Digital Plant: From Molecule to Organism
An integrative solution combining experimental biology, modelling, image analysis, engineering and statistics to understand how molecular components interact to give rise to complex plant structures.
In CPIB, we have created a heterogeneous research community where researchers from different disciplines work side-by-side to address key questions in plant biology. Through working so closely, we ensure that our models incorporate the latest experimental results and give experimental biologists the opportunity to test the latest model predictions.
Our open set up, enables experimental and theoretical biologists the opportunity to work together to test and reformulate hypotheses.
Our research into the digital plant focuses on three spatial scales:
- Cell-scale: Using bioinformatics and modelling, together with more traditional molecular-biology techniques, we are uncovering the gene regulatory networks that underpin a range of developmental processes, including anther dehiscence, tomato ripening and lateral root emergence.
- Tissue-scale: We are incorporating these single cell models into multi-cellular templates to create digital organs. As the cell-scale parameters are embedded within these templates, we see that emergent properties spontaneously arise and generate order within these structures. For example, current projects are analysing how hormone and microRNA transport lead to vasculature patterning, and are investigating how root growth is determined by the mechanical properties of the individual cells.
- Organism scale: We are taking models of individual tissues and embedding them within even larger frameworks to create virtual root or shoot networks. These will be used to predict how changes in environmental conditions (such as water, nutrient or light availability) affect growth.
Our models are principally based around the open source software OpenAlea. This provides a framework where our models can freely communicate with each other and with other members of the community.