Showing papers by "Institut national de la recherche agronomique published in 2015"
University of Paris-Sud1, French Institute of Health and Medical Research2, Institut Gustave Roussy3, Institut national de la recherche agronomique4, university of lille5, Paris Descartes University6, New York University7, Pasteur Institute8, Agency for Science, Technology and Research9, Albert Einstein College of Medicine10, Paul Sabatier University11, Centre national de la recherche scientifique12
TL;DR: A key role is revealed for Bacteroidales in the immunostimulatory effects of CTLA-4 blockade, which is found to depend on distinct Bacteroides species in mice and patients.
Abstract: Antibodies targeting CTLA-4 have been successfully used as cancer immunotherapy. We find that the antitumor effects of CTLA-4 blockade depend on distinct Bacteroides species. In mice and patients, T cell responses specific for B. thetaiotaomicron or B. fragilis were associated with the efficacy of CTLA-4 blockade. Tumors in antibiotic-treated or germ-free mice did not respond to CTLA blockade. This defect was overcome by gavage with B. fragilis, by immunization with B. fragilis polysaccharides, or by adoptive transfer of B. fragilis–specific T cells. Fecal microbial transplantation from humans to mice confirmed that treatment of melanoma patients with antibodies against CTLA-4 favored the outgrowth of B. fragilis with anticancer properties. This study reveals a key role for Bacteroidales in the immunostimulatory effects of CTLA-4 blockade.
2,360 citations
Vrije Universiteit Brussel1, Katholieke Universiteit Leuven2, University of Copenhagen3, Rega Institute for Medical Research4, Institut national de la recherche agronomique5, Technical University of Denmark6, University Hospital Heidelberg7, Molecular Medicine Partnership Unit8, Aalborg University9, University of Southern Denmark10, King's College London11
TL;DR: A unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa is reported, highlighting the need to disentangle gut microbiota signatures of specific human diseases from those of medication.
Abstract: In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication.
1,473 citations
University of Florida1, University of Bonn2, Institut national de la recherche agronomique3, Blaise Pascal University4, Stanford University5, Prince of Songkla University6, Agricultural Research Service7, University of Arizona8, International Maize and Wheat Improvement Center9, Kansas State University10, International Water Management Institute11, Washington State University12, Michigan State University13, University of Leeds14, CGIAR15, Counterintelligence Field Activity16, Spanish National Research Council17, University of Tübingen18, University of Guelph19, University of Maryland, College Park20, Texas A&M University21, Aarhus University22, Potsdam Institute for Climate Impact Research23, Indian Agricultural Research Institute24, Goddard Institute for Space Studies25, Rothamsted Research26, University of Hohenheim27, Wageningen University and Research Centre28, Chinese Academy of Sciences29, Commonwealth Scientific and Industrial Research Organisation30, China Agricultural University31, Nanjing Agricultural University32
TL;DR: The authors systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 degrees C to 32 degrees C, including experiments with artificial heating.
Abstract: Crop models are essential tools for assessing the threat of climate change to local and global food production(1). Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature(2). Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 degrees C to 32 degrees C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each degrees C of further temperature increase and become more variable over space and time.
1,461 citations
Utrecht University1, Université catholique de Louvain2, Institut national de la recherche agronomique3, Centre national de la recherche scientifique4, Université du Québec à Montréal5, Royal Society for the Protection of Birds6, University of Cambridge7, University of Padua8, University of Sussex9, Natural Resources Canada10, Purdue University11, Helmholtz Centre for Environmental Research - UFZ12, Smithsonian Institution13, University of Neuchâtel14, University of Saskatchewan15, Washington State University16, University of Bergen17, University of Stirling18
TL;DR: In this paper, a review of the global literature explores these risks and show a growing body of evidence that persistent, low concentrations of these insecticides pose serious risks of undesirable environmental impacts.
