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Team:Davidson-MissouriW
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<p>In our design, weighted items are represented by versions of <i>TetA</i> genes that confer measurably distinct levels of tetracycline resistance. We have altered the codons of the wild type <i>TetA</i> gene, optimizing and de-optimizing several segments of the coding sequence. Each <i>TetA</i> variant is coupled with a distinctive fluorescent gene, and each pair of genes is flanked by <i>lox</i> sites. In the presence of Cre protein, the <i>lox</i> mechanism either inverts or excises the coding sequence, yielding different combinations of expressed <i>TetA</i> variants. An expressed variant corresponds to an item being placed in the knapsack. Over-expression of <i>TetA</i> results in cell death, which represents exceeding the capacity of the knapsack. Under-expression of <i>TetA</i> causes the cells to stop growing due to tetracycline in the growth medium, which represents not completely filling the knapsack. Surviving cells correspond to cells within a certain range of <i>TetA</i> production and the fluorescence tag allows for comparative measurement within this range.</p> | <p>In our design, weighted items are represented by versions of <i>TetA</i> genes that confer measurably distinct levels of tetracycline resistance. We have altered the codons of the wild type <i>TetA</i> gene, optimizing and de-optimizing several segments of the coding sequence. Each <i>TetA</i> variant is coupled with a distinctive fluorescent gene, and each pair of genes is flanked by <i>lox</i> sites. In the presence of Cre protein, the <i>lox</i> mechanism either inverts or excises the coding sequence, yielding different combinations of expressed <i>TetA</i> variants. An expressed variant corresponds to an item being placed in the knapsack. Over-expression of <i>TetA</i> results in cell death, which represents exceeding the capacity of the knapsack. Under-expression of <i>TetA</i> causes the cells to stop growing due to tetracycline in the growth medium, which represents not completely filling the knapsack. Surviving cells correspond to cells within a certain range of <i>TetA</i> production and the fluorescence tag allows for comparative measurement within this range.</p> | ||
| - | <p>The team is also working to develop software tools relevant to the specific project and applicable to projects in the wider synthetic biology community.</p> | + | <p>The team is also working to develop software tools relevant to the specific project and applicable to projects in the wider synthetic biology community.</p><br> |
</div> | </div> | ||
<div id="team_box"><center><a href="https://2010.igem.org/Team:Davidson-MissouriW/Team"><img src="https://static.igem.org/mediawiki/2010/4/42/Davidson-MissouriWTEAM.jpg" alt="Team"/></center> | <div id="team_box"><center><a href="https://2010.igem.org/Team:Davidson-MissouriW/Team"><img src="https://static.igem.org/mediawiki/2010/4/42/Davidson-MissouriWTEAM.jpg" alt="Team"/></center> | ||
Revision as of 13:11, 28 July 2010
Optimizing Codons
Building weighted items through codon variation of TetA gene led to foundational advances
Details
Characterizing Cre/Lox
Randomly choosing objects to place in the knapsack using Cre/Lox recombination
Details
Measuring Gene Expression
Visualizing the knapsack problem through controlling environmental variables and manipulating gene order
Details
iGEM Davidson – Missouri Western 2010:
Foundational Advances in Biology and the Knapsack Problem
The Davidson/Missouri Western multidisciplinary team is using synthetic biology to address a mathematical problem in Escherichia coli. Specifically, we are addressing the Knapsack Problem, an NP-complete problem that asks, “Given a finite number of weighted items, can one find a subset of these items that completely fills a knapsack of fixed capacity?”
In our design, weighted items are represented by versions of TetA genes that confer measurably distinct levels of tetracycline resistance. We have altered the codons of the wild type TetA gene, optimizing and de-optimizing several segments of the coding sequence. Each TetA variant is coupled with a distinctive fluorescent gene, and each pair of genes is flanked by lox sites. In the presence of Cre protein, the lox mechanism either inverts or excises the coding sequence, yielding different combinations of expressed TetA variants. An expressed variant corresponds to an item being placed in the knapsack. Over-expression of TetA results in cell death, which represents exceeding the capacity of the knapsack. Under-expression of TetA causes the cells to stop growing due to tetracycline in the growth medium, which represents not completely filling the knapsack. Surviving cells correspond to cells within a certain range of TetA production and the fluorescence tag allows for comparative measurement within this range.
The team is also working to develop software tools relevant to the specific project and applicable to projects in the wider synthetic biology community.
Project
View the work done by Davidson and Missouri Western undergrads.
