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584 results on '"Wageningen University and Research Centre [Wageningen] (WUR)"'

101. Computational botany: advancing plant science through functional–structural plant modelling

Author: Véronique Letort, Mengzhen Kang, Jochem B. Evers, Michael Renton, Crop and Weed Ecology, Plant Sciences Group, Wageningen University and Research Centre [Wageningen] (WUR), Mathématiques et Informatique pour la Complexité et les Systèmes (MICS), CentraleSupélec, Développement et amélioration des plantes (UMR DAP), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Chinese Academy of Sciences [Changchun Branch] (CAS), and Wageningen University and Research [Wageningen] (WUR)
Subjects: 0106 biological sciences, Computer science, Active domain, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, ComputerApplications_COMPUTERSINOTHERSYSTEMS, Plant Science, PE&RC, 010603 evolutionary biology, 01 natural sciences, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Body of knowledge, Plant development, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Plant science, Botany, Life Science, Research questions, Plant system, Preface, Crop and Weed Ecology, Scientific disciplines, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany
Abstract: The need to integrate the ever-expanding body of knowledge in the plant sciences has led to the development of sophisticated modelling approaches. This special issue focuses on functional-structural plant (FSP) models, which are the result of cross-fertilization between the domains of plant science, computer science and mathematics. FSP models simulate growth and morphology of individual plants that interact with their environment, from which complex plant community properties emerge. FSP models can be used for a broad range of research questions across disciplines related to plant science. This special issue presents the latest developments in FSP modelling, including the novel incorporation of plant ecophysiological concepts and the application of FSP models to address new scientific questions. Additionally, it illustrates the breadth of model evaluation approaches that are performed. FSP modelling is a very active domain of plant research which brings together a wide range of scientific disciplines. It offers the opportunity to address questions in complex plant systems that cannot be addressed by empirical approaches alone, including questions on fundamental concepts related to plant development such as regulation of morphogenesis, as well as on applied concepts such as the relationship between crop performance and plant competition for resources.
Published: 2018
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102. beta-Carotene in the human body: metabolic bioactivation pathways - from digestion to tissue distribution and excretion

Author: Patrick Borel, Ralph Rühl, Torsten Bohn, Jaap Keijer, Charles Desmarchelier, Sedef Nehir El, Evert M. van Schothorst, Luxembourg Institute of Health (LIH), Centre recherche en CardioVasculaire et Nutrition (C2VN), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Ege university, Human and Animal Physiology [Wageningen, The Netherlands], Wageningen University [The Netherlands], Paprika Bioanalytics BT, EU-COST action POSITIVE FA 1403, EU-COST action EUROCAROTEN CA 15136, Nutrition Society. GBR., Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ege University - EGE (Izmir, Turkey), Wageningen University and Research [Wageningen] (WUR), Paprika Bioanalytics BT [Debrecen, Hungary], Nutrition humaine et lipides : Biodisponibilité, métabolisme et régulation, Université de la Méditerranée - Aix-Marseille 2-Institut National de la Recherche Agronomique (INRA)-Université de Provence - Aix-Marseille 1-IFR125-Institut National de la Santé et de la Recherche Médicale (INSERM), Wageningen University and Research Centre [Wageningen] (WUR), University of Debrecen Egyetem [Debrecen], Ege Üniversitesi, and Prémilleux, Annick
Subjects: 0301 basic medicine, Micellisation, medicine.drug_class, [SDV]Life Sciences [q-bio], Retinoic acid, Biological Availability, Medicine (miscellaneous), Pharmacology, Nuclear hormone receptor, Absorption, 03 medical and health sciences, chemistry.chemical_compound, Apo-carotenoids, medicine, Humans, Tissue Distribution, Retinoid, Receptor, Vitamin A, ComputingMilieux_MISCELLANEOUS, 030109 nutrition & dietetics, Nutrition and Dietetics, Chemistry, Retinol, beta Carotene, 3. Good health, [SDV] Life Sciences [q-bio], [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Retinoic acid receptor, 030104 developmental biology, Blood chemistry, Nuclear receptor, Digestion, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Metabolic Networks and Pathways, Drug metabolism, SNPs
Abstract: EgeUn###, beta-Carotene intake and tissue/blood concentrations have been associated with reduced incidence of several chronic diseases. Further bioactive carotenoid-metabolites can modulate the expression of specific genes mainly via the nuclear hormone receptors: retinoic acid receptor- and retinoid X receptor-mediated signalling. To better understand the metabolic conversion of beta-carotene, inter-individual differences regarding beta-carotene bioavailability and bioactivity are key steps that determine its further metabolism and bioactivation and mediated signalling. Major carotenoid metabolites, the retinoids, can be stored as esters or further oxidised and excreted via phase 2 metabolism pathways. In this review, we aim to highlight the major critical control points that determine the fate of beta-carotene in the human body, with a special emphasis on beta-carotene oxygenase 1. The hypothesis that higher dietary beta-carotene intake and serum level results in higher beta-carotene-mediated signalling is partly questioned. Alternative autoregulatory mechanisms in beta-carotene / retinoid-mediated signalling are highlighted to better predict and optimise nutritional strategies involving beta-carotene-related health beneficial mediated effects., Nutr Soc, Scottish Sect, EU-COST action POSITIVE [FA 1403]; EU-COST action EUROCAROTEN [CA 15136], The insights from EU-COST action POSITIVE (FA 1403) and EUROCAROTEN (CA 15136) are much appreciated.
Published: 2018
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103. Alteration of the characteristics of extracellular polymeric substances (EPS) extracted from the fungus Phanerochaete chrysosporium when exposed to sub-toxic concentrations of nickel (II)

Author: Eric D. van Hullebusch, Gilles Guibaud, Eldon R. Rene, Piet N.L. Lens, Feishu Cao, Yoan Pechaud, Isabelle Bourven, Laboratoire Géomatériaux et Environnement (LGE), Université Paris-Est Marne-la-Vallée (UPEM), Groupement de Recherche Eau, Sol, Environnement (GRESE), Université de Limoges (UNILIM), Sub-Department of Environmental Technology, Wageningen University and Research [Wageningen] (WUR), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-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)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, inorganic chemicals, Hydrophobicity, 010501 environmental sciences, Polysaccharide, 01 natural sciences, Microbiology, Biomaterials, Metal, 03 medical and health sciences, Extracellular polymeric substance, Nickel, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Fourier transform infrared spectroscopy, Waste Management and Disposal, 0105 earth and related environmental sciences, Chrysosporium, chemistry.chemical_classification, Phanerochaete chrysosporium, Chromatography, biology, Extraction (chemistry), Fungi, biology.organism_classification, 030104 developmental biology, chemistry, visual_art, visual_art.visual_art_medium, cardiovascular system, Molecular size, Phanerochaete, Composition (visual arts), EPS, tissues
Abstract: International audience; The fungus Phanerochaete chrysosporium was incubated at five sub-toxic concentrations of Ni2+ (0.5, 1, 5, 10 and 25 mg/L, respectively), and its metal immobilization ability as well as the alteration of some characteristics regarding the extracellular polymeric substances (EPS) were investigated. With the increased Ni2+ concentrations in the broth, higher Ni2+ amounts were measured in both intact fungal cells (biomass before EPS extraction) and EPS-free biomass (biomass after EPS extraction). The Ni2+ immobilization ability of the extracted EPS displayed a similar level at Ni2+ concentrations higher than 1 mg/L. The presence of Ni2+ in the broth decreased the zeta-potential of the intact biomass and increased cell surface hydrophobicity (CSH). Fourier transform infrared spectroscopy (FT-IR) analyses identified the presence of some functional groups, such as carboxyl, phosphoryl and hydroxyl groups, in the extracted EPS. The high hydrophobicity (>60%) of the extracted EPS was decreased by the increased Ni2+ concentration. The protein (PN) and polysaccharide (PS) content in the EPS was also affected by the increased Ni2+ concentration, and the abundance of PN-like molecules ranging from 0.5 kDa to 14 kDa was enriched. However, the fluorescence characteristics and apparent molecular weight (aMW) of the extracted EPS were not affected by the Ni2+ concentration. Therefore, one possible defense mechanism developed by the fungus towards Ni2+ stress is the adjustment of its EPS composition.
Published: 2018
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104. The impact of water and nitrogen depletion on Aphis pomi infestation in the apple orchard and its relation with the useful fauna and ants

Author: Laghfiri, M., Madani, I., Boutaleb, A.J., Blenzar, A., Jordan, Marie Odile, Sauge, Marie-Helene, Lauri, Pierre-Eric, Smaili, C., Laboratory of Biology, Faculty of Science Meknes, Université Sultan Moulay Slimane (USMS ), Laboratory of Entomology, Wageningen University and Research [Wageningen] (WUR), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Laboratory of NARI, Université Sultan Moulay Slimane - USMS (Béni Mellal, MA), Wageningen University and Research Centre [Wageningen] (WUR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), and Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Fauna, chemistry.chemical_element, Biology, chrysoperla carnea, medicine.disease_cause, Aphis pomi, besoin azoté, Infestation, Materials Chemistry, medicine, Environmental Chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nitrogendepletion, ant, Waste Management and Disposal, water deficit, réserve en eau, Vegetal Biology, useful fauna, déficit hydrique, water depletion, 15. Life on land, Pollution, Nitrogen, Horticulture, stratégie écologique, chemistry, fourmi, infestation, puceron, Orchard, Biologie végétale
Abstract: This work aims to establish an ecologically integrated strategy for pest management to assess the impact of water and nitrogen depletion on Aphis pomi infestation in the Apple orchard.The results of the study of the impact on the green Apple aphid show a significant effect on the availability of water and nitrogen on the level of Aphis pomi infestation. Indeed, the normal fertigation regime (T1 = 100%) proved to be more favorable to a prominent development of aphids, in comparison with a 25% water and nitrogen deficit regime (T2 = 75%), that minimize infestation. As for the evolution of wingless aphid and green aphid with wing, the Aphis pomi, at both regimes, the general shape of the evolution of winged curves looks like the one of the wingless ones, with small differences. The number of leaves was higher in the T1 regime than that of T2. Moreover, the study of the orientation effect on the infestation of aphids has shown that the North andthe West sides were more infested than the East and the South ones. A negative effect on Syrphesp and ChrysoperlaCarnea densities was noticed under water and nitrogen depletion.
Published: 2018
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105. Changes in Dietary Intake and Adherence to the NU-AGE Diet Following a One-Year Dietary Intervention among European Older Adults-Results of the NU-AGE Randomized Trial

Author: Anna Brzozowska, Rita Ostan, Rachel Gillings, Agnieszka Stelmaszczyk-Kusz, Agnes A M Berendsen, Lisette C. P. G. M. de Groot, Edith J. M. Feskens, Aurélie Caille, Aurelia Santoro, Ondine van de Rest, Amy Jennings, Elodie Caumon, Claudio Franceschi, Aedin Cassidy, Barbara Pietruszka, Corinne Malpuech-Brugère, Division of Human Nutrition, Wageningen University and Research [Wageningen] (WUR), Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Centro Interdipartimentale « L. Galvani» (CIG), Alma Mater Studiorum, Department of Human Nutrition, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Department of Nutrition & Preventive Medicine, Norwich Medical School, University of East Anglia [Norwich] (UEA), CHU Clermont-Ferrand, Centre de Recherche en Nutrition Humaine, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institute of Neurological Science of Bologna (IRCCS), European Project: 266486,EC:FP7:KBBE,FP7-KBBE-2010-4,NU-AGE(2011), Berendsen, A. A. M., Berendsen, Agnes A. M., van de Rest, Ondine, Feskens, Edith J. M., Santoro, Aurelia, Ostan, Rita, Pietruszka, Barbara, Brzozowska, Anna, Stelmaszczyk-Kusz, Agnieszka, Jennings, Amy, Gillings, Rachel, Cassidy, Aedin, Caille, Aurélie, Caumon, Elodie, Malpuech-Brugere, Corinne, Franceschi, Claudio, de Groot, Lisette C. P. G. M., Wageningen University and Research Centre [Wageningen] (WUR), University of Bologna, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of East Anglia, Centre Hospitalier Universitaire de Clermont-Ferrand, Unité de Nutrition Humaine - Clermont Auvergne (UNH), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)
Subjects: Male, 0301 basic medicine, medicine.medical_specialty, Mediterranean diet, Diet adherence, lcsh:TX341-641, Diet, Mediterranean, Article, law.invention, Food group, 03 medical and health sciences, Mediterranean-like diet, 0302 clinical medicine, Randomized controlled trial, law, dietary intervention, Intervention (counseling), Internal medicine, Humans, Food and Nutrition, Medicine, 030212 general & internal medicine, VLAG, Aged, Global Nutrition, Aged, 80 and over, Wereldvoeding, 030109 nutrition & dietetics, Nutrition and Dietetics, business.industry, Dietary intake, Feeding Behavior, European population, Dietary advice, Inflammaging, Diet, 3. Good health, Dietary intervention, Nutrition Assessment, Alimentation et Nutrition, Patient Compliance, Female, inflammaging, business, lcsh:Nutrition. Foods and food supply, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: Background: The Mediterranean Diet has been proposed as an effective strategy to reduce inflammaging, a chronic low grade inflammatory status, and thus, to slow down the aging process. We evaluated whether a Mediterranean-like dietary pattern specifically targeting dietary recommendations of people aged over 65 years (NU-AGE diet) could be effective to shift dietary intake of older adults towards a healthful diet. Methods: Adults aged 65&ndash, 80 years across five EU-centers were randomly assigned to a NU-AGE diet group or control group. The diet group followed one year of NU-AGE dietary intervention specifying consumption of 15 food groups plus the use of a vitamin D supplement. Participants in the diet group received counselling and individually tailored dietary advice, food products and a vitamin D supplement. Dietary intake was assessed by means of seven-day food records at baseline and one-year follow-up. A continuous NU-AGE index (0&ndash, 160 points) was developed to assess NU-AGE diet adherence. Results: In total 1296 participants were randomized and 1141 participants completed the intervention (571 intervention, 570 control). After one year, the diet group improved mean intake of 13 out of 16 NU-AGE dietary components (p &lt, 0.05), with a significant increase in total NU-AGE index (difference in mean change = 21.3 &plusmn, 15.9 points, p &lt, 0.01). Conclusions: The NU-AGE dietary intervention, based on dietary recommendations for older adults, consisting of individual dietary counselling, free healthy foods and a vitamin D supplement, may be a feasible strategy to improve dietary intake in an aging European population.
Published: 2018
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106. Nonselective Chemical Inhibition of Sec7 Domain-Containing ARF GTPase Exchange Factors

Author: Steven De Munck, Riet De Rycke, Bram Denoo, Sacco C. de Vries, Jan Hullaert, Wim Annaert, Isha Sharma, Kaija Goodman, Wim Dejonghe, Johan M. Winne, Marisa S. Otegui, François Peurois, Wim Nerinckx, Andrzej Drozdzecki, Annemieke Madder, Jacqueline Cherfils, Marine Bretou, Qing Lu, Sara Martins, Sjef Boeren, Grégory Vert, Kamila Kalinowska, Veronique Storme, Long Nguyen, Dominique Audenaert, Erika Isono, Kiril Mishev, Savvas N. Savvides, Eugenia Russinova, Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent University Hospital, Laboratory of Biochemistry, Wageningen University and Research [Wageningen] (WUR), Immunité et cancer (U932), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Plant Biotechnology and Bioinformatics, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ghent University, Compound Screening Facility, VIB, Signalisation Cellulaire et Ubiquitination chez les plantes (UBINET), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Organic and Biomimetic Chemistry Research Group, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Laboratory of Membrane Trafficking and VIB11, Center for Human Genetics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Polymer Research Group, State Univ Ghent, Department of Systems Biology, Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Ghent University [Belgium] (UGENT), Laboratoire de dynamique membranaire et maladies neurologiques (UMR 8192), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), VIB Inflammation Research Center, Laboratoire d'enzymologie et biochimie structurales (LEBS), Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Curie [Paris]-Université Paris Descartes - Paris 5 (UPD5), Universiteit Gent [Ghent], Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Université Polytechnique Hauts-de-France (UPHF)-Institut supérieur de l'électronique et du numérique (ISEN), Wageningen University and Research Centre [Wageningen] (WUR), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, ADP ribosylation factor, Endosome, [SDV]Life Sciences [q-bio], Arabidopsis, Biochemie, Endosomes, Plant Science, arabidopsis-thaliana, Biology, receptor kinase bri1, Endocytosis, Biochemistry, UBINET, Piperazines, 03 medical and health sciences, symbols.namesake, chemistry.chemical_compound, golgi network/early endosome, BIOCELL, Guanine Nucleotide Exchange Factors, Life Science, Endomembrane system, endomembrane trafficking, Research Articles, brefeldin-a, Brefeldin A, protein complexes, Arabidopsis Proteins, plasma-membrane, plant-cells, Cell Biology, Golgi apparatus, Plants, Genetically Modified, Transport protein, Cell biology, wide analysis, Protein Transport, small molecules, 030104 developmental biology, chemistry, Vacuoles, symbols, Phthalazines, Guanine nucleotide exchange factor, Protein Kinases
Abstract: International audience; Small GTP-binding proteins from the ADP-ribosylation factor (ARF) family are important regulators of vesicle formation and cellular trafficking in all eukaryotes. ARF activation is accomplished by a protein family of guanine nucleotide exchange factors (GEFs) that contain a conserved catalytic Sec7 domain. Here, we identified and characterized Secdin, a small-molecule inhibitor of Arabidopsis thaliana ARF-GEFs. Secdin application caused aberrant retention of plasma membrane (PM) proteins in late endosomal compartments, enhanced vacuolar degradation, impaired protein recycling, and delayed secretion and endocytosis. Combined treatments with Secdin and the known ARF-GEF inhibitor Brefeldin A (BFA) prevented the BFA-induced PM stabilization of the ARF-GEF GNOM, impaired its translocation from the Golgi to the trans-Golgi network/early endosomes, and led to the formation of hybrid endomembrane compartments reminiscent of those in ARF-GEF-deficient mutants. Drug affinity-responsive target stability assays revealed that Secdin, unlike BFA, targeted all examined Arabidopsis ARF-GEFs, but that the interaction was probably not mediated by the Sec7 domain because Secdin did not interfere with the Sec7 domain-mediated ARF activation. These results show that Secdin and BFA affect their protein targets through distinct mechanisms, in turn showing the usefulness of Secdin in studies in which ARF-GEF-dependent endomembrane transport cannot be manipulated with BFA.
Published: 2018
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107. Prediction of enteric methane production, yield and intensity of beef cattle using an intercontinental database

Author: Nico Peiren, Mark McGee, Zhongtang Yu, Sang Suk Lee, Sebastião de Campos Valadares Filho, Ali R. Bayat, Alexandre Berndt, Telma Teresinha Berchielli, Kristin E Hales, Angela Schwarm, André Bannink, E. Charmley, N. Andy Cole, Jan Dijkstra, Maguy Eugène, Cécile Martin, Ermias Kebreab, Carol Anne Duthie, David R. Yáñez-Ruiz, M. Niu, Michael Kreuzer, John Rooke, Les A. Crompton, David P. Casper, Christopher K. Reynolds, Juliana Duarte Messana, Padraig O'Kiely, Martin Hünerberg, Tim A. McAllister, Henk J. van Lingen, Alexander N. Hristov, Mariana Caetano, P. I. Hynd, Alex V. Chaves, Federal Office for Agriculture (Switzerland), European Commission, National Institute of Food and Agriculture (US), Department of Agriculture, Food and Marine (Ireland), Department of Animal science, University of California [Davis] (UC Davis), University of California-University of California, Farmer’s Business Network, Animal Science Department, University of Tabriz [Tabriz], Scotland's Rural College (SRUC), Institute of Agricultural Sciences, Ecole Polytechnique Fédérale de Zurich, University of Adelaide, Department of Animal and Veterinary Bioscience, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Teagasc Agriculture and Food Development Authority (Teagasc), Department of Agricultural, Food and Nutritional Science, University of Alberta, Lethbridge Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), Research Institute for Agricultural, Fisheries and Food (ILVO), Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), USDA-ARS : Agricultural Research Service, Department of Animal Science and Technology, Suncheon National University, Research and Development, EMBRAPA Southeast Livestock, School of Agriculture, Policy and Development, University of Reading (UOR), Milk Production, Production Systems, Natural resources institute Finland, Estacion Experimental del Zaidin-CSIC, Department of Animal Sciences, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Wageningen Livestock Research, Wageningen / Aeres University of Applied Sciences, Animal Nutrition Group, Wageningen University and Research [Wageningen] (WUR), Furst McNess Company, FACCE-JPI program Global Network (ANR-13-JFAC-0003-01), Scotland's Rural College (SCUR), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), United States Department of Agriculture - Agricultural Research Service, Natural Resources Institute Finland, Wageningen University and Research Centre [Wageningen] (WUR), University of California, Farmer's Business Network Inc., Universidade Federal de Viçosa (UFV), SRUC, The University of Adelaide, Université Clermont Auvergne, Dunsany, Agriculture and Agri-Food Canada, Universidade Estadual Paulista (Unesp), Animal Sciences Unit, School of Life and Environmental Sciences, CSIRO Agriculture and Food, USDA-ARS, Sunchon National University, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), University of Reading, Natural Resources Institute Finland (Luke), Estación Experimental del Zaidin (CSIC), The Ohio State University, Wageningen University & Research, The Pennsylvania State University, and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0106 biological sciences, bovin, Animal Nutrition, [SDV]Life Sciences [q-bio], Forage, Beef cattle, computer.software_genre, 7. Clean energy, 010603 evolutionary biology, 01 natural sciences, Dietary variables, Yield (wine), Linear regression, Dry matter, méthane, Empirical modeling, Geographical region, Mathematics, 2. Zero hunger, base de données, Ecology, Database, 04 agricultural and veterinary sciences, prediction, Forage content, Diervoeding, 13. Climate action, Greenhouse gas, international, marsh gas, Methane emission, 040103 agronomy & agriculture, WIAS, 0401 agriculture, forestry, and fisheries, Animal Science and Zoology, Agronomy and Crop Science, computer, Intensity (heat transfer), Predictive modelling
Abstract: Enteric methane (CH) production attributable to beef cattle contributes to global greenhouse gas emissions. Reliably estimating this contribution requires extensive CH emission data from beef cattle under different management conditions worldwide. The objectives were to: 1) predict CH production (g d animal), yield [g (kg dry matter intake; DMI)] and intensity [g (kg average daily gain)] using an intercontinental database (data from Europe, North America, Brazil, Australia and South Korea); 2) assess the impact of geographic region, and of higher- and lower-forage diets. Linear models were developed by incrementally adding covariates. A K-fold cross-validation indicated that a CH production equation using only DMI that was fitted to all available data had a root mean square prediction error (RMSPE; % of observed mean) of 31.2%. Subsets containing data with ≥25% and ≤18% dietary forage contents had an RMSPE of 30.8 and 34.2%, with the all-data CH production equation, whereas these errors decreased to 29.3 and 28.4%, respectively, when using CH prediction equations fitted to these subsets. The RMSPE of the ≥25% forage subset further decreased to 24.7% when using multiple regression. Europe- and North America-specific subsets predicted by the best performing ≥25% forage multiple regression equation had RMSPE of 24.5 and 20.4%, whereas these errors were 24.5 and 20.0% with region-specific equations, respectively. The developed equations had less RMSPE than extant equations evaluated for all data (22.5 vs. 23.2%), for higher-forage (21.2 vs. 23.1%), but not for the lower-forage subsets (28.4 vs. 27.9%). Splitting the dataset by forage content did not improve CH yield or intensity predictions. Predicting beef cattle CH production using energy conversion factors, as applied by the Intergovernmental Panel on Climate Change, indicated that adequate forage content-based and region-specific energy conversion factors improve prediction accuracy and are preferred in national or global inventories., Authors gratefully acknowledge project funding from the USDA National Institute of Food and Agriculture Federal Appropriations under Project PEN 04539 and Accession number 1000803; the Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE-JPI)’s ‘GLOBAL NETWORK’ project and the ‘Feeding and Nutrition Network’ (http://animalscience.psu.edu/fnn) of the Livestock Research Group within the Global Research Alliance for Agricultural Greenhouse Gases (www.globalresearchalliance.org); the Sesnon Endowed Chair program (UC Davis); the Swiss Federal Office of Agriculture, Berne, Switzerland; AHDB Beef and Lamb, the Scottish Government, Defra and the devolved administrations through the UK Agricultural Greenhouse Gas Inventory Research Platform; French National Research Agency through the FACCE-JPI program (ANR-13-JFAC-0003-01); the Cooperative Research Program for Agriculture Science, (Project No. PJ013448012018), RDA, Republic of Korea; the Australian Government Department of Agriculture, Fisheries and Forestry (Carbon Farming Futures Action on the Ground program; AOTGR2-0400); the financial support of the Reducing Emissions from Livestock Research Program, the National Livestock Methane Program, Meat and Livestock Australia, CSIRO and Ridley AgriProducts Pty, Ltd; the Institute of Science and Technology in Animal Science (INCTCA 465377/2014-9), the Department of Agriculture, Food and the Marine (DAFM), Ireland (AGRI-I project); European Commission through SMEthane (FP7‐SME‐262,270); Beef Cattle Research Council of the Canadian Cattlemen’s Association; the Cofund for Monitoring & Mitigation of Greenhouse Gases from Agri- and Silvi-culture (FACCE ERA-GAS)’s project Capturing Effects of Diet on Emissions from Ruminant Systems and the Dutch Ministry of Agriculture, Nature and Food Quality (AF-EU-18010 & BO-4400159-01).
Published: 2018
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108. Spatial Dimensions of the Risks of Rodenticide Use to Non-target Small Mammals and Applications in Spatially Explicit Risk Modeling

