Difference between revisions of "Team:Tokyo Tech/Proof"

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{{Tokyo_Tech}}
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<div class="column full_size judges-will-not-evaluate">
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/************************* This page setting ******************************/
<h3>★  ALERT! </h3>
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.container_top h1{
<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Medals">gold medal criterion for proof of concept</a>. </p>
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margin-top: 1px;
 
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font-size: 188%;
 
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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</head>
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<body>
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<div id="main_contents">
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<div id="page_header" class="container container_top">
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<h1 align="center">Proof of Concept</h1>
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<h2 align="center">Achievement Gold</h2>
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<div id="page_header_contents" class="container_contents">
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<p class="normal_text">Demonstrate a functional proof of concept of your project. Your proof of concept must consist of a BioBrick device; a single BioBrick part cannot constitute a proof of concept.</p>
 +
</div><!-- /page_header_contents -->
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</div><!-- /page_header -->
  
<div class="column full_size">
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<div id="Pcold" class="container">
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<div id="Pcold_header" class="container_header">
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<h2><span>1. New cold induible promoter</span></h2>
 +
</div><!-- /_header -->
 +
<div id="Pcold_contents" class="container_contents">
 +
<p class="normal_text">Here we indicated that the cold inducible promoter is a promoter that depends mainly on temperature.We performed an experiment using <a href="http://parts.igem.org/Part:BBa_K1949001">BBa_K1949001</a>.
 +
<br>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2016/e/ee/T--Tokyo_Tech--6-pr-1-1.png" height ="250"><br></div>
 +
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 6-3-1-1.  </span> Cold inducible promoter <br>
 +
the RFU of GFP / Turbidity of the samples cultivated at 18°C was higher than those cultivated at 37°C.
 +
</p></div><br>
 +
<p class="normal_text">In this experiment, each sample was cultivated at 18°C and 37°C, after that their RFU of GFP / Turbidity was measured.</p>
 +
<p class="normal_text">From the results, we found that the RFU of GFP / Turbidity of the samples cultivated at 18°C was higher than those cultivated at 37°C.</p>
 +
<p class="normal_text">The above results indicate that this promoter is induced at low temperatures.
  
 +
</p>
 +
</div><!-- /Pcold_contents -->
 +
</div><!-- /Pcold -->
  
<p>
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<div id="Rhl" class="container">
iGEM teams are great at making things work! We value teams not only doing an incredible job with theoretical models and experiments, but also in taking the first steps to make their project real.  
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<div id="Rhl_header" class="container_header">
</p>
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<h2><span>2. Rhl system assay</span></h2>
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</div><!-- /Rhl_header -->
 +
<div id="Rhl_contents" class="container_contents">
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<p class="normal_text">Here shows how we changed the rhl promoter to the one that suited our project best. We conducted an experiment using <a href="http://parts.igem.org/Part:BBa_K1949060">BBa_K1949060</a>.
 +
</p><br>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2016/1/17/T--Tokyo_Tech--6-pr-2-1.png" height ="250"><br></div>
 +
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 6-3-2-1. </span>  Our original improved Prhl(NM) is much more sensitive to C4HSL than Prhl(WT).
 +
</p></div><br>
 +
<p class="normal_text">A single point mutation was inserted in a wild type rhl promoter(<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>).</p>
 +
<p class="normal_text">In the experiment, an AHL reagent was included in the reporter, and then we measured the RFU.</p>
 +
<p class="normal_text">As a result, the mutant promoter Prhl(NM), which is stronger than a wild type promoter, was newly obtained.</p>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2016/f/f3/T--Tokyo_Tech--6-pr-2-2.png" height ="250"><br></div>
 +
<div align="center"><p class="caption" style="font-size: 16px;"><span style="font-weight: bold;">Fig. 6-3-2-2. </span> The Signal-to-Noise (SN) ratio of Prhl(NM) is higher than that of past improved Prhl(LR), and Prhl(NM) does not crosstalk to C12 unlike
 +
</p></div><br>
 +
<p class="normal_text">iGEM 2014 team Tokyo_Tech has improved the rhl promoter. However, comparing the Prhl(NM) with the Prhl(LR), the SN ratio of Prhl(NM) was higher than that of Prhl(LR). Also, the graph shows that Prhl(LR) has crosstalk with C12 at a specific proportion. If we use it in the recreation of Snow White, and the  crosstalk between the promoter and C12 will mean that the Queen eats the Poisoned Apple, which she produced herself, and dies. Therefore, this promoter cannot be used in our project.</p>
 +
<p class="normal_text">The graph also shows that Prhl(NM) almost have no crosstalk with C12.</p>
 +
<p class="normal_text">Based on the results above, we can say that we found a promoter with strong activity, and it almost have no crosstalk with C12,  which is the most suitable one for our story.</p>
  
