Biology subjects

Fontaine, C.

Publications and source records attributed to Fontaine, C..

13 recordsLinked to original sources

bioRxiv2026

Assay coverage reshapes metabolic diagnosis and the interpretation of pathway disturbance

Metabolic profiles are used to quantify disturbance, classify disease and infer biochemical function, yet these endpoints retain different information. We combine secondary analysis of 386 metabolites in six Arabidopsis thaliana mutation accumulation lines, known-disease classification in 129 public human metabolic-disease profiles, and an analytically solvable kinetic model. A conditional occupancy model separates annotation-bin breadth from hit count and measured bin sizes: the plant low-versus-high fitness comparison changes from a two-sided exact permutation p = 0.10 to p = 0.30 after calibration. Unsigned metabolite profiles achieve mean macro recall of 0.911 and 0.895 in separate EDTA and heparin subsets, compared with 0.624 and 0.382 for a burden baseline. However, controlled loss of 50% of held-out measurements reverses representation ranking in heparin, giving signed profiles a recall advantage of 0.108 with a conditional bootstrap interval of 0.063-0.155. A spectral decomposition identifies the within-pathway contrasts attenuated by smoothing. The kinetic model then shows that lower concentration and faster relaxation can coexist with reduced desired product flux, while a null-space criterion states when observations identify a metabolic task. The results connect assay coverage, diagnostic information and functional identifiability. Human performance is internally validated, and the kinetic predictions remain uncalibrated to patients.

systems biology↗

bioRxiv2026

The diel structure and robustness of plant-pollinator networks are driven by the shifting influences of plant traits

O_LISpecies interactions are increasingly recognised as temporally dynamic. For plant-pollinator networks, evidence shows that interactions vary not only seasonally but also over the diel cycle. However, we still know little about what determines their diel structure, whether this structure is important for robustness to species loss, and which plant traits are associated with the roles plants play in this structure. These gaps are fundamental, because knowing what shapes networks over the diel cycle is required to predict the effects of global change drivers, such as light pollution, that may shift the timing of interactions. C_LIO_LIUsing 22 plant-pollinator networks sampled over morning, afternoon, and night, we addressed these gaps by applying a multilayer framework to characterise their diel structure, link it to robustness, and test which plant traits are associated with plant roles across diel periods (participation, versatility) and within them (centrality). C_LIO_LIDiel structure was non-random: interactions were segregated among diel periods yet integrated through plants visited across the diel cycle. Networks were more robust to simulated species loss when interactions were on average more evenly distributed across periods and when plants were more strongly interconnected among periods, although this benefit diminished when both properties were high simultaneously. The association between plant traits and their roles shifted with the temporal scale. Across diel periods, structural traits were the stronger predictors: taller plants were visited more evenly across the diel cycle (higher participation), whereas shorter plants shared pollinators with plants from multiple periods (higher versatility), potentially mediating indirect effects among them. Within diel periods, floral visual cues became more influential, with achromatic contrast the most consistent predictor: at night, plants with brighter flowers were well visited within the period, sharing pollinators with other plants of that period (higher centrality). C_LIO_LIThese findings identify diel structure as a functional axis of network organisation and indicate that plant-pollinator networks are assembled hierarchically: structural traits set a baseline across the diel cycle, whereas light conditions determine which traits matter within periods, ultimately defining distinct temporal pathways vulnerable to global change. C_LI

ecology↗

bioRxiv2026

Population and community variability deviate from stationary expectations during transient dynamics

