid Metabolism, Obesity, 030104 developmental biology, Endocrinology, Phenotype, chemistry, Adipose Tissue, medicine.symptom, Waist Circumference, Body mass index
Abstract: Differences in white adipose tissue (WAT) lipid turnover between the visceral (vWAT) and subcutaneous (sWAT) depots may cause metabolic complications in obesity. Here we compare triglyceride age and, thereby, triglyceride turnover in vWAT and sWAT biopsies from 346 individuals and find that subcutaneous triglyceride age and storage capacity are increased in overweight or obese individuals. Visceral triglyceride age is only increased in excessively obese individuals and associated with a lower lipid removal capacity. Thus, although triglyceride storage capacity in sWAT is higher than in vWAT, the former plateaus at substantially lower levels of excess WAT mass than vWAT. In individuals with central or visceral obesity, lipid turnover is selectively increased in vWAT. Obese individuals classified as ‘metabolically unhealthy' (according to ATPIII criteria) who have small subcutaneous adipocytes exhibit reduced triglyceride turnover. We conclude that excess WAT results in depot-specific differences in lipid turnover and increased turnover in vWAT and/or decreased turnover in sWAT may result in metabolic complications of overweight or obesity., Lipid turnover in tissues can be calculated from ratios of different carbon isotopes. Here the authors use this approach to study lipid turnover in two distinct adipose tissue depots and find that, in obese individuals, visceral fat is more lipolytic than subcutaneous fat.
Published: 2017
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41. Soil carbon 4 per mille

Author: Genxing Pan, Inakwu O. A. Odeh, Igor Savin, Tor-Gunnar Vågen, Vera Leatitia Mulder, Laura Poggio, Vincent Chaplot, Damien J. Field, Alex B. McBratney, Yiyi Sulaeman, Manuel Martin, Carolyn Hedley, Denis A. Angers, Sharon M. O’Rourke, Vladimir Stolbovoy, Biswapati Mandal, Ben P. Marchant, Adam Chambers, Zueng-Sang Chen, Uta Stockmann, Dominique Arrouays, José Padarian, Keith Paustian, Anne C. Richer-de-Forges, Budiman Minasny, Bas van Wesemael, Suk Young Hong, Alessandro Gimona, Kun Cheng, Leigh A. Winowiecki, Bhabani S. Das, Chun Chih Tsui, Brendan P. Malone, Brian McConkey, Sydney Institute of Agriculture, The University of Sydney, Agriculture and Agri-Food (AAFC), InfoSol (InfoSol), Institut National de la Recherche Agronomique (INRA), Natural Resources Conservation Services (NRCS), United States Department of Agriculture, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Taiwan University [Taiwan] (NTU), Nanjing Agricultural University (NAU), Indian Institute of Technology Kharagpur (IIT Kharagpur), The James Hutton Institute, Manaaki Whenua – Landcare Research [Lincoln], Department of Agricultural Engineering,RDA, Wanju, National Institute of Agricultural Sciences, Bidhan Chandra Krishi Viswavidyalaya, British Geological Survey [Keyworth], British Geological Survey (BGS), Soil Geography and Landscape Group, Wageningen University and Research [Wageningen] (WUR), University College Dublin [Dublin] (UCD), Department of Soil and Crop Sciences [Fort Collins], Colorado State University [Fort Collins] (CSU), People's Friendship University of Russia [Moscow], Dokuchaev Soil Science Institute (SSI), Russian Academy of Agricultural Sciences, Indonesian Agency for Agricultural Research and Development (IAARD), World Agroforestry Center [CGIAR, Indonésie] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Département de Géographie (UCL GEO), Université Catholique de Louvain = Catholic University of Louvain (UCL), Agriculture and Agri-Food [Ottawa] (AAFC), Unité INFOSOL (ORLEANS INFOSOL), University of Limerick [IRLANDE] (UL), University of Limerick (UL), Biogéochimie-Traceurs-Paléoclimat (BTP), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Xi'an Jiaotong University (Xjtu), Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Hawaii Pacific University, Macaulay Institute, Rothamsted Research, Dep. of Environmental Sciences, University of Sydney, Chinese Academy of Sciences [Beijing] (CAS), Dept. of Electrical and Electronic Engineering, Hong Kong University of Science and Technology (HKUST), Université Catholique de Louvain (UCL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Nanjing Agricultural University, and Indonesian Agency for Agricultural Research and Development Ministry of Agriculture