Author: Nico W. van den Brink, Patrick Giraudoux, Clémentine Fritsch, Michael Coeurdassier, Marion Jacquot, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Wageningen University and Research [Wageningen] (WUR), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Wageningen University and Research Centre [Wageningen] ( WUR ), and Fritsch, Clémentine
Subjects: 0106 biological sciences, biology, Ecology, Range (biology), Home range, 010501 environmental sciences, Toxicology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, [SDE.ES]Environmental Sciences/Environmental and Society, Bank vole, Wood mouse, Habitat, CE - Molecular Ecology Ecotoxicology and Wildlife Management, Threatened species, Life Science, Vole, [SDE.ES] Environmental Sciences/Environmental and Society, Water vole, Environmental planning, Toxicologie, [ SDE.ES ] Environmental Sciences/Environmental and Society, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: Both target and non-target small mammals are exposed to rodenticides (AR). A better understanding of the drivers controlling this exposure is critical for the conservation of threatened small mammal species but also because they may represent important pathways of poisoning for birds of prey and carnivore mammals. Here, we consider the spatial components involved in the process of small mammal exposure to ARs with the aim to address how these can be used in spatially explicit risk assessment. We present how various drivers operate on multiple spatial scales. On continental and/or regional scales, both biogeographical distribution of small mammals and other species of conservation value and international/national regulations of AR applications (indoor vs outdoor…) could be used to identify some countries or states where exposure is more likely. For application at the local scale (i.e. few km2), we reviewed published studies that analysed the spatial pattern of small mammal exposure to ARs according to species and distance to treatments. We evidence that most of the small mammals exposed to AR are found in the immediate vicinity of treatment areas, i.e., within 100 m. Over 100 m, exposed rodents are rare but can be found until 750 m distance from treatment areas. Species traits related to spatial dimension such as habitat preferences, home range size and mobility also influence exposure. Exposure is variable, in terms of proportion of contaminated individuals and levels of residues, for species showing small home-range size and a limited spatial mobility. The level of exposure depends on whether the main habitat of the given species is similar or not to the one of the target rodent. For instance, exposure of the common vole, a grassland species, is low when ARs are used indoor while it can be highly exposed when bromadiolone is applied outdoor to control the water vole, a sympatric species. For small mammals exhibiting a relatively large home-range size and a high spatial mobility such as the wood mouse and the bank vole, the exposure is commonly reported within a lower range than target species. Although this has not been studied in details, we also address how landscape and/or habitat features may modulate exposure, suggesting that landscape management may help to mitigate the risk of ARs to small mammals. Finally, we discuss both the advantages and disadvantages of statistical, analytical or simulation models to assess potential or actual exposure of NTSM to AR in a spatially explicit way. We conclude that in order to analyse global patterns in usage and exposure risks, large scale statistical modelling should be used while for detailed site specific assessments, simulation models may be more appropriate.
Published: 2018

109. Compressive resistance of granular-scale microgels: from loose to dense packing

Author: Karin Schroën, Antoine Bouchoux, Martine Meireles, Izabella Bouhid de Aguiar, Laboratoire de génie chimique [ancien site de Basso-Cambo] (LGC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Wageningen University and Research [Wageningen] (WUR), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), European Commission - Education, Audiovisual and Culture Executive Agency (EACEA) under the program Erasmus Mundus Doctorate in Membrane Engineering - EUDIME [2011-0014], Wageningen University and Research Centre [Wageningen] (WUR), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génie Chimique (LGC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Wageningen University & Research - WUR (NETHERLANDS), and Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
Subjects: Materials science, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, [PHYS.MECA.MEMA]Physics [physics]/Mechanics [physics]/Mechanics of materials [physics.class-ph], Osmotic pressure, Colloid and Surface Chemistry, Thermal, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Génie chimique, Composite material, Génie des procédés, Food Process Engineering, Dextran, VLAG, chemistry.chemical_classification, Microgels, Compression resistance, Random close pack, Hard spheres, Polymer, 021001 nanoscience & nanotechnology, Compression (physics), 0104 chemical sciences, Confocal microscopy, chemistry, Compressibility, Deformation (engineering), 0210 nano-technology, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: International audience; Microgels are deformable and compressible particles that can be packed to concentrations that exceed the random close packing limit of hard spheres. For reaching high packing levels, one has to overcome the resistance to compression of the system. This resistance potentially originates from many different phenomena (thermal agitation effects, surface interactions, microgel deformation, interpenetration, water expulsion) that depend on the microgel properties (size, ionic charge, structure, softness). Here, we investigate granular-scale dextran-based microgels with different native water contents. The resistance to compression of the suspensions is measured through the variation of the osmotic pressure with packing concentration. In parallel, we characterize the structure of the packings in terms of polymer heterogeneity, microgel deformation, and average size using confocal microscopy. We find that all microgel suspensions resist compression in the same manner; however, the mechanisms involved clearly depend on the actual degree of compression. In the loose packing regime, the resistance originates mainly from the resistance of the microgels to their own deformation, with no or negligible deswelling; the osmotic pressure rises abruptly with concentration in analogy to compressed emulsion droplets. In the second and dense packing regime, the microgels necessarily have to expel water to withstand compression. The resistance of the packing is then similar to that of a continuous gel of the same polymer. Importantly, we find that structural macro-voids are still observable in these systems; the presence of which needs to be taken into account when modeling the osmotic resistance.
Published: 2018
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110. Compositional response of Amazon forests to climate change

Author: Eliana Jimenez-Rojas, Maria Cristina Peñuela-Mora, Nadir Pallqui Camacho, Georgia Pickavance, Rodolfo Vásquez Martínez, Gabriela Lopez-Gonzalez, Wendeson Castro, Julie Peacock, Emilio Vilanova, Julien Engel, Percy Núñez Vargas, John Terborgh, Raquel Thomas, José Luís Camargo, Alexander Parada Gutierrez, David W. Galbraith, Nallaret Davila Cardozo, Rafael Herrera Fernández, Lan Qie, Jon Lloyd, Carlos A. Quesada, Thomas E. Lovejoy, Jérôme Chave, Ima Célia Guimarães Vieira, Ricardo Keichi Umetsu, William F. Laurance, Gerardo A. Aymard C, Eurídice N. Honorio Coronado, Hirma Ramírez-Angulo, Rafael de Paiva Salomão, Sophie Fauset, Hans ter Steege, Vincent A. Vos, Antonio Carlos Lola da Costa, Luisa Fernanda Duque, Maxime Réjou-Méchain, Luis Valenzuela Gamarra, Pascal Petronelli, Damien Bonal, Roel J. W. Brienen, César I.A. Vela, Christopher Baraloto, Javier Silva Espejo, Niro Higuchi, Ana Andrade, Anand Roopsind, Simon L. Lewis, Timothy R. Baker, Fernando Elias, Armando Torres-Lezama, David A. Neill, Eric Arets, Marielos Peña-Claros, Edmar Almeida de Oliveira, Martin J. P. Sullivan, Plínio Barbosa de Camargo, Wannes Hubau, Adriana Prieto, Ted R. Feldpausch, James A. Comiskey, Ben Hur Marimon-Junior, Adriano José Nogueira Lima, Fernando Cornejo Valverde, Natalino Silva, Zorayda Restrepo Correa, Yadvinder Malhi, Jorcely Barroso, Kyle G. Dexter, Simone Aparecida Vieira, Marisol Toledo, Terry L. Erwin, Anthony Di Fiore, Victor Chama Moscoso, Oliver L. Phillips, Alejandro Araujo-Murakami, Omar Aurelio Melo Cruz, Clément Stahl, Jos Barlow, Bruno Hérault, Jhon del Aguila Pasquel, Nigel C. A. Pitman, Everton Cristo de Almeida, Luiz E. O. C. Aragão, Pieter A. Zuidema, Geertje M. F. van der Heijden, Susan G. Laurance, Marcos Silveira, Peter van der Hout, Abel Monteagudo-Mendoza, Paulo S. Morandi, Guido Pardo, René G. A. Boot, Beatriz Schwantes Marimon, James Singh, Agustín Rudas, Luzmila Arroyo, Peter J. van de Meer, Lourens Poorter, Gerardo Flores Llampazo, Frans Bongers, Emanuel Gloor, Adriane Esquivel-Muelbert, Juliana Stropp, Esteban Álvarez-Dávila, University of Leeds, School of Geography [Leeds], Imperial College London, Missouri Botanical Garden (USA), Museo de Historia Natural Noel Kempff Mercado, Universidad Autonoma Gabriel René Moreno, Fundación Con-Vida, Instituto Nacional de Pesquisas da Amazônia (INPA), Universidade do Estado de Mato Grosso (UNEMAT), Instituto de Investigaciones para el Desarrollo Forestal, Universidad de los Andes [Bogota], Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Forest Ecology and Forest Management Group, Wageningen University and Research Centre [Wageningen] (WUR), Naturalis Biodiversity Center [Leiden], Ecologie des forêts de Guyane (UMR ECOFOG), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Van der Hout Forestry Consulting, The Royal Society, University of St Andrews. School of Geography & Sustainable Development, Missouri Botanical Garden, Universidad de los Andes [Bogota] (UNIANDES), SILVA (SILVA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Lorraine (UL), Forêts et Sociétés (UPR Forêts et Sociétés), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Environnements et Sociétés (Cirad-ES), Wageningen University and Research [Wageningen] (WUR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)-AgroParisTech, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Systems Ecology
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Tropical forests, Bos- en Landschapsecologie, Biodiversity, adaptation aux changements climatiques, forêt tropicale, Forests, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, traits, CARBON STORAGE, K01 - Foresterie - Considérations générales, SDG 13 - Climate Action, Climate change, Primary Research Article, functional traits, skin and connective tissue diseases, General Environmental Science, Global and Planetary Change, GE, Ecology, Amazon rainforest, PE&RC, Geography, climate change, NEOTROPICAL FOREST, GROWTH, Vegetatie, Bos- en Landschapsecologie, Functional traits, Communauté végétale, GE Environmental Sciences, VEGETATION DYNAMICS, F40 - Écologie végétale, P40 - Météorologie et climatologie, bioclimatic niches, DROUGHT SENSITIVITY, Tropical Forest, Ecosystem, Bosecologie en Bosbeheer, Temporal Variation, Bois tropical, Vegetatie, Changement climatique, Science & Technology, Bioclimatic niches, Composition botanique, Brasil, Water, 15. Life on land, 06 Biological Sciences, Floristics, Forest Ecology and Forest Management, biodiversité forestière, functional, Season, Vegetation, Forest and Landscape Ecology, Physiology, WOOD DENSITY, Biodiversity & Conservation, 05 Environmental Sciences, DIVERSITY, Bibliomatic niches, Tropic Climate, Trees, Environmental Science(all), Dry season, Tropical climate, Forest and Landscape Ecology, Lowland Environment, Tropial forests, tropical forests, Bioclimatology, PERVASIVE ALTERATION, F70 - Taxonomie végétale et phytogéographie, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Funtional traits, Classification, Biodiversity Conservation, Seasons, TREE COMMUNITIES, Life Sciences & Biomedicine, Brazil, Tree, Temporal trends, Environmental Sciences & Ecology, 010603 evolutionary biology, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Amazonia, Niche, Environmental Chemistry, Forest, Compositional shifts, 0105 earth and related environmental sciences, Tropical Climate, Vegetation, Tropics, DAS, Carbon Dioxide, Primary Research Articles, Climatic change, 13. Climate action, Earth and Environmental Sciences, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Dioxyde de carbone, Environmental Sciences
Abstract: Funding Information: Natural Environment Research Council (NERC), Grant/Award Number: NE/ N004655/1; NERC Consortium Grants “AMAZONICA”; BIO‐RED; European Research Council (ERC); The Gordon and Betty Moore Foundation; European Union's Seventh Framework Programme, Grant/ Award Number: 282664; Royal Society, Grant/Award Number: CH160091; Royal Society Wolfson Research Merit Award. Most of the planet's diversity is concentrated in the tropics, which includes many regions undergoing rapid climate change. Yet, while climate-induced biodiversity changes are widely documented elsewhere, few studies have addressed this issue for lowland tropical ecosystems. Here we investigate whether the floristic and functional composition of intact lowland Amazonian forests have been changing by evaluating records from 106 long-term inventory plots spanning 30 years. We analyse three traits that have been hypothesized to respond to different environmental drivers (increase in moisture stress and atmospheric CO2 concentrations): maximum tree size, biogeographic water-deficit affiliation and wood density. Tree communities have become increasingly dominated by large-statured taxa, but to date there has been no detectable change in mean wood density or water deficit affiliation at the community level, despite most forest plots having experienced an intensification of the dry season. However, among newly recruited trees, dry-affiliated genera have become more abundant, while the mortality of wet-affiliated genera has increased in those plots where the dry season has intensified most. Thus, a slow shift to a more dry-affiliated Amazonia is underway, with changes in compositional dynamics (recruits and mortality) consistent with climate-change drivers, but yet to significantly impact whole-community composition. The Amazon observational record suggests that the increase in atmospheric CO2 is driving a shift within tree communities to large-statured species and that climate changes to date will impact forest composition, but long generation times of tropical trees mean that biodiversity change is lagging behind climate change. Publisher PDF
Published: 2018
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111. Production of α-1,3-L-arabinofuranosidase active on substituted xylan does not improve compost degradation by Agaricus bisporus

Author: Vos, Aurin M, Jurak, Edita, de Gijsel, Peter, Ohm, Robin A, Henrissat, Bernard, Lugones, Luis G, Kabel, Mirjam A, Wösten, Han A B, Sub Molecular Microbiology, Molecular Microbiology, Utrecht University [Utrecht], Wageningen University and Research Centre [Wageningen] (WUR), 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), Wageningen University and Research [Wageningen] (WUR), Utrecht University, Department of Bioproducts and Biosystems, Wageningen University and Research Centre, Aix-Marseille Université, Aalto-yliopisto, Aalto University, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Sub Molecular Microbiology, and Molecular Microbiology
Subjects: 0301 basic medicine, Basidiomycetes, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Agaricus, Sordariales, lcsh:Medicine, Lignin, chemistry.chemical_compound, Fungal genetics, Arabinoxylan, Food science, lcsh:Science, chemistry.chemical_classification, Mushroom, Multidisciplinary, Food Chemistry, Organic Compounds, Compost, Eukaryota, Plants, Chemistry, Physical Sciences, Wheat, Carbohydrate Metabolism, Xylans, Organic Materials, Research Article, Glycoside Hydrolases, Materials by Structure, Materials Science, Carbohydrates, Mycology, engineering.material, Polysaccharide, complex mixtures, Fungal Proteins, 03 medical and health sciences, Transformation, Genetic, Levensmiddelenchemie, Genetics, Life Science, Grasses, Cellulose, Organisms, Genetically Modified, Composting, Organic Chemistry, lcsh:R, fungi, Chemical Compounds, Organisms, Fungi, ta1182, Biology and Life Sciences, Xylan, 030104 developmental biology, chemistry, Oligomers, Waxes, engineering, lcsh:Q, Agaricus bisporus
Abstract: International audience; Agaricus bisporus consumes carbohydrates contained in wheat straw based compost used for commercial mushroom production. Double substituted arabinoxylan is part of the ~40% of the compost polysaccharides that are not degraded by A. bisporus during its growth and development. Genes encoding α-1,3-l-arabinofuranosidase (AXHd3) enzymes that act on xylosyl residues doubly substituted with arabinosyl residues are absent in this mushroom forming fungus. Here, the AXHd3 encoding hgh43 gene of Humicola insolens was expressed in A. bisporus with the aim to improve its substrate utilization and mushroom yield. Transformants secreted active AXHd3 in compost as shown by the degradation of double substituted arabinoxylan oligomers in an in vitro assay. However, carbohydrate composition and degree of arabinosyl substitution of arabinoxylans were not affected in compost possibly due to inaccessibility of the doubly substituted xylosyl residues.
Published: 2018
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112. Crop traits drive soil carbon sequestration under organic farming

Author: Andreas Gattinger, Nicolas Legay, Rubén Milla, Filipa Reis, Helena Castro, Laura B. Martínez-García, Eduardo Nascimento, Gerlinde B. De Deyn, Pablo García-Palacios, Jean-Christophe Clément, Martina Lori, Tina D'Hertefeldt, Paul Mäder, Sarah Symanczik, Lijbert Brussaard, José Paulo Sousa, Sandra Lavorel, Arnaud Foulquier, Katarina Hedlund, Pedro Martins da Silva, Adrian Müller, Helene Bracht-Jørgensen, Filipe Carvalho, Universidad Rey Juan Carlos [Madrid] (URJC), Research Institute of Organic Agriculture - Forschungsinstitut für biologischen Landbau (FiBL), Lund University [Lund], Wageningen University and Research [Wageningen] (WUR), Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Universidade de Coimbra [Coimbra], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Cités, Territoires, Environnement et Sociétés (CITERES), Centre National de la Recherche Scientifique (CNRS)-Université de Tours, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), ECO-SERVE BiodivERsA/001/2014, BiodivERsA/FACCE-JPI BiodivERsA/001/2014, ANR, NWO, FCT, MINECO, FORMAS, SNSF Spanish MINECO, NWO-ALW 864.11.003, Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Research Institute of Organic Agriculture (FiBL), Wageningen University and Research Centre [Wageningen] (WUR), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université de Tours-Centre National de la Recherche Scientifique (CNRS), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)
Subjects: 0106 biological sciences, Crop residue, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 010603 evolutionary biology, 01 natural sciences, Soil quality, climate change mitigation, Soil respiration, ecological intensification, organic farming, soil carbon stocks, "Organics" in general, Bodembiologie, 2. Zero hunger, Topsoil, Ecology, leaf nitrogen, Intensive farming, fungi, food and beverages, 04 agricultural and veterinary sciences, Soil Biology, 15. Life on land, Plant litter, PE&RC, resource economics traits, Manure, [SDE.ES]Environmental Sciences/Environmental and Society, meta-analysis, Agronomy, 13. Climate action, crop residue, 040103 agronomy & agriculture, Organic farming, 0401 agriculture, forestry, and fisheries, Environmental science, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: 1. Organic farming (OF) enhances top soil organic carbon (SOC) stocks in croplands compared with conventional farming (CF), which can contribute to sequester C. As farming system differences in the amount of C inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue traits important for soil C losses such as litter decomposition may also play a role. 2. To assess whether crop residue (leaf and root) traits determined SOC sequestration responses to OF, we coupled a global meta-analysis with field measurements across a European-wide network of sites. In the meta-analysis, we related crop species averages of leaf N, leaf-dry matter content, fine-root C and N, with SOC stocks and sequestration responses in OF vs. CF. Across six European sites, we measured the management-induced changes in SOC stocks and leaf litter traits after long-term ecological intensive (e.g. OF) vs. CF comparisons. 3. Our global meta-analysis showed that the positive OF-effects on soil respiration, SOC stocks, and SOC sequestration rates were significant even in organic farms with low manure application rates. Although fertilization intensity was the main driver of OF-effects on SOC, leaf and root N concentrations also played a significant role. Across the six European sites, changes towards higher leaf litter N in CF also promoted lower SOC stocks. 4. Our results highlight that crop species displaying traits indicative of resource-acquisitive strategies (e.g. high leaf and root N) increase the difference in SOC between OF and CF. Indeed, changes towards higher crop residue decomposability was related with decreased SOC stocks under CF across European sites. 5. Synthesis and applications. Our study emphasizes that, with management, changes in crop residue traits contribute to the positive effects of organic farming (OF) on soil carbon sequestration. These results provide a clear message to land managers: the choice of crop species, and more importantly their functional traits (e.g. leave and root nitrogen), should be considered in addition to management practices and climate, when evaluating the potential of OF for climate change mitigation.
Published: 2018
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113. Ramial wood amendments (Piliostigma reticulatum) mitigate degradation of tropical soils but do not replenish nutrient exports

Author: Jeroen C.J. Groot, Bernard Barthès, Cathy Clermont-Dauphin, Aurélien Penche, Edmond Hien, Raphaël J. Manlay, Pablo Tittonell, Laurent Cournac, Georges F. Félix, Wageningen University and Research Centre [Wageningen] (WUR), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UMR Eco&Sols, LMI IESOL, Centre IRD/ISRA de Bel Air, Institut de Recherche pour le Développement (IRD [France-Ouest]), AgroParisTech, INTA EEA Bariloche, Wageningen University and Research [Wageningen] (WUR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), LMI IESOL Intensification Ecologique des Sols Cultivés en Afrique de l’Ouest [Dakar] (IESOL), Institut de recherche pour le développement (IRD [Sénégal]), 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 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), Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), Institut de Recherche pour le Développement (IRD), WASSA project (Woody Amendments for Sudano‐Sahelian Agriculture, ERA‐ARD‐II, ConneSSA project (Connecting knowledge, scales and actors: an integrated framework for adaptive organic resource management, targeting soil aggradation and agro‐ecosystems' resilience in Sub Saharan Africa), European Project: 266603,EC:FP7:INCO,FP7-INCO-2010-3,ERAFRICA(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), and Université du Professeur Joseph Ki Zerbo
Subjects: 010504 meteorology & atmospheric sciences, sol dégradé, amendement du sol, ved/biology.organism_classification_rank.species, termites, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Farmer innovation, adaptation, 01 natural sciences, Shrub, Nutrient, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Degraded soils, Sahel, Termitidae, General Environmental Science, 2. Zero hunger, Géochimie, 04 agricultural and veterinary sciences, PE&RC, Agricultural sciences, West african, Piliostigma Reticulatum, Arbustos, Tropical soils, termite, Piliostigma reticulatum, Soil Degradation, [SDE.MCG]Environmental Sciences/Global Changes, Amendment, Soil Science, shrub material, Development, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Termites, Degradación del Suelo, Environmental Chemistry, Adaptation, Shrub material, 0105 earth and related environmental sciences, ved/biology, business.industry, Farm Systems Ecology Group, 15. Life on land, Geochemistry, Agronomy, 13. Climate action, restauration du sol, farmer innovation, 040103 agronomy & agriculture, Food processing, 0401 agriculture, forestry, and fisheries, Environmental science, Shrubs, business, Sciences agricoles
Abstract: Restoring degraded soils to support food production is a major challenge for West African smallholders who have developed local innovations to counter further degradation. The objective of this study was to evaluate a local farmer's technique that uses ramial wood (RW) as soil amendment (Piliostigma reticulatum shrub). Three treatments were applied in an experimental plot in Burkina Faso: control (no amendment), low RW (3 Mg fresh mass·ha−1·yr−1), and high RW (12 Mg fresh mass·ha−1·yr−1). RW was chipped to
Published: 2018
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114. Global trait–environment relationships of plant communities

