Team:Tokyo Tech/Experiment/Symbiosis confirmation by co-culture

From 2014.igem.org

(Difference between revisions)
 
(59 intermediate revisions not shown)
Line 1: Line 1:
<html xmlns="http://www.w3.org/1999/xhtml">
<html xmlns="http://www.w3.org/1999/xhtml">
-
<meta name="keywords" content="" />
+
<meta name="keywords" content="iGEM,2014,Tokyo_Tech,Bank E.coli" />
-
<meta name="description" content="" />
+
<meta name="description" content="iGEM2014 Wiki pages" />
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<title>Tokyo_Tech</title>
<title>Tokyo_Tech</title>
Line 9: Line 9:
<div id="header">
<div id="header">
<div id="logo">
<div id="logo">
-
<img src="https://static.igem.org/mediawiki/2014/thumb/b/b7/Tokyo_Tech_Logo.png/613px-Tokyo_Tech_Logo.png" height="150" /></h1></div>
+
 
-
        <div align="right"><img src="https://static.igem.org/mediawiki/2014/b/b4/Tokyo_Tech_Logo2.png" height="150" /></div>
+
<a href="https://2014.igem.org/Main_Page"><img src="https://static.igem.org/mediawiki/2014/thumb/8/84/Tokyo_Tech_iGEM_logo.png/794px-Tokyo_Tech_iGEM_logo.png" width="90" /></a></div>
         </div>
         </div>
<!-- end #header -->
<!-- end #header -->
 +
        <a href="http://www.titech.ac.jp/english/index.html" id="logo-link"></a>
 +
         <div id="menu">
         <div id="menu">
<ul>
<ul>
Line 20: Line 22:
<li class="current_page_item"><a href="#">Experiment</a>
<li class="current_page_item"><a href="#">Experiment</a>
  <ul>
  <ul>
-
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3oxoC12HSL_production" style="width:400px; margin-left:-135px;">C4HSL-dependent 3oxoC12HSL production</a></li>
+
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Plux and Prhl reporter assay" style="width:400px; margin-left:-135px;">Plux and Prhl reporter assay</a></li>
-
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3oxoC12HSL-dependent_C4HSL_production" style="width:400px; margin-left:-135px;">3oxoC12HSL-dependent C4HSL production</a></li>
+
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Prhl_reporter_assay" style="width:400px; margin-left:-135px;">Improved Prhl reporter assay</a></li>
-
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Symbiosis_confirmation_by_co-culture" style="width:400px; margin-left:-135px;">Symbiosis confirmation by co-culture </a></li>
+
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3OC12HSL_production" style="width:400px; margin-left:-135px;">C4HSL-dependent 3OC12HSL production</a></li>
-
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Prhl_reporter_assay" style="width:400px; margin-left:-135px;">Prhl reporter assay </a></li>
+
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production" style="width:400px; margin-left:-135px;">3OC12HSL-dependent C4HSL production</a></li>
-
+
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Symbiosis_confirmation_by_co-culture" style="width:400px; margin-left:-135px;">Mutualism Confirmation ~Co-culture Assay~</a></li>
-
  </ul>
+
     
 +
  </ul>
</li>
</li>
<li><a href="#">Modeling</a>
<li><a href="#">Modeling</a>
-
                            <ul>
+
                          <ul>
-
                                <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Modeling1" style="width:260px; margin-left:-63px;">なぞなぞ</a></li>
+
                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Overview" style="width:400px; margin-left:-135px;">Overview</a></li>
-
                                <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Modeling2" style="width:260px; margin-left:-63px;">Parameter sensitivity analysis</a></li>
+
                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Growth Conditions For Company And Customer" style="width:400px; margin-left:-135px;">Growth Conditions For Company And Customer</a></li>
-
                                <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Modeling3" style="width:260px; margin-left:-63px;">The effect of economic wave</a></li>
+
                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Analysis of C4HSL-dependent Switch" style="width:400px; margin-left:-135px;">Analysis of C4HSL-dependent Switch</a></li>
-
                            </ul>
+
                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Economic Wave"  style="width:400px; margin-left:-135px;">Economic Wave</a></li>
 +
                          </ul>
                         </li>
                         </li>
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">Parts</a></li>
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">Parts</a></li>
-
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Policy_and_Practices" style="height:45px; padding-top:4px;">Policy and Practices</a></li>
+
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Policy_and_Practices" style="height:50px; padding-top:3px;">Policy and Practices</a></li>
<li><a href="#">More</a>
<li><a href="#">More</a>
    <ul>
    <ul>
Line 58: Line 62:
-
<div id="page">
+
        <div id="page">
  <div id="content-over">
  <div id="content-over">
             <div class="post">
             <div class="post">
<h2 class="title">Experiment</h2>
<h2 class="title">Experiment</h2>
-
                 <span class="meta">Symbiosis confirmation by co-culture</span>
+
                 <span class="meta">Mutualism Confirmation ~Co-culture Assay~</span>
                 <div class="entry-long">
                 <div class="entry-long">
-
              <p>&nbsp;</p>
+
            <div id="gototop"><a href="#"><img src="https://static.igem.org/mediawiki/2014/5/55/Tokyo_Tech_Go-to-top-icon.png" height="50" /></a></div>
 +
 
