Team Virtual Plants

Overall Objectives
Scientific Foundations
New Results
Other Grants and Activities

Section: New Results

Meristem functioning and development

In axis 2 work focusses on the creation of a virtual meristem , at cell resolution, able to integrate the recent results in developmental biology and to simulate the feedback loops between physiology and growth. The approach is subdivided into several sub-areas of research.

Data acquisition and design of meristem models

Keywords : Meristem, laser microscopy, image reconstruction, cell segmentation, automatic lineaging.

Participants : Romain Fernandez, Jérôme Chopard, Frédéric Boudon, Christophe Godin, Vincent Mirabet, Jan Traas, Grégoire Malandain, Jean-Luc Verdeil.

This research theme is supported by the ATP CIRAD Meristem and the ANR GeneShape and FlowerModel projects.

Studies on plant development require the detailed observation of the tissue structure with cellular resolution. In this context it is important to develop methods that enable us to observe the inner parts of the organs, in order to analyse and simulate their behaviour. Here we focus on the apical meristems, that have been extensively studied using live imaging techniques and confocal microscopy. An important limitation of the confocal microscope lies in the data anisotropy. To overcome this limitation, we designed new protocols to achieve an accurate segmentation of the cells. Using these segmentations, a geometrical and topological representation of the meristem is built. Such representations may be used to analyze the meristem structure at cell level, to support the description of gene expression patterns and to initiate and assess virtual meristem simulations.

Transport models

Participants : Mikaël Lucas, Jérôme Chopard, Christophe Godin, Yann Guédon, Laurent Laplaze, Jan Traas, Michael Walker.

This research theme is supported by the ANR GeneShape project and a Post-doc Grant from CPIB.

The transport of plant hormones, proteines, water and sugars is critical to plant development. In particular, the active transport of the plant hormone auxin has been shown to play a key role in the initiation of organs at the shoot apex. Polar localized membrane proteins of the PIN1 and AUX/LAX family facilitate this transport and recent observations and models suggest that the coherent organization of these proteins in the L1 layer is responsible for the creation of auxin maxima, which in turn triggers organ initiation close to the meristem centre [37] [1] .

In the previous years, we built models of auxin transport in the L1 layer and inner tissues to understand the observed distribution of PIN transporters and study possible hypotheses related to their regulation. Now, we try to get farther in the understanding of auxin transport on two different systems.

Mechanical model

Participants : Jérôme Chopard, Christophe Godin, Jan Traas, Olivier Hamant [ ENS-Lyon ] .

This research theme is supported by the ANR project Virtual Flower and Geneshape projects.

The rigid cell walls that surround plant cells is responsible for their shape. These structures are under constraint due to turgor pressure inside the cell. To study the overall shape of a plant tissue and morphogenesis, its evolution throughout time, we therefore need a mechanical model of cells. We developed such a model, in which walls are characterized by their mechanical properties like the Young modulus which describes the elasticity of the material. Wall deformation results from forces due to turgor pressure. Growth results from an increase in cell wall synthesis when this deformation is too high. The final shape of the tissue integrate mechanically all the local deformation of each cell.

To model this process, we used a tensorial approach to describe both tissue deformation and stresses. Deformations were decomposed into elementary transformations that can be related to underlying biological processes. However, we showed that the observed deformations does not map directly local growth instructions given by genes and physiology in each cell. Instead, the growth is a two-stage process where genes are specifying by their activity a targeted shape for each cell (or small homogeneous region) and the final cell shape results from the confrontation between this specified shape and the physical constraints imposed by the cell neighbors. Hence the final shape of the tissue results from the integration of all these local rules and constraints at organ level. This work is being described in a paper which will be submitted for publication at the beginning of 2010.

Cell cycle model

Participants : Romain Fernandez, Christophe Godin, Pradeep Das, Jan Traas.

This research theme is supported by the ANR project Virtual Flower and Geneshape projects.

A very simple model of cell cycle is necessary to determine cell division events. Here cell division occurs when the cell volume gets above a certain threshold.

A model of cell division consistent with the observations coming from the confocal data is being investigated. The availability of 3-D geometric structures at cell resolution of real meristem and the possibility to follow their cell lineages will make it a unique opportunity to test in silico the validity of these cell division models.

Gene regulatory networks

Modelling gene activities within cells is of primary importance since cell identities correspond to stable combination of gene level activity.

Model integration

Participants : Mikaël Lucas, Michael Walker, Jérôme Chopard, Frédéric Boudon, Christophe Godin, Laurent Laplaze, Jan Traas.

This research theme is supported by the ATP CIRAD Meristem, the ANR project Carpel and the Sy-Stem European RTN Project.

Our approach consists of building a programmable tissue able to accept different modelling components. This includes a central data structure representing the tissue in either 2- or 3-D and able to grow in time, models of gene activity and regulation, models of signal exchange (physical and chemical) between cells and models of cell cycle (which includes cell division). For each modelling component, one or several approaches is investigated in depth, possibly at different temporal and spatial scales, using the data available from the partners (imaging, gene networks, and expression patterns). Approaches are compared and assessed on the same data. As an outcome of each modelling subtask, the objective of each submodel component will be to provide plugin components, corresponding to simplified versions of their models if necessary, that can be injected in the programmable tissue platform.


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