Modeling the Virtual Plant / Bioinformatics


Modeling and in vivo live imaging of the Arabidopsis shoot apical meristem

Henrik Jönsson (1) , Marcus Heisler (2) , Bruce E. Shapiro (3) , Victoria Gor (3) , G. Venugopala Reddy (2) , Elliot M. Meyerowitz (2) , Eric Mjolsness (4)
1-Complex Systems Division, Dept. of Theoretical Physics, Lund University, Lund, Sweden
2-Division of Biology, California Institute of Technology, Pasadena CA, USA
3-Jet Propulsion Laboratory, California Institute of Technology, Pasadena CA, USA
4-Institute of Genomics and Bioinformatics, University of California, Irvine CA, USA

The shoot apical meristem (SAM) is an amazing dynamical system that provides a basis for the development of the complete aboveground part of a plant. Due to the high complexity of the SAM a mathematical description of the molecular and mechanical dynamics can be a useful tool for illuminating processes during its development. The basic idea is to use current biological knowledge, and to implement a model of the dynamics for simulation on a computer. Models that survive initial validations can be used to test different hypotheses in a much faster and broader way than what is allowed for in experiments. A modeling approach can then be used to guide experiments and laboratory efforts can be directed to those most likely to answer the biological question at hand.

We are applying an approach where in vivo live imaging of proteins and cells is used together with modeling to gain a better understanding of molecular processes within the SAM. The in vivo imaging technique, where proteins are fused to GFP, is used for dynamical tracking of the subcellular locations of important proteins throughout the complete SAM for a time period of days. In parallel we are building a software platform for simulation of developmental systems where the Arabidopsis SAM is used as the main biological target. The software allows for gene regulatory networks, molecular reactions, molecular transport between cells, cell growth and division, and mechanical interactions between cells. The relatively low number of cells in the Arabidopsis SAM allows for an in silico system where all the cells can be accounted for.

In this talk I will concentrate on models for phyllotaxis. Recent studies have indicated that auxin plays an essential role in determining organ position on the shoot apical meristem flanks. In particular, the distribution of auxin, as patterned by the putative efflux carrier PIN1 appears to directly determine the site of primordial emergence. Auxin and PIN1 are the main molecules in our models, and simulations are compared to the dynamics of the in vivo localization of the PIN1 protein. In models of different resolutions we show how regular patterns of auxin concentration peaks which resemble phyllotactic patterns can be obtained. Various simulation results will be presented along with analysis of the models.

References / Literature