Early signatures of regime shifts in gene expression dynamics

Abstract

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene expression dynamics are less systematically investigated. In this paper, we consider sudden regime shifts in the gene expression dynamics described by a foldbifurcation model involving bistability and hysteresis. We consider two alternative models, Models 1 and 2, of competence development in the bacterial population B.subtilis and determine some early signatures of the regime shifts between competence and vegetative state. We use both deterministic and stochastic formalisms for the purpose of our study. The early signatures studied include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, skewness and a ratio of two mean first passage times. Some of the signatures could provide the experimental basis for distinguishing between bistability and excitability as the correct mechanism for the development of competence.

Eluding catastrophic shifts

“…Similar facilitation mechanisms appear in a vast variety of examples in population ecology (Allee effect) (19); neuroscience (synaptic facilitation) (20); systems biology (21); and, in general, climate, biological, and social sciences (1,22,23).…”

“…Predicting and anticipating catastrophic regime shifts and distinguishing them from their smoother counterparts constitutes a timely subject with a vast number of important applications, including the prevention of biodiversity collapse or radical climate changes as the result of anthropogenic pressures (21,(29)(30)(31)(32). Indeed, early warning indicators of regime shifts (such as increasingly slower return rates from perturbation and rising variance) have been proposed, and some of them have been empirically tested (9,14,30,31), even if their degree of robustness and reliability is still under debate (33,34).…”

“…Indeed, early warning indicators of regime shifts (such as increasingly slower return rates from perturbation and rising variance) have been proposed, and some of them have been empirically tested (9,14,30,31), even if their degree of robustness and reliability is still under debate (33,34). Most of these approaches rely on understanding derived from simple deterministic equations in which spatial dependence is averaged out (21,(29)(30)(31)(32). Recently, spatially explicit versions of these deterministic approaches have also been considered in the literature (35).…”

Relation between stability and resilience determines the performance of early warning signals under different environmental drivers

“…Theoretical and empirical studies have found that signatures of "critical slowing down" in the spatiotemporal dynamics may be used to indicate impending tipping points (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29). These indicators are based on the fact that the dynamics around the equilibrium of a system slows down near a tipping point (19,30,31).…”

Gated Bayesian Networks

“…While we will not delve into deeper detail why such changes may occur, the phenomenon of regime changes has been studied extensively in the fields of ecology [60,61,62], economy and finance [63,64,65,66,67], and biology [68,69]. Given the diversity of fields studying regimes, there is no general consensus of what a regime entails, nor its length or abruptness.…”