Abstract: Since their discovery in the late 1980s, neonicotinoid pesticides have become the most widely used class of insecticides worldwide, with large-scale applications ranging from plant protection (crops, vegetables, fruits), veterinary products, and biocides to invertebrate pest control in fish farming. In this review, we address the phenyl-pyrazole fipronil together with neonicotinoids because of similarities in their toxicity, physicochemical profiles, and presence in the environment. Neonicotinoids and fipronil currently account for approximately one third of the world insecticide market; the annual world production of the archetype neonicotinoid, imidacloprid, was estimated to be ca. 20,000 tonnes active substance in 2010. There were several reasons for the initial success of neonicotinoids and fipronil: (1) there was no known pesticide resistance in target pests, mainly because of their recent development, (2) their physicochemical properties included many advantages over previous generations of insecticides (i.e., organophosphates, carbamates, pyrethroids, etc.), and (3) they shared an assumed reduced operator and consumer risk. Due to their systemic nature, they are taken up by the roots or leaves and translocated to all parts of the plant, which, in turn, makes them effectively toxic to herbivorous insects. The toxicity persists for a variable period of time—depending on the plant, its growth stage, and the amount of pesticide applied. A wide variety of applications are available, including the most common prophylactic non-Good Agricultural Practices (GAP) application by seed coating. As a result of their extensive use and physicochemical properties, these substances can be found in all environmental compartments including soil, water, and air. Neonicotinoids and fipronil operate by disrupting neural transmission in the central nervous system of invertebrates. Neonicotinoids mimic the action of neurotransmitters, while fipronil inhibits neuronal receptors. In doing so, they continuously stimulate neurons leading ultimately to death of target invertebrates. Like virtually all insecticides, they can also have lethal and sublethal impacts on non-target organisms, including insect predators and vertebrates. Furthermore, a range of synergistic effects with other stressors have been documented. Here, we review extensively their metabolic pathways, showing how they form both compound-specific and common metabolites which can themselves be toxic. These may result in prolonged toxicity. Considering their wide commercial expansion, mode of action, the systemic properties in plants, persistence and environmental fate, coupled with limited information about the toxicity profiles of these compounds and their metabolites, neonicotinoids and fipronil may entail significant risks to the environment. A global evaluation of the potential collateral effects of their use is therefore timely. The present paper and subsequent chapters in this review of the global literature explore these risks and show a growing body of evidence that persistent, low concentrations of these insecticides pose serious risks of undesirable environmental impacts.
1,131 citations
TL;DR: Recent advances in the characterization of the underlying regulatory mechanisms of flavonoid biosynthesis are reviewed, with a special focus on the MBW (MYB-bHLH-WDR) protein complexes.
1,032 citations
Chalmers University of Technology1, Institut national de la recherche agronomique2, Agrocampus Ouest3, Aix-Marseille University4, University of Guelph5, Massey University6, Ege University7, Agro ParisTech8, Norwich Research Park9, Norwich University10, University of Massachusetts Amherst11, Spanish National Research Council12, Universidade Nova de Lisboa13, University of California, Davis14, Norwegian University of Life Sciences15, University of Greifswald16, Teagasc17
TL;DR: A general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements, is proposed.
Abstract: Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.
806 citations
Institut national de la recherche agronomique1, University of Lorraine2, United States Department of Energy3, Hungarian Academy of Sciences4, Clark University5, Helmholtz Centre for Environmental Research - UFZ6, Lund University7, University of Hasselt8, Universidade Federal de Viçosa9, University of Lyon10, University of Turin11, King Abdulaziz University12, Aix-Marseille University13, University of Oslo14, Swedish University of Agricultural Sciences15, Max Planck Society16, University of Bremen17, Harvard University18, Swiss Federal Institute for Forest, Snow and Landscape Research19, Pierre-and-Marie-Curie University20, University of Cologne21
TL;DR: Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of myCorrhiza-induced genes.
Abstract: To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
799 citations
University of Leeds1, University of Exeter2, Imperial College London3, James Cook University4, Environmental Change Institute5, University College London6, University of Kent7, Duke University8, National Institute of Amazonian Research9, National Institute for Space Research10, Universidad Autónoma Gabriel René Moreno11, Wageningen University and Research Centre12, University of Amsterdam13, Florida International University14, Institut national de la recherche agronomique15, Universidade Federal do Acre16, Tropenbos International17, Empresa Brasileira de Pesquisa Agropecuária18, National Chung Hsing University19, Paul Sabatier University20, National Park Service21, Amazon.com22, Federal University of Pará23, Universidade do Estado de Mato Grosso24, University of Texas at Austin25, Smithsonian Institution26, World Wide Fund for Nature27, Universidad Mayor28, Field Museum of Natural History29, Universidad Nacional de la Amazonía Peruana30, University of Los Andes31, National University of Colombia32, Museu Paraense Emílio Goeldi33, Naturalis34, Utrecht University35, University of Wisconsin–Milwaukee36, Smithsonian Tropical Research Institute37, Northumbria University38, State University of Campinas39
TL;DR: It is confirmed that Amazon forests have acted as a long-term net biomass sink, but the observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models
Abstract: Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades, with a substantial fraction of this sink probably located in the tropics, particularly in the Amazon. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models.
