Biology subjects

Moreau, J.

Publications and source records attributed to Moreau, J..

9 recordsLinked to original sources

bioRxiv2026

Model-based evaluation of Targeted-Antibacterial-Plasmids (TAPs) transfer kinetics and resensitization of pOXA-48 carbapenem-resistant Escherichia coli

Background Targeted-Antibacterial Plasmids (TAPs) are engineered mobile genetic elements that use bacterial conjugation to deliver selective CRISPR/Cas9 antibacterial activity against a specific target strain. Yet, the efficiency of TAPs is typically evaluated at a single time point, whereas the success of TAP-mediated resensitization critically depends on the dynamics of plasmid transfer and the complex interactions between bacterial subpopulations. This is the first study to evaluate the efficiency of a conjugation-based antibacterial approach at the subpopulation level, using an analytical framework analogous to that used for conventional antibiotics. Here, we investigate which process limits resensitization by TAPF-dCas9-OXA48: plasmid delivery, dCas9 activity, or the emergence of refractory and escape populations. Methods We fitted a mechanistic model of five interacting subpopulations (donors, recipients, transconjugants, escapers, and recusants) to 44 longitudinal conjugation experiments and used the fitted model to explore a range of biologically relevant scenarios. Results Using longitudinal conjugation data spanning 24 h, we show that up to 24% of recipients become recusants within 24h, refractory to further conjugation via entry exclusion, while secondary transconjugant emergence stays below 0.01%. Overall resensitization efficiency reaches up to 80%. Conclusion Plasmid transfer, rather than dCas9 repression, therefore appears to be the main bottleneck limiting the efficiency of TAPF-dCas9-OXA48 efficiency. These results identify plasmid delivery as a key engineering target for improving the performance of future TAPs.

bioinformatics↗

bioRxiv2026

High residual pesticide contamination despite contrasted feeding treatments in semi-captive bred grey partridges

Food security is one of the major ongoing global anthropic challenges, driving the intensification of agricultural systems notably through the widespread use of phyto-pharmaceutical products (PPPs). Although effective for maximizing production yields through pest control, PPP contamination is pervasive across the entire agroecosystem, raising concerns about human and non-target species exposure and health effects. Organic farming has therefore been promoted as a sustainable alternative to ensure human food security and mitigate these impacts. Yet, the pathways of PPP non-target organisms contamination are insufficiently understood. While most research has focused on ingestion as the primary route of exposure, increasing evidence suggests more complex contamination dynamics. In this study, we investigated the role of food intake in shaping PPP contamination profiles in semi-captive grey partridges (Perdix perdix). To do so, 80 birds were housed in open aviaries within an agricultural landscape and fed either conventional or organic grains over a five-month period. After drawing their PPP blood profiles at the end of the exposure period, we assessed their loads and compared the pesticide prevalence and abundance between food treatments. We found similar quantity and diversity of PPP residues in blood from conventionally- and organically-fed partridges, with few differences in specific PPP compounds. Overall, these findings suggest that food intake is not necessarily the only source of contamination for non-target organisms, with alternative pathways (e.g., inhalation, dermal contact, soil and water exposure) likely playing a substantial role. Integrating multi-pathway contamination monitoring across trophic levels within a One Health framework would now be essential to better understand and mitigate PPP contamination risks.

ecology↗

bioRxiv2025

Field-based evidence of sperm quality impairment associated with conventional farming in two passerine birds.

The detrimental effects of conventional farming on bird biodiversity are increasingly documented. Despite this, the specific impacts of both organic and conventional farming practices on bird coloration and sperm quality in natural settings remain unexplored. This study aimed to determine whether these farming practices differentially affect body mass, coloration intensity, and sperm quality in passerine birds inhabiting agricultural landscapes. We captured seven passerine species in hedgerows adjacent to fields farmed organically or conventionally, within a 250-meter radius representative of their breeding home ranges. Body mass was measured across all species, and an index of coloration intensity, based on carotenoid (yellow/orange) and melanin (black) pigments, was assessed in four species. Additionally, we evaluated three sperm quality parameters (sperm density, percentage of abnormal sperm, and intra-individual variance of sperm morphology) using fresh sperm samples collected from four species in the field. We hypothesized that birds living near conventional fields would exhibit lower body mass due to reduced food availability. Additionally, we predicted that the more favourable conditions associated with organic farming, such as greater food abundance and lower exposure to pollutants, would benefit birds, leading to enhanced coloration and improved sperm quality. Our results did not reveal any difference in body mass or coloration. The absence of observable effects might be due to several factors: methodological limitations, cross-contamination between habitats or insufficient exposure to farming practices that may hide any potential difference between the two habitats, or the intrinsic adaptive strategies of the species. However, subgroup analysis of three and four species revealed a decrease in sperm density and a higher proportion of abnormal spermatozoa in the Common Whitethroat and Common Nightingale living in conventional farming, respectively. Although our sample size was limited, we believe these findings highlight the potential negative effects of conventional farming on birds.

ecology↗

bioRxiv2025

Optimizing Antimicrobial Susceptibility Testing: Cost and Environmental Benefits of MIC Volume Reduction

The determination of Minimum Inhibitory Concentrations (MICs) is essential for evaluating antimicrobial efficacy, guiding both clinical treatment decisions and drug development. The standard broth microdilution method is widely used but requires significant reagent volumes, which can be limiting when working with novel or expensive antimicrobials. This study assesses the feasibility of reducing assay volumes without compromising MIC accuracy. We compared the MIC values obtained in standard 96-well plates (200 {micro}L) to those in 384-well plates with reduced volumes (30-50 {micro}L) for a range of Gram-negative and Gram-positive bacteria, as well as yeast species. Our results demonstrate that except for micafungin, MIC values obtained with reduced volumes remained within the acceptable variability ranges defined by EUCAST and CLSI. Evaporation, a potential source of bias in smaller volumes, was mitigated by conducting experiments in a water-saturated atmosphere. Furthermore, reduced assay volumes significantly lowered material costs and antimicrobial consumption, particularly for expensive drugs such as cefiderocol. This miniaturization approach offers a cost-effective, high-throughput alternative for antimicrobial susceptibility testing while maintaining accuracy and reproducibility.

microbiology↗

bioRxiv2025

Stable isotope probing of carbonyl sulfide and cyanate pathways in microbial thiocyanate biodegradation

Thiocyanate (SCN-) is toxic to many aquatic organisms at elevated concentrations. Historically, large amounts of SCN- were released to the environment by gold mining and coal coking. Microbial SCN- degradation provides a cost-effective approach to remediation; however, knowledge is still limited about the relative roles of the two known enzymatic SCN- biodegradation pathways. Here we applied stable carbon and nitrogen isotope probing of SCN--degrading microbial cultures to assess quantitatively the relative contributions of the cyanate (OCN-) and carbonyl sulfide (COS) pathways over a 24-hour experiment. In contrast to common assumptions, our results demonstrate that the OCN- pathway initiates before the COS pathway and can contribute up to 70% of early SCN- biodegradation. These results yield new insights into the dynamics of SCN- biodegradation, and also show that microorganisms can incorporate carbon and nitrogen from the SCN- into biomass, resolving the question of nitrogen mass balance. Our study holds implications for improving bioreactor design for SCN- bioremediation and for understanding the dynamics for sulfur, carbon and nitrogen flows from SCN- in natural environments into their respective biogeochemical cycles. ImportanceWhile the process of SCN- biodegradation has been well studied, relative contributions from the two known enzymatic pathways are still poorly resolved, hindering our ability to optimize bioremediation systems treating SCN--contaminated wastewater. Also, as SCN- biodegradation in nature impacts the biogeochemical cycling of sulfur (as well as carbon and nitrogen), a more quantitative understanding of enzymatic SCN- biodegradation pathways will yield insights into how the reactivity of this environmentally ubiquitous compound influences marine, terrestrial and atmospheric sulfur chemistry. Here we used carbon and nitrogen stable isotope probing to assess contributions to SCN- biodegradation from known enzymatic pathways in a microbial consortium grown from SCN--contaminated mine tailings. We found that the cyanate pathway dominates SCN- biodegradation initially, before activation of the carbonyl sulfide pathway. We attribute this ordering to the greater amount of bioenergy conservable via the cyanate pathway during the earliest stages of bioremediation.

