Difference between revisions of "Template:UNebraska-Lincoln/Modeling"

(Created page with "{{UNebraska-Lincoln}} <html> <p>HELLO WORLD</p> </html>")
 
Line 1: Line 1:
 
{{UNebraska-Lincoln}}
 
{{UNebraska-Lincoln}}
 
<html>
 
<html>
−
<p>HELLO WORLD</p>
+
 
 +
<h1>System Model</h1>
 +
<h2>Summary</h2>
 +
 
 +
<p>The genetic system created by the 2019 UNL iGem team was designed to identify MRSA quorum-sensing molecules, move towards their source, and produce a protein that will break down the MRSA bacteria. We modeled the protein production of our system using Simbiology in Matlab 2018b.</p>
 +
<p>To build the model, we rested upon the following assumptions:</p>
 +
<p>These reactions take place in a single e.coli cell of volume 1E-15 L. [1]</p>
 +
<p>The cell has enough RNA Polymerases, Ribosomes, and tRNAs to where they aren’t the limiting factors in reactions.</p>
 +
<p>There are the maximum amount of plasmids for each plasmid count in the cell.</p>
 +
<p>There are 40 native AraC molecules in the cell. [2]</p>
 +
<p>There is the minimum of arabinose and AIP used as input.</p>
 +
 
 +
<p>The model is broken up into two phases. The first phase begins when extracellular Arabinose enters the cell. The Arabinose binds with native AraC proteins, which dimerize and act as a transcription factor for pBad. Once the AraC dimer binds to pBad, transcription is able to initiate to produce a polycistronic mRNA strand encoding AgrA, AgrC, and SarA. This mRNA strand is then translated into the respective proteins through the three RBS sites located on the strand. AgrC then inserts itself into the cell membrane while AgrA and SarA remain in the cytoplasm.</p>
 +
 
 +
 
 
</html>
 
</html>

Revision as of 21:42, 19 October 2019

System Model

Summary

The genetic system created by the 2019 UNL iGem team was designed to identify MRSA quorum-sensing molecules, move towards their source, and produce a protein that will break down the MRSA bacteria. We modeled the protein production of our system using Simbiology in Matlab 2018b.

To build the model, we rested upon the following assumptions:

These reactions take place in a single e.coli cell of volume 1E-15 L. [1]

The cell has enough RNA Polymerases, Ribosomes, and tRNAs to where they aren’t the limiting factors in reactions.

There are the maximum amount of plasmids for each plasmid count in the cell.

There are 40 native AraC molecules in the cell. [2]

There is the minimum of arabinose and AIP used as input.

The model is broken up into two phases. The first phase begins when extracellular Arabinose enters the cell. The Arabinose binds with native AraC proteins, which dimerize and act as a transcription factor for pBad. Once the AraC dimer binds to pBad, transcription is able to initiate to produce a polycistronic mRNA strand encoding AgrA, AgrC, and SarA. This mRNA strand is then translated into the respective proteins through the three RBS sites located on the strand. AgrC then inserts itself into the cell membrane while AgrA and SarA remain in the cytoplasm.