Subjects: 010504 meteorology & atmospheric sciences, Soil Science, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Carbon sequestration, 01 natural sciences, 12. Responsible consumption, Environmental protection, Climate change, 0105 earth and related environmental sciences, 2. Zero hunger, Topsoil, Soil organic matter, 04 agricultural and veterinary sciences, Soil carbon, 15. Life on land, PE&RC, Bodemgeografie en Landschap, Climate change mitigation, Greenhouse gases, 13. Climate action, Greenhouse gas, 040103 agronomy & agriculture, Soil Geography and Landscape, 0401 agriculture, forestry, and fisheries, Soil horizon, Environmental science, Per mille, Soil carbon sequestration
Abstract: International audience; The ‘4 per mille Soils for Food Security and Climate’ was launched at the COP21 with an aspiration to increase global soil organic matter stocks by 4 per 1000 (or 0.4 %) per year as a compensation for the global emissions of greenhouse gases by anthropogenic sources. This paper surveyed the soil organic carbon (SOC) stock estimates and sequestration potentials from 20 regions in the world (New Zealand, Chile, South Africa, Australia, Tanzania, Indonesia, Kenya, Nigeria, India, China Taiwan, South Korea, China Mainland, United States of America, France, Canada, Belgium, England & Wales, Ireland, Scotland, and Russia). We asked whether the 4 per mille initiative is feasible for the region. The outcomes highlight region specific efforts and scopes for soil carbon sequestration. Reported soil C sequestration rates globally show that under best management practices, 4 per mille or even higher sequestration rates can be accomplished. High C sequestration rates (up to 10 per mille) can be achieved for soils with low initial SOC stock (topsoil less than 30 t C ha−1), and at the first twenty years after implementation of best management practices. In addition, areas which have reached equilibrium will not be able to further increase their sequestration. We found that most studies on SOC sequestration only consider topsoil (up to 0.3 m depth), as it is considered to be most affected by management techniques. The 4 per mille number was based on a blanket calculation of the whole global soil profile C stock, however the potential to increase SOC is mostly on managed agricultural lands. If we consider 4 per mille in the top 1m of global agricultural soils, SOC sequestration is between 2-3 Gt C year−1, which effectively offset 20–35% of global anthropogenic greenhouse gas emissions. As a strategy for climate change mitigation, soil carbon sequestration buys time over the next ten to twenty years while other effective sequestration and low carbon technologies become viable. The challenge for cropping farmers is to find disruptive technologies that will further improve soil condition and deliver increased soil carbon. Progress in 4 per mille requires collaboration and communication between scientists, farmers, policy makers, and marketeers.
Published: 2017
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42. Cave-dwelling Coecobrya from southern China with a survey of clypeal chaetae in Entomobryoidea (Collembola)

Author: Feng Zhang, Louis Deharveng, Anne Bedos, Nanjing Agricultural University (NAU), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), Nanjing Agricultural University, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Arthropoda, clypeal chaetotaxy, 010607 zoology, Zoology, Guangxi, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Chaeta, Cave, lcsh:Botany, lcsh:Zoology, Animalia, lcsh:QL1-991, Entomobryoidea, Ecology, Evolution, Behavior and Systematics, Taxonomy, new species, geography, geography.geographical_feature_category, biology, Ecology, Entognatha, Biodiversity, biology.organism_classification, Entomobryidae, Cave dwelling, lcsh:QK1-989, Taxon, Southern china, Collembola, Taxonomy (biology)
Abstract: International audience; Four new species of the genus Coecobrya, C. gejianbangi sp. nov., C. annulata sp. nov., C. ciliata sp. nov., and C. oculata sp. nov., are described from Guangxi caves as the representative of the genus in China. Coecobrya oculata sp. nov. of the boneti-group has 1+1 eyes and a serrate outer edge of the unguiculus. The other three species, devoid of eyes and with a tiny outer tooth on the unguiculus, are assigned here to the tenebricosa-group, assuming that the large tooth on the unguiculus is transformed into a tiny one in cave-obligate species. Clypeal chaetae in Entomobryoidea are systematically surveyed for the first time, and are found to be well diversified at species level. They have a potential taxonomical value in discriminating taxa of morphologically conserved groups.
