Difference between revisions of "Team:Tokyo Tech/Experiment/Realizing the Payoff Matrix"

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      <h1>Realizing the Payoff Matrix</h1>
 
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    <h2 class="content2">contents</h2>
 
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      <h3 class="link"><a href="#Introduction">1. Introduction</a></h3>
 
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      <h3 class="link"><a href="#Summary">2. Summary of the Experiment</a></h3>
 
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      <h3 class="link2"><a href="#Summary1">2.1. Realizing the Payoff Matrix of Prisoner A <i>coli</i></a></h3>
 
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      <h3 class="link2"><a href="#Summary2">2.2. Realizing the Payoff Matrix of Prisoner B <i>coli</i></a></h3>
 
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      <h3 class="link"><a href="#Results">3. Results</a></h3>
 
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      <h3 class="link2"><a href="#Result1">3.1. Realizing the Payoff Matrix of Prisoner A <i>coli</i></a></h3>
 
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      <h3 class="link2"><a href="#Result2">3.2. Realizing the Payoff Matrix of Prisoner B <i>coli</i></a></h3>             
 
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      <h3 class="link"><a href="#Materials">4. Materials and Methods</a></h3>
 
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      <h3 class="link2"><a href="#Const">4.1.  Construction</a></h3>
 
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      <h3 class="link2"><a href="#Protocol">4.2. Assay Protocol</a></h3>
 
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        <h3 class="link3"><a href="#Protol1">4.2.1. C4HSL-dependent CmR expression assay ([Cm] = 75 microg/mL)</a></h3>
 
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        <h3 class="link3"><a href="#Protol2">4.2.2. 3OC12HSL concentration-dependent CmR expression assay</a></h3>
 
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      <h3 class="link"><a href="#Reference">5. Reference</a></h3>
 
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          <h2 id="Introduction" class="smalltitle">1. Introduction</h2>
 
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　　　　　　<p class="text">We genetically engineered two prisoner <i>coli</i>, Prisoner A and Prisoner B.  They are able to cooperate or to defect.  The genetic circuits, with the improved chloramphenicol resistant protein(CmR) part, of Prisoner A and B are shown in Fig. 3-2-1-1.  Our goal in this project is to realize the payoff matrix (Fig. 3-2-1-2) with the four types of growth inhibition.  Using the improved plasmids we constructed, our <i>E.coli</i> version payoff matrix is realized through wet experiments. </p>
 
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;3-2-1-1.</strong>&nbsp;The genetic circuits of prisoner <i>colis</i> with the options of cooperation or defection</h4>
 
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　　　        <h2 id="Summary" class="smalltitle">2. Summary of the Experiment</h2>
 
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                <h3 id="Summary1" class="sub5">2.1. Realizing the Payoff Matrix of Prisoner A <i>coli</i></h3>
 
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                <p class="text2">The cell growth of the Prisoner <i>colis</i> containing the pairs of plasmids (1) and (2) in the lower chloramphenicol (Cm) concentration (75 microg/mL) were measured and the payoff matrix was realized.</p>
 
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;3-2-2-1.</strong>&nbsp;Cells for the experiment to realize the payoff matrix of Prisoner A <i>coli</i></h4>
 
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                <h3 id="Summary2" class="sub5">2.2. Realizing the Payoff Matrix of Prisoner B <i>coli</i></h3>
 
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                <p class="text2">We have prepared a new pair of plasmids, (3) and (4), as in the following (Fig. 3-2-2-2.).  The cell growth of the Prisoner <i>colis</i> containing the pairs of plasmids (3) and (4) in the lower chloramphenicol (Cm) concentration (75 microg/mL) and also in the lower 3OC12HSL concentration were measured and the payoff matrix was realized.</p>
 
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;3-2-2-2.</strong>&nbsp;Cells for the experiment to realize the payoff matrix of Prisoner B <i>coli</i></h4>
 
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　　　　　　<p class="text2">Using the pair of plasmids we constructed, our <i>E.coli</i> version payoff matrix with the four types of growth inhibition was replicated through wet experiments.  The cell growth of the Prisoner <i>colis</i> containing the pairs of plasmids (3) and (4), grown under the lower Cm concentration and also with the lower 3OC12HSL concentration, were observed.
 
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          <h2 id="Results" class="smalltitle">3. Results</h2>
 
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              <h3 id="Result1" class="sub5">3.1. Realizing the Payoff Matrix of Prisoner A <i>coli</i></h3>
 
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                <p class="text2">The cell growth of the Prisoner <i>colis</i> containing the pairs of plasmids (1) and (2) in the lower chloramphenicol (Cm) concentration (75 microg/mL) were measured after an eight hour incubation.  The payoff matrix was realized as the following.</p>
 
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;3-2-3-1.</strong>&nbsp;Payoff matrix of Prisoner A <i>coli</i> with 75 microg/mL Cm</h4>
 
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              <h3 id="Result2" class="sub5">3.2. Realizing the Payoff Matrix of Prisoner B <i>coli</i></h3>
 
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　　　　　　    <p class="text2">The cell growth of the Prisoner <i>colis</i> containing the pairs of plasmids (3) and (4) in the lower chloramphenicol (Cm) concentration (75 microg/mL) and in the lower 3OC12HSL concentration were measured.  The payoff matrix was realized as the following.</p>
 
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;3-2-3-2.</strong>&nbsp;Payoff matrix of Prisoner B <i>coli</i> with <i>gfp</i> in 75 microg/mL Cm and 1 nM 3OC12HSL</h4>
 
