Difference between revisions of "Team:HUST-China/Model"

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{{HUST-China}}
 
 
<html>
 
<html>
  
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    <title>Experiment</title>
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<div class="column full_size judges-will-not-evaluate">
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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://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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    </script>
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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://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<div class="column full_size">
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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 BioBrick 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. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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</div>
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<div class="clear"></div>
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        margin: 20px 0 40px 0;
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<div class="column half_size">
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<h3> Gold Medal Criterion #3</h3>
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        width:100%;
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<p>
+
    }
−
To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.
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</p>
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−
<p>
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    .tab1 {
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Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.
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        width:100%;
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</p>
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        margin: 0 0;
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</div>
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        color: #666;
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        background:#333;
 +
    }
  
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<div class="column half_size">
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    .tab1 .text-muted {
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<h3>Best Model Special Prize</h3>
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        color: #999;
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        text-decoration: line-through;
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<p>
+
    .text span{
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To compete for the <a href="https://2017.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://2017.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.
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        color: #97477c;
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<br><br>
+
    }
−
You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
+
    .text p {
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</p>
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        font-size: 14px;
 +
    }
 +
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 +
        background-color: #eee;
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        border-top: 1px solid #ccc;
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 +
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 +
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 +
    /*没有小于768px，是因为Bootstrap3以移动端优先设计*/
  
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</div>
+
    /* 小屏幕（平板，大于等于768px） */
−
<div class="clear"></div>
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 +
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        width:80%;
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        height:auto;
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 +
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−
<div class="column full_size">
+
    /* 中等屏幕（桌面显示器，大于等于992px） */
−
<h5> Inspiration </h5>
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    @media (min-width: 992px) {
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<p>
+
        .tab-h1 {
−
Here are a few examples from previous teams:
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            font-size: 28px;
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</p>
+
        }
−
<ul>
+
        .tab-p {
−
<li><a href="https://2016.igem.org/Team:Manchester/Model">Manchester 2016</a></li>
+
            font-size: 17px;
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
+
        }
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
+
        .text h3 {
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
+
            font-size: 24px;
−
</ul>
+
        }
 +
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          font-size: 12px;
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 +
        width:60%;
 +
        height:auto;
 +
        }
 +
    }
  
 +
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 +
    @media (min-width: 1200px) {
 +
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 +
            font-size: 30px;
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 +
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 +
        width:40%;
 +
        height:auto;
 +
        }
 +
    }
 +
       
  
−
</div>
+
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 +
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 +
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 +
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 +
 
 +
        @media screen and (max-width: 810px) {
 +
            #section1, #section2, #section3, #section4, #section5 {
 +
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 +
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 +
 
 +
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 +
</head>
 +
 
 +
<body data-spy="scroll" data-target="#myScrollspy" data-offset="20">
 +
      <nav class="navbar navbar-default navbar-fixed-top" style="margin-top:15px">
 +
        <div class="container">
 +
 
 +
            <div class="navbar-header">
 +
                <a href="https://2017.igem.org/Team:HUST-China" class="navbar-brand logo" style="padding:0 5px;"><img src="https://static.igem.org/mediawiki/2017/6/64/Team_HUST_China_2017_logo.png" alt="HUST_iGEM_2017_logo"></a>
 +
                <a href="https://2017.igem.org" class="navbar-brand logo" style="padding:0 5px;"><img src="https://static.igem.org/mediawiki/2017/f/f6/IGEM_2017_logo.png" alt="HUST_iGEM_2017_logo"></a>
 +
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 +
                    <span class="glyphicon glyphicon-list"></span>
 +
                </button>
 +
            </div>
 +
 
 +
 
 +
            <div class="collapse navbar-collapse" id="navbar-collapse">
 +
                <ul class="nav navbar-nav navbar-right">
 +
 
