MetExploreViz: web component for interactive metabolic network visualization

Summary: MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyse omics data in a biochemical context. Availability and implementation: Documentation and link to GIT code repository (GPL 3.0 license) are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc

The PGR Networks in France: Collaboration of users and the genetic resources centre on small grain cereals

Plant genetic resources (PGR) have been used in breeding programs for many decades to produce modern varieties by introducing genes of interest, in particular, resistance genes. Nevertheless, these resources remain underestimated if we focus on abiotic stress tolerance or new agricultural techniques, which consider productivity with regard to the environment. In recent years, new users, such as scientists and farmers, have discovered diverse sources of interest for screening and exploiting natural diversity conserved in PGR collections.In the case of the French cereals PGR Network, a share of the responsibility, based on the knowledge and ability of network members, has been decided in order to better promote the use of PGR. The main species of Triticum (wheat), Hordeum (barley), Secale (rye), ×Triticosecale (triticale), Avena (oat) genera and their wild relatives are held in the collection. By combining phenotypic and genotypic data, the whole genetic resource collection has been structured into smaller functional groups of accessions, in order to facilitate the access and meet the increasing number of different requirements for the distribution of adapted samples of accessions.New panels are being processed to give breeders and scientists new useful tools to study, for instance, stress resistance or to develop association studies. All these data obtained from the French small grain cereal Network will be progressively available through the INRA Genetic Resource Website (http://urgi.versailles.inra.fr/siregal/siregal/welcome.do)

A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Conservation ex situ des collections de céréales à paille

National audienceLe Centre de Ressources Biologiques (CRB) Céréales à Paille conserve à l'INRA de Clermont-Ferrand les espèces Triticum (blé), Hordeum (orge), Secale (seigle), Triticosecale (triticale), Avena (avoine) et leur apparentées sauvages. Les accessions, maintenues sous forme de graines au CRB, sont des ressources génétiques patrimoniales (variété de pays, lignée de sélection, variété inscrite) qui constituent un réservoir intéressant pour la recherche fondamentale (génomique et génétique), pour la création variétale et plus globalement pour la conservation de la biodiversité cultivée. La conservation ex-situ au CRB englobe plusieurs aspects : la description et l'évaluation des collections, la conservation, la régénération et la distribution des ressources génétiques ainsi que la diffusion et la gestion des informations associées à ces ressources. Parallèlement à ces activités intrinsèques, le CRB développe des connections et des partenariats avec un public large et varié (scientifiques, agriculteurs, sélectionneurs,…) ayant des intérêts différents dans l'utilisation des ressources génétiques

Certification process of small grain cereals BRC in France

In France, genetic resources are maintained in several Biological Resources Centres (BRC) spread all over the country. Most part of these BRC are involved in a quality management process. The development of quality system becomes a priority in regard of new notions (as collection of reference) and requirement at European and international levels.In this context, the French small grain cereals BRC engages itself in a certification process since March 2014. The certification's framework applied to principal missions of small grain cereals BRC:acquisition and regeneration.Each year new materials are introduced in collection for different purposes (scientific projects, evaluation networks, ie...). To be able to answer to Nagoya protocol requirement and also to be in agreement with European collection (AEGIS) philosophy, acquisition process has been clarified and standardized. Regeneration of small grain cereals genetic resources are realized at INRA Clermont-Ferrand with around 10% of the whole collection (≈ 27 000 acc.) characterized per year for primary descriptors. A part of these data is available online on SIReGal database (http://urgi.versailles.inra.fr/siregal).conservation: Active collection is maintained in a 100 m3 cold room at +4°C and 30% relative humidity. It is used to regeneration, multiplication, distribution, characterization and assessment. Base collection is maintained at -20°C in freezer as secure storage. Various tests concerning drying before storage and germination are done to improve conservation conditions. distribution: To improve access to small grain cereals collections, a work on data's curation and submission to SIReGal database has been done and it still in process. Around 4 300 samples have been distributed in 2014, mainly to researchers and breeders but also to farmers and associations. Terms and conditions of BRC have been formalized and a first survey of genetic resources' requesters was launched in autumn 2014 to better understand their expectations and to have a feedback on BRC services (seed quality, available information, delay, documentation …). Each proceeding has been well documented to clarify and improved our methodology

MetExplore: Omics data analysis in the context of metabolic networks

International audienc

What is behind the management of small grain cereals Biological Resources Centre?

