Team:KULeuven/Model/Memory

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Inspirational websites:

[http://javascript-array.com/scripts/simple_drop_down_menu/ Most basic dropdown menu, with no submenu's]
[http://jquery.com/ The javascript library used to add effects and optimise the dropdown]
[http://www.tyssendesign.com.au/articles/css/centering-a-dropdown-menu/ How to center a ul list effectively]

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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 blocks 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 increase. The system stays activated.

ODE's

Parameters

*Parameter values (Memory)*
Name	Value	Comments	Reference
Degradation Rates
d_P2ogr	0.002265 s^-1
d_{RNA_P2ogr}	0.002265 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_P22CII	0.002311 s^-1
d_{RNA_P22CII}	0,0022651 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_{antimRNA_luxI}	0.0045303 s^-1
Transcription Rates
k_P2ogr	0.0125 s^-1
k_P22CII	0.0125 s^-1
k_{AntimRNA_LuxI}	0.0094 s^-1
Dissociation Constants
K_P2ogr	4.2156	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_{R0053_P22CII}	0.1099		[http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&firstpage=10536&resourcetype=HWCIT link]
Hill Cooperativity
n	2	Used for all reactions throughout the memory submodel using Hill kinetics

Models

CellDesigner (SBML file)

Figure: CellDesigner system representation

Matlab

Problem

The OmpF promoter 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 automatically ends up in state 1 after some time (300s). This can be seen in the figure below.

Figure: Celldesigner simulation of the memory system. CIIP22(purple), P2ogr(green), AntimRNA(pink).

The system can only stay in 0-state for 300 sec. This makes it completely 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.

Describing the system

Figure: Part representation of alternative system

When this system starts Rep build up because Rep represses the Act promoter better then Act represses the Rep promoter. The Rep concentration stays high and the Act stays low. This is the 0-state. When there is light, the OmpF promoter is activated and the Act concentration is increased. This represses Rep promoter. The Rep concentration decreases and the Act promoter is activated. The Act concentration keeps increasing. When the light pulse ends the Act concentration is high enough to repress the Rep promoter, Act concentration stays high and Rep concentration stays low. This is the 1-state.

Using typical values this system can be tested in CellDesigner.

Figure: Celldesigner system representation

Parameters

These typical parameters are:

*Parameter values (alternative Memory)*
Name	Value
Degradation Rates
d_act	0.0011552 s^-1
d_{RNA_act}	0.0023105 s^-1
d_rep	0.0011552 s^-1
d_{RNA_rep}	0.0023105 s^-1
Transcription Rates
k_act	0.006 s^-1
k_rep	0.0125 s^-1
Translation rate
k_act	0,166666
k_rep	0,166666
Dissociation Constants
K_act-rep	4.2156
K_rep-act	4.2156
Hill Cooperativity
n	2

Results

CellDesigner gives the following simulation when OmpF transcription rate changes from 0.0001 to 0.01 at t=6000 sec for 2000 sec.

Figure: Celldesigner simulation of the alterative system. Act(grey), Rep(yellow)

The OmpF peak causes the Act concentration to rise and the Rep to decrease. The high Act concentration keeps the Rep concentration low. This causes the Act concentration to stay high.

New model

Describing the system

This is the same system as the alternative. The role of act is taken up by cI434 and rep by cIIP22.The output of this system is given in by RNA production that repressed the LuxI production.

CellDesigner (SBML file)

ODE's

Parameters

*Parameter values (New Memory)*
Name	Value	Comments	Reference
Degradation Rates
d_cIIP22	0.002311 s^-1		[http://www.pnas.org/content/88/12/5217.abstract?sid=27806463-33af-4a78-b964-f15872433865 link]
d_{mRNA_cIIP22}	0.00462 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_cI434	2.8822E-4 s^-1	this part has a LVA-tag, so we estimate a 40 min half-life
d_{mRNA_cI434}	0.00462 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
d_{antimRNA_luxI}	0.00462 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
cII434 regulated promotor
k_transcr	0.125 s^-1	estimate
K_m	0.8708		[http://jb.asm.org/cgi/content/abstract/187/16/5624?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=187&firstpage=5624&resourcetype=HWCIT link]
cIIP22 regulated promotor
k_transcr	0.125 s^-1	estimate
K_m	0.1099		[http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&firstpage=10536&resourcetype=HWCIT link]
translation rates
k_{transl_cI434}	0.038888 s^-1	eff. 0.07
k_{transl_cIIP22}	0,555555 s^-1	eff. 1
Hill Cooperativity
n	2	Used for all reactions throughout the memory submodel using Hill kinetics

Results

CellDesigner gives the following simulation when OmpF transcription rate changes from 0.0001 to 0.0125 at t=20000 sec for 1000 sec (17min).

There is a clear change. The cIIP22 amount drops and the cI434 increases. The high cI434 amount will repress the RNA production. These RNA amount are small and can’t be see on the graph. It might be necessary to increase the RNA production.

Team:KULeuven/Model/Memory

From 2008.igem.org

Contents

Memory

Position in the system

Describing the system

ODE's

Parameters

Models

CellDesigner (SBML file)

Matlab

Problem

Alternative

Describing the system

Parameters

Results

New model

Describing the system

CellDesigner (SBML file)

ODE's

Parameters

Results