From 2014.igem.org

Safety Modeling

Safety approach of gene expression dynamics of tetracycline regulatory system

pTRE-Tet Off System

For clinical use and application, we are required to add new features in order to manage and monitor our therapy. To make this possible, we have designed our parts under tetracycline regulatory operon which interacts with the tetracycline antibiotic. This interaction results in the inhibition of our desired proteins production. Therefore clinician may use this as an advantage to stop the treatment when necessary.
In order to realize how our system will work. We try to calculate the inhibition of production of interested protein by adding tetracycline antibiotic.
Using the SimBiology toolbox for Matlab we created a framework of the pTRE-Tet Off System (Figure 1).

We wrote down the seven chemical reactions in represent of each process.

The symbol decleration is:

X1: pCMV

Y: tTA

X2 : [TetRE -PminiCMV]

X2Y: tTA[TetRE -PminiCMV]

X3 : Luciferase

Z : Tc

YZ: [Tc-tTA]

After creating the basic framework for the model we needed to create mathematical equations for each reaction with appropriate rate constants. These equations and the corresponding values are shown below in Tables 1 and 2.

What did it show???

In order to prove the safety of our project, we added a switch of mechanism in our design and we calculate how it will change the gene expression by modeling. Then, the result of model compared with wet lab experiments to check is it reliable or not.
In our model approach, we calculated the final effect of addition of different amount of tetracycline on amount of interested protein.
Inhibition of luciferase reached %25 by adding 106 molecules tetracycline in wet and dry lab results.