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

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<h1 align="center">Proof of concept</h1>
 
<h1 align="center">Proof of concept</h1>
                        <div id="page_header_contents" class="container_contents">
 
 
<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>
 
<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>
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<h3 class="link"><a href="#Pcold">1. New cold induible promoter (Scene1 : The Magic Mirror’s answer)</a></h3>
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<h3 class="link"><a href="#Pcold">1. New cold induible promoter (Scene1 : The Magic Mirror’s Answer)</a></h3>
<h3 class="link"><a href="#Rhl">2. Rhl sysem assay (Scene2 : The Queen’s trap)</a></h3>
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<h3 class="link"><a href="#Rhl">2. Rhl sysem assay (Scene2 : The Queen’s Trap)</a></h3>
<h3 class="link"><a href="#TA">3. TA system (Scene3 : Snow White's sleep) </a></h3>
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<h3 class="link"><a href="#TA">3. TA system (Scene3 : Snow White's Sleep) </a></h3>
 
<h3 class="link"><a href="#AmiE">4. AmiE degrades C12 (Scene4 : The Prince’s rescue)</a></h3>
 
<h3 class="link"><a href="#AmiE">4. AmiE degrades C12 (Scene4 : The Prince’s rescue)</a></h3>
 
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<p class="normal_text">We are now going to expound on these points sequentially.</p>
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<p class="normal_text">These points are expounded sequentially as follows.</p>
 
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<div id="Pcold_contents" class="container_contents">
 
<div id="Pcold_contents" class="container_contents">
<p class="normal_text">Here we indicate that the cold inducible promoter is a promoter that depends mainly on temperature.<br>
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<p class="normal_text">Here we indicated that the cold inducible promoter is a promoter that depends mainly on temperature.<br>
a Pcold-gfp was constracted.<br>
+
a Pcold-gfp was constructed.<br>
<div align="center"><img src="URL"><br></div>
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<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.  </span> title
 
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> title
 
</p></div>
 
</p></div>
<p class="normal_text">In this experiment, each sample was cultivated at 18°C and 37°C, after that their RFU of GFP was measured.<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.<br>
From the experiment results it was found that the RFU of GFP of the samples cultivated at 18°C was higher than the ones cultivated at 37°C.<br>
+
From the experiment results, we found that the RFU of GFP / Turbidity of the samples cultivated at 18°C was higher than those cultivated at 37°C.<br>
From the above result, we are able to show that this promoter is a promoter induced by low temperatures.
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From the above result, we were able to show that this promoter is a promoter induced by low temperatures.
  
 
</p>
 
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<div id="Rhl_contents" class="container_contents">
 
<div id="Rhl_contents" class="container_contents">
<p class="normal_text">Here we indicate how we produced the rhl promoter that suited our project best.</p><br>
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<p class="normal_text">Here shown how we produced the rhl promoter that suited our project best.</p><br>
<div align="center"><img src="URL"><br></div>
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<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.  </span> title
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<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> Prhl(NM) vs Prhl(WT)
 
</p></div>
 
</p></div>
<p class="normal_text">A point mutation was inserted in a wild type rhl promoter.<br>
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<p class="normal_text">A single point mutation was inserted in a wild type rhl promoter(BBa_R0071).<br>
In the experiment, an AHL reagent was included in the reporter, and then the RFU of GFP was measured.<br>
+
In the experiment, an AHL reagent was included in the reporter, and then the RFU was measured.<br>
As a result, the mutant promoters Prhl(M) and Prhl(NM), which is stronger than a wild type promoter, were newly obtained.</p>
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As a result, the mutant promoters Prhl(NM), which was stronger than a wild type promoter, was newly obtained.</p>
<div align="center"><img src="URL"><br></div>
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<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; text-align: center;"><span style="font-weight: bold;">Fig.  </span> title
+
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> Pthl(NM) vs Prhl(LR)
 
</p></div>
 
</p></div>
<p class="normal_text">iGEM 2014 Tokyo_Tech has already improved the rhl promoter. However, comparing the Prhl(NM) to the Prhl(LR), Prhl(NM) did not show any crosstalk with C12 and the SN ratio of Prhl(NM) was higher than that of Prhl(LR). Also, the experiment showed that Prhl(LR) crosswalks with C12 at a specific proportion. If we use it in the recreation of Snow White, and if the promoter crosstalks with C12, it means that the Queen eats the poisoned apple, she herself produced, and dies. So this is not a promoter we can use in our project.<br>
+
<p class="normal_text">iGEM 2014 team-Tokyo_Tech has improved the rhl promoter in previous years. However, comparing the Prhl(NM) to the Prhl(LR), Prhl(NM) did not show any crosstalk with C12 and the SN ratio of Prhl(NM) was higher than that of Prhl(LR). Also, the graph shows that Prhl(LR) has crosstalks with C12 at a specific proportion. If we use it in the recreation of Snow White, and if the promoter has crosstalks with C12, it means that the Queen eats the poisoned apple, which she herself produced, and dies. Therefore, this promoter is not used in our project.<br>
 
The graph also shows that Prhl(NM) almost does not have crosstalk with C12.<br>
 
The graph also shows that Prhl(NM) almost does not have crosstalk with C12.<br>
Base on the above results, we can say that we found a promoter with strong activity, and it does not have crosstalk with C12,  which is the most suitable for our story.
+
Based on the above results, we can say that we found a promoter with strong activity, and it does not have crosstalk with C12,  which is the most suitable for our story.
  
