Difference between revisions of "Team:Shanghai United/Model"

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{{IGEM_TopBar}}
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<html lang="en">
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{{Shanghai_United}}
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        <title>Document</title>
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        <link rel="stylesheet"
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                crossorigin="anonymous"></script>
  
  
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<div class="column full_size judges-will-not-evaluate">
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</head>
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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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        #sideMenu,
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<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>
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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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<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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<h3> Gold Medal Criterion #3</h3>
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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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        }
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<br><br>
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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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<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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</p><p>
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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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</p>
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<body>
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<div class="highlight decoration_A_full">
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        <div style="height: 255px;width: 100%;display: flex;justify-content: space-around;">
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<h3> Inspiration </h3>
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                <img src="https://static.igem.org/mediawiki/2021/2/27/T--Shanghai_United--homepage01.png"
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<p>You can look at what other teams did to get some inspiration! <br />
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                        style="width: 173px; height: 89px;margin-right: 271px;margin-left: 120px;margin-top: 80px;display: block;" />
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Here are a few examples:</p>
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                <ul class="layui-nav navbar navbar-fixed-top text-center" lay-filter=""
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<ul>
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                        style="background-color:white;height: 255px;line-height: 255px;">
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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://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
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                        <li class="layui-nav-item" style="text-align: center;">
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<li><a href="https://2019.igem.org/Team:IISER_Kolkata/Model">2019 IISER Kolkata</a></li>
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                                <a href="https://2021.igem.org/Team:Shanghai_United"
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<li><a href="https://2019.igem.org/Team:Exeter/Model">2019 Exeter</li>
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                                        style="text-align: center;">Home</a>
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<li><a href="https://2019.igem.org/Team:Mingdao/Model">2019 Mingdao</a></li>
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                        </li>
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<li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li>
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<li><a href="https://2020.igem.org/Team:Leiden/Model">2020 Leiden</a></li>
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                        <li class="layui-nav-item" style="text-align: center;">
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</ul>
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                                <a href="javascript:;">Project</a>
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</div>
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                                <dl class="layui-nav-child">
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</div>
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                                        <!-- 二级菜单 -->
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                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Description">Description</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a href="https://2021.igem.org/Team:Shanghai_United/Proof_Of_Concept">Proof
 +
                                                        of Concept</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Experiments">Experiments</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Notebook">Notebook</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a href="https://2021.igem.org/Team:Shanghai_United/Results">Results</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a href="https://2021.igem.org/Team:Shanghai_United/Safety">Safety</a>
 +
                                        </dd>
 +
       
 +
                                </dl>
 +
                        </li>
 +
                        <li class="layui-nav-item" style="text-align: center;">
 +
                                <a href="javascript:;">Parts</a>
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                                <dl class="layui-nav-child">
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                                        <!-- 二级菜单 -->
 +
                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Engineering">Engineering</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a href="https://2021.igem.org/Team:Shanghai_United/Parts">Parts
 +
                                                        Collection</a>
 +
                                        </dd>
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 +
                                </dl>
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                        </li>
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                        <li class="layui-nav-item">
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                                <a href="javascript:;">Human Practice</a>
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                                <dl class="layui-nav-child">
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                                        <!-- 二级菜单 -->
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                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Fundraising">Fundraising</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Communication">Communication</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Human_Practices">Integrated Human Practices</a>
 +
                                        </dd>
 +
                                </dl>
 +
                        </li>
 +
                        <li class="layui-nav-item" style="text-align: center;">
 +
                                <a href="https://2021.igem.org/Team:Shanghai_United/Implementation">Implementation</a>
 +
                        </li>
 +
       
 +
                        <li class="layui-nav-item" style="text-align: center;">
 +
                                <a
 +
                                        href="https://2021.igem.org/Team:Shanghai_United/Entrepreneurship">Entrepreneurship</a>
 +
                        </li>
 +
       
 +
                        <li class="layui-nav-item" style="text-align: center;">
 +
                                <a href="https://2021.igem.org/Team:Shanghai_United/Model">Model</a>
 +
                        </li>
 +
       
 +
       
 +
                        <li class="layui-nav-item" style="text-align: center;">
 +
                                <a href="javascript:;">Team</a>
 +
                                <dl class="layui-nav-child">
 +
                                        <!-- 二级菜单 -->
 +
                                        <dd>
 +
                                                <a href="https://2021.igem.org/Team:Shanghai_United/Team">Team
 +
                                                        Member</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Collaborations">Collaborations</a>
 +
                                        </dd>
 +
                                        <dd>
 +
                                                <a
 +
                                                        href="https://2021.igem.org/Team:Shanghai_United/Attributions">Attributions</a>
 +
                                        </dd>
 +
                                </dl>
 +
                        </li>
 +
                </ul>
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 +
        </div>
 +
 
