Team:UC Chile/Cyanolux/Modelling

From 2012.igem.org

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<h1>Applying the model: Synechocystis promoters</h1>
<h1>Applying the model: Synechocystis promoters</h1>
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We applied our model to solve the question of which promoters should we use to meet our strategy (http://2012.igem.org/Team:UC_Chile/Cyanolux/Project_short#Strategy) goals
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We applied our model to solve the question of which promoters should we use to meet our [http://2012.igem.org/Team:UC_Chile/Cyanolux/Project_short#Strategy strategy goals
The results are shown below:
The results are shown below:
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<font size="4">Why?</font>
 
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To express bioluminescence under circadian oscillation it was essential to identify the ideal promoters that could yield highest substrate concentrations at the exact time our biolamp is on i.e. by night.
 
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Based on literature (ref) we found that suitable promoters to start our model were sigE (sll1689), Transaldolase (slr1793) and Cytochrome aa3 (sll1898).
 
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Therefore, in the following section we explain how to model the oscillation in terms of product generation under three circadian promoters: sigE (sll1689), Transaldolase (slr1793) and Cytochrome aa3 (sll1898).
 
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<font size="4">Methodology</font>
 
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Product generation by promoter
 
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From known sigE (sll1689) production data we could build up a model using MatLab software.  (Please check our script!).
 
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Basically, what we have after data adjustment is a sine function consistent with the oscillatory nature of the circadian rhythm.
 
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Generation = C*sen(2π(t-(peak-6))/12)+1
 
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The C parameter was optimized using Excel Solver’s algorithm of least squares.
 
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For Transaldolase (slr1793) and Cytochrome aa3 (sll1898) a microarray data was adjusted (using the same algorithm of least squares) to obtain:
 
Promoter Peak hour
Promoter Peak hour
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MatLab result
MatLab result
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Finally we had the protein concentrations at different times
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Finally we have the protein concentrations at different times
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[[UC-chileDiffs.m]]
[[UC-chileDiffs.m]]
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The following are the models we obtained by MatLab
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This combination of promoters was the one that best fits our strategy: Maximize substrate concentration during dusk hours
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[[File:ucchile111111.png|500px|center]]
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[[File:222222.png|500px|center]]
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[[File:33333333.png|500px|center]]
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[[File:444444.png|500px|center]]
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[[File:555555.png|500px|center]]
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[[File:666666.png|500px|center]]
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And this is the best model because it yields highest substrate concentration at the desired time (12 hr)
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[[File:ucchile111111.png|500px|center]]
[[File:ucchile111111.png|500px|center]]

Revision as of 03:49, 27 October 2012

Project: Luxilla - Pontificia Universidad Católica de Chile, iGEM 2012