Biology subjects

Boccara, M.

Publications and source records attributed to Boccara, M..

4 recordsLinked to original sources

bioRxiv2025

Membrane vesicles in freshwater ecosystems: Quantification by flow cytometry and interferometric microscopy

Membrane vesicles (MVs) are produced by cells from all domains of life and could be involved in the horizontal gene transfer (HGT). They were found in some environments as seawater and rivers but technological improvements must be required to found out their roles in the ecosystems. In this work, we developed a method using flow cytometry (FC) after lipid staining dye FM4-64 and compared the results to those obtained with Interferometric Microscopy (IM). The abundance of nanoparticles in different lakes determined by the two methods were in agreement. Moreover, nanoparticles with a high refraction index were particularly abundant suggesting that MVs could be associated with several virus particles or to very dense compounds such as iron oxides.

microbiology↗

bioRxiv2024

Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature

Loss of DNA methylation over transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritance are unknown. Here, we demonstrate at thousands of TE loci across the Arabidopsis thaliana genome, that experimentally-induced hypomethylation can be transmitted transgenerationally and reveal the role of small RNAs derived from related copies in counteracting this transmission. Using data from >700 strains collected worldwide, we uncover natural hypomethylation at hundreds of the same TE loci, often situated near stress-responsive genes. Like their experimental counterparts, most natural epivariants we tested can be inherited without DNA sequence changes and are therefore bona fide epialleles, although genetic factors modulate their recurrence or persistence. Crucially, we demonstrate that TE-mediated epiallelic variation associated with differential gene expression is generally causal and may be target of selection in specific environments, thus establishing its importance in nature.

genomics↗

bioRxiv2022

Label-free virus-antibody interaction monitoring in real-time by common-path interferometry

Viruses can affect all life forms, raising concerns about virus detection and quantification of small nanoparticles. In this paper we use a label-free, full-field, incoherently illuminated common path interferometric method to detect, track, and quantify biotic nanoparticles. The detection consists of amplifying the light scattered by single nanoparticles in the sample solution. Then, the use of single-particle tracking analysis is used to monitor the change in particle diffusive mobility. With this approach, the recognition signature of T5 phages with purified antibodies targeting the major capsid protein is detected in a few minutes. We also tracked the interaction between SPP1 phages and physiological non-purified serum-containing multiples antibodies molecules. The first interactions occur after around one minute, and the recognition signature is detectable after minutes. In addition, we have been able to differentiate two populations of similar size of empty and full (encapsulating DNA) capsids of T5 in a heterogeneous solution demonstrating the robustness of this label-free detection approach. Furthermore, by combining the diffusion coefficient to the number of tracked particles, we were able to estimate the affinity of the virus-antibodies reaction.

biophysics↗

bioRxiv2021

Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential

A genome-wide association study was undertaken to unravel marker-trait associations (MTAs) between SNP markers and yield-related traits. It involved a subset of 421 cacao accessions from the large and diverse collection conserved ex situ at the International Cocoa Genebank Trinidad. An average linkage disequilibrium (r2) of 0.10 at 5.2 Mb was found across several chromosomes. Seventeen significant (P [≤] 8.17 x 10-5 (-log10 (p) = 4.088)) MTAs of interest, which accounted for 5 to 17% of the explained phenotypic variation, were identified using a Mixed Linear Model in TASSEL version 5.2.50. The most significant MTAs identified were related to seed number and seed length on chromosome 7 and seed number on chromosome 1. Other significant MTAs involved seed length to width ratio on chromosomes 3 and 5 and seed length on chromosomes 4 and 9. It was noteworthy that several yield-related traits, viz., seed length, seed length to width ratio and seed number were associated with markers on different chromosomes, indicating their polygenic nature. Approximately 40 candidate genes that encode embryo and seed development, protein synthesis, carbohydrate transport and lipid biosynthesis and transport were identified in this study. A significant association of fruit surface anthocyanin intensity co-localised with MYB-related protein 308 on chromosome 4. Testing of a genomic selection approach revealed good predictive value (GEBV) for economic traits such as seed number (GEBV = 0.611), seed length (0.6199), seed width (0.5435), seed length to width ratio (0.5503), seed/cotyledon mass (0.6014) and ovule number (0.6325). The findings of this study could facilitate genomic selection and marker-assisted breeding of cacao thereby expediting improvement in the yield potential of cacao planting material.

genomics↗