HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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UpDown, Detecting Group Disturbances from Longitudinal Observations
No full textProvides an algorithm to detect and characterize disturbances (start, end dates, intensity) that can occur at different hierarchical levels by studying the dynamics of longitudinal observations at the unit level and group level based on Nadaraya-Watson's smoothing curves, but also a shiny app which allows to visualize the observations and the detected disturbances. Finally the package provides a dataframe mimicking a pig farming system subsected to disturbances simulated according to Le et al.(2022
Pastured rabbit systems and organic certification: European union regulations and technical and economic performance in France
No full textThis review is adapted from the article: Gidenne T., Savietto D., Fortun-Lamothe L., Huang Y. 2022. Cuniculture au pâturage et sous certification Agriculture Biologique en France: fonctionnement des systèmes, performances et règlementation. INRAE Productions Animales, 35: 201-216. https://doi.org/10.20870/productions-animales.2022.35.3.7257International audienceIn the European Union (EU), organic rabbit farming (ORF) remains uncommon (≈50 farms), found mainly in France, and to a much lesser extent in Austria, Switzerland, Spain and Italy. As rabbits are herbivorous, ORF is based mainly on grazing. This review summarises information on the functioning and performance of rabbit farming systems in France, with organic certification and/or access to pasture. Recent studies have quantified the grass intake (30 to 80 g dry matter/d/rabbit) and growth rate of rabbits on pasture (15 to 30 g/d). ORF has an extensive production cycle with a mean of 2.7 parturitions per doe and per year. The main concerns for the farmers developing ORF include available land and managing health and feeding. However, in France, a herd with 40 does on 4 ha (of pastures and complementary crops), can provide a halftime minimum salary. Since January 2022, a new regulation on ORF is applied for all EU member countries that recommends a maximum use of pasture but nevertheless allows farmers to keep a herd with 40 does on only 200 m² of pasture. It also does not require rotating rabbits on the pasture between batches of animals, wich increases the risk of parasitism. A smartphone application (GAELA) was recently developed to assist with daily management of rabbit farming, and to build a database of technical benchmarks to support the development of organic and pastured rabbit farming in France
Utilisation d'une approche multidisciplinaire pour déterminer l'étiologie de syndromes cliniques chez une espèce aviaire menacée : l'exemple de l'Outarde Houbara
No full textIn the present work, we assessed the use of a multidisciplinary diagnostic approach to successfully investigate poorly characterized pathological entities using an endangered avian species as a model: the Houbara Bustard. This species is the object of several captive breeding operations located in North Africa, the United Arab Emirates and Central Asia. We focused our attention on three conditions that could potentially jeopardize conservation efforts: high pathogenicity avian influenza (HPAI), genital infections in artificially-inseminated breeders and a respiratory syndrome affecting outdoor birds destined to be released. For the first condition, we successfully validated an RNA scope in situ hybridization (ISH) assay for the detection of the avian influenza A virus matrix gene in formalin-fixed and paraffin-embedded (FFPE) tissues. We then provided the first comprehensive description of HPAI H5N8 natural infection in the Houbara, resulting in hyperacute and acute forms exhibiting marked tissue pantropism, endotheliotropism and neurotropism. For the second condition we characterized a series of cases of peritonitis and salpingo-peritonitis. Chronic forms predominated and an ascending infection was highly suspected. Most of the cases were associated with the isolation of Escherichia coli. The identification of a variety of virulence profiles by molecular analysis of selected bacterial isolates suggested the involvement of multiple strains. Furthermore, histopathology allowed the identification of changes consistent with cystic oviductal hyperplasia, expanding the list of potential risk factors involved in the development of genital infections in the Houbara Bustard.For the third condition, we were able to shed some light on a multifactorial respiratory syndrome, focusing on long-lasting, chronic forms. A variety of viral and bacterial pathogens were detected, including potentially a novel Mycoplasma species. Environmental conditions, such as heat stress and exposure to dust storms, were considered significant contributing factors. We showed that combining