HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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The future of systems genetics in farm animal sciences, a route out of the data jungle
No full textInternational audienceFarm animal species are under intense selection on relatively small population sizes. Genetic and genomic selection has provided remarkable genetic gains in the last century. Nevertheless, current methods aiming to link genome to phenome in such populations remain limited, notably due to the difficulty to identify causal variants for complextraits. The diversity of species as well as breeds in livestock has diluted the number of genomic datasets available for each genome as compared to model organisms or human diseases. In this article we propose a systems genetics approach as an opportunity to go beyond current limits and find a way out of the data jungle, taking advantage ofnovel computational development allowing integration of omics datasets from different analyses across species. A major challenge is that systems genetics requires careful but efficient data and metadata management, as well as rigorous statistical strategies on which approach to use. Here, we highlight examples of the broad contribution systems genetics can bring to farm animal sciences, particularly across species, notably in the genome-to-phenome field within the larger scope of agricultural challenges including adaptation to environmental changes and animal welfare
Le rôle de l’environnement dans la transmission de l’antibiorésistance via la chaîne alimentaire
No full textAntimicrobial resistance is a major public health challenge. This thesis investigates the role of the environment in its dissemination through the food chain. The data show that selection pressures linked to human and veterinary uses enrich an environmental “resistome” that is widely present in soils and waters. These environments act as reservoirs where resistant genes and bacteria persist, circulate, and are transmitted. By contaminating water, as well as plant, animal, and aquaculture productions from the primary production stage, they contribute to the silent dissemination of antimicrobial resistance up to the consumer. The food chain thus emerges as a critical interface connecting the environment and human health. This work demonstrates that the environment is not a passive compartment but a structuring actor in the dissemination process, and must therefore be fully integrated into surveillance and prevention strategies within a One Health framework.L’ antibiorésistance est un défi majeur de santé publique. Cette thèse analyse le rôle de l’environnement dans sa dissémination via la chaîne alimentaire. Les données montrent que les pressions de sélection liées aux usages humains et vétérinaires enrichissent un « résistome » environnemental largement présent dans les sols et les eaux. Ces milieux constituent des réservoirs où gènes de résistance et bactéries résistantes persistent, circulent et se transmettent. En contaminant l’eau, les productions végétales, animales et aquacoles dès la production primaire, ils alimentent la dissémination silencieuse de l’antibiorésistance jusqu’au consommateur. La chaîne alimentaire apparaît ainsi comme une interface critique reliant environnement et santé humaine. Ce travail démontre que l’environnement n’est pas un compartiment passif mais un acteur structurant de la dissémination, et doit être pleinement intégré aux stratégies de surveillance et de prévention dans une approche One Health
Étude bibliographique des gliomes canins et actualités thérapeutiques
No full textCanine gliomas are brain tumors associated with a poor prognosis. The limited availability of imaging tools required for diagnosis and the high cost of current treatments restrict the collection of data on their effectiveness. However, the similarities in the development and prevalence of gliomas in both dogs and humans provide an opportunity to design new therapeutic strategies for the treatment of gliomas in veterinary medicine. This study aims to review the different therapeutic strategies for canine gliomas, and to present recent developments intended to mitigate certain adverse effects and increase treatment efficacy. The combination of radiotherapy and chemotherapy following surgical resection currently represents the treatment of choice. The development of new strategies to improve surgical precision, enhance intratumoral drug delivery, and reduce adverse effects in fields such as chemotherapy, immunotherapy, and gene therapy offers promising prospects.Les gliomes canins sont des tumeurs cérébrales de mauvais pronostic. La faible disponibilité du matériel d'imagerie nécessaire au diagnostic et le coût élevé des traitements actuels constituent une limite à l'acquisition de données sur leur efficacité. Cependant, les similitudes concernant le développement et la prévalence des gliomes chez le Chien et l'Homme constituent une opportunité de concevoir de nouvelles stratégies thérapeutiques dans le traitement des gliomes en médecine vétérinaire. Cette étude a pour objectif de recenser les différentes stratégies thérapeutiques des gliomes canins, et de présenter les nouveautés en développement pour pallier certains effets indésirables et augmenter l'efficacité des traitements. L'association de radiothérapie et de chimiothérapie suite à une résection chirurgicale constitue le traitement de choix actuellement. Le développement de nouvelles stratégies permettant d'améliorer la précision chirurgicale, la diffusion intra-tumorale des traitements, et de limiter les effets indésirables dans des domaines comme la chimiothérapie, l'immunothérapie et la thérapie génique présentent des perspectives encourageantes
Transgenerational response to an endocrine disruptor ingestion: phenotypic, genetic and epigenetic analyses in quail
No full textInternational audienceTypical prediction of an offspring’s phenotype usually focuses on the inheritance of parental alleles. However, variations across generations can also result from the transmission of non-genetic factors. Epigenetic marks such as DNA methylation offer a dynamic molecular signature of an individual’s history, as they can carry the memory of the individual’s environmental past, and probably of its ancestors. In this study, we aim to analyze in quail (Coturnix japonica) the impact of an initial supplementation with an endocrine disruptor, the genistein, on the phenotypes and epigenotypes of subsequent generations. To better disentangle the complex interplay between genetic and epigenetic effects, we designed a “mirror” breeding plan to ensure a balanced genetic structure between the group of animals issued from the treated ancestors (called epiline +) and the control group (epiline -). By recording multiple phenotypes (growth, breeding, production, behaviour) across three generations, and performing Reduced Representation Bisulfite Sequencing on blood samples for 1344 individuals, our goal is to investigate the transgenerational inheritance of an environmental effect through changes in DNA methylation profiles. Here we present the preliminary results obtained from phenotypic analysis (analysed with multiple linear regression and GLMM) and RRBS data (analysed with classical tools: BISCUIT, TrimGalore, DSS). Phenotypic analyses have shown multi and transgenerational effects for several phenotypes of interest including body weight. We are now looking to identify methylated patterns linked to phenotypic changes between generations and between groups.Funding: Région Occitanie, INRAE Animal Genetics Division, GEroNIMO (H2020 GA No 101000236)