Author: Esteban Álvarez-Dávila, Maurizio Mencuccini, Zhiyao Tang, Norbert Jürgens, Christopher Baraloto, Robert K. Peet, Jérôme Munzinger, Josep Peñuelas, Peter M. van Bodegom, Erwin Bergmeier, Wim A. Ozinga, Isabelle Aubin, Yadvinder Malhi, Michele De Sanctis, William Farfan-Rios, Marten Winter, Benjamin Blonder, Jordi Sardans, Christian Wirth, Valério D. Pillar, Nicole J. Fenton, Ilona Knollová, Jiří Doležal, Miguel D. Mahecha, Jens Kattge, Marijn Bauters, Zoltán Botta-Dukát, Francesco Maria Sabatini, Jonathan Lenoir, Peter B. Reich, Florian Jansen, Jorcely Barroso, Frédérique Louault, Anne D. Bjorkman, Alvaro G. Gutiérrez, Michael Kleyer, Matteo Dainese, Dylan Craven, Andraž Čarni, Anita K. Smyth, Gunnar Seidler, Idoia Biurrun, Ted R. Feldpausch, Javier Silva Espejo, Helge Bruelheide, Risto Virtanen, Tarek Hattab, Franziska Schrodt, Greg R. Guerin, Sandra Díaz, Anke Jentsch, Jürgen Dengler, Borja Jiménez-Alfaro, J. Hans C. Cornelissen, Kate H. Orwin, Bruno Hérault, Tomáš Černý, Stephan M. Hennekens, Erik Welk, Frederic Lens, Mohammed Abu Sayed Arfin Khan, Jacqueline Loos, Kiril Vassilev, Milan Chytrý, Jonas V. Müller, Christine Römermann, Sylvia Haider, Géraldine Derroire, Marcos Silveira, Greg H. R. Henry, Petr Petřík, Ülo Niinemets, Zygmunt Kącki, Isla H. Myers-Smith, Michael Kessler, Dirk Nikolaus Karger, Evan Weiher, Andrey Yu. Korolyuk, Richard Field, Raquel Thomas, Eric Garnier, Luis Cayuela, Brody Sandel, Cyrille Violle, Jens-Christian Svenning, Corrado Marcenò, Aaron Pérez-Haase, Daniel C. Laughlin, Pedro Higuchi, Jürgen Homeier, Ute Jandt, Fabio Attorre, Karsten Wesche, Norbert Hölzel, Oliver L. Phillips, Ingolf Kühn, Marco Schmidt, Meelis Pärtel, David A. Neill, Maria Sporbert, Mariyana Lyubenova, Oliver Purschke, Arthur Vinicius Rodrigues, Ioannis Tsiripidis, Jan Altman, Institute of Biology/Geobotany and Botanical Garden, Martin-Luther-Universität Halle Wittenberg (MLU), Universität Bayreuth, German Centre for Integrative Biodiversity Research (iDiv), UR Ecol & Dynam Syst Anthropises EDYSAN, UMR CNRS 7058, Université de Picardie Jules Verne (UPJV), Department of Botany and Zoology, Masaryk University, ALTERRA Wageningen, ALTERRA, Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Universiteit Leiden [Leiden], Fundación Con-Vida, Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Universidade Federal do Acre (UFAC), Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, National Institute of Biology [Ljubljana], Universidad Rey Juan Carlos [Madrid] (URJC), Vrije Universiteit Amsterdam [Amsterdam] (VU), Royal Institute of Technology (KTH), Department of Microelectronics and Information Technology, Kista Photonics Research Center (KPRC) (KTH), Royal Institute of Technology [Stockholm] (KTH ), AgroParisTech, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ecosystèmes et Ressources Aquatiques (UR03AGRO1), Institut National Agronomique de Tunisie, Westfälische Wilhelms-Universität Münster (WWU), Georg-August-Universität Göttingen, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Zurich, Landscape Ecology Group, University of Oldenburg, Helmholtz Zentrum für Umweltforschung (UFZ), Netherlands Centre for Biodiversity Naturalis, Institute of Ecology, Leuphana University, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Environmental Change Institute, University of Oxford [Oxford], School of Geosciences [Edinburgh], University of Edinburgh, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Universidad Estatal Amazonica, Estonian University of Life Sciences, University of Nijmegen, Global Ecology Unit CREAF-CEAB-CSIC, Universitat Autònoma de Barcelona [Barcelona] (UAB), Institute of Ecology and Earth Sciences, University of Tartu, University of Tartu, Department of Forest Resources, University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, Universität Regensburg (REGENSBURG), Universität Regensburg, Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), Dept Biol Sci, Ecoinformat & Biodivers Grp, Aarhus University [Aarhus], Aristotle University of Thessaloniki, Dept Biol, University of Oulu, University of Wisconsin-Eau Claire, Department of Botany, Senckenberg Natural History Museum, Synthesis Centre for Biodiversity Sciences, German Centre for Integrative Biodiversity Research, Universität Leipzig [Leipzig], Philips Research Europe - Hamburg, Sector Medical Imaging Systems, Philips Research, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Masaryk University [Brno] (MUNI), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour le Développement (IRD [France-Sud]), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Georg-August-University [Göttingen], Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Universitat Autònoma de Barcelona (UAB), University of Minnesota [Twin Cities] (UMN), Martin-Luther-University Halle-Wittenberg, Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN), Wageningen University and Research Centre [Wageningen] (WUR), Chercheur indépendant, Department of Ecological Modelling [UFZ Leipzig], Helmholtz Centre for Environmental Research (UFZ), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Hawkesbury Institute for the Environment [Richmond] (HIE), Western Sydney University (UWS), Bruelheide H., Dengler J., Purschke O., Lenoir J., Jimenez-Alfaro B., Hennekens S.M., Botta-Dukat Z., Chytry M., Field R., Jansen F., Kattge J., Pillar V.D., Schrodt F., Mahecha M.D., Peet R.K., Sandel B., van Bodegom P., Altman J., Alvarez-Davila E., Arfin Khan M.A.S., Attorre F., Aubin I., Baraloto C., Barroso J.G., Bauters M., Bergmeier E., Biurrun I., Bjorkman A.D., Blonder B., Carni A., Cayuela L., Cerny T., Cornelissen J.H.C., Craven D., Dainese M., Derroire G., De Sanctis M., Diaz S., Dolezal J., Farfan-Rios W., Feldpausch T.R., Fenton N.J., Garnier E., Guerin G.R., Gutierrez A.G., Haider S., Hattab T., Henry G., Herault B., Higuchi P., Holzel N., Homeier J., Jentsch A., Jurgens N., Kacki Z., Karger D.N., Kessler M., Kleyer M., Knollova I., Korolyuk A.Y., Kuhn I., Laughlin D.C., Lens F., Loos J., Louault F., Lyubenova M.I., Malhi Y., Marceno C., Mencuccini M., Muller J.V., Munzinger J., Myers-Smith I.H., Neill D.A., Niinemets U., Orwin K.H., Ozinga W.A., Penuelas J., Perez-Haase A., Petrik P., Phillips O.L., Partel M., Reich P.B., Romermann C., Rodrigues A.V., Sabatini F.M., Sardans J., Schmidt M., Seidler G., Silva Espejo J.E., Silveira M., Smyth A., Sporbert M., Svenning J.-C., Tang Z., Thomas R., Tsiripidis I., Vassilev K., Violle C., Virtanen R., Weiher E., Welk E., Wesche K., Winter M., Wirth C., Jandt U., Systems Ecology, 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 Institut de Recherche pour le Développement (IRD [France-Sud])-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Bos- en Landschapsecologie, 01 natural sciences, Ecosystem services, forests, grassland, life history traits, plant dispersal, plants, Forest and Landscape Ecology, Environmental planning, OT PB Vredepeel, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, diversité fonctionnelle, Ecology, Vegetation, Plants, Grassland, économie foliaire, Biogeography, Community Ecology, Ecosystems Research, [SDE]Environmental Sciences, Trait, Vegetatie, Bos- en Landschapsecologie, F40 - Écologie végétale, F60 - Physiologie et biochimie végétale, [SDE.MCG]Environmental Sciences/Global Changes, education, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Life History Trait, Biology, Sustainability Science, 010603 evolutionary biology, température, Life Science, prédiction, Ecosystem, Forest, 577: Ökologie, Vegetatie, Ecology, Evolution, Behavior and Systematics, climat, Plant Dispersal, Niche differentiation, Plant community, 15. Life on land, Disturbance (ecology), Vegetation, Forest and Landscape Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Scale (map), 010606 plant biology & botany
Abstract: International audience; Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait-environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.
Published: 2018
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115. Humusica 2, article 17: Techno humus systems and global change – Three crucial questions

Author: Jean-FranÃ§ois Ponge, Stefan Geisen, Jolanta Kwiatkowska-Malina, Michaã«l Aubert, Charles Benbrook, Silvia Fusaro, Tiziano Gomiero, Maria De Nobili, Giovanna Lomolino, Thomas Dilli, Andrea Vacca, Gerard Jagers, Augusto Zanella, Department of Land, Environment, Agriculture and Forestry ( TeSAF ), Universita degli Studi di Padova = University of Padua = Université de Padoue, Wageningen University and Research Centre [Wageningen] ( WUR ), Mécanismes adaptatifs : des organismes aux communautés ( MAOAC ), Muséum National d'Histoire Naturelle ( MNHN ) -Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ), Alterra Wageningen University & Research Centre ( ALTERRA ), Benbrook Consulting Services, Dipartimento di Scienze della Terra [Cagliari], Universita degli Studi di Cagliari [Cagliari], Warsaw University of Technology [Warsaw], Etude et compréhension de la biodiversité ( ECODIV ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ), Università degli Studi di Udine - University of Udine [Italie], Department of Biology, Padova University, Italy, Department of Land, Environment, Agriculture and Forestry (TeSAF), Universita degli Studi di Padova, Wageningen University and Research [Wageningen] (WUR), Mécanismes adaptatifs : des organismes aux communautés (MAOAC), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Alterra Wageningen University & Research Centre (ALTERRA), Étude et compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Normandie Université (NU)
Subjects: 0106 biological sciences, Ecology (disciplines), media_common.quotation_subject, Biodiversity, [ SDV.SA.SDS ] Life Sciences [q-bio]/Agricultural sciences/Soil study, Soil Science, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Life Science, Sociology, media_common, 2. Zero hunger, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Civilization, Ecology, Intensive farming, business.industry, Environmental ethics, 04 agricultural and veterinary sciences, 15. Life on land, PE&RC, Agricultural and Biological Sciences (miscellaneous), [ SDV.EE.ECO ] Life Sciences [q-bio]/Ecology, environment/Ecosystems, Interdependence, 13. Climate action, Agriculture, Humanity, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Dierecologie, Animal Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany, Anonymity
Abstract: Some soil scientists or biologists (14, one preferring anonymity) answered the three following questions: (1. Introduction) 2. Why is organic food better (tastes better, is healthier, richer in nutrients, contains less pesticide, etc.) than food produced with hydroponic or intensive farming techniques? 3. In a humipedon, are soil functioning, biodiversity and carbon content three interdependent and intersected aspects of a single ecosystem? In other words, can we treat these aspects as if they were inseparable in a humipedon? 4. Are agriculture and civilization (the society, culture, and way of life) interconnected? All scientists expressed affirmative answers. Nuances or in depth information were also furnished. The article allows to understand the real “agronomic challenge” that the predicted Global Change might represent for humanity.
Published: 2018
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116. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

Author: Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., Bourke, P. M., Daccord, N., Leus, L., Schulz, D., Van de Geest, H., Hesselink, T., Van Laere, K., Debray, K., Balzergue, S., Thouroude, T., Chastellier, A., Jeauffre, J., Voisine, L., Gaillard, S., Borm, T. J. A., Arens, P., Voorrips, R. E., Maliepaard, C., Neu, E., Linde, M., Le Paslier, M. C., Bérard, A., Bounon, R., Clotault, J., Choisne, N., Quesneville, H., Kawamura, K., Aubourg, S., Sakr, S., Smulders, M. J. M., Schijlen, E., Bucher, E., Debener, T., De Riek, J., Foucher, F., Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institute for Agricultural and Fisheries Research (ILVO), Institute for Agricultural and Fisheries Research, Russian State Agrarian University - Moscow Agricultural Academy named after K.A. Timiryazev, Wageningen University and Research Centre [Wageningen] (WUR), Leibniz Universität Hannover [Hannover] (LUH), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Osaka Institute of Technology (OIT), ANR-13-BSV7-0014,DODO,Identification et caractérisation des mutations DOMINANT DOUBLE (DODO) and DOUBLE FLOWER (DF) chez le pétunia et la rose(2013), 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), Research Institute for Agricultural, Fisheries and Food (ILVO), Wageningen University and Research [Wageningen] (WUR), Osaka Institute of Technology = Osaka Kogyo Daigaku (OIT), CEA-IG/CNG, ‘Région Pays de la Loire’ (Rose Genome Project, Genorose project in the framework of RFI ‘Objectif Végétal’, EPICENTER ConnecTalent grant of the Pays de la Loire), ANR [ANR-13-BSV7-0014], JSPS [JSPS KAKENHI no.17H04616], German Ministry of Economic Affairs (Aif programme ZI), Deutsche Forschungsgemeinschaft [DFG program GRK1798], TTI Green Genetics, TKI Polyploids projects [BO-26.03-002-001, BO-50-002-022], AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Leibniz Universität Hannover=Leibniz University Hannover, Cliquet, Catherine, and Blanc 2013 - Identification et caractérisation des mutations DOMINANT DOUBLE (DODO) and DOUBLE FLOWER (DF) chez le pétunia et la rose - - DODO2013 - ANR-13-BSV7-0014 - Blanc 2013 - VALID
Subjects: Male, GENUS ROSA, Arabidopsis, Haploidy, TETRAPLOID ROSE, Laboratorium voor Plantenveredeling, Genome structure, PBR Siergewassen, Tissue Culture, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, In Situ Hybridization, Fluorescence, Phylogeny, PBR Kwantitatieve aspecten, food and beverages, PBR Ornamentals, tissue culture and gene transfer, Agriculture, Genomics, PE&RC, READ ALIGNMENT, ddc:580, BIOS Applied Metabolic Systems, PBR Biodiversity and genetic variation, Genome, Plant, Agricultural genetics, GENES, SELF-INCOMPATIBILITY, Centromere, Quantitative Trait Loci, Flowers, Rosa, Fragaria, Synteny, Article, Chromosomes, Plant, PBR Quantitative aspects of Plant Breeding, BIOS Applied Bioinformatics, PBR Biodiversiteit en Genetische Variatie, [SDV.SA.HORT] Life Sciences [q-bio]/Agricultural sciences/Horticulture, Quantitative Trait, Heritable, Genetics, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Life Science, FLOWER DEVELOPMENT, Konferenzschrift, Genetic association study, Indoleacetic Acids, Arabidopsis Proteins, fungi, Genetic Variation, Sequence Analysis, DNA, MOLECULAR EVOLUTION, DNA-SEQUENCES, Plant Breeding, Fertility, ARABIDOPSIS-THALIANA, TFL1 HOMOLOG, Rosa chinensis, EPS
Abstract: Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae., A high-quality reference genome of rose is generated by sequencing a doubled haploid line. The researchers analysed the genome structure and uncovered candidate genes associated with major ornamental traits through integrated genetic and genomic analyses.
Published: 2018
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117. Humusica 2, article 11 : Histic humus systems and forms-Epihisto intergrades and dynamics

Author: Bernard Jabiol, Bas van Delft, Augusto Zanella, Maria De Nobili, Chiara Ferronato, Rein de Waal, Gilmo Vianello, Livia Vittori Antisari, Jean-François Ponge, University of Padua [Italy], Muséum national d'Histoire naturelle (MNHN), Wageningen University and Research Centre [Wageningen] (WUR), Università degli Studi di Udine - University of Udine [Italie], University of Bologna, Laboratoire d'Etudes des Ressources Forêt-Bois (LERFoB), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Zanella, Augusto, Ponge, Jean-François, De Waal, Rein, Van Delft, Ba, De Nobili, Maria, Ferronato, Chiara, Antisari, Livia Vittori, Vianello, Gilmo, Jabiol, Bernard, and Wageningen University and Research [Wageningen] (WUR)
Subjects: 010504 meteorology & atmospheric sciences, Water en Landgebruik, Histosol, Bos- en Landschapsecologie, Peats, Soil Science, Wetland, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 01 natural sciences, Humus, Soil, Water dynamics, Soil, Water and Land Use, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Bodem, Histosols, Forest and Landscape Ecology, Bog, Soil water dynamic, Vegetatie, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, Vegetation, Ecology, Water and Land Use, Peat, 04 agricultural and veterinary sciences, Humu, 15. Life on land, Agricultural and Biological Sciences (miscellaneous), Biodegradation, Soil water dynamics, Wetlands, Bodem, Water en Landgebruik, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Vegetatie, Bos- en Landschapsecologie, Vegetation, Forest and Landscape Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Geology
Abstract: International audience; The processes of formation and evolution of Histic humipedons are related to the soil/water dynamics. In a first part of the paper we present diagnostic features and horizons necessary for describing the intergrade humipedons existing between Histic and Hydro humipedons. Called Epihistic (" superficial " Histic), these humipedons are very common and help in better defining the relationships between plant and soil in semi-terrestrial environments. In a second part of the paper we set some information about biological activities and correlated environmental frames of Histic and Epihisto units. The article concludes with dynamic relationships between humipedons, describing them in fen or bog ecosystems, allowing the interpretation of complex wetlands. The present manuscript updates the description and classification of semi-terrestrial humus forms previously published by Zanella et al. (2011a, 2011b).
Published: 2018
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118. Guidelines for Biomarker of Food Intake Reviews (BFIRev) : How to conduct an extensive literature search for biomarker of food intake discovery

Author: Guy Vergères, Cristina Andres-Lacueva, Edith J. M. Feskens, Lars O. Dragsted, Qian Gao, Giulia Praticò, Lydia A. Afman, Claudine Manach, Sri Harsha Pedapati, David S. Wishart, Rosa Vázquez-Fresno, Lorraine Brennan, Marjukka Kolehmainen, Mar Garcia-Aloy, Augustin Scalbert, Hans Verhagen, Department of Nutrition, Exercise and Sports [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Section of Nutrition and Metabolism-Biomarkers Group, International Agency for Cancer Research (IACR), Agroscope, University of Eastern Finland, UCD School of Agriculture and Food Science, University College Dublin [Dublin] (UCD), Division of Human Nutrition, Wageningen University and Research Centre [Wageningen] (WUR), Department of Biological Sciences, Dartmouth College, Department of Nutrition and Food Science, Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), CIBERFES, Instituto de Salud Carlos III (ISC), European Food Safety Authority = Autorité européenne de sécurité des aliments, University of Ulster, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Wageningen University and Research [Wageningen] (WUR), Dartmouth College [Hanover], Instituto de Salud Carlos III [Madrid] (ISC), Dragsted, Laars Ove, and Universitat de Barcelona
Subjects: 0301 basic medicine, Food intake, Future studies, Endocrinology, Diabetes and Metabolism, Scientific literature, Review, Voeding, Metabolisme en Genomica, Faculty of Science, Medicine, 2. Zero hunger, Biochemical markers, Metabolisme, Metabolism and Genomics, 3. Good health, Risk analysis (engineering), Metabolisme en Genomica, Marcadors bioquímics, Alimentation et Nutrition, Biomarker (medicine), Identification (biology), Nutrition, Metabolism and Genomics, lcsh:Nutrition. Foods and food supply, lcsh:QH426-470, Special needs, lcsh:TX341-641, Ressenyes sistemàtiques (Investigació mèdica), Literature search methodology, 03 medical and health sciences, Voeding, Systematic reviews (Medical research), Genetics, Food and Nutrition, Metabolomics, Nutrition, VLAG, Global Nutrition, Wereldvoeding, business.industry, Guideline, lcsh:Genetics, 030104 developmental biology, Metabolism, Potential biomarkers, Biomarkers, Food exposure markers, Systematic review, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: FoodBAll is a project funded by the BioNH call (grant number 529051002) under the Joint Programming Initiative, "A Healthy Diet for a Healthy Life." The project is funded nationally by the respective Research Councils; the work was funded in part by a grant from the Danish Innovation Foundation (#4203-00002B) and a Semper Ardens grant from the Carlsberg Foundation to LOD, a grant from the China Scholarship Council (201506350127) to QG, a postdoc grant from the University of Rome La Sapienza ("Borsa di studio per la frequenza di corsi o attivita di perfezionamento all'estero" erogata ai sensi della legge 398/89) to GP, the Swiss National Science Foundation (40HD40_160618) in the frame of the national research program "Healthy nutrition and sustainable food protection" (NRP69) to GV, a grant from the Agence Nationale de la Recherche (#ANR-14-HDHL-0002-02) to CM, a grant from Science Foundation Ireland (SFI 14/JPI-HDHL/B3076 & SFI 11/PI/1119) to LB, a grant from the Canadian Institutes of Health Research (CIHR) to DSW, a grant from the Spanish National Grants from the Ministry of Economy and Competitiveness (MINECO) (PCIN-2014-133-MINECO Spain), an award of 2014SGR1566 from the Generalitat de Catalunya's Agency AGAUR, and funding from CIBERFES (co-funded by the FEDER Program from EU) to CAL.; Identification of new biomarkers of food and nutrient intake has developed fast over the past two decades and could potentially provide important new tools for compliance monitoring and dietary intake assessment in nutrition and health science. In recent years, metabolomics has played an important role in identifying a large number of putative biomarkers of food intake (BFIs). However, the large body of scientific literature on potential BFIs outside the metabolomics area should also be taken into account. In particular, we believe that extensive literature reviews should be conducted and that the quality of all suggested biomarkers should be systematically evaluated. In order to cover the literature on BFIs in the most appropriate and consistent manner, there is a need for appropriate guidelines on this topic. These guidelines should build upon guidelines in related areas of science while targeting the special needs of biomarker methodology. This document provides a guideline for conducting an extensive literature search on BFIs, which will provide the basis to systematically validate BFIs. This procedure will help to prioritize future work on the identification of new potential biomarkers and on validating these as well as other biomarker candidates, thereby providing better tools for future studies in nutrition and health.
Published: 2018
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119. Integrated ecological-economic fisheries models : Evaluation, review and challenges for implementation

