From 2011.igem.org

Results

Default Parameters – CASE 0

Parameter	Value
RNAP number	55
Ribosome number	150
Copies per gene	1
Repressors per promoter	2
Repressors life span and standard deviation	20 / 5 minutes
RNAs life span and standard deviation	5/ 1 minute
Repressors strength	8.33 E-4
Promoter 1 strength	50
Promoter 2 strength	5
Time-constant	1000
Cell cycle length	30 minutes
Divide-cells?	On
Increase-temperature?	Off

Without making actions

If we run the simulation with the default parameters, we can see that LacI repress the transcription of c1ts. The oscillations are caused by the division process.

We can observe that under these conditions the c1ts promoter is always repressed.

The bistable works correctly with these conditions.

Turning off the bistable

Secondly, applying 1 µmol of IPTG to induce the off-state, we observe how the protein LacI disappears. However, this state is mucho more unstable and sometimes c1ts repressors fall from the promoters they are repressing and LacI is expressed fast.

Specifically, in the second 15000 we can see that c1ts are not repressing and that allows the RNA transcription and modify the bistable state. Moreover, we can see peaks of LacI expression that are turned off by c1ts, but they should not appear if this state was perfectly stable.

Turning on the bistable

In third place, we have increased the temperature of the system in the second 6500 to see how the bistable turns on. Here we see that this process is much effective than inactivation by IPTG. In our model the total change takes place in just few seconds

Duplicating promoter 2 strength – CASE 1

Parameter	Value
Promoter 2 strength	10

Now we have focused on how parameters affect more the output of the system. Firstly duplicated the strength of the promoter 2.

Without making actions

If we don’t do any more we can see that LacI still wins the battle with c1ts

Turning off the bistable

It is logical to think that if the c1ts promoter is stronger the state 0 will be more stable. However, there are still oscillations that finish with LacI victory. In any case is interesting to remark that in this experiment a sharply increased in c1ts is produced at the end, that suggests that the competition is not so unbalanced.

Turning on the bistable

The behavior is the same that in case 0. Temperature is a effective way to turn on the bistable.

Quadruplying promoter 2 strength - CASE 2

Parameter	Value
Promoter 2 strength	20

Without making actions

Turning off the bistable

This time we can see an optimal behavior of the system. Increasing the relative strength of the c1ts promoter 4 times, we obtain a system remarkably stable.

Turning on the bistable

Increasing repressors per promotter to 4 – CASE 3

Parameter	Value
Repressors per promoter	4

In this case we have changed the number of repressors that can admit every promoter from 2 ( default value) to 4

Without making actions

We obtain a stable state with a high concentration of LacI.

Turning off the bistable

¿What if we add now IPTG? Results suggest that if we increase the number of operating sequences for both promoter the stability zone of c1ts is bigger. However, we can still see peaks of LacI expressions although they should not appear and after some hours LacI win again the battle for the control of the system.

Turning on the bistable

Increasing repressors per promoter to 6 – CASE 4

Parameter	Value
Repressors per promoter	6

This time we have increased even more the number of repressors that can be admited by every promoter.

Without making actions

Turning off the bistable

Here we obtained an interesting behavior. The system first behaves right, turning off. But in the second 6000 we can see that because of stochastic oscillations the concentration of repressor 2 decrease sharply and the repressor 1 take the control of the system. This was not the response that we wanted to obtain