 +
                    <div align="center"><p class="title-small">Contents</p></div>
 +
           <p class="info-24"><a href="#1">1. Introduction</a></p>
 +
                    <p class="info-24"><a href="#2">2. Summary of the Experiment</a></p>
 +
                    <p class="info-24"><a href="#3">3. Results</a></p>
 +
                    <p class="info-24"><a href="#4">4. Discussion</a></p>
 +
                    <p class="info-24"><a href="#5">5. Materials and Methods</a></p>                 
 +
                    <p class="info-18"><a href="#5.1">5-1. Construction</a></p>
 +
                    <p class="info-18"><a href="#5.2">5-2 Assay Protocol</a></p>
 +
                    <p class="info-24"><a href="#6">6. Reference</a></p>
 +
                    <p>&nbsp;</p>
 +
                    <div class="entry-long">&nbsp;</div>
 +
 
               <table width="900" border="0">
               <table width="900" border="0">
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center" class="title-small">Symbiosis confirmation ~co-culture assay~</div></td>
+
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                   <td colspan="2"><div align="center" class="title-small">Mutualism Confirmation ~Co-culture Assay~</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 75: Line 95:
                   <td colspan="2">&nbsp;</td>
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2"><h2>1. Summary of the experiment </h2></td>
+
                   <td colspan="2"><h2>1.Introduction </h2></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">To accomplish symbiosis of the Company cells and the Customer cells, we mixed and co-cultured the two cells.</p>
+
                   <td colspan="2"><p class="info-18">From the results so far, Company cell containing Prhl(RL)-CmR-LasI(<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>) expresses CmR and LasI in the presence of C4HSL. This enables Company to survive and to produce 3OC12HSL. (This result is showed <a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3OC12HSL_production">here</a>.) On the other hand, Customer cell containing Plux-CmR-RhlI(<a href="http://parts.igem.org/Part:BBa_K1529797">BBa_K1529797</a>) expresses CmR and RhlI in the presence of 3OC12HSL. This enables Customer to survive and to produce C4HSL. (This result is showed <a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production">here</a>.) These functions will make the mutualism of Company and Customer possible.</p></td>
-
                  <p class="info-18">Company&rsquo;s characteristics are 4HSL-dependent survival and 3OSC12HSL production, and Company&rsquo;s characteristics are the opposite from the Customer&rsquo;s. (If you want to know about the cells in more detail, please visit the project page.</p>
+
-
                  <p class="info-18">Each cells&rsquo; functions are confirmed.) These characteristics establish symbiosis between the two cells.</p>
+
-
                  <p class="info-18">This experimentation was focused on confirmation of the symbiosis and its condition. We constructed the Company cells containing GFP and the Customer cells containing RFP. By using the flow cytometer, the symbiosis and the condition become detectable. </p></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><div align="center"><img src="https://static.igem.org/mediawiki/2014/c/cf/Tokyo_Tech_Fig3-1-1.png" width="751" height="234" align="middle" /></div></td>
+
                   <td colspan="2" class="info-18"><div align="center">
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-1-2 </div></td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-1-1.png"><img src="https://static.igem.org/mediawiki/2014/e/ef/Tokyo_Tech_3-5-1-1.png" width="600"  align="middle" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"></div></td>
+
                   <td colspan="2"><div align="center"> <strong>Fig.  3-5-1-1.</strong> The genetic circuit of Company and Customer</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><h2>2.  Results</h2></td>
+
                   <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="entry-long">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 100: Line 121:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p align="center" class="head"><img src="https://static.igem.org/mediawiki/2014/0/0b/Tokyo_Tech_Fig3-3-2.png" width="627" height="226" /></p></td>
+