classical and novel diagnostic tools we were able to significantly improve the etiological diagnosis of emerging and re-merging conditions in the Houbara. This approach should be promoted to study sanitary issues in other endangered species, characterized by a limited availability of samples.Dans le travail présenté ici, nous avons évalué l’intérêt une approche diagnostique multidisciplinaire pour l’investigation d’entités pathologiques mal caractérisées en utilisant l’Outarde Houbara comme espèce modèle. Cette espèce fait l’objet de plusieurs projets d’élevages conservatoires en Afrique du Nord, au Moyen Orient et en Asie centrale. Nous nous sommes intéressés à trois entités pathologiques ayant toutes le potentiel de mettre en péril les efforts de conservation : l’influenza aviaire hautement pathogène (IAHP), les infections génitales chez les oiseaux inséminés artificiellement et un syndrome respiratoire affectant les oiseaux élevés à l’extérieur et devant à terme renforcer les populations sauvages. Pour la première entité, nous avons validé l’utilisation de l’hybridation in situ par RNAscope pour détecter le gène de matrice des virus influenza aviaires dans des tissus fixés au formol et inclus en paraffine. Cela nous a permis de décrire de manière exhaustive et pour la première fois un épisode infectieux à virus IAHP H5N8 chez l’Outarde Houbara, qui s’est manifestée par des formes cliniques suraigues à aigues de la maladie, associées à un pantropisme tissulaire, avec endothéliotropisme et neurotropisme viral. Pour la seconde entité pathologique, nous avons caractérisé une série de cas de péritonite et salpingo-péritonie associés à des infections par Escherichia coli. La diversité des profils de virulence de la bactérie, identifiée par biologie moléculaire, suggère l’implication de nombreuses souches. Les formes chroniques étaient prédominantes et une infection ascendante a été suspectée. De plus, l’examen histologique a permis l’identification de modifications tissulaires compatibles avec une hyperplasie cystique endométriale, pouvant intervenir comme facteur de risque dans le développement des infections génitales chez l’Houbara. Enfin, pour la troisième entité pathologique, nous nous sommes concentrés sur un syndrome respiratoire multifactoriel d’évolution essentiellement chronique. Divers agents pathogènes ont été détectés chez les oiseaux affectés, y compris une espèce potentiellement nouvelle de Mycoplasme. Des facteurs environnementaux, comme le stress thermique et l’exposition à des tempêtes de sable sont considérés comme des facteurs contributifs importants. Nous avons montré dans ce travail que nous améliorions considérablement le diagnostic étiologique des affections émergentes et réémergentes chez l’Outarde Houbara par une approche multidisciplinaire. Cette approche devrait être encouragée pour étudier la santé d’autres espèces menacées, notamment lors d’une disponibilité limitée en échantillons
Fusion de données omiques multiblocs à l'aide du package R Consensus OPLS
No full textInternational audienceOmics approaches have proven their value in providing a broad monitoring of biological systems. However, despite the wealth of data generated by modern analytical platforms, the analysis of a single dataset is still limited and insufficient to reveal the full biochemical complexity of biological samples. The fusion of information from several data sources constitutes therefore a relevant approach to assessing biochemical events more comprehensively. However, inherent problems encountered when analyzing single tables are amplified with the generation of multi-block datasets. Finding the relationships between data layers of increasing complexity constitutes a challenging task. Here we propose an extension to the versatile methodology combining the strength of established data analysis strategies, multi-block approaches with the Orthogonal Partial Least Squares (OPLS) framework, to offer an efficient tool as an R package for the fusion of Omics data obtained from multiple sources.The method, already available in MATLAB, has been implemented in R with additional functionalities, including multi-class response, non-linear kernels, and parallelization. The package has been validated on a published dataset (transcriptomics, plasma shotgun Mass Spectrometry (MS) lipidomics, and targeted LC-MS sphingolipids data) from living human pancreatic islet donors (n=51) with various diabetes status. Two analyses were performed: (i) a discriminant analysis to distinguish patients with impaired glucose tolerance, type 2 diabetes, and type 3c diabetes, and (ii) a regression analysis to model the level of HbA1c, a parameter of longer-term glycaemia. OPLS multiblock models enabled the identification of significant biomarkers across various blocks, leading to novel biological insights.Les approches omiques ont