Cyanobacterial cells, as living organisms, respond to changes in external factors with a wide range of adaptive mechanisms that range from circadian oscillations and changes cell growth rate to the activation of stress-response pathways and the formation of surviving structures. In order to overcome with the environmental stresses a multitude of responses are triggered, covering different levels (metabolites, proteins and transcripts), with different intensities and time lags, reflecting the complexity of the biochemical network that is defined by the genetic and structural background of the organism.
The local experimental group is focused in studying the causal connectivity of the biochemical networks by integrating metabolomic, proteomic and transcriptomic analyses to study the responses upon different environmental stimuli. Functional reconstruction of target pathways will be studied by classical enzymatic activity assays and metabolic flux analyses using stable isotope labeling. We want to study what mechanisms are behind the responses to various environmental and nutritional factors and, how they define the growth rate and the accumulation of valuable metabolites in these species.
Phototrophic growth of a cyanobacterial cell is the outcome of a coordinated interplay of multiple entangled cellular processes. Given the intrinsic complexity of these processes and their interactions, mathematical modeling provides a vital tool to describe and eventually understand the operation of cyanobacterial growth. Mathematical modeling allows us to encapsulate current knowledge and to explore the range of possible behaviors of the system.
The local Modeling Group seeks to integrate different processes relevant to understand cyanobacterial cells in natural and controlled environments, ranging from photosynthetic light reactions and metabolism, to carbon concentration mechanisms and environmental interactions. Our approach includes the construction of large-scale descriptions of selected cellular processes, as well as simpler minimal models, to understand phototrophic growth in complex environments.
The main objective of the Informatics group is to develop e-cyanobacteria.org web application providing interactive presentation of the models.
Other objectives include the following topics:
- Formal specification of biological models
- Application of formal methods to model analysis including development of relevant efficient algorithms