Published: 2016
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43. Effects of turbulence on alkaline phosphatase activity of phytoplankton and bacterioplankton in Lake Taihu

Author: Xiaoxia Han, Boqiang Qin, Jian Zhou, Céline Casenave, State Key Laboratory of Lake Science and Environment - Nanjing Institute of Geography and Limnology (NIGLAS), Chinese Academy of Sciences [Beijing] (CAS), University of Chinese Academy of Sciences, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), College of Resources and Environmental Sciences, Nanjing Agricultural University, National Natural Science Foundation of China : 41230744, Institut National de la Recherche Agronomique (INRA)-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), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), and Nanjing Agricultural University (NAU)
Subjects: lac, 0106 biological sciences, Biogeochemical cycle, Biodiversité et Ecologie, chemistry.chemical_element, 010501 environmental sciences, Aquatic Science, Biology, 01 natural sciences, Mesocosm, Biodiversity and Ecology, turbulence, alkaline phosphatase activity, phytoplankton, bacterioplankton, phosphorus deficiency, phosphorus strategy, géochimie, Phytoplankton, Phosphorus deficiency, plancton, 14. Life underwater, microbiologie, 0105 earth and related environmental sciences, Ecology, 010604 marine biology & hydrobiology, Phosphorus, Environmental and Society, fungi, Bacterioplankton, Plankton, [SDE.ES]Environmental Sciences/Environmental and Society, mathématiques appliquées, chemistry, 13. Climate action, Environmental chemistry, Alkaline phosphatase, Environnement et Société, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Alkaline phosphatase (AP), an inducible and hydrolytic enzyme, plays a key role in the biogeochemical cycle of phosphorus (P) in lakes. Activity and regulation of AP has been suggested to be affected by hydrodynamic turbulence. However, many aspects of the coupling of the AP activity (APA) and turbulence are still to be investigated and understood. In this study, mesocosm experiments were carried out to further understand the effects of turbulence on APA and the relative contribution of the different microbial groups to the total APA (TAPA). Specifically, we focused on evaluating the APA of phytoplankton (2–112 µm) and bacterioplankton (0.2–2 µm) and its relationship with P fractions under four turbulence levels. Results showed that turbulent conditions enhanced planktonic APA (PAPA) which dominated TAPA by comprising 66–93% of the total fraction. In particular, PAPA was almost two times higher in the turbulence treatments than in still-water control. On the other hand, bacterioplanktonic APA (BAPA) decreased which could be associated with the competitive advantage of bacteria in nutrient-limited conditions due to surface-to-volume ratio. The results suggest that turbulence can accelerate the biogeochemical cycle of P and plays an important role in P strategies of plankton.
Published: 2016
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44. Effects of wind wave turbulence on the phytoplankton community composition in large, shallow Lake Taihu

Author: Jianrong Ma, Pan Wu, Tingfeng Wu, Xiaoxia Han, Jian Zhou, Boqiang Qin, Yang Guijun, Céline Casenave, University of Chinese Academy of Sciences, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Nanjing Institute of Geography and Limnology (Niglas), Chinese Academy of Sciences [Beijing] (CAS), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-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), College of Resources and Environmental Sciences (CRES), Nanjing Agricultural University, School of Environmental and Civil Engineering [Wuxi], Jiangnan University, Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences (CIGIT), National Science Foundation of China : 41230744, 41471021, Water Pollution Control and Management Project : 2012ZX07503-002, European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Nanjing Agricultural University (NAU), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Cyanobacteria, lac, Health, Toxicology and Mutagenesis, Biodiversité et Ecologie, Phytoplankton community composition, Wind, 010501 environmental sciences, 01 natural sciences, cyanobacteria, Cyanobacterial blooms, Mesocosm, biodiversité, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Wind wave, Abiotic component, biology, General Medicine, Eutrophication, Pollution, 6. Clean water, onde, Oceanography, [SDE]Environmental Sciences, Seasons, Environmental Monitoring, China, Biodiversity and Ecology, Phytoplankton, Environmental Chemistry, Dominance (ecology), 14. Life underwater, Dominance, 0105 earth and related environmental sciences, Diatoms, chine, phytoplancton, Wind waves, 010604 marine biology & hydrobiology, Environmental and Society, statistique, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, wind waves, turbulence, phytoplankton community composition, dominance, cyanobacterial blooms, Turbulence, Lakes, 13. Climate action, Hydrodynamics, Environmental science, impact sur l'environnement, Environnement et Société, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay
Abstract: hal-01150611; International audience; Wind waves are responsible for some of the spatio-temporal gradients observed in the biotic and abiotic variables in large shallow lakes. However, their effects on the phytoplankton community composition are still largely unexplored especially in freshwater systems such as lakes. In this paper, using field observations and mesocosm bioassay experiments, we investigated the impact of turbulence generated by wind waves on the phytoplankton community composition (especially on harmful cyanobacteria) in Lake Taihu, a large, shallow eutrophic lake in China. The composition of the phytoplankton community varied with the intensity of wind waves in the different areas of the lake. During summer, when wind waves were strong in the central lake, diatoms and green algae seemed to dominate while harmful cyanobacteria dominated in the weakly influenced Meiliang Bay. Turbulence bioassays also showed that diatoms and green algae were favoured by turbulent mixing. The critical time for the shift of the phytoplankton community composition was approximately 10 days under turbulent conditions. However, short-term (6 days) turbulence is rather beneficial for the dominance of cyanobacteria. This study suggests that the duration of wind events and their associated hydrodynamics are key factors to understanding the temporal and spatial changes of phytoplankton communities.