prouvé leur valeur en permettant une surveillance étendue des systèmes biologiques. Cependant, malgré la richesse des données générées par les plateformes analytiques modernes, l'analyse d'un seul ensemble de données reste limitée et insuffisante pour révéler toute la complexité biochimique des échantillons biologiques. La fusion d'informations provenant de plusieurs sources de données constitue donc une approche pertinente pour évaluer les événements biochimiques de manière plus complète. Cependant, les problèmes inhérents rencontrés lors de l'analyse d'un seul ensemble de données sont amplifiés avec la génération d'ensembles de données multi blocs. Trouver les relations entre des couches de données de plus en plus complexes constitue un véritable défi. Nous proposons ici une extension de la méthodologie polyvalente combinant la force des stratégies d'analyse de données établies, les approches multi blocs avec le cadre de l'analyse des moindres carrés partiels orthogonaux (OPLS), afin d'offrir un outil efficace sous la forme d'un package R pour la fusion des données Omics obtenues à partir de sources multiples.La méthode, déjà disponible dans MATLAB, a été implémentée dans R avec des fonctionnalités supplémentaires, incluant une réponse multi-classe, les noyaux non linéaires et la parallélisation. Le package a été validé sur un ensemble de données publiées (transcriptomique, lipidomique plasma shotgun par spectrométrie de masse (MS) et données ciblées LC-MS sur les sphingolipides) provenant de donneurs vivants d'îlots pancréatiques humains (n=51) présentant différents statuts de diabète. Deux analyses ont été réalisées : (i) une analyse discriminante pour distinguer les patients présentant une intolérance au glucose, un diabète de type 2 et un diabète de type 3c, et (ii) une analyse de régression pour modéliser le niveau d'HbA1c, un paramètre de la glycémie à plus long terme. Les modèles OPLS multi blocs ont permis d'identifier des biomarqueurs significatifs dans différents blocs, ce qui a conduit à de nouvelles connaissances biologiques
An automated workflow for high-throughput 13C-fluxomics
No full textInternational audienceThe goal of isotope-based fluxomics approaches is to quantify metabolic fluxes in living organisms. 13C-fluxomics provides a detailed phenotypic description of the actual metabolic state of studied organisms. To achieve this, a combination of several experimental and computational steps is required. However, the complexity of the computational steps, coupled with the need to select the right software while manually ensuring data interoperability, makes the process error-prone, time-consuming, and hard to reproduce effectively. The objective of this project is to overcome these limitations by providing a flexible, reproducible, user-friendly, and high-throughput 13C-fluxomics workflow that integrates the tools needed for flux calculation
Services deployed on the IFB National Network of Computing Resources (NNCR)
No full textInternational audienceThe Institut Français de Bioinformatique (IFB) deploys the National Network of Computing Resources (NNCR), distributed over 10 sites, including cluster-based access to HPC as well as cloud computing, which delivers a diversity of services specifically addressed to life scientists and bioinformaticians
L'analyse d'image et sonore pour le relevé d'indicateurs de bien-être et de santé des volailles
No full textCe numéro traite de résultats de projets lauréats en 2017 et 2018 de l'appel à projet CASDAR (Compte d'Affectation Spéciale Développement Agricole et Rural), "Innovation et Partenariat" et "Recherche Technologique. Ces projets sont financés par le ministère de l'Agriculture et de la Souveraineté Alimentaire.National audienceGuaranteeing consumers that poultry farming respects animal welfare is the heart of the poultry farmer,but civil society is demanding greater transparency in farming practices. Meeting society's expectationsmust go hand in hand with the competitiveness of poultry meat production, which is globalised and highlycompetitive. The notion of animal health and welfare can be assessed using a variety of methods, andnew technologies offer an opportunity to take continuous measurements in real time, without disturbingthe animals in their living environment. Image and sound processing enables finer and more frequentanalyses than those carried out by humans. These new technologies are helping to improve monitoringand responsiveness to health problems or changes in animal behaviour through predictive analysis. TheEBroilerTrack project led by ITAVI has produced promising proofs of concept in imaging and acousticsunder controlled broiler rearing conditions. In the field of imaging, image analysis algorithms have beendeveloped to monitor individual broiler chickens on the farm, with the aim of identifying welfare and healthindicators for each animal observed. The performance of these algorithms is presented in this article. Inthe field of acoustics, the work carried out has demonstrated the benefits of using acoustic analysis tomonitor the health and well-being of broilers, in the specific case of infectious bronchitis