Author: Jan Horbowy, Elizabeth I. van Putten, Aniol Esteban, Rik C. Buckworth, Youen Vermard, Sarah Simons, Sophie Gourguet, Francois Bastardie, Rosa Mato-Amboage, Mathieu Merzéréaud, Siems Bossier, Steven Mackinson, Dorleta Garcia, Staffan Waldo, Bruce D. Mapstone, Olivier Guyader, Raúl Prellezo, Sean Pascoe, Daniel S. Holland, Paul Marchal, Stéphanie Mahévas, Clara Ulrich, Heleen Bartelings, Sonia Sanchez, Claire Macher, Ralf Doering, Didier Gascuel, Catherine M. Dichmont, Anton Paulrud, Éva E. Plagányi, Roy Deng, Rolf A. Groeneveld, Artur Palacz, L. Richard Little, Griffin Carpenter, J.M. Da-Rocha, Francesc Maynou, Michel Bertignac, Asbjørn Christensen, Rüdiger Voss, Jose A. Fernandes, Trevor Hutton, J. Rasmus Nielsen, Sigrid Lehuta, Eckhard Bethke, Hans Frost, Jörn Schmidt, Maciej T. Tomczak, Martin F. Quaas, Icarus Allen, Jordi Guillen, Jordi Lleonart, Villy Christensen, Katell G. Hamon, Eric Thunberg, Lars Ravn-Jonsen, Elizabeth A. Fulton, Olivier Thébaud, Loïc Gasche, Ayoe Hoff, Diana van Dijk, André E. Punt, DTU Aqua, National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Northeast Fisheries Science Center (NEFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Northwest Fisheries Science Center (NWFSC), Christian-Albrechts-Universität zu Kiel (CAU), CSIRO Marine and Atmosphere Research [Hobart], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Washington [Seattle], Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, Wageningen University and Research Centre [Wageningen] (WUR), Unité de recherche Sciences et Technologies Halieutiques (STH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Thünen-Institute of Sea Fisheries, New economics foundation, University of British Columbia (UBC), Universidate de Vigo, University of Copenhagen = Københavns Universitet (KU), AZTI - Tecnalia, Écologie et Modèles pour l'halieutique (EMH), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), National Marine Fisheries Research Institute, Scottish Pelagic Fishermen's Association, Laboratoire Ressources halieutiques Manche Mer du nord, IFREMER Centre Manche Mer du Nord, (HMMN), Swedish Agency for Marine Water Management, University of Southern Denmark (SDU), Stockholm University, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Swedish University of Agricultural Sciences (SLU), Wageningen University and Research [Wageningen] (WUR), Universidade de Vigo, Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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 Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Sciences et Technologies Halieutiques (STH), University of Copenhagen = Københavns Universitet (UCPH), Écologie et Modèles pour l'Halieutique (EMH), Laboratoire Ressources halieutiques Boulogne sur mer (LRHBL), and Halieutique Manche Mer du Nord (HMMN)
Subjects: 0106 biological sciences, Performance and Impact Agrosectors, Oceanography, 01 natural sciences, Performance en Impact Agrosectoren, Environmental Economics and Natural Resources, Multidisciplinary approach, International Policy, Comparative model evaluation, Bio‐economic models, Ecology, Communication, Environmental resource management, Social dynamics, Ecologically sustainable development, Performance criteria and scales and risks, Bio-economic models, Integrated ecological–economic fisheries models, Marine spatial planning and cross‐sector management, Marine conservation, Use and acceptance and implementation and communication and flexibility and complexity, Performance criteria, [SDE.MCG]Environmental Sciences/Global Changes, 5312.01 Agricultura, Silvicultura, Pesca, Management, Monitoring, Policy and Law, Aquatic Science, 010603 evolutionary biology, 12. Responsible consumption, Scales and risks, 14. Life underwater, SDG 14 - Life Below Water, bio-economic models, Internationaal Beleid, Ecology, Evolution, Behavior and Systematics, Flexibility (engineering), marine spatial planning and cross-sector management, User Friendly, WIMEK, business.industry, Marine spatial planning and cross-sector management, 010604 marine biology & hydrobiology, Marine spatial planning, Cross-sector management, Complexity, Integrated ecological-economic fisheries models, Fishery, Acceptance, 13. Climate action, Implementation, Sustainability, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, Fisheries management advice, Flexibility, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Milieueconomie en Natuurlijke Hulpbronnen
Abstract: Nielsen, J.R. ... et al.-- 29 pages, 8 figures, 2 tables, supporting information https://doi.org/10.1111/faf.12232, Marine ecosystems evolve under many interconnected and area‐specific pressures. To fulfil society's intensifying and diversifying needs while ensuring ecologically sustainable development, more effective marine spatial planning and broader‐scope management of marine resources is necessary. Integrated ecological–economic fisheries models (IEEFMs) of marine systems are needed to evaluate impacts and sustainability of potential management actions and understand, and anticipate ecological, economic and social dynamics at a range of scales from local to national and regional. To make these models most effective, it is important to determine how model characteristics and methods of communicating results influence the model implementation, the nature of the advice that can be provided and the impact on decisions taken by managers. This article presents a global review and comparative evaluation of 35 IEEFMs applied to marine fisheries and marine ecosystem resources to identify the characteristics that determine their usefulness, effectiveness and implementation. The focus is on fully integrated models that allow for feedbacks between ecological and human processes although not all the models reviewed achieve that. Modellers must invest more time to make models user friendly and to participate in management fora where models and model results can be explained and discussed. Such involvement is beneficial to all parties, leading to improvement of mo‐dels and more effective implementation of advice, but demands substantial resources which must be built into the governance process. It takes time to develop effective processes for using IEEFMs requiring a long‐term commitment to integrating multidisciplinary modelling advice into management decision‐making
Published: 2018
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120. Integration of fisheries into marine spatial planning: Quo vadis?

Author: Olivier Le Pape, Katell G. Hamon, Hans-Harald Hinrichsen, Torsten Schulze, Sarah Simons, Holger Janßen, Lorna R. Teal, J. Rasmus Nielsen, Margit Eero, Francois Bastardie, Paul Marchal, Alex Tidd, Leibniz-Institut für Ostseeforschung Warnemünde (IOW), Leibniz Association, DTU Aqua, National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Wageningen Economic Research, Wageningen University and Research Centre [Wageningen] (WUR), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institute for Marine Resources & Ecosystem Studies (IMARES), European Union through the European Community [266445], BONUS (Art 185) - EU, Wageningen University and Research [Wageningen] (WUR), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), 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: 266445,EC:FP7:KBBE,FP7-OCEAN-2010,VECTORS(2011), and Danmarks Tekniske Universitet = Technical University of Denmark (DTU)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, EBM, Performance and Impact Agrosectors, msp, Fishing, Maritime spatial planning, Fish species, Fisheries, Aquatic Science, Fisheries law, Oceanography, 01 natural sciences, Performance en Impact Agrosectoren, Competition (economics), Onderzoeksformatie, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Aquaculture and Fisheries, 14. Life underwater, SDG 14 - Life Below Water, 0105 earth and related environmental sciences, Fisheries science, ebm, business.industry, Aquacultuur en Visserij, 010604 marine biology & hydrobiology, MSP, Environmental resource management, Marine spatial planning, Life stage, Fishery, Geography, 13. Climate action, Marine governance, Marine space, Fisheries management, business
Abstract: Some of the research leading to these results has received funding from the European Union through the European Community's Seventh Framework Program (FP7/2007-2013) under Grant Agreement No. 266445 for the project "Vectors of Change in Oceans and Seas Marine Life, Impact on Economic Sectors (VECTORS)." Additional work resulted from the BONUS BALTSPACE project (Towards Sustainable Governance of Baltic Marine Space), supported by BONUS (Art 185), funded jointly by the EU and by national research funding agencies in the eight EU member states around the Baltic Sea.; International audience; The relationship between fisheries and marine spatial planning (MSP) is still widely unsettled. While several scientific studies highlight the strong relation between fisheries and MSP, as well as ways in which fisheries could be included in MSP, the actual integration of fisheries into MSP often fails. In this article, we review the state of the art and latest progress in research on various challenges in the integration of fisheries into MSP. The reviewed studies address a wide range of integration challenges, starting with techniques to analyse where fishermen actually fish, assessing the drivers for fishermen's behaviour, seasonal dynamics and long-term spatial changes of commercial fish species under various anthropogenic pressures along their successive life stages, the effects of spatial competition on fisheries and projections on those spaces that might become important fishing areas in the future, and finally, examining how fisheries could benefit from MSP. This paper gives an overview of the latest developments on concepts, tools, and methods. It becomes apparent that the spatial and temporal dynamics of fish and fisheries, as well as the definition of spatial preferences, remain major challenges, but that an integration of fisheries is already possible today. (C) 2017 The Authors. Published by Elsevier Ltd.
Published: 2018
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121. Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut

Author: Peter J. Schaap, Mark Davids, Hauke Smidt, Michael Müller, Floor Hugenholtz, Guido J. E. J. Hooiveld, Daniel Tomé, Michiel Kleerebezem, Jessica Schwarz, Davids, Mark, Kleerebezem, Michiel, Wageningen University and Research [Wageningen] (WUR), Physiologie de la Nutrition et du Comportement Alimentaire (PNCA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, This work was (co)financed by the Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative / Netherlands Organization for Scientific Research., Wageningen University and Research Centre [Wageningen] (WUR), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: Metabolic Processes, 0301 basic medicine, Protein metabolism, lcsh:Medicine, Pathology and Laboratory Medicine, Biochemistry, Fats, Mice, Voeding, Metabolisme en Genomica, chemistry.chemical_compound, Microbiologie, Medicine and Health Sciences, Systems and Synthetic Biology, Intestinal Mucosa, lcsh:Science, Protein Metabolism, Human Nutrition & Health, 2. Zero hunger, Systeem en Synthetische Biologie, Multidisciplinary, biology, Chemistry, Humane Voeding & Gezondheid, food and beverages, Genomics, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Milk Proteins, Lipids, Metabolism and Genomics, Bacterial Pathogens, Intestines, Protein catabolism, Milk, Medical Microbiology, Metabolisme en Genomica, Nutrition, Metabolism and Genomics, Pathogens, Anatomy, Energy source, Research Article, 030106 microbiology, Microbial Genomics, Microbiology, 03 medical and health sciences, Voeding, Genetics, Animals, Life Science, Host-Microbe Interactomics, Microbiome, Microbial Pathogens, VLAG, Nutrition, Clostridium, Bacteria, Catabolism, Gut Bacteria, lcsh:R, Lachnospiraceae, Organisms, Biology and Life Sciences, Fatty Acids, Volatile, biology.organism_classification, Diet, Gastrointestinal Microbiome, Amino Acid Metabolism, Gastrointestinal Tract, Metabolism, 030104 developmental biology, Fermentation, WIAS, Metagenome, lcsh:Q, Digestive System, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; Undigestible food ingredients are converted by the microbiota into a large range of metabo-lites, predominated by short chain fatty acids (SCFA). These microbial metabolites are subsequently available for absorption by the host mucosa and can serve as an energy source. Amino acids fermentation by the microbiota expands the spectrum of fermentation end-products beyond acetate, propionate and butyrate, to include in particular branched-SCFA. Here the long-term effects of high protein-diets on microbial community composition and function-ality in mice were analyzed. Determinations of the microbiota composition using phylogenetic microarray (MITChip) technology were complemented with metatranscriptome and SCFA analyses to obtain insight in in situ expression of protein fermentation pathways and the phy-logenetic groups involved. High protein diets led to increased luminal concentrations of branched-SCFA, in accordance with protein fermentation in the gut. Bacteria dominantly participating in protein catabolism belonged to the Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae families in both normal-and high-protein diet regimes. This study identifies the microbial groups involved in protein catabolism in the intestine and underpins the value of in situ metatranscriptome analyses as an approach to decipher locally active metabolic networks and pathways as a function of the dietary regime, as well as the phylogeny of the microorganisms executing them.
Published: 2018
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122. Evaluating dietary supply of microminerals as a premix in a complete plant ingredient-based diet to juvenile rainbow trout (Oncorhynchus mykiss)

Author: Catherine Mariojouls, S.J. Kaushik, Stéphanie Fontagné-Dicharry, P. Antony Jesu Prabhu, Inge Geurden, Maïté Bueno, Johan W. Schrama, Anne Surget, AgroParisTech, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Aquaculture and Fisheries Group (Wageningen University), Wageningen University and Research Centre [Wageningen] (WUR), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), The study was part of a PhD fellowship funded by INRA, under the INRA-WUR aquaculture platform, this work is also a contribution to the EU-funded project, ARRAINA: Advanced Research Initiatives for Nutrition & Aquaculture (KBBE-2011- 288925), European Project: 288925, Wageningen University and Research [Wageningen] (WUR), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, supplement, Aquatic Science, Biology, premix, 03 medical and health sciences, Ingredient, Nutrient, Animal science, Premix, Aquaculture and Fisheries, Juvenile, Fishmeal replacement, ComputingMilieux_MISCELLANEOUS, IF, Ecology, Aquacultuur en Visserij, [SDV.BA]Life Sciences [q-bio]/Animal biology, Plant based, 04 agricultural and veterinary sciences, micro mineral, Trace minerals, rainbow trout, Shrimp, 030104 developmental biology, Rainbow trout, Requirement, fishmeal replacement, Micro minerals, 040102 fisheries, WIAS, 0401 agriculture, forestry, and fisheries, trace mineral, Composition (visual arts), Whole body, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Supplement
Abstract: International audience; Two basal diets M0 and V0 were formulated with marine and plant based ingredient composition. Seven experimental diets were prepared from the two basal diets namely M0, M100, V0, V30, V60, V100 and V150 by incorporating different levels of a micromineral premix (Cu, Fe, Mn, Se and Zn). Triplicate groups of rainbow trout (initial weight: 20 g) reared at 17°C were fed one of each diet to apparent visual satiation over 12 weeks. Among the V diet fed fish, growth and feed intake exhibited maximal response at V60 level of premix inclusion; Apparent availability coefficient of Fe, Cu and Zn decreased linearly with increasing level of premix whereas apparent availability coefficient of Mn and Se was unaffected. The available dietary concentration in basal V0 diet was for Fe, 20.6; Cu, 2.8; Mn, 6.5; Zn, 17.3 and Se, 0.195 (in mg/kg DM) and in the M0 diet for Fe, 63.3; Cu, 5.2; Mn, 2.9; Zn, 35.2 and Se, 0.87 (in mg/kg DM). In reference to NRC (Nutrient requirements of fish and shrimp. Washington, DC: National Research Council, The National Academies Press, 2011) recommendations, the V0 basal diet accounted for 34.3%, 92.9%, 53.9%, 115% and 130.2% and the contribution from M0 diet for 105.5%, 173.3%, 24.2%, 234.7% and 580% of the minimal dietary inclusion levels of Fe, Cu, Mn, Zn and Se to rainbow trout, respectively. However, data on whole body mineral contents showed that normal levels were maintained only for Cu and Mn through supply from basal V0 diet. For Zn and Se, available supply even from the highest supplemented diet (V150) was not sufficient to maintain normal body mineral levels of rainbow trout in the present study. On the whole, optimal dietary inclusion levels of microminerals are altered while using fishmeal-free diets for rainbow trout.
Published: 2018
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123. Mapping local and global variability in plant trait distributions

Author: Fernando Valladares, Thomas Hickler, Benjamin Blonder, Kirk R. Wythers, Peter B. Reich, Kerry A. Brown, Ethan E. Butler, Andrés González-Melo, Enio E. Sosinski, Vanessa Minden, Nicolas Gross, Josep Peñuelas, Peter M. van Bodegom, Steven Jansen, Daniel C. Laughlin, Yusuke Onoda, Giandiego Campetella, Nathan J. B. Kraft, Bruno Enrico Leone Cerabolini, Ming Chen, Patrick Meir, Peter E. Thornton, Farideh Fazayeli, Tomas F. Domingues, Lawren Sack, Bernard Amiaud, Sandra Díaz, Dylan Craven, Ben Bond-Lamberty, Quentin D. Read, Ülo Niinemets, Gerhard Boenisch, Habacuc Flores-Moreno, Franciska T. de Vries, Chaeho Byun, Christian Wirth, Abhirup Datta, Marko J. Spasojevic, Koen Kramer, Brandon S. Schamp, Wenxuan Han, Arindam Banerjee, Joseph M. Craine, Mathew Williams, Jens Kattge, Nadejda A. Soudzilovskaia, Wesley N. Hattingh, Johannes H. C. Cornelissen, Estelle Forey, Owen K. Atkin, Hiroko Kurokawa, Department of Forest Resources, University of Minnesota, St. Paul, MN, USA, Department of Biostatistics [Baltimore], Johns Hopkins University (JHU), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences [Beijing] (CAS), University of Minnesota, Department of Computer Science and Engineering, Australian National University (ANU), German Centre for Integrative Biodiversity Research, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Environmental Change Institute, University of Oxford, Oxford, UK, Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Joint Global Change Research Institute, University Research Court, Department of Geography and Geology, Kingston University, Kingston upon Thames, UK, Seoul National University [Seoul] (SNU), University of Camerino, Department of Theoretical and Applied Sciences [Insubria], University of Insubria, Varese, Jonah Ventures, School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], Insituto Multidisciplinario de Biologia Vegetal, Universidad Nacional de Córdoba [Argentina], Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Étude et compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Etudes Biologiques de Chizé [France] (USC 1339 INRA), Institut National de la Recherche Agronomique (INRA), College of Resources and Environmental Sciences, Ministry of Agriculture, Key Laboratory of Arable Land Conservation (North China), China Agricultural University (CAU), Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences [Changchun Branch] (CAS), School of Animal, Plant & Environmental Sciences, University of the Witwatersrand [Johannesburg] (WITS), Department of Physical Geography and Ecosystem Science [Lund], Lund University [Lund], Universität Ulm - Ulm University [Ulm, Allemagne], Alterra - Green World Research, Wageningen University and Research [Wageningen] (WUR), Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, Tohoku University [Sendai], Department of Botany, University of Wyoming, Laramie, WY, USA, University of Wyoming, Laramie, Research School of Biology, Institute of Biology and Environmental Science, Carl von Ossietzky University Oldenburg, Kyoto University [Kyoto], Global Ecology Unit CREAF-CEAB-CSIC, Universitat Autònoma de Barcelona (UAB), Department of Forestry, Michigan State University, East Lansing, Department of Ecology and Evolutionary Biology, University of California, Department of Biology, Algoma University, Marie, OA, Canada, Algoma University, Institute of Environmental Sciences [Leiden] (CML), Leiden University, Laboratorio de Planejamento Ambiental, Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Climate Change Science Institute [Oak Ridge] (CCSI), UT-Battelle, LLC-UT-Battelle, LLC, Escuela Superior de Ciencias Experimentales y Tecnológicas, Departamento de Biología y Geología, Universidad Rey Juan Carlos [Madrid] (URJC), School of Geosciences [Edinburgh], University of Edinburgh, Department of Systematic Botany and Functional Biodiversity, Universität Leipzig [Leipzig], Department of Forest Resources, University of Minnesota System-University of Minnesota System, European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Biology, Butler, Ethan E., Datta, Abhirup, Systems Ecology, Environmental Change Institute, University of Oxford, Università degli Studi di Camerino = University of Camerino (UNICAM), Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, University of California (UC), Universiteit Leiden, Universität Leipzig, INRA - CEBC, Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Universitat Autònoma de Barcelona [Barcelona] (UAB), University of Minnesota [Twin Cities], Department of Energy (US), National Science Foundation (US), University of Minnesota, European Commission, Natural Environment Research Council (UK), Generalitat de Catalunya, Wageningen University and Research Centre, National Natural Science Foundation of China, and Australian Research Council
Subjects: 0106 biological sciences, Bayes theorem, Data base, 010504 meteorology & atmospheric sciences, Biodiversité et Ecologie, répartition territoriale, échelle globale, statistique spatiale, 01 natural sciences, Filosofie, spatial statistics, Leaf area, Bayes' theorem, Models, échelle locale, ComputingMilieux_MISCELLANEOUS, Priority journal, 2. Zero hunger, changement climatique, Multidisciplinary, Geography, Phosphorus, Vegetation, Plants, Statistical, PE&RC, global, Bayesian modeling, Climate, Global, Plant traits, Spatial statistics, PNAS Plus, [SDE]Environmental Sciences, Trait, Centre for Crop Systems Analysis, Statistical model, Cartography, CIENCIAS NATURALES Y EXACTAS, Nitrogen, Otras Ciencias Biológicas, Bayesian probability, plant traits, climate, Quantitative trait locus, Environment, 010603 evolutionary biology, Article, Ciencias Biológicas, Biodiversity and Ecology, Quantitative Trait, Quantitative Trait, Heritable, Spatial analysis, Heritable, Ecosystem, 0105 earth and related environmental sciences, Spatial Analysis, Models, Statistical, Plant Dispersal, diversité végétale fonctionnelle, Leaf litter, Plant, 15. Life on land, Nonhuman, modèle bayésien, Philosophy, Evergreen, 13. Climate action, Concentration (parameters), Prediction, Scale (map), Bayesian modelling, Model
Abstract: Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration—specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen (Nm) and phosphorus (Pm), we characterize how traits vary within and among over 50,000 ∼50×50-km cells across the entire vegetated land surface. We do this in several ways—without defining the PFT of each grid cell and using 4 or 14 PFTs; each model’s predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means., This research was supported as part of the Energy Exascale Earth System Model (E3SM) project, funded by the US Department of Energy, Office of Science, Office of Biological and Environmental Research (Grant DE-SC0012677 to P.B.R. and A.B.). O.K.A. acknowledges the support of the Australian Research Council (CE140100008). This research was also funded by programs from the NSF Long-Term Ecological Research (Grant DEB-1234162) and Long-Term Research in Environmental Biology (Grant DEB-1242531). A.B., F.F., and P.B.R. acknowledge funding from NSF Grant IIS-1563950. P.B.R. also acknowledges support from two University of Minnesota Institute on the Environment discovery grants. This study has been supported by the TRY initiative on plant traits (www.try-db.org). The TRY database is hosted at the Max Planck Institute for Biogeochemistry (Jena, Germany) and supported by DIVERSITAS/Future Earth, the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, and the EU H2020 project BACI (Grant 640176). B.B. acknowledges a Natural Environment Research Council (NERC) independent research fellowship NE/M019160/1. J.P. acknowledges the financial support from the European Research Council Synergy Grant ERC-SyG-2013-610028 IMBALANCE-P, the Spanish Government Grant CGL2013-48074-P, and the Catalan Government Grant SGR 2014-274. B.B.-L. was supported by the Earth System Modeling program of the US Department of Energy, Office of Science, Office of Biological and Environmental Research. K.K. acknowledges the contribution of the Wageningen University and Research Investment theme Resilience for the project Resilient Forest (KB-29-009-003). P.M. acknowledges support from ARC Grant FT110100457 and NERC Grant NE/F002149/1. W.H. acknowledges support from the National Natural Science Foundation of China (Grant 41473068) and the “Light of West China” Program of the Chinese Academy of Sciences.
Published: 2017
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124. Regulation of Orange Carotenoid Protein Activity in Cyanobacterial Photoprotection