 +
 
 +
 
 +
                    <li><a href="https://2017.igem.org/Team:HUST-China">HOME</a></li>
 +
                    <li class="dropdown">
 +
                        <a href="#" class="dropdown-toggle" data-toggle="dropdown">
 +
                            PROJECT <b class="caret"></b>
 +
                        </a>
 +
                        <ul class="dropdown-menu">
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/project/background">Background</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/Description">Description</a></li>                                       
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/Safety">Safety</a></li>
 +
                        </ul>
 +
                    </li>
 +
                    <li class="dropdown active">
 +
                        <a href="#" class="dropdown-toggle" data-toggle="dropdown">
 +
                            WETLAB <b class="caret"></b>
 +
                        </a>
 +
                        <ul class="dropdown-menu">
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/Experiments">Experiments</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/Results">Results</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/InterLab">Interlab</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/Notebook">Notebook</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/wetlab/protocols">Protocols</a></li>
 +
                        </ul>
 +
                    </li>
 +
                    <li class="dropdown">
 +
                        <a href="https://2017.igem.org/Team:HUST-China/Modeling" >
 +
                            MODELING
 +
                        </a>
 +
                    </li>
 +
                    <li class="dropdown">
 +
                        <a href="https://2017.igem.org/Team:HUST-China/Parts">
 +
                            PARTS
 +
                        </a>
 +
                    </li>
 +
                    <li class="dropdown">
 +
                        <a href="https://2017.igem.org/Team:HUST-China/Human_Practices">
 +
                            HUMAN PRACTICES
 +
                        </a>
 +
                    </li>
 +
                    <li class="dropdown">
 +
                        <a href="#" class="dropdown-toggle" data-toggle="dropdown">
 +
                            TEAM <b class="caret"></b>
 +
                        </a>
 +
                        <ul class="dropdown-menu">
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/Team">Team Roster</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:HUST-China/Attributions">Attributions</a></li>
 +
                        </ul>
 +
                    </li>
 +
 
 +
 
 +
                </ul> 
 +
            </div>
 +
        </div>
 +
    </nav>
 +
 
 +
 
 +
    <div class="tab1" style="width:100%;margin-top: 65px;">
 +
            <h1 class="tab-h1" ><strong>「Experiment」</strong></h1>
 +
    </div>
 +
 
 +
    <div class="container-fluid text">
 +
        <div class="row">
 +
            <nav class="col-sm-2" id="myScrollspy">
 +
                <div class="container-fluid">
 +
                <div class="collapse navbar-collapse" id="navbar-collapse">
 +
                <ul class="nav nav-pills nav-stacked" style="font-size:12px; text-align:center; background:#ccc;">
 +
                    <li class="active"><a href="#section1">Sensing part</a></li>
 +
                    <li><a href="#section2">Recycling part</a></li>
 +
                    <li><a href="#section3">The whole circuit </a></li>
 +
                </ul>
 +
                </div> 
 +
                </div>     
 +
            </nav>
 +
            <div class="col-sm-8">
 +
                <div id="section1" style="border: solid 1px #666; margin:5px;border-radius:10px;overflow: hidden;">   
 +
                    <h3 style="background-color:#ce6b9a;color:#ffffff; padding:10px;letter-spacing:1px;margin-top:0;">Sensing part</h3>
 +
                    <p>
 +
                        The sensing part is to achieve the awareness of the engineering bacteria on the rare earth ions in the environment.
 +
                    </p>
 +
                    <h4><strong>①Amplify</strong> </h4>
 +
                    <p>
 +
                        pmrA-B-Fe、pmrC/GFP  gene through the pcr protocol
 +
                    </p>
 +
                    <h4><strong>②Plasmid Construction</strong> </h4>
 +
                    <p>
 +
                      Coding sequences pmrA/pmrB and pmrC-GFP were cloned into the expression vector pBAD30 by restriction enzyme digestion and DNA ligation.
 +
                    </p>
 +
                    <div class="container experiment_circuit col-md-6 col-xs-6 col-md-offset-3 col-xs-offset-3">
 +
                        <img src="https://static.igem.org/mediawiki/2017/d/d5/2017_HUST_China_Experiment_image1.png" alt="experiment_circuit" class="img-responsive">
 +
                    </div>
 +
                    <div class="row col-xs-12">
 +
                        <p>
 +
                            Then we transformed these vectors into Ecoli BL21 cells.
 +
                        </p>
 +
                        <h4><strong>③Detection</strong> </h4>
 +
                        <p>
 +
                          Arabinose was used to induce expression of pmrABC system.
 +
                        </p>
 +
                        <p>
 +
                          We use the original pmrA-pmrB / Fe-pmrC-GFP circuit to test whether our
 +
                          pmrABC system works in our plasmid, then the expression and efficacy
 +
                          of LBT1-12 were tested .
 +
                        </p>
 +
                    </div>
 +
 
