Modeling

Overview

1.Gene Expression Dynamics

Analysis of the problem

The symbol declaration is:

Finally, we assigned each process with a reaction rate constant.

How did we build it?

Figure1: The diagram of reactions was designed in the SimBiology toolbox for MATLAB.

What did it show?

• Before running the model, we had to decide on how the hypoxia response element affects gene expression The pCMV promoter (distincted from HRE) expressed approximately 0.15 nM and the [HRE- pCMV] complex expressed 1.86 nM of luciferase in 12 hours. In our simulations, we show that adding hypoxia response element in our promoter design increases the protein expression approximately 20 times more in hypoxic conditions.

• This data was then used to design an experiment that could be performed in the lab to verify the model. You can visit our results page to see the comparison.

2.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]

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.

Modelling Results

Experiment Result