Team:Paris/Network analysis and design/System improvements

From 2008.igem.org

(Difference between revisions)
 
(23 intermediate revisions not shown)
Line 1: Line 1:
-
== System Improvements ==
+
{{Paris/Menu}}
 +
{{Paris/Header|System Improvements}}
 +
{{Paris/Section_contents_analysis}}
 +
 
 +
== Description ==
 +
 
 +
 
 +
== Analysis ==
 +
 
<center>
<center>
{|
{|
-
|- style="background: #649CD7;"
 
-
! colspan="4" style="background: #649CD7;" | System Improvements
 
|- style="background: #649CD7; text-align: center;"
|- style="background: #649CD7; text-align: center;"
| Name
| Name
Line 12: Line 18:
| style="background: #D4E2EF;"|Core system
| style="background: #D4E2EF;"|Core system
| Figure core system
| Figure core system
-
| Zero
+
| [[Image:Core0.png|200px|center|Simulation of the core system]]
-
| Liks core system
+
| Links core system
|- style="background: #dddddd;"
|- style="background: #dddddd;"
-
| style="background: #D4E2EF;" |Modular system
+
| style="background: #D4E2EF;" |Bimodular system
| Figure modular system
| Figure modular system
-
| **
+
| [[Image:System4.png|200px|center|Simulation of the bimodular system]]
| Links Garcia-Ojalvo
| Links Garcia-Ojalvo
|- style="background: #dddddd;"
|- style="background: #dddddd;"
-
| style="background: #D4E2EF;" |Resulting system
+
| style="background: #D4E2EF;" |Unimodular system
| Figure resulting system
| Figure resulting system
-
| ***
+
| [[Image:Oscillating.jpg]]
| Links resulting
| Links resulting
|- style="background: #dddddd;"  
|- style="background: #dddddd;"  
-
!colspan="4"  | Main conclusion: we keep S2
+
!colspan="4"  | Synchronized oscillations should be given by the unimodular system.
|}</center>
|}</center>
-
<!--
 
-
== System Improvements ==
 
-
-->
 
Core system does not oscillate. How can we enhance it?
Core system does not oscillate. How can we enhance it?
We need a 'delay' so we can:
We need a 'delay' so we can:
 +
1 add more genes to the circuit
1 add more genes to the circuit
 +
2 use quorum sensing (qs)
2 use quorum sensing (qs)
we chose quorum sensing that can allowed both 'delay' and population synchonization.
we chose quorum sensing that can allowed both 'delay' and population synchonization.
-
two ways to add it: S4 and S2.
+
two ways to add it:  
-
We first analyse S4 due to modularity.
+
*S4: Inspired from Garcia-Ojalvo: oscillating repressilator + oscillating qs module = synchronized oscillations
-
Inspired from Garcia-Ojalvo: oscillating repressilator + oscillating qs module = synchronized oscillations
+
*S2: it amounts to replace single interaction by more complex interactions: should create delay
-
we tried s4:  
+
we analyze both systems for their capacity to generate oscillations.
 +
 
 +
S2 seems more promising.
 +
 
 +
Thus we further analize S2 for its capacity to generate ''synchrionized'' oscillations (using different initial concentrations and cell populations variability).
 +
 
 +
== Conclusion ==
 +
 
 +
== Navigation ==
 +
 
 +
*[[Team:Paris/Network_analysis_and_design/System_improvements/Description|Description]]
 +
 
 +
*[[Team:Paris/Network_analysis_and_design/System_improvements/Analysis|Analysis]]
 +
 
 +
*[[Team:Paris/Network_analysis_and_design/System_improvements/Conclusions|Conclusion]]
 +
 
 +
<!--
 +
We first analyse S4 due to modularity.
damped oscillating core system + oscillating qs module = damped oscillations.
damped oscillating core system + oscillating qs module = damped oscillations.
Line 54: Line 76:
given analysis results we keep S2.
given analysis results we keep S2.
 +
-->

Latest revision as of 00:42, 30 October 2008

System Improvements


Contents

Description

Analysis

Name Description Evaluation Links
Core system Figure core system
Simulation of the core system
 Links core system
Bimodular system Figure modular system
Simulation of the bimodular system
 Links Garcia-Ojalvo
Unimodular system Figure resulting system File:Oscillating.jpg Links resulting
Synchronized oscillations should be given by the unimodular system.


Core system does not oscillate. How can we enhance it?

We need a 'delay' so we can:

1 add more genes to the circuit

2 use quorum sensing (qs)

we chose quorum sensing that can allowed both 'delay' and population synchonization. two ways to add it:

  • S4: Inspired from Garcia-Ojalvo: oscillating repressilator + oscillating qs module = synchronized oscillations
  • S2: it amounts to replace single interaction by more complex interactions: should create delay

we analyze both systems for their capacity to generate oscillations.

S2 seems more promising.

Thus we further analize S2 for its capacity to generate synchrionized oscillations (using different initial concentrations and cell populations variability).

Conclusion

Navigation


Retrieved from "http://2008.igem.org/Team:Paris/Network_analysis_and_design/System_improvements"