HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Transmission of DNA methylation: genetic or epigenetic ? A transgenerational case study in quails
No full textInternational audiencePart of the environmental story of individuals lies within their DNA methylation (DNAm). Variations in the environment can trigger changes at the DNAm level and translate to phenotypic variability, even in the progeny of the individuals directly impacted. However, the amount of environmental information transmitted between generations via epigenetic phenomena is hardly quantifiable. The present study analyses DNAm from Reduced Representation Bisulfite Sequencing (RRBS) data for 1267 quails (Coturnix japonica) within 3 successive generations following an environmental modification. Among 112,561 dinucleotides CG (CpG) used, we estimated an average heritability of DNAm of 0.24. After a sub-selection of 40 CpG sites showing high heritability and a significant difference in methylation between two epilines, we conducted methylation Quantitative Trait Loci (metQTL) analysis at those sites in order to shed light on the origin of the high heritability of those sites: genetic or epigenetic
Individual variability in metabolic and hormonal profiles for body reserve dynamics in ewes reared under indoor or outdoor farming system conditions
No full textInternational audienceThe ability of ruminants to cope with energy imbalances through alternating body reserves (BR) mobilization and accretion is a key mechanism to improve animals’ resilience and/or robustness. This study aimed to characterize individual variability in BR dynamics using plasma concentrations of key biomarkers in productive ewes. Non-esterified fatty acids, β-hydroxybutyrate, triiodothyronine, insulin, and body condition score traits were monitored longitudinally throughout the productive cycles. The study included primiparous and multiparous ewes, reared under 2 contrasting farming systems (FS), indoor (173 ewes) and outdoor (234 ewes), belonging to 2 cohorts (Coh17/18). We used functional principal component analysis and unsupervised clustering to capture biomarker variation. The optimal number of clusters was selected using the Bayesian information criterion (BIC), integrated complete-data likelihood (ICL), normalized entropy criterion (NEC), and a minimum cluster size of >5% of ewes. The decrease in BR indicated that BR mobilization occurred from mid-pregnancy (P) until weaning (W), regardless of FS or parity (Par). On the contrary, the increase in BR suggested that BR accretion occurred from W until the next P in both FS. Between 2 and 3 distinct trajectories were identified for each biomarker (BIC < 3214.38; ICL < 3237.82; NEC < 6.450), depending on Par and/or FS. Most trajectories were characterized by transient increases in biomarker concentrations during the BR mobilization period, followed by declines that sometimes continued into the BR accretion phase. Such trajectories differed mainly in biomarker concentrations at different stages and/or the time point when peaks were observed. Greater individual variability in biomarker trajectories was particularly observed around lambing. Maintaining similar trajectories across cycles in major clusters for 53 to 100% of ewes suggested that biomarker trajectories might be repeatable. In addition to individual variability, BR levels, their temporal changes, and litter size contributed to the distribution of ewes across clusters for each of the traits, with low (P ≤ 0.05), moderate (P < 0.01), and high (P < 0.001) levels of significance. These findings highlight the potential of plasma biomarkers for characterizing individual variability in BR variations in ruminants reared in different FS conditions
Early dynamics of the gut microbiota in golden retriever puppies during the first 12 h of life: A preliminary study.
