Difference between revisions of "Team:Shanghai HS ID/Model"

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<h3>★  ALERT! </h3>
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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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                    <a href="https://2021.igem.org/Team:Shanghai_HS_ID">Home</a>
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                    <a href="">Project</a>
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<h1> Modeling</h1>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Description"
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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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                                    class="sub-nav-74">Description</a></li>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Experiments"
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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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                                    class="sub-nav-74">Experiments</a></li>
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<h3> Gold Medal Criterion #3</h3>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Safety">Safety</a></li>
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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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Please see the <a href="https://2021.igem.org/Judging/Medals">2021 Medals Page</a> for more information.
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<h3>Best Model Special Prize</h3>
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                                    Collection</a></li>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Engineering"
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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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                                    class="sub-nav-74">Engineering</a></li>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Contribution"
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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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                                    class="sub-nav-74">Contribution</a></li>
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<p>You can look at what other teams did to get some inspiration! <br />
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Here are a few examples:</p>
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<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Fundraising"
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<li><a href="https://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
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<li><a href="https://2019.igem.org/Team:IISER_Kolkata/Model">2019 IISER Kolkata</a></li>
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<li><a href="https://2019.igem.org/Team:Exeter/Model">2019 Exeter</li>
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<li><a href="https://2019.igem.org/Team:Mingdao/Model">2019 Mingdao</a></li>
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<li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li>
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                <li>
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<li><a href="https://2020.igem.org/Team:Leiden/Model">2020 Leiden</a></li>
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                    <a href="https://2021.igem.org/Team:Shanghai_HS_ID/Implementation">Implementation</a>
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                    <a href="https://2021.igem.org/Team:Shanghai_HS_ID/Entrepreneurship">Entrepreneurship</a>
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        <div class="sub-title">MODEL</div>
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        <div class="article-content">In order to scientifically determine the transformation efficiency of our modified
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            L. casei (KO) and the wild L. casei (Wild), we collected the colony cultured which were pre-spread plates
 +
            with different volumes of bacteria solutions and measured their OD<sub>600</sub> after cultured for the same
 +
            hours. In
 +
            the meantime, we also aimed to explore the optimal condition for our modified L. casei’ growth by applying
 +
            different amounts of the bacteria seed solution.</div>
 +
        <div class="img-wrap no-margin">
 +
            <span>Table 1. OD<sub>600</sub> of cultured L. casei</span>
 +
            <img src="https://static.igem.org/mediawiki/2021/f/f0/T--Shanghai_HS_ID--model01.png" alt="" />
 +
        </div>
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        <div class="article-content">According to the scatter plots, we chose to use the quadratic polynomial equation
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            to build the model :
 +
        </div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/b/bd/T--Shanghai_HS_ID--model02.png" alt="" />
 +
        </div>
 +
        <div class="article-content">The coding we used is given below:</div>
 +
        <div class="article-content">
 +
            <b>
 +
                “<br />
 +
                clear;clc;<br />
 +
                v0=[50 100 150];<br />
 +
                od10=[0.035 0.289 3.84];<br />
 +
                od20=[0.255 1.984 5.21];<br />
 +
                p1=polyfit(v0,od10,2)<br />
 +
                p2=polyfit(v0,od20,2)<br />
 +
                v=[50:150];<br />
 +
                od1=polyval(p1,v);<br />
 +
                od2=polyval(p2,v);<br />
 +
                plot(v,od1,'b','LineWidth',2)<br />
 +
                hold on<br />
 +
                plot(v,od2,'r','LineWidth',2)<br />
 +
                plot(v0,od10,'k*','LineWidth',2)<br />
 +
                plot(v0,od20,'g*','LineWidth',2)<br />
 +
                hold off<br />
 +
                ”
 +
            </b>
 +
        </div>
 +
        <div class="article-content">After calculation, below are the constants of the solved quadratic polynomial
 +
            equations of the KO group and
 +
            Wild group, respectively.</div>
 +
        <div class="img-wrap no-margin">
 +
            <span style="margin-bottom: 20px;">Table 2. Model results</span>
 +
            <table id="sub-table" border="1" cellspacing="0" cellpadding="0">
 +
                <tr>
 +
                    <td>Sample</td>
 +
                    <td>p1 </td>
 +
                    <td>p2 </td>
 +
                    <td>p3 </td>
 +
                </tr>
 +
                <tr>
 +
                    <td>KO</td>
 +
                    <td>0.0007 </td>
 +
                    <td>-0.0938 </td>
 +
                    <td>3.0780 </td>
 +
                </tr>
 +
                <tr>
 +
                    <td>Wild</td>
 +
                    <td>0.0003 </td>
 +
                    <td>-0.0103 </td>
 +
                    <td>0.0230 </td>
 +
                </tr>
 +
            </table>
 +
        </div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/0/06/T--Shanghai_HS_ID--model03.png" alt="" />
 +
            <span>Figure 1. Comparison between two fitting curves of KO group(red) and Wild group(blue)</span>
 +
        </div>
 +
        <div class="article-title">Conclusion</div>
 +
        <div class="article-content">In figure 1, we can clearly see that the modified L. casei shows much higher
 +
            transformation efficiency than the wild L. casei especially when the volume of the initial bacteria seed
 +
            solution is used less than 100 uL when the difference between them is remarkable.</div>
 +
        <div class="article-title">Solution</div>
 +
        <div class="article-content">We constructed a plasmid equipped with a CRISPR-Cas9 complex that cuts and removes
 +
            a selected segment of the L. casei DNA. Our target gene is LSEI-2094. This gene is involved in the synthesis
 +
            of an enzyme that is essential in the restriction-modification system [5]. The cell's efforts to repair its
 +
            DNA induces mutations, which help to inactivate the gene and prevent the production of the enzyme. After
 +
            this modification foreign DNAs could enter and express themselves much more efficiently in L.Casei.With a
 +
            strain of bacteria ready to be tailored to our needs, the benefits are immeasurable. The benefits of L.
 +
            caseicould come to fruition if the technology is applied to popular and impactful industries such as
 +
            pharmaceuticals and food. </div>
 +
        <div class="article-content">Besides, the equation model we built for the modified L. casei as showing below,
 +
            could be used to analyze the relationship between the volume of the bacteria seed solution and its
 +
            OD<sub>600</sub>, it
 +
            could be used as a reference when we conduct the expression efficiency tests in the future. If we could
 +
            further build the relationship between the expression level and OD<sub>600</sub>, we could adjust the volume
 +
            of the
 +
            bacteria seed solution for culturing accordingly.</div>
 +
        <div class="article-content" style="text-align: center;"><b>Model for the modified L. casei: </b>f(x) =
 +
            0.0003x<sup>3</sup> -
 +
            0.0103x<sup>2</sup> + 0.0230</div>
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Revision as of 15:42, 15 October 2021

