Biology subjects

Mari, L.

Publications and source records attributed to Mari, L..

16 recordsLinked to original sources

bioRxiv2026

DNA methylation profile is not inherited in offspring of a short-lived annual fish

Parental ageing can influence offspring through non-genetic mechanisms. The contribution of epigenetic inheritance parental effects still remains poorly understood. DNA methylation is a widespread regulator of gene expression that changes during development and ageing and can also act as a mediator of intergenerational effects. We tested whether age-related changes in parental DNA methylation are transmitted to offspring in the short-lived turquoise killifish (Nothobranchius furzeri, Cyprinodontiformes). Using reduced-representation sequencing, we quantified genome-wide DNA methylation and examined methylation dynamics at individual loci. The overall proportion of methylated CpG sites increased during early ageing but declined at later ages, revealing a non-linear trajectory with substantial among-individual variation. Despite these age-related changes, we found no evidence that parental methylation patterns were transmitted to offspring, either at the genome-wide level or at individual loci. Our findings indicate that although DNA methylation undergoes pronounced age-dependent remodelling in adult killifish, these changes are not detectably inherited by the next generation. We discuss these results in the context of epigenetic inheritance and ageing in vertebrate model systems.

evolutionary biology↗

bioRxiv2026

Early life thermal plasticity and adaptive divergence among populations of Arctic charr (Salvelinus alpinus)

Climate warming alters the thermal environment experienced by ectotherms, whose physiological performance and fitness are constrained by temperature. Early life stages are often the temperature-sensitive phases of the life cycle, particularly in freshwater stenotherms such as the Arctic charr (Salvelinus alpinus). In this study, we used a common garden approach to compare the response and phenotypic plasticity of four charr populations to warmer conditions. These populations inhabit thermally contrasted lakes, including both native and introduced populations. We reared embryos at either an optimal (5{degrees}C) or a warmer (8.5{degrees}C) temperature. We tested adaptive divergence among populations in four traits (survival, incubation duration, body length and yolk sac volume) using Qst - Fst comparisons. We found that warmer temperature reduced body size, survival and incubation time, while thermal reaction norms differed among populations. Unexpectedly, populations originating from warmer environments did not consistently exhibit higher trait values under elevated temperatures. In contrast, the colder high-altitude population exhibited higher survival rates and lower yolk reserves for a given size under heat stress than the other populations. Our results highlight substantial variation among populations in responses to heat stress, emphasizing the complexity of predicting population responses to climate warming.

evolutionary biology↗

bioRxiv2025

Suppression of non-canonical autophagy induces endothelial and cardiac dysfunction

BackgroundWhile roles for canonical autophagy in the pathophysiology of cardiovascular disease have been established, we have limited understanding of the non-canonical functions of autophagy proteins in this context. LC3-asssociated endocytosis (LANDO) is a novel non-canonical function of autophagy proteins, in which LC3 (microtubule-associated protein light chain 3) is conjugated to early endosome membranes using a portion of the canonical autophagy machinery, and functions in the endocytic recycling of several plasma membrane proteins. Here we ask whether perturbation of LANDO can promote cardiovascular pathogenesis. MethodsCardiac and endothelial functions were assessed by echocardiography and flow-mediated dilatation in mice lacking Rubicon (Rubcn-/-) or the WD domain of ATG16L1 (Atg16l1{Delta}WDki), two known effectors of LANDO. Mice with conditional depletion of Rubicon in the endothelial, myeloid and cardiomyocyte compartments were used as well. Three-dimensional murine cardiac vasculature leakiness was investigated by light sheet fluorescence microcopy. Endothelial activation induced by shear stress was characterized in vitro in primary endothelial cells isolated from murine lungs and human aortic endothelial cells. Associations between genetically predicted expression of candidate genes involved in LANDO and human cardiovascular parameters were studied in the Young Finns Study and the UK Biobank. ResultsCompared to littermate controls, young Rubcn-/- and Atg16l1{Delta}WDki mice showed a decrease in cardiac and endothelial functions, as did mice with endothelium-specific deficiency. VEGFR2 recycling to the plasma membrane and nitric oxide pathway during shear stress were disrupted in LANDO-deficient primary murine and human endothelial cells. Proteomic analysis in primary human aortic endothelial cells revealed an upregulation of intracellular hemoglobin subunit alpha (Hb-) upon shear stress, which was blunted when RUBCN was ablated. Genetic expression studies uncovered several candidate genes related to LANDO that correlated with cardiovascular parameters. These included the retromer complex subunit VPS29, disruption of which decreased Hb- expression levels in human endothelial cells. ConclusionsOur data support a pivotal role of non-canonical functions of autophagy proteins in recycling VEGFR2 upon shear stress activation in endothelial cells together with Hb- expression that may contribute to the etiology of cardiovascular diseases.

