"
Team:UPO-Sevilla/Project/Basic Flip Flop/Multiagent System/Results
From 2011.igem.org
| (4 intermediate revisions not shown) | |||
| Line 2: | Line 2: | ||
<html> | <html> | ||
| + | |||
| + | <script type="text/javascript"> | ||
| + | ddmenuactual = 1; | ||
| + | $("#menuPBasic").addClass("TopMenuSelected"); | ||
| + | </script> | ||
| + | |||
<div id="principal"> | <div id="principal"> | ||
<div class="main"> | <div class="main"> | ||
| Line 11: | Line 17: | ||
<li><a href="/Team:UPO-Sevilla/Project/Overview" style="white-space: nowrap; float: left;">Project</a><ul></ul></li> | <li><a href="/Team:UPO-Sevilla/Project/Overview" style="white-space: nowrap; float: left;">Project</a><ul></ul></li> | ||
<li><a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Overview" style="white-space: nowrap; float: left;">Basic Flip Flop</a><ul></ul></li> | <li><a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Overview" style="white-space: nowrap; float: left;">Basic Flip Flop</a><ul></ul></li> | ||
| - | <li><a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Modeling/Multiagent_System" style="white-space: nowrap; float: left;">Multiagent | + | <li><a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Modeling/Multiagent_System" style="white-space: nowrap; float: left;">Multiagent Modeling</a><ul></ul></li> |
<li class="current"><a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Modeling/Multiagent_System/Results" style="white-space: nowrap; float: left;">Results</a><ul></ul></li> | <li class="current"><a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Modeling/Multiagent_System/Results" style="white-space: nowrap; float: left;">Results</a><ul></ul></li> | ||
| Line 85: | Line 91: | ||
| - | <h3>Without | + | <h3>Without doing actions</h3> |
<p>If we run the simulation with the default parameters, we can see that LacI represses the transcription of c1ts. The oscillations are caused by the cellular division process.</p> | <p>If we run the simulation with the default parameters, we can see that LacI represses the transcription of c1ts. The oscillations are caused by the cellular division process.</p> | ||
| Line 139: | Line 145: | ||
<p>Now we have focused on analyzing how some parameters affect the output of the system. Firstly, we duplicate the strength of the promoter 2. </p> | <p>Now we have focused on analyzing how some parameters affect the output of the system. Firstly, we duplicate the strength of the promoter 2. </p> | ||
| - | <h3>Without | + | <h3>Without doing actions</h3> |
<p>If the system is evolved with no inputs, we can see that LacI still wins the battle against c1ts.</p> | <p>If the system is evolved with no inputs, we can see that LacI still wins the battle against c1ts.</p> | ||
| Line 185: | Line 191: | ||
</div> | </div> | ||
| - | <h3>Without | + | <h3>Without doing actions</h3> |
<div class="center"> | <div class="center"> | ||
| Line 228: | Line 234: | ||
<p>In this case, we have changed the number of repressors that can admit every promoter from 2 ( default value) to 4</p> | <p>In this case, we have changed the number of repressors that can admit every promoter from 2 ( default value) to 4</p> | ||
| - | <h3>Without | + | <h3>Without doing actions</h3> |
<p>We obtain a stable state with a high concentration of LacI.</p> | <p>We obtain a stable state with a high concentration of LacI.</p> | ||
| Line 275: | Line 281: | ||
<p>This time we have increased even more the number of repressors that can be admited by each promoter.</p> | <p>This time we have increased even more the number of repressors that can be admited by each promoter.</p> | ||
| - | <h3>Without | + | <h3>Without doing actions</h3> |
<div class="center"> | <div class="center"> | ||
| Line 307: | Line 313: | ||
</div> | </div> | ||
<div class="left"> | <div class="left"> | ||
| - | </html>{{:Team:UPO-Sevilla/ | + | </html>{{:Team:UPO-Sevilla/leftTemplateProjectBasic}}<html> |
| + | |||
| + | <script type="text/javascript"> | ||
| + | $("#menuVBMResults").addClass("menuSelected"); | ||
| + | </script> | ||
</div> | </div> | ||
</html> | </html> | ||
{{:Team:UPO-Sevilla/footTemplate}} | {{:Team:UPO-Sevilla/footTemplate}} | ||
Latest revision as of 22:08, 27 October 2011
Simulation Results
We have performed several simulations using this model. A default set of values for the parameters is established first. Then, some parameters are modified to analyze their influence.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 doing actions
If we run the simulation with the default parameters, we can see that LacI represses the transcription of c1ts. The oscillations are caused by the cellular division process.
We can observe that under these conditions the c1ts promoter is always repressed.
The bistable works correctly under 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 much more unstable and sometimes c1ts repressors separate from the promoters they are repressing and LacI is expressed again fast.
Specifically, in the second 15000 we can see that c1ts are not repressing with enough strength, which allows the RNA transcription, modifying the bistable state. Moreover, we can see peaks of LacI expression that are turned off by c1ts, but they would not have to appear if this state was perfectly stable.
Turning on the bistable
In third place, we have increased the temperature of the system at second 6500 to see how the bistable turns on. Here we see that this process is much more effective than inactivation by IPTG.
Duplicating promoter 2 strength – CASE 1
| Parameter | Value |
|---|---|
| Promoter 2 strength | 10 |
Now we have focused on analyzing how some parameters affect the output of the system. Firstly, we duplicate the strength of the promoter 2.
Without doing actions
If the system is evolved with no inputs, we can see that LacI still wins the battle against 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 lead to a LacI victory. In any case, is interesting to remark that in this experiment a sharp increment of 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 doing 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 doing actions
We obtain a stable state with a high concentration of LacI.
Turning off the bistable
What if we add now IPTG? The results suggest that if we increase the number of operating sequences for both promoters, the stability zone of c1ts is bigger. However, we can still see unexpected peaks of LacI expression 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 each promoter.
Without doing actions
Turning off the bistable
Here we obtained an interesting behavior. The system firstly behaves right, turning off. But around second 6000 we can see that, due to stochastic oscillations, the concentration of repressor 2 decreases sharply and the repressor 1 takes the control of the system. This was not the response that we wanted to obtain.
Turning on the bistable
Temperature works as well as before
Sponsors