Published: 2015
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45. Recent Advances and Issues in Facility Location Problems

Author: Feng Chu, Said Mammar, Zhanguo Zhu, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), College of Economics and Management, Nanjing Agricultural University (NAU), and Nanjing Agricultural University
Subjects: 050210 logistics & transportation, Mathematical optimization, Facility location problems, 021103 operations research, Operations research, Matching (graph theory), Supply chain, Variant of capacitated clustering problem (VCCP), 05 social sciences, 0211 other engineering and technologies, Upstream supply network design, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], 02 engineering and technology, Multi commodity min-cost flow problem (MMCF), Facility location problem, [SPI.AUTO]Engineering Sciences [physics]/Automatic, Transshipment, [SPI]Engineering Sciences [physics], 0502 economics and business, 1-center problem, Economics, Supply network, Point location, Transshipment point, Cluster analysis
Abstract: International audience; There exist many variants of facility location problems. This chapter discusses some most recent advances and issues in this field including a capacitated plant location problem with multi commodity flow (CPLPMF), a multi-type transshipment point location problem with multi commodity flow (MTTLMF), a large scale new variant of capacitated clustering problem (VCCP), a location problem with selective matching and vehicles assignment (LCSMVA), and competitive. CPLPMF is a combination of capacitated plant location problem (CPLP) and multi commodity min-cost flow (MMCF) problem. MTTLMF is an extension of two-stage capacitated facility location problem (TSCFLP) considering both MMCF and several transshipment point (TP) types for the goal to locate TPs with appropriate types to ship different commodities from plants to customers while minimizing the total cost for opening TPs and shipment. VCCP is a new variant of the capacitated clustering problem, which describes a location-replenishment problem in upstream supply network design. © 2015 The Institute of Electrical and Electronics Engineers, Inc. All rights reserved.
Published: 2015
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46. The two-speed genomes of filamentous pathogens: waltz with plants

Author: Sylvain Raffaele, Sophien Kamoun, Suomeng Dong, Nanjing Agricultural University, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory [Norwich] (TSL), Chinese National Science Fund for Excellent Young Scholar [31422044], Laboratory of Excellence project TULIP [ANR-10-LABX-41, ANR-11-IDEX-0002-02], Gatsby Charitable Foundation, Biotechnology and Biological Sciences Research Council (BBSRC, UK), European Research Council (ERC-NGRB), European Project: 336808,EC:FP7:ERC,ERC-2013-StG,VARIWHIM(2013), and Nanjing Agricultural University (NAU)
Subjects: 0106 biological sciences, Transposable element, Virulence Factors, [SDV]Life Sciences [q-bio], Virulence, Genomics, Biology, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Genetics, Multiple time, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Pathogen, Gene, 030304 developmental biology, Plant Diseases, 0303 health sciences, Ecology, Effector, Fungal genetics, Fungi, Plants, Adaptation, Physiological, Biological Evolution, Oomycetes, Evolutionary biology, Adaptation, Genome, Fungal, Developmental Biology, 010606 plant biology & botany
Abstract: International audience; Fungi and oomycetes include deep and diverse lineages of eukaryotic plant pathogens. The last 10 years have seen the sequencing of the genomes of a multitude of species of these so-called filamentous plant pathogens. Already, fundamental concepts have emerged. Filamentous plant pathogen genomes tend to harbor large repertoires of genes encoding virulence effectors that modulate host plant processes. Effector genes are not randomly distributed across the genomes but tend to be associated with compartments enriched in repetitive sequences and transposable elements. These findings have led to the 'two-speed genome' model in which filamentous pathogen genomes have a bipartite architecture with gene sparse, repeat rich compartments serving as a cradle for adaptive evolution. Here, we review this concept and discuss how plant pathogens are great model systems to study evolutionary adaptations at multiple time scales. We will also introduce the next phase of research on this topic.
