Difference between revisions of "Team:TUDelft/DennisModel"
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<h2>TALE - Incoherent Feed Forward Loop to control gene expression</h2> | <h2>TALE - Incoherent Feed Forward Loop to control gene expression</h2> | ||
| − | <p> In our system we | + | <p> In our system we exploit a commonly applied control system known as an Incoherent Feed Forward Loop (iFFL), in which an activator regulates both a gene and a repressor of the gene ... . This control system is established through the expression of a Transcription activator-like effector (TALE) protein. TALE proteins recognize DNA by a simple DNA-binding mechanism which can be altered to recognize any sequence you want … . In our system the TALE protein binds to the promoter of a gene of interest and thus respresses the expression of it. .... Has previously described this system and shown how it can result in independence of copy number of the system. <br> |
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| − | + | We further analyzed this system through the use of modeling, which revealed that it's insensitive to many other variables as well, which hasn't been explored yet. | |
| − | Transferring genetic circuits between organisms yields large variation in most (if not all) of the parameters in the system, we exploited the robustness of this model to maintain predictability even when crossing species barriers. | + | Transferring genetic circuits between organisms yields large variation in most (if not all) of the parameters in the system, we exploited the robustness of this model to maintain predictability even when crossing species barriers. |
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Revision as of 16:44, 4 September 2019
Overview
The main goal of our project revolves around predictability. Without predictability, we cannot reliably design and implement synthetic biology solutions. However, when transferring genetic circuits between different organisms, many variables change. This dramatically increases the uncertainty of the outcome. With our modeling, we aim to demonstrate ways to make a genetic circuit independent of some of these variables, thereby decreasing this uncertainty. We couple our model with a software tool that determines a coding sequence for each gene involved in the circuit in such a way that they have similar codon usage bias across species of interest.
TALE - Incoherent Feed Forward Loop to control gene expression
In our system we exploit a commonly applied control system known as an Incoherent Feed Forward Loop (iFFL), in which an activator regulates both a gene and a repressor of the gene ... . This control system is established through the expression of a Transcription activator-like effector (TALE) protein. TALE proteins recognize DNA by a simple DNA-binding mechanism which can be altered to recognize any sequence you want … . In our system the TALE protein binds to the promoter of a gene of interest and thus respresses the expression of it. .... Has previously described this system and shown how it can result in independence of copy number of the system.
We further analyzed this system through the use of modeling, which revealed that it's insensitive to many other variables as well, which hasn't been explored yet.
Transferring genetic circuits between organisms yields large variation in most (if not all) of the parameters in the system, we exploited the robustness of this model to maintain predictability even when crossing species barriers.
Below you can find a set of questions used to establish design requirements for both our software tools and our system design
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Q1 How does the TALE protein bind to DNA?
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Q2 How does the iFFL behave?
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Q3 How can we make our system more robust?
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Q4 How does the system behave when transferring between organisms?
You can find the full model description here!
Codon usage - Cross species codon harmonization