HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Haptic Softness Perception is Invariant to Surface Texture During Pressing
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Nested PCR to optimize rpoB metabarcoding for lowconcentration and host-associated bacterial DNA
No full textInternational audienceHousekeeping genes have proven to be effective taxonomic markers for characterizing bacterial microbiota in short-read amplicon metabarcoding studies. A region of the rpoB gene has been shown to minimize Operational Taxonomic Unit (OTU) overestimation bias with a high degree of accuracy, providing better species-level taxonomic resolution
Effects of dietary supplementation with linseed and Padina pavonica algae extract on semen quality and tissue fatty acid metabolism in rabbit bucks
No full textInternational audienceThis study aimed to evaluate the effects of dietary supplementation with 5% extruded linseed, with or without 0.2% Padina pavonica algae extract, on semen quality and fatty acid metabolism in rabbit bucks. Forty-five New Zealand White rabbit bucks were divided into three groups (15 per diet) and fed for 120 days either a control diet (C), a diet supplemented with 5% linseed (L), or a linseed diet plus 0.2% algae extract (LPP). The semen characteristics, the fatty acid composition of blood, liver, and testis, and estimated indexes of lipid metabolism were assessed. The results showed that the use of linseed in both L and LPP diets had a significant effect on some semen traits (concentration, progressive motility, linearity, amplitude of lateral head displacement, beat cross frequency, acrosome reacted/capacitated sperm) compared to C group. In the tissues analysed, significant effects were observed only in relation to the linseed administration. In conclusion, while linseed positively influenced sperm quality and lipid composition of tissues, the Padina pavonica extract had only a minor effect, limited to hepatic DHA level
The VarGoats 1000 genome project dataset: an alternative approach for WGS data filtering for large-scale analysis of livestock diversity
No full textInternational audienceGoat domestication started ca. 11,000 years ago from the bezoar, Capra aegagrus, in SW Asia. Afterward, domestic goats followed the expansion of human populations out of the Fertile Crescent and spread to Europe, Asia, and Africa in a process which lasted a few thousand years. As a result, many populations became locally adapted to highly contrasting environmental conditions. Hybridization with wild goat species also occurred, playing a role in goats’ evolution through adaptive introgression. These phenomena, combined with the more recent human-mediated selection, shaped the global diversity we observe today. VarGoats is a large-scale collaborative effort to assess goat global genomic variation. Currently, the project has assembled a database of 1327 genomes from 133 local and transboundary domestic goat populations from 4 continents (Europe, Africa, Asia, and Oceania), and 45 genomes from 8 wild goat species. Variant calling followed by quality filtering procedures retained a data set of > 28M biallelic SNPs. Preliminary evaluations showed that commonly adopted variant filtering approaches relying on Minor Allele Frequency (MAF) and Linkage Disequilibrium (LD) may not be suitable to process a data set representative of global diversity across multiple species, due to notable differences in LD structure and in the presence/frequency of variants at the local vs. global scale. Thus, we devised a novel approach based on Minor Allele Count (MAC) and marker spacing (bp-space) specifically designed to avoid biases introduced by standard filtering procedures and adequately represent continental and species-specific variation. The comparison of the effects of MAF+LD pruning versus the newly proposed MAC+bp-space method showed that the latter permits to thin down the starting ca. 28M variants to ca. 13M with only a negligible reduction (1.52%) in bezoar and wild goat diversity. In contrast, the LD-based filtering would have caused a loss of 7.55% of bezoar-specific markers and of 20.59% of wild goat specific variants, potentially hampering downstream analyses
Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite
No full textInternational audienceCyathostomins are a complex of 50 intestinal parasite species infecting horses and wild equids. The massive administration of modern anthelmintic drugs has increased their relative abundance in horse helminth communities and selected drug-resistant isolates worldwide. Cylicocyclus nassatus is the most prevalent and the most abundant species. The tedious identification and isolation of these worms have hampered studies of their biology that remain largely uncharacterised. Here we have leveraged ultra-low input sequencing protocols to build a reference genome for the most prevalent horse strongyle species. Using this resource, we have established the first estimates of its genetic diversity and population structure on a gradient ranging from Ukraine (close to modern horse domestication area) to North America, while capturing a 19th-century snapshot of C. nassatus diversity in Egypt. Our results support a diverse and lowly structured global population. Modern populations displayed lower nucleotide diversity relative to the old North African isolate. We identified the first genetic candidates upon which pyrantel (an anthelmintic drug used in companion animals) selection likely applied in field populations, highlighting previously suspected genes coding for nicotinic acetylcholine receptor subunits, and identifying new candidates showing differential expression in independently evolved Caenorhabditis elegans lines. These results offer a first resource to widen current knowledge on cyathostomin biology, unravel novel aspects of pyrantel resistance mechanisms and provide candidate genes to track pyrantel resistance in the field
A Special Issue of Mass Spectrometry Reviews to Honor Professor Richard B. Cole
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Advancing Skin Ceramide analysis: innovative profiling using SupercriticalFluid Chromatography and High-Resolution Mass Spectrometry (Q-ToF)
No full textInternational audienceLipids play a crucial role in the structure and function of the skin. They are primarily composed of ceramides, fatty acids, and cholesterol. In a health context, a comprehensive characterization of the skin lipid composition is essential, as it varies in relation to skin diseases such as ichthyosis and psoriasis. The improvement of skin sample collection is a growing concern, as current methods are invasive (skin scraping), which has led to the development of new analytical methods, particularly in the extraction of these new matrices (strips, reconstructed epidermis, etc.).However, the diversity of epidermal ceramides, combined with the complexity of their structures and the lack of reference standards, presents a significant analytical challenge. To overcome this hurdle, an innovative profiling of epidermal ceramides has been implemented. This method combines Supercritical Fluid Chromatography (UPC², Waters), which is particularly suitable for nonpolar metabolites, with high-resolution Q-TOF mass spectrometry (Xevo, Waters).This analytical development has enabled the MS characterization and the relative quantification of 15 lipid sub-classes of skin ceramides. This method allows the fast profiling (10 minutes) of 300 molecular species, facilitating high-throughput applications in clinical research. The extraction method has also been improved to be adapted to various matrices (tissues, sebum from strips) while being rapid and suitable for all ceramide subfamilies, despite their differing chemical properties.Furthermore, in the study on autosomal recessive congenital ichthyosis, we have successfully demonstrated the involvement of the PNPLA1 protein (patatin-like phospholipase domain-containing1) through the analysis of epidermal ceramides. This new method has enabled the analysis of reconstructed epidermises and confirmed the role of PNPLA1 in the synthesis of certain epidermal ceramides, highlighting its impact on the skin.This approach offers a new and efficient way to analyze epidermal ceramides, providing valuable insights into skin health and disease managemen
Correcting overestimation of approximate traditional reliabilities with herd-sire interactions when young genomic bulls are used in few herds
No full textInternational audienceDifferential treatment of daughters of the same sire within a herd is modelled as the herd-sire effect. Recent changes in management practices may have led to the extensive use of certain bulls in a limited number of herds. In that case, although the effect can be well accounted for in genetic evaluation models, some approximation methods for reliabilities do not consider it correctly, leading to an overestimation of some sires’ approximated reliabilities. This study assessed the potential bias of these approximated reliabilities due to the herd-sire effect in both simulated and real dairy cattle records. Two existing methods were tested: Misztal–Wiggans, which includes a specific modification for herd-sire, and Tier–Meyer, which does not. We also modified and tested a Tier–Meyer method considering the herd-sire effect.ResultsWe observed that in the presence of the herd-sire effect, reliabilities obtained by approximations were overestimated by the Tier–Meyer method for sires with many daughters in a limited number of herds. This was true even for sires with a large number of daughters. The Misztal–Wiggans method performed correctly. We introduced a modified Tier–Meyer method that weighs the information transmitted by the daughter to the sire as a function of the herd-sire information. As a result, the modified Tier–Meyer method performed well in both simulated and real data. For cows, the inclusion of the herd-sire effect had minimal impact.ConclusionsThis study identified possible overestimation of approximated reliabilities of sires with daughters concentrated in a few herds when there is a herd-sire effect. This bias occurs when the herd-sire effect is not correctly modeled in reliability approximation methods. Methods that specifically accounted for the herd-sire effect produced unbiased reliability estimates
Socio-acoustic co-selection? Vocal encoding of sociability prevails over emotions in sheep bleats
No full textVocalisations of animals are good indicators of their emotions. Temperament is known to influence the regulation and expression of emotions. However, how animal temperament affects their vocalisations and particularly their vocal expressions of emotions remains largely unexplored. Sociability is often measured as the behavioural reactivity to social separation and is a temperament trait intrinsically linked to emotional reactivity. Most social species respond to this challenging situation using contact calls. Here, we investigated whether the acoustic structure of these calls reflect sociability, emotions or both. We used 42 female lambs from two diverging sheep lines selected for high or low sociability. High bleats were recorded both in isolation (social challenge) and before receiving a food treat (non social context) to investigate the link between vocalisations, emotions and heritable sociability. The acoustic features of isolation bleats differed between the lines, but it was not the case for pre-feeding bleats. Surprisingly, the genetic selection index and social behaviour were better predictors of the structure of isolation bleats than the arousal. Last, encoding of individuality in isolation bleats was impaired by the genetic selection. Our findings suggest a socio-acoustic co-selection: selecting for sociable animals affects vocal signatures in calls produced during a social separation
