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Fig. 4 | BMC Systems Biology

Fig. 4

From: Use of transcriptomic data for extending a model of the AppA/PpsR system in Rhodobacter sphaeroides

Fig. 4

Case (i) when only PpsRox binds and acts as a repressor of PS gene expression. Here, we show normalised SSE (sum of squared error) values as a measure of the goodness of fit. The normalised SSE values are calculated as described in the Method section. The black filled circles show the micro-array data obtained from our analysis. a Comparison of our model results with the obtained experimental data. The model best recapitulates the trends of pucB gene expression for parameters: I = 0.001, α = 6, β = 500, γ = 2.1, δ = 1, and Keq = ∞ (see parameter definitions in Additional file 1 and Table 1). Here, we have assumed that 30% O2 200–380 μM and 0% O2 = 0 μM as well as the total concentration of PpsR (PpsRtotal )= 100 nM. b A model output for the parameter combination used in panel a. It is to show that for the above combination of model parameters, the free (i.e. not bound to AppA) concentration of the reduced form of PpsR is very low in fact negligible. c The shape of the curve for different total PpsR concentrations (PpsRtotal). Note that in panel (a) and (c) level of oxygen is shown in terms of % of oxygen in the gas mixture bubbled in the culture during experiments. In panel (b) oxygen level is represented by a dimensional parameter O as it shows the simulation result obtained from the existing simple model [26]

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