National audienc

What is behind the management of small grain cereals biological centre?

The BreedWheat project and more particularly Céréales Vallée, INRA and INRA Transfert, has organized the International Wheat Innovation Workshop (IWIW) the 16th and 17th November 2015 in Clermont-Ferrand, France. Message de bienvenueL’innovation variétale doit pouvoir profiter des progrès rapides des technologies de génotypage et de phénotypage. L’objectif de ce colloque international est de faire connaître à la communauté scientifique et semencière les principales avancées sur la génomique, le séquençage, la génétique, l’écophysiologie et la caractérisation des ressources génétiques du blé tendre. Nous proposons de le faire au travers de projets et d’équipes qui travaillent dans le cadre de grands projets nationaux focalisés sur le blé. De nouvelles pistes d’applications et de recherches peuvent apparaitre de la confrontation de ces expériences entre elles et avec la communauté des céréales.Une plage importante sera dédiée aux discussions, avec des tables rondes prévues après chaque session, permettant ainsi de favoriser le dialogue entre chercheurs académiques et privés, entre chercheurs des différents projets et entre ces projets et d’autres initiatives.Ce colloque organisé par le projet français BreedWheat (Projet Investissements d’Avenir), associe WISP (Projet LOLA britannique), proWeizen (Alliance allemande pour la recherche et la sélection), CRP WHEAT (programme challenge des instituts de recherche internationaux), l’IWGSC (consortium international de séquençage du blé) et la Wheat Initiative. Il présentera les résultats obtenus dans ces projets et certains programmes associés.L’inscription est gratuite mais obligatoire et ouverte prioritairement aux partenaires des projets et programmes précités. Les personnes non partenaires devront remplir un questionnaire sur leur expertise et intérêt majeur. Les présentations orales sont principalement limitées aux partenaires des projets mais la soumission de posters est possible et fortement encouragée.The small grain cereals Biological Resources Centre (BRC), part of INRA plant BRC Networks, gathers a collection of around 27 000 accessions. A major part of the preserved accessions are patrimonial genetic resources (landraces, breeding lines, elite lines and registered cultivars), including bread wheat, durum wheat and relatives species, barleys, triticales, oats, Aegilops sp. and ryes.BRC has defined two strands of activity: The first one is related to collection's management, from acquisition of accession to sample's availability which is certified since June 2015 under French standard NF S 96-90. BRC brings its practical expertise of agronomical BRC management to quality organisation AFNOR in order to adapt this French standard at ISO level. A part of the collection is available online on SIReGal ttp://urgi.versailles.inra.fr/siregal). Annually, around 4 200 samples are freely distributed with a Material Transfer Agreement (MTA). BRC is also implicated in European Cooperative Programme for Plant Genetic Resources Cereals Networks and through this in the definition of the European collection AEGIS.The second axis concerns diversity's valorisation of collections by involvement in research programs. A core collection of 372 bread wheat accessions was defined from BRC collection (Balfourier et al, 2007) which is now highly genotyped (more than 200 000 SNPs markers) and phenotyped for a hundred traits (Bordes et al, 2008). Today, BRC participates to two main French projects: PIA Breedwheat, in which 4 600 accessions of BRC wheat collection were described at molecular and phenotype levels and CASDAR Colnator program where 570 French barley accessions will be evaluated under 2 years. Finally, BRC is also involved with private breeders in the national networks for cereal crop genetic resources. At European level, BRC is involved in FP7 Whealbi project by providing part of accessions, participating to multisite evaluation network and developing a biorepository for wheat collection