DyCeModel: a tool for 1D simulation for distribution of plant hormones controlling tissue patterning

Abstract

To study the mechanisms of growth and development, it is necessary to analyze the dynamics of the tissue patterning regulators in time and space and to take into account their effect on the cellular dynamics within a tissue. Plant hormones are the main regulators of the cell dynamics in plant tissues; they form gradients and maxima and control molecular processes in a concentration-dependent manner. Here, we present DyCeModel, a software tool implemented in MATLAB for one-dimensional simulation of tissue with a dynamic cellular ensemble, where changes in hormone (or other active substance) concentration in the cells are described by ordinary differential equations (ODEs). We applied DyCeModel to simulate cell dynamics in plant meristems with different cellular structures and demonstrated that DyCeModel helps to identify the relationships between hormone concentration and cellular behaviors. The tool visualizes the simulation progress and presents a video obtained during the calculation. Importantly, the tool is capable of automatically adjusting the parameters by fitting the distribution of the substance concentrations predicted in the model to experimental data taken from the microscopic images. Noteworthy, DyCeModel makes it possible to build models for distinct types of plant meristems with the same ODEs, recruiting specific input characteristics for each meristem. We demonstrate the tool’s efficiency by simulation of the effect of auxin and cytokinin distributions on tissue patterning in two types of Arabidopsis thaliana stem cell niches: the root and shoot apical meristems. The resulting models represent a promising framework for further study of the role of hormone-controlled gene regulatory networks in cell dynamics.

Keywords

• computer modeling
• developmental trajectory
• input data
• genetic algorithm
• phytohormones