Outil d'épi-génotypage haut-débit par capture ciblée
No full textInternational audienceAn optimized protocol to detect high-throughput DNA methylation from custom targeted sequences. Protocol Exchange (2023) hal-04214468 Detection of DNA methylation signatures through the lens of genomic imprinting. Sci Rep 14, 1694 (2024) hal-04453257 An optimized protocol to detect high-throughput DNA methylation from custom targeted sequences on 96 samples simultaneously. FEBS OpenBio (en revision)</div
Application des nouvelles approches SS/NTS pour la caractérisation des expositions aux pesticides à l’échelle nationale : le projet Ecophyto II SCREENPEST
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Développement d’une application à destination des propriétaires canins aidant au suivi des besoins du chien
No full textThis thesis is about creating a mobile app for dog owners to make it easier to find and keep track of important information about their dog’s health, food, exercise, and training. The app is meant to support the advice given during vet visits, with tips that match the dog’s lifestyle and needs. It’s divided into several sections: a health tracker with reminders for vaccines and parasite treatments; food tips that cover weight, poisoning risks, and dental care; fun games and activity ideas based on the dog’s age and breed; and info on how dogs communicate and how to help them socialize. The goal is to help owners better understand what their dogs need and to give general health advice without replacing a real vet’s opinion.Cette thèse porte sur la conception d’une application mobile destinée aux propriétaires de chiens, visant à centraliser et faciliter l’accès aux informations essentielles concernant la santé, l’alimentation, l’activité et l’éducation de leur animal. L’application a pour but de compléter les conseils donnés lors des consultations vétérinaires, adaptés en fonction de l’animal et de son mode de vie. Elle se structure en plusieurs modules : suivi de santé avec rappels de vaccination et de traitements antiparasitaires, conseils alimentaires incluant le poids, les risques d’intoxications et l’hygiène bucco-dentaire, idées de jeux et d’activités adaptées à l’âge et à la race du chien, informations sur la communication canine et la sociabilisation. L’enjeu est de sensibiliser et d’éduquer les propriétaires sur les besoins de leurs animaux, ainsi que de prodiguer des conseils portant sur la médecine préventive au sens large sans se substituer à un avis professionnel
NAPALAIR, une recherche interdisciplinaire et participative autour d'un échange écologique inégal
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Évaluation de la mesure de fréquence cardiaque par application mobile chez le chien
No full textHeart rate is defined by the number of heartbeats per minute. It is a fundamental physiological parameter for assessing an animal's cardiac activity and hemodynamic state. Although electrocardiogram is the gold standard for assessing it, this method is not routinely performed in practice due to its lack of practicality. This study aims to compare several heart rate measurement methods: electrocardiography (reference method), the traditional method (auscultation and counting heartbeats over 15 seconds, then multiplying this number by 4), and a mobile application. The results showed significant differences between the reference method and the evaluated methods, preventing strict interchangeability. However, in everyday practice, they remain good approximation tools. No influence of heart rate regularity on measurement accuracy has been demonstrated. In case of doubt, the practitioner is advised to perform an ECG.La fréquence cardiaque correspond au nombre de battements cardiaques par minute. Il s’agit d’un paramètre physiologique fondamental permettant d’évaluer l’activité cardiaque et l’état hémodynamique d’un animal. Bien que le gold standard pour la mesurer soit la réalisation d’un électrocardiogramme, il n’est pas systématiquement réalisé en pratique à cause de son manque de praticité. Cette étude a pour but de comparer plusieurs méthodes de mesures de fréquences cardiaques : l’électrocardiogramme (mesure de référence), la méthode classique (auscultation et compte des battements cardiaques sur 15 secondes, puis multiplication de ce nombre par 4) et via une application mobile. Les résultats ont montré des différences significatives entre la méthode de référence et les méthodes évaluées, empêchant leur interchangeabilité stricte. Cependant, en pratique courante, elles restent des bonnes méthodes d’approximation. Aucune influence de la régularité du rythme cardiaque n’a été mise en évidence quant à la précision des mesures. En cas de doute, il est conseillé au praticien de réaliser un ECG
Symbiotic diversification relies on an ancestral gene network in plants
No full textInternational audienceSymbioses have been fundamental to colonization of terrestrial ecosystems by plants and their evolution. Emergence of the ancient arbuscular mycorrhizal symbiosis was followed by the diversification of alternative intracellular symbioses, such as the ericoid mycorrhizae (ErM). We aimed at understanding how these diversifications occurred. We sequenced the genomes of ErM-forming liverworts, and reconstituted symbiosis under laboratory conditions. We demonstrated the existence of a nutrient-regulated symbiotic state that enables ErM and underlies intracellular colonization of plant tissues. Comparative transcriptomic analyses identified an ancestral gene module associated with intracellular symbiosis beyond ErM. Genetic manipulations in the liverwort Marchantia paleacea, phylogenetics and transactivation assays demonstrated its essential function for intracellular symbiosis. We conclude that plant have maintained, and convergently recruited, an ancestral gene module for intracellular symbioses