Published: 2015
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47. A statistical analysis of three ensembles of crop model responses to temperature and CO2 concentration

Author: Joost Wolf, Xinyou Yin, Pierre Martre, Zhengtao Zhang, H. K. Soo, Manuel Marcaida, Nadine Brisson, Patrick Bertuzzi, Soo-Hyung Kim, Yan Zhu, Roberto C. Izaurralde, L. A. Hunt, Maria I. Travasso, Christian Baron, James W. Jones, R.E.E. Jongschaap, T. Palosuo, Daniel Wallach, Jerry L. Hatfield, Christian Biernath, G. De Sanctis, Senthold Asseng, H. Yoshida, Donald S. Gaydon, Edmar Teixeira, Davide Cammarano, Alex C. Ruane, C. Nendel, T. Hasegawa, Thilo Streck, Garry O'Leary, Upendra Singh, Frank Ewert, Delphine Deryng, R. Goldberg, Bas A. M. Bouman, Peter J. Thorburn, Tao Li, Roberto Confalonieri, Myriam Adam, Jes Olesen, Reimund P. Rötter, Tamon Fumoto, Patricio Grassini, Joachim Ingwersen, Robert F. Grant, Katharina Waha, James Williams, Fulu Tao, Eckart Priesack, Pramod K. Aggarwal, Liang Tang, Sebastian Gayler, Jordi Doltra, L. Heng, Christoph Müller, J.G. Conijn, Iwan Supit, S. Naresh Kumar, Iurii Shcherbak, Jeffrey W. White, Hendrik Boogaard, Kenneth J. Boote, David Makowski, Federico Sau, Jean-Louis Durand, Mikhail A. Semenov, Claudio O. Stöckle, Marc Corbeels, Steven Hoek, Simone Bregaglio, Hiroshi Nakagawa, Philippe Oriol, Anthony Challinor, R. A. Kemanian, Carlos Angulo, Pasquale Steduto, Bruno Basso, Kurt Christian Kersebaum, Cynthia Rosenzweig, Dennis Timlin, J. Hooker, Samuel Buis, Maria Virginia Pravia, Françoise Ruget, Dominique Ripoche, Simona Bassu, Pierre Stratonovitch, Jon I. Lizaso, Balwinder Singh, Tom M. Osborne, Paul W. Wilkens, Agronomie, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de la Recherche Agronomique (INRA), International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Int Rice Res Inst, Los Banos, Philippines, Université Paris Diderot - Paris 7 (UPD7), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), International Water Management Institute, Research Program on Climate Change, Agriculture and Food Security, CGIAR, Institute of Crops Science and Resource Conservation INRES, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Department of Geological Sciences and W. K. Kellogg Biological Station, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Department of Geological Sciences [East Lansing], Agroclim (AGROCLIM), German Research Center for Environmental Health, Institute of Soil Ecololgy, Helmholtz-Zentrum München (HZM), Center for Geo-information, Alterra, Department of Agronomy, University of Florida [Gainesville] (UF), Cassandra Lab, University of Milan, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The James Hutton Institute, CGIAR ESSP Program on Climate Change, Agriculture and Food Security, International Center for Tropical Agriculture, School of Earth and Environment [Leeds] (SEE), University of Leeds, Plant Research International, Wageningen University and Research [Wageningen] (WUR), Embrapa Cerrados, Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Tyndall Centre for Climate Change Research, School of Environmental Science, University of East Anglia [Norwich] (UEA), European Commission - Joint Research Centre [Ispra] (JRC), Cantabrian Agricultural Research and Training Centre, Tsukuba, National Institute of Agro-Environmental Sciences (NIAES), Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), WESS Water and Earth System Science Competence Cluster, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), Departement of Renewable Resources, University of Alberta, Department of Agronomy and Horticulture, University of Nebraska [Lincoln], University of Nebraska System-University of Nebraska System, National Laboratory for Agriculture and Environment, International Atomic Energy Agency [Vienna] (IAEA), Centre for Geo-Information, Agriculture Department, University of Reading (UOR), Department of Plant Agriculture, University of Guelph, Institute of Soil Science and Land Evaluation, University of Hohenheim, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Instituto Nacional de Investigación Agropecuaria (INIA), Institute of Landscape System Analysis, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), College of the Environment, School of Environmental and Forest Sciences, University of Washington, Department Produccion Vegetal, Fitotecnia, Universidad Politécnica de Madrid (UPM), Potsdam Institute for Climate Impact Research (PIK), National Agriculture and Food Research