Team:KULeuven/Model/Memory

{{:Team:KULeuven/Tools/Navigation_Bar}}

== [https://static.igem.org/mediawiki/2008/0/05/Memory.zip Memory] ==

=== Position in the system ===

=== Describing the system ===
This system must activate the cell death system after one light pulse. As long as there is no light, there is no P2ogr, no CIIP22 and a lot of antimRNA_LuxI. The antimRNA_LuxI blokes the cell death system. When light is turned on OmpF increases. This causes P2ogr and CIIP22 to increase and antimRNA_LuxI to decrease. This activates the system. When light is turned off, the P2ogr concentration is large enough to maintain itself. This way antimRNA doesn't encrease. The system stayes activated.

==== ODE's ====

==== Parameters ====

{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"
|+ ''Parameter values (Memory)''
! width=15% | Name
! width=15% | Value
! width=40% | Comments
! width=10% | Reference
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates
|-
| d<sub>P2ogr</sub>
| 0.002265 s<sup>-1</sup>
|
|
|-
| d<sub>RNA_P2ogr</sub>
| 0.002265 s<sup>-1</sup>
| 
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
|-
| d<sub>P22CII</sub>
| 0.002311 s<sup>-1</sup>
|
|
|-
| d<sub>RNA_P22CII</sub>
| 0,0022651 s<sup>-1</sup>
| 
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
|-
| d<sub>antimRNA_luxI</sub> 
| 0.0045303 s<sup>-1</sup>
| 
| 
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
|-
| k<sub>P2ogr</sub>
| 0.0125 s<sup>-1</sup>
| 
|  
|-
| k<sub>P22CII</sub>
| 0.0125 s<sup>-1</sup>
| 
| 
|-
| k<sub>AntimRNA_LuxI</sub>
| 0.0094 s<sup>-1</sup>
| 
| 
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Constants
|-
| K<sub>P2ogr</sub>
| 4.2156 [M]
| Used in two reactions for activator control at the transcription of P2ogr mRNA and CIIP22 mRNA
| [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=P22+c2+repressor&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=258&resourcetype=HWCIT link]
|-
| K<sub>R0053_P22CII</sub>
| 0.1099 [M]
| R0053 is the P22 cII promoter region
| 
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Hill Cooperativity 
|-
| n<sub></sub>
| 2
| Used for all reactions throughout the memory submodel using Hill kinetics
| 
|-
|}

=== Models ===

==== CellDesigner ====

[[Image:Memory.png|600px|center|Memory]]

==== Matlab ====

=== Problem ===

The OmpF promotor is not ideal. When there is no light the transcription rate is still 0.00005. This means that P2ogr will slowly build up, activating the system. In this case the memory is in 0-state when the stationary state isn't reached yet. The 1-state is the stationary state. So the system automaticly ends up in state 1 after some time (300s). This can be seen in the figure below.
[[Image:mem_no_act.png|600px|center|mem_no_act]]
The system can only stay in 0-state for 300 sec. This makes it completly useless.

===Alternative===
In the previous system the 0-state isn't actively maintained. It's just 'not stationary state'. So we need to search mathematical system that has 2 stationary states. A possible solution is given below.
[[Image:Alt.png|600px|center|alt]]
When this system starts Rep build up because Rep represses the Act promoter beter then Act represses the Rep promoter. The Rep concentration stayes high and the Act stayes low. This is the 0-state. When there is light, the OmpF promotor is activated and the Act concentration is encreased. This respesses Rep promoter. The Rep concentration decreases and the Act promoter is activated. The Act concentration keeps encreasing. When the light pulse ends the Act concetration is high enough to repress the Rep promotor, Act concentration stayes high and Rep concentration stayes low. This is the 1-state
Using typical value this system can be tested in CellDesigner. 
[[Image:Alt_celldesigner.png|600px|center|alt_CD]]
These typical parameters are:

{| width=40% style="border: 1px solid #003E81; background-color: #EEFFFF;"
|+ ''Parameter values (alternative Memory)''
! width=20% | Name
! width=20% | Value
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates
|-
| d<sub>act</sub>
| 0.0011552 s<sup>-1</sup>
|-
| d<sub>RNA_act</sub>
| 0.0023105 s<sup>-1</sup>
|-
| d<sub>rep</sub>
| 0.0011552 s<sup>-1</sup>
|-
| d<sub>RNA_rep</sub>
| 0.0023105 s<sup>-1</sup>
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
|-
| k<sub>act</sub>
| 0.006 s<sup>-1</sup>
|-
| k<sub>rep</sub>
| 0.0125 s<sup>-1</sup>
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation rate
|-
| k<sub>act</sub>
| 0,166666 [M]
|-
| k<sub>rep</sub>
| 0,166666 [M]
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Constants
|-
| K<sub>act-rep</sub>
| 4.2156 [M]
|-
| K<sub>rep-act</sub>
| 4.2156 [M]
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Hill Cooperativity 
|-
| n<sub></sub>
| 2
|-
|}
CellDesigner gives the following simulation when OmpF transcription rate changes from 0.0001 to 0.01 at t=6000 sec for 2000 sec.
[[Image:alt_CDplot.png|600px|center|alt_CDplot]]
The OmpF peak causes the Act concantration to rise and the Rep to descrease. The high Act concentration keeps the Rep concetration low and it's own high. So this system works.