Difference between revisions of "Team:Shanghai high school/Model"

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<p>This page is used by the judges to evaluate your team for the <a href="https://2021.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2021.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of 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. </p>
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<p>Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page. </p>
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    <!--图片-->
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<h3> Gold Medal Criterion #3</h3>
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    <div class="page-header">
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<p>
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        <img src="https://static.igem.org/mediawiki/2021/f/fd/T--Shanghai_high_school--bg_1.png" alt="">
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Use modeling to gain insight into how your project works or should be implemented. Explain your model's assumptions, data, parameters, and results in a way that anyone could understand.
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        <h1>Modeling</h1>
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<br><br>
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    </div>
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Please see the <a href="https://2021.igem.org/Judging/Medals">2021 Medals Page</a> for more information.
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−
</p>
+
  
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</div>
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    <!--内容-->
 +
    <div class="content-small">
 +
        <section class="article p-t-54 p-b-54">
 +
            <p>In order to determine the optimum induction duration of our engineered BL21 strains for the antigen protein
 +
                expression which is designed to induce neutralizing antibody immune response inside the human body, we
 +
                conducted several Western Blot and collected the gray value which was calculated by ImageJ to quantify the
 +
                protein expression against hours.</p>
  
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<div class="column two_thirds_size">
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            <section>
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<h3>Best Model Special Prize</h3>
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                <h1 class="title">PET28a-VP7qe</h1>
  
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<p>Models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices. Synthetic biology is an engineering discipline and part of engineering is simulation and modeling to determine system behavior before building your design. 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 before or in conjunction with experiments in the wetlab.
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                <div class="img-container">
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</p><p>
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                    <span class="figure">Table 2. the protein expression of PET28a-VP7</span>
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To compete for the <a href="https://2021.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2021.igem.org/Judging/Judging_Form">judging form</a>.
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                    <img src="https://static.igem.org/mediawiki/2021/6/63/T--Shanghai_high_school--img_modeling_1.jpg" alt="">
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</p>
+
                </div>
  
−
</div>
+
                <p>principle of linear model is the least square method, which we have learned in school. So here we go
 +
                    straight to the linear model (to assume the growth rate constant): and the model results analyzed by
 +
                    Matlab are showing below (figure 1, 2) .</p>
  
 +
                <div class="img-container m-t-12">
 +
                    <img src="https://static.igem.org/mediawiki/2021/2/22/T--Shanghai_high_school--img_modeling_2.jpg" alt="">
 +
                    <span class="figure">Figure 1. Model result of VP7 when IPTG concentration was given 1mM</span>
 +
                </div>
  
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<div class="column third_size">
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                <div class="img-container">
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<div class="highlight decoration_A_full">
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                    <img src="https://static.igem.org/mediawiki/2021/f/ff/T--Shanghai_high_school--img_modeling_3.jpg" alt="">
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<h3> Inspiration </h3>
+
                    <span class="figure">Figure 2. Model result of VP7 when IPTG concentration was given 2mM</span>
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<p>You can look at what other teams did to get some inspiration! <br />
+
                </div>
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Here are a few examples:</p>
+
−
<ul>
+
−
<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
+
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<li><a href="https://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
+
−
<li><a href="https://2019.igem.org/Team:IISER_Kolkata/Model">2019 IISER Kolkata</a></li>
+
−
<li><a href="https://2019.igem.org/Team:Exeter/Model">2019 Exeter</li>
+
−
<li><a href="https://2019.igem.org/Team:Mingdao/Model">2019 Mingdao</a></li>
+
−
<li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li>
+
−
<li><a href="https://2020.igem.org/Team:Leiden/Model">2020 Leiden</a></li>
+
−
</ul>
+
−
</div>
+
−
</div>
+
  
