Biology subjects

Charest, J.

Publications and source records attributed to Charest, J..

2 recordsLinked to original sources

bioRxiv2025

Dark matter of an orchid: metagenome of the microbiome associated with the rhizosphere of Dactylorhiza traunsteineri

Plant microbiota forms complex co-associations with its host, promoting health in natural environments. Root-associated bacteria (RAB) colonize root compartments and can modulate plant functions by producing bioactive compounds as part of their secondary metabolism. We present an in-depth analysis of the rhizosphere-associated microbiome of the endangered marsh orchid Dactylorhiza traunsteineri. Using deep sequencing of 16S rRNA genes, we identified Proteobacteria, Actinobacteria, Myxococcota, Bacteroidota, and Acidobacteria as predominant phyla associated with the rhizosphere of D. traunsteineri. Using deep shotgun metagenomics and de novo assembly, we extracted high-quality metagenome-assembled genomes (MAGs), revealing significant metabolic and biosynthetic potentials of the D. traunsteineris RABs. Our study offers a comprehensive investigation into the microbial community of the D. traunsteineri rhizosphere, highlighting a potential novel source of critical bioactive substances. Our study offers novel insights and a robust platform for future investigations into D. traunsteineris rhizosphere, crucial for understanding plant-microbe interactions and aiding conservation efforts for endangered orchids.

microbiology↗

bioRxiv2024

Comparison of compartmental analytical BOLD fMRI models against Monte Carlo simulations performed over cortical micro-angiograms

BOLD fMRI arises from a physiological and physical cascade of events taking place at the level of the cortical microvasculature which constitutes a medium with complex geometry. Several analytical models of the BOLD contrast have been developed but these have not been compared directly against detailed bottom-up modeling methods. Using a 3D modeling method based on experimentally measured images of mice microvasculature and Monte Carlo simulations, we quantified the accuracy of two analytical models to predict the amplitude of the BOLD response from 1.5T to 7T, for different TE and for both gradient echo and spin echo acquisition protocols. We also showed that accounting for the tridimensional structure of the microvasculature results in more accurate prediction of the BOLD amplitude, even if the values for SO2 were averaged across individual vascular compartments. A secondary finding is that modeling the venous compartment as two individual compartments results in more accurate prediction of the BOLD amplitude compared to standard homogenous venous modeling, arising from the bimodal distribution of venous SO2 across the microvasculature in our data.

biophysics↗