 +
        <!--banner-->
 +
        <div style="width:100%;position: relative;">
 +
                <img style="width:100%;" src="https://static.igem.org/mediawiki/2021/9/95/T--Shanghai_United--homepage08.jpg"></img>
 +
                <p style="color:white;font-size:48px;position: absolute;font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:48px; font-weight:bold;display: block;bottom: 100px;left: 100px;">Model</p>
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        </div>
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 +
        <!--text-->
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                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">In order to determine the effective concentration range
 +
                            of the arsenic (</span><span style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">C</span><span
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                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">2</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">H</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">6</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">AsNaO</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">5</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">), we tested the </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">fluorescence intensity generated by a</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">n</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> ARSD/amilGFP transformed </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px; font-style:italic">E. coli</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> reacting for 1 hour in C</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">2</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">H</span><span
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                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">6</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">AsNaO</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">5</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">solutions.</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> </span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">&#xa0;</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">The initial data is showing belo</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">w and we also used the value of the fluorescence
 +
                            intensity when the arsenic concentration is zero as the baseline for the primary elimination.</span></p>
 +
                        <p style="font-size:22px; line-height:150%; margin:20px auto; orphans:0; text-align:center; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">Table 1. Fluorescence intensity of E.
 +
                            coli/</span><span style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">ArsD</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:9pt;">_amilGFP </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">in C</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; ">2</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">H</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; ">6</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">AsNaO</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; ">5</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px"> </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">solutions</span></p>
 +
                        <img src="https://static.igem.org/mediawiki/2021/b/b6/T--Shanghai_United--model01.jpg" width="600" style="display: block;margin: 10px auto;">
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">&#xa0;</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:36px; font-weight:bold">Model I</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">According to the scatter plots, there seemed some
 +
                          </span><span style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">ups and downs which would cause difficulties
 +
                            also less accuracy to build the model. We also thought to use the exponential equation or logarithmic equation
 +
                            to fit our data but the fitting degrees turn out quite low. Therefore, we chose to use </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">the </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">piecewise</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">H</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">ermite</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">interpolation</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">method to build the model and finally drew the fitting
 +
                            curve.</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">&#xa0;</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">Coding we used is giving below:</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">“</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">clear;clc;</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">x0=[0 10 20
 +
                            50 100 150];</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">y0=[0
 +
                            48345.77778 45807.44444 390431.2222 258369.1111 245812.5556];</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">x=[0:0.5:150];</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">y=interp1(x0,y0,x</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">,</span><span
 +
                            style="color:#a020f0; font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">'pchip'</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">);</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">ymax=max(y);</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">i=find(y==max(y))</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">xmax=x(i)</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">plot(x,y,</span><span
 +
                            style="color:#a020f0; font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">'LineWidth'</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">,2)</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">hold
 +
                          </span><span style="color:#a020f0; font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">on</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> </span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">plot(xmax,max(y),</span><span
 +
                            style="color:#a020f0; font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">'r*'</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">,</span><span
 +
                            style="color:#a020f0; font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">'LineWidth'</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">,2)</span></p>
 +
                        <p style="margin:0pt; orphans:0; widows:0"><span style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">hold
 +
                          </span><span style="color:#a020f0; font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">off</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">&#xa0;</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">”</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><img
 +
                            src="https://static.igem.org/mediawiki/2021/b/b0/T--Shanghai_United--model02.jpg" width="600" alt=""
 +
                            style="display:block;margin: 10px auto;" />
 +
                        </p>
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:center; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">Figure 1. </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">The f</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">itting curve of E.
 +
                            coli/ArsD</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">_amilGFP</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px"> by piecewise Hermite
 +
                            interpolation</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">In figure 1, we noticed that the </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">f</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">luorescence intensity</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> started to decline as the concentration of the arsenic
 +
                            increases after 50 ug/L. It is probably that the arsenic affects the growth of the engineered strain, the
 +
                            biosensor when the concentration exceeds 50ug/L. Therefore, we would ind</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">icate the effective detection range of our biosensor (E.
 +
                            coli/ArsD_amilGFP) to be 0~50 ug/L for the arsenic (</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">C</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">2</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">H</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">6</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">AsNaO</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:7pt; vertical-align:sub">5</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">).</span></p>
 +
                        <p style="margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">&#xa0;</span></p>
 +
                        <p style="font-size:12pt; line-height:150%; margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:36px; font-weight:bold">Model II</span></p>
 +
                        <p style="font-size:22px; line-height:150%; margin:10px auto; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">As we have determined the effective detection range of
 +
                            our arsenic biosensor, we thought to further analyze the relationship</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> between the </span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">f</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">luorescence intensity</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px"> and the concentration of the arsenic.</span></p>
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:justify; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">Therefore, we only picked the data when the
 +
                            concentration is not higher than 50 ug/L and adopted the following equation with the fitting degree, 1 by
 +
                            MATLAB:</span></p>
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:center; widows:0"><img
 +
                        src="https://static.igem.org/mediawiki/2021/8/81/T--Shanghai_United--model03.jpg" width="500" alt=""
 +
                        style="-aw-left-pos:0pt; -aw-rel-hpos:column; -aw-rel-vpos:paragraph; -aw-top-pos:0pt; -aw-wrap-type:inline" />   
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:center; widows:0"><img
 +
                            src="https://static.igem.org/mediawiki/2021/3/3b/T--Shanghai_United--model04.jpg" width="500" alt=""
 +
                            style="-aw-left-pos:0pt; -aw-rel-hpos:column; -aw-rel-vpos:paragraph; -aw-top-pos:0pt; -aw-wrap-type:inline" />
 +
                        </p>
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:center; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">Figure 2. Model result of </span><img
 +
                            src="https://static.igem.org/mediawiki/2021/8/81/T--Shanghai_United--model03.jpg" width="200" alt=""
 +
                            style="-aw-left-pos:0pt; -aw-rel-hpos:column; -aw-rel-vpos:paragraph; -aw-top-pos:0pt; -aw-wrap-type:inline" />
 +
                        </p>
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:center; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">&#xa0;</span></p>
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:center; widows:0"><img
 +
                            src="https://static.igem.org/mediawiki/2021/c/ca/T--Shanghai_United--model06.jpg" width="500" alt=""
 +
                            style="-aw-left-pos:0pt; -aw-rel-hpos:column; -aw-rel-vpos:paragraph; -aw-top-pos:0pt; -aw-wrap-type:inline" />
 +
                        </p>
 +
                        <p style="font-size:22px; line-height:150%; margin:0pt; orphans:0; text-align:center; widows:0"><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">Figure 3. </span><span
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                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">The f</span><span
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                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:16px">itting curve of </span><img
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                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">According to the model result of the cubic polynomial
 +
                            equation, it could establish the direct quantitative relationship between arsenic co</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">ncentration and fluorescence intensity, which means we
 +
                            could read the fluorescence intensity to get the value of the arsenic amount. Hence, this model could be used
 +
                            for the numerical display screen set up in the future to facilitate the application and enh</span><span
 +
                            style="font-family:'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;line-height: 200%; font-size:22px">ance the functionality.</span></p>
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Latest revision as of 10:29, 19 October 2021

