http://2011.igem.org/wiki/index.php?title=Special:Contributions/Lyl&feed=atom&limit=50&target=Lyl&year=&month=2011.igem.org - User contributions [en]2024-03-29T12:12:56ZFrom 2011.igem.orgMediaWiki 1.16.0http://2011.igem.org/Team:UNIST_Korea/human_practice/acknowledgementTeam:UNIST Korea/human practice/acknowledgement2011-10-04T17:58:01Z<p>Lyl: </p>
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<font size=6><font color=cc0099><center>ACKNOWLEDGMENT<br/></font></font><br/></center><br/><br/><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <img src="https://static.igem.org/mediawiki/2011/9/9a/Ykcho.jpg" height="270" width="200">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br />
<img src="https://static.igem.org/mediawiki/2011/8/80/CMKIM.jpg"height="270" width="200" align="center"> <br/><br />
<font color=maroon><br />
<center>Dr.Yoon Kyoung Cho &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dr.Cheol Min Ghim<br/><br />
<br />
Associate Professor &nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Assistant Professor<br/><br />
<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;School of NanoBiochemical Science &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;School of NanoBiochemical Science<br/><br />
<br />
UNIST,Korea &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;UNIST , Korea<br/></center><br />
<br />
<br/><br />
<center>We thank Dr. Cho and Dr. Ghim for their financial and technical support throughout our project</center><br />
<br/><br/><br/><br/><br />
<br />
<center><font size=6><font color=cc0099>Special Thanks to <br/></center></font></font><br/><br />
<font color=maroon><center>Dr. Sung Kuk Lee </center><br />
<br />
<center>Ms. Young Shin Ryu<br/></center><br />
<br />
<center>Ms. Euna Lee<br/></center><br />
<center>Mr. JaeMyung Lee<br/></center><br />
<br />
<center>Ms. Goo Hee Kim<br/></center><br />
<br />
<center>Ms Jung Min Park<br/></center><br />
<br />
<center>Mr. SungHun Jung<br/></center><br />
<br />
<center>Mr. HyunMo Yang<br/></center><br />
<br />
<center>Ms. Vinuselvi Parisutham<br/></center><br />
<br />
<center>Mr. Min Choi<br/></center><br />
<center>Mr. Yong Sun Park<br/></center><br />
<br />
<br />
<br />
<br />
<center>for their solid encouragements, technical assistance, scientific discussions and motivations<center/><br/><br />
<br />
<center><font size=4>We also thank all members of NBC for their kind support and solid encouragement<br/></center></font></font><br/><br/><br />
<br/><br/><br />
<font size=6><font color=cc0066>ATTRIBUTIONS<br/></font></font><br/><br />
EeSeul Shin- Light Sensor Module<br/><br />
JaeSung Yoo- Temperature Sensor Module<br/><br />
Bokeun Song- Signal Processor Module<br/><br />
Yu-Lim Lee- Lysis Module <br/><br />
------------------------<br/><br />
Min Choi-Web programing<br/><br />
Yong Sun Park-Web programing<br/><br />
<br />
</font><br />
<br />
<br />
<br />
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</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/human_practice/acknowledgementTeam:UNIST Korea/human practice/acknowledgement2011-10-04T17:55:04Z<p>Lyl: </p>
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<font size=6><font color=cc0099><center>ACKNOWLEDGMENT<br/></font></font><br/></center><br/><br/><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <img src="https://static.igem.org/mediawiki/2011/9/9a/Ykcho.jpg" height="270" width="200">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br />
<img src="https://static.igem.org/mediawiki/2011/8/80/CMKIM.jpg"height="270" width="200" align="center"> <br/><br />
<font color=maroon><br />
<center>Dr.Yoon Kyoung Cho &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dr.Cheol Min Ghim<br/><br />
<br />
Associate Professor&nbsp &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Assistant Professor<br/><br />
<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;School of NanoBiochemical Science &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;School of NanoBiochemical Science<br/><br />
