Biology subjects

Arpin, C.

Publications and source records attributed to Arpin, C..

6 recordsLinked to original sources

bioRxiv2026

Responses of dairy cows following a change in housing system and social group: a living lab experiment

To investigate how the disturbances associated with a relocation to a bedded-pack barn, such as a housing system change, a milking system change and a social regrouping, impacts the behavior of lactating dairy cows, 38 cows from a total of 9 tie-stall or free-stall commercial farms were moved to a newly built bedded-pack barn on an enrollment basis, with a social regrouping occurring after 2 weeks. Scan sampling of video data was done to assess behavior expression in the pen, and live data was collected to assess milking reactivity and animal handling procedures. Results indicate that the cows adapted quickly to the relocation to the new housing system as there were no changes in the locations in the pen, the body positions or the behaviors of cows in time between arrival and regrouping. The social regrouping had a bigger impact with a decrease in 16% of the observed time spent lying and an increase of 9.7% of the observed time spent feeding. Cows also adapted quickly to the milking procedures with a rapid decrease in the occurrence of negative social interactions between cows at the parlor, and in needing less human-animal manipulations and less time to be brought to the parlor. The housing system of origin had a slight effect on behaviors with cows from tie-stalls spending 1.7 times more of the observed time lying than free-stall cows, and free-stall cows spending 1.6 times more of the observed time feeding than tie-stall cows. This study provides a better understanding of how dairy cows respond to disturbances and is encouraging for producers that need to make changes to their current housing system as cows were shown to be quickly adaptable to the challenges presented to them. SummaryDairy cows from cubicle systems were shown to adapt quickly after a relocation to a bedded pack barn, the first use of a milking parlor, and a social regrouping. This was supported by limited changes observed in their behaviors after the disturbances, and observed deviations were temporary and short-lived. Animal handling procedures also observed a quick improvement in time with the trips to the milking parlor needing 2x less time and 3.5x fewer physical contacts from handlers after 5 days. These results are encouraging to producers needing to make changes to their barns.

zoology↗

bioRxiv2024

In silico modelling of CD8 T cell immune response links genetic regulation to population dynamics

The CD8 T cell immune response operates at multiple temporal and spatial scales, including all the early complex biochemical and biomechanical processes, up to long term cell population behavior. In order to model this response, we devised a multiscale agent-based approach using Simuscale software. Within each agent (cell) of our model, we introduced a gene regulatory network (GRN) based upon a piecewise deterministic Markov process (PDMP) formalism. Cell fate - differentiation, proliferation, death - was coupled to the state of the GRN through rule-based mechanisms. Cells interact in a 3D computational domain and signal to each other via cell-cell contacts, influencing the GRN behavior. Results show the ability of the model to correctly capture both population behaviour and molecular time-dependent evolution. We examined the impact of several parameters on molecular and population dynamics, and demonstrated the add-on value of using a multiscale approach by showing that a higher degradation rate for the protein controlling cell death induces a later peak in the response.

systems biology↗

bioRxiv2022

CD8 memory precursor cells generation is a continuous process

In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T cells collected during the postinfection expansion phase. We used different tools to reconstruct the developmental trajectory that CD8 T cells followed after activation. Cells that exhibited a memory precursor signature were identified and positioned on this trajectory. We found that memory precursors are generated continuously with increasing numbers being generated over time. Similarly, expression of genes associated with effector functions was also found to be raised in memory precursors at later time points. The ability of cells to enter quiescence to differentiate into memory cells was confirmed by BrdU pulse-chase experiment in vivo. Analysis of cell counts indicates that the vast majority of memory cells are generated at later time points from cells that have extensively divided.

immunology↗

bioRxiv2019

Emergence of B2-ST131-C2 and A-ST617 Escherichia coli clones producing both CTX-M-15- and CTX-M-27 and ST147 NDM-1 positive Klebsiella pneumoniae in the Tunisian community.

