Team:NYMU-Taipei/Modeling/Ethanol

Ethanol model

Background:

TrxC promoter is an oxyR-activated promoter. Behind trxC promoter are several terminals to inhibit T7 polymerase-producing gene from being opened easily ; namely, it will not open until the concentration of oxyR is high enough, which means the bees are facing disastrous infection. Once oxyR concentration overcomes the threshold and conquers the terminal obstacles, T7 polymerase is produced and will bind to T7 promoter, which is a specific promoter binding only to T7 polymerase. Behind the T7promoter are enzyme PDC and ADH-producing genes, which will convert pyruvate to ethanol, and thus kill spores of Nosema Ceranae.

Pathway of ethanol:

[[File:]]

PDC= pyruvate decarboxylase; ADH= Acetaldehyde

Aims

1.To simulate how many terminal do we need as a threshold to have the T7 polymerase-producing gene open at a proper 　　time.
2.To simulate the threshold concentration of oxyR to conquer the terminal.
3.To determine the time of opening to see if the circuit could open in time (useful).

　　As for how we measure promoter strengths, we choose PoPS, which is the rate of RNA polymerase binding to the DNA and trigger the transcription of the certain gene.
　　It is assumed that the dose of pyruvate is sufficient in bees’ body through enough proliferation/copy number of Beecoli; the possibility of RNApolymerase skipping terminators is assumed to be proportional to time span; equilibrium between pyruvate and acetaldehyde is dominantly rightward, while equilibrium between acetaldehyde and ethanol is bidirectional; concentration of ethanol will not easily decrease and will sustain for a period of time.

Equation1: