Prediction of UV dose-dependent threshold and validation results on wild type yeast cells at 20 J/m2 and 30 J/m2 UV doses. The figure shows the experimental measurements on WT cells irradiated at 20 J/m2 UV dose (top part) and at 30 J/m2 UV dose (bottom part), as well as the comparison with the corresponding simulation results. As the aim of these experiments was not to carry out a precise quantification of the PCNA ubiquitylated isoforms, but only to verify the prediction of computational analysis, they were conducted with a single repetition. (A-C) Comparison between the value of western blot quantification deriving from a single experiment, and the dynamics of mono-, di- and tri-ubiquitylated PCNA isoforms emerging from 100 independent stochastic simulations, executed starting from the same initial conditions (see Table 2 for molecular amounts and Table 3 for reaction constants), with an estimated number of DNA lesions equal to 4005 (A) and 6007 (C). Colored areas indicate the amplitude of stochastic fluctuations around the mean value . Data are plotted by using the units representation (see Additional file 5). (B-D) Comparison between the ratio of experimental (, left bars) and simulated (, right bars) ubiquitylated PCNA isoforms at every sampled time point. Mean and standard deviation bars of simulated results are plotted by using the normalized representation (see Additional file 5).
Amara et al. BMC Systems Biology 2013 7:24 doi:10.1186/1752-0509-7-24