<br />
UNIST,Korea &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;UNIST , Korea<br/></center><br />
<br />
<br/><br />
<center>We thank Dr. Cho and Dr. Ghim for their financial and technical support throughout our project</center><br />
<br/><br/><br/><br/><br />
<br />
<center><font size=6><font color=cc0099>Special Thanks to <br/></center></font></font><br/><br />
<font color=maroon><center>Dr. Sung Kuk Lee </center><br />
<br />
<center>Ms. Young Shin Ryu<br/></center><br />
<br />
<center>Ms. Euna Lee<br/></center><br />
<center>Mr. JaeMyung Lee<br/></center><br />
<br />
<center>Ms. Goo Hee Kim<br/></center><br />
<br />
<center>Ms Jung Min Park<br/></center><br />
<br />
<center>Mr. SungHun Jung<br/></center><br />
<br />
<center>Mr. HyunMo Yang<br/></center><br />
<br />
<center>Ms. Vinuselvi Parisutham<br/></center><br />
<br />
<center>Mr. Min Choi<br/></center><br />
<center>Mr. Yong Sun Park<br/></center><br />
<br />
<br />
<br />
<br />
<center>for their solid encouragements, technical assistance, scientific discussions and motivations<center/><br/><br />
<br />
<center><font size=4>We also thank all members of NBC for their kind support and solid encouragement<br/></center></font></font><br/><br/><br />
<br/><br/><br />
<font size=6><font color=cc0066>ATTRIBUTIONS<br/></font></font><br/><br />
EeSeul Shin- Light Sensor Module<br/><br />
JaeSung Yoo- Temperature Sensor Module<br/><br />
Bokeun Song- Signal Processor Module<br/><br />
Yu-Lim Lee- Lysis Module <br/><br />
------------------------<br/><br />
Min Choi-Web programing<br/><br />
Yong Sun Park-Web programing<br/><br />
<br />
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<b>July 5</b></br> We took a tour of the lab, learnt basic laboratory safety rule and learnt basic techniques like how to prepare LB-Medium, how to use the autoclave. We inoculated <i>E. coli</i> strain SCS110 so that we will make competent cell tomorrow. We also prepared ice coldwater and glycerol for tomorrow’s experiment.<br/><br/><br/><br />
<b>July 6</b></br> We learnt how to make Electro Competent Cell. While JaeSung and Eeseul were busy making Comp cell, Bokeun and YuLim were busy setting PCR and recovering Biobrick Parts. We made a list of the biobrick parts we would use in our experiment and we tried to recover those plasmids from the DNA kit box we obtained from iGEM. <br/><br/><br/><br />
<b>July 7</b></br> We saw pretty colonies on our plates we made yesterday. We failed to recover all of the biobrick parts we aimed for. So, we tried to recover them once again. We also have transformed the pSIM5 plasmid carrying the lambda red system into SCS110 to perform gene knockout. Then our instructor, Vinu tried to explain us the use of lambda red system for gene knockouts. We were excited with the function of exo, gamma and beta proteins. We inoculated SCS110 pSIM5 cells for tomorrow’s experiment. Eeseul made a PCR product that is to be used to knockout our target gene. <br/><br/><br/><br />
<b>July 8</b></br> We tried to knock out gene. SCS110 is a comparatively slow growing cell. It was funny to induce cells at 42⁰C and immediately cooling them and making electrocompetent for transformation. <br/><br/><br/><br />
<b>July 9</b></br> We were excited to see tiny small colonies on our Kanamycin plates. We went ahead to do a colony PCR to check for the true deletion. At the end of the day, we confirmed that we have deleted our gene, EnvZ. We were so excited because now we can make our <i>E. coli</i> to sense light. Our instructor advised us to remove the kanamycin cassette before we proceed to check the light sensing ability. <br/><br/><br/><br />
<b>July 11</b></br> We inoculated the SCS110 ∆envZ strains to make competent cell and transform pCP20 plasmid, which would help us to remove the kanamycin cassette. <br/><br/><br/><br />
