Fiber Optic Sensing System for Temperature and Gas Monitoring in Coal Waste Pile Combustion Environments

International audienceIt is presented an optical fiber sensing system projected to operate in the demanding conditions associated with coal waste piles in combustion. Distributed temperature measurement and spot gas sensing are requirements for such a system. A field prototype has been installed and is continuously gathering data, which will input a geological model of the coal waste piles in combustion aiming to understand their dynamics and evolution. Results are presented on distributed temperature and ammonia measurement, being noticed any significant methane emission in the short time period considered. Carbon dioxide is also a targeted gas for measurement, with validated results available soon. The assessment of this technology as an effective and reliable tool to address the problem of monitoring coal waste piles in combustion opens the possibility of its widespread application in view of the worldwide presence of coal related fires

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

IWGSC Sequence Repository: Moving towards tools to facilitate data integration for the reference sequence of wheat

URGI is a genomics and bioinformatics research unit at INRA (French National institute for Agricultural Research), dedicated to plants and crop parasites. We develop and maintain a genomic and genetic Information System called GnpIS that manages multiple types of wheat data. Under the umbrella of the IWGSC (International Wheat Genome Sequencing Consortium), we have set up a Sequence Repository on the Wheat@URGI website to store, browse and BLAST the data being generated by the wheat genome project: http://wheat-urgi.versailles.inra.fr/Seq-Repository. The repository holds the wheat physical maps, the chromosome survey sequence data for the individual chromosomes of breadwheat, draft sequences for diploid and tetraploid wheats and provides browsable access to the BAC-based reference sequence for chromosome 3B, the first of the chromosomes to be completed by the consortium. I will highlight the new features and data available in the Sequence Repository (e.g., new BLAST functionalities) and, in particular, present what we have done to address needs and concerns raised during the IWGSC S&P workshop last year. In addition, I will open the discussion about the future needs for tools to facilitate the integration of data to produce the reference sequence

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Defaunated and invaded insular tropical rainforests will not recover alone: recruitment limitation factors disentangled by hierarchical models of spontaneous and assisted regeneration

International audience1. Most tropical forests are now severely degraded and their ability to recover is highly dependent on frugivores which ensure seed dispersal for most woody plants. The global collapse of large vertebrates therefore raises major concerns about tropical forest succession, but few field studies have been conducted to disentangle recruitment limitations during disrupted succession.2. This study took place on Réunion (Mascarenes) where all large native frugivores have been extinct since human colonisation in 1665 and where multiple invasions threaten native ecosystems. We set up 20 experimental blocks on a lava flow dated back to 1800, in plant-impoverished post-defaunation vegetation bordered by old-growth forests. We assessed fecundity, seed dispersal and seedling recruitment of the complete fleshy-fruited plant community and used Bayesian analyses to disentangle the impact of multiple factors on these key processes. In the same blocks, we sowed four native trees assumed to be disperserless to test their capacity to establish, controlling for two additional post-dispersal limitations (seed predation and competition with invasive plants).3. On the flow, small-seeded native plants were fairly dispersed but did not recruit, probably due to strong competition with invasive plants; the few native species that recruited somehow were mostly medium-seeded plants that were still dispersed; large-seeded plants were absent from seed rain (which shows that invasive frugivores did not replace extinct ones) and subsequently from spontaneous recruitment. Instead, some alien plants, notably the tiny-seeded highly-dispersed Clidemia hirta and the medium-seeded Psidium cattleianum largely dominated seedling recruitment. Native plants recruited better at the forest margin, including some large-seeded species nearby mother trees.4. Sown large-seeded species were able to emerge and survive in all plots whatever the treatment, which demonstrates that dispersal loss was the primary cause of regeneration failure on the flow. Synthesis. The strong modulation of the establishment capacity of native plants by seed mass shows that invasive plants win by forfeit of large-seeded plants after native frugivores loss. Our study emphasises the fundamental role of dispersal loss and competition with invasive plants in the disruption of ecological succession, as well as the urgency of restoring seed dispersal and strengthening biosecurity regulations.1. La plupart des forêts tropicales sont aujourd'hui gravement dégradées et leur capacité à se reconstruire après perturbation dépend fortement des frugivores qui assurent la dispersion des graines. L'effondrement global des grands vertébrés soulève donc des inquiétudes majeures pour la la succession écologique en forêt tropicale, mais peu d'études de terrain ont été menées pour démêler les limitations du recrutement dans ce contexte.2. Cette étude se déroule à la Réunion (archipel des Mascareignes) où tous les grands frugivores indigènes ont disparu depuis la colonisation humaine en 1665 et où de multiples invasions menacent les écosystèmes indigènes. Nous installons 20 blocs expérimentaux sur une coulée de lave datant de 1800, dans une végétation post‐défaunation très appauvrie et flanquée de forêts anciennes. Nous évaluons la fécondité, la dispersion des graines et le recrutement des plantules pour l’ensemble des plantes à fruits charnus, et nous utilisons des analyses bayésiennes pour démêler l'impact de multiples facteurs sur ces trois processus clés. Dans les mêmes blocs, nous semons quatre arbres indigènes supposés sans disperseur afin de tester leur capacité à s'établir, en contrôlant deux limitations post‐dispersion supplémentaires (prédation des graines et compétition avec les plantes envahissantes).3. Sur la coulée de 1800, les plantes indigènes à petites graines sont relativement bien dispersées mais ne peuvent recruter spontanément, probablement en raison d'une forte compétition avec les plantes envahissantes; les quelques espèces indigènes capables de recruter sont principalement des plantes à graines moyennes qui sont encore dispersées; les plantes à grosses graines sont absentes de la pluie de graines (ce qui montre aussi que les frugivores introduits n'ont pas fonctionnellement remplacé les espèces éteintes) et par conséquent du recrutement spontané. A l’opposé, certaines plantes exotiques dominent très largement le recrutement, notamment l’espèce à petites graines Clidemia hirta qui archi‐domine la dispersion et l’espèce à graines moyennes Psidium cattleianum. Les plantes indigènes recrutent davantage à la limite de la forêt ancienne, y compris certaines espèces à grosses graines à proximité des semenciers.4. Les espèces à grosses graines semées sont capables de lever et survivre dans tous les blocs, quel que soit le traitement, ce qui démontre que la perte de la dispersion est la cause principale de leur absence sur les coulées historiques du Piton de la Fournaise.Synthèse . La forte modulation de la capacité d'établissement des plantes indigènes par la masse de graine montre que les plantes envahissantes gagnent par forfait des plantes indigènes à grosses graines. Notre étude souligne le rôle fondamental de la perte de la dispersion depuis l’extinction des frugivores indigènes et de la compétition avec les plantes envahissantes dans l’altération de la succession écologique, ainsi que l'urgence de restaurer la dispersion des graines et de renforcer les réglementations en matière de biosécurité

