HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Influence du sexe des fœtus adjacents sur le poids de naissance et les caractéristiques placentaires du chiot
No full textThe relation between sex surrondings, birth weight and placental characteristics has been been investigated in dogs yet. In other species (rodents, rabbits), the number of male fetuses surrounding a given fetus influences its physical, physiological, and behavioral traits. To explore the impact of the fetal environment in the canine species, 17 uterus containing 166 Boerboel puppies were mapped during scheduled cesarean sections. The position of the puppies in the uterus, their sex, and their weight were recorded. The placental attachment zone was weighed and measured. This study did not reveal any correlation between the fetal environment and the characteristics of the feto-placental unit: neither the number of male fetuses surrounding a given fetus, the number of male fetuses located between the apex of the uterine horn and a fetus, nor the total number of fetuses located upstream showed any influence.L’influence du sexe des fœtus adjacents sur le poids de naissance et les caractéristiques placentaires dans l’espèce canine n’a jamais encore jamais été étudiée à ce jour. Dans d’autres espèces (rongeurs, lapins) le nombre de fœtus mâles entourant un fœtus donné influence ses caractéristiques physiques, physiologiques et comportementales. Pour explorer l’impact de l’environnement fœtal dans l’espèce canine, 17 utérus, comprenant 166 chiots de race Boerboel, ont été cartographiés lors de césariennes programmées. La position dans l’utérus des chiots, leur sexe et leurs poids ont été identifiés. La zone d’attachement placentaire a été pesée et mesurée. Cette étude n’a pas permis de mettre en évidence de lien entre l’environnement fœtal et les caractéristiques de l’unité foeto-placentaire : ni le nombre de fœtus mâles entourant un fœtus donné, ni le nombre de fœtus mâles situés entre l’apex de la corne et un fœtus, ni le nombre de fœtus totaux situés en amont n’ont montré d’influence
Virus influenza aviaires : facteurs modulant l'évolution vers les formes hautement pathogènes
No full textLow pathogenicity avian influenza viruses (LPAIV) belonging to subtypes H5 and H7 are capable of evolving into high pathogenicity avian influenza viruses (HPAIV), following the acquisition of a polybasic cleavage site in their hemagglutinin (HA). HA can then be cleaved by intracellular and ubiquitous proteases, enabling the virus to replicate systemically. The newly emerged HPAIV must then become the predominant variant in order to be transmitted to new hosts, thus ensuring its successful emergence. During this process, the VIAHP interacts with the population of viral variants, and the interactions could be of different kinds depending on the host. We therefore wanted to see whether the host's innate immune response played a role in variant emergence. The first part of the thesis involved the testing of an innate immunity inhibitor, named ruxolitinib, in ducks infected with a HPAIV. We were able to see that administration of ruxolitinib increased viral replication and also that this molecule effectively inhibited Mx1 expression in ducks. The second part of the thesis focused on coinfections in embryonated eggs and TOCs, in order to mimic the competition between a newly emerged HPAIV and its LPAIV precursor. We used ruxolitinib in these models to see whether modulating the innate immune response had an impact on the emergence of the HP variant. Under our experimental conditions, we did not observe any effect of the innate immune response on the interactions between the variants. The next objective will be to carry out these coinfections in ducks. This work contributes to the understanding of the factors influencing the emergence of HPAIV, whose epizootics have a major impact on public and animal health.Les virus influenza aviaires faiblement pathogènes (VIAFP) appartenant aux sous-types H5 et H7 sont capables d’évoluer en virus influenza aviaires hautement pathogènes (VIAHP), suite à l’obtention d’un site de clivage polybasique au niveau de leur hémagglutinine (HA). HA peut alors être clivée par des protéases intracellulaires et ubiquitaires et le virus est ainsi capable de se répliquer de manière systémique. Le VIAHP nouvellement apparu doit ensuite devenir majoritaire pour être transmis à de nouveaux hôtes, et ainsi son émergence sera réussie. Au cours de ce processus, le VIAHP interagit avec la population de variants viraux, et les interactions pourraient être de différente nature en fonction de l’hôte. Nous avons donc voulu voir si la réponse immunitaire innée de l’hôte jouait un rôle dans l’émergence des variants. La première partie de la thèse a consisté dans l’essai d’un inhibiteur de l’immunité innée, le ruxolitinib, dans des canards infectés par un VIAHP. Nous avons pu voir que l’administration du ruxolitinib permettait d’augmenter la réplication virale et aussi que cette molécule inhibait efficacement l’expression de Mx1 chez les canards. La deuxième partie de la thèse était centrée sur les co-infections dans des œufs embryonnés et des TOC, afin de mimer la compétition entre un VIAHP nouvellement apparu et son précurseur VIAFP. Nous avons utilisé le ruxolitinib dans ces modèles afin de voir si le fait de moduler la réponse immunitaire innée avait un impact sur l’émergence du variant HP. Dans nos conditions expérimentales, nous n’avons pas observé d’effet de la réponse immunitaire innée sur les interactions entre les variants. Le prochain objectif sera de réaliser ces co-infections dans des canards. Ces travaux contribuent à la compréhension des facteurs influençant l’émergence de VIAHP, dont les épizooties ont un impact important sur la santé publique et animale
