Karanam, A. R. | bioRxiv Science

bioRxiv2023

Eukaryotic chemotaxis under periodic stimulation shows temporal gradient dependence

When cells of the social amoeba Dictyostelium discoideum are starved of nutrients they start to synthesize and secrete the chemical messenger and chemoattractant cyclic Adenosine Mono Phosphate (cAMP). This signal is relayed by other cells, resulting in the establishment of periodic waves. The cells aggregate through chemotaxis towards the center of these waves. We investigated the chemotactic response of individual cells to repeated exposure to waves of cAMP generated by a microfluidic device. When the period of the waves is short, the chemotactic ability of the cells was found to increase upon exposure to more waves, suggesting the development of a longer-term memory. This effect was not significant for longer wave periods. We show that the experimental results are consistent with a model that includes a slowly rising and decaying component that is activated by the temporal gradient of cAMP concentration. The observed enhancement in chemotaxis is relevant to populations in the wild: once sustained, periodic waves of the chemoattractant are established, it is beneficial to cells to improve their chemotactic ability in order to reach the aggregation center sooner.

biophysics↗

bioRxiv2021

BoolSim, a Graphical Interface for Open Access Boolean Network Simulations and Use in Guard Cell CO2 Signaling

Signaling networks are at the heart of almost all biological processes. Most of these networks contain a large number of components and often the connections between these components are either not known, or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to more detailed mathematical models but can be difficult to implement. Therefore, open source format of such models for community use is desirable. Here we present BoolSim, a freely available graphical user interface (GUI) that allows users to easily construct and analyze Boolean networks. BoolSim can be applied to any Boolean network. We demonstrate BoolSims application using a previously published network for abscisic acid-driven stomatal closure in Arabidopsis. We also show how BoolSim can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested and the model was iteratively modified based on experiments showing that ABA closes stomata even at near zero CO2 concentrations (1.5 ppm CO2). One Sentence SummaryThis study presents an open-source, graphical interface for the simulation of Boolean networks and applies it to an abscisic acid signaling network in guard cells, extended to include input from CO2.

plant biology↗