Team:KULeuven/Model/Output

From 2008.igem.org

(Difference between revisions)
(→References)
(→References)
Line 93: Line 93:
=== References ===
=== References ===
-
 
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
<head>
<head>
Line 110: Line 109:
<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">“IGEM:Tsinghua/2007/Projects/RAP - OpenWetWare”; http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation.</td></tr>
<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">“IGEM:Tsinghua/2007/Projects/RAP - OpenWetWare”; http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation.</td></tr>
<tr><td colspan="2">&nbsp;</td></tr>
<tr><td colspan="2">&nbsp;</td></tr>
-
<tr style="vertical-align:top;"><td>[5]</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>
+
<tr style="vertical-align:top;"><td>[5]</td><td style="padding-left:4pt;">M. Gonzalez et al., “Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues required for proteolysis,” <span style="font-style:italic;">Genes Dev.</span>,  vol. 12, Dec. 1998, pp. 3889-3899. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1101/gad.12.24.3889&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Lon-mediated%20proteolysis%20of%20the%20Escherichia%20coli%20UmuD%20mutagenesis%20protein%3A%20in%20vitro%20degradation%20and%20identification%20of%20residues%20required%20for%20proteolysis&amp;rft.jtitle=Genes%20Dev.&amp;rft.volume=12&amp;rft.issue=24&amp;rft.aufirst=Martin&amp;rft.aulast=Gonzalez&amp;rft.au=Martin%20Gonzalez&amp;rft.au=Ekaterina%20G.%20Frank&amp;rft.au=Arthur%20S.%20Levine&amp;rft.au=Roger%20Woodgate&amp;rft.date=1998-12-15&amp;rft.pages=3889-3899"></span></td></tr>
<tr><td colspan="2">&nbsp;</td></tr>
<tr><td colspan="2">&nbsp;</td></tr>
-
<tr style="vertical-align:top;"><td>[6]</td><td style="padding-left:4pt;">“Part:BBa B0032 - partsregistry.org”; http://partsregistry.org/Part:BBa_B0032.</td></tr>
+
<tr style="vertical-align:top;"><td>[6]</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>
<tr><td colspan="2">&nbsp;</td></tr>
<tr><td colspan="2">&nbsp;</td></tr>
<tr style="vertical-align:top;"><td>[7]</td><td style="padding-left:4pt;">“Part:BBa J23109 - partsregistry.org”; http://partsregistry.org/Part:BBa_J23109.</td></tr>
<tr style="vertical-align:top;"><td>[7]</td><td style="padding-left:4pt;">“Part:BBa J23109 - partsregistry.org”; http://partsregistry.org/Part:BBa_J23109.</td></tr>
 +
<tr><td colspan="2">&nbsp;</td></tr>
 +
<tr style="vertical-align:top;"><td>[8]</td><td style="padding-left:4pt;">J.P. McDonald et al., “Regulation of UmuD cleavage: role of the amino-terminal tail,” <span style="font-style:italic;">Journal of Molecular Biology</span>,  vol. 282, Oct. 1998, pp. 721-730. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1006/jmbi.1998.2044&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Regulation%20of%20UmuD%20cleavage%3A%20role%20of%20the%20amino-terminal%20tail&amp;rft.jtitle=Journal%20of%20Molecular%20Biology&amp;rft.volume=282&amp;rft.issue=4&amp;rft.aufirst=John%20P&amp;rft.aulast=McDonald&amp;rft.au=John%20P%20McDonald&amp;rft.au=Erinn%20E%20Maury&amp;rft.au=Arthur%20S%20Levine&amp;rft.au=Roger%20Woodgate&amp;rft.date=1998-10-02&amp;rft.pages=721-730"></span></td></tr>
<tr><td colspan="2">&nbsp;</td></tr>
<tr><td colspan="2">&nbsp;</td></tr>
</table></body>
</table></body>
 +
</html>
</html>

Revision as of 10:38, 8 September 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 activated by tetR. 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 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.

Sim output 1.png
Sim output 2.png

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

Sim output 3.png

Sensitivity Analysis

Sens output2.png

References

Bibliography

[1]“Berkeley2006-RiboregulatorsMain - IGEM”; http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain.
 
[2]F.J. Isaacs et al., “Engineered riboregulators enable post-transcriptional control of gene expression,” Nat Biotech, vol. 22, Jul. 2004, pp. 841-847.
 
[3]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.
 
[4]“IGEM:Tsinghua/2007/Projects/RAP - OpenWetWare”; http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation.
 
[5]M. Gonzalez et al., “Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues required for proteolysis,” Genes Dev., vol. 12, Dec. 1998, pp. 3889-3899.
 
[6]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.
 
[7]“Part:BBa J23109 - partsregistry.org”; http://partsregistry.org/Part:BBa_J23109.
 
[8]J.P. McDonald et al., “Regulation of UmuD cleavage: role of the amino-terminal tail,” Journal of Molecular Biology, vol. 282, Oct. 1998, pp. 721-730.
 

Retrieved from "http://2008.igem.org/Team:KULeuven/Model/Output"