Biology subjects

Gauthier, M.

Publications and source records attributed to Gauthier, M..

9 recordsLinked to original sources

bioRxiv2026

Genetic differentiation between two locations along an ocean/river gradient captures the signature of intragenerational selection in the European eel (Anguilla anguilla)

AO_SCPLOWBSTRACTC_SCPLOWMigration events can act as strong selective filters by spatially sorting individuals according to their migration ability, behaviour, and associated functional traits. The European eel, a panmictic and threatened fish, presents various estuarine migration patterns at juvenile stage (glass eel), ranging from sedentarization in brackish/saltwater of the estuary (non-migrant phenotype) to upstream colonisation of freshwater ecosystems (migrant phenotype). We hypothesize that migration propensity is partly genetically determined in glass eel, and that migration-related genotypes are spatially sorted during estuarine migration. To test these hypotheses, we first collected six pools of individuals over three years at two extreme sites along a gradient from ocean to Adour River tidal limit (Ocean vs. Upstream). Secondly, we collected additional glass eels and phenotypically sorted migrant vs. non-migrant individuals using an experimental device mimicking alternating tidal currents, producing two other pools. Whole genome pool sequencing and analysis of these eight pools generated 18.99 106 SNP variants. Controlling for linked selection through a local score approach, we found five best outlier SNPs with a significant genetic differentiation between Ocean vs. Upstream sites (average FST = 0.21) compared to the pangenomic estimate (FST = 0.0086). These five SNPs were all found in the same gene (gpb2), involved in interferon-mediated antiviral immune responses. We also found 28 best outlier SNPs with a significant genetic differentiation between migrant vs. non-migrant phenotypes (average FST = 0.51). They were located in genes mainly involved in neuronal development, cell migration and tissue remodelling, transcriptional regulation, and metabolic or stress-related processes. Our results support that variation in eel migration propensity is partly genetically determined and that, while panmixia maintains high level of genetic diversity, spatial sorting could promote intra-generational genetic divergence between habitats of European eels. However, the absence of shared genes among the best outliers between in-situ and experimental contrasts suggests a complex and context-dependent genetic control of migration.

evolutionary biology↗

bioRxiv2025

Deciphering spatiotemporal patterns of rhizodeposition with a functional-structural root model: RhizoDep

Rhizodeposition, i.e. the release of organic matters by roots, constitutes a significant fraction of the plant carbon (C) budget and plays a key role in soil-plant interactions. However, its spatial and temporal dynamics remain poorly understood. We developed RhizoDep, a new functional-structural root model that simulates 3D root growth, respiration, and rhizodeposition based on C balance and root morphology at the individual root segment level. Our model successfully reproduced the dynamics of belowground C flows observed in a previous pulse-labelling field experiment on spring wheat. Our simulations revealed that root C exudation largely dominated over mucilage secretion and cap cells sloughing in terms of C release. The spatial distribution of exudation rate along the roots was driven by the preferential unloading of sugars to support root elongation and emergence, and was modulated by the formation of apoplastic barriers. Furthermore, our results demonstrated that, for a given C allocation flow to roots, variations in root hairs or lateral root number had minimal effects on rhizodeposition, whereas changes in root tissue density had a significant impact. RhizoDep offers a new opportunity to explore the dynamics of C exchange at the plant-soil interface and to identify traits and environmental conditions that favor rhizodeposition. HighlightUsing the new model RhizoDep, we simulated distinct spatial and temporal patterns of rhizodeposition along the roots of spring wheat over its complete growth cycle, and identified their main drivers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/646173v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@155786borg.highwire.dtl.DTLVardef@54c1b1org.highwire.dtl.DTLVardef@784ca9org.highwire.dtl.DTLVardef@1f0f09d_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Sex-dependent effects of stress on insular cortex-to-nucleus accumbens synaptic plasticity