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          <h2 id="Materials" class="smalltitle">4. Materials and Methods</h2>
 
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              <h3 id="Const" class="sub5">4.1.  Construction</h3>
 
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              <h3 class="sub5">-Strain</h3>
 
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　　　　　　    <p class="text2">All the samples were JM2.300 strain.</p>
 
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              <h3 class="sub5">-Plasmids</h3>
 
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　　　　　　    <p class="text2">(1) Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1) + Plac_lasI (pSB3K3)</p>
 
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                  <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/b/be/Tokyo_Tech_Pcon_rhlR_TT_Plux_CmRssrA_Plac_lasI.png"/>
 
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-1.</strong></h4>
 
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　　　　　　    <p class="text2">(2) Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1) + promoter less_lasI (pSB3K3)</p>
 
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                  <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/2/24/Tokyo_Tech_Pcon_rhlR_TT_Plux_CmRssrA_lasI.png"/>
 
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-2.</strong></h4>
 
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　　　　　　    <p class="text2">(3) Pcon_<i>lasR</i>_TT_Plux_<i>CmRssrA</i> (pSB6A1) + Pcon_<i>gfp</i>_<i>rhlI</i> (pSB3K3)</p>
 
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                  <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/c/cf/Tokyo_Tech_Pcon_lasR_TT_Plux_CmRssrA_Pcon_gfp_rhlI.png"/>
 
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-3.</strong></h4>
 
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　　　　　　    <p class="text2">(4) Pcon_<i>lasR</i>_TT_Plux_<i>CmRssrA</i> (pSB6A1) + promoter less_<i>rhlI</i> (pSB3K3)</p>
 
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                  <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/7/77/Tokyo_Tech_Pcon_lasR_TT_Plux_CmRssrA_rhlI.png"/>
 
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-4.</strong></h4>
 
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              <h3 id="Protocol" class="sub5">4.2. Assay Protocol</h3>
 
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              <h3 id="Protol1" class="sub6">4.2.1. C4HSL-dependent CmR expression assay ([Cm] = 75 microg/mL)</h3>
 
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                    <p class="text4">
 
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<strong>-samples</strong><br>
 
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(1) Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1) ＋ Plac_lasI (pSB3K3)<br>
 
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(2) Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1) ＋ promoter less_lasI (pSB3K3)<br>
 
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                    <p class="text4"><br>
 
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<strong>-Procedure</strong><br>
 
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1. Prepare overnight cultures (n=2) for the samples in 3 mL LB medium, containing ampicillin (50 microg/mL) and kanamycin (30 microg/mL) at 37°C for 12 hours.<br>
 
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2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp (50 microg/mL) and Kan (30 microg/mL) and grow the cells at 37°C until the observed OD590 reaches 0.5.<br>
 
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3. Centrifuge 1 mL of the sample at 5000g, RT for 1 minute.<br>
 
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4. Suspend the pellet in 1mL of LB containing Amp and Kan.<br>
 
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5. Add 30 microL of suspension in the following medium.<br>
 
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&nbsp;&nbsp;&nbsp;①)LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + 50 microM C4HSL (30 microL) + Chloramphenicol (75 microg/mL)<br>
 
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&nbsp;&nbsp;&nbsp;②)LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (30 microL) + Chloramphenicol (75 microg/mL)<br>
 
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6.Grow the samples of cells at 37°C for more than 8 hours.<br>
 
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7.Measure optical density every hour. (If the optical density is over 0.9, dilute the cell medium to 1/5.)<br><br>
 
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              <h3 id="Protol2" class="sub6">4.2.2. 3OC12HSL concentration-dependent CmR expression assay</h3>
 
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                    <p class="text4">
 
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<strong>-samples</strong><br>
 
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(3) Pcon_<i>lasR</i>_TT_Plux_<i>CmRssrA</i> (pSB6A1) ＋ Pcon_<i>gfp</i>_<i>rhlI</i> (pSB3K3)<br>
 
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(4) Pcon_<i>lasR</i>_TT_Plux_<i>CmRssrA</i> (pSB6A1) ＋ promoter less_<i>rhlI</i> (pSB3K3)<br>
 
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<br>
 
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<strong>-Procedure</strong><br>
 
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1. Prepare overnight cultures (n=2) for the samples in 3 mL LB medium, containing ampicillin (50 microg/mL) and kanamycin (30 microg/mL) at 37°C for 12 hours.<br>
 
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2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp (50 microg/mL) and Kan (30 microg/mL) and grow the cells at 37°C until the observed OD590 reaches 0.5.<br>
 
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3. Centrifuge 1 mL of the sample at 5000g, RT for 1 minute.<br>
 
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4. Suspend the pellet in 1mL of LB containing Amp and Kan.<br>
 
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5.Add 30 microL of suspension in the following medium.<br>
 
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&nbsp;&nbsp;&nbsp;a) LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + 1 microM 3OC12HSL (3 microL) + Chloramphenicol (75 microg/mL)<br>
 
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&nbsp;&nbsp;&nbsp;b) LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (3 microL) + Chloramphenicol (75 microg/mL)<br>
 
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6. Grow the samples of cells at 37°C for more than 8 hours.<br>
 
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&nbsp;&nbsp;&nbsp;Measure optical density every hour.  (If the optical density is over 0.9, dilute the cell medium to 1/5.)<br><br></p>
 
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          <h2 id="Reference" class="smalltitle">5. Reference</h2>
 
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　　　　　　<p class="text">1. Bo Hu <em>et al.</em> (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5): e10619</p>
 
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Latest revision as of 12:45, 18 September 2015