Simulating leaf growth dynamics through Metropolis-Monte Carlo based energy minimization

Abstract: Throughout their life span, plants maintain the ability to generate new organs, such as leaves. This is normally done in an orderly way by activating limited groups of dormant cells to divide and grow. It is currently not understood how that process is precisely regulated. We have used the VirtualLeaf framework for plant organ growth modeling to simulate the typical developmental stages of leaves of the model plant Arabidopsis thaliana. For that purpose the Hamiltonian central to the Monte-Carlo based mechanical equilibration of VirtualLeaf was modified. A basic two-dimensional model was defined starting from a rectangular grid with a dynamic phytohormone gradient that spatially instructs the cells in the growing leaf. Our results demonstrate that such a mechanism can indeed reproduce various spatio-temporal characteristics of leaf development and provides clues for further model development. (C) 2015 Elsevier B.V. All rights reserved

The Role of Tissue Cell Polarity in Monocot Development

Nature exhibits huge diversity in organ shape, and yet all organs start as small bud-like peripheral outgrowths. Combinations of different spatial and temporal developmental switches in shape determine final organ shape. In plants shape arises through growth, which is defined by axiality and growth rates. Here I tested three hypotheses for how developmental switches in shape could arise: (1) growth rates alone are altered, (2) axiality alone is altered (3) both growth rates and axiality are altered. Using a multidisciplinary approach I explored which of the hypotheses was true for developmental switches in shape during organ development in two monocot models: early grass leaf development and the Hooded barley mutant. Developmental switches in shape were first volumetrically described using 3D imaging. Using this framework, computational models were generated to formulate hypotheses which could account for the switches in shape. Model predictions were then tested using whole-mount immunolocalisation of SISTER OF PINFORMED 1 (SoPIN1), gene expression, and cell division and shape analyses. Synthetic biology was also used to generate a set of transgenic tools for future testing of the models. I found that a developmental switch in shape during early grass leaf development may arise through alterations in growth rates alone (hypothesis 1). In contrast, ectopic flower and wing formation in Hooded may arise through modulation of growth rates and axiality combined (hypothesis 2). In this case a single gene, BKn3, triggers the growth change, possibly through directly influencing tissue cell polarity (if axiality is defined by a polarity based axiality system), with differential effects on shape depending on where it is expressed. This suggests that novel developmental switches in shape could evolve due to single gene mutations, and that during evolution, modulation of growth may have been redeployed in different spatial and temporal patterns to trigger novel changes in shape, ultimately changing final form