physiology↗

bioRxiv2025

Reactive persistence of riverine metapopulations

Understanding the conditions that favor the persistence of metapopulations inhabiting riverine landscapes (riverscapes) is critical to guiding conservation and restoration efforts aimed at preserving biodiversity and ecological integrity in freshwater environments. In this study, we present a modeling framework to examine the transient persistence of fluvial metapopulations---the temporary occupation of riverscape patches by a metapopulation expected to become extinct in the long run. Our approach is theoretically grounded in the concept of ecological reactivity, which effectively complements asymptotic stability analysis in the study of the short-term response of ecological systems to impulsive perturbations of otherwise stable steady states. Our results suggest that, under ecohydrological conditions conducive to reactive metapopulation extinction equilibria, a metapopulation asymptotically bound to extinction can still colonize parts of the riverscape for significant periods of time. We also find that, in the presence of repeated positive perturbations of the extinction equilibrium, the temporal scales associated with these transient phenomena may allow for reactive pseudo-persistence. This phenomenon involves an arbitrarily long delay in the eventual extinction of the metapopulation, which may occur well below the deterministic extinction threshold. Identifying the ecohydrological drivers of reactivity-driven metapopulation persistence and the riverscape patches that contribute most to transient metapopulation dynamics over different temporal scales may provide valuable suggestions for the spatial prioritization of conservation and restoration efforts.

ecology↗

bioRxiv2025

Does generalism drive pollinators' abundance, persistence and regional distribution? Insights from an ecological model

The functioning of plant-pollinator mutualistic networks is crucial for ecosystem service provisioning and biodiversity maintenance. However, multiple drivers of global change are causing an alarming decline of wild pollinators abundance and richness. We propose an ecological, process-based mathematical model describing the dynamics of pollinators and plants, properly mediated by reward resources. Our model explicitly accounts for the main interactions of both facilitative and competitive nature that occur both within and between the two guilds. We apply our model to a broad set of real communities in fragmented landscapes to investigate the mechanisms that link the architecture of the interaction networks, the pollinators temporal persistence and abundance at the community level, and their rarity at the landscape level. Our results suggest that few generalist pollinators form a core of abundant, persistent and widely distributed species, while a lower number of mutualistic partners is generally associated with low abundance, low persistence and high turnover between patches. Specialists, however, are crucial to maintaining high levels of biodiversity within the community. This finding highlights the importance of ecological connectivity, through which local extinctions can be counter-balanced by recolonizations. Our analysis shows how a mechanistic model accounting for the structure of plant-pollinator networks can serve as a tool to investigate important ecological mechanisms driving community composition, dynamics and the resulting species distribution patterns.

ecology↗

bioRxiv2025

Effects of neuromuscular priming with spinal cord transcutaneous stimulation on lower limb motor performance in young active males