Document

Model

In order to determine the effective concentration range of the arsenic (C2H6AsNaO5), we tested the fluorescence intensity generated by an ARSD/amilGFP transformed E. coli reacting for 1 hour in C2H6AsNaO5 solutions.

 

The initial data is showing below and we also used the value of the fluorescence intensity when the arsenic concentration is zero as the baseline for the primary elimination.

Table 1. Fluorescence intensity of E. coli/ArsD_amilGFP in C2H6AsNaO5 solutions

 

Model I

According to the scatter plots, there seemed some ups and downs which would cause difficulties also less accuracy to build the model. We also thought to use the exponential equation or logarithmic equation to fit our data but the fitting degrees turn out quite low. Therefore, we chose to use the piecewise Hermite interpolation method to build the model and finally drew the fitting curve.

 

Coding we used is giving below:

“

clear;clc;

x0=[0 10 20 50 100 150];

y0=[0 48345.77778 45807.44444 390431.2222 258369.1111 245812.5556];

x=[0:0.5:150];

y=interp1(x0,y0,x,'pchip');

ymax=max(y);

i=find(y==max(y))

xmax=x(i)

plot(x,y,'LineWidth',2)

hold on

plot(xmax,max(y),'r*','LineWidth',2)

hold off

 

”

Figure 1. The fitting curve of E. coli/ArsD_amilGFP by piecewise Hermite interpolation

In figure 1, we noticed that the fluorescence intensity started to decline as the concentration of the arsenic increases after 50 ug/L. It is probably that the arsenic affects the growth of the engineered strain, the biosensor when the concentration exceeds 50ug/L. Therefore, we would indicate the effective detection range of our biosensor (E. coli/ArsD_amilGFP) to be 0~50 ug/L for the arsenic (C2H6AsNaO5).

 

Model II

As we have determined the effective detection range of our arsenic biosensor, we thought to further analyze the relationship between the fluorescence intensity and the concentration of the arsenic.

Therefore, we only picked the data when the concentration is not higher than 50 ug/L and adopted the following equation with the fitting degree, 1 by MATLAB:

Figure 2. Model result of

 

Figure 3. The fitting curve of

According to the model result of the cubic polynomial equation, it could establish the direct quantitative relationship between arsenic concentration and fluorescence intensity, which means we could read the fluorescence intensity to get the value of the arsenic amount. Hence, this model could be used for the numerical display screen set up in the future to facilitate the application and enhance the functionality.

CONTACT INFO Please scan the following QR codes to find more about us on Weibo、Bilibili、Wechat !