Difference between revisions of "Team:TUDelft/DennisModel"

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     <p> 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. <br>
 
     <p> 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. <br>
 
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We first mapped all the moving parts that influence the expression levels of the gene of interest
 
  
 
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   <p> In our system we make use of a commonly applied control system called an Incoherent Feed Forward Loop (iFFL).  This control system is established through the expression of a Transcription activator-like effector (TALE) protein which binds to the promoter of a gene of interest and thus repressing the expression, developed by … .  TALE proteins recognize DNA by a simple DNA-binding mechanism which can be altered to recognize any sequence you want … . <br>
 
   <p> In our system we make use of a commonly applied control system called an Incoherent Feed Forward Loop (iFFL).  This control system is established through the expression of a Transcription activator-like effector (TALE) protein which binds to the promoter of a gene of interest and thus repressing the expression, developed by … .  TALE proteins recognize DNA by a simple DNA-binding mechanism which can be altered to recognize any sequence you want … . <br>
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Based on our modeling of this system we can show that this system gives expression levels independent of copy number which has previously been described by ... . However, further analyzation of this model reveals that its insensitive to many variables, which previously haven't been explored.
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Below you can find a set of questions used to establish design requirements for both our software tools and our system design
 
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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Revision as of 16:23, 4 September 2019

Sci-Phi 29


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 make use of a commonly applied control system called an Incoherent Feed Forward Loop (iFFL). This control system is established through the expression of a Transcription activator-like effector (TALE) protein which binds to the promoter of a gene of interest and thus repressing the expression, developed by … . TALE proteins recognize DNA by a simple DNA-binding mechanism which can be altered to recognize any sequence you want … .

Based on our modeling of this system we can show that this system gives expression levels independent of copy number which has previously been described by ... . However, further analyzation of this model reveals that its insensitive to many variables, which previously haven't been explored.
Below you can find a set of questions used to establish design requirements for both our software tools and our system design

Codon usage - Cross species codon harmonization