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Week 6

Monday

Dry Work

Modelling

On friday, the two models for a proposed threshold switching system were created. Model 6.2 (competition between activator and repressor for a site on the DNA) was investigated; For different 'arabinose' (or other proposed input) and repressor concentrations the final level of output from the system was plotted. It was hoped that for different input levels (shown in the below graphs by the different green lines of output) the position of switching to low output would take place at different repressor levels due to the competitive nature of the system. Investigation into refining the model will take place. It is important to remember that whilst total output is what is seen, plotting rates of output production is necessary; the 'switching level' could be considered to be the point at which the rate of output production becomes zero. A standard way of designing this switching level is required.

Rate of output production against time for a series of set repressor levels showed that different steady rates of production were rapidly obtained (figure 1 below). The final rate of production (representative of the steady state) was plotted against repressor level, showing that the 'switching level' would occur in the region where the rate falls to zero (figure 2). Ideally, our system would have a well defined switching point, with a much sharper rise to high rates of output. This would likely be achieved by increasing hill coefficients, requiring a system with a greater degree of cooperativity.

Figure 1

figure 2

Ideally, for each set repressor level, the output will have a non-zero rate of production at different levels of arabinose input. The most useful plot here is rate of output against input concentration, with different set repressor levels as different lines on the same graph. This is equivalent to the competitive inhibtion of enzyme action, a sample plot of such a case is given below (figure 3).

figure 3

The feasibility of such a system investigated, the question is how to implement such a system?