HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
Not a member yet
16577 research outputs found
Sort by
Empowering bioinformatics communities with Nextflow and nf-core
No full textInternational audienceStandardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia
Significant improvements in targeted UHPLC-ESI-MS/MS analysis of the reactive aldehydes 4-hydroxy-2(E)-nonenal and 4-hydroxy-2(E)-hexenal and application to rat serum.
No full textInternational audienceThe elevated risk of colorectal cancer (CRC) induced by red or processed meat rich diets is now established. Those haem-iron rich diets induce luminal lipid peroxidation, one of the most recognised hypotheses explaining CRC promotion. Due to their known toxic properties, quantification of reactive aldehydes such as 4-hydroxy-2 (E)-nonenal (HNE) and 4-hydroxy-2(E)-hexenal (HHE) as lipid peroxidation end-products in biological fluids is of upmost importance. Following previous works on faecal waters, an UHPLC-ESI-MS/MS method has been developed and validated for HNE and HHE quantification in rat serum, using deuterated internal standards (ISs). After protein precipitation (PP) and solid phase extraction (SPE), LC-ESI-MS/MS analysis was achieved by MRM. The use of a brominated derivatisation reagent allowed using the bromine isotopes for selective detection of both HNE and HHE based on diagnostic transitions. This new method was validated according to the European Medicines Agency (EMA) guidelines. Our method proved to efficiently determine HNE and HHE serum concentrations with the required sensitivity (nM range) in serum of rats fed diets rich or not in red meat and different fatty acid compositions
Worldwide analysis of microRNA polymorphism variability in domestic goa
No full textInternational audienceMicroRNAs (miRNAs) are a type of small non-coding RNAs involved in the post-transcriptional repression of target mRNA transcripts, and responsible for the fine-tuning of numerous molecular mechanisms regulating cell metabolism. The presence of single nucleotide polymorphisms (SNP) in miRNA genes is known to affect their expression dynamics and binding affinity toward targeted mRNAs, thus potentially modifying gene regulatory networks. Since domestication, goats have spread worldwide adapting to diverse environmental conditions. However, a comprehensive analysis of how evolutionary forces across and within continental regions have influenced the genome-wide distribution of miRNA polymorphisms in domestic goats is still lacking. By using whole-genome sequencing data from 1,059 domestic goats with African, Asian, American and European origins, we have identified SNPs located within and around goat miRNA genes. In doing so, we have found that miRNA SNPs display very low alternative allele frequencies (median alternative allele frequency of 0.38%) and that the distribution of SNPs within and around miRNA genes is uneven. Remarkably, the stem, loop and neighboring regulatory regions of precursor miRNA hairpins show a significantly higher SNP density compared with the miRNA seed, which determines the binding affinity to target mRNAs. This outcome is probably explained by the occurrence of strong purifying selection removing polymorphisms with potential effects on gene regulatory networks linked to miRNA function. Moreover, we have detected a differential segregation of miRNA SNPs across and within continental regions, with an enriched segregation of putatively high impact polymorphisms, i.e., those located in the seed and other biologically relevant regions of miRNA genes, in isolated goat populations with a low census and reduced heterozygosity. Such information could be useful to investigate the phenotypic consequences of miRNA polymorphisms disrupting gene regulatory networks in domestic goats, as well as to assess their potential impact on adaptation and fitness
Putative erythema annulare centrifugum in two Peruvian hairless and one Chinese crested dog
No full textInternational audienceDas Erythema annulare centrifugum (EAC) ist eine entzündliche Hauterkrankung, die beim Menschen durch distinktive ringförmige erythematöse Läsionen charakterisiert wird. Es wurden drei haarlose Hunde untersucht, die klinische und histologische Merkmale aufwiesen, die auf eine EAC hinwiesen. Eine Glukokortikoid Verabreichung per os oder topisch führte zu einer völligen klinischen Abheilung.Erythema annulare centrifugum (EAC) is an inflammatory skin condition characterised in humans by distinctive annular erythematous lesions. Three hairless dogs were examined with clinical and histological features suggestive of EAC. Oral or topical glucocorticoid administration led to complete clinical resolution.El eritema anular centrífugo (EAC) es una afección cutánea inflamatoria que se caracteriza en humanos por lesiones eritematosas anulares distintivas. Se examinaron tres perros sin pelo con características clínicas e histológicas sugestivas de EAC. La administración oral o tópica de glucocorticoides produjo una resolución clínica completa.L' Erythema annulare centrifugum (EAC) est une affection cutanée inflammatoire caractérisée chez l'homme par des lésions érythémateuses annulaires distinctives. Trois chiens sans poils ont été examinés et présentaient des caractéristiques cliniques et histologiques suggérant un EAC. L'administration orale ou topique de glucocorticoïdes a permis une résolution clinique complète.遠心性環状紅斑(EAC)は、人において遠心状に紅斑病変が核だすることを特徴とした炎症性皮ふ疾患お一つである。 遠心性環状紅斑(EAC)は、ヒトでは特徴的な環状紅斑性病変によって特徴づけられる炎症性皮膚疾患である。EACを示唆する臨床的および組織学的特徴を有する3頭のヘアレスドッグを認めた。経口または局所グルココルチコイド投与により、臨床症状は完全に消失した。O eritema anular centrífugo (EAC) é uma doença inflamatória da pele caracterizada por lesões eritematosas anulares distintas em humanos. Três cães sem pelos foram examinados com características clínicas e histológicas sugestivas de EAC. A administração de glicocorticoide oral ou tópico levou à resolução clínica completa
