Team:KULeuven/Model/Output

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== Output ==
== Output ==
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=== Position in the system ===
=== Position in the system ===
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The output system is one of three modules directly linked to the output of the light sensor (black-box) the input for is OmpF. The output system is a simple gene regulation, of which transcription is activated by OmpF. The output signal is CFP (cyan fluorescent protein).
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The output system is one of three modules directly linked to the input. The output system is a simple gene regulation, of which transcription is repressed by TetR - and can be activated by anhydrotetracyclin. The output signal is GFP (green fluorescent protein).
In the applied project of dealing with Crohn's disease this would be replaced by the drug necessary to cure the local inflammation. The drug concentration would be proportional to the amount of local inflammation sensed.
In the applied project of dealing with Crohn's disease this would be replaced by the drug necessary to cure the local inflammation. The drug concentration would be proportional to the amount of local inflammation sensed.
=== Describing the system ===
=== Describing the system ===
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see also: [https://2008.igem.org/Team:KULeuven/Project/Output Project:Output]
[[Image:Output_BioBrick.jpg|center]]
[[Image:Output_BioBrick.jpg|center]]
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<a href="https://static.igem.org/mediawiki/2008/d/d1/Output.pdf">
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<a href="https://static.igem.org/mediawiki/2008/6/66/OutputODE.pdf">
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60">
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates
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|-
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| d<sub>CFP</sub> (protein)
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| d<sub>GFP</sub>
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| 1.05E-4 s<sup>-1</sup>
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| d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup>
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|  
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| LVA-tag reduces lifetime to 40 minutes
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| [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
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| [https://2008.igem.org/Team:KULeuven/Model/Output#References [1<html>]</html>] [https://2008.igem.org/Team:KULeuven/Model/Output#References [4<html>]</html>]
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|-
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| d<sub>RNA_CFP</sub> (mRNA)
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| d<sub>mRNA_GFP</sub>
| 0.0023 s<sup>-1</sup>
| 0.0023 s<sup>-1</sup>
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|  
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| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
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| [https://2008.igem.org/Team:KULeuven/Model/Output#References [2<html>]</html>]
|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
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|-
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| k<sub>CFP</sub>
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| TetR_var_transcr_rate
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| OmpF dependent
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| p(TetR) dependent
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|
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| (GFP) between 5E-5 and 0.0125 s<sup>-1</sup> ~ [aTc]
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| [https://2008.igem.org/Team:KULeuven/Model/Output#References [3<html>]</html>]
|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
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|-
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| k<sub>CFP</sub>
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| k<sub>GFP</sub>
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| 0.05 s<sup>-1</sup>
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| 0.167 s<sup>-1</sup>
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| RBS is B0032 (efficiency of 0.3)
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| translation rate for B0032 RBS (0.3 relative efficiency)
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|  
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| [https://2008.igem.org/Team:KULeuven/Model/Output#References [5<html>]</html>]
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|}
=== Models ===
=== Models ===
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==== CellDesigner ([https://static.igem.org/mediawiki/2008/d/d9/Output_v2.zip SBML file]) ====
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==== CellDesigner ([https://static.igem.org/mediawiki/2008/5/53/Output_CellDesigner.zip SBML file]) ====
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The Output model represented in CellDesigner:
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[[Image:Output_CellDesigner.png|500px|center|Output]]
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[[Image:output_v2.png|500px|center|Output]]
 
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Several simulations were conducted, the following two show the transient respons and eventual saturation of the output system to a low and a high step signal as input, respectively. We see that there is a great distinction in the number of CFP molecules between the two input signals.
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==== Matlab ([https://static.igem.org/mediawiki/2008/1/16/Output_Matlab.zip SBML file]) ====
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[[Image:Sim_output_1.png|780px|center]]
 
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[[Image:Sim_output_2.png|780px|center]]
 
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Next figure shows the switching behaviour of the output system to an light signal turning off and on:
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[[Image:Output_Matlab.jpg|center]]
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[[Image:Sim_output_3.png|780px|center]]
 