This study investigated the effects of non-invasive spinal cord transcutaneous stimulation (scTS) applied during an exercise-based priming protocol on the neuromuscular performance of lower limbs in young active males. Twelve volunteers (age: 22.7{+/-}2.1 years) participated in this randomized crossover, sham-controlled study. Maximal voluntary contraction and low-level torque steadiness of knee extensors as well as maximal explosive extension of lower limbs were assessed before and after the priming protocol with scTS or sham stimulation over a total of four experimental sessions. Further, characteristics of evoked potentials to scTS related to spinal circuitry excitability were assessed in supine position before and after the scTS priming protocol. The exercise component of the [~]25-minute priming protocol consisted of low-volume, low- and high-intensity lower limb motor tasks. scTS priming protocol tended to increase or maintain maximum isometric torque during knee extension (4.7%) as well as peak force (0.2%) and rate of force development (6.0%) during explosive lower limb extensions, whereas Sham priming protocol tended to decrease them (-4.3%, -3.3% and -15.1% respectively). This resulted in significant interactions (p=0.001 to 0.018) and medium-large differences between scTS and Sham protocols. These findings were associated with meaningful trends of some neurophysiological variables. Conversely, priming protocols did not affect low-level torque steadiness. Overall, the application of scTS during the proposed priming protocol enhanced lower limb maximal performance compared to Sham priming protocol. Future studies are warranted to assess the implementation of optimized scTS and exercise-based priming protocols during training and rehabilitation programs that include high-intensity neuromuscular efforts. NEW & NOTEWORTHYSpinal cord transcutaneous stimulation applied during an exercise-based priming protocol enhanced relevant aspects of lower limb maximal performance during isometric and explosive efforts when compared to sham stimulation; this was associated with meaningful trends of some neurophysiological variables. Conversely, neither priming protocol modulated the control of low-level, non-fatiguing torque steadiness task.

physiology↗

bioRxiv2025

Conspecific brood parasitism in the barn swallow (Hirundo rustica)

Conspecific brood parasitism (CBP) has been reported in many altricial avian species, yet its prevalence and underlying behavioural mechanisms remain poorly understood. We studied CBP in the barn swallow (Hirundo rustica), a species in which conspecific brood parasitism has been reported. We conducted parentage analysis on 1945 barn swallow broods involving 7816 offspring. Samples were collected over 12 breeding seasons at 5 colonies/populations. Contrary to expectations, we identified only six cases of CBP (0.3 % of broods). By identifying all individuals involved, i.e. the parasitic females, the female hosts and the males that fathered the parasitic eggs, we determined these cases of CBP resulted most likely from either a failed nest take-over (three times), the disappearance of a female partner or a disruption caused by researchers while only one case could be interpreted as a result of females mixed reproductive tactic. Based on a review of the literature on CBP in seven other Hirundinidae, we conclude that the only reliable evidence for CBP comes from cliff swallows (Petrochelidon pyrrhonata). Studies on other species either failed to identify the parasitic females or do not present sufficient evidence supporting the occurrence of CBP. Several studies relied on the appearance of two eggs in a nest within 24 hours to conclude that CBP occurred. However, based on the parentage analysis, we show that CBP only occurred in one out of 11 such cases in our barn swallow data. Our findings highlight that CBP is rare in our barn swallow populations, and have been likely overestimated in other studies. We emphasize the importance of frequent nest checks and rigorous genetic validation in CBP research. Overall, our results challenge existing assumptions about the prevalence of CBP and provide insights into the behavioural mechanisms that lead to CBP, with ecological and evolutionary implications.

ecology↗

bioRxiv2025

Recent breeding experience improves egg ejection behaviour

Recognizing ones own eggs is crucial for birds, especially for hosts of brood parasites that must identify and reject different-looking parasitic eggs. While birds seem to possess a template image of their eggs, whether it is innate or learnt remains unclear. We addressed this question by experimentally inserting either artificial mimetic eggs (ME) or non-mimetic eggs (NME) into the nests of barn swallows (Hirundo rustica) during pre-laying stage. Our individually marked population allowed a unique comparison between naive first-time breeders and experienced females, as well as females with old (from a previous season) and recent (from the previous breeding attempt within the same season) experience allowing to investigate the role of memory. We found that both naive and experienced females ejected ME and NME at similar rates, indicating that the template image is neither innate nor learnt and does not play a primary role in egg recognition. Instead, our findings suggest that awareness of own egg-laying is the crucial mechanism at play, and may facilitate nest sanitation behaviour. Finally, we provide the first evidence that this mechanism improves with recent breeding experience. Future studies should investigate the role of non-visual factors that may modulate nest sanitation, such as endocrine regulation.

