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

 
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              <h1>Demonstrate</h1>
 
              <h1>Demonstrate</h1>
 
            </div>
 
            </div>
            <h5>We analyzed the experimental data through modeling.</h5>
+
          <small class="bigtitle">Response to nickel ions:</small>
<small class="bigtitle">1.Assumptions:</small>
+
<p>We added nickel ions in the medium of strain K2304002. After 2h (200rpm, 37 ℃, LB), we centrifuged the culture medium at 12000 r / min. The red precipitate appeared at the bottom of the centrifuge tube,while the blank control group produced very little, or none of the red precipitation. This indicates that KL2304002 can be induced by Ni ions to produce RFP.</p>
<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>
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<div align="center" style="margin:10px 0;">
<p>The degradation of and other substances are linear.</p>
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    <img src="//2017.igem.org/wiki/images/8/89/Hbut-newresult-1.png" alt="this is a photo">
<p>Each cell has the same state.</p>
+
    </div>
<p>The reaction in the process satisfies the first-order kinetic reaction.</p>
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<small class="bigtitle">Specific response:</small>
<small class="bigtitle">2. Transcription Repression and Release Repression</small>
+
<p>In order to detect whether strain K2304002 is also induced by other ions,</p>
<div align="center" style="margin:10px 0;">
+
<p>We mixed samples using Cd<sup>2 +</sup>, Co<sup>2 +</sup>, Cu<sup>2 +</sup>, Fe<sup>3 +</sup>, and Ni<sup>2 +</sup>in LB medium, with a concentration of 0.01 mmol / L .</p>
<img src="https://static.igem.org/mediawiki/2017/5/5f/Hbut-demon-1.png" alt="this is a photo">
+
<p>We cultured the samples at 200rpm, 37 ℃ overnight.</p>
</div>
+
<p>The next day we observed them with a fluorescence microscope. Excitation light is Blue background light.</p>
<div align="center" style="margin:10px 0;">
+
<div align="center" style="margin:10px 0;">
<img src="https://static.igem.org/mediawiki/2017/f/fd/Hbut-demon-2.png" alt="this is a photo">
+
    <img src="//2017.igem.org/wiki/images/4/4f/Hbut-newresult-2.png" alt="this is a photo">
</div>
+
    </div>
<div align="center" style="margin:10px 0;">
+
<p>Clearly, only the sample with Ni ions showed red fluorescence, the other groups had no red fluorescence. Note that the iron ions reacted with the substance in the culture medium,so that there is an impurity in the field of view.</p>
<img src="https://static.igem.org/mediawiki/2017/d/db/Hbut-demon-3.png" alt="this is a photo">
+
</div>
+
<div align="center" style="margin:10px 0;">
+
<img src="https://static.igem.org/mediawiki/2017/a/a7/Hbut-demon-4.png" alt="this is a photo">
+
</div>
+
<h5>Using the assumption about the first-order kinetic reaction,</h5>
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<h5>Give:</h5>
+
<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>
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<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">
+
</div>
+
+
+
<h5>According to the formula’s deformation and derivation, </h5>
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<h5>gives:</h5>
+
  
<div align="center" style="margin:10px 0;">
 
<img src="https://static.igem.org/mediawiki/2017/5/5c/Hbut-demon-7.png" alt="this is a photo">
 
</div>
 
 
  
<small class="bigtitle">4. Incomplete Repression</small>
+
<small class="bigtitle">Qualitative testing:</small>
<h5>Under incomplete repression, the bacteria express red fluorescent proteins without the presence of nickel ions.</h5>
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<p>K304002 was cultured at different concentrations of nickel ions, and the fluorescence intensity was measured every hour. We found that different concentrations of nickel ions caused inconclusive differences in fluorescence intensity.</p>
<h5>The incomplete repression of promoters is a major issue in our fluorescence system. This issue was particularly observed in following diagram.</h5>
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<div align="center" style="margin:10px 0;">
<h5>The common formulation of the Hill equation is as follows:</h5>
+
    <img src="//2017.igem.org/wiki/images/1/1d/Hbut-newresult-3.png" alt="this is a photo">
<div align="center" style="margin:10px 0;">
+
    </div>
<img src="https://static.igem.org/mediawiki/2017/3/30/Hbut-demon-8.png" alt="this is a photo">
+
</div>
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<h5>Consequently, we modeled incomplete repression by using the ratio of occupied promoter concentration to total promoter concentration.</h5>
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<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">
+
</div>
+
  