No full textMetExploreViz, online visualisation tool for metabolic networks
No full textInternational audienceThe study of metabolism is now an integral part of research projects aimed at understanding organism responses to biotic and abiotic stress. In this context, Genome-Scale Metabolic Networks (GSMNs) offer a framework for describing the metabolic functioning of living organisms. They represent all biochemical reactions occurring within a cell or tissue, providing a structure for interpreting metabolomic, transcriptomic, and fluxomic data. In particular, GSMNs encode the interplay between metabolites (substrates and products of reactions) which can be measured using metabolomics.The key challenge is to extract knowledge from the thousands of connected elements in GSMNs. To help address these challenges, the bioinformatics community have developed network visualisation tools to aid in data interpretation. The goal of this discipline is to capture the essence of complex datasets and propose the most effective ways to represent them. Beyond GSMNs, representing biological data as networks is a particularly effective approach for visualizing diverse data types in the context of systems biology.Our tool, MetExploreViz (https://metexplore.toulouse.inrae.fr/metexploreviz-ui/), has been developed since 2018 to facilitate the understanding and exploration of metabolic knowledge and related omics data. MetExploreViz is an online tool dedicated to the visualisation of metabolic networks. The most recent release offers technical enhancements and a standalone website. It offers a range of features such as visualisation of metabolic networks as interactive graphs, mapping of omics data directly onto the network, visualisation of flux distributions and application of a hierarchical layout to improve readability and interpretation.These advancements reinforce MetExploreViz as a versatile and accessible solution for researchers seeking to extract meaningful insights from complex metabolic datasets. MetExploreViz is also part of the MetExplore ecosystem, a database dedicated to metabolic networks that provides users with a variety of analysis and interpretation tools, making it a comprehensive platform for metabolomics research
Diagramme de Venn avec R: Tutoriel pour la construction de diagrammes de Venn avec R
No full texthttps://lcauquil.pages-forge.inrae.fr/mon_blog/posts/026_venn_diagram
Etudes pratiques sanitaires préventives et curatives en élevages de poules d'ornement de France métropolitaine
No full textAn epidemiological feature of ornamental (fancy) chicken flocks is that the owners regularly take part in live poultry exhibitions. Little is known about their sanitary practices, given their intermediate status between professional and amateur backyard poultry farming. Moreover, they are not systematically in contact with veterinarians specialized in poultry farming. In this study, we conducted a survey on 60 ornamental chicken owners to describe types of diseases in their flocks, along with prevention and treatment practices, as well as their expectations with regard to their veterinarians. We found that the use of self-medication was high, and that farmers had high expectations of their veterinarians, underlining spaces for improvement in terms of veterinary careLes élevages de poules d’ornement présentent la particularité épidémiologique que les éleveurs.euses participent régulièrement à des expositions de volailles vivantes. On connaît peu leurs pratiques sanitaires du fait de leur situation intermédiaire entre élevage professionnel et basse-cour ; et ils ne sont généralement pas suivi par des vétérinaires spécialisés en aviculture. Dans cette étude, nous avons mené une enquête auprès de 60 éleveurs de poules d’ornement pour décrire les problèmes sanitaires rencontrés, les pratiques de prévention et de traitement et les attentes vis-à-vis de leur prise en charge vétérinaire. Il s’avère que le recours à l’automédication est important et que les attentes vis-à-vis de leurs vétérinaires sont importantes, soulignant ainsi des marges de progrès en termes de prise en charge
Validation des méthodes de prélèvement et de conservation dans l’étude du microbiote intestinal chez le chat
No full textMany studies on the feline intestinal microbiota have been carried out but the results obtained don’t seem to be reproducible. Our goal was to provide guidelines on the sampling and storage methods that can be carried out in the context of a clinical study. The study was carried out on twenty-three healthy adult cats and the effects were studied using principal component and multivariate analyses. The factors that do not seem to generate greater variability than inter-individual variability are the type of litter, the sampling time, the week effect and the storage method when the stools are collected two hours after their emission. The method of collecting fecal samples as well as the storage of stools collected less than fifteen minutes after their emission at +4C° for one week seem to generate greater variability than inter-individual variability.De nombreuses études sur le microbiote intestinal félin ont été réalisées mais les résultats obtenus ne semblent pas être reproductibles. Notre objectif a été de donner des lignes directrices sur les méthodes de prélèvement et de conservation réalisables dans le cadre d’une étude clinique. L’étude s’est réalisée chez vingt-trois chats adultes sains et les effets ont été étudiés à partir d’analyses en composantes principales et multivariées. Les facteurs qui ne semblent pas engendrer une variabilité plus forte que la variabilité interindividuelle sont le type de litière, le délai de prélèvement, l’effet semaine et le mode de conservation lorsque les selles sont récoltées deux heures après leur émission. La méthode de prélèvement d’échantillons fécaux ainsi que la conservation des selles prélevées à moins de quinze minutes après leur émission à +4C° pendant une semaine semblent engendrer une variabilité plus forte que la variabilité interindividuelle