 +
</div><!-- /Rhl_contents -->
 +
</div><!-- /Rhl -->
  
<h4> What should we do for our proof of concept? </h4>
+
<div id="TA" class="container">
<p>  
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<div id="TA_header" class="container_header">
You can assemble a device from BioBricks and show it works. You could build some equipment if you're competing for the hardware award. You can create a working model of your software for the software award. Please note that this not an exhaustive list of activities you can do to fulfill the gold medal criterion. As always, your aim is to impress the judges!
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<h2><span>3. TA system</span></h2>
</p>
+
</div><!-- /TA_header -->
 +
<div id="TA_contents" class="container_contents">
 +
<p class="normal_text">Here shows the inhibition of the <span style="font-style : italic">E. coli´</span>s growth and translation by MazF and the resuscitation of them by MazE. We performed an experiment using <a href="http://parts.igem.org/Part:BBa_K1949100">BBa_K1949100</a> and <a href="http://parts.igem.org/Part:BBa_K1949102">BBa_K1949102</a>.
  
</div>
+
 +
</p><br>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2016/e/eb/T--Tokyo_Tech--6-pr-3-1.png" height ="250"><br></div>
 +
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 6-3-3-1. </span> After inhibiting cell growth by MazF, it was resuscitated by expression of MazE.
 +
</p></div><br>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2016/2/24/T--Tokyo_Tech--6-pr-3-2.png" height ="250"><br></div>
 +
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 6-3-3-2. </span> After inhibiting expression of GFP by MazF, it was resuscitated by expression of MazE.
 +
</p></div><br>
 +
<p class="normal_text">In this experiment, MazF was expressed by arabinose, and after 2 h MazE was expressed by IPTG. </p>
 +
<p class="normal_text">From the results, it was found that the turbidity of the sample without MazE almost did not rise at all. However, it was also found that if IPTG is added, and the MazE will be expressed, the <span style="font-style : italic">E. coli</span> will recover its growth.</p>
 +
<p class="normal_text">Also, if only the MazF is working, the RFU of GFP barely rise. If MazE is induced, the RFU of GFP will rise. <a href="https://2016.igem.org/Team:Tokyo_Tech/Toxin_Assay/Overview"><a href="https://2016.igem.org/Team:Tokyo_Tech/Toxin_Assay/mazEF_System_Assay">Read mazEF system Assay page</a>.
 +
</a></p>
 +
<p class="normal_text">As the result above, we concluded that MazF inhibits the <span style="font-style : italic">E. coli'</span>s growth and translation. However, MazE resuscitates the growth and translation stopped by MazF.</p>
 +
<p class="normal_text">Althrough this experiment, we indicated that the TA system functions properly.</p>
  
 +
</div><!-- /TA_contents -->
 +
</div><!-- /TA -->
  
 +
<div id="AmiE" class="container">
 +
<div id="AmiE_header" class="container_header">
 +
<h2><span>4. Degredation of C12 by AmiE </span></h2>
 +
</div><!-- /AmiE_header -->
 +
<div id="AmiE_contents" class="container_contents">
 +
<p class="normal_text">Here it is indicated that AmiE degrades AHL selectively. We performed an experiment using <a href="http://parts.igem.org/Part:BBa_K1949052">BBa_K1949052</a>.
  
</div>
+
</p><br>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2016/7/75/T--Tokyo_Tech--6-pr-4-1.png" height ="250"><img src="https://static.igem.org/mediawiki/2016/9/94/T--Tokyo_Tech--6-pr-4-2.png" height ="250"></div><br>
 +
<p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 6-3-4-1. </span> AmiE degrades C12  &nbsp;
 +
<span style="font-weight: bold;">Fig. 6-3-4-2. </span> AmiE barely degrades C4 <br>
 +
C12 is greatly degraded. On the other hand, the C4 is barely degraded by AmiE.
 +
</p><br>
 +
<p class="normal_text">In this experiment, it was examined whether AHLs would be degraded after the addition of 3OC12HSL(C12) and C4HSL(C4) molecules into a culture of <span style="font-style : italic">E. coli</span> that expresses AmiE.<br>
 +
From the results, it was found that the C12 added into a culture of AmiE expressing <span style="font-style : italic">E. coli</span> is greatly degraded. On the other hand, the C4 added into this culture, is barely degraded.</p>
 +
<p class="normal_text">From the above result, we showed that AmiE selectively degraded AHL molecules.
 +
</p>
  