<b>July 12</b></br> We failed to remove the kanamycin cassette. Our instructor advised us to try it again.<br />
We tried again. Eeseul got a lot of stress in removing the kanamycin cassette. So YuLim tried to remove the kanamycin cassette. <br/><br/><br/><br />
<b>July 13</b></br> YuLim also failed to remove the kanamycin cassette. Vinu advised us to give up this strain, as the plasmid pCP20 may not be compatible with SCS110 host strain. So we decided to use MG1655. We inoculated MG1655 pSIM5 strain to delete kanamycin cassette. <br/><br/><br/><br />
<b>July 14</b></br> Eeseul tried to delete envZ gene in MG1655. JaeSung and Bokeun were busy writing Safety rule and Abstract which is due for tomorrow. YuLim and Vinu tried to isolate the genomic DNA from Streptococcus which they will use it to amplify the Dpn cassette. It was little hard and a long boring procedure as it is a gram-positive bacterium. But, finally they got a good yield. <br/><br/><br/><br />
<b>July 16</b></br> We were busy learning the Vector NTI program in order to design our primers. It was little hard at the beginning but we started mastering it soon. <br/><br/><br/><br />
<b>July 18</b></br> We were still busy designing primers for our future experiments. Primers for Gibson’s Assembly was little difficult. We took care of adding RBS and additional bases for restriction sites. Finally at the end of the day almost all of our primers were being designed. Now, our instructor will check our primers and place an order for our primers. <br/><br/><br/><br />
<b>July 21</b></br> Our primers have come. Our instructor explained us the ways to process our primers. JaeSung went crazy about the calculation and finally Bokeun helped him fix his problem. Everybody rushed to set our PCRs. YuLim got all of her holin genes successfully. But she failed to get her Dpn PCR product. Vinu suggested that she should try a gradient PCR. So, she went ahead to set a gradient PCR. <br/><br/><br/><br />
<b>July 22</b></br> YuLim still failed to get her PCR product. Vinu suggested Dpn digestion of the genomic DNA itself to confirm if Streptococcus DNA we had really has a Dpn gene. To our suspicion, Streptococcus DNA was digested by Dpn suggesting it has no Dpn. Vinu tried to place order for another Streptococcus strain from KCTC. Bokeun went ahead to clone his fimE gene into a plasmid pACYC. <br/><br/><br/><br />
<b>July 23</b></br> Bokeun and JaeSung are done with their cloning, they luckily got one colony, and that had their target gene inserted. Bokeun was extremely excited with it. We transformed 3 plasmids (light receptors, fimE and GFP) into one strain. JaeSung went on to check the expression of mRNA at different temperatures. The preliminary result was promising and he was able to see some difference based on the temperature. <br/><br/><br/><br />
<b>July 25</b></br> JaeSung went on to screen for the cells Bokeun made to find one cell, which carries all 3 plasmids. He used TECAN microplate reader to screen for the cell. Finally he got one colony that contains all 3 plasmids. And Eeseul streaked it on a plate. <br/><br/><br/><br />
<b>July 26</b></br> The last day's plate was completely green the next day. Then we realized that TECAN is dark. So, in our cell darkness lead to fimE expression which in turn inverted all of the promoters of GFP making GFP expression constitutive. So, we learnt that we should take care of darkness when we use fimE system. <br/><br/><br/><br />
<b>July 27-29</b></br> We went for a workshop on Climate Change. We explained the audience about iGEM and our goal. We were explaining our project for the first time to a group of people. We were excited with that. We celebrated the day with alcohol. <br/><br/><br/><br />
<b>August 1</b></br> We deleted the envZ gene and integrated cI gene into the chromosome of MG1655 using lambda red system. <br/><br/><br/><br />
<b>August 3</b></br> We tried to transform the light sensing biobricks and the reporter gene into the envZ deleted strain<br/><br/><br/><br />