Author: Céline Bourcier de Carbon, Diana Kirilovsky, Léa Comolet, Adjélé Wilson, Adrien Thurotte, Fugui Xiao, Rocío López-Igual, Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Laboratory of Biophysics, Wageningen University and Research Centre [Wageningen] ( WUR ), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Wageningen University and Research [Wageningen] (WUR)
Subjects: Models, Molecular, 0106 biological sciences, Cyanobacteria, MESH : Escherichia coli, Light, Physiology, [SDV]Life Sciences [q-bio], MESH : Synechocystis, MESH : Models, Biological, Plant Science, Orange (colour), MESH: Synechocystis, 01 natural sciences, polycyclic compounds, Phycobilisomes, MESH : Bacterial Proteins, MESH : Light, MESH: Bacterial Proteins, Carotenoid, chemistry.chemical_classification, 0303 health sciences, MESH: Escherichia coli, Synechocystis, food and beverages, MESH : Protein Binding, Articles, Fluorescence, Biofysica, Biochemistry, MESH : Mutation, MESH: Models, Molecular, Protein Binding, MESH : Fluorescence, MESH: Mutation, MESH : Models, Molecular, Biophysics, macromolecular substances, Biology, Models, Biological, 03 medical and health sciences, Bacterial Proteins, Escherichia coli, Genetics, Life Science, MESH: Protein Binding, MESH: Phycobilisomes, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], Orange carotenoid protein, organic chemicals, MESH: Fluorescence, MESH: Models, Biological, biology.organism_classification, MESH: Light, MESH : Phycobilisomes, chemistry, Photoprotection, Mutation, bacteria, Phycobilisome, Excess energy, 010606 plant biology & botany
Abstract: International audience; Plants, algae, and cyanobacteria have developed mechanisms to decrease the energy arriving at reaction centers to protect themselves from high irradiance. In cyanobacteria, the photoactive Orange Carotenoid Protein (OCP) and the Fluorescence Recovery Protein are essential elements in this mechanism. Absorption of strong blue-green light by the OCP induces carotenoid and protein conformational changes converting the orange (inactive) OCP into a red (active) OCP. Only the red orange carotenoid protein (OCP(r)) is able to bind to phycobilisomes, the cyanobacterial antenna, and to quench excess energy. In this work, we have constructed and characterized several OCP mutants and focused on the role of the OCP N-terminal arm in photoactivation and excitation energy dissipation. The N-terminal arm largely stabilizes the closed orange OCP structure by interacting with its C-terminal domain. This avoids photoactivation at low irradiance. In addition, it slows the OCP detachment from phycobilisomes by hindering fluorescence recovery protein interaction with bound OCP(r). This maintains thermal dissipation of excess energy for a longer time. Pro-22, at the beginning of the N-terminal arm, has a key role in the correct positioning of the arm in OCP(r), enabling strong OCP binding to phycobilisomes, but is not essential for photoactivation. Our results also show that the opening of the OCP during photoactivation is caused by the movement of the C-terminal domain with respect to the N-terminal domain and the N-terminal arm.
Published: 2015
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125. NDIR Gas Sensor for Spatial Monitoring of Carbon Dioxide Concentrations in Naturally Ventilated Livestock Buildings

Author: Julio Mosquera, Nadège Edouard, Hendrik Jan van Dooren, Ilda de Fátima Ferreira Tinôco, Nico W.M. Ogink, Luciano Mendes, Research Institute for Agricultural, Fisheries and Food (ILVO), Wageningen University and Research [Wageningen] (WUR), Department of Agricultural Engineering, Universidade Federal de Vicosa (UFV), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Institute for Agricultural and Fisheries Research, Wageningen University and Research Centre [Wageningen] (WUR), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
Subjects: 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Farm Technology, lcsh:Chemical technology, 01 natural sciences, Biochemistry, Analytical Chemistry, chemistry.chemical_compound, Co2 concentration, ventilation rate, Environmental monitoring, batiment, dairy barn, lcsh:TP1-1185, teneur en dioxyde de carbone, Instrumentation, élevage laitier, Equipment Design, Housing, Animal, Atomic and Molecular Physics, and Optics, Dairying, Ventilation rate, vache laitière, CO2 mass balance, Carbon dioxide, impact environnemental, Livestock, Female, Emissions & Manure Valorisation, Barn (unit), Environmental Monitoring, spectrométrie infrarouge, Emissie & Mestverwaarding, spectroscopie photoacoustique, Article, Photo acoustic spectroscopy, photo acoustic spectroscopy, Ratio method, TRACER, Animals, Electrical and Electronic Engineering, 0105 earth and related environmental sciences, business.industry, 010401 analytical chemistry, Environmental engineering, Dairy barn, Open-path laser, Carbon Dioxide, Ventilation, 0104 chemical sciences, Field monitoring, open-path laser, laser, chemistry, WIAS, Environmental science, Agrarische Bedrijfstechnologie, Cattle, business
Abstract: The tracer gas ratio method, using CO2 as natural tracer, has been suggested as a pragmatic option to measure emissions from naturally ventilated (NV) barns without the need to directly estimate the ventilation rate. The aim of this research was to assess the performance of a low-cost Non-Dispersive Infra-Red (NDIR) sensor for intensive spatial field monitoring of CO2 concentrations in a NV dairy cow house. This was achieved by comparing NDIR sensors with two commonly applied methods, a Photo-Acoustic Spectroscope (PAS) Gas Monitor and an Open-Path laser (OP-laser). First, calibrations for the NDIR sensors were obtained in the laboratory. Then, the NDIR sensors were placed in a dairy cow barn for comparison with the PAS and OP-laser methods. The main conclusions were: (a) in order to represent the overall barn CO2 concentration of the dairy cow barn, the number of NDIR sensors to be accounted for average concentration calculation was dependent on barn length and on barn area occupation, and (b) the NDIR CO2 sensors are suitable for multi-point monitoring of CO2 concentrations in NV livestock barns, being a feasible alternative for the PAS and the OP-laser methods to monitor single-point or averaged spatial CO2 concentrations in livestock barns.
Published: 2015
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126. Bio-alteration of metallurgical wastes by Pseudomonas aeruginosa in a semi flow-through reactor

Author: Eric D. van Hullebusch, Piet N.L. Lens, Jérôme Labanowski, Nang Htay Yin, Arnaud Gauthier, Yann Sivry, Caroline Avril, Nicolas Seignez, Laboratoire Géomatériaux et Environnement (LGE), Université Paris-Est Marne-la-Vallée (UPEM), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Université de Poitiers-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), 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), Sub-Department of Environmental Technology, Wageningen University and Research [Wageningen] (WUR), Wageningen University and Research Centre [Wageningen] (WUR), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Equipe Sols et Environnement, Laboratoire Génie Civil et géoEnvironnement Lille Nord de France (LGCgE), EA 4515, Institut Supérieur d' Agriculture, Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), and Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Blast furnace, Siderophore, Environmental Engineering, Leaching rates, Heterotroph, Siderophores, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, chemistry.chemical_element, Biomass, Zinc, 010501 environmental sciences, Management, Monitoring, Policy and Law, 010502 geochemistry & geophysics, 01 natural sciences, Bioreactors, Metals, Heavy, Bioreactor, Leachate, Waste Management and Disposal, 0105 earth and related environmental sciences, Waste Products, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Chemistry, Spectrophotometry, Atomic, Metallurgy, Slag, General Medicine, 6. Clean water, Culture Media, Biodegradation, Environmental, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Lead, 13. Climate action, visual_art, [SDE]Environmental Sciences, Pseudomonas aeruginosa, visual_art.visual_art_medium, Bio/weathering, Environmental Pollutants, Slags
Abstract: International audience; Metallurgical activities can generate a huge amount of partially vitrified waste products which are either landfilled or recycled. Lead Blast Furnace (LBF) slags are often disposed of in the vicinity of metallurgical plants, and are prone to weathering, releasing potentially toxic chemical components into the local environment. To simulate natural weathering in a slag heap, bioweathering of these LBF slags was studied in the presence of a pure heterotrophic bacterial strain (Pseudomonas aeruginosa) and in a semi-flow through reactor with intermittent leachate renewal. The evolution of water chemistry, slag composition and texture were monitored during the experiments. The cumulative bulk release of dissolved Fe, Si, Ca and Mg doubled in the presence of bacteria, probably due to the release of soluble complexing organic molecules (e.g. siderophores). In addition, bacterial biomass served as the bioadsorbent for Pb, Fe and Zn as 70-80% of Pb and Fe, 40-60% of Zn released are attached to and immobilized by the bacterial biomass.
Published: 2015
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127. Improving the performance of remote sensing models for capturing intra- and inter-annual variations in daily GPP : An analysis using global FLUXNET tower data

Author: Piero Toscano, Petra D'Odorico, Beverly E. Law, Eddy Moors, Mark A. Friedl, Olivier Roupsard, Georg Wohlfahrt, Andrej Varlagin, Leonardo Montagnani, M. Verma, Alessandro Cescatti, Barbara Marcolla, Damien Bonal, M. A. Arain, Gerard Kiely, T. A. Black, Boston University [Boston] (BU), California Institute of Technology (CALTECH), Oregon State University (OSU), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), University College London, University of British Columbia (UBC), University of Innsbruck, European Academy of Bolzano, Alterra, Wageningen University and Research Centre [Wageningen] (WUR), Free University of Bozen-Bolzano, Autonomous Province of Bolzano (APB), Edmund Mach Foundation (FEM), Institute of Biometeorology, Russian Academy of Sciences [Moscow] (RAS), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Tropical Agricultural Centre for Research and Higher Education, JRC Institute for Environment and Sustainability (IES), European Commission - Joint Research Centre [Ispra] (JRC), McMaster University [Hamilton, Ontario], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Wageningen University and Research [Wageningen] (WUR), 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)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
Subjects: Atmospheric Science, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Biome, FLUXNET, 0211 other engineering and technologies, 02 engineering and technology, Gross primary productivity, 01 natural sciences, FluxNet, Temporal scales, Global and Planetary Change, Forestry, Remote sensing, Variation saisonnière, Remote sensing (archaeology), P01 - Conservation de la nature et ressources foncières, Modèle mathématique, Télédétection, Context (language use), Settore BIO/07 - ECOLOGIA, Mesure, Modélisation environnementale, Scientific activity, 021101 geological & geomatics engineering, 0105 earth and related environmental sciences, Seasonal, Analyse de données, Modeling, Lagged effects, Productivité primaire, 15. Life on land, Climate Resilience, 13. Climate action, Klimaatbestendigheid, Environmental science, Spatial variability, U30 - Méthodes de recherche, Cycle du carbone, Agronomy and Crop Science
Abstract: Accurate and reliable estimates of gross primary productivity (GPP) are required for monitoring the global carbon cycle at different spatial and temporal scales. Because GPP displays high spatial and temporal variation, remote sensing plays a major role in producing gridded estimates of GPP across spatiotemporal scales. In this context, understanding the strengths and weaknesses of remote sensing-based models of GPP and improving their performance is a key contemporary scientific activity. We used measurements from 157 research sites (similar to 470 site-years) in the FLUXNET "La Thuile" data and compared the skills of 11 different remote sensing models in capturing intra- and inter-annual variations in daily GPP in seven different biomes. Results show that the models were able to capture significant intra-annual variation in GPP (Index of Agreement = 0.4-0.80) in all biomes. However, the models' ability to track inter-annual variation in daily GPP was significantly weaker (IoA < 0.45). We examined whether the inclusion of different mechanisms that are missing in the models could improve their predictive power. The mechanisms included the effect of sub-daily variation in environmental variables on daily GPP, factoring-in differential rates of GPP conversion efficiency for direct and diffuse incident radiation, lagged effects of environmental variables, better representation of soil-moisture dynamics, and allowing spatial variation in model parameters. Our analyses suggest that the next generation remote sensing models need better representation of soil-moisture, but other mechanisms that have been found to influence GPP in site-level studies may not have significant bearing on model performance at continental and global scales. Understanding the relative controls of biotic vis-a-vis abiotic factors on GPP and accurately scaling up leaf level processes to the ecosystem scale are likely to be important for recognizing the limitations of remote sensing model and improving their formulation. (C) 2015 Elsevier B.V. All rights reserved.
Published: 2015
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128. Eight principles of integrated pest management

Author: Barzman, Marco, Bàrberi, Paolo, Nicholas, A., Birch, E., Boonekamp, Piet, Dachbrodt-Saaydeh, Silke, Graf, Benno, Hommel, Bernd, Jensen, Jens Erik, Kiss, Jozsef, Kudsk, Per, Lamichhane, Jay Ram, Messéan, Antoine, Moonen, Anna-Camilla, Ratnadass, Alain, Ricci, Pierre, Sarah, Jean-Louis, Sattin, Maurizio, Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institut National de la Recherche Agronomique (INRA), Institute of Life Sciences, Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP), The James Hutton Institute, Plant Research International, Wageningen University and Research [Wageningen] (WUR), Federal Research Centre for Cultivated Plants, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Plant Protection and Fruit and Vegetable Extension, Agroscope, Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, SEGES, Plant Protection Institute [Budapest] (ATK NOVI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Department of Agro-ecology, Aarhus University [Aarhus], Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Direction Générale Déléguée à la Recherche et à la Stratégie (Cirad-Dgdrs), Institute of Agro-Environmental and Forest Biology, Consiglio Nazionale delle Ricerche [Roma] (CNR), Scuola Superiore Sant'Anna [Pisa], Wageningen University and Research Centre [Wageningen] (WUR), Julius Kühn Institute (JKI), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (Cirad-Persyst-UPR 103 HORTSYS), 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), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Barzman, Marc
Subjects: 0106 biological sciences, Protection Intégrée des Cultures, Approche système, Computer science, Integrated farming, [SDV]Life Sciences [q-bio], H02 - Pesticides, Gestion intégrée des ravageurs, 01 natural sciences, Santé publique, Protection des plantes, Sustainable agriculture, Cropping system, media_common, 2. Zero hunger, Résistance aux insecticides, Integrated pest management, Agroécologie, Europe, S50 - Santé humaine, Integrated pest management . Europe, Pesticides . Alternatives . Systems approach . Resilient cropping system . Sustainable agriculture, Biological regulation, Integrated Pest Management, Pesticides, P02 - Pollution, Environmental Engineering, Accord international, Integrated pest management . Europe, Biointeractions and Plant Health, media_common.cataloged_instance, European union, Lutte intégrée, Environmental planning, Sustainable development, Lutte chimique, Pesticides . Alternatives . Systems approach . Resilient cropping system . Sustainable agriculture, 15. Life on land, Lutte biologique, Crop protection, Pesticide, Systems approach, 010602 entomology, Alternatives, Agronomy, Protection de l'environnement, 13. Climate action, Toxicité des pesticides, Agronomy and Crop Science, Cropping, 010606 plant biology & botany, Resilient cropping system
Abstract: The use of pesticides made it possible to increase yields, simplify cropping systems, and forego more complicated crop protection strategies. Over-reliance on chemical control, however, is associated with contamination of ecosystems and undesirable health effects. The future of crop production is now also threatened by emergence of pest resistance and declining availability of active substances. There is therefore a need to design cropping systems less dependent on synthetic pesticides. Consequently, the European Union requires the application of eight principles (P) of Integrated Pest Management that fit within sustainable farm management. Here, we propose to farmers, advisors, and researchers a dynamic and flexible approach that accounts for the diversity of farming situations and the complexities of agroecosystems and that can improve the resilience of cropping systems and our capacity to adapt crop protection to local realities. For each principle (P), we suggest that (P1) the design of inherently robust cropping systems using a combination of agronomic levers is key to prevention. (P2) Local availability of monitoring, warning, and forecasting systems is a reality to contend with. (P3) The decision-making process can integrate cropping system factors to develop longer-term strategies. (P4) The combination of non-chemical methods that may be individually less efficient than pesticides can generate valuable synergies. (P5) Development of new biological agents and products and the use of existing databases offer options for the selection of products minimizing impact on health, the environment, and biological regulation of pests. (P6) Reduced pesticide use can be effectively combined with other tactics. (P7) Addressing the root causes of pesticide resistance is the best way to find sustainable crop protection solutions. And (P8) integration of multi-season effects and trade-offs in evaluation criteria will help develop sustainable solutions.
Published: 2015
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129. Place branding, embeddedness and endogenous rural development: Four European cases

Author: Mechthild Donner, Fatiha Fort, Lummina Horlings, Sietze Vellema, Urban and Regional Studies Institute, Marchés, Organisations, Institutions et Stratégies d'Acteurs (UMR MOISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Planning Department, University of Groningen, Knowledge, Technology and Innovation group, Wageningen University and Research Centre [Wageningen] (WUR), 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 de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National 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), Wageningen University and Research [Wageningen] (WUR), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM)
Subjects: Economic growth, Strategy and Management, rural areas, développement endogène, 0211 other engineering and technologies, WASS, développement régional, 02 engineering and technology, milieu rural, intégration, Economic geography, place branding, Marketing, 05 social sciences, SAFFRON, 021107 urban & regional planning, food network, REGIONS, Gestion et management, embeddedness, Technologie and Innovatie, Knowledge Technology and Innovation, Kennis, [SHS.GESTION]Humanities and Social Sciences/Business administration, France, image de marque, irlande, Embeddedness, Context (language use), ireland republic, vertical integration, Place branding, 0502 economics and business, PORTUGAL, QUALITY, TERRITORIALISATION, AGENDA, business.industry, regional development, public image, Public diplomacy, FRAMEWORK, endogenous development, Brand management, Brand extension, allemagne, food networks, Business administration, Business, Rural area, Kennis, Technologie and Innovatie, 050212 sport, leisure & tourism, Tourism
Abstract: This article deals with place branding on the regional scale, in the rural context of food and tourism networks in Europe. Place branding is linked to the concepts of endogenous rural development, territory and embeddedness, by analysing how the valorisation of specific rural assets takes shape. The overall objective is to provide more understanding of how the branding of rural regions can contribute to endogenous rural development.Four European regional rural cases on place branding are explored, two from France, one from Ireland and one from Germany. Described are pre-conditions for branding, brand management, cooperation forms and development outcomes. The analysis is based on interviews as primary data and various secondary data. The cases all involve multiple stakeholders, and integrate the capacities and needs of local people. The findings show different levels of societal, structural and territorial embeddedness, and that higher degrees of embeddedness contribute to a successful branding process. The results indicate that place branding can support endogenous rural development and benefits from the adoption of common values and joint reflections on brand extensions, although there remains a need for more consistent impact measurement methods.
Published: 2017
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130. Modulation of the gut microbiota impacts nonalcoholic fatty liver disease: A potential role for bile acids

Author: Wieneke Dijk, Tom Houben, J. Mark Brown, Stanley L. Hazen, Rinke Stienstra, Jacques Vervoort, Aafke W. F. Janssen, Guido J. E. J. Hooiveld, Ko Willems van Dijk, Lily Boutens, Sander Kersten, Folkert Kuipers, Stéphane Mandard, Zeneng Wang, Nieke van der Bolt, Saeed Katiraei, Ronit Shiri-Sverdlov, Center for Liver, Digestive and Metabolic Diseases (CLDM), Nutrition, Metabolism and Genomics Group [Wageningen, The Netherlands], Wageningen University and Research Centre [Wageningen] ( WUR ), Department of Molecular Genetics [Maastricht, The Netherlands], Maastricht University [The Netherlands], Department of Human Genetics [Leiden, The Netherlands], Leiden University Medical Center (LUMC), Department of Medicine [Nijmegen, The Netherlands], Radboud University Nijmegen Medical Center [The Netherlands], Department of Cellular and Molecular Medicine [Ohio, USA], Lerner Research Institute Cleveland Clinic [USA], Equipe LIPNESS (LNC - U1231) ( LIPNESS ), Lipides - Nutrition - Cancer [Dijon - U1231] ( LNC ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Department of Pediatrics and Laboratory Medicine [Groningen, The Netherlands], University Medical Center Groningen - UMCG [The Netherlands], Department of Medicine [Leiden, The Netherlands], Laboratory of Biochemistry [Wageningen, The Netherlands], This research was supported by The Netherlands Cardiovascular Research Committee IN-CONTROL grant (CVON 2012-03) and the Rembrandt Institute for Cardiovascular Research 2012. TMA and TMAO analyses were supported by grants from the National Institutes of Health and the Office of Dietary Supplements (HL103866, HL122283, and AA024333).LPS measurement was supported by the Institut National de la Santé et de la Recherche Médicale (INSERM, Centre de Recherches U1231), and the French Government Grant managed by the French National Research Agency under the program 'Investissements d’Avenir' ANR-11-LABX-0021., Wageningen University and Research [Wageningen] (WUR), Radboud University Medical Center [Nijmegen], Cleveland Clinic, Equipe LIPNESS (LNC - U1231) (LIPNESS), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), University Medical Center Groningen [Groningen] (UMCG), Genetica & Celbiologie, Moleculaire Genetica, RS: NUTRIM - R2 - Liver and digestive health, RS: NUTRIM - R2 - Gut-liver homeostasis, Mandard, Stéphane, and Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: Male, 0301 basic medicine, obesity, Gut flora, Galactans, Gastroenterology, Biochemistry, antibiotics, Mannans, STEATOHEPATITIS, Voeding, Metabolisme en Genomica, chemistry.chemical_compound, Liver disease, Endocrinology, Non-alcoholic Fatty Liver Disease, Fibrosis, Antibiotics, Plant Gums, Nonalcoholic fatty liver disease, Heptaic inflammation, FIBROSIS, hepatic fibrosis, Research Articles, Human Nutrition & Health, biology, Bile acid, Humane Voeding & Gezondheid, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Metabolism and Genomics, Anti-Bacterial Agents, 3. Good health, Intestine, L-CARNITINE, Liver, GUAR GUM, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Metabolisme en Genomica, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nutrition, Metabolism and Genomics, [ SDV.MHEP.HEG ] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, medicine.medical_specialty, medicine.drug_class, Biochemie, Celbiologie en Immunologie, QD415-436, Gut microbiota, METABOLISM, Diet, High-Fat, digestive system, DIET, 03 medical and health sciences, Voeding, INFLAMMATION, INTESTINAL MICROBIOTA, Internal medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, Hepatic inflammation, Obesity, intestine, VLAG, Nutrition, Inflammation, Bile acids and salts, hepatic inflammation, Biological Transport, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Cell Biology, Glucose Tolerance Test, medicine.disease, Taurocholic acid, biology.organism_classification, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Gastrointestinal Microbiome, Mice, Inbred C57BL, MICE, 030104 developmental biology, chemistry, Cell Biology and Immunology, Steatohepatitis, Hepatic fibrosis, TRIMETHYLAMINE-N-OXIDE
Abstract: Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide, yet the pathogenesis of NAFLD is only partially understood. Here, we investigated the role of the gut bacteria in NAFLD by stimulating the gut bacteria via feeding mice the fermentable dietary fiber, guar gum (GG), and suppressing the gut bacteria via chronic oral administration of antibiotics. GG feeding profoundly altered the gut microbiota composition, in parallel with reduced diet-induced obesity and improved glucose tolerance. Strikingly, despite reducing adipose tissue mass and inflammation, GG enhanced hepatic inflammation and fibrosis, concurrent with markedly elevated plasma and hepatic bile acid levels. Consistent with a role of elevated bile acids in the liver phenotype, treatment of mice with taurocholic acid stimulated hepatic inflammation and fibrosis. In contrast to GG, chronic oral administration of antibiotics effectively suppressed the gut bacteria, decreased portal secondary bile acid levels, and attenuated hepatic inflammation and fibrosis. Neither GG nor antibiotics influenced plasma lipopolysaccharide levels. In conclusion, our data indicate a causal link between changes in gut microbiota and hepatic inflammation and fibrosis in a mouse model of NAFLD, possibly via alterations in bile acids.-Janssen, A. W. F., T. Houben, S. Katiraei, W. Dijk, L. Boutens, N. van der Bolt, Z. Wang, J. M. Brown, S. L. Hazen, S. Mandard, R. Shiri-Sverdlov, F. Kuipers, K. Willems van Dijk, J. Vervoort, R. Stienstra, G. J. E. J. Hooiveld, and S. Kersten. Modulation of the gut microbiota impacts nonalcoholic fatty liver disease: a potential role for bile acids.
Published: 2017
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131. Soil-landscape controls on the impact of extreme warm and dry events on terrestrial ecosystems within continental Europe and the Mediterranean Basin

