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Team:UCSF/Modeling
From 2013.igem.org
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If we can get this result from our model, then it would help us figure out how much inducer to add to our experiments in order to get the desired result. | If we can get this result from our model, then it would help us figure out how much inducer to add to our experiments in order to get the desired result. | ||
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| - | Before getting into any modeling, we had to first figure out what the design of the synthetic circuit would be. It’s essentially the same diagram as the one shown on the synthetic circuit page (link here), but we added letters to represent each variable for our model. (R:C – gRNA/dCas9 complex; R – gRNA; C – dCas9; L – low inducible promoter; H – high inducible promoter) | + | Before getting into any modeling, we had to first figure out what the design of the synthetic circuit would be. It’s essentially the same diagram as the one shown on the synthetic circuit page (link here), but we added letters to represent each variable for our model. <br>(R:C – gRNA/dCas9 complex; R – gRNA; C – dCas9; L – low inducible promoter; H – high inducible promoter) |
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| - | <br><b><FONT COLOR="#008000"> | + | <br><b><FONT COLOR="#008000">ASSUMPTIONS: </FONT COLOR="#008000"></b>While creating the model for our system, we made a few assumptions about some of the aspects of the model that would be impossible for us to know within a few months. We made four assumptions: 1) protein degradation is linear; 2) protein production is based on a hill function and also depends on inducer concentration; 3) repression is governed by a hill function and depends on the concentration of dCas9 and gRNA complex; and 4) that the binding and unbinding of dCas9 and gRNA complex happens much faster than the production/degradation of gRNA and fluorescent proteins (the complex is at <a href="http://en.wikipedia.org/wiki/Steady_State_theory#Quasi-steady_state" target="_blank">Quasi Steady State</a><span>). |
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Revision as of 18:14, 19 September 2013
The primary goal of the modeling portion for the synthetic circuit project is to create a model that will allow us to predict how our circuit will react to different concentrations of inducer. Since our circuit should express GFP at lower inducer concentrations and RFP at high inducer concentrations, we should expect the graph to look something like the one below:
If we can get this result from our model, then it would help us figure out how much inducer to add to our experiments in order to get the desired result.
Before getting into any modeling, we had to first figure out what the design of the synthetic circuit would be. It’s essentially the same diagram as the one shown on the synthetic circuit page (link here), but we added letters to represent each variable for our model.
(R:C – gRNA/dCas9 complex; R – gRNA; C – dCas9; L – low inducible promoter; H – high inducible promoter)
(R:C – gRNA/dCas9 complex; R – gRNA; C – dCas9; L – low inducible promoter; H – high inducible promoter)
ASSUMPTIONS: While creating the model for our system, we made a few assumptions about some of the aspects of the model that would be impossible for us to know within a few months. We made four assumptions: 1) protein degradation is linear; 2) protein production is based on a hill function and also depends on inducer concentration; 3) repression is governed by a hill function and depends on the concentration of dCas9 and gRNA complex; and 4) that the binding and unbinding of dCas9 and gRNA complex happens much faster than the production/degradation of gRNA and fluorescent proteins (the complex is at Quasi Steady State).