<b>August 10</b></br> Our strain containing the light plasmid and reporter plasmids are ready. We made a quick check of its functionality in the presence and absence of light. <br/><br/><br/><br />
<b>August 13</b></br> We got the new Streptococcus DNA and successfully amplified the Dpn genes. Gibson’s assembly works very well. <br/><br/><br/><br />
<b>August 16</b></br> YuLim completed cloning Holin and Dpn into a plasmid without the prmoter. <br/><br/><br/><br />
<b>August 17</b></br> YuLim went on to put the promoters in front of Holin and Dpn. She has two kinds of promoter one is a inversion promoter, ptrc* and another is a Constitutive Promoter. She is aware that it is not as easy to clone the promoters, as it was to clone the genes. She was causing in using specific strains for each promoters. (pL promoter into ECNR2; Dpn into SCS110). <br/><br/><br/><br />
<b>September 4</b></br> Eeseul repeated the mRNA-GFP. However, she had difficulty in understanding the GFP expression as she made a temperature shift at the early log phase. She had to deal with a slow growing and fast growing strain. So, she gave up the experiment as she could not predict her output and even the control was not as expected. Bokeun tried to check the effect of different concentration of glucose on the light receptor. He could see a good cross talk of the light and the osmo-regulator. <br/><br/><br/><br />
<b>September 5</b></br> JaeSung repeated the mRNA experiment even when his control gave good result. He could not see any difference in GFP expression with temperature dependent riboswitch. <br/><br/><br/><br />
<b>September 7</b></br> JaeSung tried to check the effect of light on cI expression by following GFP expression every one hour. After one day of tiresome experiment, he got a very good result. <br/><br/><br/><br />
<b>September 8</b></br> We had a deep discussion on Synthetic Biology and iGEM to Science Specialized High Schools in Korea and in Singapore. <br/><br/><br/><br />
<b>September 11</b></br> Eeseul tried to check the effect of cross-talk between the osmo-regulator and the light receptor using salt. She found no cross-talk with salt. YuLim was almost done with her cloning of Holin and Dpn cassette. Now she is ready to check their functionality. <br/><br/><br/><br />
<b>September 18</b></br> Bokeun and Eeseul tried to prove the cross-talk using various sugars such as Arabinose and Glucose. They found a similar pattern even when they used arabinose or glucose. <br/><br/><br/><br />
<b>September 21</b></br> We had a group presentation with all members of our department. It was our first official presentation. We were excited and we got many good feed backs. <br/><br/><br/><br />
<b>September 22</b></br> We were busy making our websites and documenting the results. We were aware that the wiki would freeze soon. <br/><br/><br/><br />
<b>September 23</b></br> We went on to clone Holin and Dpn under the control of pBAD promoter as the light promoter did not work<br/><br/><br/><br />
<b>September 28</b></br> We cloned the riboswitch regulated GFP into pTrc promoter to check for a significant change in GFP with temperature. We still could not see any significant changes in GFP. <br/><br/><br/><br />
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<font size=6><font color=cc0099><center>ACKNOWLEDGMENT<br/></font></font><br/></center><br/><br/><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <img src="https://static.igem.org/mediawiki/2011/9/9a/Ykcho.jpg" height="270" width="270">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br />
<img src="https://static.igem.org/mediawiki/2011/8/80/CMKIM.jpg"height="270" width="270" align="center"> <br/><br />
<font color=maroon><br />
<center>Dr.Yoon Kyoung Cho &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dr.Cheol Min Ghim<br/><br />
<br />
Associate Professor&nbsp &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Assistant Professor<br/><br />
