Biology subjects

Perret, S.

Publications and source records attributed to Perret, S..

10 recordsLinked to original sources

bioRxiv2026

Large-scale exposure of southern seabirds to avian cholera Pasteurella multocida: scavengers as sentinels at different spatial scales

Seabird communities represent spatially structured social networks within which potential sentinels could inform us where multi-host pathogens could be present. Pasteurella multocida, the agent of avian cholera, is responsible for recurrent massive seabird mortality events on remote Amsterdam Island, Southern Indian Ocean, but little is known about its broad spatial occurrence. To explore its distribution and whether avian scavengers and predators could be used as sentinels, we screened 18 southern seabird species from 11 islands for antibodies against P. multocida (2634 plasma samples). We detected widespread but heterogeneous exposure among host populations. High seroprevalences were found in widely roaming predators and scavengers (giant petrels (Macronectes spp), and brown skua (Stercorarius antarcticus)), which could represent efficient sentinels at broad scales. Antibodies were also detected over a series of years in a non-migratory scavenger, the lesser sheathbill (Chionis minor) and an abundant penguin species, the king penguin (Aptenodytes patagonicus), suggesting that the bacterium was circulating locally at some sites. This broad scale serological screening of whole seabird host communities provides critical information to assess disease emergence risks in the context of global change.

ecology↗

bioRxiv2025

Coastal winds are stronger and impact seabird behaviour and fitness in a warming Arctic

The Arctic is warming nearly four times faster than the rest of the planet. This unprecedented warming is profoundly altering environmental conditions. Coastal areas, which are crucial for biodiversity and human activities, are at the forefront of these changes. Among the major environmental changes expected in coastal regions are shifts in wind regimes and an increase in storm frequency. Using an interdisciplinary approach, we demonstrated that (1) wind conditions in Arctic coastal regions during summer are changing, resulting in a rise in strong wind events. (2) These large-scale changes in wind dynamics influence the movements and fitness of seabirds, with broader impacts on panarctic socio-ecosystems. To demonstrate these effects, we used a long-term study of little auks (Alle alle), the most abundant Arctic seabird species and an ecological indicator of Arctic coastal ecosystems. We showed that during strong wind events, little auks significantly reduce the visits to the colony. These behavioural changes negatively impact their fitness as inferred from chick growth rates. Overall, strong wind events disrupt the delicate balance between parental investment and self-maintenance in this long-lived species. Over time, such pressures may drive shifts in life-history traits, potentially affecting population dynamics.

ecology↗

bioRxiv2025

Genome-scale metabolic modeling of Ruminiclostridium cellulolyticum: a microbial cell factory for valorization of lignocellulosic biomass

The development of sustainable biotechnological processes requires a transition from the traditional fermentation of refined substrates towards the valorization of waste materials such as lignocellulosic biomass. Although these so-called recalcitrant substrates cannot be degraded by model industrial organisms, they can be degraded by microbial consortia through a process of anaerobic digestion, where different community members are able to break down polysaccharides of varied complexity. Among these microbes, Ruminiclostridium cellulolyticum stands out as a promising candidate for fermentation of lignocellulose due to its ability to degrade both cellulose and hemicellulose. In this work, we present an updated genome-scale metabolic model for R. cellulolyticum strain H10. The model was manually curated with experimental data and the pathways for degradation of cellulose and hemicellulose (arabinoxylan and xyloglucan) were reconstructed and annotated with full detail. The model enables the simulation of the fermentation profile of lignocellulosic materials of various compositions, facilitating the use of this organism as a potential workhorse for sustainable biotechnology, and it provides a valuable template for the reconstruction and optimization of lignocellulose degradation pathways in related organisms.

systems biology↗

bioRxiv2025

Disentangling urbanisation, climate effects and their interaction on ornamental colourations

