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Team:TU Delft-Leiden/Modeling/Landmine
From 2014.igem.org
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$$ P_{R} + DNT \ \overset{k_{on}}{\underset{k_{off}}{\rightleftharpoons}} \ P_{A} \tag{1} $$ | $$ P_{R} + DNT \ \overset{k_{on}}{\underset{k_{off}}{\rightleftharpoons}} \ P_{A} \tag{1} $$ | ||
| + | |||
| + | $$ P_{A} \ \xrightarrow{s_{A}} \ P_{A} + mRNA \tag{2} $$ | ||
| + | |||
| + | $$ P_{R} \ \xrightarrow{s_{R}} \ P_{R} + mRNA \tag{3} $$ | ||
| + | |||
| + | $$ mRNA \ \xrightarrow{s_{P}} \ mRNA + R \tag{4} $$ | ||
| + | |||
| + | $$ mRNA \ \xrightarrow{d_{m}} \ \emptyset \tag{5} $$ | ||
</p> | </p> | ||
Revision as of 19:39, 26 September 2014
Landmine Module
An important part of our iGEM project is a promoter sensitive to landmines, first described by Yagur-Kroll et al. [1]. We will use two of the promoters described in this paper, ybiJ and ybiFB2A1, in our project. Of these promoters, not much is known other than the fact that they have a DNT/TNT-dependent response curve (see figure 1). Our goal was to find a model which would be able to reproduce the response curves of both promoters.
Our first approach was to solve a system of Ordinary Differential Equations (ODEs) resembling the transcription and translation of a gene activated by the DNT-sensitive promoter. The ODEs were derived from the following system of reactions: $$ P_{R} + DNT \ \overset{k_{on}}{\underset{k_{off}}{\rightleftharpoons}} \ P_{A} \tag{1} $$ $$ P_{A} \ \xrightarrow{s_{A}} \ P_{A} + mRNA \tag{2} $$ $$ P_{R} \ \xrightarrow{s_{R}} \ P_{R} + mRNA \tag{3} $$ $$ mRNA \ \xrightarrow{s_{P}} \ mRNA + R \tag{4} $$ $$ mRNA \ \xrightarrow{d_{m}} \ \emptyset \tag{5} $$