Under complex perturbation regimes, biodiversity dynamics show temporal variability in species and community abundance around long-term population trends. Many species indeed show long-term declines while other species increase, putting natural communities far from stationary regimes, while variability is often studied near equilibrium. We contribute to bridging this gap by investigating population and community variability during long-term trends caused by press perturbations in stochastic models of population dynamics. By estimating the deterministic changes in mean and variance during the transient regime, we show that population variability deviates from stationary expectations. Moreover, the deviation strongly depends on the sign of the population trends: increases generate excesses of variability while declines generate deficits. Scaling up to community variability, we propose a decomposition of community variability deviation, allowing to highlight that community variability in the transient regime depends on how the press perturbation is distributed within species relative abundances and growth rates. These results challenge the equilibrium assumption and open new perspectives for the study of the variability of ecological systems under multiple perturbation types.

ecology↗

bioRxiv2025

Androgen receptor imprints satellite cells stemness and preserves their reservoir for lifelong regeneration and optimal repair

Skeletal muscle stem cells (MuSC) are the guardians of muscle regeneration, sustaining tissue integrity through a delicate balance of quiescence, activation, and lineage commitment. While numerous molecular cues have been implicated in regulating these processes, the influence of androgen receptor (AR) signaling, an essential hormonal pathway for male muscle physiology, has remained largely unexplored. Here, we show that AR expression defines quiescent MuSC and acts as a safeguard of their dormancy. Integrated multi-omic analyses reveal a redistribution of AR binding from quiescence-maintenance loci to regulatory elements driving activation and metabolic reprogramming during repair. Loss of AR in young adult mice disrupts this balance, precipitating premature cell-cycle entry, skewed division modalities, depletion of the stem cell reservoir, and destabilization of the niche. These defects converge with hallmarks of aging-associated androgen decline, while androgen supplementation restores regenerative competence. Together, our findings establish AR signaling as a pivotal determinant of MuSC fate and a cornerstone of skeletal muscle homeostasis.

developmental biology↗

bioRxiv2025

Biodiversity temporal trends are reshaping food web structure and redundancy in riverine ecosystems

Biodiversity temporal changes are expected to profoundly impact ecosystem functioning and stability, yet large-scale empirical evidence remains limited. Bridging this gap requires aligning biodiversity temporal trends with food web theory and Biodiversity-Ecosystem Functioning research, both of which provide strong predictions about the ecological consequences of biodiversity loss. Most insights on those consequences currently rely on spatial comparisons of ecological communities, assuming they reflect temporal trends--a space-for-time substitution. Here, we analyze biodiversity and food web time series from over 400 riverine fish communities across France (1995-2018) to evaluate how biodiversity temporal trends reshape food web structure and community functioning. We examine relationships among species richness, community biomass, and three key food web metrics: connectance, weighted average trophic level, and trophic pathway redundancy. We also test the space-for-time hypothesis using spatial gradients and a theoretical food web model. Our structural equation models and robustness analysis reveal that declines in species richness strongly correlate with reduced community biomass, with top trophic-level species playing a disproportionate role in food web changes. Declining biomass is associated with the loss of top trophic levels and decreased connectance, while temporal changes in species richness negatively correlates with changes in connectance. Both biomass and species richness declines reduce trophic pathway redundancy, suggesting that biodiversity loss weakens community robustness to future perturbations. Our findings align with food web theory and Biodiversity-Ecosystem Functioning research, support the validity of space-for-time approaches for basic food web metrics, and demonstrate the relevance of food web metrics as indicators of ecosystem function and fragility. SignificanceRates of biodiversity loss raise urgent concerns about ecosystem functioning and stability, yet how biodiversity trends directly impact these critical processes remains unclear. For instance, food web & Biodiversity-Ecosystem Functioning research has delivered strong predictions about the ecological consequences of biodiversity loss but lack of empirical assessment. Using an extensive dataset of riverine fish communities, we link biodiversity trends to temporal changes in food web structure. We demonstrate that temporal changes in species richness and community biomass consistently associate with altered food web structure. We found that declining biodiversity reduces trophic pathway redundancy, likely increasing ecosystem vulnerability to perturbations. Our findings suggest that food web structure metrics could serve as valuable indicators for monitoring ecosystem health and guiding conservation strategies.