Urbanisation and climate change can both affect phenotype expression across taxa. Most evidence collected so far has focused on exploring these two phenomena on isolation. Currently, the combined effects of climate change and urbanisation remain underexplored, despite being among the greatest challenges faced by biodiversity. Here, we use a decade-long, individual-based study of urban and forest great tits (Parus major) to analyse urbanisation, climate and their interactive effects on yellow breast colouration, a carotenoid-based trait. We find that urban birds exhibit duller colourations than forest counterparts, being 10-20% less chromatic, with first-year birds and males being more negatively impacted by cities. Additionally, birds in the city are more sexually dichromatic than in the forest. Over the decade, colouration differences between habitats remain stable, following a similar quadratic temporal pattern. Finally, while climate has a weak effect on colouration, urban birds appear more sensitive to its influence than forest birds. Our results indicate urbanisation has a stronger impact than last decade climatic variation on great tit colouration, though both factors may interact. The heightened sensitivity of first-year birds and increased sexual dichromatism in cities may alter the strength of natural and sexual selection on this trait in urban environments.

ecology↗

bioRxiv2024

A deep learning approach to detect and visualise sexual dimorphism in monomorphic species

Sex recognition is facilitated by dimorphism in some traits. However, humans often fail to find the traits that allow to distinguish between sexes in other species. Deep learning has the potential to surpass humans in identifying cryptic differences between sexes, but, so far, has rarely been used to assess sexual dimorphism. In this study, we evaluated (i) the ability of a fine-tuned classification neural network, EfficientNet, to find differences between sexes in a species that appears monomorphic to humans, the sociable weaver (Philetairus socius). We then assessed (ii) the benefits of Grad-CAM visualisation techniques to understand which parts of the individuals are used by the network to differentiate the sexes. We trained 10-folds cross-validation models on more than 4,500 pictures of the head from more than 1,300 individuals. Our results show that the network can predict sex of sociable weavers with an accuracy of 76%, which is considerably higher than humans performance, and that the model was similarly good at predicting females and males. When interpreting the probability of being classified to one sex, our results further reveal an effect of the interaction of sex with age on the confidence score of the models which shows that younger males are less masculine than older ones, and older females more masculine than younger ones. Finally, using Grad-CAM we found that the model mostly uses the beak region to predict the sex of individuals. Overall, this work shows that artificial intelligence has the potential to be a non-invasive sexing tool, surpassing human capabilities and aiding in pinpointing potential cryptic dimorphic body parts that have yet to be identified. In birds, half of the worlds species appear sexually monomorphic to humans, and re-evaluation of species dimorphism with this type of methods could deepen our understanding of the effect of selection on animal traits.

zoology↗

bioRxiv2023

Cities as parasitic burden? Malaria prevalence and diversity along an urbanization gradient in great tits

Urbanization is a worldwide phenomenon that modifies the environment. By affecting the reservoirs of pathogens and the body and immune conditions of hosts, urbanization alters the epidemiological dynamics and diversity of diseases. Cities could act as areas of pathogen dilution or amplification, depending on whether urban features have positive or negative effects on vectors and hosts. In this study, we focused on a host species and investigated the prevalence and diversity of avian malaria parasites (Plasmodium/Haemoproteus sp. and Leucocytozoon sp.) in great tits (Parus major) living across an urbanization gradient. In general, we observed high prevalence in adult birds (from 95% to 100%), yet lower prevalence in fledglings (from 0% to 38%). We found a slight tendency for increased Plasmodium sp. prevalence with increasing urbanization in adults. Urban nestlings had higher Plasmodium sp. infection rates than non-urban nestlings. We found evidence of higher diversity of parasites in the most natural urban park; however, parasite diversity was similar across other urbanization levels (e.g. from a little artificialized park to a highly anthropized industrial area). Parasite lineages were not habitat specific. Only one Plasmodium sp. lineage (YWT4) was associated with urban areas and some rare lineages (e.g., AFR065) were present only in a zoo area, perhaps because of the presence of African birds. This study suggests that urbanization can lead to a parasite amplification effect and can favor different avian malaria lineages.

ecology↗

bioRxiv2021

Arsenal of Nanobodies for Broad-Spectrum Countermeasures against Current and Future SARS-CoV-2 Variants of Concerns