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==== Matlab ([https://static.igem.org/mediawiki/2008/1/16/Output_Matlab.zip SBML file]) ====
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=== Simulations ===
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The diagram for the output system is shown below:
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Several simulations were conducted. The following two show the transient respons and eventual saturation of the output system to a low (left figure) and a high (right figure) input signal (TetR = 5E-5 vs 0.0125 s<sup>-1</sup>). There is a great distinction in the number of GFP molecules between the two input signals. All graphs have amounts (number of molecules in the cell) plotted vs time, measured in seconds.
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[[Image:Output_Matlab.jpg|center]]
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<div class="center">
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<div class="noborder" style="width: 1050px;">
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<img src="https://static.igem.org/mediawiki/2008/7/74/Sim_output_1.png" style="float: left; width: 450px; height: 400px; margin: 0 15px;" />
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<img src="https://static.igem.org/mediawiki/2008/3/3b/Sim_output_2.png" style="float: left; width: 450px; height: 400px; margin: 0 5px;" />
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</div></div></html>
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Another two simulations have been conducted, matching the solutions found by CellDesigner, the low input respons (0.0005 OmpF s<sup>-1</sup>) is on the left, the high input respons (0.025 OmpF s<sup>-1</sup>) on the right:
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The next figure shows the switching behaviour of the output system to an light signal turning on and off:
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{| align="center"
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[[Image:Sim_output_3.png|450px|center]]
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|[[Image:Sim_output_low_input.jpg|center|450px]]
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|[[Image:Sim_output_high_input.jpg|center|450px]]
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|}
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Next figure demonstrates the switching behaviour and concides with the results predicted by CellDesigner:
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=== Sensitivity Analysis ===
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[[Image:Sim_output_switch_input.jpg|center]]
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[[Image:Sens output2.png|center]]
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=== References ===
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
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<title>Bibliography</title>
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</head>
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<body>
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<table style="border-collapse:collapse;line-height:1.1em;">
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<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">“ETHZ/Parameters - IGEM07”; https://2007.igem.org/ETHZ/Parameters.</td></tr>
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<tr><td colspan="2">&nbsp;</td></tr>
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<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” <span style="font-style:italic;">Proceedings of the National Academy of Sciences of the United States of America</span>,  vol. 99, Jul. 2002, pp. 9697–9702. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1073/pnas.112318199&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Global%20analysis%20of%20mRNA%20decay%20and%20abundance%20in%20Escherichia%20coli%20at%20single-gene%20resolution%20using%20two-color%20fluorescent%20DNA%20microarrays&amp;rft.jtitle=Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20of%20the%20United%20States%20of%20America&amp;rft.stitle=Proc%20Natl%20Acad%20Sci%20U%20S%20A.%20&amp;rft.volume=99&amp;rft.issue=15&amp;rft.aufirst=Jonathan%20A.&amp;rft.aulast=Bernstein&amp;rft.au=Jonathan%20A.%20Bernstein&amp;rft.au=Arkady%20B.%20Khodursky&amp;rft.au=Pei-Hsun%20Lin&amp;rft.au=Sue%20Lin-Chao&amp;rft.au=Stanley%20N.%20Cohen&amp;rft.date=2002-07-23&amp;rft.pages=9697%E2%80%939702"></span></td></tr>
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<tr><td colspan="2">&nbsp;</td></tr>
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<tr style="vertical-align:top;"><td>[3]</td><td style="padding-left:4pt;">M. Bon, S.J. McGowan, and P.R. Cook, “Many expressed genes in bacteria and yeast are transcribed only once per cell cycle,” <span style="font-style:italic;">FASEB J.</span>,  vol. 20, Aug. 2006, pp. 1721-1723. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1096/fj.06-6087fje&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Many%20expressed%20genes%20in%20bacteria%20and%20yeast%20are%20transcribed%20only%20once%20per%20cell%20cycle&amp;rft.jtitle=FASEB%20J.&amp;rft.volume=20&amp;rft.issue=10&amp;rft.aufirst=Michael&amp;rft.aulast=Bon&amp;rft.au=Michael%20Bon&amp;rft.au=Simon%20J.%20McGowan&amp;rft.au=Peter%20R.%20Cook&amp;rft.date=2006-08-01&amp;rft.pages=1721-1723"></span></td></tr>
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<tr><td colspan="2">&nbsp;</td></tr>
 +
<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">J.B. Andersen et al., “New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria,” <span style="font-style:italic;">Applied and Environmental Microbiology</span>,  vol. 64, Jun. 1998, pp. 2240–2246. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=New%20Unstable%20Variants%20of%20Green%20Fluorescent%20Protein%20for%20Studies%20of%20Transient%20Gene%20Expression%20in%20Bacteria&amp;rft.jtitle=Applied%20and%20Environmental%20Microbiology&amp;rft.stitle=Appl%20Environ%20Microbiol.%20&amp;rft.volume=64&amp;rft.issue=6&amp;rft.aufirst=Jens%20Bo&amp;rft.aulast=Andersen&amp;rft.au=Jens%20Bo%20Andersen&amp;rft.au=Claus%20Sternberg&amp;rft.au=Lars%20Kongsbak%20Poulsen&amp;rft.au=Sara%20Petersen%20Bj%C3%B8rn&amp;rft.au=Michael%20Givskov&amp;rft.au=S%C3%B8ren%20Molin&amp;rft.date=1998-06&amp;rft.pages=2240%E2%80%932246"></span></td></tr>
 +
<tr><td colspan="2">&nbsp;</td></tr>
 +
<tr style="vertical-align:top;"><td>[5]</td><td style="padding-left:4pt;">“Part:BBa B0032 - partsregistry.org”; http://partsregistry.org/Part:BBa_B0032.</td></tr>
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<tr><td colspan="2">&nbsp;</td></tr>
 +
 