ecology↗

bioRxiv2025

Transcriptomic analysis of chronic chikungunya in the Reunionese CHIKGene cohort uncovers a shift in gene expression more than 10 years after infection

AimIn 2005-2006, a chikungunya epidemic of unprecedented magnitude hit Reunion Island, which raised a public health concern through the substantial proportions of long-lasting manifestations. To understand the pathophysiology underlying chronic chikungunya (CC), we designed the CHIKGene cohort study and collected blood samples from 133 subjects diagnosed with CC and from 86 control individuals that had recovered within 3 months, 12-to-15 years after exposure. MethodsWe conducted bulk RNAseq analysis on peripheral blood mononuclear cells to find differentially expressed genes (DEGs), gene set enrichment analysis (GSEA) and gene ontologies to uncover top-level enriched terms associated with DEGs, and weighted gene correlation network analysis (WGCNA) to elucidate underlying cellular processes. ResultsAmong 1549 DEGs, gene expression analysis identified 10 top genes including NR4A2 and TRIM58 (upregulated in CC), IGHG3 and IGHV3-49 (downregulated in CC) linked to immune regulation, OSBP2 (upregulated in CC) and SEMA6B (downregulated in CC) linked to neuronal homeostasis and axon guidance, respectively. GSEA and WGCNA unveiled cellular processes such as "Metabolism of RNA" and "Cell Cycle". ConclusionsThis study uncovers a shift in gene expression of CC subjects. IGHG3 and IGHV3-49 gene shut-offs spotlight the importance of neutralizing antibodies against chikungunya virus in the progression to chronic disease. Human diseases associations highlight connections to rheumatoid arthritis, nervous and cardiac systems. GSEA and WGCNA bounce the hypotheses of a persistent viral reservoir or an increased susceptibility to RNA viral pathogens with new onset infections. Together, our findings might offer potential targets for therapeutic options aimed at alleviating chronic chikungunya.

bioinformatics↗

bioRxiv2024

Weather explains inter-annual variability, but not the temporal decline, in insect biomass

In a recent publication, Muller et al. (2023) re-analysed, in light of new data, the dataset of the highly cited paper of Hallmann et al. (2017) showing a strong decline in insect biomass in Germany between 1989 and 2016. In their re-analysis, Muller et al. completed Hallmann et als model with a focus on modelling the effects of weather conditions on insect biomass. They also included temporal changes in habitat as additional predictors, using the same variables as Hallmann et al., which although not entirely satisfactory due to the scarcity of historical habitat data, represent the best available data. While they trained their model on the Hallmann et al.s dataset, Muller et al. validated it with an independent dataset. These upgraded analyses are a nice demonstration of the strong impact of climatic conditions on annual insect biomass. However, Muller et al. conclusion that "temporal variation in weather conditions explained most of the temporal changes in insect biomass whereas temporal changes in habitat conditions played only a minor role" was overstated. Here we argue that their methodological approach was unsuitable to draw such conclusion, because of omitted variable bias. We show that more appropriate analyses produce a pattern opposite to the main conclusion of Muller et al.: there is a significant temporal decline in insect biomass not explained by weather conditions.

ecology↗

bioRxiv2022

Influence of sex-limited mimicry on extinction risk in Aculeata: a theoretical approach.