767 citations
TL;DR: In this article, a review of the potential of dark fermentation of organic biomasses and its potential in green energy-efficient green chemistry applications is presented, with a brief review on the simulation and modeling of the dark fermentation processes and their energy balance.
711 citations
Wageningen University and Research Centre1, Rutgers University2, Spanish National Research Council3, Naturalis4, University of Leeds5, Institut national de la recherche agronomique6, Michigan State University7, University of Freiburg8, University of California, Berkeley9, University of New England (United States)10, University of Vermont11, University of California, Davis12, National University of Singapore13, Hungarian Academy of Sciences14, University of Göttingen15, Cornell University16, Swedish University of Agricultural Sciences17, Stellenbosch University18, Centre national de la recherche scientifique19, Simon Fraser University20, University of Reading21, University of Würzburg22, Plant & Food Research23, University of Giessen24, University of Texas at Austin25, University of Bern26, Hebrew University of Jerusalem27, Lund University28, Federal University of Bahia29
TL;DR: It is shown that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species, suggesting that cost-effective management strategies to promote crop pollination should target a different set of species than management Strategies to promote threatened bees.
Abstract: There is compelling evidence that more diverse ecosystems deliver greater benefits to people, and these ecosystem services have become a key argument for biodiversity conservation. However, it is unclear how much biodiversity is needed to deliver ecosystem services in a cost-effective way. Here we show that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species. Across crops, years and biogeographical regions, crop-visiting wild bee communities are dominated by a small number of common species, and threatened species are rarely observed on crops. Dominant crop pollinators persist under agricultural expansion and many are easily enhanced by simple conservation measures, suggesting that cost-effective management strategies to promote crop pollination should target a different set of species than management strategies to promote threatened bees. Conserving the biological diversity of bees therefore requires more than just ecosystem-service-based arguments.
698 citations
Wellcome Trust Sanger Institute1, University of Oxford2, Genentech3, Vita-Salute San Raffaele University4, University of Turin5, European Bioinformatics Institute6, University of Paris-Sud7, King Abdulaziz University8, Western General Hospital9, Institut national de la recherche agronomique10, University of Leicester11, International Potato Center12, Joint Genome Institute13, Queen Mary University of London14, French Institute for Research in Computer Science and Automation15, University of Trento16, University of Chile17, Pfizer18, Pompeu Fabra University19, Catalan Institution for Research and Advanced Studies20, Seoul National University21, Ontario Institute for Cancer Research22, University of California, Los Angeles23, Iowa State University24, Peking University25, University of Cambridge26, Karolinska Institutet27, University of Rennes28, Cold Spring Harbor Laboratory29
TL;DR: The latest version of the BioMart Community Portal comes with many new databases that have been created by the ever-growing community and comes with better support and extensibility for data analysis and visualization tools.
Abstract: The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
University of Grenoble1, Centre national de la recherche scientifique2, Austral University of Chile3, Queen's University4, Coordenadoria de Aperfeiçoamento de Pessoal de Nível Superior5, Universidade Federal do Rio Grande do Sul6, Universidade Federal de Goiás7, State University of Campinas8, Sewanee: The University of the South9, Academy of Sciences of the Czech Republic10, Federal University of Rio Grande do Norte11, University of Montpellier12, Swedish University of Agricultural Sciences13, Institut national de la recherche agronomique14, Tohoku University15, United Nations University16, University of Florida17, Université du Québec à Montréal18, University of Maryland, College Park19, Université de Sherbrooke20, Landcare Research21, Spanish National Research Council22, Lund University23, University of Tokyo24, Algoma University25, Natural History Museum26, Umeå University27
TL;DR: This paper conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits.
Abstract: Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, we conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the total trait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies.
Utrecht University1, Institut national de la recherche agronomique2, French Institute of Health and Medical Research3, University of Sussex4, Natural Resources Canada5, Purdue University6, Helmholtz Centre for Environmental Research - UFZ7, Smithsonian Institution8, University of Saskatchewan9, Université catholique de Louvain10, Washington State University11, University of Bergen12
TL;DR: Enough knowledge exists to conclude that existing levels of pollution with neonicotinoids and fipronil resulting from presently authorized uses frequently exceed the lowest observed adverse effect concentrations and are thus likely to have large-scale and wide ranging negative biological and ecological impacts on a wide range of non-target invertebrates in terrestrial, aquatic, marine and benthic habitats.
