HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Image and sound analysis for poultry health and welfare indicators
No full textThis issue deals with the results of winning projects in 2017 and 2018 from the CASDAR (Compte d'Affectation Spéciale Développement Agricole et Rural) call for projects, ‘Innovation and Partnership’ and ‘Technological Research. These projects are funded by the Ministry of Agriculture and Food.International 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 expectations must go hand in hand with the competitiveness of poultry meat production, which is globalised and highly competitive. The notion of animal health and welfare can be assessed using a variety of methods, and new technologies offer an opportunity to take continuous measurements in real time, without disturbing the animals in their living environment. Image and sound processing enables finer and more frequent analyses than those carried out by humans. These new technologies are helping to improve monitoring and responsiveness to health problems or changes in animal behaviour through predictive analysis. The EBroilerTrack project led by ITAVI has produced promising proofs of concept in imaging and acoustics under controlled broiler rearing conditions. In the field of imaging, image analysis algorithms have been developed to monitor individual broiler chickens on the farm, with the aim of identifying welfare and health indicators for each animal observed. The performance of these algorithms is presented in this article. In the field of acoustics, the work carried out has demonstrated the benefits of using acoustic analysis to monitor the health and well-being of broilers, in the specific case of infectious bronchitis
Use of enzymes to facilitate the recycling and disposal of materials
No full textInternational audienc
L' élevage français : contexte actuel, enjeux et perspectives d’avenir
No full textFrance is one of Europe's leading livestock producers. Therefore, livestock farming is playing a key role, both economically and culturally. In recent years, however, the sector has faced a lot of challenges: difficult weather conditions, health crises, an economic instability, a negative public image, ageing farmers, and a growing rift between farmers and consumers. The latter criticise livestock farming for its impacts on the climate and on the animal welfare. This raises concerns about the future of livestock farming and the place of farmers in society. This paper presents five scenarios, based on bibliographical data, and compares them in the face of future challenges: a massive intensification, an agro-ecological approach, a sustainable industrialisation, a greening of livestock farming based on intensive practices, and finally, a vegan perspective, with no animal exploitation. Three of them seem to offer answers to most of the issues raised.La France est l'une des principales puissances européennes en production animale. L'élevage y joue donc un rôle clé, à la fois économique et culturel. Pourtant, ces dernières années, le secteur est confronté à de nombreux défis : conditions climatiques difficiles, crises sanitaires, instabilité économique, image négative auprès du public, vieillissement des agriculteurs, et une rupture grandissante entre éleveurs et citoyens. Ces derniers reprochent à l'élevage son impact sur le climat et le bien-être animal. Cela soulève des inquiétudes sur l'avenir de l'élevage et la place des éleveurs dans la société. Cet écrit présente cinq scénarios, issus de données bibliographiques, et les confronte face aux enjeux futurs : une intensification massive, une approche agroécologique, une industrialisation durable, un verdissement de l’élevage intensif, et enfin, une perspective végane, sans exploitation animale. Trois d'entre eux offrent des réponses à la majorité des enjeux soulevés
Single cell tracing of Pomc neurons reveals recruitment of ‘Ghost’ subtypes with atypical identity in a mouse model of obesity