Nanobodies offer several potential advantages over mAbs for the control of SARS-CoV-2. Their ability to access cryptic epitopes conserved across SARS-CoV-2 variants of concern (VoCs) and feasibility to engineer modular, multimeric designs, make these antibody fragments ideal candidates for developing broad-spectrum therapeutics against current and continually emerging SARS-CoV-2 VoCs. Here we describe a diverse collection of 37 anti-SARS-CoV-2 spike glycoprotein nanobodies extensively characterized as both monovalent and IgG Fc-fused bivalent modalities. The panel of nanobodies were shown to have high intrinsic affinity; high thermal, thermodynamic and aerosolization stability; broad subunit/domain specificity and cross-reactivity across many VoCs; wide-ranging epitopic and mechanistic diversity; high and broad in vitro neutralization potencies; and high neutralization efficacies in hamster models of SARS-CoV-2 infection, reducing viral burden by up to six orders of magnitude to below detectable levels. In vivo protection was demonstrated with anti-RBD and previously unreported anti-NTD and anti-S2 nanobodies. This collection of nanobodies provides a therapeutic toolbox from which various cocktails or multi-paratopic formats could be built to tackle current and future SARS-CoV-2 variants and SARS-related viruses. Furthermore, the high aerosol-ability of nanobodies provides the option for effective needle-free delivery through inhalation.

bioengineering↗

bioRxiv2021

Leaf area index estimation of even-aged oak (Quercus petraea) forests using in situ stand dendrometric parameters

The leaf area index (LAI) is a key characteristic of forest stand aboveground net productivity (ANP), and many methods have been developed to estimate the LAI. However, every method has flaws, e.g., methods may be destructive, require means or time and/or show intrinsic bias and estimation errors. A relationship using basal area (G) and stand age to estimate LAI was proposed by Sonohat et al. (2004). We used literature data in addition to data form measurements campaign made in the northern half of France to build a data set with large ranges of pedoclimatic conditions, stand age and measured LAI. We validated the Sonohat et al. (2004) relationship and attempted to improve or modify it using other stand/dendrometric characteristics that could be predictors of the LAI. The result is a series of three models using the G, age and/or quadratic mean diameter (Dg), and the models were able to estimate the LAI of an oak only even-aged forest stand with good confidence (root mean square error, RMSE < 0.75) While G is the main predictor here, age and Dg could be used conjointly or exclusively given the available data, with variable precision in the estimations. Although these models could not, by construction, relate to the interannual variability of the LAI, they may provide the theoretical LAI of an untouched forest (no meteorological, biotic or anthropogenic perturbation) in recent years. additionally, the use of this model may be more interesting than an LAI measurement campaign, depending on the means to be invested in such a campaign.

ecology↗

bioRxiv2020

Rapid, high-yield production of full-length SARS-CoV-2 spike ectodomain by transient gene expression in CHO cells

Recombinant forms of the spike protein of SARS-CoV-2 and related viruses have proven difficult to produce with good yields in mammalian cells. Given the panoply of potential COVID-19 diagnostic tools and therapeutic candidates that require purified spike protein and its importance for ongoing SARS-CoV-2 research, we have explored new approaches for spike production and purification. Three transient gene expression methods based on PEI-mediated transfection of CHO or HEK293 cells in suspension culture in chemically-defined media were compared for rapid production of full-length SARS-CoV-2 ectodomain. A high-cell-density protocol using DXB11-derived CHOBRI/rcTA cells gave substantially better yields than the other methods. Different forms of the spike were expressed, including the wild-type SARS-CoV-2 sequence and a mutated/stabilized form (to favor expression of the full-length spike in prefusion conformation), with and without fusion to putative trimerization domains. An efficient two-step affinity purification method was also developed. Ultimately, we have been able to produce highly homogenous preparations of full-length spike, both monomeric and trimeric, with yields of 100-150 mg/L. The speed and productivity of this method support further development of CHO-based approaches for recombinant spike protein manufacturing.

bioengineering↗

bioRxiv2019

Density-dependent selection mediates harvest-induced evolution

Rapid life-history changes caused by size-selective harvesting are often interpreted as a response to direct harvest selection against a large body size. However, similar trait changes may result from a harvest-induced relaxation of natural selection for a large body size via density-dependent selection. Here, we show evidence of such density-dependent selection favouring large-bodied individuals at high population densities, in replicated pond populations of medaka fish. Harvesting, in contrast, selected medaka directly against large-bodied medaka and, in parallel, decreased medaka population densities. Five years of harvesting were enough for harvested and unharvested medaka populations to inherit the classically-predicted trait differences, whereby harvested medaka grew slower and matured earlier than unharvested medaka. We demonstrate that this life-history divergence was not driven by direct harvest selection for a smaller body size in harvested populations, but by density-dependent natural selection for a larger body size in unharvested populations.

evolutionary biology↗