Shanghai_HS_ID

MODEL
In order to scientifically determine the transformation efficiency of our modified L. casei (KO) and the wild L. casei (Wild), we collected the colony cultured which were pre-spread plates with different volumes of bacteria solutions and measured their OD600 after cultured for the same hours. In the meantime, we also aimed to explore the optimal condition for our modified L. casei’ growth by applying different amounts of the bacteria seed solution.
Table 1. OD600 of cultured L. casei
According to the scatter plots, we chose to use the quadratic polynomial equation to build the model :
The coding we used is given below:
“
clear;clc;
v0=[50 100 150];
od10=[0.035 0.289 3.84];
od20=[0.255 1.984 5.21];
p1=polyfit(v0,od10,2)
p2=polyfit(v0,od20,2)
v=[50:150];
od1=polyval(p1,v);
od2=polyval(p2,v);
plot(v,od1,'b','LineWidth',2)
hold on
plot(v,od2,'r','LineWidth',2)
plot(v0,od10,'k*','LineWidth',2)
plot(v0,od20,'g*','LineWidth',2)
hold off
”
After calculation, below are the constants of the solved quadratic polynomial equations of the KO group and Wild group, respectively.
Table 2. Model results
Sample p1 p2 p3
KO 0.0007 -0.0938 3.0780
Wild 0.0003 -0.0103 0.0230
Figure 1. Comparison between two fitting curves of KO group(red) and Wild group(blue)
Conclusion
In figure 1, we can clearly see that the modified L. casei shows much higher transformation efficiency than the wild L. casei especially when the volume of the initial bacteria seed solution is used less than 100 uL when the difference between them is remarkable.
Solution
We constructed a plasmid equipped with a CRISPR-Cas9 complex that cuts and removes a selected segment of the L. casei DNA. Our target gene is LSEI-2094. This gene is involved in the synthesis of an enzyme that is essential in the restriction-modification system [5]. The cell's efforts to repair its DNA induces mutations, which help to inactivate the gene and prevent the production of the enzyme. After this modification foreign DNAs could enter and express themselves much more efficiently in L.Casei.With a strain of bacteria ready to be tailored to our needs, the benefits are immeasurable. The benefits of L. caseicould come to fruition if the technology is applied to popular and impactful industries such as pharmaceuticals and food.
Besides, the equation model we built for the modified L. casei as showing below, could be used to analyze the relationship between the volume of the bacteria seed solution and its OD600, it could be used as a reference when we conduct the expression efficiency tests in the future. If we could further build the relationship between the expression level and OD600, we could adjust the volume of the bacteria seed solution for culturing accordingly.
Model for the modified L. casei: f(x) = 0.0003x3 - 0.0103x2 + 0.0230
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