No full textInternational audienceThe hypothalamus contains a remarkable diversity of neurons that orchestrate behavioural and metabolic outputs in a highly plastic manner. Neuronal diversity is key to enabling hypothalamic functions and, according to the neuroscience dogma, it is predetermined during embryonic life. Here, by combining lineage tracing of hypothalamic pro-opiomelanocortin (Pomc) neurons with single-cell profiling approaches in adult male mice, we uncovered subpopulations of ‘Ghost’ neurons endowed with atypical molecular and functional identity. Compared to ‘classical’ Pomc neurons, Ghost neurons exhibit negligible Pomc expression and are ‘ invisible’ to available neuroanatomical approaches and promoter-based reporter mice for studying Pomc biology. Ghost neuron numbers augment in diet-induced obese mice, independent of neurogenesis or cell death, but weight loss can reverse this shift. Our work challenges the notion of fixed, developmentally programmed neuronal identities in the mature hypothalamus and highlight the ability of specialised neurons to reversibly adapt their functional identity to adult-onset obesogenic stimuli
L'Altruisme en matière de Données Personnelles de Santé et le Défi du Consentement dans la Recherche Scientifique : Une Articulation Difficile entre les Actes de l'UE
No full textInternational audienceThe paper explores the challenges in implementing data altruism, focusing on personal health data altruism for scientific research purposes. The analysis highlights conceptual gaps and lack of clarity of the Data Governance Act (DGA) provisions and their unclear interplay with the General Data Protection Regulation (GDPR). Ethical considerations regarding the relationship between altruism and solidarity-based systems are discussed, along with legal issues surrounding the scope of data altruism and consent requirements in different scenarios of personal health data altruism for scientific research. The discussion extends to existing optout practices in scientific research and their recognition, pointing out potential drawbacks of an overly restrictive emphasis on consent in the context of data altruism. The conclusion highlights the conceptual and ethical shortcomings of data altruism, advocates for the development of an integrative approach to altruism within health data-sharing organisations encouraging collaboration and recognition of contributors to not-for-profit research in the public interest. Ultimately, the paper supports the development of new approaches to participation in research through dynamic opt-out mechanisms in health systems and emphasises the need for clearer regulatory guidance to unlock the full potential of health data altruism.Cet article explore les défis liés à la mise en œuvre de l'altruisme en matière de données en se concentrant sur les données personnelles de santé et leur réutilisation à des fins de recherche scientifique. L'analyse met en évidence les lacunes conceptuelles et le manque de clarté des dispositions de la loi sur la gouvernance des données (DGA) et les difficultés liées à l'interaction de ses dispositions avec le règlement général sur la protection des données (GDPR). Des considérations éthiques concernant la relation entre l'altruisme et les systèmes fondés sur la solidarité sont examinées, ainsi que des questions juridiques concernant la portée de l'altruisme en matière de données et les exigences en matière de consentement dans différents scénarios d'altruisme à des fins de recherche scientifique. La discussion s'étend aux pratiques actuelles d'opt-out dans la recherche scientifique et à leur reconnaissance, soulignant les inconvénients potentiels d'une approche trop restrictive basée sur le consentement dans le contexte de l'altruisme des données. La conclusion met en évidence les lacunes conceptuelles et éthiques de l'altruisme en matière de données et plaide pour le développement d'une approche intégrée au sein des organisations de partage des données de santé, en encourageant la collaboration et la reconnaissance des contributeurs à la recherche à but non lucratif dans l'intérêt public. Enfin, le document soutient le développement de nouvelles approches de la participation à la recherche par le biais de mécanismes dynamiques d'opt-out à construire dans les systèmes de santé et souligne la nécessité d'une orientation réglementaire plus claire pour libérer tout le potentiel de l'altruisme dans ce secteur
Relationship between vaginal microbiota composition at whelping and neonatal mortality in the dog
No full textInternational audienc
Exposition maternelle à un mélange complexe de toxiques environnementaux durant la folliculogenèse et le développement embryonnaire préimplantatoire : étude des conséquences sur l'ovaire et sur la descendance aux stades embryonnaire et postnatal