 
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<div id="TA_contents" class="container_contents">
 
<div id="TA_contents" class="container_contents">
<p class="normal_text">Here we indicate the inhibition of the <span style="font-style : italic">E. Coli</span>´s multiplication and inhibition of translation by MazF and the restarting of them by MazE.<br>
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<p class="normal_text">Here shown 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.<br>
We constructed a circuit that includes mazEF .
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We constructed the circuit that includes <span style="font-style : italic">mazEF</span>.
 
</p><br>
 
</p><br>
<div align="center"><img src="URL"><br></div>
+
<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.  </span> title
 
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> title
 
</p></div>
 
</p></div>
<p class="normal_text">In this experiment, MazF was expressed by arabinose , and after 2 hours MazE was expressed by IPTG. <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>
From the experiment results, it was found that the turbility of the sample without MazE almost did not rise at all. However, it was also found that if IPTG is added, and the MazE is expressed, the <span style="font-style : italic">E. Coli</span> will restart its multiplication.<br>
+
Also, if only the MazF is working, the RFU of GFP barely rise But if MazE is induced, the RFU of GFP will rise. <a href="https://2016.igem.org/Team:Tokyo_Tech/Toxin_Assay">(Link: Toxin assay)</a><br>
+
As the result above, it was concluded that MazF interrupts the multiplication of <span style="font-style : italic">E. Coli</span> and translation. However, MazE restarted the multiplication and translation stopped by MazF.<br>
+
Through this experiment, we showed that the TA system functions properly.</p>
+
<div align="center"><img src="URL"><br></div>
+
 
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> title
 
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> title
 
</p></div>
 
</p></div>
+
<p class="normal_text">In this experiment, MazF was expressed by arabinose, and after 2 h MazE was expressed by IPTG. <br>
 +
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 is expressed, the <span style="font-style : italic">E. coli</span> will recover its growth.<br>
 +
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">(Link: Toxin assay)</a><br>
 +
As the result above, we concluded that MazF inhibits the <span style="font-style : italic">E. coli'</span>s growth and translation. However, MazE recovers the growth and translation stopped by MazF.<br>
 +
Althrough this experiment, we indicated that the TA system functions properly.</p>
 +
 
 
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<div id="AmiE" class="container">
 
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<div id="AmiE_header" class="container_header">
 
<div id="AmiE_header" class="container_header">
<h2><span>4. AmiE degrades C12 </span></h2>
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<h2><span>4. AmiE degrades C12</span></h2>
 
</div><!-- /AmiE_header -->
 
</div><!-- /AmiE_header -->
 
<div id="AmiE_contents" class="container_contents">
 
<div id="AmiE_contents" class="container_contents">
<p class="normal_text">Here we indicate that the AmiE decomposes AHL selectively.
+
<p class="normal_text">Here it is indicated that AmiE degrades AHL selectively.
 
</p><br>
 
</p><br>
<div align="center"><img src="URL"><br></div>
+
<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>
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> title
+
<p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.  </span> title1 &nbsp;
</p></div>
+
<span style="font-weight: bold;">Fig.  </span> title2
<p class="normal_text">In this experiment, it was examined whether AHL would be degraded after the addition of 3OC12HSL and C4HSL molecules into a culture of <span style="font-style : italic">E. Coli</span> that express AmiE.<br>
+
</p>
From the experiment 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 in this culture, is barely degraded.<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 above result, we were able to show that AmiE selectively degrades AHL molecules.
+
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.<br>
 +
From the above result, we showed that AmiE selectively degraded AHL molecules.
 
</p>
 
</p>
  

Revision as of 15:24, 14 October 2016

1. New cold induible promoter

Here we indicated that the cold inducible promoter is a promoter that depends mainly on temperature.
a Pcold-gfp was constructed.


Fig. title

In this experiment, each sample was cultivated at 18°C and 37°C, after that their RFU of GFP / Turbidity was measured.
From the experiment results, we found that the RFU of GFP / Turbidity of the samples cultivated at 18°C was higher than those cultivated at 37°C.
From the above result, we were able to show that this promoter is a promoter induced by low temperatures.

2. Rhl system assay

Here shown how we produced the rhl promoter that suited our project best.



Fig. Prhl(NM) vs 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 the RFU was measured.
As a result, the mutant promoters Prhl(NM), which was stronger than a wild type promoter, was newly obtained.


Fig. Pthl(NM) vs Prhl(LR)

iGEM 2014 team-Tokyo_Tech has improved the rhl promoter in previous years. However, comparing the Prhl(NM) to the Prhl(LR), Prhl(NM) did not show any crosstalk with C12 and the SN ratio of Prhl(NM) was higher than that of Prhl(LR). Also, the graph shows that Prhl(LR) has crosstalks with C12 at a specific proportion. If we use it in the recreation of Snow White, and if the promoter has crosstalks with C12, it means that the Queen eats the poisoned apple, which she herself produced, and dies. Therefore, this promoter is not used in our project.
The graph also shows that Prhl(NM) almost does not have crosstalk with C12.
Based on the above results, we can say that we found a promoter with strong activity, and it does not have crosstalk with C12, which is the most suitable for our story.

3. TA system

Here shown the inhibition of the E. coli´s growth and translation by MazF and the resuscitation of them by MazE.
We constructed the circuit that includes mazEF.



Fig. title


Fig. title

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 is 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. (Link: Toxin assay)
As the result above, we concluded that MazF inhibits the E. coli's growth and translation. However, MazE recovers the growth and translation stopped by MazF.
Althrough this experiment, we indicated that the TA system functions properly.

4. AmiE degrades C12

Here it is indicated that AmiE degrades AHL selectively.



Fig. title1   Fig. title2

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.