Biology subjects

Vural, D.

Publications and source records attributed to Vural, D..

6 recordsLinked to original sources

bioRxiv2021

Extinction in complex communities as driven by adaptive dynamics

In a complex community, species continuously adapt to each other. On rare occasions, the adaptation of a species can lead to the extinction of others, and even its own. "Adaptive dynamics" is the standard mathematical framework to describe evolutionary changes in community interactions, and in particular, predict adaptation driven extinction. Unfortunately, most authors implement the equations of adaptive dynamics through computer simulations, that require assuming a large number of questionable parameters and fitness functions. In this study we present analytical solutions to adaptive dynamics equations, thereby clarifying how outcomes depend on any computational input. We develop general formulas that predict equilibrium abundances over evolutionary time scales. Additionally, we predict which species will go extinct next, and when this will happen.

ecology↗

bioRxiv2021

Suppressing evolution through environmental switching

Ecology and evolution under changing environments are important in many subfields of biology with implications for medicine. Here, we explore an example: the consequences of fluctuating environments on the emergence of antibiotic resistance, which is an immense and growing problem. Typically, high doses of antibiotics are employed to eliminate the infection quickly and minimize the time under which resistance may emerge. However, this strategy may not be optimal. Since competition can reduce fitness and resistance typically has a reproductive cost, resistant mutants fitness can depend on their environment. Here we show conditions under which environmental varying fitness can be exploited to prevent the emergence of resistance. We develop a stochastic Lotka-Volterra model of a microbial system with competing phenotypes: a wild strain susceptible to the antibiotic, and a mutant strain that is resistant. We investigate the impact of various pulsed applications of antibiotics on population suppression. Leveraging competition, we show how a strategy of environmental switching can suppress the infection while avoiding resistant mutants. We discuss limitations of the procedure depending on the microbe and pharmacodynamics and methods to ameliorate them.

ecology↗

bioRxiv2019

Evolution of specialization in dynamic fluids

Previously we found mechanical factors involving diffusion and fluid shear promote evolution of social behavior in microbial populations Uppal and Vural (2018). Here, we extend this model to study the evolution of specialization using realistic physical simulations of bacteria that secrete two public goods in a dynamic fluid. Through this first principles approach, we find physical factors such as diffusion, flow patterns, and decay rates are as influential as fitness economics in governing the evolution of community structure, to the extent that when mechanical factors are taken into account, (1) Generalist communities can resist becoming specialists, despite the invasion fitness of specialization (2) Generalist and specialists can both resist cheaters despite the invasion fitness of free-riding. (3) Multiple community structures can coexist despite the opposing force of competitive exclusion. Our results emphasize the role of spatial assortment and physical forces on niche partitioning and the evolution of diverse community structures.

bioinformatics↗

bioRxiv2017

Interdependence Theory of Tissue Failure: Bulk and Boundary Effects

The mortality rate of many complex multicellular organisms increase with age, which suggests that net aging damage is accumulative, despite remodeling processes. But how exactly do little mishaps in the cellular level accumulate and spread to become a systemic catastrophe? To address this question we present experiments with synthetic tissues, an analytical model consistent with experiments, and a number of implications that follow the analytical model. Our theoretical framework describes how shape, curvature and density influences the propagation of failure in a tissue subject to oxidative damage. We propose that aging is an emergent property governed by interaction between cells, and that intercellular processes play a role that are at least as important as intracellular ones.

biophysics↗

bioRxiv2017

Shearing in flow environment promotes evolution of social behavior in microbial populations

It is advantageous for microbes to form social aggregates when they commonly benefit from secreting a public good. However, cooperating microbial groups can be evolutionarily unstable, since a cheating strain that does not secrete the public good can reproduce quicker and take over. Here we study the effects of fluid advection patterns on group reproduction as a mechanism to enable or enhance social behavior in microbial populations. We use a realistic advection-diffusion-reaction model to describe microbial growth and mutation in a flow environment. Social groups arise naturally from our model as self-reproducing Turing patterns that can avoid mutant takeovers at steady state. Our central finding is that flow shear enables and promotes social behavior in microbes by limiting the spread of cheating strains. Regions of the flow domain with higher shear admits high cooperativity and large population density, whereas low shear regions are devoid of life due to opportunistic mutations.

bioinformatics↗

bioRxiv2017

Cheater-altruist synergy in immunopathogenic ecological public goods games

Much research has focused on the deleterious effects of free-riding in public goods games, and a variety of mechanisms that suppresses cheating behavior. Here we argue that under certain conditions cheating behavior can be beneficial to the population. In a public goods game, cheaters do not pay for the cost of the public goods, yet they receive the benefit. Although this free-riding harms the entire population in the long run, the success of cheaters may aid the population when there is a common enemy that antagonizes both cooperators and cheaters. Here we study models in which an immune system antagonizes a cooperating pathogen. We investigate three population dynamics models, and determine under what conditions the presence of cheaters help defeat the immune system. The mechanism of action is that a polymorphism of cheaters and altruists optimizes the average growth rate. Our results give support for a possible synergy between cooperators and cheaters in ecological public goods games.

ecology↗