Biology subjects

Mobilia, M.

Publications and source records attributed to Mobilia, M..

8 recordsLinked to original sources

bioRxiv2026

Dynamics of fluctuating populations in multi-state switching environments

Microbial populations generally evolve in fluctuating environments under time-varying conditions. These are often described by binary switching models, sometimes seen as coarse-grained feast-famine cycles, in which resource availability switches abruptly between abundant and scarce conditions. However, experimental studies suggest that feast-famine environments actually exhibit more complex temporal dynamics. Here, we study how two strains, one growing slightly slower than the other, compete for the same resources in fluctuating environments comprising a finite number of intermediate states, each having its own carrying capacity. Environmental switching between these states and their carrying capacities represents gradual changes in nutrient availability. This class of multi-state stochastic switching models can be interpreted as a coarse-grained description of feast-famine cycles and allows us to investigate strain competition under the gradual recovery and depletion of resources. By computational and analytical means, we characterise the population dynamics in these multi-state fluctuating environments. In particular, we study how the switching rates and distribution of carrying capacities affect the population-size statistics, fixation probability, and mean fixation time. By comparing these results with their counterparts in binary environments, we clarify how the frequency and amplitude of environmental fluctuations influence population dynamics in coarse-grained feast-famine cycles.

biophysics↗

bioRxiv2025

Impaired Chylomicron Secretion Results in Reduced Body Fat and Increased Intestinal Fatty Acid Oxidation by Activation of Autophagy

Intestinal absorption of dietary lipid is essential for systemic lipid homeostasis; however, elevated postprandial plasma lipid levels are associated with obesity and increased risk for atherosclerotic cardiovascular disease. In humans and rodents, biological sex impacts dietary triglyceride absorption and males tend to have higher postprandial triglyceride levels compared to females, but the physiological basis for this is not well understood. Here, we show that the gene DENND5B is associated with body composition in humans and mice and that genetic deletion of Dennd5b in mice prevents postprandial plasma triglyceride elevations in both sexes. Our findings establish a role for this protein in intestinal chylomicron secretion and reveal a biological sex-biased differential impact of its deletion on body composition, dietary fatty acid uptake, and intestinal metabolism. Mechanistically, our findings implicate autophagy and mitochondrial beta oxidation in coping with enterocyte lipid accumulation due to impaired chylomicron secretion. This work extends the emerging concept that the intestinal epithelium may play a prominent role in oxidation of diet-derived fatty acids and suggests that this process may contribute to biological sex-based differences in postprandial lipemia and body composition. HighlightsO_LIThe DENND5B gene is required for dietary triglyceride absorption and is associated with metabolic phenotypes in humans and mice. C_LIO_LIDisruption of chylomicron secretion differentially affects body composition, dietary lipid absorption, and intestinal metabolic activity in male and female mice. C_LIO_LIIn mice, genetic disruption of Dennd5b results in lower body fat in both sexes, and increased lean mass only in males. C_LIO_LIMetabolic phenotypes in Dennd5b-deficient mice are driven by reduced absorption of dietary lipid characterized by enterocyte lipid retention and increased fecal lipid excretion. C_LIO_LIImpaired chylomicron secretion in Dennd5b-/- mice induces autophagy-mediated disposal of cellular triglyceride and increased fatty acid oxidation in intestinal tissue. C_LI

