Biology subjects

Billoir, E.

Publications and source records attributed to Billoir, E..

4 recordsLinked to original sources

bioRxiv2025

Effects of dibutyl phthalate (DBP) on life history traits and population dynamics of Daphnia magna: comparison of two exposure regimes

AbstractPhthalates are chemical products used as additives in the synthesis of plastics to increase their flexibility and resistance. Among the most frequently detected phthalates in the environment is dibutyl phthalate (DBP). Although ubiquitous in freshwater environments at concentrations in the ng/L to {micro}g/L range, studies on the effects of DBP on Daphnia magna have overlooked the potential effects of exposure at low concentrations ({micro}g/L order) and without solvent. Our work focuses on the chronic effects of DBP on life history traits (survival, growth, reproduction) in the freshwater model species, D. magna (Crustacea). Organisms were exposed to two exposure regimes: from the beginning of embryonic development or from the adult stage, at the third brood, when most of the energy investment in growth is complete. The results obtained show that the DBP exposure regime is an essential parameter in the effects on D. magna life history traits. While no significant response was observed in organisms exposed at the adult stage, disturbances to survival, growth and reproduction were observed at concentrations as low as the {micro}g/L range in organisms exposed at the beginning of embryonic development. The results also demonstrated that exposure to a concentration gradient of DBP results in different dose-dependent response typologies, depending on the life history traits measured. For survival, the dose-response relationship was non-monotonic, with greater juvenile mortality at intermediate concentrations (100, 280 and 500 {micro}g/L) than at higher concentrations (1000 and 2000 {micro}g/L). For effects on growth and reproduction, the responses followed classic monotonic dose-response relationships with low sensitivities. At the end of the experiment, the EC10-25d values were 1.01 {micro}g/L for reproduction and 79.22 {micro}g/L for growth. However, when calculated at earlier timepoints, the EC10-4d and the EC10-7d for growth were 0.25 {micro}g/L and 1.16 {micro}g/L. Furthermore, projecting these results to the population level suggests that exposure to DBP from early embryonic development leads to a decrease in growth rate and a change in population structure.

physiology↗

bioRxiv2024

Cluefish: mining the dark matter of transcriptional data series with over-representation analysis enhanced by aggregated biological prior knowledge

Interpreting transcriptomic data presents significant challenges, particularly in non-targeted approaches. While modern functional enrichment methods are well-suited for experimental designs involving two conditions, they are less applicable to data series. In this context, we developed Cluefish, a free and open-source, semi-automated R workflow designed for untargeted, comprehensive biological interpretation of transcriptomic data series. Cluefish applies over-representation analysis on pre-clustered protein-protein interaction networks, using clusters as anchors to identify smaller, more specific biological functions. Innovative features, including cluster merging and recovery of isolated genes through shared biological contexts, enable a more complete exploration of the data. We applied Cluefish to an in-house dataset with zebrafish exposed to a dose-gradient of dibutyl phthalate, and to two published toxicology datasets featuring different organisms. Combined with DRomics, a tool for dose-response analysis--Cluefish identified gene clusters deregulated at low doses and linked to biological functions overlooked by the standard approach. Notably, it revealed that retinoid signalling disruption may be the most sensitive pathway affected by dibutyl phthalate during zebrafish development, potentially leading to morphological changes. The Cluefish workflow aims to provide valuable clues for biological hypothesis generation and experimental validation. It is freely available at https://github.com/ellfran-7/cluefish. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/627334v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@19d9903org.highwire.dtl.DTLVardef@1a8a118org.highwire.dtl.DTLVardef@1e84c3aorg.highwire.dtl.DTLVardef@1e4ac35_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Effects of water nutrient concentrations on stream macroinvertebrate community stoichiometry: a large-scale study

Basal resources generally mirror environmental nutrient concentrations in the elemental composition of their tissue, meaning that nutrient alterations can directly reach consumer level. An increased nutrient content (e.g. phosphorus) in primary and detrital resources under nutrient enriched conditions should favour taxa with a high demand for this nutrient. With the nutrient demand of a taxon being correlated to the elemental composition of its body tissue (e.g. phosphorus content), such above described species shifts likely alter the overall community stoichiometry. However, studies addressing stoichiometry at community level are rare and most often restricted to lacustrine planktonic systems, single streams or limited experimental setups. Relying on a stoichiometric database for >200 taxa and >1300 standardized sampling events of macroinvertebrate assemblages from the French national monitoring programme, we investigated the effect of water phosphorus and nitrogen load on stream macroinvertebrate community stoichiometry. Community stoichiometry was significantly affected by water phosphorus concentration and the effect was strongest at low levels of nitrogen. While we could not confirm our hypothesis of increasing community %P (and decreasing C:P, N:P) with increasing water phosphorus concentrations for the overall community, it clearly followed this pattern for both Insecta and Malacostraca. General differences in the elemental composition among major taxonomic groups and a shift among these groups over the nutrient gradient probably explain the response of community stoichiometry. Our results show that assumptions from Ecological Stoichiometry Theory also hold at the community level, at least for two dominant taxa, and on a large spatial scale, with likely consequences for nutrient cycling and ecosystem function.

ecology↗

bioRxiv2023

DRomics, a workflow to model and make sense of dose-response (multi-)omics data in (eco)toxicology

Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.

bioinformatics↗