Abstract: We assessed the state of knowledge regarding the effects of large-scale pollution with neonicotinoid insecticides and fipronil on non-target invertebrate species of terrestrial, freshwater and marine environments. A large section of the assessment is dedicated to the state of knowledge on sublethal effects on honeybees (Apis mellifera) because this important pollinator is the most studied non-target invertebrate species. Lepidoptera (butterflies and moths), Lumbricidae (earthworms), Apoidae sensu lato (bumblebees, solitary bees) and the section “other invertebrates” review available studies on the other terrestrial species. The sections on freshwater and marine species are rather short as little is known so far about the impact of neonicotinoid insecticides and fipronil on the diverse invertebrate fauna of these widely exposed habitats. For terrestrial and aquatic invertebrate species, the known effects of neonicotinoid pesticides and fipronil are described ranging from organismal toxicology and behavioural effects to population-level effects. For earthworms, freshwater and marine species, the relation of findings to regulatory risk assessment is described. Neonicotinoid insecticides exhibit very high toxicity to a wide range of invertebrates, particularly insects, and field-realistic exposure is likely to result in both lethal and a broad range of important sublethal impacts. There is a major knowledge gap regarding impacts on the grand majority of invertebrates, many of which perform essential roles enabling healthy ecosystem functioning. The data on the few non-target species on which field tests have been performed are limited by major flaws in the outdated test protocols. Despite large knowledge gaps and uncertainties, enough knowledge exists to conclude that existing levels of pollution with neonicotinoids and fipronil resulting from presently authorized uses frequently exceed the lowest observed adverse effect concentrations and are thus likely to have large-scale and wide ranging negative biological and ecological impacts on a wide range of non-target invertebrates in terrestrial, aquatic, marine and benthic habitats.
TL;DR: This work proposes the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard, to facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters.
Abstract: A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.
Pasteur Institute1, Osaka University2, National Presto Industries3, University of Tokyo4, Institut national de la recherche agronomique5, French Institute of Health and Medical Research6, Paris Descartes University7, Technische Universität München8, Research Institute of Molecular Pathology9, University of Erlangen-Nuremberg10, Kyoto University11
TL;DR: It is reported that microbiota-induced Tregs express the nuclear hormone receptor RORγt and differentiate along a pathway that also leads to TH17 cells, and acts as a key factor in balancing immune responses at mucosal surfaces.
Abstract: Changes to the symbiotic microbiota early in life, or the absence of it, can lead to exacerbated type 2 immunity and allergic inflammations. Although it is unclear how the microbiota regulates type 2 immunity, it is a strong inducer of proinflammatory T helper 17 (TH17) cells and regulatory T cells (Tregs) in the intestine. Here, we report that microbiota-induced Tregs express the nuclear hormone receptor RORγt and differentiate along a pathway that also leads to TH17 cells. In the absence of RORγt+ Tregs, TH2-driven defense against helminths is more efficient, whereas TH2-associated pathology is exacerbated. Thus, the microbiota regulates type 2 responses through the induction of type 3 RORγt+ Tregs and TH17 cells and acts as a key factor in balancing immune responses at mucosal surfaces.
Norwich Research Park1, University of California, Riverside2, University of Florida3, West Bengal State University4, Mediterranea University of Reggio Calabria5, Agro ParisTech6, University of Nice Sophia Antipolis7, Deakin University8, National Research Council9, College of Horticulture10, University of Massachusetts Amherst11, James Hutton Institute12, University of Tennessee13, Agriculture and Agri-Food Canada14, Oregon State University15, Agricultural Research Service16, University of Alabama at Birmingham17, University of Warwick18, University of Worcester19, Utrecht University20, Virginia Tech21, University of Manitoba22, Cornell University23, International Potato Center24, Wageningen University and Research Centre25, Institut national de la recherche agronomique26, North Carolina State University27
TL;DR: A survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance received 263 votes from 62 scientists in 15 countries for a total of 33 species and the Top 10 species are provided.
Abstract: Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
TL;DR: In this paper, the authors focus on an analysis of planted forests data from the 2015 Forests Resources Assessment of the U.N. Food and Agriculture Organization (FRA 2015) and suggest that climate impacts, especially from extreme climatic events will affect planted forests in the future and that forest health impacts can also be expected to increase.
