Biology subjects

Le Floch, E.

Publications and source records attributed to Le Floch, E..

5 recordsLinked to original sources

bioRxiv2025

Diclofenac stress responses and biotransformation pathways in the marine diatom Phaeodactylum tricornutum

Effects of organic contaminants (OCs) on phytoplankton physiology were extensively studied in the last years while a knowledge gap exists regarding the ability of phytoplankton to transform OCs. Knowledge about biotransformation pathways in these organisms lag far behind that of other microorganisms. A better understanding of biotransformation pathways would help identify biomarkers of contaminants exposure, improve microalgae-based water remediation strategies and help better assess contaminants persistence and trophic transfer in natural aquatic environments. The present study investigated diclofenac (DCF) physiological effects, transcriptional responses and metabolism in the marine diatom Phaeodactylum tricornutum with the aim of getting an insight on detoxifications pathways. P. tricornutum did not result in significant removal capacity of DCF from the exposure medium. Bioconcentration factors varied depending on the exposure concentration (3.9 and 2.7 for 1.5 mg L-1 and 10 mg L-1 DCF respectively) but remained relatively low. DCF resulted in mild physiological effects on P. tricornutum but gene expression analysis indicated that multiple molecular functions and biological processes were altered by DCF exposure. Transcriptomic analysis suggested increased nutrients and energy requirements possibly associated with the contaminant stress and detoxification metabolism. CYP gene expression was not significantly regulated upon DCF exposure but 4-Hydroxy Diclofenac (OH-DCF), a metabolite generally associated with CYP enzymatic activity, was detected. However, CYP gene expression was not significantly regulated upon DCF exposure. Five additional DCF metabolites with high molecular weight were detected. These metabolites were not previously described in the literature and were suggested to be generated via amino acid (or peptides) conjugation. Gene ontology analysis indicated that amino acid and peptide biosynthetic pathways were regulated upon DCF exposure supporting a possible correlation between organic contaminants detoxification responses and amino acid and protein content in phytoplankton cells. Our findings contribute to highlighting the diversity of biotransformation pathways in phytoplankton and provide mechanistic information about contaminants detoxification.

microbiology↗

bioRxiv2023

Copy Number Variants and heritability estimates on UKBiobank data

Copy Number Variants (CNVs) are sometimes used to perform association studies. The aim of this paper was to study the use of CNVs in another context: heritability estimation. We wanted to assess the impact of using CNVs in these estimates, either alone, or in conjunction with Single Nucleotide Polymorphisms (SNPs). Using real SNP and CNV data from UK Biobank, we simulated phenotypes depending either on one or the two type(s) of data. We showed that mixed models, usually used for estimating heritability on SNP data, were also capable of estimating CNV heritability and to properly decipher between CNV and SNP heritabilities when phenotypes depend on both types of data. However CNV heritability estimation becomes more challenging when it is only supported by the few relatively common CNVs. Finally we estimated CNV and SNP heritabilities for two real phenotypes from UK Biobank (height and hypertension) but only hypertension showed a small but non-null CNV heritability of about 1.7%.

genetics↗

bioRxiv2022

Genetic population structure across Brittany and the downstream Loire basin provides new insights on the demographic history of Western Europe

European genetic ancestry originates from three main ancestral populations - Western hunter-gatherers, early European farmers and Yamnaya Eurasian herders - whose edges geographically met in present-day France. Despite its central role to our understanding of how the ancestral populations interacted and gave rise to modern population structure, the population history of France has remained largely understudied. Here, we analysed the high-coverage whole-genome sequences and genome-wide genotype profiles of respectively 856 and 3,234 present-day individuals from the northern half of France, and merged them with publicly available present-day and ancient Europe-wide genotype datasets. We also explored, for the first time, the whole-genome sequences of six mediaeval individuals (300-1100 CE) from Western France to gain insights into the genetic impact of what is commonly known as the Migration Period in Europe. We found extensive fine-scale population structure across Brittany and the downstream Loire basin, emphasising the need for investigating local populations to better understand the distribution of rare and putatively deleterious variants across space. Overall, we observed an increased population differentiation between the northern and southern sides of the river Loire, which are characterised by different proportions of steppe vs. Neolithic-related ancestry. Samples from Western Brittany carry the largest levels of steppe ancestry and show high levels of allele sharing with individuals associated with the Bell Beaker complex, levels that are only comparable with those found in populations lying on the northwestern edges of Europe. Together, our results imply that present-day individuals from Western Brittany retain substantial legacy of the genetic changes that occurred in Northwestern Europe following the arrival of the Bell Beaker people c. 2500 BCE. Such genetic legacy may explain the sharing of disease-related alleles with other present-day populations from Western Britain and Ireland.

genetics↗

bioRxiv2020

Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects.

Neuroimaging-genetics cohorts gather two types of data: brain imaging and genetic data. They allow the discovery of associations between genetic variants and brain imaging features. They are invaluable resources to study the influence of genetics and environment in the brain features variance observed in normal and pathological populations. This study presents a genome wide haplotype analysis for 123 brain sulcus opening value (a measure of sulcal width) across the whole brain that include 16,304 subjects from UK Biobank. Using genetic maps, we defined 119,548 blocks of low recombination rate distributed along the 22 autosomal chromosomes, and analyzed 1,051,316 haplotypes. To test associations between haplotypes and complex traits, we designed three statistical approaches. Two of them use a model that includes all the haplotypes for a sin gle block, while the last approach considers one model by haplotype. All the statistics produced were assessed as rigorously as possible. Thanks to the rich imaging dataset at hand, we used resampling techniques to assess False Positive Rate for each statistical approach in a genome-wide and brain-wide context. The results on real data show that genome-wide haplotype analyses are more sensitive than single-SNP approach and account for local complex Linkage Disequilibrium (LD) structure, which makes genome-wide haplotype analysis an interesting and statistically sound alternative to the single-SNP counterpart.

bioinformatics↗

bioRxiv2019

Tissue-specific expression of young small-scale duplications in human central nervous system regions

BackgroundThe duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional specialization of the adult human central nervous system has not yet been well described. ResultsOur work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue Expression (GTEx) consortium. Interestingly, we found that paralogs were associated with region-specific expression in CNS, suggesting their involvement in the differentiation of these territories. Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs. Indeed, we found that small scale duplicated genes (SSDs) and in particular ySSDs (SSDs younger than the 2 rounds of whole genome duplications) were more CNS region-specific than other paralogs. Next, by studying the two paralogs of ySSD pairs, we observed that when they were region-specific, they tend to be specific to the same region more often than for other paralogs, showing the high co-expression of ySSD pairs. Extension of this analysis to families of paralogs showed that the families with co-expressed gene members (i.e. homogeneous families) were enriched in ySSDs. Furthermore, these homogeneous families tended to be region-specific families, where the majority of their gene members were specifically expressed in the same region. ConclusionsOverall, our study suggests the major involvement of ySSDs in the differentiation of human central nervous system territories. Therefore, we show the relevance of exploring region-specific expression of paralogs at the intra-organ level.

genomics↗