Difference between revisions of "Team:SCUT/Modeling"

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<h2> Modeling</h2>
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<h4>Note</h4>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
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<h2>Measurement</h2>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
 
  
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<h3>Overview</h3>
 
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Here are a few examples from previous teams:
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The function of E.coli W3110 in our project is to monitor and then absorb the cadmium ion in waste water. In order to simulate how it worked and made it simple for us to evaluate the result, we strive vigorously to establish a precise mathematical model of the procedure. The whole system was the divided into two devices. After that, we went even further. We optimized our system, trying to get a more efficient system so that it could be more powerful to process the toxic cadmium ion. We decided to follow the length of ECs.
 
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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In addition, we got enough quantitative data of some biobricks which we were going to submit. We hope to submit those biobricks together with their own relatively accurate parameters. We believe, by doing so, we may conform better to the meaning of synthetic biology.
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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As was discussed before, there are two devices of our system, one was named bio-sensor and the other, of course, was named bio-effector. And here we will just briefly talk about them.
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The former also has two main parts: PcadA, which is the cadmium ion induced promotor; and Ptet, which is simply Tetracycline induced promoter. These two components respectively linked with RFP gene and with cjBlue gene. This kind of method leads a result that when the concentration of cadmium ion is below the low limit of detection, the system is blue, otherwise it’s red instead. Based on the strength of these two promotors, we built a mathematical model to predict the capacity of processing the cadmium ion.
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The core of Bio-effector is csgA-EC compound. CsgA-EC, whose function is decreasing the concentration of cadmium ion by using chelation, is the unit of our E.coli’s curli. We also built a model about that based on their chelating equilibrium constant and use it to do the same thing as last model we have talked about.
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However, not everything went well, because of the lack of time, we failed to knock out the gene of csgA of wild type on time, we could only gain our referential parameters from multitudinous literatures and establish a similar model. Another great pity is that crippled by our poor measuring apparatus, we merely did some preliminary data measurement and treatment.
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<img src="https://static.igem.org/mediawiki/parts/b/b5/2015SCUTsystem1.jpg">
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<p>Figure 1</p>
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<img src="https://static.igem.org/mediawiki/parts/b/b3/2015SCUTsystem2.jpg">
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<p>Figure 2</p>
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<img src="https://static.igem.org/mediawiki/parts/6/66/2015SCUTsystem3.jpg">
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<p>Figure 3</p>
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Figure 1, Figure 2 and Figure 3 show the color change and the capacity of cadmium adsorption of the whole system in different initial concentration of extracellular cadmium ion.
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<h3>About Us</h3>
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In 2015, we SCUT teams won top ten innovative and entrepreneurial team set up by SCUT.Because of the strong support of the college, our team is being on the right track, and increasing understanding of the subject and experience.
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<h3 style="margin-left:20px;">Thanks</h3>
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<ul>
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<li>Zhang Zhenwu,Prof. Guo Shouqian,Dr. Li, Dr. Li Cheng,Dr. Wang Meng,Chen Kejie</li>
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<li>Guangzhou Municipal Environmental Protection Bureau<br/>
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Revision as of 20:40, 18 September 2015

Team:SCUT

Measurement

Overview

The function of E.coli W3110 in our project is to monitor and then absorb the cadmium ion in waste water. In order to simulate how it worked and made it simple for us to evaluate the result, we strive vigorously to establish a precise mathematical model of the procedure. The whole system was the divided into two devices. After that, we went even further. We optimized our system, trying to get a more efficient system so that it could be more powerful to process the toxic cadmium ion. We decided to follow the length of ECs.

In addition, we got enough quantitative data of some biobricks which we were going to submit. We hope to submit those biobricks together with their own relatively accurate parameters. We believe, by doing so, we may conform better to the meaning of synthetic biology.

As was discussed before, there are two devices of our system, one was named bio-sensor and the other, of course, was named bio-effector. And here we will just briefly talk about them.

The former also has two main parts: PcadA, which is the cadmium ion induced promotor; and Ptet, which is simply Tetracycline induced promoter. These two components respectively linked with RFP gene and with cjBlue gene. This kind of method leads a result that when the concentration of cadmium ion is below the low limit of detection, the system is blue, otherwise it’s red instead. Based on the strength of these two promotors, we built a mathematical model to predict the capacity of processing the cadmium ion.

The core of Bio-effector is csgA-EC compound. CsgA-EC, whose function is decreasing the concentration of cadmium ion by using chelation, is the unit of our E.coli’s curli. We also built a model about that based on their chelating equilibrium constant and use it to do the same thing as last model we have talked about.

However, not everything went well, because of the lack of time, we failed to knock out the gene of csgA of wild type on time, we could only gain our referential parameters from multitudinous literatures and establish a similar model. Another great pity is that crippled by our poor measuring apparatus, we merely did some preliminary data measurement and treatment.

Figure 1

Figure 2

Figure 3

Figure 1, Figure 2 and Figure 3 show the color change and the capacity of cadmium adsorption of the whole system in different initial concentration of extracellular cadmium ion.

About Us

In 2015, we SCUT teams won top ten innovative and entrepreneurial team set up by SCUT.Because of the strong support of the college, our team is being on the right track, and increasing understanding of the subject and experience.

Thanks

  • Zhang Zhenwu,Prof. Guo Shouqian,Dr. Li, Dr. Li Cheng,Dr. Wang Meng,Chen Kejie
  • Guangzhou Municipal Environmental Protection Bureau

COPYRIGHT ©2015-SCUT