Team:NUDT CHINA/Notebook

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<h3>The Transformation of Our iGEM Ideas</h3></p><p>
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Originally, we were attracted by the <i>Shortest Path Problem</i>, which aims to find the shortest path in a directed graph that can link the beginning node and ending node. Be inspired, we decided to design a cascade pathway <i>in vivo</i> which can help us read out the answer of Shortest Path Problem directly by the life stage of <i>E. coli</i>.
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<p>The main problem in the design are:</p>
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<li>how to describe a route in <i>E. coli</i>;</li>
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<li>how to build different routes in <i>E. coli</i>;</li>
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<li>how to compare the length of different pathways.</li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA">Home</a> </li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA/Team">Team</a> </li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA/Project">Project</a> </li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA/Parts">Parts</a> </li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA/Modeling">Modeling</a> </li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA/Notebook">Notebook</a> </li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA/Safety">Safety</a> </li>
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<li><a href="https://2014.igem.org/Team:NUDT_CHINA/Attributions">Attributions</a> </li>
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To solve the first problem, we built devices that contains promoter, RBS, target gene (CDS) and terminator to simulate the nodes and lines in directed graph: the promoters are nodes and the target fragment are lines. When the promoter is activated, the target gene can coding protein which then activate the next promoter as regulatory element. This regulatory process can describe how a man the walking in a directed graph: he departed from the node P1, went through the line L and finally arrived at the spot P2. In this way, theoretically, we can describe any given directed graph in <i>E. coli</i>. (For further details about the coding of the graph, please refer to the project profile of our wiki) (Fig. 1)</p>
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<p><center><img src="https://static.igem.org/mediawiki/2014/0/04/NUDT_CHINA_Notes_idea_3part.png" width="302" heigth="128" /><br>
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Fig. 1 One promoter and one target gene can simulate one node and one line
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After building one complete graph in <i>E. coli</i>, different route should be labelled and tested independently so that we can get the length indirectly by the time of whole travel from beginning to ending. Then we can selected the quickest one as the shortest route. However, we are stuck in the second problem: how to build different route.</p>
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<h5>First design:</h5></p>
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In each regulatory unit, three different restrict enzyme sites are put between the promoter and RBS, target gene and terminator, terminator and next promoter, respectively. (Fig. 2)
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<img src="https://static.igem.org/mediawiki/2014/5/58/NUDT_CHINA_Notes_idea_3part_fig2.png" width="302" height="119" />
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<br>Fig. 2 the position of three different restrict enzyme sites</center>
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Revision as of 15:27, 17 October 2014


The Transformation of Our iGEM Ideas

Originally, we were attracted by the Shortest Path Problem, which aims to find the shortest path in a directed graph that can link the beginning node and ending node. Be inspired, we decided to design a cascade pathway in vivo which can help us read out the answer of Shortest Path Problem directly by the life stage of E. coli.

The main problem in the design are:

  • how to describe a route in E. coli;
  • how to build different routes in E. coli;
  • how to compare the length of different pathways.

To solve the first problem, we built devices that contains promoter, RBS, target gene (CDS) and terminator to simulate the nodes and lines in directed graph: the promoters are nodes and the target fragment are lines. When the promoter is activated, the target gene can coding protein which then activate the next promoter as regulatory element. This regulatory process can describe how a man the walking in a directed graph: he departed from the node P1, went through the line L and finally arrived at the spot P2. In this way, theoretically, we can describe any given directed graph in E. coli. (For further details about the coding of the graph, please refer to the project profile of our wiki) (Fig. 1)


Fig. 1 One promoter and one target gene can simulate one node and one line

After building one complete graph in E. coli, different route should be labelled and tested independently so that we can get the length indirectly by the time of whole travel from beginning to ending. Then we can selected the quickest one as the shortest route. However, we are stuck in the second problem: how to build different route.

First design:

In each regulatory unit, three different restrict enzyme sites are put between the promoter and RBS, target gene and terminator, terminator and next promoter, respectively. (Fig. 2)


Fig. 2 the position of three different restrict enzyme sites

WELCOME TO iGEM 2014!

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On this page you can document your project, introduce your team members, document your progress
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Home Team Official Team Profile Project Parts Modeling Notebook Safety Attributions

Notebook

You should make use of the calendar feature on the wiki and start a lab notebook. This may be looked at by the judges to see how your work progressed throughout the summer. It is a very useful organizational tool as well.

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