Difference between revisions of "Team:HBUT-China/Demonstrate"

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        <li><img src="https://static.igem.org/mediawiki/2017/5/55/HBUT-logo2.png" height="45"/></li>
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        <li><a href='https://2017.igem.org/Team:HBUT-China'>HOME</a></li>
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              <li ><a href='https://2017.igem.org/Team:HBUT-China/Team'>Team</a></li>
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              <li ><a href='https://2017.igem.org/Team:HBUT-China/Description'>Description</a></li>
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              <li ><a href='https://2017.igem.org/Team:HBUT-China/Design'>Design</a></li>
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              <li ><a href='https://2017.igem.org/Team:HBUT-China/Experiments'>Experiments</a></li>
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              <li ><a href='https://2017.igem.org/Team:HBUT-China/Notebook'>Notebook</a></li>
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              <li ><a href='https://2017.igem.org/Team:HBUT-China/Demonstrate'>Demonstrate</a></li>
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              <li ><a href='https://2017.igem.org/Team:HBUT-China/Attributions'>Attributions</a></li>
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<h1>Demonstrate</h1>
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      <div class="oneByOne_item">
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<h3>Gold Medal Criterion #4</h3>
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        <a href="javascript:;"><img src="https://static.igem.org/mediawiki/2017/5/55/HBUT-logo2.png" width="300" class="wp1_3 slide1_bot"/></a>                
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        <span class="txt1">Nickel ion!</span>      
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<p>
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        <span class="txt2">Heavy metal pollutants!</span>                                  
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Teams that can show their system working under real world conditions are usually good at impressing the judges in iGEM. To achieve gold medal criterion #4, convince the judges that your project works. There are many ways in which your project working could be demonstrated, so there is more than one way to meet this requirement. This gold medal criterion was introduced in 2016, so check our what 2016 teams did to achieve a their gold medals!
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        <span class="txt3 short">For this year¡¯s iGEM Competition, our team will be focusing on putting forward a biological approach to detect nickel ions as a heavy metal contaminant in the natural environment</span>                                   
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Please see the <a href="https://2017.igem.org/Judging/Medals">2017 Medals Page</a> for more information.
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        <span class="txt1 blue txt_right2">In order to achieve this goal, we use a nickel-sensitive repressive promoter (pncrA)</span>      
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</p>
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        <span class="txt1 blue txt_right2">In the absence of nickel ions, the repressor protein (NcrB) binds to the promoter, preventing the expression of the subsequent gene</span>
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              <h1>Demonstrate</h1>
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            </div>
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            <h5>We analyzed the experimental data through modeling.</h5>
 +
<small class="bigtitle">1.Assumptions:</small>
 +
<h5>We made four assumptions in order to simplify some of the aspects of the model. Many similar assumptions have been made in the literature.</h5>
 +
<p>The degradation of  and other substances are linear.</p>
 +
<p>Each cell has the same state.</p>
 +
<p>The reaction in the process satisfies the first-order kinetic reaction.</p>
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<small class="bigtitle">2. Transcription Repression and Release Repression</small>
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<div align="center" style="margin:10px 0;">
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<img src="https://static.igem.org/mediawiki/2017/5/5f/Hbut-demon-1.png" alt="this is a photo">
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</div>
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<div align="center" style="margin:10px 0;">
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<img src="https://static.igem.org/mediawiki/2017/f/fd/Hbut-demon-2.png" alt="this is a photo">
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</div>
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<div align="center" style="margin:10px 0;">
 +
<img src="https://static.igem.org/mediawiki/2017/d/db/Hbut-demon-3.png" alt="this is a photo">
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</div>
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<div align="center" style="margin:10px 0;">
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<img src="https://static.igem.org/mediawiki/2017/a/a7/Hbut-demon-4.png" alt="this is a photo">
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</div>
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<h5>Using the assumption about the first-order kinetic reaction,</h5>
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<h5>Give：</h5>
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<div align="center" style="margin:10px 0;">
 +
<img src="https://static.igem.org/mediawiki/2017/b/b3/Hbut-demon-5.png" alt="this is a photo">
 +
</div>
 +
 +
<small class="bigtitle">3. Quasi-steady-state Approximation (QSSA)</small>
 +
<h5>Ordinary differential equations are too difficult to be solved, in order to get the solution of the equations, quasi-steady-state approximation is necessary.</h5>
 +
<h5>We use the approximate conditions as little as possible and try to make the quasi steady state of matter consistent with the actual situation.</h5>
 +
 +
<div align="center" style="margin:10px 0;">
 +
<img src="https://static.igem.org/mediawiki/2017/4/4a/Hbut-demon-6.png" alt="this is a photo">
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</div>
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<h5>According to the formula’s deformation and derivation, </h5>
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<h5>gives：</h5>
  
