Development of whole-plant metabolic models
Plants have organs with specialized tissues, each of them fulfilling specific functions during the life of a plant. Our group is interested in understanding the complex metabolic interactions between these subsystems. We reconstruct metabolic models of interacting cells, tissues and organs up to whole-plant metabolic models and we are currently in the course of integrating plant anatomical features into our metabolic models. In collaboration with the Szymanski group (IPK, FZ Jülich) we have developed Plant-Ed - a strategy computer game for SciCom and teaching. The game uses a whole-plant metabolic model dynamic flux-balance analysis to allow the gamer to develop resource allocation strategies for optimal growth and survival.
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Modeling and analysis of C3, C4 and CAM photosynthesis
Plants perform photosynthesis to convert light energy into chemical energy, supporting carbon and nitrogen assimilation and facilitating plant growth. Most plants employ C3 photosynthesis, where CO2 is directly fixed by the enzyme rubisco in the Calvin-Benson-Basham cycle. However, this process leads to photorespiration when rubisco fixes O2 instead of CO2. To overcome this, C4 and CAM photosynthesis have evolved as efficient alternatives, separating carbon fixation and rubisco activity to reduce photorespiration and increase water-use efficiency. Our research employs large-scale metabolic models to study the constraints and energetics of C3, C3-C4 intermediate, C4, and CAM photosynthesis. Additionally, we investigate the energetics of guard cell metabolism, which controls stomatal opening and water-gas exchange on leaf surfaces.
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Software development for metabolic network reconstruction and curation
Modelling predictions strongly depend on the quality of the underlying metabolic network reconstruction. These network reconstructions comprise hundreds to thousands of reactions which are typically assembled from metabolic pathway databases and are thus sensitive to annotation errors and error propagation. To address this issue we are supplying open-source software packages which offer coherent and reproducible curation workflows to the community. Recently, we developed CobraMod - a pathway-centric curation tool for constraint-based metabolic models.