Biology subjects

Petit, E.

Publications and source records attributed to Petit, E..

11 recordsLinked to original sources

bioRxiv2026

Integrating multi-host modelling with empirical wildlife-livestock contacts reveals an essential population in a pathogen reservoir

Infections at the animal-human or wildlife-livestock interfaces have severe health and socio-economic consequences. Combined with empirical data, mathematical models can contribute to a better understanding of the reservoirs of these infections, which is a priority for mitigating their impact by using appropriate management interventions. Taking brucellosis in the Bargy massif (French Alps) as an example of a zoonosis at the wildlife-livestock interface, we developed and calibrated a multi-host model integrating data on direct and environment-mediated cross-species contacts from field observations. Estimates of the basic reproduction number (R0) allowed to identify the population of Alpine ibex (Capra ibex) and its environment as an essential host in the reservoir, driving both pathogen maintenance (within-species R0[≥]1: 1.66, 95% credible interval: 1.42-2.03) and its transmission to livestock (between-species R0>0: 0.035, 0.01-0.05). Our approach can be adapted to other multi-host pathogens, which will contribute to improve the understanding and management of these complex systems.

ecology↗

bioRxiv2026

A mosaic of genomic architectures underpins parasitism loss in a jawless vertebrate

Lampreys are the only ancestrally parasitic vertebrate lineage, yet parasitism has been repeatedly lost alongside a suite of life-history changes, such as loss of migration and juvenile feeding and accelerated maturation. Combining whole-genome resequencing, haplotype-resolved assemblies, hybrid-zone genotyping, multi-tissue transcriptomics, and sperm phenotyping, we map this life-history syndrome in European Lampetra to six chromosomes spanning a mosaic of genomic architectures: a [~]20 Mb low-recombination region on chromosome 1 lacking chromosomal rearrangements within Lampetra but involving inter-specific rearrangements across deep lamprey lineages; a translocated inversion with ecotype-dependent sperm-velocity effects; and ecotype-divergent deletions overlapping genes crucial for nervous system (CNTNAP2) and reproductive development (FSHR). However, this genomic basis is not shared with a convergent sister lineage, pointing to independent routes to a recurring life-history transition in lampreys.

evolutionary biology↗

bioRxiv2024

Proteomic profiling of UV damage repair patches uncovers histone chaperones with central functions in chromatin repair

DNA damage compromises not only genome stability but also the integrity of the chromatin template, which plays a central role in controlling cell identity. Our understanding of chromatin repair mechanisms is very incomplete. To bridge this knowledge gap, here we devise a novel proteomic strategy to characterize dynamic changes in the chromatin landscape during the repair of UV-induced DNA lesions in human cells, in a quantitative, unbiased and time-resolved manner. Thus, we identify the histone chaperones DNAJC9 and MCM2 as central players in chromatin repair. We demonstrate that DNAJC9 and MCM2 are independently recruited to sites of UV damage repair. DNAJC9 provides new H3-H4 histones to CAF-1 and HIRA chaperones for deposition into chromatin and also stimulates old H3-H4 histone recovery. DNAJC9 cooperates with MCM2 to coordinate old and new histone dynamics during UV damage repair. Together, our proteomic dataset provides a molecular framework for further dissecting epigenome maintenance mechanisms.