 +
</div><!-- /AmiE_contents -->
 +
</div><!-- /AmiE -->
 +
</div><!-- /main_contents -->
 +
</body>
 
</html>
 
</html>

Latest revision as of 02:58, 20 October 2016

1. New cold induible promoter

Here we indicated that the cold inducible promoter is a promoter that depends mainly on temperature.We performed an experiment using BBa_K1949001.


Fig. 6-3-1-1. Cold inducible promoter
the RFU of GFP / Turbidity of the samples cultivated at 18°C was higher than those cultivated at 37°C.


In this experiment, each sample was cultivated at 18°C and 37°C, after that their RFU of GFP / Turbidity was measured.

From the results, we found that the RFU of GFP / Turbidity of the samples cultivated at 18°C was higher than those cultivated at 37°C.

The above results indicate that this promoter is induced at low temperatures.

2. Rhl system assay

Here shows how we changed the rhl promoter to the one that suited our project best. We conducted an experiment using BBa_K1949060.



Fig. 6-3-2-1. Our original improved Prhl(NM) is much more sensitive to C4HSL than Prhl(WT).


A single point mutation was inserted in a wild type rhl promoter(BBa_R0071).

In the experiment, an AHL reagent was included in the reporter, and then we measured the RFU.

As a result, the mutant promoter Prhl(NM), which is stronger than a wild type promoter, was newly obtained.


Fig. 6-3-2-2. The Signal-to-Noise (SN) ratio of Prhl(NM) is higher than that of past improved Prhl(LR), and Prhl(NM) does not crosstalk to C12 unlike


iGEM 2014 team Tokyo_Tech has improved the rhl promoter. However, comparing the Prhl(NM) with the Prhl(LR), the SN ratio of Prhl(NM) was higher than that of Prhl(LR). Also, the graph shows that Prhl(LR) has crosstalk with C12 at a specific proportion. If we use it in the recreation of Snow White, and the crosstalk between the promoter and C12 will mean that the Queen eats the Poisoned Apple, which she produced herself, and dies. Therefore, this promoter cannot be used in our project.

The graph also shows that Prhl(NM) almost have no crosstalk with C12.

Based on the results above, we can say that we found a promoter with strong activity, and it almost have no crosstalk with C12, which is the most suitable one for our story.

3. TA system

Here shows the inhibition of the E. coli´s growth and translation by MazF and the resuscitation of them by MazE. We performed an experiment using BBa_K1949100 and BBa_K1949102.



Fig. 6-3-3-1. After inhibiting cell growth by MazF, it was resuscitated by expression of MazE.



Fig. 6-3-3-2. After inhibiting expression of GFP by MazF, it was resuscitated by expression of MazE.


In this experiment, MazF was expressed by arabinose, and after 2 h MazE was expressed by IPTG.

From the results, it was found that the turbidity of the sample without MazE almost did not rise at all. However, it was also found that if IPTG is added, and the MazE will be expressed, the E. coli will recover its growth.

Also, if only the MazF is working, the RFU of GFP barely rise. If MazE is induced, the RFU of GFP will rise. Read mazEF system Assay page.

As the result above, we concluded that MazF inhibits the E. coli's growth and translation. However, MazE resuscitates the growth and translation stopped by MazF.

Althrough this experiment, we indicated that the TA system functions properly.

4. Degredation of C12 by AmiE

Here it is indicated that AmiE degrades AHL selectively. We performed an experiment using BBa_K1949052.



Fig. 6-3-4-1. AmiE degrades C12   Fig. 6-3-4-2. AmiE barely degrades C4
C12 is greatly degraded. On the other hand, the C4 is barely degraded by AmiE.


In this experiment, it was examined whether AHLs would be degraded after the addition of 3OC12HSL(C12) and C4HSL(C4) molecules into a culture of E. coli that expresses AmiE.
From the results, it was found that the C12 added into a culture of AmiE expressing E. coli is greatly degraded. On the other hand, the C4 added into this culture, is barely degraded.

From the above result, we showed that AmiE selectively degraded AHL molecules.