Biology subjects

Vergne, J.

Publications and source records attributed to Vergne, J..

3 recordsLinked to original sources

bioRxiv2026

Adaptive evolution of transcriptome and transcriptomic plasticity in stable and fluctuating environments

Adaptation to new environments often involves multiple genes and can induce substantial changes in biological systems, but the overall consequences of the genetic response to specific environmental pressures remain poorly understood. Here, we investigate the large-scale effects of adaptation to new temperature regimes on the whole transcriptome from experimental evolution carried on the fungus Zymoseptoria tritici. Two distinct strains from the wild were grown in constant cool (17{degrees}C), constant warm (23{degrees}C), and fluctuating temperature environments, for about 250 clonal generations. The expression of > 10,000 genes was estimated by RNA-seq before and after evolution at several temperatures. We observed massive convergent change in both gene expression and gene expression plasticity. Fluctuating environments did not favor plastic gene expression in general, although fluctuating populations did evolve towards the optimal reaction norms. Some of our observations were at odds with common expectations; adaptive mutations were highly pleiotropic, and adaptation to stable temperature conditions did not match gene expression plasticity. We thus showed that the evolution of complex biological systems follow some general patterns which challenge gene-centered or quantitative genetics predictions.

evolutionary biology↗

bioRxiv2024

Perception/action coupling in children with autism: insights from looking time and pupil dilation measurements

The objective of this study was to characterize, through indices extracted from eye-tracking measurements, the spontaneous distinction of videos of daily actions with a variable perception/action coupling, depending on whether, for the same action, the video was presented in the forward reading direction (strong coupling), or in the backward reading direction (weaker coupling). 17 pairs of videos of daily actions performed by adults were viewed by 36 typically developing children and 28 children with ASD aged 7-18 years. During the exposure phase, they watched two videos of the same action (forward and backward) presented successively, before looking at these two videos in competition, in a second visual preference phase. During the exposure phase, all participants paid similar general attention to each of the videos. We found greater pupillary dilation for backward than forward actions in both groups, but significantly less in the ASD group. In the visual preference phase, both groups showed significantly greater looking times for backward actions over forward ones, with no difference between groups. If TD children perceived the kinematics of the backward videos as violating their expectations given the strong perception/action coupling they had already built over that action, on the contrary, the lower increased in pupil dilation found in ASD children could reflect altered perception/action coupling. This study confirms the validity of looking time and pupil dilation as behavioral and physiological markers that could be used in a 10-mn eye-tracking test to explore perception/action coupling in childhood and in ASD. Lay summaryPeople with ASD often have difficulty understanding the actions of others. The fine understanding of actions requires a coupling between the action we observe, and its representation stored in our memory. This process might be challenged in autism. Here we used a 10-mn eye-tracking test to explore perception/action coupling in ASD. Participants were watching videos of daily actions. Looking time and pupil dilation were measured while participants watched videos of daily actions, and were found to be relevant indexes.

neuroscience↗

bioRxiv2023

Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites

Transcriptomic studies have revealed that fungal pathogens of plants activate the expression of numerous biosynthetic gene clusters (BGC) exclusively when in presence of a living host plant. The identification and structural elucidation of the corresponding secondary metabolites remain challenging. Here we adapted a polycistronic vector for efficient, seamless and cost-effective cloning of biosynthetic genes using in vivo assembly (also called transformation-assisted recombination) directly in Escherichia coli followed by heterologous expression in Saccharomyces cerevisiae. Two vectors were generated with different auto-inducible yeast promoters and selection markers. The effectiveness of these vectors was validated with fluorescent proteins. As a proof-of-principle, we applied our approach to the Colletochlorin family of molecules. These polyketide secondary metabolites were known from the phytopathogenic fungus Colletotrichum higginsianum but had never been linked to their biosynthetic genes. Considering the requirement for an halogenase, and by applying comparative genomics, we identified a BGC putatively involved in the biosynthesis of Colletochlorins in C. higginsianum. Following the expression of those genes in S. cerevisiae, we could identify the presence of the precursor Orsellinic acid, Colletochlorins and their non-chlorinated counterparts, the Colletorins. In conclusion, the polycistronic vectors described herein were adapted for the host S. cerevisiae and allowed to link the Colletochlorin compound family to their corresponding biosynthetic genes. This system will now enable the production and purification of infection-specific secondary metabolites of fungal phytopathogens. More widely, this system could be applied to any fungal BGC of interest.

microbiology↗