HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Evaluating low-pass genotyping strategies using PARSEC, a scalable and modular Nextflow pipeline
No full textInternational audienceLow-pass sequencing combined with genotype imputation offers a cost-effective alternative to SNP arrays for high-resolution genotyping in large-scale genomic studies. However, it requires specific algorithms and computational resources. We present PARSEC, a modular and scalable Nextflow pipeline for processing low-pass sequencing data and performing genotype imputation using three state-of-the-art tools: Stitch, Beagle, and Glimpse.We used PARSEC on a real-world dataset of 1,050 pig offsprings of 12 founders by subsampling their sequencing data to various depths. PARSEC scales efficiently with large datasets and supports different imputation strategies.Our results show that tools tailored for low-pass data (Stitch and Glimpse) significantly outperform Beagle, a general-purpose imputation tool. Furthermore, we demonstrate that joint imputation of closely related individuals using Stitch is more accurate than using a reference haplotype panel with Glimpse.We also monitored resource usage across all scenarios, confirming that PARSEC can process large cohorts using widely accessible computational infrastructure.PARSEC provides a user-friendly, reproducible, and portable solution for large-scale low-pass sequencing projects. Beyond its practical utility as a bioinformatics pipeline, it also offers methodological insights into low-pass sequencing and imputation strategies. As such, it is a valuable tool both for implementing large-scale studies and for guiding methodological decisions in population genomics and association research
An advanced stochastic framework for the simulation of transgenerational hologenomic data
No full textInternational audienceA holobiont is made up of a host organism together with its microbiota. In the context of animal breeding, the holobiont can be viewed as the single unit upon which selection operates. Therefore, integrating microbiota data into genomic prediction models may be a promising approach to improve predictions of phenotypic and genetic values. Nevertheless, there is a paucity of hologenomic transgenerational data to address this hypothesis, and thus to fill this gap, we propose a new simulation framework. Our approach, an R Implementation of a Transgenerational Hologenomic Model-based Simulator (RITHMS) is an open-source package, builds upon simulated transgenerational genotypes from the MoBPS package and incorporates distinctive characteristics of the microbiota, notably vertical and horizontal transmission as well as modulation due to the environment and host genetics. In addition, RITHMS can account for a variety of selection strategies and is adaptable to different genetic architectures. We simulated transgenerational hologenomic data using RITHMS under a wide variety of scenarios, varying heritability, microbiability, and microbiota heritability. We found that simulated data accurately preserved key characteristics across generations, notably microbial diversity metrics, exhibited the expected behavior in terms and correlation between taxa and of modulation of vertical and horizontal transmission, response to environmental effects and the evolution of phenotypic values depending on selection strategy. Our results support the relevance of our simulation framework and illustrate its possible use for building a selection index balancing genetic gain and microbial diversity. RITHMS is an advanced, flexible tool for generating transgenerational hologenomic data that incorporate the complex interplay between genetics, microbiota and environment
Pharmacokinetic data for the manuscript "Population pharmacokinetic modeling of sulfadimethoxine, sulfadizine and sulfamethoxazole combined to trimethoprim in pigs"
No full textThe column: - "ID corresponds to the number of the individual (i.e. pig) - "Time" corresponds to the sampling time - "Amount (mg/kg)" corresponds to the amount of drug received/kg - "Administration" and "Route" correspond to the administration route - "Weight" corresponds to the weight of each pig in kg - "Observation" corresponds to the amount of drug quantified - "Censoring" and "Limit of quantification" correspond to the censoring of the data - "Obs_ID" corresponds to the molecule studied - "Phase" corresponds to the combination (TMP/SDZ or SMX or SDMX) for each data obtained - "OCC" corresponds to the week of cross-over - "Outliers" corresponds to any events during the experiment - "Formulation" corresponds to the veterinary product administered.International audienceDataset associated to the manuscript "Population pharmacokinetic modeling of sulfadimethoxine, sulfadizine and sulfamethoxazole combined to trimethoprim in pigs". The dataset contains all the data (e.g. observations, time, censoring...) used for the population modeling described in the manuscript
Bilan d’une étude de séroprévalence des Orthoflavivirus West Nile, Usutu et du virus de l’encéphalite à tiques sur un échantillon de la population équine de Gironde en 2023
No full textA seroprevalence study of West Nile virus (WNV), Usutu virus (USUV), and Tick-borne encephalitis virus (TBEV) was conducted in Gironde in the spring of 2023, following the emergence of WNV in equids in this department in 2022. The serological status of 494 horses, located in three geographical areas (Confluence, Intermediate Zone, and Arcachon Basin), was assessed through blood sampling for these three viruses. The results showed an overall seroprevalence of 14% for the three orthoflaviviruses, with the highest rates observed in the Confluence zone : 9% for WNV and 5% for USUV. Housing type (exclusive pasture) and the distance to the nearest Special Protection Area (SPA) for birds were identified as significant risk factors for WNV seropositivity. This study, the first of its kind on the French Atlantic coast, demonstrates active circulation of WNV in this region as well as the presence of USUV in equids.Une étude de séroprévalence des Orthoflavivirus West Nile (WNV), Usutu (USUV) et Tick-borne encephalitis virus (TBEV) a été réalisée en Gironde, au printemps 2023, suite à l’émergence du WNV chez les équidés dans ce département en 2022. Le statut sérologique de 494 chevaux, répartis sur trois zones géographiques (Confluence, Zone intermédiaire et Bassin d'Arcachon), a été établi par prélèvement sanguin pour ces trois virus. Les résultats montrent une séroprévalence globale de 14% pour les trois orthoflavivirus, avec les taux les plus élevés observés dans la zone de Confluence : 9% pour WNV et 5% pour USUV. Le type d’hébergement (pâturage exclusif) et la distance par rapport à la zone de protection spéciale des oiseaux (SPA) la plus proche étaient des facteurs de risque significatifs pour la séropositivité au WNV. Cette étude, la première sur la côte atlantique française, démontre une circulation active du WNV dans cette région, ainsi que la présence du virus USUV chez les équidés
Les profils métaboliques simulés révèlent des biais dans les méthodes d'enrichissement de voies
No full textInternational audienceIntroduction Initially developed for transcriptomics data, pathway analysis (PA) methods can introduce biases when applied to metabolomics data, especially if input parameters are not chosen with care. This is particularly true for exometabolomics data, where there can be many metabolic steps between the measured exported metabolites in the profile and internal disruptions in the organism. However, evaluating PA methods experimentally is practically impossible when the sample’s “true" metabolic disruption is unknown. Objectives This study aims to show that PA can lead to non-specific enrichment, potentially resulting in false assumptions about the true cause of perturbed metabolic states. Methods Using in silico metabolic modelling, we can create disruptions in metabolic networks. SAMBA, a constraint-based modelling approach, simulates metabolic profiles for entire pathway knockouts, providing both a known disruption site as well as a simulated metabolic profile for PA methods. PA should be able to detect the known disrupted pathway among the significantly enriched pathways for that profile. Results Through network-level statistics, visualisation, and graph-based metrics, we show that even when a given pathway is completely blocked, it may not be significantly enriched when using PA methods with its corresponding simulated metabolic profile. This can be due to various reasons such as the chosen PA method, the initial pathway set definition, or the network’s inherent structure. Conclusion This work highlights how some metabolomics data may not be suited to typical PA methods, and serves as a benchmark for analysing, improving and potentially developing new PA tools
HLA Class Ib and MICA/MICB Expression in Human Tissues and Cell Types: Reshuffling Immune Players
No full textInternational audienceAbnormal expression of HLA class Ib, MICA and MICB molecules is associated with the evolution of pathological conditions and clinical settings. Here, we use RNA‐sequencing data from two publicly‐available projects, from different human organs and tissues and at single‐cell level, to present their transcriptional expression throughout the human body, in comparison to that of HLA class Ia, HLA class II, their costimulatory molecules, and the main HLA transcription factors. Our analyses for 21 target genes reveal that median gene expression differs by orders of magnitude and that the classical/non‐classical HLA distinction is not absolute for overall expression. Sixteen of the 21 target genes show correlated expressions, although careful analyses of individual expression patterns in tissues and organs highlight specificities. Tissue and organ expression patterns reveal that the lymphoid organs, lungs, and gastrointestinal tract organs display the highest expression of the HLA and HLA‐related genes. At single‐cell level, adipocytes, endothelial cells, and immune cells all have unexpectedly close expression patterns. The expression pattern of the 21 target genes in non‐immune organs, such as the lung or colon, and in non‐immune cells like adipocytes, questions the role of these organs and cell types in immune homeostasis and suggests additional, non‐immune functions of these molecules. The lack of impact of the HLA transcription factors studied here on HLA regulation in non‐immune tissues also supports a role for additional HLA transcription factors in these tissues. Finally, classical/non‐classical HLA classification based on molecule structure and genetic polymorphism does not seem to extend to their expression