AO_SCPLOWBSTRACTC_SCPLOWPositive ecological interactions can play a role in community structure and species co-existence. A well-documented case of mutualistic interaction is Mullerian mimicry, the convergence of colour pattern in defended species living in sympatry. By reducing predation pressure, Mullerian mimicry may limit local extinction risks of defended species, but this positive effect can be weakened by undefended mimics (Batesian mimicry). While mimicry was well-studied in neotropical butterflies, it remains surprisingly poorly studied in wasps and bees (Hymenoptera: Aculeata). However, only females are defended in Aculeata and this female-limited defence may modulate the effect of Mullerian mimicry on extinction risks. Here, we focus on the effect of Mullerian mimicry on extinction risk in Aculeata, using a population dynamics model for two species. We show that Mullerian mimicry has a positive effect on species co-existence, but this effect depends on the sex-ratio. We found that the probability of extinction increases as the proportion of undefended males increases in the population, however co-existence still occurs if females are sufficiently abundant or noxious. Furthermore, we detected a destabilising effect of dual sex-limited mimicry (when each sex resembles a different model) on species co-existence. In a context of massive population decline caused by anthropic activities, our findings highlight the potential importance of Mullerian mimicry as an overlooked mechanism linked to extinction risk in wasp and bee species.

ecology↗

bioRxiv2022

Controversy over the decline of arthropods: a matter of temporal baseline?

AO_SCPLOWBSTRACTC_SCPLOWRecently, a number of studies have reported somewhat contradictory patterns of temporal trends in arthropod abundance, from decline to increase. Arthropods often exhibit non-monotonous variation in abundance over time, making it important to account for temporal coverage in interpretation of abundance trends, which is often overlooked in statistical analysis. Combining four recently analysed datasets that led to contrasting outcomes, we first show that temporal abundance variations of arthropods are non-monotonous. Using simulations, we show non-monotony is likely to bias estimated linear abundance trends. Finally, analysing empirical data, we show that heterogeneity in estimated abundance trends is significantly related to the variation in temporal baseline of analysed time series. Once differences in baseline years, habitats and continents are accounted for, we do not find any statistical difference in estimated linear abundance trends among the four datasets. We also show that short time series produce more stochastic abundance trends than long series, making the dearth of old and long-term time series a strong limitation in the assessment of temporal trends in arthropod abundance. The lack of time series with a baseline year before global change acceleration is likely to lead to an underestimation of global change effects on biodiversity.

ecology↗

bioRxiv2020

Relationship between the composition of the digestive microbiota and the concentrations of opportunistic pathogens in intensive care patients.

ObjectiveInfections caused by multidrug-resistant Gram-negative bacilli (MDR-GNB) are a major issue in intensive care. The intestinal and oropharyngeal microbiota being the reservoir of MDR-GNB. Our main objective was to assess the link between the composition of the intestinal and tracheal microbiota and colonization by MDR-GNB. MethodsWe performed a 2-month prospective, monocentric cohort study in the medical intensive care unit of our hospital. Patients ventilated >3 days and spontaneously passing faeces were included. A faecal sample and an endotracheal aspiration (EA) were collected twice a week. MDR-GNB but also Enterococcus faecium and yeasts (as potential dysbiosis surrogate markers) were detected by culture methods. The composition of the intestinal and tracheal microbiota was assessed by 16S profiling. ResultsWe collected 62 couples of faeces and EA from 31 patients, including 18 faeces and 9 EA positive for MDR-GNB. We did not observe a link between the diversity and the richness of the intestinal microbiota and the MDR-GNB intestinal relative abundance (RA). Conversely, we observed a negative link between the intestinal diversity and richness and the RA of Enterococcus spp. (p<0.001). ConclusionThe intestinal MDR-GNB RA was not associated to the diversity nor the richness of the intestinal microbiota, but that of Enterococcus spp. was.

microbiology↗

bioRxiv2019

Wild pollinator activities negatively related to honey bee colony densities in urban context