 +
 
 +
                    <div class="table-responsive" style="padding: 10px 100px; text-align: center; font-size:14px;">
 +
                        <table class="table">
 +
                          <thead>
 +
                              <tr>
 +
                                <th style="text-align: center;">gene circuit</th>
 +
                                <th style="text-align: center;">vector</th>
 +
                                <th style="text-align: center;">description</th>
 +
                              </tr>
 +
                          </thead>
 +
                          <tbody>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/Fe-pmrC-GFP</td>
 +
                                    <td>pBAD30</td>
 +
                                    <td>Test whether our pmrABC system works in our plasmid</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT1-pmrC-GFP </td>
 +
                                    <td>pBAD30</td>
 +
                                    <td> Detecting effectiveness of protein LBT1</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT2-pmrC-GFP</td>
 +
                                    <td>pBAD30 </td>
 +
                                    <td> Detecting effectiveness of protein LBT2</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT3-pmrC-GFP</td>
 +
                                    <td>pBAD30 </td>
 +
                                    <td>Detecting effectiveness of protein LBT3</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT4-pmrC-GFP</td>
 +
                                    <td> pBAD30 </td>
 +
                                    <td>Detecting effectiveness of protein LBT4</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT5-pmrC-GFP</td>
 +
                                    <td>pBAD30</td>
 +
                                    <td>Detecting effectiveness of protein LBT5</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT6-pmrC-GFP </td>
 +
                                    <td>pBAD30</td>
 +
                                    <td> Detecting effectiveness of protein LBT6</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT7-pmrC-GFP</td>
 +
                                    <td>pBAD30 </td>
 +
                                    <td> Detecting effectiveness of protein LBT7</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT8-pmrC-GFP</td>
 +
                                    <td>pBAD30 </td>
 +
                                    <td>Detecting effectiveness of protein LBT8</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT9-pmrC-GFP</td>
 +
                                    <td> pBAD30 </td>
 +
                                    <td>Detecting effectiveness of protein LBT9</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT10-pmrC-GFP</td>
 +
                                    <td>pBAD30 </td>
 +
                                    <td> Detecting effectiveness of protein LBT10</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT11-pmrC-GFP</td>
 +
                                    <td>pBAD30 </td>
 +
                                    <td>Detecting effectiveness of protein LBT11</td>
 +
                                  </tr>
 +
                                  <tr>
 +
                                    <td>pmrA-pmrB/LBT12-pmrC-GFP </td>
 +
                                    <td> pBAD30 </td>
 +
                                    <td>Detecting effectiveness of protein LBT12</td>
 +
                                  </tr>
 +
                               
 +
                          </tbody>
 +
                        </table>
 +
                    </div>
 +
                </div>
 +
 
 +
 
 +
                <div id="section2" style="border: solid 1px #666; margin:5px;border-radius:10px;overflow: hidden;">
 +
                    <h3 style="background-color:#ce6b9a;color:#ffffff; padding:10px;letter-spacing:1px; margin-top:0;">Recycling part </h3>
 +
                    <p>
 +
                            The recycling part is to capture the rare earth ions in the environment and to anchor our cells over the silicon net.
 +
                    </p>
 +
                    <h4><strong>①With appropriate primers, PCR was carried out to amplify target gene oprf-LBT1-12 and oprf-Si tag.</strong> </h4>
 +
                    <div class="container experiment_circuit col-md-6 col-xs-6 col-md-offset-3 col-xs-offset-3">
 +
                        <img src="https://static.igem.org/mediawiki/2017/7/73/2017_HUST_China_Experiment_image2.png" alt="experiment_circuit" class="img-responsive">
 +
                    </div>
 +
                    <h4 class="col-xs-12"><strong>②Then we constructed two vectors to achieve expression of LBT and Si-tag.</strong> </h4>
 +
                    <div class="container experiment_circuit col-md-6 col-xs-6 col-md-offset-3 col-xs-offset-3">
 +
                        <img src="https://static.igem.org/mediawiki/2017/7/78/2017_HUST_China_Experiment_image3.png" alt="experiment_circuit" class="img-responsive">
 +
                    </div>
 +
                    <p class="col-xs-12">
 +
                        We cloned the sequence of oprf-LBT and Si-tag into the vector pET28α in order to make the sequence be tagged N-terminally with a 6×His tag. 6×His tag is an affinity tag which allows the tagged recombinant protein to be purified in the process of affinity purification.
 +
                    </p>
 +
                    <h4><strong>③Detection</strong> </h4>
 +
                    <p>
 +
                      In the meanwhile,we added the FLAG tag to achieve that whether the LBTs and the Si tag was expressed on the cell membrane.
 +
                    </p>
 +
                </div>
 +
 