Defaunated and invaded insular tropical rainforests will not recover alone: recruitment limitation factors disentangled by hierarchical models of spontaneous and assisted regeneration

<ol> <li>Most tropical forests are now severely degraded and their ability to recover is highly dependent on frugivores which ensure seed dispersal for most woody plants. The global collapse of large vertebrates therefore raises major concerns about tropical forest succession, but few field studies have been conducted to disentangle recruitment limitations during disrupted succession.</li> <li>This study took place on Réunion (Mascarenes) where all large native frugivores have been extinct since human colonisation in 1665 and where multiple invasions threaten native ecosystems. We set up 20 experimental blocks on a lava flow dated back to 1800, in plant-impoverished post-defaunation vegetation bordered by old-growth forests. We assessed fecundity, seed dispersal and seedling recruitment of the complete fleshy-fruited plant community and used Bayesian analyses to disentangle the impact of multiple factors on these key processes. In the same blocks, we sowed four native trees assumed to be disperserless to test their capacity to establish, controlling for two additional post-dispersal limitations (seed predation and competition with invasive plants).</li> <li>On the flow, small-seeded native plants were fairly dispersed but did not recruit, probably due to strong competition with invasive plants; the few native species that recruited somehow were mostly medium-seeded plants that were still dispersed; large-seeded plants were absent from seed rain (which shows that invasive frugivores did not replace extinct ones) and subsequently from spontaneous recruitment. Instead, some alien plants, notably the tiny-seeded highly-dispersed <em>Clidemia hirta</em> and the medium-seeded <em>Psidium cattleianum</em> largely dominated seedling recruitment. Native plants recruited better at the forest margin, including some large-seeded species nearby mother trees.</li> <li>Sown large-seeded species were able to emerge and survive in all plots whatever the treatment, which demonstrates that dispersal loss was the primary cause of regeneration failure on the flow. </li> <li> <em>Synthesis</em><strong>.</strong> The strong modulation of the establishment capacity of native plants by seed mass shows that invasive plants win by forfeit of large-seeded plants after native frugivores loss. Our study emphasises the fundamental role of dispersal loss and competition with invasive plants in the disruption of ecological succession, as well as the urgency of restoring seed dispersal and strengthening biosecurity regulations.</li> </ol&gt

Plan de gestion de données de la Plateforme de Bioinformatique des Plantes de l'URGI (PlantBioinfoPF): PGD PlantBioinfoPF

