Team:UC Chile/Cyanolux/Modelling

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<h1>Why Modelling?:</h1>
<h1>Why Modelling?:</h1>
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Synechocystis transcriptional circadian oscillation makes  it an exceptional chassis if time control of synthetic metabolic processes is desired.
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Nevertheless, the  functionality of some of these processes depends upon precise timing.
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While there are hundreds of genes known to oscillate in Synechocystis genome -each with its own peak, strenght and amplitude- it can be tricky to choose the right ones.
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Here is where our modeling approach comes on stage.
<h1>Model Overview:</h1>
<h1>Model Overview:</h1>
<h2>Model Application</h2>
<h2>Model Application</h2>
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Our model works as a user-friendly black box. The user´s input is the desired time of protein concentration peak and the program´s output is a list of suggested promoters.
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It can be adjusted to take as input the time on which enzymatic products concentration peaks , or to maximize an intermediate metabolite that depends not just on production but also consumption.
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Finally, its logical design can be applied to any other organism that exhibits circadian oscillation.
<h2>What´s inside the box?</h2>
<h2>What´s inside the box?</h2>
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We took all the microarray data available of promoter of Synechocystis grown on normal conditions. Conveniently, these arrays already have a filter: they only contain cycling promoters
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The microarray data points were adjusted by a least squares algorithm into sine functions for each promoter.
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equa1
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Where k, theta and y are parameters to adjust.
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x is protein concentration
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This equation accounts for protein production and its included into this form of universal balance equation:
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equa2
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Where HL is protein´s half life
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The resulting plot of this equation predicts protein concentration over time.
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For example (plot screenshot)
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As a complement, we developed a list of relative promoter strengths. We took one promoter present in all datasets to make a relative scale, then,  we transformed it to an absolute scale using a promoter quantitatively characterized in literature by comparing it to the relative scale promoter.
<h1>Extended Model</h1>
<h1>Extended Model</h1>
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The approach can be extended to consider as input the product of the protein enzymatic activity instead of the protein itself.
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Moreover, it can be adjusted to a two-protein model in which protein 1 produces the metabolite and protein 2 consumes it.
<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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The results are shown below:
<font size="4">Why?</font>
<font size="4">Why?</font>

Revision as of 02:11, 27 October 2012

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