Organization (NARO), Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Institute of Landscape Systems Analysis, Department of Economic Development Jobs, Transport and Resources, Grains Innovation Park, Department of Agroecology, Aarhus University [Aarhus], Walker Institute, NCAS Climate, Natural Resources Institute Finland, Department of Plant Science, Pennsylvania State University (Penn State), Penn State System-Penn State System, German Research Center for Environmental Health, Institute of Soil Ecology, Department Biologia Vegetal, Computational and Systems Biology Department, Rothamsted Research, Department of Geological Sciences and W.K. Kellogg Biological Station, International Maize and Wheat Improvement Centre [Inde] (CIMMYT), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), International Fertilizer Development Center (IFDC), College of the Environment, School of Environmental and Forest Science, University of Washington [Seattle], FAO Sub-regional Office for Eastern Africa [Addis Ababa, Ethiopie] (FAO), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), Biological Systems Engineering, Washington State University (WSU), Plant Production Systems and Earth System Science, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Sustainable Production, Plant & Food Research, ARS Crop Systems and Global Change Laboratory, United States Department of Agriculture, CIRN, Institute for Climate and Water, Instituto Nacional de Tecnología Agropecuaria (INTA), Agriculture, Agrosystèmes Cultivés et Herbagers (ARCHE), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Arid-Land Agricultural Research Center, Texas AgriLife Research and Extension, Texas A&M University System, Centre for Crop Systems Analysis, State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University (BNU), Metaprogramme ACCAF, 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Helmholtz Zentrum München = German Research Center for Environmental Health, Università degli Studi di Milano = University of Milan (UNIMI), University of Nebraska–Lincoln, Université de Toulouse (UT)-Université de Toulouse (UT), Natural Resources Institute Finland (LUKE), Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Nanjing Agricultural University (NAU), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Agricultural and Biological Engineering Department, University of Florida [Gainesville], Institute of Crop Science and Resource Conservation INRES, International Rice Research Institute, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), UE Agroclim (UE AGROCLIM), Wageningen University and Research Centre [Wageningen] (WUR), Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Eberhard Karls Universität Tübingen, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), National Agriculture and Food Research Organization, International Maize and Wheat Improvement Centre (CIMMYT), Food and Agricultural Organization (FAO), New Zealand Institute for Plant and Food Research Limited, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Beijing Normal University, Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, University of Bonn (Rheinische Friedrich-Wilhelms), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères ( P3F ), Institut National de la Recherche Agronomique ( INRA ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Institut National de la Recherche Agronomique ( INRA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Territoires, Environnement, Télédétection et Information Spatiale ( UMR TETIS ), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture ( IRSTEA ) -AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ), Department of Geological Sciences, W.K. Kellogg Biological Station, Michigan State Univ, Dept Geol Sci, E Lansing, MI 48823 USA, UE Agroclim ( UE AGROCLIM ), Helmholtz-Zentrum München ( HZM ), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes ( EMMAH ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Institut National de la Recherche Agronomique ( INRA ), Invergowrie, School of Earth and Environment [Leeds] ( SEE ), Wageningen University and Research Centre [Wageningen] ( WUR ), Agro-ecologyand Sustainable Intensification of Annual Crops, Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ), University of East Anglia [Norwich] ( UEA ), European Commission - Joint Research Centre [Ispra] ( JRC ), National Institute for Agro-Environmental Sciences, Commonwealth Scientific and Industrial Research Organisation, NASA Goddard Institute