molecular biology↗

bioRxiv2023

Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration

Seasonal migrations are central ecological processes connecting populations, species and ecosystems in time and space. Land migrations, such as those of ungulates, are particularly threatened by habitat transformations and fragmentation, climate change and other environmental changes caused by anthropogenic activities. Mountain ungulate migrations are neglected because they are relatively short, although traversing highly heterogeneous altitudinal gradients particularly exposed to anthropogenic threats. Detecting migration routes of these species and understanding their drivers is therefore of primary importance to predict connectivity and preserve ecosystem functions and services. The populations of Alpine ibex Capra ibex, an iconic species endemic to the Alps, have all been reintroduced from the last remnant source population. Because of their biology and conservation history, Alpine ibex populations are mostly disconnected. Hence, despite a general increase in abundance and overall distribution range, their conservation is strictly linked to the interplay between external threats and related behavioral responses, including space use and migration. By using 337 migratory tracks from 425 GPS-collared individuals from 15 Alpine ibex populations distributed across their entire range, we (i) identified the environmental drivers of movement corridors in both spring and autumn and (ii) compared the abilities of three modeling approaches to predict migratory movements between seasonal ranges of the 15 populations. Trade-offs between energy expenditure, food, and cover seemed to be the major driver of migration routes: steep south-facing snow-free slopes were selected while high elevation changes were avoided. This revealed the importance of favorable resources and an attempt to limit energy expenditures and perceived predation risk. Based on these findings, we provided efficient connectivity models to inform conservation of Alpine ibex and its habitats, and a framework for future research investigating connectivity in migratory species.

ecology↗

bioRxiv2021

Effect of landscape structure on genetic structure of the Lesser horseshoe bat (Rhinolophus hipposideros) in Britanny colonies

Some species are difficult to observe and others, need to be not disturbed because of their vulnerability. In response to the difficulty of studying the dispersal behaviors of these species, some areas of biology have been combined in order to access the information despite practical limitations. Here we present the combination of several methodologies from landscape ecology to non- invasive population genetics that allow us to obtain important information on Rinolophus hipposideros, a vulnerable European bat. We genotyped 18 georeferrenced colonies in Brittany (France) from droppings collected in their refuges. We used 6 microsatellite markers in order to obtain the genetic distances between them. On the other hand we calculated Euclidian distances between the refuges occupied by these colonies and some ecological distances with the Pathmatrix module of ArcGis 3.2. We tested hypothesis about the difficulty of dispersal of the species in areas without forest cover or with a low density of hedges. Thanks to the Monmonier algorithm we could infer possible genetic barriers between the colonies and we could compare their location to the presence of landscape barriers (areas with little tree cover). We detected a pattern of isolation by distance that reveals limited dispersal capacities in the species but no pattern linked to ecological distances. We found that some of the neighboring colonies with greater genetic distances between them were located in areas with low density of hedges which could suggest an impact of this landscape element in their movements. Finer studies should allow us to conclude on the need or not of forest cover in the dispersal of this species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/470144v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@1efb190org.highwire.dtl.DTLVardef@17287c8org.highwire.dtl.DTLVardef@3072c7org.highwire.dtl.DTLVardef@bf84a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2021

The Role of Low Molecular Weight Fungal Metabolites in Grapevine Trunk Disease Pathogenesis: Eutypa Dieback and Esca

Eutypa dieback and Esca are serious grapevine trunk diseases (GTDs) caused by fungal consortia causing large economic losses in vineyards. Depending on the disease the species involved include Eutypa lata, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. There is a need to understand the complex pathogenesis mechanisms used by these causative fungi to develop treatments for the diseases they cause. Low molecular weight metabolites (LMW) are known to be involved in non-enzymatic oxygen radical generation in fungal degradation of wood by some Basidiomycota species, and as part of our work to explore the basis for fungal consortia pathogenesis, LMW metabolite involvement by the causal GTD fungi was explored. The GTD fungal pathogens examined, Eutypa lata, Phaeoacremonium minimum and Phaeomoniella chlamydospora, were found to produce low molecular weight iron binding metabolites that preferentially reduced iron or redox cycled to produce hydrogen peroxide. Uniquely, different LMW metabolites isolated from the GTD fungi promoted distinct chemistries that are important in a type of non-enzymatic catalysis known as chelator-mediated Fenton (CMF) reactions. CMF chemistry promoted by LMW metabolites from these fungi allowed for the generation of highly reactive hydroxyl radicals under conditions promoted by the fungi. We hypothesize that this new reported mechanism may help to explain the necrosis of woody grapevine tissue as a causal mechanism important in pathogenesis in these two grapevine trunk diseases. IMPORTANCEUnderstanding the pathogenesis of grape trunk diseases (GTDs) is the key to the development of disease control and treatment. While fungal extracellular enzyme systems are typically cited relative to their fungal mechanisms in pathogenesis, non-enzymatic mechanisms have been less studied in this regard and the role of low molecular weight (LMW) fungal metabolites in GTD development is quite limited. In this article, we demonstrate that GTD-causative fungal pathogens Eutypa lata, Phaeoacremonium minimum and Phaeomoniella chlamydospore produce LMW phenolic metabolites under iron-restricted conditions. These metabolites undergo a series of redox reactions, with different fungi producing metabolites that preferentially either reduce iron, or generate hydrogen peroxide, under conditions simulating grapevine woody tissue. These conditions have the potential to promote generation of highly damaging hydroxyl radicals through a mechanism that appears to be similar to non-enzymatic chelator-mediated Fenton (CMF) chemistry which is involved in fungal degradation of wood by non-related fungal orders. This is the first report of CMF chemistry promoted by GTD-causative fungi under laboratory conditions and the research suggests an alternate pathway that may contribute to pathogenesis in GTDs, and a potential target for vine protection.

