In the initial phase, we shall focus on reactions that occur in PSII after an exposure to a strong actinic light. Later, we shall add the other important components of the photosynthetic machinery and assume also moderate and low irradiance.
Motivation: The evolution of photosynthesis is, among other constraints, driven by selection of genes for photochemical energy conversion that is robust and, yet effective, in a fluctuating light environment. Variable cloud cover, moving canopy and ocean waves are among the dynamic factors that have been shaping the photosynthetic regulation since the first ancestors of modern plants emerged. It is sensible to assume that the regulatory networks concerting the activity of the two photosystems and of the coupled dark reactions are tuned to be highly responsive to a fluctuating light (Pearcy 1990, Pearcy et al. 1994, Kuelheim et al. 2002, Zhu 2004). Similarly to complex technical systems (Csete and Doyle 2002), the dynamic regulation of photosynthesis relies on an interplay of multiple sensory, transmission and executive modules that can be studied by the tools of systems biology.
Here, we offer an open web platform for modeling and reverse engineering of photosynthetic dynamism. We shall implement and share models of photosynthesis using the universal standard of Systems Biology Mark-Up Languange (SBML, http://sbml.org). The photosynthetic response to particular light protocols will be simulated using primarily MATLAB and Simulink (MathWorks, http://www.mathworks.com). We are aware of parallel projects that are also oriented towards resolution of photosynthetic regulatory networks (e.g., Giersch 2000, Lebedeva et al. 2002, Zhu 2004). By offering an open web platform, we search for a pathway that is more rapid and with a faster feedback than achieved in printed journals.
First, we present two modeling projects:
- Highly structured fluorescence transients reflecting photosynthetic regulation were discovered in harmonically modulated irradiance (Nedbal and Brezina 2002, Nedbal et al. 2003). Molecular basis of the observed non-linear, upper harmonic modulation of the output signal is unknown. We predict that the newly discovered phenomenon will be instrumental in identifying the regulatory interactions that are responsible for the dynamism of photosynthesis in fluctuating light.
- The rapid OJIP fluorescence rise has been observed (Neubauer and Schreiber 1987, Strasser et al., 1995) and described using molecular models of Photosystem II (Stirbet et al. 1998, Lazar 2003). We feel that the model deserves further verification and refinement (Vredenberg and Bulychev 2002).
Credits: The models will be confronted with a database of experiments that are carried out using imaging and non-imaging fluorometers of Photon Systems Instruments, spol. s r.o. (Brno, Czech Republic, http://www.psi.cz). The experiments will be done in the Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic (http://www.uek.cas.cz) and of the Institute of Physical Biology of the University of South Bohemia, Nove Hrady (http://www.greentech.cz).
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