<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>
+
 
<div align="center" style="margin:10px 0;">
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<p>Therefore, we tried to find a way to perform qualitative testing. We used different concentrations of nickel ions to induce the strain in OD0.8, and detected the fluorescence intensity every other hour by fluorescence spectrophotometer. And finally we found with a nickel ion concentration of 10-6mmol / L to 10-4mmol / L, that the correlation between fluorescence intensity and nickel ion concentration is the highest. So it has the application value of qualitative detection.</p>
  <img src="https://static.igem.org/mediawiki/2017/9/95/Hbut-demon-10.png" alt="this is a photo">
+
<div align="center" style="margin:10px 0;">
    </div>
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    <img src="//2017.igem.org/wiki/images/f/f3/Hbut-demon-new2.png" alt="this is a photo">
<h5>So, the fluorescence intensity can be obtained without considering the cytotoxicity of Nickel Ions:</h5>
+
    </div>
<div align="center" style="margin:10px 0;">
+
 
<img src="https://static.igem.org/mediawiki/2017/9/9d/Hbut-demon-11.png" alt="this is a photo">
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<p>This is the conclusion we have made so far, and if we continue to experiment, we believe we can find a better application mode, or an exact detectable interval. After that, we will be able to further study its measurement accuracy.</p>
</div>
+
 
<h5>The para meters for the production function are:</h5>
+
 
<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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<small class="bigtitle">Application:</small>
<h5><i>K<sub>d</sub></i>-half maximal effective concentration of N-Ni</h5>
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<p>We designed a kit, including 10ml centrifuge tubes, filter columns (containing 0.22 M filter membrane), the national standard concentration of nickel ion solution 50ml(3μg/L), pure water 20ml, engineering bacteria 5ml.</p>
<h5><i>n</i>-Hill coefficient for induction. </h5>
+
 
<h5>Added Variable, The differential equation of was updated by:</h5>
+
<p>Here is the Instructions:</p>
<div align="center" style="margin:10px 0;">
+
<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">
+
    <img src="//2017.igem.org/wiki/images/2/29/Hbut-demon-new1.png" alt="this is a photo">
</div>
+
    </div>
<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">
+
</div>
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        </div>
 
        </div>
 
         <div class="col-lg-2"></div>
 
         <div class="col-lg-2"></div>

Latest revision as of 01:48, 2 November 2017

  • \
Response to nickel ions:

We added nickel ions in the medium of strain K2304002. After 2h (200rpm, 37 ℃, LB), we centrifuged the culture medium at 12000 r / min. The red precipitate appeared at the bottom of the centrifuge tube,while the blank control group produced very little, or none of the red precipitation. This indicates that KL2304002 can be induced by Ni ions to produce RFP.

this is a photo
Specific response:

In order to detect whether strain K2304002 is also induced by other ions,

We mixed samples using Cd2 +, Co2 +, Cu2 +, Fe3 +, and Ni2 +in LB medium, with a concentration of 0.01 mmol / L .

We cultured the samples at 200rpm, 37 ℃ overnight.

The next day we observed them with a fluorescence microscope. Excitation light is Blue background light.

this is a photo

Clearly, only the sample with Ni ions showed red fluorescence, the other groups had no red fluorescence. Note that the iron ions reacted with the substance in the culture medium,so that there is an impurity in the field of view.

Qualitative testing:

K304002 was cultured at different concentrations of nickel ions, and the fluorescence intensity was measured every hour. We found that different concentrations of nickel ions caused inconclusive differences in fluorescence intensity.

this is a photo

Therefore, we tried to find a way to perform qualitative testing. We used different concentrations of nickel ions to induce the strain in OD0.8, and detected the fluorescence intensity every other hour by fluorescence spectrophotometer. And finally we found with a nickel ion concentration of 10-6mmol / L to 10-4mmol / L, that the correlation between fluorescence intensity and nickel ion concentration is the highest. So it has the application value of qualitative detection.

this is a photo

This is the conclusion we have made so far, and if we continue to experiment, we believe we can find a better application mode, or an exact detectable interval. After that, we will be able to further study its measurement accuracy.

Application:

We designed a kit, including 10ml centrifuge tubes, filter columns (containing 0.22 M filter membrane), the national standard concentration of nickel ion solution 50ml(3μg/L), pure water 20ml, engineering bacteria 5ml.

Here is the Instructions:

this is a photo