Morphogenesis and gene regulatory networks in plants and animals:

A complex systems modelling approach

Growth of biological organisms is influenced by genes in individual cells and by interactions between cells. MORPHEX seeks to understand how interactions between genes cause cells to differentiate, grow and divide, and how exchanges between cells contribute to this process. The results should improve understanding of why the growing process sometimes fails, and how to overcome this. It will also lead to the expansion of computer-based experimentation on virtual organisms, and to the development of a generic platform for model-driven experimentation.

The main objective of the project is to obtain via a modelling and simulation approach a better understanding of the structure and dynamics of metabolic pathways of gene regulatory networks involved in the morphogenesis of animals and plants. We will concentrate on the development of two kind of sponges and on the organogenesis of carpel and anthers of a flowering plant. We will tackle the complexity involved in these processes by using concepts and tools arising from complex systems science. On the one side morphogenesis of sponges and organogenesis in flowering plants share many common concerns and approaches which justify the feasability of tackling them within a common complex systems framework. On the other side they consider distinguished features and methods of analysis that will guarantee a minimal genericity in the tools designed for the modelling process. The following problems will be addressed: provide a general model allowing to describe the underlying complex systems at different hiearchical levels in the same formalism; provide tools to extract concrete models description from experimental data; provide a way to conduct in-silico experiments. These tools will be applied on real data in order to significatively progress on the initial biological problems and will also be used to develop a modelguided data collection process. Moreover, the simulation tools will be modular enough to be customised or extended in the future for modelling complex systems arising from other fields. Our global goals can be summarised by three measurable and verifiable objectives: to build patiotemporal atlases of gene expression for flowering plants (for carpel and anther) and one for sponges; to web design, implement and finely tune models of development for reproductive organs in flowering plants and for sponges; to develop a customisable modelling and simulation platform adapted to the study of free complex systems in the context of development biology.
The freshwater sponge Lubomirskia baicalensis represents one of the most structured sponge species. The green colour of the specimens originates from the green algae which live in symbiosis with this animal.
An x-ray image of the freshwater sponge Lubomirskia baicalensis demonstrates the complex architectural structure of the hard skeleton of this animal.

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