Team:KULeuven/Model/Output

From 2008.igem.org

(Difference between revisions)

Latest revision as of 22:47, 29 October 2008

dock/undock dropdown

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

ODE's

Parameters

*Parameter values (Output)*
Name	Value	Comments	Reference
Degradation Rates
d_GFP	d_LVA = 2.814E-4 s^-1	LVA-tag reduces lifetime to 40 minutes	[1] [4]
d_{mRNA_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
k_GFP	0.167 s^-1	translation rate for B0032 RBS (0.3 relative efficiency)	[5]

Models

CellDesigner (SBML file)

Matlab (SBML file)

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:

Sensitivity Analysis

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.

@@ Line 1: / Line 1: @@
+{{:Team:KULeuven/Tools/Styling}}
+{{:Team:KULeuven/Tools/Scripting}}
 {{:Team:KULeuven/Tools/Header}}
-<div style="float: right;">[[Image:pictogram_output.png|120px]]</div>
+[[Image:pictogram_output.png|120px|right]]
 == Output ==
@@ Line 7: / Line 9: @@
 === 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).
+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.
@@ Line 21: / Line 23: @@
 <body>
 <p>
-<a href="https://static.igem.org/mediawiki/2008/d/d1/Output.pdf">
+<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">
 </a>
@@ Line 43: / Line 45: @@
 | d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup>
 | LVA-tag reduces lifetime to 40 minutes
-| [https://2008.igem.org/Team:KULeuven/Model/Output#References [1]] [https://2008.igem.org/Team:KULeuven/Model/Output#References [4]]
+| [https://2008.igem.org/Team:KULeuven/Model/Output#References [1<html>]</html>] [https://2008.igem.org/Team:KULeuven/Model/Output#References [4<html>]</html>]
 |-
 | d<sub>mRNA_GFP</sub>
 | 0.0023 s<sup>-1</sup>
 |
-| [https://2008.igem.org/Team:KULeuven/Model/Output#References [2]]
+| [https://2008.igem.org/Team:KULeuven/Model/Output#References [2<html>]</html>]
 |-
 ! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
@@ Line 55: / Line 57: @@
 | p(TetR) dependent
 | (GFP) between 5E-5 and 0.0125 s<sup>-1</sup> ~ [aTc]
-| [https://2008.igem.org/Team:KULeuven/Model/Output#References [3]]
+| [https://2008.igem.org/Team:KULeuven/Model/Output#References [3<html>]</html>]
 |-
 ! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
@@ Line 62: / Line 64: @@
 | 0.167 s<sup>-1</sup>
 | translation rate for B0032 RBS (0.3 relative efficiency)
-| [https://2008.igem.org/Team:KULeuven/Model/Output#References [5]]
+| [https://2008.igem.org/Team:KULeuven/Model/Output#References [5<html>]</html>]
 |}
@@ Line 79: / Line 81: @@
 === 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.
+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.
-[[Image:Sim_output_1.png|780px|center]]
+<html>
-[[Image:Sim_output_2.png|780px|center]]
+<div class="center">
+<div class="noborder" style="width: 1050px;">
+<img src="https://static.igem.org/mediawiki/2008/7/74/Sim_output_1.png" style="float: left; width: 450px; height: 400px; margin: 0 15px;" />
+<img src="https://static.igem.org/mediawiki/2008/3/3b/Sim_output_2.png" style="float: left; width: 450px; height: 400px; margin: 0 5px;" />
+</div></div></html>
-Next figure shows the switching behaviour of the output system to an light signal turning off and on:
+The next figure shows the switching behaviour of the output system to an light signal turning on and off:
-[[Image:Sim_output_3.png|780px|center]]
+[[Image:Sim_output_3.png|450px|center]]
 === Sensitivity Analysis ===
@@ Line 93: / Line 99: @@
 === References ===
 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
 <head>
@@ Line 101: / Line 106: @@
 <body>
 <table style="border-collapse:collapse;line-height:1.1em;">
-<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">“ETHZ/Parameters - IGEM07”; http://parts.mit.edu/igem07/index.php/ETHZ/Parameters.</td></tr>
+<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">“ETHZ/Parameters - IGEM07”; https://2007.igem.org/ETHZ/Parameters.</td></tr>
 <tr><td colspan="2">&nbsp;</td></tr>
 <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>