<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;School of NanoBiochemical Science &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;School of NanoBiochemical Science<br/><br />
<br />
UNIST,Korea &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; UNIST , Korea<br/></center><br />
<br />
<br/><br />
<center>We thank Dr. Cho and Dr. Ghim for their financial and technical support throughout our project</center><br />
<br/><br/><br/><br/><br />
<br />
<center><font size=6><font color=cc0099>Special Thanks to <br/></center></font></font><br/><br />
<font color=maroon><center>Dr. Sung Kuk Lee </center><br />
<br />
<center>Ms. Young Shin Ryu<br/></center><br />
<br />
<center>Ms. Euna Lee<br/></center><br />
<center>Mr. JaeMyung Lee<br/></center><br />
<br />
<center>Ms. Goo Hee Kim<br/></center><br />
<br />
<center>Ms Jung Min Park<br/></center><br />
<br />
<center>Mr. SungHun Jung<br/></center><br />
<br />
<center>Mr. HyunMo Yang<br/></center><br />
<br />
<center>Ms. Vinuselvi Parisutham<br/></center><br />
<br />
<center>Mr. Min Choi<br/></center><br />
<center>Mr. Yong Sun Park<br/></center><br />
<br />
<br />
<br />
<br />
<center>for their solid encouragements, technical assistance, scientific discussions and motivations<center/><br/><br />
<br />
<center><font size=4>We also thank all members of NBC for their kind support and solid encouragement<br/></center></font></font><br/><br/><br />
<br/><br/><br />
<font size=6><font color=cc0066>ATTRIBUTIONS<br/></font></font><br/><br />
EeSeul Shin- Light Sensor Module<br/><br />
JaeSung Yoo- Temperature Sensor Module<br/><br />
Bokeun Song- Signal Processor Module<br/><br />
Yu-Lim Lee- Lysis Module <br/><br />
------------------------<br/><br />
Min Choi-Web programing<br/><br />
Yong Sun Park-Web programing<br/><br />
<br />
</font><br />
<br />
<br />
<br />
<br />
<br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/human_practice/acknowledgementTeam:UNIST Korea/human practice/acknowledgement2011-10-04T17:23:36Z<p>Lyl: </p>
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<font size=6><font color=cc0099><center>ACKNOWLEDGMENT<br/></font></font><br/><center/><br />
<img src="https://static.igem.org/mediawiki/2011/9/9a/Ykcho.jpg" height="270" width="270"><br />
<img src="https://static.igem.org/mediawiki/2011/8/80/CMKIM.jpg"height="270" width="270" align="right"><br/><br />
<font color=maroon><br />
<table width="80%" border="0" align="center"bgcolor="#F5F5DC"><br />
<tr><br />
<th><align="center">Dr.Yoon Kyoung Cho<br/>Associate Professor<br/>School of NanoBiochemical Science<br/>UNIST,Korea</th><br />
<th><align="center">Dr.Cheol Min Ghim<br/>Assistant Professor<br/>School of NanoBiochemical Science<br/>UNIST , Korea</th><br />
</tr><br />
</table><br />
<br/><br />
<center>We thank Dr. Cho and Dr. Ghim for their financial and technical support throughout our project</center><br />
<br/><br/><br />
<br />
<center><font size=6><font color=blue>Special Thanks to <br/></center></font></font><br/><br />
<center>Dr. Sung Kuk Lee </center><br />
<br />
<center>Ms. Young Shin Ryu<br/></center><br />
<br />
<center>Ms. Euna Lee<br/></center><br />
<center>Mr. JaeMyung Lee<br/></center><br />
<br />
<center>Ms. Goo Hee Kim<br/></center><br />
<br />
<center>Ms Jung Min Park<br/></center><br />
<br />
<center>Mr. SungHun Jung<br/></center><br />
<br />
<center>Mr. HyunMo Yang<br/></center><br />
<br />
<center>Ms. Vinuselvi Parisutham<br/></center><br />
<br />
<center>Mr. Min Choi<br/></center><br />
<center>Mr. Yong Sun Park<br/></center><br />
<br />
<br />
<br />
<br />
<center>for their solid encouragements, technical assistance, scientific discussions and motivations<center/><br/><br />
<br />
<center><font size=4>We also thank all members of NBC for their kind support and solid encouragement<br/></center></font></font><br/><br/><br />
<br />
<font size=6><font color=blue>ATTRIBUTIONS<br/></font></font><br/><br />