L'attachement de l’homme au chien : étude chez le chien âgé
No full textThe dog’s importance in human society has significantly evolved since domestication and has been totally transformed. As for the owner attachment to his older dog, the central thematic of this tesis. A survey which enrolled 56 olders dogs owner was contucted using the french traduction of the LAPS questionary. Results identify keys factors impacting the quality of this human-senior dog relationship. However, a very large number of variable initially tested do not show statistic significant relation with the bonding mecanism. Therefore, conclusions are limited. The determination of these parameters can be applied in veterinaries clinicals. It can be used to manage relational disordes that may be encountered into the human-dog dyad.La place que détient le chien dans la société humaine a bien évolué depuis l’ère de la domestication et s’est totalement transformée. Il en est de même pour la notion d’attachement du propriétaire envers son chien âgé, sujet central de cette thèse. Une enquête auprès de 56 propriétaires de chiens séniors a été menée en s’appuyant sur l’utilisation de la traduction française du questionnaire LAPS. Cette dernière a permis de mettre en évidence des facteurs clefs de variation modulant la qualité de cette relation homme-chien âgé. Toutefois, un nombre élevé de variables initialement testées ne semblent pas avoir de relation statistiquement significative avec l’attachement, ce qui limite les conclusions qui peuvent en être déduites. La détermination de ces paramètres peut s’appliquer au sein des cabinets vétérinaires. Celle-ci permettra de prendre en charge certaines difficultés relationnelles qui peuvent être rencontrées au sein d’une dyade homme-chien
Reaching the limit: moving beyond antimicrobial use indicators
No full textInternational audienceWe analysed trends in antimicrobial use for conventional broiler chicken production in France based on a dataset of 193,526 sales for 2,120 farms and 33,831 flocks for 2015-2023, including 21,218 antibiotic prescriptions. We found the percentage of flocks prescribed antibiotics dropped from 65% in 2013 to 20% in 2023, plateauing in 2020-2023 where it oscillated between 13% and 23%, and observed an reduction in the use of critical antibiotics. A multiple correspondence analysis and hierarchical clustering on principal components of 1940 antibiotic prescriptions and associated clinical data for 2021-22 produced five clusters of antibiotic prescribing patterns, each characterised by a specific clinical context. These findings indicate that antimicrobial prescribing patterns can be characterised by a combination of clinical indicators in addition to traditional AMU metrics. This calls for a shift to a more sustainable approach to monitoring antimicrobial stewardship, using integrated indicators which consider both AMU and the clinical context
Inférence post hoc pour l'analyse différentielle de données Hi-C
No full textInternational audienceHi-C data provide insights into the three-dimensional organization of thegenome by measuring interactions between genomic positions along the chromatin. Thisthree-dimensional structure plays a crucial role in regulating gene expression. Differentialanalysis aims to identify genomic regions that display significant differences in structurebetween two different biological conditions. Here, we propose to use a post hoc inferencestrategy on results obtained from pixel-level differential analysis. This makes it possible toquantify signal in arbitrary clusters of pixels and thus to identify differential genomic regions.Les données Hi-C fournissent une information sur l'organisation tridimensionnelle du génome à partir de mesures d'interactions entre positions génomiques le long de la chromatine. Cette structure en trois dimensions a un rôle important dans la régulation de l'expression des gènes. L'objectif de l'analyse différentielle est d'identifier, à partir de réplicats obtenus dans deux conditions biologiques différentes, des régions génomiques qui présentent des différences significatives de structure entre les deux conditions. Ici, nous proposons de nous appuyer sur des outils d'inférence post hoc couplés à de l'analyse différentielle restreinte aux pixels. Il est ainsi possible de quantifier la présence d'interactions différentielles dans des sous-ensembles de pixels arbitrairement choisis permettant ainsi d'identifier les régions génomiques les plus différentielles