Minnesota/15 July 2009

Patrick Today there was an extended discussion about the validity of the model surrounding its condition of modeling a single tetO1 and tetO2 (and lacO1 when necessary) for each cell (it does not split on division, so each cell has one). This was done to simplify the model. Unfortunately the question arose that perhaps the model is not accurate since the cells in the experimental section are high plasmid cells (~300 plasmids). Each plasmid has 300 tetO1 and tetO2 sites then.

Several options for correcting this were thought up. One was that since the operons are mainly in competition with non-specific DNA (nsDNA), reducing the amount of nsDNA could yield more accurate (although most likely not different) results. Another option was the increase the amount of tetO1 and tetO2 to 300. This posed several problems, most specifically the issue surrounding linking these operons into a complex such as tetO1:tetO2.

This method would add a significant amount of equations, Currently there are ten tetR2-tetO1 related equations, and ten tetR2-tetO2 equations. With this method there would be 10*10 = 100 equations, an increase of 80 equations. All of that for something that would more likely result in little or no improvement to the model.

In the end it was determined the model was accurate enough for our purposes.