Évolution de l'épidémiologie des virus de l'influenza aviaire hautement pathogene chez les oiseaux sauvages depuis 2020 : une revue de la litterature
No full textInternational audienceLes virus de l'influenza aviaire hautement pathogène (IAHP), en particulier les virus H5 du clade 2.3.4.4b, ont causé des épizooties dévastatrices chez les oiseaux sauvages et domestiques ainsi que des transmissions significatives aux mammifères, particulièrement depuis 2020. Notre étude cherche à comprendre le rôle des oiseaux sauvages dans la transmission et la propagation des virus IAHP entre 2020 et 2023 à l'échelle mondiale. En analysant la littérature existante et les cas déclarés chez les oiseaux sauvages dans le monde, nous montrons que les populations sauvages ont fortement contribué à la circulation de ces virus. De nombreuses espèces d'oiseaux sauvages sont impactées, à une échelle mondiale et dans certains cas de manière massive. Certaines espèces d'anatidés, notamment des canards et des oies, sont souvent mentionnées pour leur rôle dans la diffusion des virus via des mouvements migratoires. Ce travail souligne l'importance de poursuivre les recherches et la collaboration afin d'atténuer les impacts de ce virus sur la santé animale et humaine
Effective mortality thresholds for reporting suspicion of highly pathogenic avian influenza in mule ducks
No full textInternational audienceEffective mortality thresholds are critical for timely reporting and management of highly pathogenic avian influenza. Using standard modelling techniques, we evaluated the performance of different mortality thresholds in mule duck flocks. Using an eightfold increase of the mortality for two consecutive days compared to the average mortality the previous week led to a perfect classification of all flocks used for validation (12 affected and 18 non-affected flocks). A fixed daily threshold of 0.25% showed a perfect sensitivity and a good specificity (3 false positives/18). Our results fill a knowledge gap and can inform HPAI surveillance policy in non-vaccinated mule ducks
How to Study the Mechanobiology of Intestinal Epithelial Organoids? A Review of Culture Supports, Imaging Techniques, and Analysis Methods
No full textInternational audienceMechanobiology studies how mechanical forces influence biological processes at different scales, both in homeostasis and in pathology. Organoids, 3D structures derived from stem cells, are particularly relevant tools for modeling tissues and organs in vitro. They currently constitute one of the most suitable models for mechanobiology studies. This review provides an overview of existing or applicable approaches to organoids for mechanical studies. We first present the different types of culture supports, including hydrogels and organ‐on‐chip. We then discuss advanced imaging techniques, particularly suitable for studying the physical properties of cells, allowing the visualization of mechanical forces and cellular responses. We also describe the approaches and tools available to observe the organoids by microscopy. Finally, we present analytical methods, including computational models and biophysical measurement approaches, which facilitate the quantification of mechanical interactions. This review aims to provide the most comprehensive overview possible of the methods, instrumentations, and tools available to conduct a mechanobiological study on organoids
Proximal tubule-on-chip as a model for predicting cation transport and drug transporter dynamics
No full textInternational audienceDeciphering the sources of variability in drug responses requires to understand the processes modulating drug pharmacokinetics. However, pharmacological research suffers from poor reproducibility across clinical, animal, and experimental models. Predictivity can be improved by using Organs-on-Chips, which are more physiological, human-oriented, micro-engineered devices that include microfluidics. OoC are particularly relevant at the fundamental and preclinical stages of drug development by providing more accurate assessment of key pharmacokinetic events. We have developed a proximal tubule-on-a-chip model combining commercial microfluidic and chip technologies. Using the RPTEC/TERT1 cell line, we set up a dual-flow system with antiparallel flows to mimic the dynamics of blood and urine. We assessed transporters mRNA expression, cellular polarization and protein expression via immunofluorescence, and monitored the transcellular transport of prototypic xenobiotics by determining their efflux ratios. Our results show that flow exposure significantly modulate mRNA expression of drug membrane transporters. Dynamic conditions also enhance cell polarization, as evidenced by preferential basal and apical expressions of Na + /K + -ATPase, P-gp, OCT2, and MATE1 , as well as the cellular secretory profile. We demonstrated unidirectional transcellular transport of metformin with a higher efflux than influx ratio, inhibited with OCT2 inhibitor, thus confirming the relevance of our proximal tubule-on-a-chip set up for cation transport investigations. Our proximal tubule-on-a-chip can also be used to explore the interactions between transporters, xenobiotics, and endogenous metabolites, possibly involved in the variability of individual drug responses. This study provides additional evidence that OoC can help bridge the gaps between systemic and local pharmacokinetics
Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle
No full textInternational audienceIncreased evidence suggests that cattle are the primary host of Influenza D virus (IDV) and may contribute to respiratory disease in this species. The aim of this study was to detect and characterise IDV in the Swedish cattle population using archived respiratory samples. This retrospective study comprised a collection of a total 1763 samples collected between 1 January 2021 and 30 June 2024. The samples were screened for IDV and other respiratory pathogens using real-time reverse transcription quantitative PCR (rRT-qPCR). Fifty-one IDV-positive samples were identified, with a mean cycle threshold (Ct) value of 27 (range: 15-37). Individual samples with a Ct value of <30 for IDV RNA were further analysed by deep sequencing. Phylogenetic analysis was performed by the maximum likelihood estimation method on the whole IDV genome sequence from 16 samples. The IDV strains collected in 2021 (n = 7) belonged to the D/OK clade, whereas samples from 2023 (n = 4) and 2024 (n = 5) consisted of reassortants between the D/OK and D/660 clades, for the PB2 gene. This study reports the first detection of IDV in Swedish cattle and the circulation of D/OK and reassortant D/OK-D/660 in this population.</div
Escobase and AcR: Escherichia coli databases of genomes and acid resistance genes from isolates from cattle farms
No full textAbstract Escherichia coli is a gram-negative bacterium commonly found in mammals and birds’ intestinal microbiota. It can be easily isolated and has been studied for more than nine decades, making it an ideal model organism. It is mainly commensal but occasionally pathogenic, expressing virulence factors, antibiotic-resistance and acid-resistance genes, which contribute to its ability to persist and colonize diverse environments. Its multi-resistance, combined with the virulence of certain pathotypes (e.g. STEC), poses a recurring threat to public health, as treatment for clinical infections is not always straightforward. The remarkable propensity of E. coli for diversification and genomic variability is often referred to as an open pangenome. This project’s objective was to create the ‘Escobase’ database ( Es cherichia co li data base ), which is comprised exclusively of Escherichia coli isolates from cattle farms, allowing us to generate a reference set of genomes that can be used for comparative genomics on samples from cattle and cattle farms. Using the annotated E. coli genomes, we further built a catalog of predicted proteins that help E. coli survive in low pH environments, often encountered when the bacteria traverse through the intestine. We believe these two databases will be of great help to the community, and we plan to keep improving them and publish updated versions in the future
A comprehensive review and benchmark of differential analysis tools for Hi-C data
No full textInternational audienceMotivation The 3D organization of the genome plays a crucial role in various biological processes. Hi-C technology is widely used to investigate chromosome structures by quantifying 3D proximity between genomic regions. While numerous computational tools exist for detecting differences in Hi-C data between conditions, a comprehensive review and benchmark comparing their effectiveness is lacking. Results This study offers a comprehensive review and benchmark of 10 generic tools for differential analysis of Hi-C matrices at the interaction count level. The benchmark assesses the statistical methods, usability, and performance (in terms of precision and power) of these tools, using both real and simulated Hi-C data. Results reveal a striking variability in performance among the tools, highlighting the substantial impact of preprocessing filters and the difficulty all tools encounter in effectively controlling the false discovery rate across varying resolutions and chromosome sizes. Availability The complete benchmark is available at https://forgemia.inra.fr/scales/replication-chrocodiff using processed data deposited at https://doi.org/10.57745/LR0W9R. Contact [email protected]
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
No full textInternational audienceMore than 50% of families with suspected rare monogenic diseases remain unsolved after whole-genome analysis by short-read sequencing (SRS). Long-read sequencing (LRS) could help bridge this diagnostic gap by capturing variants inaccessible to SRS, facilitating long-range mapping and phasing and providing haplotype-resolved methylation profiling. To evaluate LRS's additional diagnostic yield, we sequenced a rare-disease cohort of 98 samples from 41 families, using nanopore sequencing, achieving per sample-.363 average coverage and 32-kb read N50 from a single flow cell. Our Napu pipeline generated assemblies, phased variants, and methylation calls. LRS covered, on average, coding exons in X280 genes and 5 known Mendelian disease-associated genes that were not covered by SRS. In comparison to SRS, LRS detected additional rare, functionally annotated variants, including structural variants (SVs) and tandem repeats, and completely phased 87% of protein-coding genes. LRS detected additional de novo variants and could be used to distinguish postzygotic mosaic variants from prezygotic de novos. Diagnostic variants were established by LRS in 11 probands, with diverse underlying genetic causes including de novo and compound heterozygous variants, large-scale SVs, and epigenetic modifications. Our study demonstrates LRS's potential to enhance diagnostic yield for rare monogenic diseases, implying utility in future clinical genomics workflows