                   <td colspan="2"><h2>2.Summary of the Experiment</h2></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p align="center"><strong>Fig. 3-3-2. </strong>Growth of the two cells when co-cultured</p></td>
+
                   <td colspan="2"><p class="info-18">To characterize the mutualism of Company cell and Customer cell, we cultivated both of them in different ratio and measured the growth. We constructed the Company cell containing GFP and the Customer cell containing RFP. After cultivating both of them for six hours in the same medium, we detected the mutualism by checking the fluorescence intensity of GFP with flow cytometer. We measured the optical density every hour during the culturing. </p></td>
 +
                </tr>
 +
                <tr></p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-2-1.png"><img src="https://static.igem.org/mediawiki/2014/3/39/Tokyo_Tech_3-5-2-1.png" width="750" align="middle" /></div></td></tr>
 +
                <tr><td colspan="2"><div align="center"><strong>Fig. 3-5-2-1. </strong>The flow chart of co-culture assay</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 109: Line 136:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><h2>3.  Materials and methods</h2></td>
+
                   <td colspan="2" class="entry-long">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 115: Line 142:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="head">3-1  Construction</p></td>
+
                   <td colspan="2"><h2>3. Results</h2></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="head">-Strain</p></td>
+
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-3-1.png"><img src="https://static.igem.org/mediawiki/2014/b/b8/Tokyo_Tech_3-5-3-1.png" width="500" align="middle" /></div></td></tr>
 +
                <tr>
 +
                   <td colspan="2"><p align="center"><strong>Fig. 3-5-3-1. </strong>The growth of the two cells when co-cultured</p> </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">All the samples were JM2.300 strain</p></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="head">-Plasmids</p></td>
+
                   <td colspan="2"><p class="info-18">Fig.3-5-3-1 shows the optical densities of Company and Customer after they were co-cultured for 6 hours. These values were evaluated below: </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">A. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR-LasI (pSB3K3) ...Company (type1)</p></td>
+
                   <td colspan="2"><p class="info-18">The optical density of Company cell = the optical density after co-culturing for 6 h x the ratio of the cells with the fluorescence of GFP. </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">B. Ptet-GFP-Ptet-RhiR (pSB6A1), Prhl-CmR-LasI (pSB3K3) ...Company (type2)</p></td>
+
                   <td colspan="2"><p class="info-18">The optical density of Customer cell = the optical density after co-culturing for 6 h x the ratio of the  cells without fluorescence of GFP. </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">C. Ptet-GFP-Ptet-RhiR (pSB6A1), Prhl(RL)-CmR-lasI (pSB3K3) ...Company (type3)</p></td>
+
                   <td colspan="2"><p class="info-18">As a result, the co-cultured samples were able to grow better than the samples single  cultured . It means that only Customer cell can grow little by little in the medium with 100 microg/mL Chloramphenicol because of the leak of Plux promoter (Company cell can’t grow since it contains Prhl promoter which has less leak.) However, in the co-culture experiment, Customer produced C4HSL by the leakage and it induced CmR and LasI expression of Company. LasI produced 3OC12HSL, and it induced CmR and RhlI expression of Customer. This positive feedback might cause the mutualism of Company and Customer. </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">D. Ptet-RFP-Ptet-LuxR (pSB6A1), Plux-CmR-RhlI (pSB3K3) ...Customer</p></td>
+
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                  <tr>
 +
                  <td colspan="2"><h2>4. Discussion</h2></td>
 +
                </tr>
 +
                <tr>
 +
