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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]
The dropdown has been created and developed by the KULeuven team.
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<ul>
<li>
<a href="https://2008.igem.org/Team:KULeuven">Home</a>
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<a>The Team</a>
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<a href="https://2008.igem.org/Team:KULeuven/Team/LabsandGroups">Research Labs and Groups</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Students">Students</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Instructors">Instructors</a>
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<a href="https://2008.igem.org/Team:KULeuven/Team/Pictures">Pictures</a>
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<a>The Project</a>
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<a href="https://2008.igem.org/Team:KULeuven/Project">Summary</a>
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<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Project/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Evaluation">End Evaluation</a>
<a href="https://2008.igem.org/Team:KULeuven/Literature">Literature</a>
<a href="https://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a>
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<li>
<a>Ethics</a>
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</div>
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<li>
<a>Submitted Parts</a>
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<a href="https://2008.igem.org/Team:KULeuven/Parts">Listing</a>
<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a>
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<li>
<a>Modeling</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Sensitivity">Sensitivity Analysis</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a>
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<a>Data Analysis</a>
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<a href="https://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a>
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<a>New Parts</a>
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<a href="https://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a>
</div>
</span>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a>
</div>
</li>
<li>
<a>Software</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a>
<a href="https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a>
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<li>
<a>Notebook</a>
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<a href="https://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a>
<a href="https://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a>
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<a>Reports</a>
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<a href="https://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a>
<a href="https://2008.igem.org/Team:KULeuven/Weekly Meetings">Weekly</a>
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<a>Lab Data</a>
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<a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a>
<a href="https://2008.igem.org/Team:KULeuven/Primers">Primers</a>
<a href="https://2008.igem.org/Team:KULeuven/Ligation">Ligation</a>
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<a href="https://2008.igem.org/Team:KULeuven/Tools">Tools</a>
<a href="https://2008.igem.org/Team:KULeuven/Press">Press</a>
<a href="https://2008.igem.org/Team:KULeuven/Guestbook">Guestbook</a>
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Contents |
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
| Name | Value | Comments | Reference |
|---|---|---|---|
| Degradation Rates | |||
| dP2ogr | 0.002265 s-1 | ||
| dRNA_P2ogr | 0.002265 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dP22CII | 0.002311 s-1 | ||
| dRNA_P22CII | 0,0022651 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dantimRNA_luxI | 0.0045303 s-1 | ||
| Transcription Rates | |||
| kP2ogr | 0.0125 s-1 | ||
| kP22CII | 0.0125 s-1 | ||
| kAntimRNA_LuxI | 0.0094 s-1 | ||
| Dissociation Constants | |||
| KP2ogr | 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] |
| KR0053_P22CII | 0.1099 | R0053 is the P22 cII promoter region | |
| Hill Cooperativity | |||
| n | 2 | Used for all reactions throughout the memory submodel using Hill kinetics | |
Models
CellDesigner
- 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.
- 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 value this system can be tested in CellDesigner.
- Figure: Celldesigner system representation
These typical parameters are:
| Name | Value | ||
|---|---|---|---|
| Degradation Rates | |||
| dact | 0.0011552 s-1 | ||
| dRNA_act | 0.0023105 s-1 | ||
| drep | 0.0011552 s-1 | ||
| dRNA_rep | 0.0023105 s-1 | ||
| Transcription Rates | |||
| kact | 0.006 s-1 | ||
| krep | 0.0125 s-1 | ||
| Translation rate | |||
| kact | 0,166666 | ||
| krep | 0,166666 | ||
| Dissociation Constants | |||
| Kact-rep | 4.2156 | ||
| Krep-act | 4.2156 | ||
| Hill Cooperativity | |||
| n | 2 | ||
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 (SBML file)
CellDesigner