The Plant Bioinformatics Facility (PlantBioinfoPF - doi:10.15454/1.5572414581735654E12) supports research activities in plant genetics and genomics. It is hosted by URGI, an INRAE research unit. The services offered by the platform cover database design, software engineering, software hosting, data integration and training. The platform's activities benefit from URGI's research activities (data integration, annotation of repeats, study of genome structure and evolution). PlantBioinfoPF belongs to IFB (Institut Français de Bioinformatique), the French node of the Elixir European network of bioinformatics platforms. It has been certified by INRAE's ISC (Infrastructure Scientifique Collective) committee and by the GIS IBISA (Groupement d'Intérêt Scientifique - Infrastructures en Biologie Sante et Agronomie) as a national strategic platform. The platform also belongs to the INRAE Research Infrastructure BioinfOmics and is part of the Saclay Plant Science Network and the Biosphera Graduate School. It is ISO9001 v. 2015 certified.PlantBioinfoPF's data management plan describes the lifecycle of the data managed by the platform via 3 management modes: 1) "Information Systems" details the management of data in our Information systems (GnpIS warehouse and pPlantBioinfoPF's data management plan describes the various stages in the lifecycle of the data managed by the platform via 3 management modes: 1) "Information systems" details the management of data in our Information systems (GnpIS warehouse and data federation portals), 2) "Software" details the management of the source code of the software we develop and 3) "Genome analysis" details the management of data as part of our genome analyses.La plateforme de bioinformatique des plantes, PlantBioinfoPF (Plant Bioinformatics Facility - doi:10.15454/1.5572414581735654E12) soutient les activités de recherche en génétique et génomique sur les plantes. Elle est hébergée par l'URGI, une unité de recherche INRAE. Les services offerts par la plateforme couvrent la conception de bases de données, l'ingénierie logicielle, l'hébergement de logiciels, l'intégration de données et la formation. Les activités de la plateforme bénéficient des activités de recherche de l'URGI (intégration de données, annotation de répétitions, étude de la structure et de l'évolution des génomes). PlantBioinfoPF appartient à l'IFB (Institut Français de Bioinformatique), noeud français du réseau européen de plateformes de bioinformatiques Elixir. Elle a été labellisée par le comité ISC (Infrastructure Scientifique Collective) d'INRAE et par le GIS IBISA (Groupement d'Intérêt Scientifique - Infrastructures en Biologie Sante et Agronomie) comme plateforme stratégique nationale. La plateforme appartient également à l'Infrastructure de Recherche INRAE BioinfOmics et elle fait partie du réseau Science des Plantes de Saclay et la Graduate School Biosphera. Elle est certifiée ISO9001 v. 2015.Le plan de gestion de données de PlantBioinfoPF décrit les différentes étapes du cycle de vie des données gérées par la plateforme via 3 modes de gestion : 1) "Systèmes d’information" détaille la gestion des données dans nos systèmes d’Information (entrepôt GnpIS et portails de fédération de données), 2) "Logiciel" détaille la gestion des codes source des logiciels que nous développons et 3) "Analyse des génomes" détaille la gestion des données dans le cadre de nos analyses de génomes

Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case study on grain legumes

International audienceWhile the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain largely understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data.Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including quantitative trait loci (QTL), RNA-seq datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling main traits across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programme

Translational research opportunities in grain legumes: where are we?

International audienceResearchers are under constant pressure to provide solutions to meet the challenges of a growing world population and advance One Health. Translational biology can play an important role in achieving these goals by transforming basic research discoveries into practice quickly and efficiently. In plants, basic science can indeed be translated into methods to developand improve crop varieties and thus achieve food security in a sustainable and safe way. Grain legumes are an important source of protein for animal and human nutrition. They are part of a large plant family with several, closely-related, agronomically-important crops. As the demand for plant-based protein continues to grow, more land is being devoted to these crops, but many environmental influences still constrain their productivity. Improving the response of grain legumes to limiting factors is key to ensuring the stability of yield and grain quality. Here, we report the development of OrthoLegKB, aknowledge graph database for grain legumes. The framework relies heavily on orthology and synteny relationships to build bridges between species, and transfer and/or compare information between them. Users can integrate published and unpublished data related to their species of interest including genetic, genomic and transcriptomic information. Heterogeneous datasets from multiple species can be accessed and explored with quasi-instantaneous query times, allowing relevant biological questions to be addressed, hypotheses to be generated, and information from a single or group of species to be transferred to others. OrthoLegKB is a significant step towards translational approaches in grain legumes and a great tool for research and breeding. The number of legume species will be constantly increased. Future developments to accommodate pangenomic datasets as well as proteomic and metabolomic information will further enrich the query capabilities