No full textXenobiotics, notably endocrine-disrupting chemicals, are an integral part of human exposome nowadays. The last decades have been marked by increased experimental data attesting their deleterious effects on diverse biological functions, including reproduction. However, risk assessment has been based essentially on protocols studying scenarios often not relevant to human reality. Efforts within the scientific community are thus shifting the focus from studies on isolated toxicants at non-physiological doses, but relevant studies remain a minority at the moment. The investigations of this thesis aim to evaluate reproductive effects of a complex and relevant exposure on two generations. They target an exposure during folliculogenesis and preimplantation embryonic development, since these processes are periconceptional windows of vulnerability while fundamentally contributing to the development and the integrity of the reproductive function. To address relevancy, the experimental design is a key element of this work. We studied a mixture comprising eight environmental toxicants (BDE-47, BPS, HCB, -HCH, DDE, PFOA, PFOS et DEHP) that are representative of the childbearing women exposure. Exposure protocol was designed to reproduce, within the model rabbit, circulating levels similar to those encountered in rather highly exposed women. In a first study, we showed that female rabbits (F0) exposed during 17 post-natal weeks presented alterations of terminal folliculogenesis and testosterone levels. Reassuringly these perturbations did not impact ovarian reserve of primordial follicles, ovulation nor the ability to reproduce at an early stage of sexual maturity. In a second study, the experiments targeted the progeny of F0 exposed preconceptionnally and/or during the beginning of preimplantation development. Preimplantation development did not show abnormality despite maternal exposure. Nevertheless, the study of DNA methylation profile at the blastocyst stage reported a global hypomethylation in exposed embryos. The direction and the location of this methylation differential raise the question on the impacts of an ancestral exposure on the future development and health of the progeny, especially considering the importance of embryonic epigenetic reprogramming. The last part of the work showed that F1 individuals did not exhibit abnormal phenotypes. Neonatal survival and development until adult stage was similar in all exposure conditions. Gonadal and gametic parameters measured in adults did not cast doubt on the integrity on males and females reproductive function. These findings were then confirmed with the results of their breeding once sexual maturity was acquired. In conclusion, our work revealed negative effects of the mixture at the molecular levels of ovarian processes without immediate repercussions on female reproductive function. The following experiments on F1 progeny did not highlight altered developmental and reproductive parameters. These results suggest that exposure of the gametes and preimplantation embryo is potentially not the only contributor to the deleterious multigenerational effects of environmental exposures reported in the literature. Lastly, the data recorded routinely to monitor general health of F0 and F1 animals unexpectedly revealed punctual alterations of lipid metabolism thus questioning the impact of the mixture specifically on the metabolic function.Les xénobiotiques, notamment les perturbateurs endocriniens, font aujourd'hui partie intégrante de l'exposome de l'être humain. Les dernières décennies ont été marquées par une augmentation des données attestant leurs effets néfastes sur diverses fonctions biologiques incluant la fonction de reproduction. L'évaluation de ces risques est basée principalement sur des protocoles qui étudient des situations souvent peu pertinentes pour la réalité humaine. Des efforts au sein de la communauté scientifique permettent de s'éloigner des études sur des toxiques isolés à des doses non physiologiques, néanmoins elles restent minoritaires. Les travaux de cette thèse avaient ainsi pour objectif d'évaluer les effets reproducteurs d'une exposition complexe et pertinente sur deux générations. La période d'exposition étant un paramètre important, ces travaux ciblent la folliculogenèse et le développement embryonnaire préimplantatoire. Ces dernières contribuent fondamentalement au développement et à l'intégrité de la fonction de reproduction et constituent des fenêtres péri-conceptionnelles de vulnérabilité. Nous avons étudié un mélange