for Space Studies ( GISS ), NASA Goddard Space Flight Center ( GSFC ), University of Nebraska-Lincoln, International Atomic Energy Agency [Vienna] ( IAEA ), University of Reading ( UOR ), UMR 1248 Agrosystèmes et Développement Territorial (AGIR), Agro-ecology and Sustainable Intensification of Annual Crops, Instituto Nacional de Investigación Agropecuaria, Leibniz Centre for Agricultural Landscape Research, Universidad Politécnica de Madrid ( UPM ), Potsdam Institute for Climate Impact Research ( PIK ), Centre for Environment Science and Climate Resilient Agriculture ( CESCRA ), Indian Agricultural Research Institute ( IARI ), PennState University [Pennsylvania] ( PSU ), W.K. Kellogg Biological Station, Department of Geological Sciences, International Maize and Wheat Improvement Centre ( CIMMYT ), International Fertilizer Development Center ( IFDC ), Food and Agricultural Organization ( FAO ), Washington State University ( WSU ), Instituto Nacional de Tecnología Agropecuaria, Agrosystèmes Cultivés et Herbagers ( ARCHE ), Institut National Polytechnique [Toulouse] ( INP ) -Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Supérieure Agronomique de Toulouse, and Texas A and M University ( TAMU )
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Atmospheric Science, 010504 meteorology & atmospheric sciences, F62 - Physiologie végétale - Croissance et développement, 01 natural sciences, Statistics, Aardobservatie en omgevingsinformatica, Climate change, Crop model, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Triticum, Mathematics, 2. Zero hunger, Global and Planetary Change, Mathematical model, Air, Forestry, Regression analysis, 04 agricultural and veterinary sciences, PE&RC, [ SDE.MCG ] Environmental Sciences/Global Changes, Rendement des cultures, Plant Production Systems, Statistical model, Modèle mathématique, Atmosphère, Earth Observation and Environmental Informatics, Yield, Crop Physiology, P40 - Météorologie et climatologie, [SDE.MCG]Environmental Sciences/Global Changes, Oryza sativa, Zea mays, Earth System Science, Emulator, Agro Water- en Biobased Economy, Alterra - Centrum Bodem, Precipitation, Croissance, 0105 earth and related environmental sciences, Meta-model, Changement climatique, Hydrology, Modélisation des cultures, Crop yield, Simulation modeling, Soil Science Centre, 15. Life on land, Température, Laboratorium voor Phytopathologie, Climate Resilience, 13. Climate action, Klimaatbestendigheid, Yield (chemistry), Plantaardige Productiesystemen, Laboratory of Phytopathology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Leerstoelgroep Aardsysteemkunde, Plante de culture, Agronomy and Crop Science, Dioxyde de carbone
Abstract: Ensembles of process-based crop models are increasingly used to simulate crop growth for scenarios of temperature and/or precipitation changes corresponding to different projections of atmospheric CO2 concentrations. This approach generates large datasets with thousands of simulated crop yield data. Such datasets potentially provide new information but it is difficult to summarize them in a useful way due to their structural complexities. An associated issue is that it is not straightforward to compare crops and to interpolate the results to alternative climate scenarios not initially included in the simulation protocols. Here we demonstrate that statistical models based on random-coefficient regressions are able to emulate ensembles of process-based crop models. An important advantage of the proposed statistical models is that they can interpolate between temperature levels and between CO2 concentration levels, and can thus be used to calculate temperature and [CO2] thresholds leading to yield loss or yield gain, without rerunning the original complex crop models. Our approach is illustrated with three yield datasets simulated by 19 maize models, 26 wheat models, and 13 rice models. Several statistical models are fitted to these datasets, and are then used to analyze the variability of the yield response to [CO2] and temperature. Based on our results, we show that, for wheat, a [CO2] increase is likely to outweigh the negative effect of a temperature increase of +2 degrees C in the considered sites. Compared to wheat, required levels of [CO2] increase are much higher for maize, and intermediate for rice. For all crops, uncertainties in simulating climate change impacts increase more with temperature than with elevated [CO2]. (C) 2015 Elsevier B.V. All rights reserved.