Stress is an important risk factor for the development of psychiatric disorders and men and women tend to react differently to stress. Sex differences are also observed in many stress-related psychiatric disorders such as depression, anxiety disorders or addiction. Therefore, identifying specific neuroadaptations induced by stress, in males and females, is a necessary step to the understanding of stress-related sex dimorphism in these disorders. Here, we tested the hypotheses that acute stress could affect plasticity in the anterior insular cortex (aIC)-nucleus accumbens core (NAcC) pathway, two structures involved in the stress response, in a sex-dependent manner. Using in vivo extracellular recordings in anesthetized rats, we show that synaptic plasticity in the aIC-NAcC pathway is different between male and female rats. Whereas in males, long-term potentiation and long-term depression were equally induced, in females, there was mostly a long-term potentiation induced. Moreover, stress affected synaptic plasticity in the aIC-NAcC differently in male and female rats. In males, stress induced a loss of long-term-depression that lasted for at least 24h, whereas in females, stress induced less neurons displaying LTP, which did not last. These results demonstrate that integration of aIC information to NAcC is different between males and females. This study provides mechanistic support for differential reactivity to stress between males and females that may relate to stress-related psychiatric disorders and sex dimorphism in these disorders.

neuroscience↗

bioRxiv2022

Encoding social preference by interhemispheric neurons in the Insula

The Insula is a multisensory relay that participates in socio-emotional processing through multiple projections to sensory, cognitive, emotional, and motivational regions. Interestingly, the Insula interhemispheric projection to the contralateral Insula is a strong but understudied projection. Using cutting-edge neuroanatomy, ex vivo and in vivo electrophysiology associated with specific circuit manipulation, we unraveled the nature and role of Insula interhemispheric communication in social and anxiety processing in mice. In this study, we 1) characterized the anatomical and molecular profile of the interhemispheric neurons of the Insula, 2) highlighted that stimulation of this neuronal subpopulation triggers excitation in the Insula interhemispheric circuit 3) uncovered their engagement in social processing. In conclusion, this study demonstrates that interhemispheric neurons of the Insula constitute a unique class of Insula neurons and proposes new meaningful insights into the neuronal mechanisms underlying social behavior.

neuroscience↗

bioRxiv2022

Microfluidic device combining hydrodynamic and dielectrophoretic trapping for the controlled contact between single micro-sized objects and application to adhesion assays

The understanding of cell-cell and cell-matrix interactions via receptor and ligand binding relies on our ability to study the very first events of their contact. Of particular interest is the interaction between a T cell receptor and its cognate peptide-major histocompatibility complex. Indeed analyzing their binding kinetics and cellular avidity in large-scale low-cost and fast cell sorting would largely facilitate the access to cell-based cancer immunotherapies. We thus propose a microfluidic tool able to independently control two types of micro-sized objects, put them in contact for a defined time and probe their adhesion state. The device consists in hydrodynamic traps holding the first type of cells from below against the fluid flow, and a dielectrophoretic system to force the second type of object to remain in contact to the first one. First the device is validated by performing an adhesion frequency assay between fibroblasts and fibronectin coated bead. Then, a study is conducted on the modification of the cellular environment to match the dielectrophoretic technology requirements without modifying the cells viability and interaction functionalities. Finally, we demonstrate the capability of the developed device to put cancer cells and a population of T cells in contact and show the discrimination between specific and non specific interactions based on pairs lifetime.

