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

(Prototype team page)
 
Line 1: Line 1:
−
{{IGEM_TopBar}}
+
<html lang="en">
−
{{Shanghai_Metro_HS}}
+
−
<html>
+
  
 +
<head>
 +
    <meta charset="UTF-8">
 +
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
    <title>Shanghai_Metro_HS</title>
 +
    <link rel="stylesheet"
 +
        href="https://2021.igem.org/wiki/index.php?title=Template:Shanghai_Metro_HS/Main_CSS&action=raw&ctype=text/css" />
 +
</head>
  
 +
<body>
 +
    <nav class="head-nav clearfix">
 +
        <div class="top-block"></div>
 +
        <div class="top-nav-bar">
 +
            <ul class="clearfix">
 +
                <span class="small-logo"></span>
 +
                <li>
 +
                    <a href="https://2021.igem.org/Team:Shanghai_Metro_HS">Home</a>
 +
                </li>
 +
                <li>
 +
                    <a href="">Project</a>
 +
                    <div class="sub-nav">
 +
                        <ul>
 +
                            <li class="current-sub-nav">
 +
                                <a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Description"
 +
                                    class="sub-nav-74">Description</a>
 +
                            </li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Experiments"
 +
                                    class="sub-nav-74">Experiments</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Results"
 +
                                    class="sub-nav-74">Results</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Proof_Of_Concept"
 +
                                    class="sub-nav-52">Proof Of
 +
                                    Concept</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Notebook"
 +
                                    class="sub-nav-52">Notebook</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Safety">Safety</a></li>
 +
                        </ul>
 +
                    </div>
 +
                </li>
 +
                <li>
 +
                    <a href="">Parts</a>
 +
                    <div class="sub-nav">
 +
                        <ul>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Collection"
 +
                                    class="sub-nav-74">Parts Collection</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Engineering"
 +
                                    class="sub-nav-74">Engineering</a></li>
 +
                        </ul>
 +
                    </div>
 +
                </li>
 +
                <li>
 +
                    <a href="">Human Practices</a>
 +
                    <div class="sub-nav">
 +
                        <ul>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Human_Practices"
 +
                                    class="sub-nav-74">Integrated Human Practice</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Communication"
 +
                                    class="sub-nav-74">Communication</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Fundraising"
 +
                                    class="sub-nav-74">Fundraising</a></li>
 +
                        </ul>
 +
                    </div>
 +
                </li>
 +
                <li>
 +
                    <a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Implementation">Implementation</a>
 +
                </li>
 +
                <li>
 +
                    <a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Entrepreneurship">Entrepreneurship</a>
 +
                </li>
 +
                <li class="active">
 +
                    <a href="#">Model</a>
 +
                </li>
 +
                <li>
 +
                    <a href="">Team</a>
 +
                    <div class="sub-nav">
 +
                        <ul>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Members" class="sub-nav-74">Team
 +
                                    Members</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Attributions"
 +
                                    class="sub-nav-74">Attributions</a></li>
 +
                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_HS/Collaborations"
 +
                                    class="sub-nav-74">Collaborations</a></li>
 +
                        </ul>
 +
                    </div>
 +
                </li>
 +
            </ul>
 +
        </div>
 +
    </nav>
 +
    <div class="sub-banner">
 +
        <img src="https://static.igem.org/mediawiki/2021/a/a4/T--Shanghai_Metro_HS--Team_Members01.png" alt="" />
 +
        <span>MODEL</span>
 +
    </div>
 +
    <div class="sub-content no-margin-top">
 +
        <div class="article-content">
 +
            As our goal is to produce the additive that could secret PKC enzyme to help degrade the cellulose in silage,
 +
            we want to ensure that our engineered strain can make the best of itself at its best condition. From this
 +
            perspective, we designed several different induction conditions for protein expression and decided to build
 +
            the model to determine the optimal condition for our engineered strain to “work” better.<br />
 +
            Below is the initial data:
 +
        </div>
 +
        <div class="img-wrap no-margin">
 +
            <span>Table 1. The gray value of E. coli/PKC-OP under different concentrations of IPTG against time</span>
 +
            <img src="https://static.igem.org/mediawiki/2021/0/03/T--Shanghai_Metro_HS--model01.png" alt="" />
 +
        </div>
 +
        <div class="article-content">
 +
            In table 1, gray values were measured by Image J in order to quantify the protein expression level. In this
 +
            case, we tested three concentrations of IPTG to conduct induction.<br />
 +
            According to the scatter plots, we noticed that the cubic polynomial equation could fit the trends very well
 +
            with all fitting degrees higher than 0.98.
 +
        </div>
 +
        <div class="article-content">Cubic polynomial equation: </div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/a/ab/T--Shanghai_Metro_HS--model02.png" alt="">
 +
            <span>Figure 1. The model result when IPTG concentration equals 0.01 mM</span>
 +
        </div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/3/35/T--Shanghai_Metro_HS--model03.png" alt="">
 +
            <span>Figure 2. The fitting curve of the model when IPTG concentration equals 0.01 mM</span>
 +
        </div>
 +
        <div class="article-content">When E. coli/PKC-OP is induced by 0.01mM IPTG, it indicates that before 12 hours
 +
            there is a peak at 7 hours when the protein was expressed the best. Otherwise, if there is enough time
 +
            given, the protein could be expressed more after 18 hours and the induction duration to be chosen will
 +
            depend on the production plan.</div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/f/f8/T--Shanghai_Metro_HS--model04.png" alt="">
 +
            <span>Figure 3. The model result when IPTG concentration equals 0.1 mM</span>
 +
        </div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/c/ce/T--Shanghai_Metro_HS--model05.png" alt="">
 +
            <span>Figure 4. The fitting curve of the model when IPTG concentration equals 0.1 mM</span>
 +
        </div>
 +
        <div class="article-content">When E. coli/PKC-OP is induced by 0.1mM IPTG, we can see that the basic trend of
 +
            the protein expression level is increasing as the induction time increases. In this case, we would suggest
 +
            the least induction time to be 8 hours.</div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/e/ea/T--Shanghai_Metro_HS--model06.png" alt="">
 +
            <span>Figure 5. The model result when IPTG concentration equals 1 mM</span>
 +
        </div>
 +
        <div class="img-wrap no-margin">
 +
            <img src="https://static.igem.org/mediawiki/2021/3/3d/T--Shanghai_Metro_HS--model07.png" alt="">
 +
            <span>Figure 6. The fitting curve of the model when IPTG concentration equals 1 mM</span>
 +
        </div>
 +
        <div class="article-content">When E. coli/PKC-OP was induced by 1 mM IPTG, it shows a clear increasing trend of
 +
            the protein expression
 +
            level as the induction time increases.</div>
 +
        <div class="article-content"><b>Comparison</b></div>
 +
        <div class="article-content">In order to further analyze the effect of the IPTG concentration on the protein
 +
            expression level of E.
 +
            coli/PKC-OPO, we put these three lines on the same page as shown in figure 7 and the coding is given below:
 +
        </div>
 +
        <div class="article-content">
 +
            “<br />
 +
            clear;clc;<br />
 +
            t0=[3 5 8 12 20];<br />
 +
            grey001=[21173.401 26062.4 27973.278 25035.036 37106.845];<br />
 +
            grey01=[17101.066 21654.681 27102.823 25365.43 32166.652];<br />
 +
            grey1=[19705.53 22921.471 25004.723 27629.166 33671.986];<br />
 +
            p001=polyfit(t0,grey001,3);<br />
 +
            p01=polyfit(t0,grey01,3);<br />
 +
            p1=polyfit(t0,grey1,3);<br />
 +
            t=[0:0.1:22];<br />
 +
            y001=polyval(p001,t);<br />
 +
            y01=polyval(p01,t);<br />
 +
            y1=polyval(p1,t);<br />
 +
            plot(t,y001,t,y01,t,y1,'LineWidth',1)<br />
  