As pollinator decline is increasingly reported in natural and agricultural environments, cities are perceived as shelters for pollinators because of low pesticide exposure and high floral diversity throughout the year. This has led to the development of environmental policies supporting pollinators in urban areas. However, policies are often restricted to the promotion of honey bee colony installations, which resulted in a strong increase in apiary numbers in cities. Recently, competition for floral resources between wild pollinators and honey bees has been highlighted in semi-natural contexts, but whether urban beekeeping could impact wild pollinators remains unknown. Here, we show that in the city of Paris (France), wild pollinator visitation rates is negatively correlated to honey bee colony densities present in the surrounding (500m - slope = -0.614; p = 0.001 - and 1000m - slope = -0.489; p = 0.005). More particularly, large solitary bees and beetles were significantly affected at 500m (respectively slope = -0.425, p = 0.007 and slope = - 0.671, p = 0.002) and bumblebees were significantly affected at 1000m (slope = - 0.451, p = 0.012). Further, lower interaction evenness in plant-pollinator networks was observed with honey bee colony densities within 1000 meter buffers (slope = -0.487, p = 0.008). Finally, honey bees tended to focus their foraging activity on managed rather than spontaneous plant species (student t-test, p = 0.001) whereas wild pollinators equally visited managed and spontaneous species. We advocate responsible practices mitigating the introduction of high density of hives in urban environments. Future studies are needed to deepen our knowledge about the potential negative interactions between wild and domesticated pollinators.

ecology↗

bioRxiv2019

Segregation of floricolous ants along latitudinal and urbanization gradients

Recent call has been made to study the biogeography of species interactions in order to better understand ecosystems states and processes, as well as their response to global anthropogenic disturbances. Ants (Formicidae) are a dominant group of arthropods with a central role in ecosystem functioning. Many ant species, those feeding on liquids, are floricolous and consume nectar. The biogeography of ant-flower interactions is still poorly studied and especially in temperate area. Here we quantify variations in ant-flower interaction frequency in response to latitudinal and urbanization gradients at a country scale.\n\nWe used data from a flower-visitor monitoring program that includes pictures on 2511 flower plants across Continental France (Mainland) and over 4 years. We analysed the occurrence of the ant-flower interactions along two gradients: latitude and urbanization, this for 10 ant taxa corresponding to different taxonomical level (from family to species).\n\nAnts visited 26 % of the sampled plants. Most of the observed ant-flower interaction involved the subfamily Formicinae (82.1 %), followed by Myrmicinae and Dolichoderinae (6.9 % and 4.6 % respectively). Globally, (i) the probability of occurrence was negatively related to latitudes (ii) and to urbanization at lower latitude. (iii) Responses to latitude among sub families, genus and species level responses were segregated and taxonomically aggregated.\n\nAt lower taxonomic levels we found clear latitudinal niche partitioning among ant taxa suggesting that competition, on both evolutionary and ecological time scales, is a major process structuring ant communities. Finally, our results highlight that the effects of large scale perturbation like urbanization can vary and affect latitudinal gradient.

ecology↗

bioRxiv2018

Proteomic Analysis of Urine from California Sea Lions (Zalophus californianus): a Resource for Urinary Biomarker Discovery

Urinary markers for the assessment of kidney diseases in wild animals are limited, in part, due to the lack of urinary proteome data, especially for marine mammals. One of the most prevalent kidney diseases in marine mammals is caused by Leptospira interrogans, which is the second most common etiology linked to stranding of California sea lions (Zalophus californianus). Urine proteins from eleven sea lions with leptospirosis kidney disease and eight sea lions without leptospirosis or kidney disease were analyzed using shotgun proteomics. In total, 2694 protein groups were identified and 316 were differentially abundant between groups. Major urine proteins in sea lions were similar to major urine proteins in dogs and humans except for the preponderance of resistin, lysozyme C, and PDZ domain containing 1, which appear to be over-represented. Previously reported urine protein markers of kidney injury in humans and animals were also identified. Notably, neutrophil gelatinase-associated lipocalin, osteopontin, and epidermal fatty acid binding protein were elevated over 20-fold in the leptospirosis-infected sea lions. Consistent with leptospirosis infection in rodents, urinary proteins associated with the renin-angiotensin system were depressed, including neprilysin. This study represents a foundation from which to explore the clinical use of urinary protein markers in California sea lions.\n\nAbbreviations

biochemistry↗