physiology↗

bioRxiv2025

Fixation and extinction in time-fluctuating spatially structured metapopulations

Bacteria evolve in volatile environments and complex spatial structures. Migration, fluctuations and environmental variability therefore have a significant impact on the evolution of microbial populations. Here, we consider a class of spatially explicit metapopulation models arranged as regular (circulation) graphs where wild-type and mutant cells compete in a time-fluctuating environment in which demes (subpopulations) are connected by slow cell migration. The carrying capacity is the same at each deme and endlessly switches between two values associated to harsh and mild environmental conditions. It is known that environmental variability can lead to population bottle-necks, following which the population is prone to fluctuation-induced extinction. Here, we analyse how slow migration, spatial structure, and fluctuations affect the phenomena of fixation and extinction on clique, cycle, and square lattice metapopulations. When the carrying capacity remains large, bottlenecks are weak and deme extinction can be ignored. The dynamics is thus captured by a coarse-grained description within which the probability and mean time of fixation are obtained analytically. This allows us to show that, in contrast to what happens in static environments, the mutant fixation probability depends on the rate of migration. We also show that the fixation probability and mean fixation time can exhibit a non-monotonic dependence on the switching rate. When the carrying capacity is small under harsh conditions, bottlenecks are strong, and the metapopulation evolution is shaped by the coupling of deme extinction and strain competition. This yields rich dynamical scenarios, among which we identify the best conditions to eradicate mutants without dooming the metapopulation to extinction. We offer an interpretation of these findings in the context of an idealised treatment strategy and discuss possible generalisations of our models.

biophysics↗

bioRxiv2024

Slow spatial migration can help eradicate cooperative antimicrobial resistance in time-varying environments

Antimicrobial resistance (AMR) is a global threat and combating its spread is of paramount importance. AMR often results from a cooperative behaviour with shared drug protection. Microbial communities generally evolve in volatile, spatially structured settings. Migration, space, fluctuations, and environmental variability all have a significant impact on the development and proliferation of AMR. While drug resistance is enhanced by migration in static conditions, this changes in time-fluctuating spatially structured environments. Here, we consider a two-dimensional metapopulation consisting of demes in which drug-resistant and sensitive cells evolve in a time-changing environment. This contains a toxin against which protection can be shared (cooperative AMR). Cells migrate between demes and connect them. When the environment and the deme composition vary on the same timescale, strong population bottlenecks cause fluctuation-driven extinction events, countered by migration. We investigate the influence of migration and environmental variability on the AMR eco-evolutionary dynamics by asking at what migration rate fluctuations can help clear resistance and what are the near-optimal environmental conditions ensuring the quasi-certain eradication of resistance in the shortest possible time. By combining analytical and computational tools, we answer these questions by determining when the resistant strain goes extinct across the entire metapopulation. While dispersal generally promotes strain coexistence, here we show that slow-but-nonzero migration can speed up and enhance resistance clearance, and determine the near-optimal conditions for this phenomenon. We discuss the impact of our findings on laboratory-controlled experiments and outline their generalisation to lattices of any spatial dimension. Author summaryAs the number of microbes resisting antimicrobial drugs grows alarmingly, it is of paramount importance to tackle this major societal issue. Resistant microbes often inactivate antibiotic drugs in the environment around them, and hence offer protection to drug-sensitive bacteria in a form of cooperative behaviour. Moreover, microbes typically are distributed in space and live in time-changing environments, where they are subject to random fluctuations. Environmental variability, fluctuations, and spatial dispersal all have a strong influence on the drug resistance of microbial organisms. Here we investigate the temporal evolution of antimicrobial resistance in time-varying spatial environments by combining computational and mathematical means. We study the dynamics of drug-resistant and sensitive cells in the presence of an antimicrobial drug, when microbes are spatially distributed across a (two-dimensional) grid of well-mixed sub-populations (demes). Cells migrate between neighbouring demes, connecting these sub-populations, and are subject to sudden changes of environment, homogeneously across all demes. We show that when the environment and the deme composition vary on the same timescale, the joint effect of slow migration and fluctuations can help eradicate drug resistance by speeding up and enhancing the extinction probability of resistant bacteria. We also discuss how our findings can be probed in laboratory experiments, and outline their generalisation to lattices of any dimension.

biophysics↗

bioRxiv2023

Enhancement of High-Density Lipoprotein-Associated Protease Inhibitor Activity Prevents Atherosclerosis Progression