comprenant huit toxiques environnementaux (BDE-47, BPS, HCB, -HCH, DDE, PFOA, PFOS et DEHP) représentatifs de l'exposition de la femme en âge de procréer. Le protocole d'exposition a été construit afin de reproduire chez le modèle lapin des niveaux plasmatiques comparables à ceux mesurés chez les femmes ayant une forte exposition. Dans une première partie, les travaux ont montré que l'exposition de femelles exposées durant 17 semaines a induit des perturbations significatives de la folliculogenèse terminale et la production de testostérone. De manière rassurante, ces altérations n'ont pas mis en péril la réserve ovarienne en follicules primordiaux, ni les capacités à ovuler et à concevoir des lapines à l'âge de jeune adulte. Dans une seconde partie, les travaux ont ciblé la descendance (F1) de femelles exposées pré-conceptionnellement et/ou durant le début du développement préimplantatoire. Le développement préimplantatoire de ces F1 ne présentait pas d'anomalies malgré l'exposition maternelle. En revanche, l'étude de leur profil de méthylation au stade blastocyste rapporte une hypo-méthylation globale. Le sens et la localisation de ce différentiel de méthylation posent la question des répercussions de cette exposition ancestrale sur la santé future de la descendance, étant donné l'importance de cette période de reprogrammation épigénétique. Les derniers travaux sur ces individus F1 n'ont étonnamment pas montré de phénotype inquiétant. La survie néonatale et le développement jusqu'à l'âge adulte se sont révélés similaires chez tous les groupes d'exposition. Aucune altération des paramètres gonadiques et gamétiques mesurés à l'âge adulte n'a posé de doute sur l'intégrité de leur fonction de reproduction et ce constat a été confirmé par leurs mise à la reproduction une fois l'âge adulte atteint. En conclusion, ces travaux ont démontré des effets négatifs ovariens suite à l'exposition directe aux toxiques néanmoins ils n'induisent pas de répercussions immédiates sur la reproduction. Par la suite, l'étude de la descendance des lapines exposées péri-conceptionnellement n'a pas soulevé d'impacts développementaux et reproducteurs. Ces résultats suggèrent que les gamètes exposés et/ou l'embryon exposé ne sont potentiellement pas les seuls contributeurs des effets délétères multigénérationnels rapportés dans la littérature. De manière inattendue, différentes informations recueillies en routine sur la santé générale des individus F0 et F1 ont rapporté des perturbations ponctuelles du métabolisme lipidique, questionnant l'impact du mélange plus spécifiquement sur la fonction métabolique
Metabarcoding, FROGS training - Oct. 2024
No full textMasterThis training session, in webinar, is designed to help you to deal with NGS data of 16S, 18S, ITS, COI, and other DNAs produced with MiSeq/HiSeq from Illumina technologies in the Galaxy workbench. You will discover how to use a Galaxy instance, run bioinformatics analysis on your data (clean reads, clusterize them, do the taxonomic affiliation, etc.) and perform statistics to interpret your results with the FROGS pipeline. With FROGS you can also make functional inference and hypothesize what metabolic functions are present in a microbial community.Biologists interested in microbiota from various environments (intestinal, soil, aquatic, food, etc.) use genetic markers to know their composition and follow their evolution - metabarcoding. FROGS is a software package for accurate, simple and robust processing of metabarcoding sequencing reads. FROGS uses standard methods and tools combined with original and innovative approaches (such as the support of yeast and fungal markers). FROGS offers in addition to the expected outputs (abundance table of the species in the environment and their affiliations), numerous graphs and statistics allowing biologists an enriched support of their analyses. Its use is open to both non-experts and experts thanks to the launch of the tools via the Galaxy platforms or via the command line.Our objective is to make future FROGS users autonomous in the use of the 28 proposed tools and in the interpretation of the results obtained
The copper-based nanopesticide Kocide 3000® worsens development of colitis in mice as a function of sex, and disrupts the intestinal barrier function in an enteroid-derived epithelial cell monolayer model from mouse gut organoids