Author: Mulder, Vera Leatitia, van Eck, Christel Melissa, Friedlingstein, Pierre, Arrouays, Dominique, Regnier, Pierre, Soil Geography and Landscape Group, Wageningen University and Research Centre [Wageningen] (WUR), Department of Geosciences, Environment and Society, Université Libre de Bruxelles [Bruxelles] (ULB), College of Engineering, Mathematics and Physical Sciences, University of Exeter, Unité INFOSOL (ORLEANS INFOSOL), Institut National de la Recherche Agronomique (INRA), Wageningen University and Research [Wageningen] (WUR), Université libre de Bruxelles (ULB), and InfoSol (InfoSol)
Subjects: changement climatique, France, Soil-landscape control, Extreme climatic event, Terrestrial ecosystem, Large extent, [SDV]Life Sciences [q-bio], europe du sud, bassin méditerranéen, cartographie des sols, southern Europe, soil sciences, sciences du sol, europe, global change
Abstract: Vegetation activity within continental Europe and the Mediterranean Basin is changing and extreme warm and dry events cause substantial reductions in vegetation activity. This region covers a wide variety of climate regimes, soil and land cover types. Distinguishing the response of the vegetation to extreme heat, drought and compound events as a function of land cover type, climate regime and soil type allows to better explain regional and local differences in vegetation response. This research analyses the temporal evolution of the impact of extreme heat, drought and compound events on the observed NDVI during the growing season, aggregated by land cover, soil and climate types. The results show 31% reduction of the median vegetation activity, though highly variable depending on local conditions in climate, soil and vegetation type. The maximum impact was observed for extreme warm and dry compound events, one month after the extreme event occurrence, and recovery took up to 4 months. Furthermore, the impact of extreme heat and drought on vegetation activity increases when moving to colder climates with the largest change occurring in high latitude natural land cover types. The soil properties affecting the impact of extreme droughts on vegetation activity were mainly related to root depth limitations, water regulating properties and ecophysiological properties. Within a temperate climate, water availability and water regulating properties of the soil were found most important; in water limiting conditions those showing limiting root development con- ditions linked to abrupt textural changes (e.g. Luvisol), accumulated salts (e.g. Solonchak) or unfavorable soil structure (compaction, swelling/shrinking) were more impacted and had a slower recovery. Within a hot and dry temperate climate, there were major differences in the overall productivity rather than a different response to extreme events. These differences were mainly related to growth limiting conditions due to accumulated salts in the soil profile (e.g. Calcisol, Solonchak). Furthermore, it was found that vegetation activity of stable forest ecosystems was strongly impacted by extreme climatic events, especially in Northern Europe. The controlling fac- tors defining the impact of extreme warm and dry events were found to be a complex combinatory of soil, climate and ecophysiological properties (e.g. Podzols and mycorrhiza networks in Northern Europe). With the expected increase of extreme climatic events, the current stable and productive sys- tems will be most affected and large reductions in vegetation activity can be expected, partly due to the lack of ecophysiological adaptation of plants towards the change in climate.
Published: 2017

132. Genetic determinism of flowering regularity over years in an apple multi-family population

Author: Baptiste Guitton, Jean-Baptiste Durand, Evelyne Costes, Eric van de Weg, Marco C. A. M. Bink, Alix Allard, Modelling and Inference of Complex and Structured Stochastic Systems (MISTIS ), 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 polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-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)-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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Plant Breeding, Wageningen University and Research [Wageningen] (WUR), Biometris, Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), 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)-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), 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), Modelling and Inference of Complex and Structured Stochastic Systems (MISTIS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut National Polytechnique de Grenoble (INPG), 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)-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)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), 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), Wageningen University and Research Center (WUR), Wageningen University and Research Centre [Wageningen] (WUR), 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)-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), 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 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), and 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)
Subjects: déterminisme génétique, Correlation coefficient, initiation florale, Entropy, Population, Floral induction, alternance de production, pommier, Markov models, Apple tree, Horticulture, Quantitative trait locus, Biennial bearing, Generalized linear mixed model, modèle de markov, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Statistics, Botany, Pedigree based analysis, education, Malus x domestica, malus domestica, education.field_of_study, Vegetal Biology, Genetic architecture, Bayes factor, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Geography, Tree breeding, Biologie végétale
Abstract: UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières; International audience; Irregular flowering over years is commonly observed in fruit trees and is assumed to be, at least partly, under genetic control. This study aimed atpredicting genotype flowering behaviours and at detecting QTL associated to regularity, in a multi-family apple tree population. Successions of vegetative and floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families, observed at two experimental sites. Sequences were analysed using Markovian and linear mixed models including year and site effects.Indices of flowering regularity, periodicity and synchronicity were estimated, at tree and axis scales. First indices were derived from the Biennial Bearing Index (BBI). A second index was the auto-regressive correlation coefficient between flowering in consecutive years. A third index quantified the synchronicity of meristems within the trees through the measure of differences in the predictability of flowering over years, from a probabilistic viewpoint. These three types of indices were used to predict tree behaviour and to detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of the three indices efficiently predicted andclassified the genotype behaviours despite few miss-classifications. Four common QTLs for BBIs and auto-regressive coefficient were highlighted (on LG4, 5, 8 and 10) and one for synchronicity (on LG9) in the integrated multi-family map, thus revealing the complex genetic architecture of the considered traits. This study proposes a posteriori sampling of axes within trees as a relevant and time-savingmethod to estimate tree flowering behaviours. Coupled to appropriate statistical indices, it is efficient to evaluate the tree breeding values for flowering regularity.In apple tree, biennial bearing appeared to result from high AS synchronism in flowering, i.e. with all axes alternatively flowering or not in a given year, whereas regularity resulted from either asynchronous alternating or regular flowering of AS.
Published: 2017
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133. Stb16q-mediated resistance against Zymoseptoria tritici is conferred by a new class of R gene

Author: Saintenac, Cyrille, Cambon, Florence, Faris, Justin, Xu, Steven, Marande, William, Berges, Helene, Ghaffary, Mahmod Tabib, Aouini, Lamia, Kema, Gert Hj, Robert, Olivier, Langin, Thierry, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Cereal Crops Research Unit, USDA-ARS : Agricultural Research Service, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Seed and Plant Improvement Research Department, Agricultural Research, Education and Extension Organisation (AREEO ), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Florimond Desprez, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), United States Department of Agriculture - Agricultural Research Service, Wageningen University and Research Centre [Wageningen] (WUR), ProdInra, Archive Ouverte, and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: [SDV] Life Sciences [q-bio], blé, wheat, [SDV]Life Sciences [q-bio]
Abstract: Book of abstracts p. 61 ISBN: 978-3-900932-48-0Book of abstracts p. 61ISBN: 978-3-900932-48-0; Stb16q-mediated resistance against Zymoseptoria tritici is conferred by a new class of R gene. 13. International Wheat Genetics Symposium
Published: 2017

134. Hydrophobic features of EPS extracted from anaerobic granular sludge: an investigation based on DAX-8 resin fractionation and size exclusion chromatography

Author: Yoan Pechaud, Isabelle Bourven, Feishu Cao, Eric D. van Hullebusch, Piet N.L. Lens, Gilles Guibaud, Laboratoire Géomatériaux et Environnement (LGE), Université Paris-Est Marne-la-Vallée (UPEM), Groupement de Recherche Eau, Sol, Environnement (GRESE), Université de Limoges (UNILIM), Sub-Department of Environmental Technology, Wageningen University and Research Centre [Wageningen] (WUR), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research [Wageningen] (WUR), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Polymers, Size-exclusion chromatography, Formaldehyde, Fractionation, 010501 environmental sciences, Chemical Fractionation, 01 natural sciences, Applied Microbiology and Biotechnology, EPS extraction, 03 medical and health sciences, chemistry.chemical_compound, Extracellular polymeric substance, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Anaerobiosis, DAX-8 resin Hydrophobicity, Sodium dodecyl sulfate, 0105 earth and related environmental sciences, Chromatography, Ethanol, Sewage, Elution, Anaerobic granular sludge, SEC/absorbance 210 nm, General Medicine, Hydrogen-Ion Concentration, Molecular Weight, 030104 developmental biology, chemistry, Reagent, Chromatography, Gel, Hydrophobic and Hydrophilic Interactions, Biotechnology
Abstract: International audience; The hydrophobic fractionation of extracellular polymeric substances (EPS) extracted from anaerobic granular sludge was performed on the DAX-8 resin (two elution pH conditions, i.e., pH 2 and pH 5 were tested). The impact of seven different EPS extraction methods on EPS hydrophobicity features was assessed. The results showed that the extraction methods and bulk solution pH influenced dramatically the biochemical composition of the EPS, and in turn, the hydrophobicity determined. Besides, EPS extracting reagents i.e., formaldehyde, ethanol, sodium dodecyl sulfate (SDS), and Tween 20 not only introduced extra carbon content in the total organic carbon (TOC) measurement but also interacted with the DAX-8 resin. By comparing the apparent molecular weight (aMW) distribution of untreated and pH-adjusted EPS samples, more complete EPS aMW information was preserved at pH 5. Thus, elution at pH 5 was preferred in this study for the qualitative analysis of EPS hydrophobic features. The hydrophobic fraction of EPS retained by the resin at pH 5 was ascribed to a wide aMW range, ranging from >440 to 0.3 kDa. Within this range, EPS molecules ranging from 175 to 31 kDa were mostly retained by the DAX-8 resin, which indicates that these EPS molecules are highly hydrophobic.
Published: 2017
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135. Host-related factors explaining interindividual variability of carotenoid bioavailability and tissue concentrations in humans

Author: Charles Desmarchelier, Wilhelm Stahl, Ralph Rühl, Patrick Borel, Lars O. Dragsted, Torsten Bohn, Charlotte Svendler Nielsen, Jaap Keijer, Luxembourg Institute of Health, Nutrition, obésité et risque thrombotique (NORT), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Nutrition, Exercise and Sports [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institute of Biochemistry and Molecular Biology II [Düsseldorf, Germany], University Hospital Düsseldorf, MTA-DE Public Health Research Group of the Hungarian Academy of Sciences [Debrecen, Hungary], University of Debrecen [Hungary]-Faculty of Public Health [Debrecen, Hungary], Paprika Bioanalytics BT [Debrecen, Hungary], Wageningen University and Research Centre [Wageningen] (WUR), Human and Animal Physiology [Wageningen, The Netherlands], Wageningen University [The Netherlands], EU COST action POSITIVE FA-1403., Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Debrecen Egyetem [Debrecen], Wageningen University and Research [Wageningen] (WUR), and Borel, Patrick
Subjects: 0301 basic medicine, appareil intestinal, Apolipoprotein B, Adipose tissue, Review, Intestinal absorption, polymorphisme génétique, Biodistribution, absorption digestive, Faculty of Science, genetic polymorphism, Tissue Distribution, Carotenoid, 2. Zero hunger, chemistry.chemical_classification, Biological Variation, Individual, intestinal absorption, food and beverages, prévention des maladies chroniques, métabolisme tissulaire, carotenoid, 3. Good health, Intestine, Observational Studies as Topic, Liver, Biochemistry, Absorption, Genetic polymorphisms, Macula lutea, Human and Animal Physiology, Alimentation et Nutrition, Digestion, Signal Transduction, Biotechnology, Transcriptional Activation, medicine.medical_specialty, Reviews, Biological Availability, Biology, 03 medical and health sciences, carotenoide, microbiote, Internal medicine, medicine, Humans, Food and Nutrition, biodistribution, VLAG, Lipid metabolism, Metabolism, prevention of chronic disease, Lipid Metabolism, Carotenoids, Diet, Bioavailability, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, 030104 developmental biology, Endocrinology, chemistry, WIAS, Fysiologie van Mens en Dier, biology.protein, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science, Chylomicron
Abstract: Absorption; Biodistribution; Genetic polymorphisms; Intestine; Macula lutea; International audience; Carotenoid dietary intake and their endogenous levels have been associated with a decreased risk of several chronic diseases. There are indications that carotenoid bioavailability depends, in addition to the food matrix, on host factors. These include diseases (e.g. colitis), life-style habits (e.g. smoking), gender and age, as well as genetic variations including single nucleotide polymorphisms that govern carotenoid metabolism. These are expected to explain interindividual differences that contribute to carotenoid uptake, distribution, metabolism and excretion, and therefore possibly also their association with disease risk. For instance, digestion enzymes fostering micellization (PNLIP, CES), expression of uptake/efflux transporters (SR-BI, CD36, NPC1L1), cleavage enzymes (BCO1/2), intracellular transporters (FABP2), secretion into chylomicrons (APOB, MTTP), carotenoid metabolism in the blood and liver (LPL, APO C/E, LDLR), and distribution to target tissues such as adipose tissue or macula (GSTP1, StARD3) depend on the activity of these proteins. In addition, human microbiota, e.g. via altering bile-acid concentrations, may play a role in carotenoid bioavailability. In order to comprehend individual, variable responses to these compounds, an improved knowledge on intra-/interindividual factors determining carotenoid bioavailability, including tissue distribution, is required. Here, we highlight the current knowledge on factors that may explain such intra-/interindividual differences.
Published: 2017
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136. A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Author: Brett Williams, Jill M. Farrant, José M. Jiménez-Gómez, Henk W. M. Hilhorst, Eef Jonkheer, Thamara Hesselink, Mariana Aline Silva Artur, Wilco Ligterink, Elio Schijlen, Harm Nijveen, Martijn F.L. Derks, Maria Cecília D. Costa, Melvin J. Oliver, Sagadevan G. Mundree, Julio Maia, Laboratory of Plant Physiology, Wageningen University and Research Centre [Wageningen] (WUR), Department of Molecular and Cell Biology, University of Cape Town, Bioinformatics Group, Wageningen University, Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Department of Plant Breeding and Genetics, Cornell University, Bioscience, Wageningen Plant Research International, Wageningen University and Research Center (WUR), University of Missouri [Columbia], University of Missouri System, Midwest Area (MWA) - Plant Genetic Resources Unit (PGRU), United States Department of Agriculture - Agricultural Research Service, CAPES–Brazilian Federal Agency for Support and Evaluation of Graduate Education (BEX0428/09-04, BEX0857/14-9), South African Research Chairs Initiative of the DST and NRF of SA (Grant No 98406), Wageningen University and Research [Wageningen] (WUR), Cornell University [New York], University of Missouri [Columbia] (Mizzou), and USDA-ARS : Agricultural Research Service
Subjects: 0106 biological sciences, 0301 basic medicine, dessèchement, Bioinformatics, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, Drought tolerance, Resurrection plant, Plant Science, Biology, 01 natural sciences, Genome, Transcriptome, Desiccation tolerance, 03 medical and health sciences, Magnoliopsida, BIOS Applied Bioinformatics, Phylogenetics, Botany, Bioinformatica, Life Science, Laboratorium voor Plantenfysiologie, Desiccation, Gene, genome, Phylogeny, Plant Proteins, 2. Zero hunger, ved/biology, food and beverages, xerophyta viscosa, 15. Life on land, Droughts, 030104 developmental biology, BIOS Applied Metabolic Systems, EPS, transcription, Laboratory of Plant Physiology, 010606 plant biology & botany
Abstract: Desiccation tolerance is common in seeds and various other organisms, but only a few angiosperm species possess vegetative desiccation tolerance. These 'resurrection species' may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance, we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration. Data revealed induction of transcripts typically associated with desiccation tolerance in seeds and involvement of orthologues of ABI3 and ABI5, both key regulators of seed maturation. Dehydration resulted in both increased, but predominantly reduced, transcript abundance of genomic 'clusters of desiccation-associated genes' (CoDAGs), reflecting the cessation of growth that allows for the expression of desiccation tolerance. Vegetative desiccation tolerance in X. viscosa was found to be uncoupled from drought-induced senescence. We provide strong support for the hypothesis that vegetative desiccation tolerance arose by redirection of genetic information from desiccation-tolerant seeds.
Published: 2017
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137. An Insight in the Reproductive Biology of Therophilus javanus (Hymenoptera, Braconidae, and Agathidinae), a Potential Biological Control Agent against the Legume Pod Borer (Lepidoptera, Crambidae)

Author: Barry R. Pittendrigh, Manuele Tamò, Djibril Aboubakar Souna, Antonino Cusumano, Aimé H. Bokonon-Ganta, Anne-Nathalie Volkoff, Marc Ravallec, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), International Institute of Tropical Agriculture (IITA), International Institute of Tropical Agriculture, Faculté des Sciences Agronomiques (FSA), University of Abomey Calavi (UAC), Wageningen University and Research Centre [Wageningen] (WUR), Michigan State University [East Lansing], Michigan State University System, Aboubakar Souna D., Bokonon-Ganta A., Ravallec M., Cusumano A., Pittendrigh B.R., Volkoff A.-N., Tamo M., International Institute of Tropical Agriculture (IITA-Benin), International Institute of Tropical Agriculture [Nigeria] (IITA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Wageningen University and Research [Wageningen] (WUR)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Article Subject, Biological pest control, Parasitism, Zoology, 010603 evolutionary biology, 01 natural sciences, follicle, Parasitoid, Lepidoptera genitalia, Crambidae, Maruca vitrata, lcsh:Zoology, lcsh:QL1-991, Laboratory of Entomology, Caterpillar, Ecology, Evolution, Behavior and Systematics, biology, fungi, biology.organism_classification, Laboratorium voor Entomologie, ovariole, 010602 entomology, vitellarium, Settore AGR/11 - Entomologia Generale E Applicata, Agronomy, Insect Science, caterpillar, oogenesi, EPS, 017-4066, Braconidae, Research Article
Abstract: Therophilus javanus is a koinobiont, solitary larval endoparasitoid currently being considered as a biological control agent against the pod borer Maruca vitrata, a devastating cowpea pest causing 20–80% crop losses in West Africa. We investigated ovary morphology and anatomy, oogenesis, potential fecundity, and egg load in T. javanus, as well as the effect of factors such as age of the female and parasitoid/host size at oviposition on egg load. The number of ovarioles was found to be variable and significantly influenced by the age/size of the M. vitrata caterpillar when parasitized. Egg load also was strongly influenced by both the instar of M. vitrata caterpillar at the moment of parasitism and wasp age. The practical implications of these findings for improving mass rearing of the parasitoid toward successful biological control of M. vitrata are discussed.
Published: 2017
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138. Does the recoupling of dairy and crop production via cooperation between farms generate environmental benefits? A case-study approach in Europe

Author: O. Barrantes, Jérémy Berland, M.C. Hanegraaf, Eimear M. Ruane, Thomas Nesme, Sylvain Pellerin, Silvia Marton, H. Korevaar, J. Regan, Interactions Sol Plante Atmosphère (ISPA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Life Cycle Assessment, Institute for Sustainability Sciences, Agroscope, Swiss Federal Institute of Technology, Departamento de Ciencias Agrarias y del Medio Natural, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Teagasc Food Research Centre [Fermoy, County Cork, Ireland], Nutriënten Management Instituut, SARL Déshyouest, Coopedom, Plant Research International, Wageningen University and Research Centre [Wageningen] (WUR), Interactions Sol Plante Atmosphère (UMR ISPA), Teagasc Food Research Centre [Fermoy, Ireland], Wageningen University and Research [Wageningen] (WUR), and Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, agriculture durable, Land Use and Food Security, Soil Science, Plant Science, 010501 environmental sciences, farm specialisation, crop-livestock integration, Nutrient cycling, 01 natural sciences, Ecosystem services, Sustainable agriculture, resource use efficiency, Dairy production, 0105 earth and related environmental sciences, relation élevage agriculture, 2. Zero hunger, dairy production, farm censuses, business.industry, Intensive farming, Landgebruik en Voedselzekerheid, nutrient cycling, 04 agricultural and veterinary sciences, 15. Life on land, Product (business), sustainable agriculture, Crop-livestock integration, enquête en exploitation agricole, Agronomy, Agriculture, Resource use efficiency, Sustainability, 040103 agronomy & agriculture, Farm specialisation, 0401 agriculture, forestry, and fisheries, Livestock, Business, Arable land, ecosystem services, Agronomy and Crop Science
Abstract: The intensification of agriculture in Europe has contributed significantly to the decline of mixed crop-livestock farms in favour of specialised farms. Specialisation, when accompanied by intensive farming practices, leaves farms poorly equipped to sustainably manage by-products of production, capture beneficial ecological interactions, and adapt in a volatile economic climate. An often proposed solution to overcome these environmental and economic constraints is to recouple crop and livestock production via cooperation between specialised farms. If well-managed, synergies between crop and livestock production beyond farm level have the potential to improve feed and fertiliser autonomy, and pest regulation. However, strategies currently used by farmers to recouple dairy livestock and crop production are poorly documented; there is a need to better assess these strategies using empirical farm data. In this paper, we employed farm surveys to describe, analyse and assess the following strategies: (1) Local exchange of materials among dairy and arable farms; (2) Land renting between dairy and arable farms; (3) Animal exchanges between lowland and mountainous areas; and (4) Industrially mediated transfers of dehydrated fodder. For each strategy, cooperating farm groups were compared to non-cooperating farm groups using indicators of metabolic performance (input autonomy, nutrient cycling and use efficiency), and ecosystem services provision. The results indicate that recoupling of crop and dairy production through farm cooperation gives farmers access to otherwise inaccessible or underutilised local resources such as land, labour, livestock feed or organic nutrients. This in turn leads to additional outlets for by-products (e.g. animal manure). Farmers' decisions about how to allocate the additional resources accessed via cooperation essentially determine if the farm diversifies, intensifies or expands operations. The key finding is that in three of the four crop-livestock integration strategies assessed, these newly accessed resources facilitated more intensive farming practices (e.g. higher stocking rate or number of milking cows per hectare) on cooperating dairy farms relative to non-cooperating, specialised dairy farms. As a consequence, cooperation was accompanied by limited environmental benefits but helped to improve resource use efficiency per unit of agricultural product produced. This article provides a critical step toward understanding real-world results of crop-livestock cooperation beyond the farm level relative to within-farm crop-livestock integration. As such, it brings practical knowledge of vital importance for policy making to promote sustainable farming.
Published: 2017
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139. Genetic and nongenetic factors contributing to differences in αS-casein phosphorylation isoforms and other major milk proteins