                   <td colspan="2"><p class="info-18">Before conducting this experiment, we checked whether the mutualism could be achieved by mathematical modeling (Go to <a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Growth_Conditions_For_Company_And_Customer">modeling page</a>.) This modeling results showed that the mutualism between the Company and Customer is significantly affected by the initial cell concentration. Therefore, we conducted this assay with the following conditions as preliminary experiment. The experimental results are shown below. </p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">E. Ptet-GFP-Ptet-RhlR (pSB6A1), PlacIq-CmR (pSB3K3) ...Negative control (company)</p></td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-4-1.png"><img src="https://static.igem.org/mediawiki/2014/1/14/Tokyo_Tech_3-5-4-1.png" width="500" align="middle" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">F. Ptet-RFP-Ptet-LuxR (pSB6A1), PlacIq-CmR (pSB3K3) ...Negative control (customer)</p></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-5-4-1.</strong> The preliminary experiment results</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 148: Line 186:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="head">3-2 Assay Protocol</p></td>
+
                   <td colspan="2"><p class="info-18">Fig. 3-5-4-1 shows that the mutualism cannot be achieved when the initial population density is too low. Also, when the initial population density is too high, the mutualism cannot be characterized because of reaching a saturation of  population before the measurement. </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><ol>
+
                   <td colspan="2"><p class="info-18">Additionally, it was found that Customer could survive in the presence of chloramphenicol even when its initial population density was low(Go to the <a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production">3OC12HSL-dependent growth experiment page</a>).  </p></td>
-
                    <li class="info-18">1. Prepare 2 overnight cultures for each samples A~F in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12 h.</li>
+
-
                  </ol></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><ol>
+
                   <td colspan="2"><p class="info-18">Based on these results, we estimated that the proper condition in our experiment is adding 300 microL of Company cell and 100 microL of Customer cell to 2.6 mL of LB medium.(See Materials and methods for the detailed procedures). </p></td>
-
                    <li class="info-18">2. Dilute the overnight cultures to 1 / 100 in fresh LB medium (3 mL) containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) [fresh culture].                     </li>
+
-
                  </ol></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><ol>
+
                   <td colspan="2"><p class="info-18">So we characterized the mutualism between Company and Customer with the following conditions. </p></td>
-
                    <li class="info-18">3. Incubate the fresh cultures in 37°C until the observed OD590 reaches 0.5. If the OD becomes over 0.5, dilute to 0.5.</li>
+
-
                  </ol></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><ol>
+
                   <td colspan="2">&nbsp;</td>
-
                    <li class="info-18">4. Take 1 mL of the sample, and centrifuge at 5000x g, 1 min., 25°C.</li>
+
-
                  </ol></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">5. Remove the supernatant.</td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Detailed result of Co-culture assay.png"><img src="https://static.igem.org/mediawiki/2014/8/81/Detailed_result_of_Co-culture_assay.png" width="500"/></a></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><ol>
+
                   <td colspan="2"><p align="center"><strong>Fig. 3-5-4-2. </strong>Detailed result of Co-culture assay </p></td>
-
                    <li class="info-18">6. Add 1 mL of LB (containing 50 microg / mL ampicilin, 30 microg / mL kanamycin and Cm) and suspend.</li>
+
-
                  </ol></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">7. Add the suspension to 3mL of LB medium as listed below.</td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">LB contains 50 microg / mL ampicilin, 30 microg / mL kanamycin, and Cm.</td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Optical Density.png"><img src="https://static.igem.org/mediawiki/2014/4/4c/Optical_Density.png" width="500"/></a></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td width="21" class="info-18">&nbsp;</td>
+
                   <td colspan="2"><p align="center"><strong>Fig. 3-5-4-3.</strong> Optical Density </p></td>
-
                  <td width="869" class="info-18">A 30 microL + D 30 microL</td>
+
                 </tr>
                 </tr>
-
               