CTX-M ESBLs have been increasingly reported from human enterobacteria isolates in Tunisia. NDM-1 carbapenemase was recently reported in isolates from Tunisian Hospitals. During a 2-month period (December 2017 to January 2018), we have collected 23 ESBL-producing Enterobacteriaceae (ESBL-E) from urines of patients hospitalized in three health care facilities and from community, situated in two distinct Tunisian geographical regions. They were divided into 15 Escherichia coli and eight Klebsiella pneumoniae. The aim of this study was to characterize ESBL-E with regard to their {beta}-lactamase content and their epidemiological relationship. The results indicated a high rate (47%) of E. coli producing both CTX-M group-1 and -9. For the first time, we demonstrated the presence of E. coli having concomitantly CTX-M-15 and CTX-M-27 which belong to two sequences types (ST), ie. A-ST617 (2 isolates) and B2-ST131 subclade C2 (2 isolates). All four E. coli isolates carried a multireplicon IncF with an identical allelic combination, F31:A4:B1. This study reports also the first description of K. pneumoniae belonging to the clone ST147 carrying the carbapenemase NDM-1 in the Tunisian community. In conclusion, our data confirms the need for monitoring the resistance to extended-spectrum cephalosporins and to carbapenems among enterobacteria in Tunisia.

microbiology↗

bioRxiv2019

Investigation of Inter-Individual Variability in CD8 T Cell Responses with Nonlinear Mixed Effects Models

To develop vaccines it is mandatory yet challenging to account for inter-individual variability during immune responses. Even in laboratory mice, T cell responses of single individuals exhibit a high heterogeneity that may come from genetic backgrounds, intra-specific processes (e.g. antigen-processing and presentation) and immunization protocols. To account for inter-individual variability in CD8 T cell responses in mice, we propose a dynamical model coupled to a statistical, nonlinear mixed effects model. Average and individual dynamics during a CD8 T cell response are characterized in different immunization contexts (vaccinia virus and tumor). On one hand, we identify biological processes that generate inter-individual variability (activation rate of naive cells, the mortality rate of effector cells, and dynamics of the immunogen). On the other hand, introducing categorical covariates to analyze two different immunization regimens, we highlight the steps of the response impacted by immunogens (priming, differentiation of naive cells, expansion of effector cells and generation of memory cells). The robustness of the model is assessed by confrontation to new experimental data. Our approach allows to investigate immune responses in various immunization contexts, when measurements are scarce or missing, and contributes to a better understanding of inter-individual variability in CD8 T cell immune responses.

immunology↗

bioRxiv2018

Model-based assessment of the Role of Uneven Partitioning of Molecular Content on Heterogeneity and Regulation of Differentiation in CD8 T-cell Immune Responses

Activation of naive CD8 T-cells can lead to the generation of multiple effector and memory subsets. Multiple parameters associated with activation conditions are involved in generating this diversity that is associated with heterogeneous molecular contents of activated cells. Naive cell polarisation upon antigenic stimulation and the asymmetric division that results are known to be a major source of heterogeneity and cell fate regulation. The consequences of stochastic uneven partitioning of molecular content upon subsequent divisions remain unclear. Here we aim at studying the impact of uneven partitioning on molecular-content heterogeneity and then on the immune response dynamics at the cellular level. To do so, we introduce a multiscale mathematical model of the CD8 T-cell immune response in the lymph node. In the model, cells are described as agents evolving and interacting in a 2D environment while a set of differential equations, embedded in each cell, models the regulation of intra and extracellular proteins involved in cell differentiation. Based on the analysis of in silico data at the single cell level, we show that immune response dynamics can be explained by the molecular-content heterogeneity generated by uneven partitioning at cell division. In particular, uneven partitioning acts as a regulator of cell differentiation and induces the emergence of two coexisting subpopulations of cells exhibiting antagonistic fates. We show that the degree of unevenness of molecular partitioning, along all cell divisions, affects the outcome of the immune response and can promote the generation of memory cells.

immunology↗