BackgroundInflammatory cells within atherosclerotic lesions secrete various proteolytic enzymes that contribute to lesion progression and destabilization, increasing the risk for an acute cardiovascular event. The relative contributions of specific proteases to atherogenesis is not well understood. Elastase is a serine protease, secreted by macrophages and neutrophils, that may contribute to the development of unstable plaque. We have previously reported interaction of endogenous protease-inhibitor proteins with high-density lipoprotein (HDL), including alpha-1-antitrypsin, an inhibitor of elastase. These findings support a potential role for HDL as an endogenous modulator of protease activity. In this study, we test the hypothesis that enhancement of HDL-associated elastase inhibitor activity is protective against atherosclerotic lesion progression. MethodsWe designed an HDL-targeting protease inhibitor (HTPI) that binds to HDL and confers elastase inhibitor activity. Lipoprotein binding and the impact of HTPI on atherosclerosis was examined using mouse models. ResultsHTPI is a small (1.6 kDa) peptide with an elastase inhibitor domain, a soluble linker, and an HDL-targeting domain. When incubated with human plasma ex vivo, HTPI predominantly binds to HDL. Intravenous administration of HTPI to mice resulted in its binding to plasma HDL and increased elastase inhibitor activity on isolated HDL. Accumulation of HTPI within plaque was observed after systemic administration to Apoe-/- mice. To examine the effect of HTPI treatment on atherosclerosis, prevention and progression studies were performed using Ldlr-/- mice fed Western diet. In both study designs, HTPI-treated mice had reduced lipid deposition in plaque. Histology and immunofluorescence staining of aortic root sections were used to examine the impact of HTPI on lesion morphology and inflammatory features. ConclusionsThese data support the hypothesis that HDL-associated anti-elastase activity can improve the atheroprotective potential of HDL and highlight the potential utility of HDL enrichment with anti-protease activity as an approach for stabilization of atherosclerotic lesions.

physiology↗

bioRxiv2023

Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance

There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can often be viewed as a cooperative behavior leading to the coexistence of resistant and sensitive cells in large populations and static environments. This picture is however greatly altered by the fluctuations arising in volatile environments, in which microbial communities commonly evolve. Here, we study the eco-evolutionary dynamics of a population consisting of an antimicrobial resistant strain and microbes sensitive to antimicrobial drugs in a time-fluctuating environment, modeled by a carrying capacity randomly switching between states of abundance and scarcity. We assume that antimicrobial resistance is a shared public good when the number of resistant cells exceeds a certain threshold. Eco-evolutionary dynamics is thus characterized by demographic noise (birth and death events) coupled to environmental fluctuations which can cause population bottlenecks. By combining analytical and computational means, we determine the environmental conditions for the long-lived coexistence and fixation of both strains, and characterize a fluctuation-driven antimicrobial resistance eradication mechanism, where resistant microbes experience bottlenecks leading to extinction. We also discuss the possible applications of our findings to laboratory-controlled experiments.

biophysics↗

bioRxiv2020

Microbial species interactions determine community diversity in fluctuating environments

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.

ecology↗

bioRxiv2019

Spatial patterns emerging from a stochastic process near criticality

There is mounting empirical evidence that many communities of living organisms display key features which closely resemble those of physical systems at criticality. We here introduce a minimal model framework for the dynamics of a community of individuals which undergoes local birth-death, immigration and local jumps on a regular lattice. We study its properties when the system is close to its critical point. Even if this model violates detailed balance, within a physically relevant regime dominated by fluctuations, it is possible to calculate analytically the probability density function of the number of individuals living in a given volume, which captures the close-to-critical behavior of the community across spatial scales. We find that the resulting distribution satisfies an equation where spatial effects are encoded in appropriate functions of space, which we calculate explicitly. The validity of the analytical formulae is confirmed by simulations in the expected regimes. We finally discuss how this model in the critical-like regime is in agreement with several biodiversity patterns observed in tropical rain forests.

ecology↗