−
<div class="column full_size judges-will-not-evaluate">
+
            ”
−
<h3>★  ALERT! </h3>
+
        </div>
−
<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>
+
        <div class="img-wrap no-margin">
−
<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2021.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
+
            <img src="https://static.igem.org/mediawiki/2021/2/21/T--Shanghai_Metro_HS--model08.png" alt="">
−
</div>
+
            <span>Figure 7. Comparison graph of the fitting curves of three models</span>
−
 
+
        </div>
−
 
+
        <div class="article-content">Based on the graph where we can see several cross points’ coordinates of lines, we
−
<div class="clear"></div>
+
            could adjust the IPTG concentration according to the induction time which could be pre-decided by the
−
 
+
            production plan in the future. </div>
−
 
+
        <div class="article-content" style="padding-left: 30px; box-sizing:border-box;">When the induction time is given
−
<div class="column full_size">
+
            less
−
<h1> Modeling</h1>
+
            than 2.5 hours, 1 mM IPTG would be more recommended;</div>
−
 
+
        <div class="article-content" style="padding-left: 30px; box-sizing:border-box;">When the induction time is given
−
<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>
+
            during 2.5 hours 10.2 hours, 0.01 mM IPTG would be
−
 
+
            more recommended;
−
<p>Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page. </p>
+
        </div>
−
 
+
        <div class="article-content" style="padding-left: 30px; box-sizing:border-box;">When the induction time is given
−
</div>
+
            during 10.2 hours ~ 19 hours, 1 mM IPTG would be
−
<div class="clear"></div>
+
            more recommended;</div>
−
 
+
        <div class="article-content" style="padding-left: 30px; box-sizing:border-box;">When the induction time is given
−
<div class="column full_size">
+
            very enough like more than 19 hours, 0.01 mM IPTG
−
<h3> Gold Medal Criterion #3</h3>
+
            would be
−
<p>
+
            more
−
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.
+
            recommended.</div>
−
<br><br>
+
    </div>
−
Please see the <a href="https://2021.igem.org/Judging/Medals">2021 Medals Page</a> for more information.
+
    <footer class="footer">
−
</p>
+
        <section class="footer-wrap">
−
 