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</table></body>
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Latest revision as of 22:47, 29 October 2008

  dock/undock dropdown  

Pictogram output.png

Contents

Output

Position in the system

The output system is one of three modules directly linked to the input. The output system is a simple gene regulation, of which transcription is repressed by TetR - and can be activated by anhydrotetracyclin. The output signal is GFP (green fluorescent protein).

In the applied project of dealing with Crohn's disease this would be replaced by the drug necessary to cure the local inflammation. The drug concentration would be proportional to the amount of local inflammation sensed.

Describing the system

see also: Project:Output

Output BioBrick.jpg

ODE's

Parameters

Parameter values (Output)
Name Value Comments Reference
Degradation Rates
dGFP dLVA = 2.814E-4 s-1 LVA-tag reduces lifetime to 40 minutes [1] [4]
dmRNA_GFP 0.0023 s-1 [2]
Transcription Rates
TetR_var_transcr_rate p(TetR) dependent (GFP) between 5E-5 and 0.0125 s-1 ~ [aTc] [3]
Translation Rates
kGFP 0.167 s-1 translation rate for B0032 RBS (0.3 relative efficiency) [5]

Models

CellDesigner (SBML file)

Output


Matlab (SBML file)

Output Matlab.jpg


Simulations

Several simulations were conducted. The following two show the transient respons and eventual saturation of the output system to a low (left figure) and a high (right figure) input signal (TetR = 5E-5 vs 0.0125 s-1). There is a great distinction in the number of GFP molecules between the two input signals. All graphs have amounts (number of molecules in the cell) plotted vs time, measured in seconds.

The next figure shows the switching behaviour of the output system to an light signal turning on and off:

Sim output 3.png

Sensitivity Analysis

Sens output2.png

References

Bibliography

[1]“ETHZ/Parameters - IGEM07”; https://2007.igem.org/ETHZ/Parameters.
 
[2]J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702.
 
[3]M. Bon, S.J. McGowan, and P.R. Cook, “Many expressed genes in bacteria and yeast are transcribed only once per cell cycle,” FASEB J., vol. 20, Aug. 2006, pp. 1721-1723.
 
[4]J.B. Andersen et al., “New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria,” Applied and Environmental Microbiology, vol. 64, Jun. 1998, pp. 2240–2246.
 
[5]“Part:BBa B0032 - partsregistry.org”; http://partsregistry.org/Part:BBa_B0032.
 

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