Integrative Multimodal Metabolomics to Early Predict Cognitive Decline Among Amyloid Positive Community-Dwelling Older Adults
No full textInternational audienceAlzheimer’s disease is strongly linked to metabolic abnormalities. We aimed to distinguish amyloid-positive people who progressed to cognitive decline from those who remained cognitively intact. We performed untargeted metabolomics of blood samples from amyloid-positive individuals, before any sign of cognitive decline, to distinguish individuals who progressed to cognitive decline from those who remained cognitively intact. A plasma-derived metabolite signature was developed from Supercritical Fluid chromatography coupled with high-resolution mass spectrometry (SFC-HRMS) and nuclear magnetic resonance (NMR) metabolomics. The 2 metabolomics data sets were analyzed by Data Integration Analysis for Biomarker discovery using Latent approaches for Omics studies (DIABLO), to identify a minimum set of metabolites that could describe cognitive decline status. NMR or SFC-HRMS data alone cannot predict cognitive decline. However, among the 320 metabolites identified, a statistical method that integrated the 2 data sets enabled the identification of a minimal signature of 9 metabolites (3-hydroxybutyrate, citrate, succinate, acetone, methionine, glucose, serine, sphingomyelin d18:1/C26:0 and triglyceride C48:3) with a statistically significant ability to predict cognitive decline more than 3 years before decline. This metabolic fingerprint obtained during this exploratory study may help to predict amyloid-positive individuals who will develop cognitive decline. Due to the high prevalence of brain amyloid-positivity in older adults, identifying adults who will have cognitive decline will enable the development of personalized and early interventions
The Salmonella virulence protein PagN contributes to the advent of a hyper-replicating cytosolic bacterial population
No full textInternational audienceSalmonella enterica subspecies enterica serovar Typhimurium is an intracellular pathogen that invades and colonizes the intestinal epithelium. Following bacterial invasion, Salmonella is enclosed within a membrane-bound vacuole known as a Salmonella-containing vacuole (SCV). However, a subset of Salmonella has the capability to prematurely rupture the SCV and escape, resulting in Salmonella hyper-replication within the cytosol of epithelial cells. A recently published RNA-seq study provides an overview of cytosolic and vacuolar upregulated genes and highlights pagN vacuolar upregulation. Here, using transcription kinetics, protein production profile, and immunofluorescence microscopy, we showed that PagN is exclusively produced by Salmonella in SCV. Gentamicin protection and chloroquine resistance assays were performed to demonstrate that deletion of pagN affects Salmonella replication by affecting the cytosolic bacterial population. This study presents the first example of a Salmonella virulence factor expressed within the endocytic compartment, which has a significant impact on the dynamics of Salmonella cytosolic hyper-replication
Classical BSE dismissed as the cause of CWD in Norwegian red deer despite strain similarities between both prion agents
No full textInternational audienceThe first case of CWD in a Norwegian red deer was detected by a routine ELISA test and confirmed by western blotting and immunohistochemistry in the brain stem of the animal. Two different western blotting tests were conducted independently in two different laboratories, showing that the red deer glycoprofile was different from the Norwegian CWD reindeer and CWD moose and from North American CWD. The isolate showed nevertheless features similar to the classical BSE (BSE-C) strain. Furthermore, BSE-C could not be excluded based on the PrPSc immunohistochemistry staining in the brainstem and the absence of detectable PrPSc in the lymphoid tissues. Because of the known ability of BSE-C to cross species barriers as well as its zoonotic potential, the CWD red deer isolate was submitted to the EURL Strain Typing Expert Group (STEG) as a BSE-C suspect for further investigation. In addition, different strain typing in vivo and in vitro strategies aiming at identifying the BSE-C strain in the red deer isolate were performed independently in three research groups and BSE-C was not found in it. These results suggest that the Norwegian CWD red deer case was infected with a previously unknown CWD type and further investigation is needed to determine the characteristics of this potential new CWD strain