No full textInternational audienceNanoparticles (NPs) can cross gut barrier, interact with immune cells and alter gut microbiota with health concerns. Kocide 3000® (K3) is a copper (Cu(OH2))-based nanopesticide, but the intestinal effects of Cu-NPs compared to Cu-based conventional (non-nano) pesticide have not received attention. We aim to evaluate in mice the impact of K3 exposure on microbiota-dependent colitis, and the gut barrier tolerance to K3 using an enteroid-derived monolayer (EDM) model and immune cells from mesenteric lymph nodes (MLN) in comparison to Kocide 2000® (K2), a non-nanosized form.Female mice were exposed to a control, K3 or K2-enriched diet from pregnancy to weaning of pups. All doses were adjusted for Cu content, and mice were exposed to 0, 0.25 and 25mg of K3/kg bw/d, or 0.215mg of K2/kg bw/d. Male and female offspring (F1) were fed as their mother until adulthood and colitis was induced by dextran sulfate sodium (DSS; 2% in drinking water) for 7 days, followed by a 5-day recovery, and disease activity was monitored daily. EDM were cultured from intestinal crypt stem cells of naïve mice and exposed for 24h to Cu-adjusted doses of K3 (0.025-25µg/ml) or K2 (0.0215-21.5µg/ml). LDH release was assessed for cytotoxicity, and gene expression of gut barrier homeostasis markers by qPCR. Genotoxicity was studied by 53BP1 and γH2AX immunostaining. MLN cells from naïve mice were stimulated (PMA/ionomycine or anti-CD3/anti-CD28) in the presence of K3 or K2 for 48h, and cytokine levels measured for direct effects of K3 and K2.At 25mg of K3/kg/d (Cu NOAEL), F1 males were more susceptible to DSS-induced colitis, while females were protected. Colitis activity at 0.25mg of K3/kg/d and 0.215mg of K2/kg/d (Cu ADI) was not different from controls. To decipher the K3-related mechanisms in support of the colitis flare in males, the direct impact of K3 on EDM and MLN cells was evaluated. A slight cytotoxicity on EDM was noted at 25µg/mL of K3 only. Neither genotoxic nor oxidative stress effects were reported for K2 and K3 regardless of dose. Exposure of the EDM to K3 resulted in a decrease in the stem cell marker Lgr5, suggesting impaired epithelial renewal, while an increased mucin-producing gene Muc2 expression occurred. Downregulation of the antimicrobial peptide genes S100a8 and (dose-dependently) Reg3γ occurred after K3 exposure, possibly promoting gut dysbiosis. Interestingly, EDM alterations were not reported after K2 treatment, highlighting K3 effects linked to nanoformulation. Finally, no effect in cytokine production by MLN cells was reported whatever the treatment.These data show that long-term exposure to K3 through the diet aggravates colitis in a sex-dependent manner. As the immune cells do not respond to K3, the exacerbation of colitis could be due to Cu-NP-evoked disruption of the gut barrier integrity and its secretory functions. In addition to proper biocidal properties of Cu, this could aggravate the pro-inflammatory dysbiosis in DSS-treated males
Metabolomic & lipidomic information contained in Dried Blood Spot (DBS) vs. serum
No full textInternational audienceDBS (Dried Blood Spot) are used for the screening of neonatal diseases and monitoring adults suffering from certain diseases in clinical context. DBS is a self-sampling device which is less invasive and requires less sample than a blood test. They can be sent by mail to the hospital allowing everyone to get access easily to biological analysis even in remote area or for elderly patients with mobility problems. Their use in new contexts has been widespread: carrying out anti-doping tests, the research of biomarkers of galactosemia or detection of cancer. In this work, we propose to compare quantitative data and exploratory metabolomic data between DSB and serum. For quantitative data, we quantified 6 short-chain fatty acids (SCFA), 20 bile acids, 20 tryptophan intermediates and 8 organic acids from TCA cycle. Two trends emerge: the first one is that the majority of the serum information is found in DBS. The second one is that DBS brings complementary information not found in serum. Indeed, an overlay of the metabolic cards of serum and DBS highlights a wider metabolic coverage for DBS. These results make it possible to envisage the use of DBS in both quantitative and exploratory metabolomic analyses. However, building up a cohort can last several months or years, so it will be necessary to clearly define the impact of storage conditions (temperature, hygrometry and light exposure) as well as its lasting