Biology subjects

Laroche, J.

Publications and source records attributed to Laroche, J..

7 recordsLinked to original sources

bioRxiv2026

New whole slide image analysis method for detection and quantification of hepatocellular vacuolization in European flounder (Platichthys flesus) in multipollutant exposure context

A new whole slide image analysis method was developed for hepatocellular vacuolization detection and quantification in European flounder (Platichthys flesus) liver. Histopathological quantification allows a better understanding of how contaminants and biotic factors might influence lesion pathogenesis in a multipollutant exposure context. One of the main findings is the significant difference in the extent of the pathology between the polluted and the control sites,with P. flesus sampled in the Seine estuary presenting a higher proportion of tissue affected by hepatocellular vacuolation (6.88 sd. 3.01%) compared to fish sampled in the Canche estuary (5.46 sd. 2.86%). This result is coherent with the previous qualitative histological assessment done on the same histological samples, it helps validate the method and brings new insight into the pathology intensity level with the level of contamination on each site. The other main finding is the potential synergetic effect of the pollutant mixture on the pathology. The multipollutant analysis showed a positive mixture effect on the proportion of tissue affected by hepatocellular vacuolation in fish from the Seine estuary, while this effect is not observed in fish sampled in the Canche estuary. This study highlights the benefits of developing novel bio-image analysis methods for environmental research. Histopathological diagnostic quantification allows a better understanding of the potential factors inducing and exacerbating the pathology, as well as the potential mixture effect in a context of multipollutant contamination.

pathology↗

bioRxiv2025

Development and validation of an exome-wide SNP genotyping array for genomic prediction, GWAS and assessment of introgressive hybridization between black and red spruces, and transferability to white and Norway spruces

Introgressive hybridization plays a major role in shaping the evolutionary dynamics and adaptive potential of forest trees. In this study, we developed and validated an exome-wide bispecific SNP genotyping array (Pmr25k) for the closely related species black spruce (Picea mariana) and red spruce (Picea rubens), two ecologically and economically important North American conifers that form a widespread hybrid zone in eastern Canada. Exome capture and sequencing of pooled red spruce samples yielded over 25,000 high-quality SNPs, which were used in conjunction with a previously developed black spruce gene SNP resource of over 97,000 high-quality SNPs, to construct the bispecific genotyping array. The final array comprised 21,573 successfully manufactured SNPs, representing 14,200 distinct gene loci, of which 85% were segregating when both species were considered together. More than 4000 segregating SNPs could also be successfully used and genotyped in each of white spruce (Picea glauca) and Norway spruce (Picea abies), highlighting the conserved nature of DNA attachment sites and presence of homologous SNPs for many gene loci. The Pmr25k array thus provides an efficient and reliable high-throughput genotyping tool to investigate introgression, genetic adaptation at the gene level, and to assist genomic-based prediction for breeding and conservation efforts in boreal spruces.

genomics↗

bioRxiv2025

Comparison of spatio-temporal dynamics and composition in size-fractionated and unfractionated Northwestern Atlantic microbial communities

Size fractionation is a widely applied approach to target specific microbial size ranges, differentiating between larger particle-associated, and smaller free-living microorganisms. To characterize its impact on microbial diversity and its comparability to unfractionated samples, we analyzed 16 weekly ocean samples across five depths during a spring bloom. A universal marker was used to characterize prokaryotes, eukaryotes and chloroplasts comparing single (0.2 {micro}m) or sequential (3 {micro}m and 0.2 {micro}m) filtration. We analyzed unfractionated, fractionated (small and large fractions) and de-fractionated samples. The particle-associated fraction defines the most different community from the other fractions, and combining size fractions (de-fractionating) before or after sequencing produces a community that is most similar to unfractionated samples in terms of composition, and richness dynamics with the exception of very rare taxa. Between 75% and 97% of features are shared, but some discrepancies in relative abundances were unresolved, including for some lineages of free-living Proteobacteria like OM43. The richness trends were consistent, and ANCOM detected at most one significantly different feature between fractionated, and de-fractionated samples, highlighting the similarity in community composition and temporal dynamics between the sets.

molecular biology↗

bioRxiv2023

Contrasting levels of transcriptome-wide SNP diversity and decoupled patterns of molecular and functional adaptive variation in conifers

Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. Their analysis also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of [~]350 Mya between conifers and Angiosperms, we also uncovered a set of 20 key genes presumably under positive selection in both lineages.

plant biology↗

bioRxiv2021

Interpersonal synchronization of movement intermittency

Most animal species group together and coordinate their behavior in quite sophisticated manners for mating, hunting or defense purposes. In humans, coordination at a macroscopic level (the pacing of movements) is evident both in daily life (e.g., walking) and skilled (e.g., music and dance) behaviors. By examining the fine structure of movement, we here show that interpersonal coordination is established also at a microscopic - sub-movement - level. Natural movements appear as marked by recurrent (2-3 Hz) speed breaks, i.e., submovements, that are traditionally considered the result of intermittency in (visuo)motor control. In a series of interpersonal motor coordination tasks, we demonstrate that submovements are not independent between interacting partners but produced in a tight temporal relation that reflects the directionality in the partners informational coupling. These findings unveil a potential core mechanism for behavioral coordination that is based on between-persons synchronization of the intrinsic dynamics of action-perception cycles.

neuroscience↗

bioRxiv2020

The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions

BackgroundManipulative parasites are thought to liberate molecules in their external environment acting as manipulation factors with biological functions implicated in their hosts physiological and behavioural alterations. These manipulation factors are part of a complex mixture called the secretome. While the secretomes of various parasites have been described, there is very little data for a putative manipulative parasite. It is necessary to study the molecular interaction between a manipulative parasite and its host to better understand how such alterations evolve. MethodsHere, we used proteomics to characterize the secretome of a model cestode with a complex life cycle based on trophic transmission. We studied Schistocephalus solidus during the life stage in which behavioural changes take place in its obligatory intermediate fish host, the threespine stickleback (Gasterosteus aculeatus). We produced a novel genome sequence and assembly of S. solidus to improve protein coding gene prediction and annotation for this parasite. We then described the whole worms proteome and its secretome during fish host infection using LC-MS/MS. ResultsA total of 2 290 proteins were detected in the proteome of S. solidus, and 30 additional proteins were detected specifically in the secretome. We found that the secretome contains proteases, proteins with neural and immune functions, as well as proteins involved in cell communication. We detected Receptor-type tyrosine-protein phosphatases, which were reported in other parasitic systems to be manipulation factors. We also detected 12 S. solidus-specific proteins in the secretome that may play important roles in host-parasite interactions. ConclusionsOur results suggest that S. solidus liberates molecules with putative host manipulation functions in the host and that many of them are species specific.

genomics↗

bioRxiv2019

Soybean Haplotype Map (GmHapMap): A Universal Resource for Soybean Translational and Functional Genomics

Here we describe the first worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1,007 Glycine max accessions and yielding 15 million variants. The number of unique haplotypes plateaued within this collection (4.3 million tag SNPs) suggesting extensive coverage of diversity within the cultivated germplasm. We imputed GmHapMap variants onto 21,618 previously genotyped (50K array/210K GBS) accessions with up to 96% success for common alleles. A GWAS performed with imputed data enabled us to identify a causal SNP residing in the NPC1 gene and to demonstrate its role in controlling seed oil content. We identified 405,101 haplotypes for the 55,589 genes and show that such haplotypes can help define alleles. Finally, we predicted 18,031 putative loss-of-function (LOF) mutations in 10,662 genes and illustrate how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for soybean genomics and breeding.

plant biology↗