TL;DR: In this paper, the potential advantages of eco-functional intensification in organic farming by intercropping cereal and grain legume species sown and harvested together are reviewed based on a literature analysis reinforced with integration of an original dataset of 58 field experiments conducted since 2001 in contrasted pedo-climatic European conditions.
Abstract: World population is projected to reach over nine billion by the year 2050, and ensuring food security while mitigating environmental impacts represents a major agricultural challenge. Thus, higher productivity must be reached through sustainable production by taking into account climate change, resources rarefaction like phosphorus and water, and losses of fertile lands. Enhancing crop diversity is increasingly recognized as a crucial lever for sustainable agro-ecological development. Growing legumes, a major biological nitrogen source, is also a powerful option to reduce synthetic nitrogen fertilizers use and associated fossil energy consumption. Organic farming, which does not allow the use of chemical, is also regarded as one prototype to enhance the sustainability of modern agriculture while decreasing environmental impacts. Here, we review the potential advantages of eco-functional intensification in organic farming by intercropping cereal and grain legume species sown and harvested together. Our review is based on a literature analysis reinforced with integration of an original dataset of 58 field experiments conducted since 2001 in contrasted pedo-climatic European conditions in order to generalize the findings and draw up common guidelines. The major points are that intercropping lead to: (i) higher and more stable grain yield than the mean sole crops (0.33 versus 0.27 kg m−2), (ii) higher cereal protein concentration than in sole crop (11.1 versus 9.8 %), (iii) higher and more stable gross margin than the mean sole crops (702 versus 577 € ha−1) and (iv) improved use of abiotic resources according to species complementarities for light interception and use of both soil mineral nitrogen and atmospheric N2. Intercropping is particularly suited for low-nitrogen availability systems but further mechanistic understanding is required to propose generic crop management procedures. Also, development of this practice must be achieved with the collaboration of value chain actors such as breeders to select cultivars suited to intercropping.
TL;DR: This work proposes 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 the authors' capacity to adapt crop protection to local realities.
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.
TL;DR: It is demonstrated that rapamycin partially reversed the protein expression patterns of EndoMT, improved experimental PAH, and decreased the migration of human pulmonary artery endothelial cells, providing the proof of concept that Endo MT is druggable.
Abstract: Background—The vascular remodeling responsible for pulmonary arterial hypertension (PAH) involves predominantly the accumulation of α-smooth muscle actin–expressing mesenchymal-like cells in obstructive pulmonary vascular lesions. Endothelial-to-mesenchymal transition (EndoMT) may be a source of those α-smooth muscle actin–expressing cells. Methods and Results—In situ evidence of EndoMT in human PAH was obtained by using confocal microscopy of multiple fluorescent stainings at the arterial level, and by using transmission electron microscopy and correlative light and electron microscopy at the ultrastructural level. Findings were confirmed by in vitro analyses of human PAH and control cultured pulmonary artery endothelial cells. In addition, the mRNA and protein signature of EndoMT was recognized at the arterial and lung level by quantitative real-time polymerase chain reaction and Western blot analyses. We confirmed our human observations in established animal models of pulmonary hypertension (monocrotal...
TL;DR: An overview of advancements in the understanding of all aspects of plant meiosis, including recombination, chromosome synapsis, cell cycle control, chromosome distribution, and the challenge of polyploidy is provided.
Abstract: Meiosis is the cell division that reshuffles genetic information between generations. Recently, much progress has been made in understanding this process; in particular, the identification and functional analysis of more than 80 plant genes involved in meiosis have dramatically deepened our knowledge of this peculiar cell division. In this review, we provide an overview of advancements in the understanding of all aspects of plant meiosis, including recombination, chromosome synapsis, cell cycle control, chromosome distribution, and the challenge of polyploidy.
Blaise Pascal University1, Institut national de la recherche agronomique2, University of Florida3, University of Bonn4, Goddard Institute for Space Studies5, Commonwealth Scientific and Industrial Research Organisation6, International Water Management Institute7, Michigan State University8, Agro ParisTech9, CGIAR10, University of Leeds11, University of Tübingen12, University of Alberta13, International Atomic Energy Agency14, University of Reading15, University of Guelph16, University of Hohenheim17, University of Maryland, College Park18, Potsdam Institute for Climate Impact Research19, Indian Agricultural Research Institute20, Department of Environment and Primary Industries21, Aarhus University22, Rothamsted Research23, Food and Agriculture Organization24, Washington State University25, Wageningen University and Research Centre26, Chinese Academy of Sciences27, International Trademark Association28, United States Department of Agriculture29
TL;DR: It is concluded that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics, and argued that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.