Familiarisation avec un nouvel automate d’hématologie, le ProCyte One (Idexx) chez le chien et le chat
No full textThis work aimed to produce eight clinical cases intended for veterinary practitioners, highlighting the specific features of the ProCyte One (Idexx). Blood samples from selected cats and dogs were chosen for their clinical relevance and were first analyzed using the XN-V (Sysmex) or ProCyte Dx (Idexx) analyzers, then subsequently analyzed with the ProCyte One. A blood smear was systematically performed to allow comparison of the results with those obtained from the analyzers during the preparation of the clinical cases.Ce travail avait pour objectif de réaliser huit cas cliniques, à destination des vétérinaires praticiens, illustrant les particularités du ProCyte One (Idexx). Les spécimens sanguins des chats et des chiens retenus ont été sélectionnés pour leur intérêt et après analyses par l’automate XN-V (Sysmex) ou le ProCyte Dx (Idexx), avant d’être analysés avec le ProCyte One. Un frottis sanguin a systématiquement été réalisé et a permis de comparer les résultats à ceux des analyseurs lors de la rédaction des cas cliniques
Perception de la restriction alimentaire et bien-être du veau laitier : une approche expérimentale par le conditionnement
No full textDairy calves are typically fed restricted amounts of milk. Although feed restriction affects observed behaviours and physiology, the perception calves remains poorly understood. After reviewing existing knowledge about the effects of milk restriction on calves’ welfare, we used a conditioned place preference experiment to explore how calves perceive feed restriction. The results do not allow us to draw any conclusions, but some findings are encouraging and invite further research in this areLes veaux laitiers sont couramment restreints en quantité de lait. Si cette restriction a des conséquences comportementales et physiologiques, sa perception par les veaux reste mal comprise. Après avoir fait une revue des connaissances des conséquences de la restriction alimentaire sur le bien-être du veau, nous avons réalisé des expériences de préférence de lieu conditionnée afin d’explorer la perception de la restriction alimentaire par les veaux. Ces expériences ne nous ont pas permis de tirer de conclusions claires même si des résultats encourageants nous invitent à continuer les recherches à ce sujet
A review of the regulation of plastics used in agriculture and for food to inform public policies and support the transition towards sustainable agrifood food systems
No full textInternational audienceA review of the regulation of plastics used in agriculture and for food to inform public policies and support the transition towards sustainable agrifood food systems
Preparedness, prevention and control related to zoonotic avian influenza
No full textAbstract A risk assessment framework was developed to evaluate the zoonotic potential of avian influenza (AI), focusing on virus mutations linked to phenotypic traits related to mammalian adaptation identified in the literature. Virus sequences were screened for the presence of these mutations and their geographical, temporal and subtype‐specific trends. Spillover events to mammals (including humans) and human seroprevalence studies were also reviewed. Thirty‐four mutations associated with five phenotypic traits (increased receptor specificity, haemagglutinin stability, neuraminidase specificity, enhanced polymerase activity and evasion of innate immunity) were shortlisted. AI viruses (AIVs) carrying multiple adaptive mutations and traits belonged to both low and highly pathogenic subtypes, mainly to A(H9N2), A(H7N9), A(H5N6) and A(H3N8), were sporadic and primarily detected in Asia. In the EU/EEA, H5Nx viruses of clade 2.3.4.4b, which have increased opportunities for evolution due to widespread circulation in birds and occasional cases/outbreaks in mammals, have acquired the highest number of zoonotic traits. Adaptive traits, such as enhanced polymerase activity and immune evasion, were frequently acquired, while receptor‐specific mutations remained rare. Globally, human cases remain rare, with the majority overall due to A(H5N1), A(H5N6), A(H7N9) and A(H9N2) that are among the subtypes that tend to have a higher number of adaptive traits. The main drivers of mammalian adaptation include virus and host characteristics, and external factors increasing AIV exposure of mammals and humans to wild and domestic birds (e.g. human activities and ecological factors). Comprehensive surveillance of AIVs targeting adaptive mutations with whole genome sequencing in animals and humans is essential for early detection of zoonotic AIVs and efficient implementation of control measures. All preparedness, preventive and control measures must be implemented under a One Health framework and tailored to the setting and the epidemiological situation; in particular, enhanced monitoring, biosecurity, genomic surveillance and global collaboration are critical for mitigating the zoonotic risks of AIV