Team:TzuChiU Formosa/Project
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+ | <li><a class="qmitem-s" href="https://2013.igem.org/Team:TzuChiU_Formosa/Project"><span style="font-weight: bold;">Projects</span></a></li> | ||
<li><a class="qmitem-s" href="https://2013.igem.org/Team:TzuChiU_Formosa/Protocol"><span style="font-weight: bold;">Protocol</span></a></li> | <li><a class="qmitem-s" href="https://2013.igem.org/Team:TzuChiU_Formosa/Protocol"><span style="font-weight: bold;">Protocol</span></a></li> | ||
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<li><a class="qmitem-s" href="https://2013.igem.org/Team:TzuChiU_Formosa/Safety"><span style="font-weight: bold;">Safety</span></a></li> | <li><a class="qmitem-s" href="https://2013.igem.org/Team:TzuChiU_Formosa/Safety"><span style="font-weight: bold;">Safety</span></a></li> | ||
</ul></li> | </ul></li> | ||
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<table style="border: 5px hidden rgb(14, 150, 25); height: 250px; background-color: rgb(255, 255, 255); width: 800px; margin-left: 30px; align="left" cellpadding="5" cellspacing="5" frame="none" rules="ALL"> | <table style="border: 5px hidden rgb(14, 150, 25); height: 250px; background-color: rgb(255, 255, 255); width: 800px; margin-left: 30px; align="left" cellpadding="5" cellspacing="5" frame="none" rules="ALL"> | ||
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The reason why we have chosen to use the IPTG induction is because this inducible system complies with the need of our experiment. After IPTG is added, it will combine with LacI thus detaching from the sequence from the Lac operator. This will then activate transcription to our antisense gene and the transcribed antisense mRNA will bind to resistant gene CamR. If we have successfully knocked down CamR, and it cannot be cultured onto the LB plate, then it proves that our idea has worked! | The reason why we have chosen to use the IPTG induction is because this inducible system complies with the need of our experiment. After IPTG is added, it will combine with LacI thus detaching from the sequence from the Lac operator. This will then activate transcription to our antisense gene and the transcribed antisense mRNA will bind to resistant gene CamR. If we have successfully knocked down CamR, and it cannot be cultured onto the LB plate, then it proves that our idea has worked! | ||
+ | <br> | ||
+ | <br><hr> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <font size="4"><b>Our plan</b></font> | ||
+ | <br> | ||
+ | <br> | ||
+ | The figure below is the composite we plan to use in our project: | ||
+ | <br> | ||
+ | <br> | ||
+ | <img src="https://static.igem.org/mediawiki/2013/d/d3/Project_1.png" width="550px"><br><br> | ||
+ | We intend to make use of the iGEM biobricks and the parts we constructed to compose an IPTG inducible system, via the Biobrik Assembly Kit. The T7 promoter(<a href="http://parts.igem.org/Part:BBa_I719005">BBa_I719005</a>)、T7 terminator(<a href="http://parts.igem.org/Part:BBa_K731721">BBa_K731721</a>) and Lac promoter(<a href="http://parts.igem.org/Part:BBa_I14032">BBa_I14032</a>) are igem biobricks. Joining the biobrick with our Lac operator+CamR antisense (<a href="http://parts.igem.org/Part:BBa_K1222984">BBa_K1222984</a>), (<a href="http://parts.igem.org/Part:BBa_K1222983">BBa_K1222983</a>), (<a href="http://parts.igem.org/Part:BBa_K1222982">BBa_K1222982</a>), (<a href="http://parts.igem.org/Part:BBa_K1222981">BBa_K1222981</a>) and LacI (<a href="http://parts.igem.org/Part:BBa_K1222003">BBa_K1222003</a>) would be the IPTG inducible system part (<a href="http://parts.igem.org/Part:BBa_K1222000">BBa_K1222000</a>) we are going to submit. | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | The figure below is the biobrick assemble kit overview: | ||
+ | <br> | ||
+ | <br> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2013/9/9c/Project_2.png" width="600px" height="600px" > | ||
+ | |||
</td></font> | </td></font> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td><font face="calibri" size="5px"><br><br><br><br>Result</font></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td><font color="black" face="Calibri" size="3"> | ||
+ | <br> | ||
+ | <font size="4"><b>Group one: pSB1C3</b></font> | ||
+ | <br> | ||
+ | <br> | ||
+ | <ol> | ||
+ | <dl> | ||
+ | <dd> | ||
+ | <li> | ||
+ | We have successfully obtained the pSB1C3 vector and the insert we have designed (<a href="http://parts.igem.org/Part:BBa_K1222987">BBa_K1222987</a>、<a href="http://parts.igem.org/Part:BBa_K1222986">BBa_K1222986</a>、<a href="http://parts.igem.org/Part:BBa_K1222985">BBa_K1222985</a>、<a href="http://parts.igem.org/Part:BBa_K1222984">BBa_K1222984</a>、<a href="http://parts.igem.org/Part:BBa_K1222983">BBa_K1222983</a>、<a href="http://parts.igem.org/Part:BBa_K1222982">BBa_K1222982</a>、<a href="http://parts.igem.org/Part:BBa_K1222981"> BBa_K1222981</a>). After ligation, we transformed the plamid think DH5α. | ||
+ | </ol> | ||
+ | </dl> | ||
+ | <br> | ||
+ | <br> | ||
+ | <img src="https://static.igem.org/mediawiki/2013/4/44/Result_1.png" height="500px"> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <img src="https://static.igem.org/mediawiki/2013/3/38/Result_2.png" width="400px"> | ||
+ | |||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <ol start="2"> | ||
+ | <dl> | ||
+ | <dd> | ||
+ | <li>We have Picked a single colony of the bacteria cultured and performed streaking. According to each quadrant of single colony, we have done a colony PCR but only a primer dimer band was shown. We conjecture that this is because the specificity of the primer is not high enough. | ||