Abstract: Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but such studies are difficult to organize and have only recently begun. We report on the largest ensemble study to date, of 27 wheat models tested in four contrasting locations for their accuracy in simulating multiple crop growth and yield variables. The relative error averaged over models was 24-38% for the different end-of-season variables including grain yield (GY) and grain protein concentration (GPC). There was little relation between error of a model for GY or GPC and error for in-season variables. Thus, most models did not arrive at accurate simulations of GY and GPC by accurately simulating preceding growth dynamics. Ensemble simulations, taking either the mean (e-mean) or median (e-median) of simulated values, gave better estimates than any individual model when all variables were considered. Compared to individual models, e-median ranked first in simulating measured GY and third in GPC. The error of e-mean and e-median declined with an increasing number of ensemble members, with little decrease beyond 10 models. We conclude that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics. We argue that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.
TL;DR: The agronomic, plant breeding, and transgenic approaches that are used to remediate Fe deficiency of plants on calcareous soils are discussed, and ways to increase the Fe content and bioavailability of the edible parts of crops to improve human diet are suggested.
Agriculture and Agri-Food Canada1, University of Sydney2, Institut national de la recherche agronomique3, Aix-Marseille University4, university of lille5, University of Amsterdam6, American Museum of Natural History7, Leibniz Association8, Ruhr University Bochum9, Universidade Nova de Lisboa10, Federal University of Paraná11, Agro ParisTech12, University of Perugia13, Tuscia University14, Pasteur Institute15, Spanish National Research Council16, Second Military Medical University17, University of Pretoria18, King Abdulaziz University19, Staatliches Museum für Naturkunde Stuttgart20
TL;DR: A novel high fidelity primer pair for TEF1α has potential as a supplementary DNA barcode with superior resolution to ITS, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
Abstract: Primer development and testing by partners in the
European Consortium of Microbial Resource Centres (EMbaRC) was supported
through funding of the European Community’s Seventh Framework
Programme (FP7, 2007–2013), Research Infrastructures action, under grant
agreement no. FP7-228310. Part of sequencing work in CBS was supported
by Fonds Economische Structuurversterking (FES), Dutch Ministry of Education,
Culture and Science grant BEK/BPR-2009/137964-U). WM and VR
were supported by research grant NH&MRC #APP1031952. Genome mining
at CBS and AAFC, and primer development and testing at AAFC, were supported
by grants from the A.P. Sloan Foundation Programme on the Microbiology
of the Built Environment. We acknowledge the Deanship of Scientific
Research (DSR), King Abdulaziz University, under grant No. 1-965/1434 HiCi
for technical and financial support. AY was supported by Fundacao para a
Ciencia e a Tecnologia (Portugal), project PTDC/BIA-BIC/4585/2012. MPM
was supported by grant CGL2012-359 (Spain).
Macquarie University1, University of Western Sydney2, Imperial College London3, University of Technology, Sydney4, University of Lleida5, Commonwealth Scientific and Industrial Research Organisation6, University of Antwerp7, University of Gothenburg8, Swedish University of Agricultural Sciences9, Lund University10, James Cook University11, Kansas State University12, Colorado State University13, University of Paris-Sud14, Brookhaven National Laboratory15, Oak Ridge National Laboratory16, Tuscia University17, Tohoku University18, Kyoto University19, University of Exeter20, Institut national de la recherche agronomique21, International Sleep Products Association22, University of Melbourne23, University of Auckland24, Spanish National Research Council25, University of Edinburgh26, Charles Darwin University27, Forestry Commission28, Ishikawa Prefectural University29, University of Helsinki30, Obihiro University of Agriculture and Veterinary Medicine31, University of New Mexico32, Federal University of Pará33, Technical University of Denmark34, Pontifical Catholic University of Peru35, University of Oxford36, Northeast Normal University37
TL;DR: In this paper, the authors present a database of globally distributed stomatal conductance (g(s) obtained in the field for a wide range of plant functional types (PFTs) and biomes.