Published: 2015
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48. Identification and functional characterization of sex pheromone receptors in the common cutworm (Spodoptera litura)

Author: Shuwei Yan, Shuang-Lin Dong, Guirong Wang, Yang Liu, Jin Zhang, Emmanuelle Jacquin-Joly, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences (CAAS), Nanjing Agricultural University, 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), National Basic Research Program of China [2012CB114104], National Natural Science Foundation of China [31230062, 31071752], Beijing Natural Science Foundation [6132028], Nanjing Agricultural University (NAU), and 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)
Subjects: 0106 biological sciences, Male, Patch-Clamp Techniques, Physiology, Xenopus, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Spodoptera litura, Action Potentials, Spodoptera, 01 natural sciences, Pheromones, Lepidoptera genitalia, 03 medical and health sciences, Behavioral Neuroscience, Physiology (medical), Botany, Animals, Amino Acid Sequence, Cloning, Molecular, Spodoptera littoralis, Receptor, Phylogeny, 030304 developmental biology, Xenopus oocytes, 0303 health sciences, biology, Sequence Homology, Amino Acid, fungi, pheromone receptor, biology.organism_classification, Sensory Systems, Receptors, Pheromone, Cell biology, 010602 entomology, Sex pheromone, Oocytes, Pheromone, Noctuidae, RNA, Female, Sequence Alignment
Abstract: International audience; Male moths can finely discriminate the sex pheromone emitted by conspecific females from similar compounds. Pheromone receptors, expressed on the dendritic membrane of sensory neurons housed in the long trichoid sensilla of antennae, are thought to be associated with the pheromone reception. In this study, we identified and functionally characterized 4 pheromone receptors from the antennae of Spodoptera litura (Lepidoptera: Noctuidae). A tissue distribution analysis showed that the expression of the 4 SlituPRs was restricted to antennae. In addition, SlituOR6 and SlituOR13 were specifically expressed in male antennae whereas SlituOR11 and SlituOR16 were male-biased. Functional investigation by heterologous expression in Xenopus oocytes revealed that SlituOR6 was specifically tuned to the second major pheromone component, Z9,E12-14:OAc, SlituOR13 was equally tuned to Z9,E12-14:OAc and Z9-14:OAc, with a small response to the major pheromone component Z9,E11-14:OAc, SlituOR16 significantly responded to the behavioral antagonist Z9-14:OH, whereas SlituOR11 did not show response to any of the pheromone compounds tested in this study. Our results provide molecular data to better understand the mechanisms of sex pheromone detection in the moth S. litura and bring clues to investigate the evolution of the sexual communication channel in closely related species through comparison with previously reported pheromone receptors in other Spodoptera species.
Published: 2015
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49. Single machine scheduling with resource allocation and learning effect considering the rate-modifying activity

Author: Zhanguo Zhu, Feng Chu, Ming Liu, Linyan Sun, School of Management, Xi'an Jiaotong University (Xjtu), College of Economics and Management, Nanjing Agricultural University (NAU), Laboratoire d'Optimisation des Systèmes Industriels (LOSI), Institut Charles Delaunay (ICD), Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS), Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), State Key Laboratory for Mechanical Manufacturing Systems Engineering, School of Economics and Management, Tongji University, and Nanjing Agricultural University
Subjects: 0209 industrial biotechnology, Mathematical optimization, 021103 operations research, Single-machine scheduling, Learning effect, Computer science, Scheduling, Applied Mathematics, 0211 other engineering and technologies, Regular polygon, Rate-modifying activity, 02 engineering and technology, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Static memory allocation, Scheduling (computing), 020901 industrial engineering & automation, Modeling and Simulation, Max-min fairness, Modelling and Simulation, Resource allocation
Abstract: International audience; This paper addresses a single machine scheduling problem in which the actual job processing times are determined by resource allocation function, its position in a sequence and a rate-modifying activity simultaneously. We discuss two objective functions with two resource allocation functions under the consideration of a rate-modifying activity. We show that the problems are solvable in O(n4) time for a linear resource allocation function and are solvable in O(n2logn) time for a convex resource allocation function.
Published: 2013
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50. Single machine scheduling with past-sequence-dependent delivery times and learning effect

Author: Zhanguo Zhu, Ming Liu, Feng Chu, Yunfei Fang, College of Economics and Management, Nanjing Agricultural University (NAU), Dalian University of Technology, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), and Nanjing Agricultural University
Subjects: Rate-monotonic scheduling, Mathematical optimization, Single-machine scheduling, Job shop scheduling, Least slack time scheduling, Computer science, Dynamic priority scheduling, Flow shop scheduling, Round-robin scheduling, Fair-share scheduling, Learning effects, Common due date, Total completion time, Learning process, Scheduling jobs, Polynomial-time algorithms, Absolute difference, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: International audience; This paper studies single-machine scheduling problem with time-dependent delivery times and learning effect. The delivery time of a job is proportional to its waiting time in the system, i.e., the length of the already scheduling jobs. That is, the delivery times are past-sequence-dependent (psd). Delivery time denotes the time a job required to be delivered to the customer. It is assumed that the learning process reflects a decrease in the process time as a function of the number of repetitions, i.e., as a function of the job position in the sequence. We respectively consider the following objectives: the minimization of the makespan, the total completion time, the total absolute differences in completion times and the sum of earliness, tardiness and common due date penalty. We develop polynomial time algorithms to optimally solve these problems.
Published: 2013
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