Author: Guy Miranda, H. Bovenhuis, A. Delacroix-Buchet, M.H.P.W. Visker, Patrice Martin, Didier Boichard, Zih-Hua Fang, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), Casdar From'Mir, Erasmus Mundus EGS-ABG, Apisgene, and Wageningen University and Research Centre [Wageningen] (WUR)
Subjects: 0301 basic medicine, Gene isoform, genetic variant, [SDV]Life Sciences [q-bio], Biology, Animal Breeding and Genomics, 03 medical and health sciences, Casein, Lactation, Genetic variation, Genetics, medicine, Fokkerij en Genomica, Lactation stage, Genetic variant, 2. Zero hunger, phosphorylation, French Montbéliarde, 0402 animal and dairy science, 04 agricultural and veterinary sciences, bovine Montbéliarde breed, Heritability, race bovine montbeliarde, 040201 dairy & animal science, Phenotype, casein haplotype, variation génétique, 030104 developmental biology, medicine.anatomical_structure, Casein haplotype, Biochemistry, WIAS, Phosphorylation, Animal Science and Zoology, Composition (visual arts), Food Science
Abstract: Relative concentrations of αS-casein (αS-CN) phosphorylation isoforms vary considerably among milk of individual cows. We aimed to explore to what extent genetic and other factors contribute to the variation in relative concentrations of αS-CN phosphorylation isoforms and the phosphorylation degree of αS-CN defined as the proportion of isoforms with higher degrees of phosphorylation. We also investigated the associations of genetic variants of milk proteins and casein haplotypes with relative concentrations of αS-CN phosphorylation isoforms and with the phosphorylation degree of αS-CN in French Montbéliarde cattle from the cheese production area of Franche-Comté. Detailed milk protein composition was determined by liquid chromatography coupled with electrospray ionization mass spectrometry from 531 test-day morning milk samples. Parity, lactation stage, and genetic variation of cows contributed to the phenotypic variation in relative concentrations of individual αS-CN phosphorylation isoforms and in the phosphorylation degree of αS-CN. As lactation progressed, we observed a significant increase for relative concentrations of αS-CN isoforms with higher degrees of phosphorylation (αS1-CN-9P, αS2-CN-13P, and αS2-CN-14P) as well as for the phosphorylation degree of both αS1-CN and αS2-CN. Furthermore, the β-CN I variant was associated with a greater proportion of isoforms with lower degrees of phosphorylation (αS1-CN-8P, αS2-CN-10P, and αS2-CN-11P); the β-CN B variant was associated with a greater proportion of isoforms with higher degrees of phosphorylation (αS1-CN-9P, αS2-CN-12P to αS2-CN-14P). The heritability estimates were low to moderate for relative concentrations of αS2-CN phosphorylation isoforms (0.07 to 0.32), high for relative concentrations of αS1-CN-8P (0.84) and αS1-CN-9P (0.56), and moderate for phosphorylation degrees of αS1-CN (0.37) and αS2-CN (0.23). Future studies investigating relations between the phosphorylation degree of αS-CN and technological properties of milk will be beneficial for the dairy industry.
Published: 2017
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140. Effect of production quotas on economic and environmental values of growth rate and feed efficiency in sea cage fish farming

Author: Hans Komen, J.A.M. van Arendonk, Marc Vandeputte, Mathieu Besson, Edwige Quillet, I.J.M. de Boer, Joël Aubin, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Animal Breeding and Genomics Centre, Wageningen University and Research Centre [Wageningen] (WUR), Animal Production Systems group, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Sol Agro et hydrosystème Spatialisation (SAS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research [Wageningen] (WUR), 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 la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Besson, Mathieu
Subjects: Environmental Impacts, 0301 basic medicine, Atmospheric Science, Economics, [SDV]Life Sciences [q-bio], Social Sciences, lcsh:Medicine, Aquaculture, Agricultural science, Environmental impact assessment, Economic impact analysis, lcsh:Science, Life-cycle assessment, Climatology, 2. Zero hunger, Dierlijke Productiesystemen, Multidisciplinary, Ecology, Agriculture, 04 agricultural and veterinary sciences, Eutrophication, Chemistry, Models, Economic, Physical Sciences, Fish Farming, Environmental Economics, Research Article, Conservation of Natural Resources, Pollutants, Animal feed, Climate Change, Fish farming, Fisheries, Biology, Animal Breeding and Genomics, Feed conversion ratio, Animal Production Systems, 03 medical and health sciences, Animals, Environmental Chemistry, Life Science, Seawater, Fokkerij en Genomica, 14. Life underwater, Sea bass, Ecosystem, Stock (geology), Ecology and Environmental Sciences, lcsh:R, 0402 animal and dairy science, Biology and Life Sciences, Animal Feed, 040201 dairy & animal science, Economic Analysis, 030104 developmental biology, Seafood, Economic Impact Analysis, 13. Climate action, Earth Sciences, WIAS, Bass, lcsh:Q, Agricultural Economics
Abstract: In sea cage fish farming, production quotas aim to constrain the impact of fish farming on the surrounding ecosystem. It is unknown how these quotas affect economic profitability and environmental impact of genetic improvement. We combined bioeconomic modelling with life cycle assessment (LCA) to calculate the economic (EV) and environmental (ENV) values of thermal growth coefficient (TGC) and feed conversion ratio (FCR) of sea bass reared in sea cages, given four types of quota commonly used in Europe: annual production (Qprod), annual feed distributed (Qannual_ feed), standing stock (Qstock), and daily feed distributed (Qdaily_ feed). ENV were calculated for LCA impact categories climate change, eutrophication and acidification. ENV were expressed per ton of fish produced per year (ENV(fish)) and per farm per year (ENV(farm)). Results show that irrespective of quota used, EV of FCR as well as ENV(fish) and ENV(farm) were always positive, meaning that improving FCR increased profit and decreased environmental impacts. However, the EV and the ENV(fish) of TGC were positive only when quota was Qstock or Qdaily_ feed. Moreover, the ENV(farm) of TGC was negative in Qstock and Qdaily_ feed quotas, meaning that improving TGC increased the environmental impact of the farm. We conclude that Qstock quota and Qdaily_ feed quota are economically favorable to a genetic improvement of TGC, a major trait for farmers. However, improving TGC increases the environmental impact of the farm. Improving FCR represents a good opportunity to balance out this increase but more information on its genetic background is needed to develop breeding programs improving FCR.
Published: 2017
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141. A test of the hierarchical model of litter decomposition

Author: Aimée T. Classen, Daniel S. Maynard, Thomas W. Crowther, J. Hans C. Cornelissen, Paul Kardol, G F Ciska Veen, David A. Wardle, Mark A. Bradford, Wim H. van der Putten, Anne Bonis, Gregory S. Newman, Grégoire T. Freschet, Stephen A. Wood, Maria Viketoft, Ella M. Bradford, Richard S.P. Logtestijn, William R. Wieder, Marta Manrubia-Freixa, Jonathan R. De Long, Yale University [New Haven], Netherlands Institute of Ecology (NIOO-KNAW), 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), Rubenstein School Environment and National Resources, University of Vermont [Burlington], Center Macroecology, Evolution and Climate, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Vrije Universiteit Amsterdam [Amsterdam] (VU), Institute for Integrative Biology [Zürich] (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour le Développement (IRD [France-Sud]), Swedish University of Agricultural Sciences (SLU), Yale School Forestry & Environment Studies, Nanyang Technological University [Singapour], National Center for Atmospheric Research [Boulder] (NCAR), The Nature Conservancy, Wageningen University and Research [Wageningen] (WUR), Research was supported by grants to M.A.B. from the US National Science Foundation (DEB-1457614), The Royal Netherlands Academy of Arts and Sciences (Visiting Professors Programme), and the Netherlands Production Ecology & Resource Conservation Programme for Visiting Scientists. G.F.V. was supported by an NWO-VENI from the Netherlands Organisation for Scientific Research (863.14.013). M.M.-F. and W.H.v.d.P. were supported by a European Research Council grant (ERC-Adv 260-55290), and G.T.F. by grant EC2CO-Multivers., 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), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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)-Centre National de la Recherche Scientifique (CNRS), University of Vermont, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Wageningen University and Research Centre [Wageningen] (WUR), Terrestrial Ecology (TE), and Systems Ecology
Subjects: 0106 biological sciences, Biogeochemical cycle, Climate, Climate Change, Ecosystem ecology, Climate change, Atmospheric sciences, 010603 evolutionary biology, 01 natural sciences, Hierarchical database model, Decomposer, Carbon cycle, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Decomposition (computer science), SDG 13 - Climate Action, Life Science, Laboratorium voor Nematologie, Ecology, Evolution, Behavior and Systematics, Soil Microbiology, Biomass (ecology), Ecology, 04 agricultural and veterinary sciences, 15. Life on land, Models, Theoretical, PE&RC, Europe, 13. Climate action, international, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, EPS, Laboratory of Nematology
Abstract: International audience; Our basic understanding of plant litter decomposition informs the assumptions underlying widely applied soil biogeochemical models, including those embedded in Earth system models. Confidence in projected carbon cycle-climate feedbacks therefore depends on accurate knowledge about the controls regulating the rate at which plant biomass is decomposed into products such as CO2. Here we test underlying assumptions of the dominant conceptual model of litter decomposition. The model posits that a primary control on the rate of decomposition at regional to global scales is climate (temperature and moisture), with the controlling effects of decomposers negligible at such broad spatial scales. Using a regional-scale litter decomposition experiment at six sites spanning from northern Sweden to southern France-and capturing both within and among site variation in putative controls-we find that contrary to predictions from the hierarchical model, decomposer (microbial) biomass strongly regulates decomposition at regional scales. Furthermore, the size of the microbial biomass dictates the absolute change in decomposition rates with changing climate variables. Our findings suggest the need for revision of the hierarchical model, with decomposers acting as both local- and broad-scale controls on litter decomposition rates, necessitating their explicit consideration in global biogeochemical models.
Published: 2017
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142. Diversity and carbon storage across the tropical forest biome

Author: Connie J. Clark, Kofi Affum-Baffoe, Lan Qie, Timothy R. Baker, Abel Monteagudo-Mendoza, Lise Zemagho, Yadvinder Malhi, Javier Silva Espejo, Patricia Alvarez-Loayza, Lindsay F. Banin, Jefferson S. Hall, Ima Célia Guimarães Vieira, H. Priyadi, Jérôme Chave, Fernando Cornejo Valverde, Peter M. Umunay, J. W. Ferry Slik, Martin Gilpin, Ana Andrade, Andrew R. Marshall, Alvaro Cogollo Pacheco, Bonaventure Sonké, Rodrigo Sierra, Jan Bogaert, Emanuel Gloor, Christopher Baraloto, Guido Pardo, Nicholas J. Berry, Simon L. Lewis, Georgia Pickavance, Axel Dalberg Poulsen, Ismayadi Samsoedin, Vincent A. Vos, Carlos Cerón, Jean-Louis Doucet, Peter S. Ashton, William F. Laurance, Wannes Hubau, Thomas E. Lovejoy, Eric Chezeaux, Zorayda Restrepo, Aida Cuni-Sanchez, Kanehiro Kitayama, Everton Cristo de Almeida, Luiz E. O. C. Aragão, Sophie Fauset, Nadir Pallqui Camacho, Jan Reitsma, Corneille E. N. Ewango, Percy Núñez Vargas, Hans ter Steege, John Terborgh, Roel J. W. Brienen, Jean-François Bastin, Kamariah Abu Salim, Jon C. Lovett, Beatriz Schwantes Marimon, Simon Willcock, Marisol Toledo, Ben Hur Marimon Junior, Serge K. Begne, Greta C. Dargie, Carlos A. Quesada, Terese B. Hart, Martin J. P. Sullivan, Terry Sunderland, Ted R. Feldpausch, Eurídice N. Honorio Coronado, Stuart J. Davies, Lera Miles, Sean C. Thomas, Lip Khoon Kho, Lisa Steel, Jaques Mukinzi, Marie Noel Djuikouo K., Rafael de Paiva Salomão, Terry L. Erwin, Ervan Rutishauser, Edmar Almeida de Oliveira, Rafael Herrera, Shin-ichiro Aiba, Faustin Mpanya Lukasu, Damien Bonal, Sylvester Tan, Esteban Alvarez Dávila, Marielos Peña-Claros, José Luís Camargo, Lee J. T. White, James A. Comiskey, Hermann Taedoumg, Maxime Réjou-Méchain, Pascal Petronelli, Jean-Remy Makana, Ophelia Wang, Richard B. Primack, Gerardo A. Aymard C, Charles De Cannière, Luis Valenzuela Gamarra, Gabriela Lopez-Gonzalez, Leandro Maracahipes, Kuswata Kartawinata, Michael Balinga, Victor Chama Moscoso, Susan G. Laurance, Marcos Silveira, David Harris, Miguel E. Leal, Paulo S. Morandi, John Tshibamba Mukendi, Frans Bongers, Joey Talbot, Douglas Sheil, Reuben Nilus, John R. Poulsen, Oliver L. Phillips, Sch Geog, University of Nottingham, Dept Geog, University College of London [London] (UCL), Plant Systemat & Ecol Lab, Université de Yaoundé, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Instituto Nacional de Pesquisas da Amazônia (INPA), United Nations Environment Programme World Conservation Monitoring Centre, Missouri Botanical Garden (USA), Universidad Nacional San Antonio Abad del Cusco, Center for International Forestry Research (CIFOR), Coll Marine & Environm Sci, James Cook University, Leiden University, Agence Nationale des Parcs Nationaux du Gabon, Ecole de Terrain en Ecologie Tropicale (ECOTROP), Mensurat Unit, Forestry Research Institute of Ghana, Grad Sch Sci & Engn, Kagoshima University, Inst Biodiversidade & Floresta, Universidade Federal do Oeste do Pará, Universidade Federal do Mato Grosso (UFMT), Ctr Trop Conservat, Duke University [Durham], Universidad Nacional de Colombia, Coll Life & Environm Sci, University of Exeter, Dept Organism & Evolutionary Biol, Harvard University [Cambridge], Programa Ciencias Agro & Mar, Herbario Universitario PORT, Ctr Ecol & Hydrol, Dept Biol Sci, Int Ctr Trop Bot, Florida International University (FIU), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (Cirad-Es-UPR 105 BSEF), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Sch Geosci, University of Edinburgh, Biodivers & Landscape Unit, Université de Liège, Gembloux Agro-Bio Tech [Gembloux], Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Forest Ecol & Forest Management Grp, Wageningen University and Research Centre [Wageningen] (WUR), Projeto Dinam Biol Fragmentos Florestais, Herbario Alfredo Paredes, Universidad Agraria del Ecuador, Rougier Gabon, Nicholas Sch Environm, Duke University, Jardín Botánico de Medellín, Inventory & Monitoring Program, National Park Service, Smithsonian Institution, Andes to Amazon Biodiversity Program, Instituto de Investigaciones de la Amazonía Peruana, Smithsonian Tropical Research Institute, Landscape Ecol & Vegetal Prod Syst Unit, Université Libre de Bruxelles [Bruxelles] (ULB), Dept Bot & Plant Physiol, Fac Sci, University of Buea, Wildlife Conservation Society, Centre de Formation et de Recherche en Conservation Forestière (CEFRECOF), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Ctr Ecol, Instituto Venezolano de Investigaciones Cientificas (IVIC), Inst Geog & Reg Forsch, University of Vienna, Royal Botanic Garden Edinburgh, Lukuru Wildlife Res Fdn, Div Vertebrate Zool, National Museum of Natural History, Herbarium Bogoriense, Indonesian Institute of Sciences, Integrat Res Ctr, Field Museum of Natural History [Chicago, USA], Trop Peat Res Inst, Biol Res Div, Malaysian Palm Oil Board, Kyoto University, Ctr Trop Environm & Sustainabil Sci, Coll Sci & Engn, Dept Environm Sci & Policy, George Mason University, Fac Sci Agron, University of Kisangani, Sch Geog & Environm, University of Oxford, Universidade Federal de Goiás [Goiânia] (UFG), Flamingo Land LTD, Dept Environm, CIRCLE, University of York, Salonga Natl Pk, sabah Parks, Universidad Autonoma del Beni, Inst Boliviano Invest Forestal, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Natural History Museum [Oslo], University of Oslo (UiO), Southern Swedish Forest Res Ctr, Swedish University of Agricultural Sciences (SLU), Bur Waarderburg, Fundación Con-Vida, CarboForExpert, Fac Sci, Environm & Life Sci, University of Brunei Darussalam (Biology Department), Museu Paraense Emílio Goeldi, Forestry Research and Development Agency (FORDA), Norwegian University of Life Sciences (NMBU), Geoinformática y Sistemas , Cia. Ltda (GeoIS), Museu Univ, Universidade Federal do Acre (UFAC), World Wide Fund for Nature, CTFS AA Asia Program, Fac Forestry, University Stefan cel Mare of Suceava (USU), Sch Forestry & Environm Studies, Yale University [New Haven], Centro de Investigación y Promoción del Campesinado Norte Amazónico, Sch Earth Sci & Environm Sustainabil, Northern Arizona University [Flagstaff], Biol Sci, Liverpool John Moore University (ljmu), Sch Environm Nat Resources & Geog, Bangor University, European Research Council (ERC), Gordon and Betty Moore Foundation, David and Lucile Packard Foundation, European Union's Seventh Framework Programme 283080, 282664, Natural Environment Research Council (NERC) Urgency Grants, NERC Consortium Grant 'AMAZONICA' NE/F005806/1, NERC Consortium Grant 'TROBIT' NE/D005590/1, NERC Consortium Grant 'BIO-RED' NE/N012542/1, NERC New Investigators Grant, Royal Society, Centre for International Forestry (CIFOR), Gabon's National Parks Agency (ANPN), NERC PhD Studentship, UNEP-WCMC, NERC research fellowship NE/I021160/1, Royal Society University Research Fellowship ERC Advanced Grant (T-FORCES), Phillip Leverhulme Prize, Royal Society Wolfson Research Merit Award, NERC studentship, RGS-IBG Henrietta Hutton Grant, National Council for Science and Technology Development of Brazil (CNPq) PELD/403725/2012-7, CNPq/PPBio/457602/2012-0, National Council for Science and Technology Development of Brazil (CNPq) Productivity Grant, Leverhulme Trust under the Valuing the Arc project, Missouri Botanical Garden, Sullivan, Martin J. P., Université de Yaoundé I, Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Florida International University [Miami] (FIU), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (UPR BSEF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Wageningen University and Research [Wageningen] (WUR), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Université libre de Bruxelles (ULB), University of Vienna [Vienna], Indonesian Institute of Sciences (LIPI), University of Oxford [Oxford], Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Southern Swedish Forest Research Centre, Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Université de Toulouse (UT), James Cook University (JCU), Universiteit Leiden, Agence Nationale des Parcs Nationaux du Gabon (ANPN), Harvard University, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Royal Botanic Garden [Edinburgh]
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, INCREASES, ALPHA-DIVERSITY, [SDV]Life Sciences [q-bio], Biome, Biodiversity, COMPLEMENTARITY, forêt tropicale, Forests, 01 natural sciences, AMAZONIAN FORESTS, Tropic Climate, biodiversité, biomasse aérienne des arbres, conservation des forêts, Tropical climate, stockage du carbone, Biomass (ecology), Multidisciplinary, PRODUCTIVITY, Agroforestry, Ecology, Plants, PE&RC, Classification, Tropical ecology, Chemistry, séquestration du carbone, biome, diversité variétale, protection de la forêt, P01 - Conservation de la nature et ressources foncières, ABOVEGROUND BIOMASS, tropical forest, Asia, F60 - Physiologie et biochimie végétale, TREE ALPHA-DIVERSITY, forêt amazonienne, CONSERVATION, 010603 evolutionary biology, Article, Ecology and Environment, Phénomènes atmosphériques, Forest ecology, Life Science, Bosecologie en Bosbeheer, Forest, AFRICAN RAIN-FORESTS, WOOD PRODUCTION, BIODIVERSITY, CLIMATE, K70 - Dégâts causés aux forêts et leur protection, atténuation des effets du changement climatique, 0105 earth and related environmental sciences, Tropical Climate, Western Hemisphere, TREE SPECIES RICHNESS, Tropics, Plant, 15. Life on land, Forest Ecology and Forest Management, Carbon, biodiversité forestière, DOMINANCE, 13. Climate action, Earth and Environmental Sciences, Africa, Alpha diversity, Americas, structure de la canopée
Abstract: Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-Tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity., 0, SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2017
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143. Assessing environmental impacts of genetically modified plants on non-target organisms: The relevance of in planta studies

Author: Marco Nuti, Jeremy Sweet, Antoine Messéan, Jozsef Kiss, Christoph C. Tebbe, Salvatore Arpaia, Joop J. A. van Loon, Joe N. Perry, A. Nicholas E. Birch, DTE-BBC, Research Centre Trisaia, Italian National Agency for New Tecnologies Energy and Sustainable Economic Development (ENEA), The James Hutton Institute, Plant Protection Institute [Budapest] (ATK NOVI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Laboratory of Entomology, Wageningen University and Research [Wageningen] (WUR), Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institut National de la Recherche Agronomique (INRA), Universita degli studi di Pisa, University of Greenwich, Sweet Environmental Consultants, Thünen Institute of Biodiversity, European Project: 289706, Wageningen University and Research Centre [Wageningen] (WUR), Arpaia, S., Birch, A. N. E., Kiss, J., van Loon, J. J. A., Messean, A., Nuti, M., Perry, J. N., Sweet, J. B., Tebbe, C. C., and University of Pisa - Università di Pisa
Subjects: 0301 basic medicine, Environmental Engineering, [SDV]Life Sciences [q-bio], Bacillus thuringiensis, Genetically modified crops, Biology, Environment, Risk Assessment, 03 medical and health sciences, Non target, Ecological relationship, Environmental Chemistry, Relevance (law), media_common.cataloged_instance, Ecosystem services, European Union, Laboratory of Entomology, European union, Waste Management and Disposal, Insect resistance, media_common, Environmental risk assessment, 2. Zero hunger, Ecology, business.industry, fungi, food and beverages, 15. Life on land, Laboratorium voor Entomologie, Plants, Genetically Modified, Pollution, Biotechnology, 030104 developmental biology, Risk management, Sustainable management, Non-target organisms, Insect-plant interactions, EPS, business, Environmental Monitoring
Abstract: In legal frameworks worldwide, genetically modified plants (GMPs) are subjected to pre-market environmental risk assessment (ERA) with the aim of identifying potential effects on the environment. In the European Union, the EFSA Guidance Docuinent introduces the rationale that GMPs, as well as their newly produced metabolites, represent the potential stressor to be evaluated during ERA. As a consequence, during several phases of ERA for cultivation purposes, it is considered necessary to use whole plants or plant parts in experimental protocols. The importance of in planta studies as a strategy to address impacts of GMPs tin non-target organislns is demonstrated, to evaluate both effects due to the intended modification in plant phenotype (e.g. expression of Cry proteins) and effects due to unintended modifications in plant phenotype resultihg from the transformation process (e.g. due to somaclonal variations or pleiotropic effects). In planta tests are also necessary for GMPs in which newly expressed metabolites cannot easily be studied in vitro. This paper reviews the scientific literature supporting the choice of in planta studies as a fundamental tool in ERA of GMPs in cultivation dossiers; the evidence indicates they can realistically mimic the ecological relationships occurring in their receiving environments and provide important insights into the biology and sustainable management of GMPs.
Published: 2017
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144. Un regard au-delà des métriques classiques pour la comparaison de modèles - les leçons d'une étude d'intercomparaison internationale de modèles