Salpingo-peritonitis in captive African Houbara bustards ( Chlamydotis undulata )
No full textInternational audienceCaptive breeding of endangered species, such as the African Houbara bustard (Chlamydotis undulata) is an essential part of conservation programmes. However, several factors may negatively impact the health and reproductive performance of captive animals, including genital infections. Between 2010 and 2023, a total of 439 cases of salpingo-peritonitis were diagnosed in a flock of African Houbara breeders belonging to a Moroccan conservation project, relying exclusively on artificial insemination and artificial incubation of eggs (annual prevalence from 0.07% to 1.64%). To improve the overall knowledge of reproductive pathology in this avian species, a representative sample of 14 cases registered in 2022 were characterized, combining gross pathology, histopathology, microbiology and molecular biology. Overall, 4/14 bustards died spontaneously and exhibited septicaemic changes, while 10/14 euthanized birds presented signs consistent with chronic salpingo-peritonitis and oviductal impaction. The latter was further confirmed at histopathology and, in eight bustards, was associated with mucosal changes resembling cystic endometrial hyperplasia, a condition commonly reported in mammals and potentially predisposing to secondary bacterial infections. Escherichia coli was isolated from the reproductive tract of 12/14 birds. Molecular characterization of nine selected isolates revealed the presence of several virulence factors associated with avian pathogenic E. coli. The variety of virulence, as well as antimicrobial sensitivity profiles identified, combined with the pathological presentation, suggested the involvement of multiple bacterial strains. Overall, in addition to the presence of specific virulence genes, management and host-related factors should also be considered as important determinants of the pathogenic potential of E. coli in captive African Houbaras.RESEARCH HIGHLIGHTSFirst comprehensive description of salpingo-peritonitis in African Houbaras.First report of cystic oviductal hyperplasia in African Houbaras.Escherichia coli isolated from the reproductive tract of the majority of birds.Several virulence and antimicrobial sensitivity profiles identified
Authors' response: Statistical methodology critique and alternative approaches in H5Nx avian influenza seroprevalence study among French cats
No full textInternational audienc
The bacterial faecal microbiota shifts during the transition period in dairy cows
No full textInternational audienceBackgroundIn dairy cows, the transition period around parturition is a critical period with the highest incidence of infectious and metabolic diseases compared to the rest of the lactation. Over the past few years, several studies have highlighted the central role of the microbiota in health and disease. In mammals, gut microbiota is typically studied by analysing faecal samples. In cattle, most research on the gastrointestinal microbiota has focused on the ruminal microbiota, while the composition and evolution of the faecal microbiota in transitioning dairy cows remain poorly studied. We aimed to describe the composition of the faecal bacterial microbiota in a large number of dairy cows around parturition on commercial farms. Faecal samples were collected three weeks before and one week after calving from a cohort of 411 Holstein dairy cows in their 2nd and 3rd lactations across 25 dairy herds. DNA was extracted from faeces, and the 16S rRNA gene (hypervariable region V3-V4) was sequenced after amplification.ResultsA loss of microbial diversity was observed after calving, with no significant association with the lactation rank. The analysis identified different genera when comparing pre- and post-calving samples, indicating significant changes in the faecal microbiota of dairy cows after calving compared to the dry period, closer to calving. Among the major changes, Verrucomicrobiota were less abundant in the two unknown genera from the phylum after calving. In contrast, the proportion of Bifidobacterium was higher after than before calving.ConclusionShifts in faecal microbiota around calving may be attributed to changes in diet composition, feed intake modifications, or physiological changes from the dry period to lactation. However, other factors such as genetic background and health factors may also influence the microbiota composition. This could be further investigated to identify biomarkers for predicting imbalances or identifying maladaptation to the lactation stage
Exploration of different ion excitation modes in tandem mass spectrometry to optimize structural information and identification levels in metabolomics and exposomics