 
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">Fig. 3-5-4-2 revealed that when the amount of Company is 300 microL, the mutualism can be achieved in the range of 60 to 200 microL of Customer.  </p></td>
-
                   <td class="info-18">B 30 microL + D 30 microL</td>
+
                </tr>
 +
                  <tr>
 +
                   <td colspan="2"><p class="info-18">Fig. 3-5-4-3 shows the time-dependent change of optical density. The growth of the cells in mutualism was faster than that of in single culture.  </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td colspan="2">&nbsp;</td>
-
                   <td class="info-18">C 30 microL + D 30 microL</td>
+
                </tr>
 +
                  <tr>
 +
                   <td colspan="2"><p class="info-18">From these results described above, our Company and Customer constructed a mutualistic relationship. </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td colspan="2">&nbsp;</td>
-
                   <td class="info-18">D 30 microL + E 30 microL</td>
+
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><h2>5. Materials and methods</h2></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><h1>5-1  Construction</h1></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><p class="head">-Strain</p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><p class="info-18">All the samples were JM2.300 strain</p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><p class="head">-Plasmids</p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">A. Ptet-GFP-Ptet-RhlR  (pSB6A1), Prhl(RL)-CmR-LasI (pSB3K3) ...Company</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Fig.3-5-5-1.png"><img src="https://static.igem.org/mediawiki/2014/6/62/Fig.3-5-5-1.png" width="300"/></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><p align="center"><strong>Fig. 3-5-5-1.</strong></p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">B. Ptet-LuxR-Plac-RFP  (pSB6A1), Plux-CmR-RhlI (pSB3K3) ...Customer</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Fig.3-5-5-2.png"><img src="https://static.igem.org/mediawiki/2014/5/56/Fig.3-5-5-2.png" width="300"/></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><p align="center"><strong>Fig. 3-5-5-2.</strong></p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><h1>5-2 Assay Protocol</h1></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">1. Prepare  overnight cultures for each samples A and B in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12 h.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">2. Dilute the overnight cultures to 1 / 100 in fresh LB medium (3 mL) containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) [fresh culture].                    </td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">3. Incubate the fresh cultures in 37°C until the observed OD590  reaches 0.5.If the OD becomes over  0.5, dilute to 0.5 with LB medium.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">4. Add  the culture to LB medium as below.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td width="21" class="info-18">&nbsp;</td>
 +
                  <td width="869" class="info-18">LB medium contains 50 microg / mL ampicillin, 30  microg / mL kanamycin and 100 microg / mL chloramphenicol.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
                   <td class="info-18">&nbsp;</td>
                   <td class="info-18">&nbsp;</td>
-
                   <td class="info-18">A 30 microL + F 30 microL</td>
+
                   <td class="info-18">&#8226; A 300 microL + B 130 microL+ LB medium 2.57 mL</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
                   <td class="info-18">&nbsp;</td>
                   <td class="info-18">&nbsp;</td>
-
                   <td class="info-18">B 30 microL + F 30 microL</td>
+
                   <td class="info-18">&#8226; A 300 microL + LB medium 2.7 mL</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
                   <td class="info-18">&nbsp;</td>
                   <td class="info-18">&nbsp;</td>
-
                   <td class="info-18">C 30 microL + F 30 microL</td>
+
                   <td class="info-18">&#8226; B 130 microL + LB medium 2.87 mL</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><ol>
+
                   <td colspan="2" class="info-18">5. Incubate these samples at 37°C for 6 h. (During  that time, measure the optical density every one hour.)</td>
-
                    <li class="info-18">8. Incubate these samples at 37°C for 6 h.</li>
+
-
                  </ol></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">(During that time, measure the optical density every one hour.)</td>
+
                   <td colspan="2" class="info-18">6. Measure the fluorescence intensity with a flow  cytometer (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company).</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><ol>
+
                   <td colspan="2">&nbsp;</td>
-
                    <li class="info-18">9. Measure the fluorescence intensity with a flow cytometer (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company).</li>
+
                </tr>
-
                   </ol></td>
+
                <tr>
 +
                   <td colspan="2" class="entry-long">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 230: Line 320:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><h2>4. Reference</h2></td>
+
                   <td colspan="2"><h2>6. Reference</h2></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">&nbsp;</td>
+
                   <td colspan="2" class="info-18">1. Bo  Hu et al. (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS  ONE 5(5): e10619</td>
                 </tr>
                 </tr>
               </table>
               </table>
Line 244: Line 334:
   </div>
   </div>
<!-- end #page -->
<!-- end #page -->
 +
</div>
</div>

