bioRxiv Science⌕ Search

Biology subjects

Tarantino, R.

Publications and source records attributed to Tarantino, R..

2 recordsLinked to original sources

Agent-based modelling of a nematode system provides general insights into the evolutionary constraints and modulators of phenotypic plasticity, bet-hedging, and environmental homeostasis

In this study, I implemented an agent-based model aimed at exploring the competition between plastic and non-plastic genotypes of the dimorphic nematode Pristionchus pacificus in a digital environment with periodic fluctuations in food resources. Simulation scenarios monitoring frequency and time until fixation of two alleles of the developmental switch gene eud-1 were performed to capture emerging eco-evolutionary patterns generated by the interplay of three main variables, namely the intrinsic cost of plasticity, the timescale of environmental fluctuations, and the individual degree of plasticity. Interestingly, while intermediate-to-long periods of environmental stability and higher levels of plasticity might favour plastic strategists in a cost-free condition, the introduction and increase of inherent costs of plasticity could select for genotypes with either very low or high sensitivity to environmental cues, induce a sequential collapse in the frequency of fixation of plastic strains and time of coexistence between strains, and make invasions by non-plastic mutants/immigrants more likely until a plateau is reached. In addition, asymmetries in fitness between the two alternative phenotypes might be an almost necessary condition to enable the invasion of a non-plastic population by plastic genotypes. Collectively, while confirming previous theoretical findings, these outcomes may also uncover the sensitivity of a nematode system involving stochastic, conditional, and constitutive phenotype production to even small changes in key variables, suggesting the existence of phase transitions and critical evolutionary constraints.

evolutionary biology↗

An Agent-Based Model of Protein Polymerization Dynamics: Focus on the Actin System

Actin polymerization is a critical cellular process involved in a wide range of activities, from cell motility to cytokinesis. The complex behavior of this molecular system, resulting in three different phases (i.e., nucleation, elongation, and steady state) is clear by looking at the way these dynamics emerge from a large number of interactions between different proteins, regulatory elements, and signaling pathways. In this article, we present an agent-based model of actin polymerization dynamics implemented with the NetLogo simulation platform and focus on the time evolution of actin filaments length distribution in two dimensions starting from a pool of free G-actin monomers. Stochastic simulations were able to reproduce all main steps of the polymerization process in vitro, as well as two emerging patterns which have been previously discovered using alternative approaches, namely global treadmilling of F-actin filaments and competition between nucleation and elongation. The ability of the model to replicate relevant theoretical and experimental findings makes this new tool suitable for simulating complex molecular mechanisms by manipulating a limited set of parameters.

systems biology↗