 +
                <div id="section3" style="border: solid 1px #666; margin:5px;border-radius:10px;overflow: hidden;">       
 +
                    <h3 style="background-color:#ce6b9a;color:#ffffff; padding:10px;letter-spacing:1px; margin-top:0;">Construction of the whole circuit</h3>
 +
                    <p>
 +
                      All of our part should be built in one plasmid. Therefore, we use endonuclease and ligase to  replace the GFP by Oprf-LBT and Oprf-Si tag.
 +
                    </p>
 +
                    <div class="container experiment_circuit col-md-6 col-xs-6 col-md-offset-3 col-xs-offset-3" style="padding: 5px;">
 +
                        <img src="https://static.igem.org/mediawiki/2017/5/58/2017_HUST_China_Experiment_image4.png" alt="experiment_circuit" class="img-responsive">
 +
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 +
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Revision as of 13:34, 27 October 2017

Experiment

「Experiment」

Sensing part

The sensing part is to achieve the awareness of the engineering bacteria on the rare earth ions in the environment.

①Amplify

pmrA-B-Fe、pmrC/GFP gene through the pcr protocol

②Plasmid Construction

Coding sequences pmrA/pmrB and pmrC-GFP were cloned into the expression vector pBAD30 by restriction enzyme digestion and DNA ligation.

experiment_circuit

Then we transformed these vectors into Ecoli BL21 cells.

③Detection

Arabinose was used to induce expression of pmrABC system.

We use the original pmrA-pmrB / Fe-pmrC-GFP circuit to test whether our pmrABC system works in our plasmid, then the expression and efficacy of LBT1-12 were tested .

gene circuit vector description
pmrA-pmrB/Fe-pmrC-GFP pBAD30 Test whether our pmrABC system works in our plasmid
pmrA-pmrB/LBT1-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT1
pmrA-pmrB/LBT2-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT2
pmrA-pmrB/LBT3-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT3
pmrA-pmrB/LBT4-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT4
pmrA-pmrB/LBT5-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT5
pmrA-pmrB/LBT6-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT6
pmrA-pmrB/LBT7-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT7
pmrA-pmrB/LBT8-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT8
pmrA-pmrB/LBT9-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT9
pmrA-pmrB/LBT10-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT10
pmrA-pmrB/LBT11-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT11
pmrA-pmrB/LBT12-pmrC-GFP pBAD30 Detecting effectiveness of protein LBT12

Recycling part

The recycling part is to capture the rare earth ions in the environment and to anchor our cells over the silicon net.

①With appropriate primers, PCR was carried out to amplify target gene oprf-LBT1-12 and oprf-Si tag.

experiment_circuit

②Then we constructed two vectors to achieve expression of LBT and Si-tag.

experiment_circuit

We cloned the sequence of oprf-LBT and Si-tag into the vector pET28α in order to make the sequence be tagged N-terminally with a 6×His tag. 6×His tag is an affinity tag which allows the tagged recombinant protein to be purified in the process of affinity purification.

③Detection

In the meanwhile,we added the FLAG tag to achieve that whether the LBTs and the Si tag was expressed on the cell membrane.

Construction of the whole circuit

All of our part should be built in one plasmid. Therefore, we use endonuclease and ligase to replace the GFP by Oprf-LBT and Oprf-Si tag.

experiment_circuit