Latest revision as of 03:33, 18 October 2014

Tokyo_Tech

Experiment

Mutualism Confirmation ~Co-culture Assay~

Contents

         

1. Introduction

2. Summary of the Experiment

3. Results

4. Discussion

5. Materials and Methods

5-1. Construction

5-2 Assay Protocol

6. Reference

 

 

 
Mutualism Confirmation ~Co-culture Assay~
 
 

1.Introduction

From the results so far, Company cell containing Prhl(RL)-CmR-LasI(BBa_K1529302) expresses CmR and LasI in the presence of C4HSL. This enables Company to survive and to produce 3OC12HSL. (This result is showed here.) On the other hand, Customer cell containing Plux-CmR-RhlI(BBa_K1529797) expresses CmR and RhlI in the presence of 3OC12HSL. This enables Customer to survive and to produce C4HSL. (This result is showed here.) These functions will make the mutualism of Company and Customer possible.

Fig. 3-5-1-1. The genetic circuit of Company and Customer
 
 
 

2.Summary of the Experiment

To characterize the mutualism of Company cell and Customer cell, we cultivated both of them in different ratio and measured the growth. We constructed the Company cell containing GFP and the Customer cell containing RFP. After cultivating both of them for six hours in the same medium, we detected the mutualism by checking the fluorescence intensity of GFP with flow cytometer. We measured the optical density every hour during the culturing.

Fig. 3-5-2-1. The flow chart of co-culture assay
 
 
 

3. Results

Fig. 3-5-3-1. The growth of the two cells when co-cultured

 

Fig.3-5-3-1 shows the optical densities of Company and Customer after they were co-cultured for 6 hours. These values were evaluated below:

The optical density of Company cell = the optical density after co-culturing for 6 h x the ratio of the cells with the fluorescence of GFP.

The optical density of Customer cell = the optical density after co-culturing for 6 h x the ratio of the cells without fluorescence of GFP.

As a result, the co-cultured samples were able to grow better than the samples single cultured . It means that only Customer cell can grow little by little in the medium with 100 microg/mL Chloramphenicol because of the leak of Plux promoter (Company cell can’t grow since it contains Prhl promoter which has less leak.) However, in the co-culture experiment, Customer produced C4HSL by the leakage and it induced CmR and LasI expression of Company. LasI produced 3OC12HSL, and it induced CmR and RhlI expression of Customer. This positive feedback might cause the mutualism of Company and Customer.

 

4. Discussion

Before conducting this experiment, we checked whether the mutualism could be achieved by mathematical modeling (Go to modeling page.) This modeling results showed that the mutualism between the Company and Customer is significantly affected by the initial cell concentration. Therefore, we conducted this assay with the following conditions as preliminary experiment. The experimental results are shown below.

 
Fig. 3-5-4-1. The preliminary experiment results
 

Fig. 3-5-4-1 shows that the mutualism cannot be achieved when the initial population density is too low. Also, when the initial population density is too high, the mutualism cannot be characterized because of reaching a saturation of population before the measurement.

Additionally, it was found that Customer could survive in the presence of chloramphenicol even when its initial population density was low(Go to the 3OC12HSL-dependent growth experiment page).

Based on these results, we estimated that the proper condition in our experiment is adding 300 microL of Company cell and 100 microL of Customer cell to 2.6 mL of LB medium.(See Materials and methods for the detailed procedures).

So we characterized the mutualism between Company and Customer with the following conditions.

 

Fig. 3-5-4-2. Detailed result of Co-culture assay

 

Fig. 3-5-4-3. Optical Density

Fig. 3-5-4-2 revealed that when the amount of Company is 300 microL, the mutualism can be achieved in the range of 60 to 200 microL of Customer.

Fig. 3-5-4-3 shows the time-dependent change of optical density. The growth of the cells in mutualism was faster than that of in single culture.

 

From these results described above, our Company and Customer constructed a mutualistic relationship.

 

5. Materials and methods

5-1 Construction

-Strain

All the samples were JM2.300 strain

-Plasmids

A. Ptet-GFP-Ptet-RhlR (pSB6A1), Prhl(RL)-CmR-LasI (pSB3K3) ...Company
 

Fig. 3-5-5-1.

B. Ptet-LuxR-Plac-RFP (pSB6A1), Plux-CmR-RhlI (pSB3K3) ...Customer
 

Fig. 3-5-5-2.

 

5-2 Assay Protocol

1. Prepare overnight cultures for each samples A and B in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12 h.
2. Dilute the overnight cultures to 1 / 100 in fresh LB medium (3 mL) containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) [fresh culture].
3. Incubate the fresh cultures in 37°C until the observed OD590 reaches 0.5.If the OD becomes over 0.5, dilute to 0.5 with LB medium.
4. Add the culture to LB medium as below.
  LB medium contains 50 microg / mL ampicillin, 30 microg / mL kanamycin and 100 microg / mL chloramphenicol.
  • A 300 microL + B 130 microL+ LB medium 2.57 mL
  • A 300 microL + LB medium 2.7 mL
  • B 130 microL + LB medium 2.87 mL
5. Incubate these samples at 37°C for 6 h. (During that time, measure the optical density every one hour.)
6. Measure the fluorescence intensity with a flow cytometer (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company).
 
 
 

6. Reference

1. Bo Hu et al. (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5): e10619