Team:TU-Munich/Modeling/Kill Switch

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Kill Switch Modeling

Purpose

The idea of our kill switch is to kill off our moss, as soon as it leaves the filter system. For this purpose two methods were proposed:

1. siRNA method: When some trigger is activated, siRNA is expressed inhibiting the expression of a vital gene
2. nuclease method: When some trigger is activated, a nuclease is released destroying the DNA of the cell

To decide between these two methods we modelled the vitality V of the cell (a number between 0 and 1, so a perfectly functional cell has V=1, a dead cell V=0) and depending on the tested method the concentration of siRNA R and nuclease N as appropriate. Both concentrations are normalized to the unit interval [0,1].

siRNA Model

Governing equations

We determined the governing equations of this model to be the following:

with initial conditions V(0) = 1 and R(0) = 0, where at the time t=0 the trigger is activated.

Calculation of stable points and analysis

The steady points V* and R* of this system have to satisfy Defining we get the following quadratic equation for the steady point of V

If α = 1, the unique steady point is .

To analyze the stability of these the eigenvalues of the Hessian matrix H must be computed. The eigenvalues are

These are both negative, so this is a stable point, i.e. an attractor.

If α ≠ 1, the steady points are

Now only one of these is in the sensible range, because

• for α > 1:
• for α < 1:

So there is only one steady point in this range, namely:

By expanding the fraction by we can rewrite V* as

So using the results from above, we get:

Now look at the eigenvalues of the Hessian matrix to analyze the stability

Defining , the eigenvalues are given by

So , which means that this is a stable attractor.

Result of the modelling

So for the siRNA there always is a stable point for the vitality between 0 and 1, so the moss is not killed-off completely, just impeded in its growth.

Interpretation

This result makes intuitive sense, because as the function of the cell is repressed the cell produces less of the inhibiting siRNA, which leads to a regeneration of the cell. Eventually a steady state at a lower vitality is reached, where the vitality stays constant.

Nuclease Modell

Governing equations

We determined the governing equations of this model to be the following:

with initial conditions V(0) = 1 and N(0) = 0, where at the time t=0 the trigger is activated.

Calculation of stable points and analysis

The steady points V* and N* of this system have to satisfy

The Hessian matrix of this system for the stable point is easy to solve

Conclusions

For a functional kill-switch it is necessary, that the cells are actually killed completely and not just live on with reduced vitality. So based on our modelling results the siRNA approach is not satisfactory, while the nuclease satisfies the requirement. As a result the team pursued the nuclease approach leading to our final kill-switch.

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85354 Freising, Germany

Email: igem@wzw.tum.de
Phone: +49 8161 71-4351