microbiology↗

bioRxiv2020

Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens

Improvements in the biological control of agricultural pests require improvements in the phenotyping methods used by practitioners to select efficient biological control agent (BCA) populations in industrial rearing or field conditions. Consistent inter-individual variations in behaviour (i.e. animal personality) probably affect BCA efficiency, but have never been taken into account in the development of phenotyping methods, despite having characteristics useful for phenotyping: repeatable (by definition), often heritable, etc. We developed a video-tracking method targeting animal personality traits and evaluated the feasibility of its use for genetic improvement in the BCA Trichogramma evanescens, by phenotyping 1,049 individuals from 24 isogenic lines. We found consistent individual variations in boldness, activity and exploration. Personality differences between the 24 isogenic lines suggested a genetic origin of the variations in activity and exploration (broad-sense heritability estimates of 0.06 to 0.11) and revealed a trade-off between exploration and fecundity.

ecology↗

bioRxiv2019

A global perspective on microbial diversity in the terrestrial deep subsurface

While recent efforts to catalogue Earths microbial diversity have focused upon surface and marine habitats, 12% to 20% of Earths bacterial and archaeal biomass is suggested to inhabit the terrestrial deep subsurface, compared to [~]1.8% in the deep subseafloor 1-3. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities 4-6. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Here, we show the diversity of bacterial communities in deep subsurface groundwater is controlled by aquifer lithology globally, by using 16S rRNA gene datasets collected across five countries on two continents and from fifteen rock types over the past decade. Furthermore, our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, likely as a function of the diverse metabolic strategies of these taxa. Despite this similarity, evidence was found not only for aquifer-specific microbial communities, but also for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacterial OTUs across the localities. This finding implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, that may play an important role in colonising and sustaining microbial habitats in the deep terrestrial subsurface. An in-silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

microbiology↗

bioRxiv2019

Development of senescence biomarkers in the common woodlouse

Senescence, the decline of physiological parameters with increasing age, is a quasi-ubiquitous phenomenon in the living world. The observed patterns of senescence, however, can markedly differ across species and populations, between sexes, and even among individuals. To identify the drivers of this variation in senescence, experimental approaches are essential and involve the development of tools and new study models. Current knowledge of the senescence process is mostly based on studies on vertebrates and main information about senescence in invertebrates is mostly limited to model organisms such as Caenorhabditis elegans or Drosophila melanogaster. In this context, we tested whether biomarkers of vertebrate ageing could be used to study senescence in a new invertebrate model: the common woodlouse Armadillidium vulgare (Latreille, 1804). More specifically, we looked for the effect of age in woodlouse on three well-established physiological biomarkers of ageing in vertebrates: immune cells (cell size, density, and viability), {beta}-galactosidase activity, and the gene expression of telomerase reverse transcriptase (TERT), an essential subunit of telomerase protein. We found that the size of immune cells was higher in older individuals, whereas their density and viability decreased, and that the {beta}-galactosidase activity increased with age, whereas the TERT gene expression decreased. These findings demonstrate that woodlouse displays age-related changes in biomarkers of vertebrate senescence, with different patterns depending on gender. The tools used in studies of vertebrate senescence can thus be successfully used in studies of senescence of invertebrates such as the woodlouse. The application of commonly used tools to new biological models offers a promising approach to assess the diversity of senescence patterns across the tree of life.

evolutionary biology↗

bioRxiv2017

MEG-BIDS: an extension to the Brain Imaging Data Structure for magnetoencephalography

We present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG provides direct measurement of brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS has provided a solution to structure the organization of magnetic resonance imaging (MRI) data, which nature and acquisition parameters are different. Despite the lack of standard data format for MEG, MEG-BIDS is a principled solution to store, organize and share the typically-large data volumes produced. It builds on BIDS for MRI, and therefore readily yields a multimodal data organization by construction. This is particularly valuable for the anatomical and functional registration of MEG source imaging with MRI. With MEG-BIDS and a growing range of software adopting the standard, the MEG community has a solution to minimize curation overheads, reduce data handling errors and optimize usage of computational resources for analytics. The standard also includes well-defined metadata, to facilitate future data harmonization and sharing efforts.

neuroscience↗