Team:Aberdeen Scotland/parameters

Internal Dynamics Parameters
When modeling any process, it is essential to use parameters which reflect reality, otherwise the model will not give accurate predictions. Thus we spend a considerable time researching, analysing and estimating parameters so that our model will reflect real life behaviour as accuratly as possible.

= Calculating promoter strengths =

A brief discription of how some of our promoter strengths were calculated follows:

The paper "Measuring the activity of BioBrick promoters using an in vivo reference standard" published in the Journal of Biological Engineering makes J23101 their reference standard, giving it a strength of 0.03 POPS.

We can directly compare the strengths of all the J series constititive promoters using other promoters in the above paper and the promoters in the standard registry of parts website. From this page we can calculate that if J23101 =0.03 pops then our original LuxI and LuxR promoter J23107 has a strength of ~0.018 POPS and our ammended model LuxR promoter has a strength of ~0.01 POPS. We also find that our constitutive Antiholin promoter has a strength of ~0.0066 POPS

LuxR promoter polymerase per second (PoPS) The following BioBrick F2620 defines the LuxR responsive promoter. This has been assessed as having 6.6 PoPS promoter activity, i.e. 6.6 RNA polymerisation events per second. However, this seemed unlikely; the most active promoter in E.coli has about 2 polymerisations per second. At the iGEM meeting in Edinburgh this year Dr Stansfield attended on behalf of the team were he met Barry Canton, the actual experimenter who deduced the 6.6 PoPS. When questioned he stated that he measured the PoPS value in PoPs per cell; the LuxR promoter/GFP construct was on a ‘15 copies per cell’ plasmid, thus there were 15 copies of the LuxR promoter. The actual PoPS = 6.6/15 = 0.44 PoPS   i.e. consistent with known E.coli promoters.

An estimate for the strength of different E.coli promoters, including lambda P(L) is in the following paper:

Journal of Molecular Biology Volume 292, Issue 1, Activities of constitutive promoters in Escherichia coli1

S.-T Liang1, 2, M Bipatnath1, Y.-C Xu1, S.-L Chen2, P Dennis3

It states the PoPs values for several promoters as:

Pspc, 26 polymerase initiations per minute P(L), 17 polymerase initiations per minute Pbla  1.7 polymerase initiations per minute PRNAI, 17 polymerase initiations per minute

Using the P(L) strength of 17 polymerase initiations per minute we can easily calculate the PoPs value.