HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
Not a member yet
16577 research outputs found
Sort by
Thoracic Ultrasonography Findings and Their Association With Respiratory Pathogens in 221 Young Beef Cattle at Fattening Farms: A Cross‐Sectional Study
No full textInternational audienceABSTRACT Background Thoracic ultrasonography (TUS) could improve antibiotic treatment selection in cattle with respiratory diseases. Hypothesis/Objectives Evaluate the association between respiratory pathogens and consolidations on TUS in feedlot cattle, at both individual and group levels. Animals A total of 221 bulls, aged 8.8 months and weighing 322.5 ± 160 kg, from nine farms. Methods Cross‐sectional study including all data from clinical examinations and TUS collected weekly during the first month on feed. Pathogens were assessed by seroconversion (all animals) and qPCR on nasal swabs (sick animals). At the individual level, the association between pathogen detection and TUS consolidation was investigated using univariate logistic regression, and the ability of consolidation size to differentiate bacterial from non‐bacterial pneumonia was assessed using receiver operating characteristic curves. Principal component analysis identified clusters at the group level based on pathogen detection and TUS results. Results At the individual level, bulls infected with multiple pathogens (odds ratio [OR], 8.1; 95% confidence interval [CI], 2.21–29.8) or a single virus (OR, 5.49; 95% CI, 1.42–21.3) were more likely to have consolidations than those not infected. A total consolidation size > 14 cm 2 in the scanned thoracic region differentiated bacterial from non‐bacterial pneumonia with a sensitivity of 47.8% (95% CI, 36.4–83.3) and specificity of 94.1% (95% CI, 60.0–100.0). These results were consistent at the group level; clustering based on bacterial versus non‐bacterial etiology correlated with the number and size of consolidations. Conclusions and Clinical Importance Consolidation size could help differentiate bacterial from non‐bacterial pneumonia, guiding treatment at both individual and group levels
Technical recommendations for analyzing oxylipins by liquid chromatography–mass spectrometry
No full textInternational audienceSeveral oxylipins are potent lipid mediators that regulate diverse aspects of health and disease and whose quantitative analysis by liquid chromatography–mass spectrometry (LC-MS) presents substantial technical challenges. As members of the lipidomics community, we developed technical recommendations to ensure best practices when quantifying oxylipins by LC-MS
RNA-Seq data provide new insights into the molecular regulation of breast muscle glycogen reserves, a key factor in muscle function and meat quality in chickens
No full textInternational audienceResearch is needed to better understand the molecular mechanisms that influence muscle glycogen reserves in chickens due to their critical influence on muscle function and meat quality. In this study, breast muscle RNA sequencing data (RNA-Seq) were used to compare the transcriptomic profile of two original chicken lines divergently selected for breast muscle ultimate pH, which is a proxy for glycogen reserves. Weighted gene co-expression network analysis (WGCNA) of muscle and jejunum RNA-Seq data was also performed to highlight biological processes specifically involved in the gut-muscle dialogue that may contribute to the divergence in glycogen reserves between the two lines. Breast muscle RNA-Seq analysis of 4-week-old birds from the 15th generation of selection, in which glycogen reserves in the pHu-line were twice as high as that in the pHu+ line, revealed 2676 differentially expressed genes (Padj <= 0.05). Functional analysis of the genes overexpressed in the pHu-line highlighted enrichment in processes related to energy production from a wide range of substrates and pathways, as well as to processes involved in development of blood and lymph tissue. Diverse processes were enriched for genes overexpressed in the pHu+ line: muscle development and remodeling, lipid metabolism, immune response and inflammation, which suggested molecular changes much larger than those for carbohydrate metabolism. WGCNA revealed 64 modules of co-expressed genes. One, which contained 30 % genes expressed in the jejunum and 70 % genes expressed in the muscle, was correlated (P <= 0.05) with muscle glycogen reserves and several indicators of intestinal anatomy and health. Functional analysis of it showed an enrichment of processes related to transmission of nerve information and tissue oxygenation that seem to be involved in the gut-muscle dialogue that mediates establishment of breast muscle glycogen reserves. Finally, the study found that transcriptional regulations observed in muscle of the pHu+ line were similar to those in muscle afflicted with "wooden breast", which highlighted a dysfunction of mitochondrial metabolism and suggested several potential gene markers for both conditions
IntronSeeker
No full textFinding and removing introns from RNA-Seq de novoassemblies with IntronSeeke
Straight from the Horse’s Mouth: Timing and Zoogeography of Domesticated Horse Arrivals in Mongolia and China
No full textInternational audienceThe timing, geographical pathways, and earliest uses for horses (Equus caballus) in East Asia have long been a scientific puzzle vigorously debated by scholars with different backgrounds across diverse disciplinary fields. Over the past two decades, a wide range of high-resolution evidence has been presented documenting the multi-regional dispersion of domesticated horses, but questions still abound, especially in the eastern regions of Eurasia. This study provides a rigorous critique of this body of evidence and advances hypotheses as to when and where domesticated horses first arrived in Mongolia and China. We present the earliest ancient DNA evidence for the DOM2 genetic lineage of modern domesticated horses in Mongolia and evaluate a comprehensive dataset of radiocarbon dates for East Asian domesticated horses using a Bayesian statistical approach that is powerful but seldom utilized by archaeologists. Our genetic and chronological evidence demonstrates that horses far to the east in Mongolia, interred in monumental prone burial contexts, were domesticated and contemporaneous with the earliest horses documented in western regions of Mongolia and Xinjiang. These results both complicate and clarify major questions related to the occurrence of domesticated horses within the greater region and help to explain the development of horse culture(s) and knowledge on the eastern steppe and at the Late Shang capital of Yinxu
Pig and quail CpG methylation datasets from short and long read sequencing technologies
No full textInternational audienceCpG methylation, a key epigenetic mark involved in gene regulation, development, and other biological processes, is commonly analyzed using Whole-Genome Bisulfite Sequencing (WGBS). However, bisulfite treatment causes significant DNA degradation. Enzymatic Methyl-seq (EM-seq) offers a short-read alternative that preserves DNA integrity but requires conversion steps, limiting its compatibility with downstream analyses. Third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and PacBio, enable direct detection of DNA modifications without altering the DNA, providing simultaneous genome and epigenome information. This work presents a comprehensive dataset combining long- and short-read sequencing data, including ONT, PacBio, Enzymatic Methyl-seq, and WGBS, for two agronomically relevant species: pig (Sus scrofa) and quail (Coturnix japonica). Data quality evaluation reveals high nucleotide quality scores for PacBio and short reads, robust alignment rates for long reads, and inter-method correlations in CpG methylation calling ranging from 0.76 to 0.99. This dataset is a valuable resource for training methylation callers and represents the first combined methylation dataset for these species, providing an essential benchmark for assessing emerging sequencing technologies
PigOptim : an individual-based model for the assessment of technic, economic and environmental performance (with life cycle assessment) of fattening pigs.
No full textPigOptim is an open-source software developed for scientific research based on simulation of fattening-pig units.It is released under the GNU GPL-3.0 license with additional terms restricting commercial use and requiring citation in scientific publications. This software is a derivative work of the following registered programs:Mogador, registered with the Agence de Protection des Programmes (APP) under: IDDN.FR.001.460024.000.S.C.2022.000.10000EcoAlim, registered with the Agence de Protection des Programmes (APP) under: IDDN.FR.001.010027.000.S.P.2024.000.3010
In Vitro Dermal Absorption of Key Colour Developers in Thermal Paper: A Focus on Bisphenol A, Bisphenol S and Pergafast 201
No full textInternational audienc
Prédiction de l’efficacité digestive dans deux systèmes de production conventionnel et biologique
No full textInternational audienceL’efficacité digestive, composante de l’efficacité alimentaire, est un caractère d’intérêt pour la filière porcine afin de limiter les impacts environnementaux et le coût de l’aliment dans le coût de production (Gilbert et al., 2017). La capacité des porcs à digérer les aliments comme les co-produits de l’alimentation humaine, produits localement, est aussi un enjeu sociétal et d’évolution des systèmes d’élevage. Des développements méthodologiques récents à l’aide de la spectrométrie dans le proche infrarouge (SPIR) ont rendu la mesure de l’efficacitédigestive accessible pour un plus grand nombre d’animaux dans des conditions d’élevage. Une étude précédente en porcs Large White a permis de mettre en évidence une variabilité génétique des coefficients d’utilisation digestive (CUD) suffisante pour envisager une sélection (Déru et al., 2021). Le but de cette étude était de comparer les prédictions de CUD d’animaux élevés dans deux systèmes de production contrastés pour leurs ressources alimentaires, un système avec un aliment conventionnel, et un système en agriculture biologique avec fourrages
Genotype-by-Environment Interactions and Response to Selection for Milk Production Traits in Lacaune Sheep from Greece and France
No full textInternational audienceThe objective of the study was two-fold and is as follows: (i) to investigate genotype-by-environment (G × E) interactions for milk yield and composition in purebred Lacaune sheep reared intensively in Greece and semi-extensively in France, and (ii) to estimate the potential genetic gain of selection based on genetic evaluations jointly calculated in both countries compared to each country separately. A total of 1658 Lacaune ewes from 4 intensive farms in Northern Greece and 4859 Lacaune ewes from 186 semi-extensive farms in Southern France were used. Ewes in the two countries were daughters or granddaughters of the same rams (6 common sires and 11 common grandsires). Individual ewe milk yield was recorded monthly, and milk samples were collected to assess their chemical composition. The total milk yield and milk component content were calculated. Results showed a strong genetic correlation for milk yield (0.86 ± 0.13, p < 0.05) and protein content (0.88 ± 0.12, p < 0.05) between the two countries, suggesting no strong evidence of G × E interaction. In the case of fat content, a moderate correlation was found (0.59 ± 0.21, p < 0.05) indicating some degree of sire re-ranking. Results suggest that a joint genetic evaluation and selection of Lacaune sheep in Greece and France is feasible. Simulations showed that selection across countries is estimated to increase genetic gain up to 68.17% and 0.16% in Greece and France, respectively, as compared to selection within a country