Author: Jiri Nossent, Jan De Niel, Fabrizio Fenicia, Laurène Bouaziz, Gilles Drogue, Benjamin Grelier, Claudia Brauer, Tanja de Boer-Euser, Fernando Lobo Pereira, Hubert H. G. Savenije, Guillaume Thirel, Patrick Willems, Benjamin Dewals, Delft University of Technology (TU Delft), Deltares system, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Wageningen University and Research [Wageningen] (WUR), Université de Liège, Centre d'Etude et de Recherche en Géographie de l'Aménagement des Paysages et de l'Environnement (CERGAPE - LOTERR), Université de Lorraine (UL), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Flanders Hydraulics Research, Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Wageningen University and Research Centre [Wageningen] (WUR), Swiss Federal Institute for Environmental Science and Technology [Dübendorf] (EAWAG), aucun, Hydrosystèmes et bioprocédés (UR HBAN), Earth System Sciences, and Hydrology and Hydraulic Engineering
Subjects: Meteorology, Hydrological modelling, 0208 environmental biotechnology, Flow (psychology), Hydrograph, 02 engineering and technology, Hydrology and Quantitative Water Management, lcsh:Technology, lcsh:TD1-1066, modelling, MODELE, models, MODELE HYDROLOGIQUE, hydrography, Earth and Planetary Sciences (miscellaneous), Econometrics, Life Science, Relevance (information retrieval), lcsh:Environmental technology. Sanitary engineering, Hydrological model, lcsh:Environmental sciences, Water Science and Technology, General Environmental Science, lcsh:GE1-350, Protocol (science), WIMEK, Flood myth, lcsh:T, Model validation, lcsh:Geography. Anthropology. Recreation, hydrological model, MODELISATION, 020801 environmental engineering, Catchment hydrology, lcsh:G, OA-Fund TU Delft, HYDROGRAPHIE, [SDE]Environmental Sciences, Generalized extreme value distribution, General Earth and Planetary Sciences, Environmental science, Hydrology, Hydrologie en Kwantitatief Waterbeheer
Abstract: International collaboration between research institutes and universities is a promising way to reach consensus on hydrological model development. Although model comparison studies are very valuable for international cooperation, they do often not lead to very clear new insights regarding the relevance of the modelled processes. We hypothesise that this is partly caused by model complexity and the comparison methods used, which focus too much on a good overall performance instead of focusing on a variety of specific events. In this study, we use an approach that focuses on the evaluation of specific events and characteristics. Eight international research groups calibrated their hourly model on the Ourthe catchment in Belgium and carried out a validation in time for the Ourthe catchment and a validation in space for nested and neighbouring catchments. The same protocol was followed for each model and an ensemble of best-performing parameter sets was selected. Although the models showed similar performances based on general metrics (i.e. the Nash–Sutcliffe efficiency), clear differences could be observed for specific events. We analysed the hydrographs of these specific events and conducted three types of statistical analyses on the entire time series: cumulative discharges, empirical extreme value distribution of the peak flows and flow duration curves for low flows. The results illustrate the relevance of including a very quick flow reservoir preceding the root zone storage to model peaks during low flows and including a slow reservoir in parallel with the fast reservoir to model the recession for the studied catchments. This intercomparison enhanced the understanding of the hydrological functioning of the catchment, in particular for low flows, and enabled to identify present knowledge gaps for other parts of the hydrograph. Above all, it helped to evaluate each model against a set of alternative models.
Published: 2017
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145. Whole dairy matrix or single nutrients in assessment of health effects: Current evidence and knowledge gaps

Author: Arne Astrup, Sabita S. Soedamah-Muthu, Lisette C. P. G. M. de Groot, Ulf Risérus, Didier Dupont, Richard Ipsen, Jean Michel Lecerf, Ian Givens, Marie-Caroline Michalski, Michelle C. McKinley, Didier Rémond, Tanja K. Thorning, Jean-Philippe Bonjour, Alan R. Mackie, Hanne Christine Bertram, Tine Tholstrup, Emma L. Feeney, Connie M. Weaver, Medical and Clinical Psychology, Department of Nutrition, Exercise and Sports [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Food Science, Cornelle University, Department of Internal Medicine, Huntsman Cancer Institute, Human Nutrition, University of Glasgow, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Food for Health Ireland, University College Dublin [Dublin] (UCD), Food Science, Università degli Studi di Udine - University of Udine [Italie], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), School of Food Science and Nutrition, University of Leeds, Queen's University [Belfast] (QUB), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Centre de Recherche en Nutrition Humaine Rhône Alpes (CRNH Rhône Alpes), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Department of Public Health and Caring Sciences, Uppsala University, Division of Human Nutrition, Wageningen University and Research Centre [Wageningen] (WUR), Nutrition Science, Purdue University [West Lafayette], Institute for Food, Nutrition and Health, University of Reading (UOR), Groupement Europeen d'Interet Economique (GEIE), European Milk Forum, France, 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 Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Wageningen University and Research [Wageningen] (WUR), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Nutrition and Disease, Bioavailability, dairy nutrients, Medicine (miscellaneous), Disease, structure de l'aliment, dairy structure, Nutrient, Voeding en Ziekte, dairy proteins, 2. Zero hunger, ddc:616, Minerals, Nutrition and Dietetics, Milk Proteins, Whole dairy, dairy product, Cardiovascular Diseases, phosphorous, Nutritive Value, MFGM, Dairy Nutrients, Biological Availability, Biology, Body weight, Dairy Structure, Bone health, Bone and Bones, produit laitier, fermented dairy products, 03 medical and health sciences, Humans, Food structure, Fermented Dairy, VLAG, Global Nutrition, Wereldvoeding, 030109 nutrition & dietetics, blood lipids, business.industry, whole dairy, Dairy Protein, Body Weight, Feeding Behavior, Health indicator, Dietary Fats, Coronary heart disease, Biotechnology, Diet, Diabetes Mellitus, Type 2, Phosphorous, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Calcium, Dairy Products, business, relation alimentation santé, Blood Lipids, Dairy foods, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: Foods consist of a large number of different nutrients that are contained in a complex structure. The nature of the food structure and the nutrients therein (i.e., the food matrix) will determine the nutrient digestion and absorption, thereby altering the overall nutritional properties of the food. Thus, the food matrix may exhibit a different relation with health indicators compared to single nutrients studied in isolation. The evidence for a dairy matrix effect was presented and discussed by an expert panel at a closed workshop, and the following consensus was reached: 1) Current evidence does not support a positive association between intake of dairy products and risk of cardiovascular disease (i.e., stroke and coronary heart disease) and type 2 diabetes. In contrast, fermented dairy products, such as cheese and yogurt, generally show inverse associations. 2) Intervention studies have indicated that the metabolic effects of whole dairy may be different than those of single dairy constituents when considering the effects on body weight, cardiometabolic disease risk, and bone health. 3) Different dairy products seem to be distinctly linked to health effects and disease risk markers. 4) Different dairy structures and common processing methods may enhance interactions between nutrients in the dairy matrix, which may modify the metabolic effects of dairy consumption. 5) In conclusion, the nutritional values of dairy products should not be considered equivalent to their nutrient contents but, rather, be considered on the basis of the biofunctionality of the nutrients within dairy food structures. 6) Further research on the health effects of whole dairy foods is warranted alongside the more traditional approach of studying the health effects of single nutrients. Future diet assessments and recommendations should carefully consider the evidence of the effects of whole foods alongside the evidence of the effects of individual nutrients. Current knowledge gaps and recommendations for priorities in future research on dairy were identified and presented Whole dairy matrix or single nutrients in assessment of health effects: current evidence and knowledge gaps (PDF Download Available). Available from: https://www.researchgate.net/publication/316112054_Whole_dairy_matrix_or_single_nutrients_in_assessment_of_health_effects_current_evidence_and_knowledge_gaps [accessed Dec 15 2017].
Published: 2017
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146. Characterizing a region on BTA11 affecting β-lactoglobulin content of milk using high-density genotyping and haplotype grouping

Author: Nicolas Bedere, Henk Bovenhuis, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), Wageningen University and Research Centre [Wageningen] (WUR), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, haplotype, Genotyping Techniques, beta lactoglobuline bovine, Lactoglobulins, Animal Breeding and Genomics, Biology, β-lactoglobulin, Polymorphism, Single Nucleotide, 03 medical and health sciences, Dairy cow, Bovine, Haplotype, Association study, Genetic variation, Genetics, Animals, SNP, Fokkerij en Genomica, Genetics(clinical), dairy cows, Gene, Genotyping, Genetics (clinical), Selection (genetic algorithm), 2. Zero hunger, variabilité génétique animale, 0402 animal and dairy science, Chromosome Mapping, food and beverages, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Agricultural sciences, Milk, 030104 developmental biology, Haplotypes, vache laitière, Mutation, Chromosomal region, Mutation (genetic algorithm), région génomique, WIAS, Sciences agricoles, Research Article
Abstract: Background: Milk β-lactoglobulin (β-LG) content is of interest as it is associated with nutritional and manufacturing properties. It is known that milk β-LG content is strongly affected by genetic factors. In cattle, most of the genetic differences are associated with a chromosomal region on BTA11, which contains the β-LG gene. The aim of this study was to characterize this region using 777 k SNP data (BovineHDbeadChip) and perform a haplotype-based association study. A statistical approach was developed to build haplotypes that capture the genetic variation associated with this genomic region. Results: The SNP with the most significant effect on β-lactoglobulin content was one of the 2 causal mutations responsible for the β-lactoglobulin protein variants A/B. Haplotypes based on 2 to 5 selected lead SNP were clustered in groups with different effects on β-lactoglobulin content. Four different groups were identified suggesting that β-lactoglobulin variant A and B can be further refined in A1, A2, B1 and B2. Conclusions: This study showed that β-lactoglobulin protein variants A/B do not explain all genetic variation associated with the tail part of BTA11 but this region contains more than one mutation with an effect on β-lactoglobulin content. These findings can be used for selection of cows with higher cheese yield, which is desirable for the dairy industry.
Published: 2017
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147. Looking beyond general metrics for model comparison - lessons from an international model intercomparison study

Author: de Boer-Euser, T., Bouaziz, L., De Niel, J., Brauer, C., Dewals, B., Drogue, G., Fenicia, F., Grelier, B., Nossent, J., Pereira, F., Savenije, H., Thirel, Guillaume, Willems, P., Delft University of Technology (TU Delft), Deltares system, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Wageningen University and Research Centre [Wageningen] (WUR), Université de Liège, Centre d'Etude et de Recherche en Géographie de l'Aménagement des Paysages et de l'Environnement (CERGAPE - LOTERR), Université de Lorraine (UL), Swiss Federal Institute for Environmental Science and Technology [Dübendorf] (EAWAG), aucun, Flanders Hydraulics Research, Hydrosystèmes et bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Wageningen University and Research [Wageningen] (WUR), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), and Hydrosystèmes et Bioprocédés (UR HBAN)
Subjects: modelling, MODELE, models, MODELE HYDROLOGIQUE, hydrography, HYDROGRAPHIE, [SDE]Environmental Sciences, hydrological model, MODELISATION
Abstract: International audience; International collaboration between research institutes and universities is a promising way to reach consensus on hydrological model development. Although model comparison studies are very valuable for international cooperation, they do often not lead to very clear new insights regarding the relevance of the modelled processes. We hypothesise that this is partly caused by model complexity and the comparison methods used, which focus too much on a good overall performance instead of focusing on a variety of specific events. In this study, we use an approach that focuses on the evaluation of specific events and characteristics. Eight international research groups calibrated their hourly model on the Ourthe catchment in Belgium and carried out a validation in time for the Ourthe catchment and a validation in space for nested and neighbouring catchments. The same protocol was followed for each model and an ensemble of best-performing parameter sets was selected. Although the models showed similar performances based on general metrics (i.e. the Nash-Sutcliffe efficiency), clear differences could be observed for specific events. We analysed the hydrographs of these specific events and conducted three types of statistical analyses on the entire time series: cumulative discharges, empirical extreme value distribution of the peak flows and flow duration curves for low flows. The results illustrate the relevance of including a very quick flow reservoir preceding the root zone storage to model peaks during low flows and including a slow reservoir in parallel with the fast reservoir to model the recession for the studied catchments. This intercomparison enhanced the understanding of the hydrological functioning of the catchment, in particular for low flows, and enabled to identify present knowledge gaps for other parts of the hydrograph. Above all, it helped to evaluate each model against a set of alternative models.
Published: 2017
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148. Dietary and health biomarkers-time for an update

Author: Giulia Praticò, Claudine Manach, Augustin Scalbert, Edith J. M. Feskens, David S. Wishart, Qian Gao, Lars O. Dragsted, Department of Nutrition, Exercise and Sports [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Department of Biological Sciences, The Open University [Milton Keynes] (OU), Nutrition and Metabolism Section, Biomarkers Group, International Agency for Cancer Research (IACR), Division of Human Nutrition, Wageningen University and Research Centre [Wageningen] (WUR), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Wageningen University and Research [Wageningen] (WUR), and Dragsted, Lars O.
Subjects: 0301 basic medicine, Food intake, Metabolomics, Biomarker, Nutrition, Ontology, Classification, Validation, Databases, Review, lcsh:QH426-470, Endocrinology, Diabetes and Metabolism, lcsh:TX341-641, Clinical nutrition, Biology, Bioinformatics, 03 medical and health sciences, aliment santé pour l'homme, Environmental health, approche nutritionnelle, Genetics, Food and Nutrition, Food components, VLAG, 2. Zero hunger, Global Nutrition, Wereldvoeding, 030109 nutrition & dietetics, Dietary intake, Nutritional status, Healthy diet, 3. Good health, lcsh:Genetics, 030104 developmental biology, Dietary biomarkers, Alimentation et Nutrition, Commentary, Biomarker (medicine), biomarker, lcsh:Nutrition. Foods and food supply, biomarqueur, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: FoodBAll is a project funded by the BIO-NH call under the Joint Programming Initiative, "a Healthy Diet for a Healthy Life" (grant number 529051002). The project is funded nationally by the respective Research Councils; the work was funded in part by a grant from the Danish Innovation Foundation (#4203-00002B) and a Semper Ardens grant from the Carlsberg Foundation to LOD, a postdoc grant from the University of Rome La Sapienza ("Borsa di studio per la frequenza di corsi o attivita di perfezionamento all'estero" erogata ai sensi della legge 398/89) to GP, a grant from the China Scholarship Council (201506350127) to QG, a grant from the Agence Nationale de la Recherche (#ANR-14-HDHL-0002-02) to CM, and a grant from the Canadian Institutes of Health Research (CIHR) to DSW.; In the dietary and health research area, biomarkers are extensively used for multiple purposes. These include biomarkers of dietary intake and nutrient status, biomarkers used to measure the biological effects of specific dietary components, and biomarkers to assess the effects of diet on health. The implementation of biomarkers in nutritional research will be important to improve measurements of dietary intake, exposure to specific dietary components, and of compliance to dietary interventions. Biomarkers could also help with improved characterization of nutritional status in study volunteers and to provide much mechanistic insight into the effects of food components and diets. Although hundreds of papers in nutrition are published annually, there is no current ontology for the area, no generally accepted classification terminology for biomarkers in nutrition and health, no systematic validation scheme for these biomarker classes, and no recent systematic review of all proposed biomarkers for food intake. While advanced databases exist for the human and food metabolomes, additional tools are needed to curate and evaluate current data on dietary and health biomarkers. The Food Biomarkers Alliance (FoodBAll) under the Joint Programming Initiative-A Healthy Diet for a Healthy Life (JPI-HDHL)-is aimed at meeting some of these challenges, identifying new dietary biomarkers, and producing new databases and review papers on biomarkers for nutritional research. This current paper outlines the needs and serves as an introduction to this thematic issue of Genes & Nutrition on dietary and health biomarkers
Published: 2017
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149. When experts disagree : the need to rethink indicator selection for assessing sustainability of agriculture

Author: Eddie A.M. Bokkers, Isabelle Le Quellec, Imke J.M. de Boer, Claus G. Sørensen, Jayson Benge, Frank W. Oudshoorn, Marion Sautier, Henrik Moller, Christian Schader, Jon Manhire, Evelien M. de Olde, Catriona J. MacLeod, Fleur Marchand, Richard W. McDowell, Andrew Barber, Stephan Halloy, Charles N. Merfield, Christian Bockstaller, Katharine Legun, Erika Szymanski, John Reid, Jay Whitehead, Wageningen University and Research [Wageningen] (WUR), Aarhus University [Aarhus], University of Otago [Dunedin, Nouvelle-Zélande], Research Institute for Agricultural, Fisheries and Food (ILVO), Ecosystem management research group - ECOBE (Wilrijk, Belgium), University of Antwerp (UA), AgResearch Ltd, Lincoln University, New Zealand, Manaaki Whenua – Landcare Research [Lincoln], 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, Universidad Internacional de la Rioja (UNIR), Laboratoire Agronomie et Environnement (LAE), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), SEGES, University of Canterbury [Christchurch], Research Institute of Organic Agriculture - Forschungsinstitut für biologischen Landbau (FiBL), contract AGRB1201, Wageningen University and Research Centre [Wageningen] (WUR), Institute for Agricultural and Fisheries Research, Landcare Research [Lincoln], and Research Institute of Organic Agriculture (FiBL)
Subjects: Economics and Econometrics, 010504 meteorology & atmospheric sciences, Process (engineering), Geography, Planning and Development, Dashboard (business), Landgebruiksplanning, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Context (language use), Indicateur, 010501 environmental sciences, Management, Monitoring, Policy and Law, Temperate agriculture, 01 natural sciences, Animal Production Systems, 12. Responsible consumption, Land Use Planning, Multi-criteria assessment, Sustainability organizations, Biology, Durabilité, 0105 earth and related environmental sciences, 2. Zero hunger, Sustainable development, Dierlijke Productiesystemen, business.industry, Sustainability assessment, Environmental resource management, Evaluation Multicritère, Indicator selection, 15. Life on land, Environmental economics, Chemistry, Ranking, 13. Climate action, Transparency (graphic), Sustainability, WIAS, Exploitation agricole, business, Engineering sciences. Technology
Abstract: Sustainability indicators are well recognized for their potential to assess and monitor sustainable development of agricultural systems. A large number of indicators are proposed in various sustainability assessment frameworks, which raises concerns regarding the validity of approaches, usefulness and trust in such frameworks. Selecting indicators requires transparent and well-defined procedures to ensure the relevance and validity of sustainability assessments. The objective of this study, therefore, was to determine whether experts agree on which criteria are most important in the selection of indicators and indicator sets for robust sustainability assessments. Two groups of experts (Temperate Agriculture Research Network and New Zealand Sustainability Dashboard) were asked to rank the relative importance of eleven criteria for selecting individual indicators and of nine criteria for balancing a collective set of indicators. Both ranking surveys reveal a startling lack of consensus amongst experts about how best to measure agricultural sustainability and call for a radical rethink about how complementary approaches to sustainability assessments are used alongside each other to ensure a plurality of views and maximum collaboration and trust amongst stakeholders. To improve the transparency, relevance and robustness of sustainable assessments, the context of the sustainability assessment, including prioritizations of selection criteria for indicator selection, must be accounted for. A collaborative design process will enhance the acceptance of diverse values and prioritizations embedded in sustainability assessments. The process by which indicators and sustainability frameworks are established may be a much more important determinant of their success than the final shape of the assessment tools. Such an emphasis on process would make assessments more transparent, transformative and enduring.
Published: 2017
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150. EuMIXFOR empirical forest mensuration and ring width data from pure and mixed stands of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) through Europe

Author: Michael Heym, Hubert Sterba, Tomáš Čihák, Jerzy Skrzyszewski, Tzvetan Zlatanov, Miren del Río, Maciej Pach, Viktor Kurylyak, Fabio Lombardi, Vít Šrámek, Hans Pretzsch, Václav Hurt, Indrė Ruškytkė, Renzo Motta, Buraczyk Włodzimierz, Lars Drössler, Ricardo Ruiz-Peinado, Gerald Dirnberger, David I. Forrester, Magnus Löf, Lluís Coll, Kamil Bielak, Marek Fabrika, Quentin Ponette, Dejan Stojanović, Jan den Ouden, Christian Ammer, Admir Avdagić, Géraud de Streel, Kris Verheyen, Andrés Bravo-Oviedo, Gediminas Brazaitis, Ignacio Barbeito, Chair Forest Growth & Yield Sci, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Dept Silviculture & Forest Syst Management, INIA-CIFOR, Sustainable Forest Management Res Inst, Universitad de Valladolid, Dept Silviculture, Forest Research Institute, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Dept Forest & Soil Sci, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Laboratoire d'Etudes des Ressources Forêt-Bois (LERFoB), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Inst Forest Biol & Silviculture, Fac Forest Sci & Ecol, Aleksandras Stulginskis University, Dept Agr & Forest Engn Forest Sci, Universitat de Lleida, Dept Forest Management & Geodesy, Fac Forestry, Technical University in Zvolen (TUZVO), Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences (SLU), Ukrainian National Forestry University (UNFU), Dipartimento AGR, Università degli Studi Mediterranea di Reggio Calabria, Inst Lowland Forestry & Environm, University of Novi Sad, Forest Ecol & Forest Management Grp, Wageningen University and Research [Wageningen] (WUR), Dept Agr Forest & Food Sci DISAFA, University of Turin, Fac Biosci Engn, Université Catholique de Louvain = Catholic University of Louvain (UCL), Earth and Life Institute [Louvain-La-Neuve] (ELI), Forestry & Game Management Res Inst, Fac Forestry, University Stefan cel Mare of Suceava (USU), Georg-August-University [Göttingen], Fac Biosci Engn, Forest & Nat Lab, Universiteit Gent = Ghent University [Belgium] (UGENT), COST Association during COST Action (EuMIXFOR: European mixed forests - Integration Scientific Knowledge in Sustainable Forest Management) FP1206, Technical University of Munich (TUM), Swiss Federal Institute for Forest Snow and Landscape Research (WSL), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Technical University of Zvolen, Southern Swedish Forest Res Ctr, Wageningen University and Research Centre [Wageningen] (WUR), Université Catholique de Louvain, Université Catholique de Louvain (UCL), Georg-August-Universität Göttingen, Ghent University [Belgium] (UGENT), and Heym, Michael
Subjects: 0106 biological sciences, Empirical data, [SDV]Life Sciences [q-bio], Forest management, PRODUCTIVITY, GROWTH, YIELD, forest stand, fagus sylvatica, 010603 evolutionary biology, 01 natural sciences, pinus sylvestris, résultat empirique, Mixed and monospecific stands, Fagus sylvatica, Bosecologie en Bosbeheer, largeur de cerne, Beech, Mixed stand dynamics, Ecology, biology, Agroforestry, dendométrie, Scots pine, peuplement mixte, Forestry, 15. Life on land, biology.organism_classification, PE&RC, Forest Ecology and Forest Management, European beech, %22">Pinus , Geography, peuplement forestier, EuMIXFOR data, europe, peuplement pur, 010606 plant biology & botany
Abstract: Key message This data set provides unique empirical data from triplets of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) across Europe. Dendrometric variables are provided for 32 triplets, 96 plots, 7555 trees and 4695 core samples. These data contribute to our understanding of mixed stand dynamics. Dataset access at http://dx.doi.org/10.5061/dryad.8v04m. Associated metadata available at https://metadata-afs.nancy.inra.fr/geonetwork/apps/georchestra/? uuid=b3e098ca-e681-4910-90990e25d3b4cd52&hl=eng.; Key message :This data set provides unique empirical data from triplets of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) across Europe. Dendrometric variables are provided for 32 triplets, 96 plots, 7555 trees and 4695 core samples.These data contribute to our understanding of mixed stand dynamics.Dataset access at http://dx.doi.org/10.5061/dryad.8v04m.Associated metadata available at https://metadata-afs.nancy.inra.fr/geonetwork/apps/georchestra/? uuid=b3e098ca-e681-4910-90990e25d3b4cd52&hl=eng.
Published: 2017
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