+
            <div class="footer-contact">CONTACT INFO</div>
−
</div>
+
            <p class="margin-bottom-20">Email: igemteamceres@gmail.com</p>
−
 
+
            <p><i style="color: #2d2d2d;">WeChat Official Account: iGEM Ceres</i></p>
−
<div class="column two_thirds_size">
+
        </section>
−
<h3>Best Model Special Prize</h3>
+
    </footer>
−
 
+
</body>
−
<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.
+
<script>
−
</p><p>
+
    let liTags = document.querySelectorAll(".top-nav-bar > ul > li");
−
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>.  
+
    let len = liTags.length;
−
</p>
+
    for (let i = 0; i < len; i++) {
−
 
+
        liTags[i].onclick = function (e) {
−
</div>
+
            //先移除所有的点击样式
−
 
+
            for (let j = 0; j < len; j++) {
−
 
+
                liTags[j].classList.remove("active");
−
<div class="column third_size">
+
            }
−
<div class="highlight decoration_A_full">
+
            //再添加点击样式
−
<h3> Inspiration </h3>
+
            let li = e.currentTarget;
−
<p>You can look at what other teams did to get some inspiration! <br />
+
            li.classList.add("active");
−
Here are a few examples:</p>
+
        }
−
<ul>
+
    }
−
<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
+
</script>
−
<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>
+
  
 
</html>
 
</html>

Revision as of 16:28, 14 October 2021

Shanghai_Metro_HS

MODEL
As our goal is to produce the additive that could secret PKC enzyme to help degrade the cellulose in silage, we want to ensure that our engineered strain can make the best of itself at its best condition. From this perspective, we designed several different induction conditions for protein expression and decided to build the model to determine the optimal condition for our engineered strain to “work” better.
Below is the initial data:
Table 1. The gray value of E. coli/PKC-OP under different concentrations of IPTG against time
In table 1, gray values were measured by Image J in order to quantify the protein expression level. In this case, we tested three concentrations of IPTG to conduct induction.
According to the scatter plots, we noticed that the cubic polynomial equation could fit the trends very well with all fitting degrees higher than 0.98.
Cubic polynomial equation:
Figure 1. The model result when IPTG concentration equals 0.01 mM
Figure 2. The fitting curve of the model when IPTG concentration equals 0.01 mM
When E. coli/PKC-OP is induced by 0.01mM IPTG, it indicates that before 12 hours there is a peak at 7 hours when the protein was expressed the best. Otherwise, if there is enough time given, the protein could be expressed more after 18 hours and the induction duration to be chosen will depend on the production plan.
Figure 3. The model result when IPTG concentration equals 0.1 mM
Figure 4. The fitting curve of the model when IPTG concentration equals 0.1 mM
When E. coli/PKC-OP is induced by 0.1mM IPTG, we can see that the basic trend of the protein expression level is increasing as the induction time increases. In this case, we would suggest the least induction time to be 8 hours.
Figure 5. The model result when IPTG concentration equals 1 mM
Figure 6. The fitting curve of the model when IPTG concentration equals 1 mM
When E. coli/PKC-OP was induced by 1 mM IPTG, it shows a clear increasing trend of the protein expression level as the induction time increases.
Comparison
In order to further analyze the effect of the IPTG concentration on the protein expression level of E. coli/PKC-OPO, we put these three lines on the same page as shown in figure 7 and the coding is given below:
“
clear;clc;
t0=[3 5 8 12 20];
grey001=[21173.401 26062.4 27973.278 25035.036 37106.845];
grey01=[17101.066 21654.681 27102.823 25365.43 32166.652];
grey1=[19705.53 22921.471 25004.723 27629.166 33671.986];
p001=polyfit(t0,grey001,3);
p01=polyfit(t0,grey01,3);
p1=polyfit(t0,grey1,3);
t=[0:0.1:22];
y001=polyval(p001,t);
y01=polyval(p01,t);
y1=polyval(p1,t);
plot(t,y001,t,y01,t,y1,'LineWidth',1)
”
Figure 7. Comparison graph of the fitting curves of three models
Based on the graph where we can see several cross points’ coordinates of lines, we could adjust the IPTG concentration according to the induction time which could be pre-decided by the production plan in the future.
When the induction time is given less than 2.5 hours, 1 mM IPTG would be more recommended;
When the induction time is given during 2.5 hours 10.2 hours, 0.01 mM IPTG would be more recommended;
When the induction time is given during 10.2 hours ~ 19 hours, 1 mM IPTG would be more recommended;
When the induction time is given very enough like more than 19 hours, 0.01 mM IPTG would be more recommended.
CONTACT INFO

Email: igemteamceres@gmail.com

WeChat Official Account: iGEM Ceres