No full textInternational audienceOne of the primary applications of mass spectrometry is to elucidate the molecular structure of compounds by analyzing their fragmentation profiles. This is achieved through tandem mass spectrometry (MS/MS), where specific precursor ions are isolated and subsequently excited using collision-, photon-, or electron-based activation methods. This excitation induces unimolecular dissociation, producing characteristic fragment ions1.Despite the valuable structural insights provided by MS/MS, challenges remain in precisely identifying specific classes of compounds within endogenous (metabolome) and exogenous (exposome) domains. These limitations hinder the generation of comprehensive spectral data, which is crucial for the accurate interpretation of complex "omics" datasets. This project aims to evaluate the potential of various fragmentation modes complementary to the classical collision induced dissociation (CID) method, such as Higher-energy Collision Dissociation (HCD), Ultraviolet Photodissociation (UVPD), and Electron-induced dissociation (EID), in enriching structural information for compounds whose fragmentation using CID yields limited insights. For that, a set of compounds including pesticides, toxins, persistent organic pollutants (POPs), lipids and others was selected to assess richness structural information and feed spectral databases dedicated to metabolomics2 and exposomics3.Once excitation strategies validating various MS/MS approaches on complex biological matrices, the project will provide original information for annotation/identification of molecules and metabolites, with new structural information not accessible through conventional methods. Furthermore, the project will also take advantage of in silico approaches for dissociation spectra of unknown molecules using molecular networks. The ability of the excitation methods explored in this project to support this data processing approach will also be assessed.As first results, preliminary data comparing CID, HCD and UVPD on several compounds will be presented to highlight the complementarity of these different excitation modes.References :1.Bayat.P. et al., Mass Spectrometry Reviews, 2020.2.Paulhe. N. et al, Metabolomics, 2022.3.Meijer. J. et al, Environment International, 202
Multidisciplinary Tracking of Highly Pathogenic Avian Influenza A(H5N1) Outbreak in Griffon Vultures, Southern Europe, 2022
No full textInternational audienceSince 2021, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus has affected wild bird populations globally. Griffon vultures (Gyps fulvus), a species hitherto considered unexposed, experienced an HPAI H5N1 outbreak in 2022 in southern Europe, leading to moderate mortality and reduced breeding success. The integration of virological, serologic, phylogenetic, and ecologic data revealed a short yet intense viral circulation and a probable common source of infection. The dissemination across Spain and France was likely caused by frequent interpopulation movements of birds. This integrated overview of the 2022 HPAI outbreak in vultures provides novel insights into the role of large-scale movements of wild birds in the spread of such disease. Understanding the epidemiologic dynamics of HPAI H5N1 in these scavenger species is crucial because the birds play vital roles in ecosystem functioning. Their susceptibility to this virus highlights potential broader ecologic effects of the ongoing outbreaks
Obesity induces phenotypic switching of gastric smooth muscle cells through the activation of the PPARD/PDK4/ANGPTL4 pathway
No full textInternational audienceBackground Clinical research has identified stomach dysmotility as a common feature of obesity. However, the specific mechanisms driving gastric emptying dysfunction in patients with obesity remain largely unknown. In this study, we investigated potential mechanisms by focusing on the homeostasis of gastric smooth muscle. Methods An obese mouse model was established using a high-fat diet (HFD). Immunofluorescence analysis and Western blotting were employed to assess smooth muscle status using stage-specific markers. An in vitro culture model of differentiated human gastric smooth muscle cells (SMCs) was treated with lipids, siRNA-peptide-based nanoparticles and pharmaceutical compounds. Global lipidomic and RNA sequencing analyses were performed. The findings were evaluated in patients with obesity, using gastric samples from individuals who underwent sleeve gastrectomy, to evaluate their clinical relevance. Results The smooth muscle layers in gastric tissue from both mice fed on a HFD as well as patients with obesity exhibited altered differentiation status. Treatment of differentiated human gastric SMCs with lipids phenocopies these alterations and is associated with increased expression of PDK4 and ANGPTL4 . Inhibition of PDK4 or ANGPTL4 upregulation prevents these lipid-induced modifications. PPARD activation stimulates PDK4 and ANGPTL4 upregulation, leading to SMC dedifferentiation. Notably, PDK4 and ANGPTL4 levels correlate with immaturity and alteration of gastric smooth muscle in patients with obesity. Conclusions Obesity triggers a phenotypic change in gastric SMCs, driven by the activation of the PPARD/PDK4/ANGPTL4 pathway. These mechanistic insights offer potential biomarkers for diagnosing stomach dysmotility in patients with obesity