Abstract: Stomatal conductance (g(s)) is a key land-surface attribute as it links transpiration, the dominant component of global land evapotranspiration, and photosynthesis, the driving force of the global carbon cycle. Despite the pivotal role of g(s) in predictions of global water and carbon cycle changes, a global-scale database and an associated globally applicable model of g(s) that allow predictions of stomatal behaviour are lacking. Here, we present a database of globally distributed g(s) obtained in the field for a wide range of plant functional types (PFTs) and biomes. We find that stomatal behaviour differs among PFTs according to their marginal carbon cost of water use, as predicted by the theory underpinning the optimal stomatal model(1) and the leaf and wood economics spectrum(2,3). We also demonstrate a global relationship with climate. These findin g(s) provide a robust theoretical framework for understanding and predicting the behaviour of g(s) across biomes and across PFTs that can be applied to regional, continental and global-scale modelling of ecosystem productivity, energy balance and ecohydrological processes in a future changing climate.
TL;DR: In this article, the authors present a review of agroecological and management sciences to identify two facts that explain the lack of practical applications: (1) the occurrence of high uncertainties about relations between agricultural practices, ecological processes, and ecosystem services, and (2) the site-specific character of agricultural practices required to deliver expected ecosystem services; they also show that an adaptive management approach, focusing on planning and monitoring, can serve as a framework for developing and implementing learning tools tailored for biodiversity-based agriculture.
Abstract: Intensive agriculture has led to several drawbacks such as biodiversity loss, climate change, erosion, and pollution of air and water. A potential solution is to implement management practices that increase the level of provision of ecosystem services such as soil fertility and biological regulation. There is a lot of literature on the principles of agroecology. However, there is a gap of knowledge between agroecological principles and practical applications. Therefore, we review here agroecological and management sciences to identify two facts that explain the lack of practical applications: (1) the occurrence of high uncertainties about relations between agricultural practices, ecological processes, and ecosystem services, and (2) the site-specific character of agroecological practices required to deliver expected ecosystem services. We also show that an adaptive-management approach, focusing on planning and monitoring, can serve as a framework for developing and implementing learning tools tailored for biodiversity-based agriculture. Among the current learning tools developed by researchers, we identify two main types of emergent support tools likely to help design diversified farming systems and landscapes: (1) knowledge bases containing scientific supports and experiential knowledge and (2) model-based games. These tools have to be coupled with well-tailored field or management indicators that allow monitoring effects of practices on biodiversity and ecosystem services. Finally, we propose a research agenda that requires bringing together contributions from agricultural, ecological, management, and knowledge management sciences, and asserts that researchers have to take the position of “integration and implementation sciences.”
TL;DR: It is shown that PopP2 directly acetylates a key lysine within an additional C-terminal WRKY transcription factor domain of RRS1-R that binds DNA, causing loss of WRKY-DNA binding and transactivating functions needed for defense gene expression and disease resistance.
TL;DR: In this paper, the authors focus on the different alternatives of digestate valorisation, apart from land applications, such as the use of the digestate liquor for replacing freshwater and nutrients in algae cultivation, and the conversion of solid digestate into added-value products (char or activated carbons) through a pyrolysis process.
Abstract: In the agricultural sector of many European countries, biogas production through anaerobic digestion (AD) is becoming a very fast-growing market. AD is a simple and robust process that biologically converts an organic matrix into biogas and digestate, the latter corresponding to the anaerobically non-degraded fraction. So far, digestate has been mostly used at farm-scales for improving soils. However, its ever-increasing production induces problems related to transport costs, greenhouse-gas emissions during storage and high nitrogen content that constrains its use to land application only. Consequently, research on alternative valorisation routes to reduce its environmental impact and to improve the economical profitability of AD plants should draw increasing interest in the future. This review therefore focuses on the different alternatives of digestate valorisation, apart from land applications: (I) the use of the digestate liquor for replacing freshwater and nutrients in algae cultivation; (II) the use of solid digestate for energy production through biological (i.e. AD, bioethanol) or thermal processes (i.e. combustion, hydrothermal carbonization and pyrolysis); (III) the conversion of solid digestate into added-value products (char or activated carbons) through a pyrolysis process.
TL;DR: A set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana are developed, suitable for any transformable plant species.
Abstract: The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species.
TL;DR: An update of the knowledge on potyvirus multiplication, movement, and transmission and on potYvirus/plant compatible interactions including pathogenicity and symptom determinants is presented and information on biotechnological applications of potyviruses is provided.
Abstract: Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.