Team:KULeuven/Model/Output

From 2008.igem.org

(Difference between revisions)
m (→ODE's)
Line 1: Line 1:
 +
{{:Team:KULeuven/Tools/Styling}}
{{:Team:KULeuven/Tools/Header}}
{{:Team:KULeuven/Tools/Header}}

Revision as of 12:12, 3 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 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 (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”; http://parts.mit.edu/igem07/index.php/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.
 

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