animal behavior and cognition↗

bioRxiv2024

Machine learning outcompetes human assessment in identifying eggs of a conspecific brood parasite

Avian brood parasitism provides an exceptional system for studying coevolution. While conspecific brood parasitism (CBP) is more common than interspecific parasitism, it is less studied due to the challenge of detecting parasitic eggs, which closely resemble those of the host. Although molecular genotyping can accurately detect CBP, its high cost has led researchers to explore egg appearance as a more accessible alternative. Barn swallows (Hirundo rustica) are considered conspecific brood parasites, but identifying parasitic eggs has traditionally relied on human visual assessment. Here, we used UV-visible photographs of non-parasitized barn swallow clutches and simulated parasitism to compare the accuracy of human assessment with automated methods. In two games, participants and models identified parasitic eggs from six or two options. While humans performed better than chance (72% and 87% accuracy), they still made significant errors. In contrast, the automated supervised model was far more reliable, achieving 95% and 97% accuracy. We think that the model outperformed humans due to its ability to analyse a broader range of visual information, including UV reflectance, which humans cannot perceive. We recommend using supervised models over human assessment for identifying conspecific parasitic eggs and highlight their potential to advance research on evolution of egg colouration.

zoology↗

bioRxiv2023

Helminth ecological requirements shape the impact of climate change on the hazard of infection

Outbreaks and spread of infectious diseases are often associated with seasonality and changes caused by global warming. Free-living stages of soil-transmitted helminths are highly susceptible to environmental drivers, however, how multiple climatic variables affect helminth species, and the long-term consequences of these interactions, is poorly understood. We used experiments on nine trichostrongylid species to develop a temperature- and humidity-dependent model of infection hazard, which was then implemented at the European scale under climate change scenarios. Intestinal and stomach helminths exhibited contrasting climatic responses, with the former group strongly affected by temperature while the latter primarily impacted by humidity. These differences generated seasonal changes in the timing and intensity of the infection hazard and spatial heterogeneities within and between the two groups. A future range expansion of both groups toward northern latitudes is expected to create new opportunities for the co-circulation of the studied helminth species.

ecology↗

bioRxiv2023

Phosphatidylserine clustering by membrane receptors triggers LC3-associated phagocytosis.

LC3-associated phagocytosis (LAP) represents a non-canonical function of autophagy proteins in which ATG8 family proteins (LC3 and GABARAP proteins) are lipidated onto single-membrane phagosomes as particles are engulfed by phagocytic cells1-4. LAP plays roles in innate immunity5, inflammation and anti-cancer6 responses and is initiated upon phagocytosis of particles that stimulate Toll-like receptors (TLR), Fc-receptors, and upon engulfment of dying cells6. However, how this molecular route is initiated remains elusive. Here we report that receptors that engage LAP enrich phosphatidylserine (PS) in the phagosome membrane via membrane-proximal domains that are necessary and sufficient for LAP to proceed. Subsequently, PS recruits the Rubicon-containing PI3-kinase complex to initiate the enzymatic cascade leading to LAP. Manipulation of plasma membrane PS content, PS-binding by Rubicon, or the PS-clustering domains of receptors prevents LAP and phagosome maturation. We found that pharmacologic inhibition of PS clustering promotes the ability of dendritic cells to induce anti-cancer responses to engulfed tumor cells. Therefore, the initiation of LAP represents a novel mechanism of PS-mediated signal transduction upon ligation of surface receptors.