 +
                <p>Therefore, we can have the curves of these two models about PET28a-VP7 protein expression against hours
 +
                    (figure 3, 4).</p>
 +
 +
                <p>As seen below, these two curves present very similar trends with very close k value (curvature). So it
 +
                    indicates that the concentration of IPTG might not affect that much on the protein expression of
 +
                    PET28a-VP7, just a slight promotion. As the increase rate during the induction for the strain PET28a-VP7
 +
                    keeps almost constant, the protein expression level could be proportional to the induction duration.</p>
 +
 +
                <div class="img-container m-t-12">
 +
                    <img src="https://static.igem.org/mediawiki/2021/b/bb/T--Shanghai_high_school--img_modeling_4.jpg" alt="">
 +
                    <span class="figure">Figure 3. Curve of VP7 model when IPTG concentration was given 1mM</span>
 +
                </div>
 +
 +
                <div class="img-container">
 +
                    <img src="https://static.igem.org/mediawiki/2021/9/99/T--Shanghai_high_school--img_modeling_5.jpg" alt="">
 +
                    <span class="figure">Figure 4. Curve of VP7 model when IPTG concentration was given 2mM</span>
 +
                </div>
 +
            </section>
 +
 +
            <section>
 +
                <h1 class="title">PET28a-VP7-LTB</h1>
 +
 +
                <div class="img-container">
 +
                    <span class="figure">Table 2. the protein expression of PET28a-VP7-LTB</span>
 +
                    <img src="https://static.igem.org/mediawiki/2021/8/81/T--Shanghai_high_school--img_modeling_6.jpg" alt="">
 +
                </div>
 +
 +
                <p>After analysis, the data conforms to the S-type growth trend, so the Logistic Equation commonly used in
 +
                    biological growth, population growth, infectious diseases and other models is selected.</p>
 +
 +
                <img src="https://static.igem.org/mediawiki/2021/d/d3/T--Shanghai_high_school--img_modeling_11.jpg" alt="" style="width: 30%">
 +
 +
                <p>And its analytic expression is:</p>
 +
 +
                <img src="https://static.igem.org/mediawiki/2021/e/e2/T--Shanghai_high_school--img_modeling_12.jpg" alt="" style="width: 25%">
 +
 +
                <p>Here we imported the data by Matlab, the model results all indicate good fitting degrees as showing below
 +
                    in figure 5, 6.</p>
 +
 +
                <div class="img-container">
 +
                    <img src="https://static.igem.org/mediawiki/2021/f/f7/T--Shanghai_high_school--img_modeling_7.jpg" alt="">
 +
                    <span class="figure">Figure 5. Model result of VP7-LTB when IPTG concentration was given 1mM</span>
 +
                </div>
 +
 +
                <div class="img-container">
 +
                    <img src="https://static.igem.org/mediawiki/2021/9/93/T--Shanghai_high_school--img_modeling_8.jpg" alt="">
 +
                    <span class="figure">Figure 6. Model result of VP7-LTB when IPTG concentration was given 2mM</span>
 +
                </div>
 +
 +
                <p>In addition, here we obtained the curves of above models showing below (figure 7, 8). </p>
 +
 +
                <p>When IPTG concentration was given 1mM, VP7-LTB expresses the most fast during the third hour of the
 +
                    induction and it starts to flatten out after 4 hours. So we could imply that our engineered strain
 +
                    PET28a-VP7-LTB would start its maximum response efficiency after 2 hours and its optimum induction
 +
                    duration will be 4 hours around.</p>
 +
 +
                <p>When IPTG concentration was given 2 mM, the strain expresses the fast in the second hour of the induction
 +
                    but it is also earlier to get the steady phase which the peak of gray value is 120 around. In this case,
 +
                    the optimum induction duration of VP7-LTB shall be 2 hours.</p>
 +
 +
                <div class="img-container m-t-12">
 +
                    <img src="https://static.igem.org/mediawiki/2021/c/c4/T--Shanghai_high_school--img_modeling_9.jpg" alt="">
 +
                    <span class="figure">Figure 7. Curve of VP7-LTB model when IPTG concentration was given 1mM</span>
 +
                </div>
 +
 +
                <div class="img-container">
 +
                    <img src="https://static.igem.org/mediawiki/2021/2/2c/T--Shanghai_high_school--img_modeling_10.jpg" alt="">
 +
                    <span class="figure">Figure 8. Curve of VP7-LTB model when IPTG concentration was given 2mM</span>
 +
                </div>
 +
            </section>
 +
        </section>
 +
    </div>
 +
 +
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 +
            <span>Contact Email: 1649407718@qq.com; 2796437537@qq.com</span>
 +
            <span>Wechat Search ‘Dr Oral’ and follow us!</span>
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Revision as of 12:55, 27 September 2021

Modeling

In order to determine the optimum induction duration of our engineered BL21 strains for the antigen protein expression which is designed to induce neutralizing antibody immune response inside the human body, we conducted several Western Blot and collected the gray value which was calculated by ImageJ to quantify the protein expression against hours.

PET28a-VP7qe

Table 2. the protein expression of PET28a-VP7

principle of linear model is the least square method, which we have learned in school. So here we go straight to the linear model (to assume the growth rate constant): and the model results analyzed by Matlab are showing below (figure 1, 2) .

Figure 1. Model result of VP7 when IPTG concentration was given 1mM
Figure 2. Model result of VP7 when IPTG concentration was given 2mM

Therefore, we can have the curves of these two models about PET28a-VP7 protein expression against hours (figure 3, 4).

As seen below, these two curves present very similar trends with very close k value (curvature). So it indicates that the concentration of IPTG might not affect that much on the protein expression of PET28a-VP7, just a slight promotion. As the increase rate during the induction for the strain PET28a-VP7 keeps almost constant, the protein expression level could be proportional to the induction duration.

Figure 3. Curve of VP7 model when IPTG concentration was given 1mM
Figure 4. Curve of VP7 model when IPTG concentration was given 2mM

PET28a-VP7-LTB

Table 2. the protein expression of PET28a-VP7-LTB

After analysis, the data conforms to the S-type growth trend, so the Logistic Equation commonly used in biological growth, population growth, infectious diseases and other models is selected.

And its analytic expression is:

Here we imported the data by Matlab, the model results all indicate good fitting degrees as showing below in figure 5, 6.

Figure 5. Model result of VP7-LTB when IPTG concentration was given 1mM
Figure 6. Model result of VP7-LTB when IPTG concentration was given 2mM

In addition, here we obtained the curves of above models showing below (figure 7, 8).

When IPTG concentration was given 1mM, VP7-LTB expresses the most fast during the third hour of the induction and it starts to flatten out after 4 hours. So we could imply that our engineered strain PET28a-VP7-LTB would start its maximum response efficiency after 2 hours and its optimum induction duration will be 4 hours around.

When IPTG concentration was given 2 mM, the strain expresses the fast in the second hour of the induction but it is also earlier to get the steady phase which the peak of gray value is 120 around. In this case, the optimum induction duration of VP7-LTB shall be 2 hours.

Figure 7. Curve of VP7-LTB model when IPTG concentration was given 1mM
Figure 8. Curve of VP7-LTB model when IPTG concentration was given 2mM
Contact Email: 1649407718@qq.com; 2796437537@qq.com Wechat Search ‘Dr Oral’ and follow us!