+ | </ol> | ||
+ | </dl> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <img src="https://static.igem.org/mediawiki/2013/7/75/Result_3.png" width="700px"> | ||
+ | <br><br><br><br><br><br> | ||
+ | <ol start="3"> | ||
+ | <dl> | ||
+ | <dd> | ||
+ | <li> | ||
+ | While performing the experiment above, we have also attempted to clone lac I. Firstly, we designed a primer with regard to lac I on the pET11d and used TGradient Thermocycler to test several annealing temperatures (Tm) but unfortunately, we did not succeed. We assume that this is because the sequence for lac I is too large hence, it cannot be cloned out at once. We then tried overlapping PCR and designed several groups of primers. Again, we did not manage to succeed. | ||
+ | </ol> | ||
+ | </dl> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | |||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <font size="4"><b>Group two: pET11d</b></font> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <ol> | ||
+ | <dl> | ||
+ | <dd> | ||
+ | <li> | ||
+ | Since the pET11d plasmid contains the lac I gene, so to make up for the previous group (group 1), we have decided to use pET11d. Successfully we managed to get the pET11d vector and our designed antisense insert (<a href="http://parts.igem.org/Part:BBa_K1222994">BBa_K1222994</a>, <a href="http://parts.igem.org/Part:BBa_K1222995">BBa_K1222995</a>, <a href="http://parts.igem.org/Part:BBa_K1222996">BBa_K1222996</a>, <a href="http://parts.igem.org/Part:BBa_K1222997">BBa_K1222997</a>, <a href="http://parts.igem.org/Part:BBa_K1222998">BBa_K1222998</a>, <a href="http://parts.igem.org/Part:BBa_K1222988">BBa_K1222988</a>, <a href="http://parts.igem.org/Part:BBa_K1222989">BBa_K1222989</a>), which includes GFP and Ampicillin. After ligation, we transformed it into BL21 but nothing grew on the agar plate. The control group (Ampicillin free) proved that there is nothing wrong with the competent cell and in fact we have obtained a complete plasmid from digestion. Therefore, we assume the reasons could be the following: | ||
<br> | <br> | ||
<br> | <br> | ||
- | </tr> | + | a. Unsuccessful ligation |
- | <tr> | + | <br> |
+ | b. The size of the plasmid is too large | ||
+ | <br> | ||
+ | c. Probably BL21 already contains a plasmid (T7 polymerase sequence) therefor the chances of it would not accept another plasmid | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | One of the main reason is that there is not enough time on hand so the result displayed is our experiment for now. We will still continue working on the experiment to complete our idea and design. | ||
+ | </ol> | ||
+ | </dl> | ||
+ | <img src="https://static.igem.org/mediawiki/2013/5/58/Result_4.png" width="500px"> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | |||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2013/d/d7/Result_5.png" width="450px"> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | |||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <font size="4"><b>Due to the problems above, we have already carried out some solutions:</b></font> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | <ol> | ||
+ | <dl> | ||
+ | <dd> | ||
+ | <li>We have redesigned a new higher specificity check primer for the pSB1C3 colony PCR. | ||
+ | <li>According to pSB1C3 the lac I for this group: | ||
+ | <br>a. We have once again designed another overlapping primer, repetitively trying to clone the lac I sequence from the pET11d | ||
+ | <br>b. Not only did we attempt cloning the lac I off pET11d, we also tried cloning other plasmids with the lac I sequence such as PQE80L. This is to increase the probability of us getting the lac I gene. | ||
+ | <br> | ||
+ | <br> | ||
+ | <li>In accordance to pET11d, we have tried some minor alterations to the transformation protocol in this experiment such as: | ||
+ | <br>a. Increasing the time of heat shock and | ||
+ | <br>b. Make use of electroporation to prepare competent cell. | ||
+ | We plan to give it a try, carry out these alterations and complete the experiment in the near future. | ||
+ | |||
+ | |||
+ | |||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td><font face="calibri" size="5px"><br><br><br><br>Brand New Design</font></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td><br><br><br><br><br><font color="black" face="Calibri" size="3"> | ||
+ | <img src="https://static.igem.org/mediawiki/igem.org/6/6f/2013-09-28_080927.png" width="750px"> | ||
+ | <br> | ||
+ | <br> | ||
+ | <br> | ||
+ | |||
+ | At first, we started off this project baring the thought that " Are organisms able to perform an easier mechanism to carry out our desired plan? " Now that the competition is right around the corner, it seems like we still need a little extra time to prove the feasibility of the experiment. <br> | ||
+ | <br> | ||
+ | A few weeks ago, we have seen a paper called "DNA targeting specificity of RNA-guided Cas9 nucleases" which gave us a moment of epiphany! We have then realized that if we could add the CRISPR/Cas9 mechanism to our experiment, the results would probably be much closer to our expectation than it is now. Our team members then spent some extra time redesigning the proposal by adding both conjugation and CRISPR to our original plan. In doing this we hope to design a more powerful and effective system that complies more with our expectations.<br> | ||
+ | <br> | ||
+ | <br> | ||
+ | </font> | ||
+ | </tr> | ||
+ | <tr> | ||
</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
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+ | <br> | ||
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Latest revision as of 01:56, 28 September 2013