bioengineering↗

bioRxiv2021

Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis

SO_SCPLOWUMMARYC_SCPLOWState-of-the-art methods for single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis (DEA) often rely on strong distributional assumptions that are difficult to verify in practice. Furthermore, while the increasing complexity of clinical and biological single-cell studies calls for greater tool versatility, the majority of existing methods only tackle the comparison between two conditions. We propose a novel, distribution-free, and flexible approach to DEA for single-cell RNA-seq data. This new method, called ccdf, tests the association of each gene expression with one or many variables of interest (that can be either continuous or discrete), while potentially adjusting for additional covariates. To test such complex hypotheses, ccdf uses a conditional independence test relying on the conditional cumulative distribution function, estimated through multiple regressions. We provide the asymptotic distribution of the ccdf test statistic as well as a permutation test (when the number of observed cells is not sufficiently large). ccdf substantially expands the possibilities for scRNA-seq DEA studies: it obtains good statistical performance in various simulation scenarios considering complex experimental designs (i.e. beyond the two condition comparison), while retaining competitive performance with state-of-the-art methods in a two-condition benchmark. We apply ccdf to a large publicly available scRNA-seq dataset of 84,140 SARS-CoV-2 reactive CD8+ T cells, in order to identify the diffentially expressed genes across 3 groups of COVID-19 severity (mild, hospitalized, and ICU) while accounting for seven different cellular subpopulations.

bioinformatics↗

bioRxiv2019

dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate

RNA-seq studies are growing in size and popularity. We provide evidence that the most commonly used methods for differential expression analysis (DEA) may yield too many false positive results in some situations. We present dearseq, a new method for DEA which controls the FDR without making any assumption about the true distribution of RNA-seq data. We show that dearseq controls the FDR while maintaining strong statistical power compared to the most popular methods. We demonstrate this behavior with mathematical proofs, simulations, and a real data set from a study of Tuberculosis, where our method produces fewer apparent false positives.

bioinformatics↗

bioRxiv2019

Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol

Metabarcoding is often presented as an alternative identification tool to compensate for coarse taxonomic resolution and misidentification encountered with traditional morphological approaches. However, metabarcoding comes with two major impediments which slow down its adoption. First, the picking and destruction of organisms for DNA extraction are time and cost consuming and do not allow organism conservation for further evaluations. Second, current metabarcoding protocols include a PCR enrichment step which induces errors in the estimation of species diversity and relative biomasses. In this study, we first evaluated the capacity of capture enrichment to replace PCR enrichment using controlled freshwater macrozoobenthos mock communities. Then, we tested if DNA extracted from the fixative ethanol (etDNA) of the same mock communities can be used as an alternative to DNA extracted from pools of whole organisms (bulk DNA). We show that capture enrichment provides more reliable and accurate representation of species occurrences and relative biomasses in comparison with PCR enrichment for bulk DNA. While etDNA does not permit to estimate relative biomasses, etDNA and bulk DNA provide equivalent species detection rates. Thanks to its robustness to mismatches, capture enrichment is already an efficient alternative to PCR enrichment for metabarcoding and, if coupled to etDNA, is a time-saver option in studies where presence information only is sufficient.

molecular biology↗

bioRxiv2018

Platypus Induced Pluripotent Stem Cells: the Unique Pluripotency Signature of a Monotreme

Summary StatementThe generation and transcriptome analysis of the first induced pluripotent stem cells from the platypus reveals SOX2 has been a key driver of the expanded pluripotency regulatory network in placental mammals.\n\nABSTRACTThe mechanisms by which pluripotency has evolved remain unclear. To gain insight into the evolution of mammalian pluripotency we have generated induced pluripotent stem cells (piPSCs) from the platypus. Deep sequencing of the piPSC transcriptome revealed that piPSCs robustly express the core eutherian pluripotency factors OCT4, SOX2 and NANOG. Given the more extensive role of SOX3 over SOX2 in avian pluripotency, our data indicate that between 315 million years and 166 million years ago primitive mammals replaced the role of SOX3 in the vertebrate pluripotency network with SOX2. DAX1/NR0B1 is not expressed in piPSCs and an analysis of the platypus DAX1 promoter revealed the absence of a proximal SOX2-binding DNA motif known to be critical for DAX1 expression in eutherian pluripotent stem cells, suggesting that the acquisition of SOX2 responsiveness by DAX1 has facilitated its recruitment into the pluripotency network of eutherians. We further show that the expression ratio of X chromosomes to autosomes (X1-5 X1-5:AA) is approximately equal to 1 indicating that there is no upregulation of X-linked genes and that there is no preference for silencing of maternal or paternal alleles (ie imprinting).

cell biology↗