Team/CINVESTAV-IPN-UNAM MX/equations.htm

The proteins in our regulatory system constitute a network of intermingling elements whose behavior can be narrow into basic interaction rules. Primarily in this part of the modeling we focused on the PpsR and AppA anti-repressor/repressor system and chose to model it using a system of ordinary differential equations. The systemӳ repressive activity varies with the redox (O2) state of the cell and Light intensity and thus we wondered how exactly these two variables affect the overall repressive level of PpsR over the expression of PS genes.

To do this we based ourselves on a previous work that had attempted to study this same regulatory system. [Pandey, Rakesh Flockerzi, Dietrich Hauser, Marcus JB Straube, Ronny. 2011. Modeling the light- and redox-dependent interaction of PpsR/AppA in Rhodobacter sphaeroides.] In addition to contacting the responsible authors and discussing this model, we chose to improve it based on recent publications and preliminary experimental results i.e. we introduced a more subtle way light and oxygen affects the protein concentration dynamic, which is exactly what we were interested in understanding better.

Because all this was done in Mathematica, we were able to generate an interactive graphical representation of the repressive strength over a range of conditions. This is really the strength of our work because with this model, we can make predictions in sillico as to how the organism will react to a given environmental surrounding and then go back to the lab and validate that prediction.