cell biology↗

bioRxiv2022

Modeling the contribution of antibodies to the within-host dynamics of single and dual helminth infections in a natural system

Within-host models of infection can provide important insights into the processes that affect parasite spread and persistence in host populations. However, modeling is often limited by the availability of empirical data, a problem commonly encountered in natural systems. Here, we used six years of immune-infection observations of two gastrointestinal helminths (Trichostrongylus retortaeformis and Graphidium strigosum) from a population of European rabbits (Oryctolagus cuniculus) to develop an age-dependent, within-host mathematical model that explicitly included species-specific and cross-reacting antibody (IgA and IgG) responses to each helminth in hosts with single or dual infections. Different models of single infection were formally compared to test alternative mechanisms of parasite regulation. The two models that best described single infections of each helminth species were then coupled through antibody cross-immunity to examine how the presence of one species could alter the host immune response to, and the within-host dynamics of, the other species. For both single infections, model selection suggested that either IgA or IgG responses could equally explain the observed parasite intensities at different host age. However, the strength of this response drastically changed between the two helminths, being stronger against T. retortaeformis than against G. strigosum and causing contrasting age-intensity profiles. When the two helminths coinfect the same host, we found a decrease of the species-specific immune response to both species together with an asymmetric cross-immune response driven by IgG. Changes in the level and affinity of antibodies from single to dual infections contributed to the significant increase of both helminth abundances. By combining mathematical modeling with immuno-infection data, our work provides a model framework for disentangling some of the complexities generated by host-parasite and parasite-parasite interactions from natural systems. Our approach thus offers a tractable general tool to examine immune-infection relationships within hosts. Author summaryThe host immune response often plays a critical role in regulating parasite dynamics and transmission. We developed a mathematical model to evaluate whether and how the observed variation in host antibody responses could explain the relative differences in the abundance of two parasite species in hosts with single and dual infections from a natural rabbit population. Our results indicated that either IgA or IgG could describe the contrasting trends of the two parasites in rabbits with single infections. Specifically, antibodies appeared to control T. retortaeformis, while the effect was less clear for G. strigosum. For dual infections, we found a weaker specific antibody response against both helminths and an asymmetric cross-immunity, which could explain the significantly greater intensities observed for T. retortaeformis and, secondly, for G. strigosum. Our within-host mathematical framework provides a plausible mechanism for the mediated role of antibodies in hosts with single and dual parasite infections, and how the strength of these infection-immune interactions changes with host age. This model framework offers a way forward to our understanding of the within-host processes that generate individual variation in infection and is relatively flexible to be applied to other natural systems.

immunology↗

bioRxiv2021

The Enemy of my Enemy is my Friend: Immune-Mediated Facilitation Contributes to Fitness of Co-Infecting Helminths

Our conceptual understanding of immune-mediated interactions between parasites is rooted in the theory of community ecology. One of the limitations of this approach is that most of the theory and empirical evidence has focused on resource or immune-mediated parasite competition and yet, there is ample evidence of positive interactions between species that could be generated by immune-mediated facilitation. Here, we develop an immuno-epidemiological framework and apply it to longitudinal infection data of two gastrointestinal helminths that infect a population of free-living rabbits to investigate, through model testing, the mechanisms of immune-mediated facilitation in dual infections. Simulations show that weakened, species-specific IgA antibody responses and unequal, albeit low, IgA cross-reactions explain higher parasite intensities in dual compared to single infections, for both helminths. Simulations also show that rabbits with dual infections shed more free-living stages that survive fort longer in the environment, implying greater onward transmission than hosts with single infections. These findings support the hypothesis that the two helminths interact through immune-mediated facilitation which contributes to greater fitness and the long-term co-circulation of both species in the host population.

