Difference between revisions of "Team:Shanghai City United/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_City_United">Home</a>
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                    <a href="">Project</a>
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<h1> Modeling</h1>
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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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                                <a href="https://2021.igem.org/Team:Shanghai_City_United/Description"
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                                    class="sub-nav-74">Description</a>
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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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                            <li><a href="https://2021.igem.org/Team:Shanghai_City_United/Proof_Of_Concept"
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<h3> Gold Medal Criterion #3</h3>
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                                    class="sub-nav-52">Proof Of Concept</a></li>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_City_United/Notebook"
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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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                            <li><a href="https://2021.igem.org/Team:Shanghai_City_United/Collection"
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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">Parts Collection</a></li>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_City_United/Engineering"
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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">Engineering</a></li>
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<h3> Inspiration </h3>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_City_United/Human_Practices"
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<p>You can look at what other teams did to get some inspiration! <br />
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                                    class="sub-nav-74">Integrated Human Practice</a></li>
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Here are a few examples:</p>
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                                    class="sub-nav-74">Communication</a></li>
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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_City_United/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_City_United/Implementation">Implementation</a>
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                    <a href="https://2021.igem.org/Team:Shanghai_City_United/Entrepreneurship">Entrepreneurship</a>
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        <div class="sub-title">MODEL</div>
 +
        <div class="article-content">In order to determine the optimal duration of our engineered Lactobacillus reuteri
 +
            to express the most enzyme activities, we used the SppIP to induce the expression of L. reuteri by several
 +
            hours and the enzyme activity was measured by DNS assay.</div>
 +
        <div class="article-content">Below is the data of the units of enzyme activity of our engineered L. reuteri:
 +
        </div>
 +
        <div class="article-content">Table 1.</div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/e/ed/T--Shanghai_City_United--MODEL01.png" alt="" />
 +
        </div>
 +
        <div class="article-content">According to the scatter plots, we notice that the data when the induction time is
 +
            24 hours and 48 hours quite deviate from the trend. In order to find the optimal induction time of our
 +
            engineered L. reuteri, we attempted several methods to build the model and wish to contribute to predicting
 +
            the optimal condition for our product, L. reuteri/pSIP403-PUS-xyn AM to work.</div>
 +
        <div class="article-title">MODEL I_Hermite interpolation</div>
 +
        <div class="article-content">In order to obtain a curve of units of enzyme activity against induction time
 +
            without kicking out any data, we introduced Hermite interpolation by MATLAB and the coding is given below:
 +
        </div>
 +
        <div class="article-content">
 +
            “<br />
 +
            clear;clc;<br />
 +
            t0=[0 3 8 12 16 24 48];<br />
 +
            y1=[38.60214035 52.4481485 149.8437352 139.0661995 98.70252865 80.32957666 81.82593049];<br />
 +
            y2=[61.23685955 93.09593712 158.2536225 134.1414907 127.1521924 72.90463112 81.31451842];<br />
 +
            y0=(y1+y2)/2<br />
 +
            t=[0:0.5:48];<br />
 +
            y=interp1(t0,y0,t,'pchip');<br />
 +
            ymax=max(y)<br />
 +
            i=find(y==max(y));<br />
 +
            tmax=t(i)<br />
 +
            plot(t,y,'LineWidth',2)<br />
 +
            hold on<br />
 +
            plot(tmax,ymax,'r*','LineWidth',2)<br />
 +
            hold off<br />
 +
            ”
 +
        </div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/5/5a/T--Shanghai_City_United--MODEL02.png" alt="" />
 +
            <span>Figure 1. The fitting curve of the model by Hermite interpolation</span>
 +
        </div>
 +
        <div class="article-content">In figure 1, we could easily predict that the optimal induction time would be 8
 +
            hours for the engineered L. reuteri and it would tend to decline to the least value (around 80 U/mL) after
 +
            that.</div>
 +
        <div class="article-title">MODEL II_Fourier Function</div>
 +
        <div class="article-content">After deleting the data in 48 hours as it seriously deviated from the
 +
            trend, the model built by the Fourier function fits the data very well and the model result is given below
 +
            with a high fitting degree, 1.</div>
 +
        <div class="article-content">The second-order Fourier Function:</div>
 +
        <div class="article-content" style="padding-left: 30px; box-sizing: border-box;">
 +
            f(x) = a0 + a<sub>1</sub>cos(wx) + b<sub>1</sub>sin(wx) + a<sub>2</sub>cos(2wx) + b<sub>2</sub>sin(2wx)
 +
        </div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/5/57/T--Shanghai_City_United--MODEL03.png" alt="" />
 +
            <span>Figure 2. The model result by Fourier function</span>
 +
        </div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/5/5e/T--Shanghai_City_United--MODEL04.png" alt="" />
 +
            <span>Figure 3. The fitting curve of the model built by Fourier function</span>
 +
        </div>
 +
        <div class="article-content">According to the fitting curve we built based on Fourier function, there are
 +
            several ups and downs but the top point lies down to (9, 157). Therefore, it would be recommended that the
 +
            optimal induction time is 9 hours. But this model has its limit that it only fits the trend before 24 hours.
 +
        </div>
 +
        <div class="article-title">MODEL III_Quartic Polynomial</div>
 +
        <div class="article-content">After deleting the data in 24 and 48 hours, we chose to use the quartic polynomial
 +
            function to adapt to our data.</div>
 +
        <div class="article-content">The quartic polynomial function:</div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/4/41/T--Shanghai_City_United--MODEL05.png" alt="" />
 +
        </div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/a/a9/T--Shanghai_City_United--MODEL06.png" alt="" />
 +
            <span>Figure 4. The model result by quartic polynomial function</span>
 +
        </div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/a/a8/T--Shanghai_City_United--MODEL07.png" alt="" />
 +
            <span>Figure 5. The fitting curve of the model built by quartic polynomial function</span>
 +
        </div>
 +
        <div class="article-content">According to the fitting curve built by the quartic polynomial function which only
 +
            works before 16 hours, we will recommend the induction time of our engineered L. reuteri is 9 hours.</div>
 +
        <div class="article-title">Conclusion</div>
 +
        <div class="article-content">Based on the models above, 8~9 hours would be the most recommended induction time
 +
            for our engineered L. reuteri to express the enzyme and work best. In addition, above models would also
 +
            contribute to the application of our product - "drink" for poultry in the future as the reference to analyze
 +
            the expiry time, stability, store conditions .</div>
 +
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            <div class="footer-contact">Contact Info.</div>
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            <p class="margin-bottom-10">WeChat Official Account:<i>谷饲嘉Grain Fed Plus</i></p>
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            <p>Email：<i>xxkk5905@gmail.com</i></p>
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Revision as of 06:14, 16 October 2021