microbiology↗

bioRxiv2021

Male differentiation in the marine copepod Oithona nana reveals the development of a new nervous ganglion linked to Lin12-Notch-Repeat protein-associated proteolysis

BackgroundCopepods are among the most numerous animals, and play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest density of copepods, and as being the most cosmopolite copepods. The Oithona male paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is typically less mobile and often feeding. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein-protein interaction approaches. ResultsImmunofluorescence of {beta}3- and -tubulin revealed two male-specific nervous ganglia in the lateral first segment of the Oithona nana males prosome. In parallel, transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed only in males. Furthermore, most of the LDPGs (27%) coded for proteins having predicted proteolytic activity, and non-LDPG proteolysis-associated transcripts showed a male-specific enrichment. Using yeast double-hybrid assays, we constructed a protein-protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins. ConclusionsFor the first time, our study describes the lateral nervous ganglia of O. nana males, unique to copepods. We also demonstrated a role of LDPGs and their associated proteolysis in male-specific physiology, and we hypothesize a role of the LDPGs in the development of the lateral ganglia through directed lysis of the extracellular matrix for the growth of neurites and genesis of synapses.

molecular biology↗

bioRxiv2021

Surfactin stimulated by pectin molecular patterns and root exudates acts as a key driver of Bacillus-plant mutualistic interaction

Bacillus velezensis is considered as model species belonging to the so-called B. subtilis complex that typically evolved to dwell in the soil rhizosphere niche and establish intimate association with plant roots. This bacterium provides protection to its natural host against diseases and represents one of the most promising biocontrol agents. However, the molecular basis of the cross-talk that this bacterium establishes with its natural host has been poorly investigated. We show here that these plant-associated bacteria have evolved some polymer-sensing system to perceive their host and that in response, they increase the production of the surfactin-type lipopeptide. Furthermore, we demonstrate that surfactin synthesis is favoured upon growth on root exudates and that this lipopeptide is a key component used by the bacterium to optimize biofilm formation, motility and early root colonization. In this specific nutritional context, the bacterium also modulates qualitatively the pattern of surfactin homologues co-produced in planta and mainly forms variants that are the most active at triggering plant immunity. Surfactin represents a shared good as it reinforces the defensive capacity of the host. ImportanceWithin the plant-associated microbiome, some bacterial species are of particular interest due to the disease protective effect they provide via direct pathogen suppression and/or stimulation of host immunity. While these biocontrol mechanisms are quite well characterized, we still poorly understand the molecular basis of the cross talk these beneficial bacteria initiate with their host. Here we show that the model species Bacillus velezensis stimulates production of the surfactin lipopeptide upon sensing pectin as cell surface molecular pattern and upon feeding on root exudates. Surfactin favors bacterial rhizosphere fitness on one hand and primes the plant immune system on the other hand. Our data therefore illustrate how both partners use this multifunctional compound as unique shared good to sustain mutualistic interaction.