ecology↗

bioRxiv2021

Analysis of amino acid change dynamics reveals SARS-CoV-2 variant emergence

Since its emergence in late 2019, the diffusion of SARS-CoV-2 is associated with the evolution of its viral genome1,2. The co-occurrence of specific amino acid changes, collectively named virus variant, requires scrutiny (as variants may hugely impact the agents transmission, pathogenesis, or antigenicity); variant evolution is studied using phylogenetics3-6. Yet, never has this problem been tackled by digging into data with ad hoc analysis techniques. Here we show that the emergence of variants can in fact be traced through data-driven methods, further capitalizing on the value of large collections of SARS-CoV-2 sequences. For all countries with sufficient data, we compute weekly counts of amino acid changes, unveil time-varying clusters of changes with similar - rapidly growing - dynamics, and then follow their evolution. Our method succeeds in timely associating clusters to variants of interest/concern, provided their change composition is well characterized. This allows us to detect variants emergence, rise, peak, and eventual decline under competitive pressure of another variant. Our early warning system, exclusively relying on deposited sequences, shows the power of big data in this context, and concurs to calling for the wide spreading of public SARS-CoV-2 genome sequencing for improved surveillance and control of the COVID-19 pandemic.

bioinformatics↗

bioRxiv2019

Modelling plastics exposure for the marine biota: Risk maps for fin whales in the Pelagos Sanctuary (North-Western Mediterranean)

The Mediterranean basin is among the most impacted marine ecoregions globally, being at the same time semi-enclosed by densely populated countries and crossed by trafficked maritime routes. Such anthropogenic pressure threatens both the qual-ity of its waters and the high biodiversity living in them, making the role of Marine Protected Areas (MPAs) crucial for pre-serving species suitable habitats. Under the European Union Marine Strategy Framework Directive, marine litter has been recognized as one of the principal causes of marine pollution, and public awareness on its environmental and biological impacts is raising. Using a quantitative and data-driven modelling approach, here we assess the presence of plastic waste within the feeding grounds of the fin whale Balaenoptera physalus, an endangered cetacean for which there is increasing evidence of impacts due to microplastic ingestion. To this end, we analyze a decade (2000 - 2010) of advection patterns of marine plastic litter, modelled with a Lagrangian approach. Particles are released in the MPA Pelagos, the International Sanctuary for the Protection of Mediterranean Marine Mammals (North-Western Mediterranean, between France, Italy and Monaco), from different sources (i.e., untreated waste along coasts, plastic discharged from rivers and plastic pollution released along maritime shipping routes). Risk of exposure of fin whales to microplastic pollution is evaluated by interlacing plastic litter distribution maps obtained through modelling with maps of suitable habitats obtained from the elaboration of satellite chlorophyll-a data in species-specific visited areas. Our modelling results show that all the three main sources of plastic litter taken into account clearly contribute to impacting cetaceans in the Sanctuary, yet in a different manner. The procedure formalized here can be extended to assess the risk caused by plastic pollution in other MPAs as well as to evaluate possible impacts on other taxa, thus informing targeted actions to tackle the complex issue of marine litter.

ecology↗

bioRxiv2018

Prawn aquaculture as a method for schistosomiasis control and poverty alleviation: a win-win approach to address a critical infectious disease of poverty

Recent evidence suggests crustacean snail predators may aid schistosomiasis control programs by targeting the environmental component of the parasites life cycle through predation of the snail species that serve as intermediate hosts of the parasite. We evaluate costs, benefits, and potential synergies between schistosomiasis control and aquaculture of giant prawns using an integrated bio-economic-epidemiologic model. We identified combinations of stocking density and aquaculture cycle length that maximize profit and offer disease control benefits for sustainable schistosomiasis control. We consider two prawn species in sub-Saharan Africa: the endemic, non-domesticated Macrobrachium vollenhovenii, and the non-native, domesticated Macrobrachium rosenbergii. We find that, at profit-optimal densities, both M. rosenbergii and M. vollenhovenii can complement conventional control approaches (mass drug treatment of people) and lead to sustainable schistosomiasis control. We conclude that integrated aquaculture strategies can be a win-win strategy in terms of health and sustainable development in schistosomiasis endemic regions of the world.

epidemiology↗