Shanghai_City_United

MODEL
In order to determine the optimal duration of our engineered Lactobacillus reuteri to express the most enzyme activities, we used the SppIP to induce the expression of L. reuteri by several hours and the enzyme activity was measured by DNS assay.
Below is the data of the units of enzyme activity of our engineered L. reuteri:
Table 1.
According to the scatter plots, we notice that the data when the induction time is 24 hours and 48 hours quite deviate from the trend. In order to find the optimal induction time of our engineered L. reuteri, we attempted several methods to build the model and wish to contribute to predicting the optimal condition for our product, L. reuteri/pSIP403-PUS-xyn AM to work.
MODEL I_Hermite interpolation
In order to obtain a curve of units of enzyme activity against induction time without kicking out any data, we introduced Hermite interpolation by MATLAB and the coding is given below:
“
clear;clc;
t0=[0 3 8 12 16 24 48];
y1=[38.60214035 52.4481485 149.8437352 139.0661995 98.70252865 80.32957666 81.82593049];
y2=[61.23685955 93.09593712 158.2536225 134.1414907 127.1521924 72.90463112 81.31451842];
y0=(y1+y2)/2
t=[0:0.5:48];
y=interp1(t0,y0,t,'pchip');
ymax=max(y)
i=find(y==max(y));
tmax=t(i)
plot(t,y,'LineWidth',2)
hold on
plot(tmax,ymax,'r*','LineWidth',2)
hold off
”
Figure 1. The fitting curve of the model by Hermite interpolation
In figure 1, we could easily predict that the optimal induction time would be 8 hours for the engineered L. reuteri and it would tend to decline to the least value (around 80 U/mL) after that.
MODEL II_Fourier Function
After deleting the data in 48 hours as it seriously deviated from the trend, the model built by the Fourier function fits the data very well and the model result is given below with a high fitting degree, 1.
The second-order Fourier Function:
f(x) = a0 + a1cos(wx) + b1sin(wx) + a2cos(2wx) + b2sin(2wx)
Figure 2. The model result by Fourier function
Figure 3. The fitting curve of the model built by Fourier function
According to the fitting curve we built based on Fourier function, there are several ups and downs but the top point lies down to (9, 157). Therefore, it would be recommended that the optimal induction time is 9 hours. But this model has its limit that it only fits the trend before 24 hours.
MODEL III_Quartic Polynomial
After deleting the data in 24 and 48 hours, we chose to use the quartic polynomial function to adapt to our data.
The quartic polynomial function:
Figure 4. The model result by quartic polynomial function
Figure 5. The fitting curve of the model built by quartic polynomial function
According to the fitting curve built by the quartic polynomial function which only works before 16 hours, we will recommend the induction time of our engineered L. reuteri is 9 hours.
Conclusion
Based on the models above, 8~9 hours would be the most recommended induction time for our engineered L. reuteri to express the enzyme and work best. In addition, above models would also contribute to the application of our product - "drink" for poultry in the future as the reference to analyze the expiry time, stability, store conditions .
Contact Info.

WeChat Official Account:谷饲嘉Grain Fed Plus

Email：xxkk5905@gmail.com