microbiology↗

bioRxiv2020

Numerical Instabilities in Analytical Pipelines Lead to Large and Meaningful Variability in Brain Networks

The analysis of brain-imaging data requires complex processing pipelines to support findings on brain function or pathologies. Recent work has shown that variability in analytical decisions, small amounts of noise, or computational environments can lead to substantial differences in the results, endangering the trust in conclusions1-7. We explored the instability of results by instrumenting a connectome estimation pipeline with Monte Carlo Arithmetic8,9 to introduce random noise throughout. We evaluated the reliability of the connectomes, their features10,11, and the impact on analysis12,13. The stability of results was found to range from perfectly stable to highly unstable. This paper highlights the potential of leveraging induced variance in estimates of brain connectivity to reduce the bias in networks alongside increasing the robustness of their applications in the classification of individual differences. We demonstrate that stability evaluations are necessary for understanding error inherent to brain imaging experiments, and how numerical analysis can be applied to typical analytical workflows both in brain imaging and other domains of computational science. Overall, while the extreme variability in results due to analytical instabilities could severely hamper our understanding of brain organization, it also leads to an increase in the reliability of datasets.

neuroscience↗

bioRxiv2019

Proteolysis and neurogenesis modulated by LNR domain proteins explosion support male differentiation and sacrificial behaviour in the iteroparous crustacean Oithona nana.

Copepods are the most numerous animals and play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest numerical density, as the most cosmopolite copepod and iteroparous. The Oithona male paradox obliges it to alternate feeding (immobile) and mating (mobile) phases. As the molecular basis of this trade-off is unknown, we investigated this sexual dimorphism at the molecular level by integrating genomic, transcriptomic and protein-protein interaction analyses.\n\nWhile a ZW sex-determination system was predicted in O. nana, a fifteen-year time-series in the Toulon Little Bay showed a biased sex ratio toward females (male / female ratio < 0.15{+/-}0.11) highlighting a higher mortality in male. Here, the transcriptomic analysis of the five different developmental stages showed enrichment of Lin12-Notch Repeat (LNR) domains-containing proteins coding genes (LDPGs) in male transcripts. The male also showed enrichment in transcripts involved in proteolysis, nervous system development, synapse assembly and functioning and also amino acid conversion to glutamate. Moreover, several male down-regulated genes were involved in the increase of food uptake and digestion. The formation of LDP complexes was detected by yeast two-hybrid, with interactions involving proteases, extracellular matrix proteins and neurogenesis related proteins.\n\nTogether, these results suggest that the O. nana male hypermotility is sustained by LDP-modulated proteolysis allowing the releases and conversions of amino acid into the excitatory neurotransmitter glutamate. This process could permit new axons and dendrites formation suggesting a sexual nervous system dimorphism. This could support the hypothesis of a sacrificial behaviour in males at the metabolic level.

molecular biology↗

bioRxiv2019

Linking Allele-Specific Expression And Natural Selection In Wild Populations

Allele-specific expression (ASE) is a widely studied molecular mechanism at cell, tissue and organism levels. Here, we extrapolated the concept of ASE to the population-scale (psASE), aggregating ASEs detected at smaller scales. We developed a novel approach to detect psASE based on metagenomic and metatranscriptomic data of environmental samples containing communities of organisms. This approach which measures the deviation between the frequency and the relative expression of biallelic loci, was applied on samples collected during the Tara Oceans expedition (2009-2013), in combination to new Oithona similis transcriptomes, a widespread marine copepod. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 587 (2.3%) were targeted by psASE in at least one population. The distribution of SNVs targeted by psASE in different populations is significantly shaped by population genomic differentiation (p-value = 9.3x10-9), supporting a partial genetic control of psASE. To investigate the link between evolution and psASE, loci under selection were compared to loci under psASE. A significant amount of SNVs (0.6%) were targeted by both selection and psASE (p-values < 9.89x10-3), supporting the hypothesis that natural selection and ASE may lead to the same phenotype. Population-scale ASE offers new insights into the gene regulation control in populations and its link with natural selection.

genomics↗