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<div align="center" style="margin:10px 0;">
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<img src="https://static.igem.org/mediawiki/2017/5/5c/Hbut-demon-7.png" alt="this is a photo">
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</div>
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<div class="column half_size">
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<small class="bigtitle">4. Incomplete Repression</small>
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<h5>Under incomplete repression, the bacteria express red fluorescent proteins without the presence of nickel ions.</h5>
 +
<h5>The incomplete repression of promoters is a major issue in our fluorescence system. This issue was particularly observed in following diagram.</h5>
 +
<h5>The common formulation of the Hill equation is as follows:</h5>
 +
<div align="center" style="margin:10px 0;">
 +
<img src="https://static.igem.org/mediawiki/2017/3/30/Hbut-demon-8.png" alt="this is a photo">
 +
</div>
 +
<h5>Consequently, we modeled incomplete repression by using the ratio of occupied promoter concentration to total promoter concentration.</h5>
 +
<div align="center" style="margin:10px 0;">
 +
<img src="https://static.igem.org/mediawiki/2017/a/a9/Hbut-demon-9.png" alt="this is a photo">
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</div>
  
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<h4> What should we do for our demonstration?</h4>
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<h5>In view of the fact that is difficult to be measured and have same trend to , we used the concentration of nickel ions to approximate the equation.</h5>
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<div align="center" style="margin:10px 0;">
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<h5> Standard teams </h5>
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  <img src="https://static.igem.org/mediawiki/2017/9/95/Hbut-demon-10.png" alt="this is a photo">
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    </div>
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<p>  
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<h5>So, the fluorescence intensity can be obtained without considering the cytotoxicity of Nickel Ions:</h5>
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If you have built a proof of concept system, you can demonstrate it working under real world conditions. If you have built a biological device that is intended to be a sensor, can you show it detecting whatever it is intended to sense. If it is intended to work in the field, you can show how this might work using a simulated version in the lab, or a simulation of your device in the field.<strong> Please note biological materials must not be taken out of the lab</strong>.
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<div align="center" style="margin:10px 0;">
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</p>
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<img src="https://static.igem.org/mediawiki/2017/9/9d/Hbut-demon-11.png" alt="this is a photo">
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</div>
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<h5>The para meters for the production function are:</h5>
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<h5><i>A</i>-basal expression level of promoter</h5>
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<h5><i>B</i>-maximal expression level of promoter</h5>
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<h5><i>K<sub>d</sub></i>-half maximal effective concentration of N-Ni</h5>
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<h5><i>n</i>-Hill coefficient for induction. </h5>
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<h5>Added Variable, The differential equation of was updated by:</h5>
 +
<div align="center" style="margin:10px 0;">
 +
<img src="https://static.igem.org/mediawiki/2017/3/3b/Hbut-demon-12.png" alt="this is a photo">
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</div>
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<h5>The solution of this differential equation is as follows：</h5>
 +
<div align="center" style="margin:10px 0;">
 +
<img src="https://static.igem.org/mediawiki/2017/2/22/Hbut-demon-13.png" alt="this is a photo">
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</div>
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  <p>copyright &copy;  2017 IGEM-HBUT-China All rights reserved.</p>
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<h5> Special track teams </h5>
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<p>
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Special track teams can achieve this medal criterion by bringing their work to the Jamboree and showcasing it in the track event. Art & Design, Measurement, Hardware and Software tracks will all have showcase events at the Giant Jamboree.<strong> Please note biological materials must not be taken out of the lab</strong>.
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Revision as of 09:25, 21 October 2017

Demonstrate

We analyzed the experimental data through modeling.
1.Assumptions:
We made four assumptions in order to simplify some of the aspects of the model. Many similar assumptions have been made in the literature.

The degradation of and other substances are linear.

Each cell has the same state.

The reaction in the process satisfies the first-order kinetic reaction.

2. Transcription Repression and Release Repression
this is a photo
this is a photo
this is a photo
this is a photo
Using the assumption about the first-order kinetic reaction,
Give：
this is a photo
3. Quasi-steady-state Approximation (QSSA)
Ordinary differential equations are too difficult to be solved, in order to get the solution of the equations, quasi-steady-state approximation is necessary.
We use the approximate conditions as little as possible and try to make the quasi steady state of matter consistent with the actual situation.
this is a photo
According to the formula’s deformation and derivation,
gives：
this is a photo
4. Incomplete Repression
Under incomplete repression, the bacteria express red fluorescent proteins without the presence of nickel ions.
The incomplete repression of promoters is a major issue in our fluorescence system. This issue was particularly observed in following diagram.
The common formulation of the Hill equation is as follows:
this is a photo
Consequently, we modeled incomplete repression by using the ratio of occupied promoter concentration to total promoter concentration.
this is a photo
In view of the fact that is difficult to be measured and have same trend to , we used the concentration of nickel ions to approximate the equation.
this is a photo
So, the fluorescence intensity can be obtained without considering the cytotoxicity of Nickel Ions:
this is a photo
The para meters for the production function are:
A-basal expression level of promoter
B-maximal expression level of promoter
Kd-half maximal effective concentration of N-Ni
n-Hill coefficient for induction.
Added Variable, The differential equation of was updated by:
this is a photo
The solution of this differential equation is as follows：
this is a photo