EeSeul Shin- Light Sensor Module<br/><br />
JaeSung Yoo- Temperature Sensor Module<br/><br />
Bokeun Song- Signal Processor Module<br/><br />
Yu-Lim Lee- Lysis Module <br/><br />
------------------------<br/><br />
Min Choi-Web programing<br/><br />
Yong Sun Park-Web programing<br/><br />
<br />
</font><br />
<br />
<br />
<br />
<br />
<br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/human_practice/human_practiceTeam:UNIST Korea/human practice/human practice2011-10-04T17:21:27Z<p>Lyl: </p>
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<font face=calibri><font size="7" color=cc0099><center>Human Practice</font></center><br />
<br/><br/><br/><br />
<font color=maroon><br />
<p align="justify">Media Attention: We published an article in Korean language to introduce synthetic biology and iGEM competition to all universities in Korea. To do this we gathered a simple description of the projects of all 4 iGEM teams from South Korea (KAIST , KOREA UNIV. , CBNU, UNIST) and finally summarized it. We believe that this article would reach all universities of Korea and would motivate few other undergraduates to join hands for Synthetic Biology. Visit <a href=http://www.ksbb.or.kr/home/kor/>http://www.ksbb.or.kr/home/kor/</a> for more details.<br />
</br></br></p><br />
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<th><img src="https://static.igem.org/mediawiki/2011/5/5f/%EC%B9%B4%EC%9D%B4%EC%8A%A4%ED%8A%B8.png"></th><br />
<th><img src="https://static.igem.org/mediawiki/2011/3/34/%EA%B3%A0%EB%A0%A4%EB%8C%80.png"></th></tr><br />
<tr><th>KAIST</th><th>KOREA</th></tr><br />
<tr><th><img src="https://static.igem.org/mediawiki/2011/9/99/%EC%B6%A9%EB%B6%81%EB%8C%80.png"></th><br />
<th><img src="https://static.igem.org/mediawiki/2011/e/e3/UNIST.png"></th></tr><br />
<tr><th>CBNU</th><th>UNIST</th></tr></table></center><br />
<br />
<br/><br/><br/><br />
<br />
<font size="5">Collaboration with CBNU_KOREA TEAM</font><br/><br />
<br />
<p style="float:left"><img src="https://static.igem.org/mediawiki/2011/c/c2/Logo_UNIST.gif" height="70" align="right"><br />
<p style="float:left"><img src="https://static.igem.org/mediawiki/2011/7/77/CBNU.jpg" height="70"> <br />
<p align="justify">UNIST_KOREA Team & CBNU_KOREA Team held a regular meeting once at a month . We shared our idea and discussed how to prepare for iGEM competetion. Computer engineers from ChungBuk National University helped us a lot in terms of modeling. We provide a sequence analysis and other molecular analysis. We are planning to have a nice trip in the HongKong! <br/><br/></p><br />
<br/><br/><br />
<br />
<br />
<font size="5">Sowing Synthetic Seeds in the Young Minds of High School Students</font><br/><br/><br />
<p style="float:right"><img src="https://static.igem.org/mediawiki/2011/6/6d/%ED%95%84%EB%A6%AC%ED%95%80%EC%82%AC%EB%9E%8C%EB%93%A4.png" hspace=30/></p><p style="justify">On September 3rd, we organized a small symposium with high school students from Korea Science Academy and National University of Singapore. The students belonged to mathematics and science departments. We discussed future aspects of synthetic biology and its detailed applications for bio-fuel production. We believe that the seeds to harvest synthetic fruits should be laid even from the very young age.<br/><br/><br/><br/><br/><br/></p><br />
<br />
<br />
<font size="5">Special lecture on synthetic biology – August 24th </font><br/><br/><br />
<p style="float:left"><img src="https://static.igem.org/mediawiki/2011/a/ad/%EC%9B%8C%ED%81%AC%EC%83%BE2.png" hspace=30></p><p style="justify">We organized a special lecture on synthetic biology (Synthetic Biology : Advances and Threats) to non-biologists in UNIST Students from different departments like Electrical Engineering Department, Chemical Engineering Department, Technology management and Physics department were present at the session. We discussed the possible strategies we have to control the Genetically Modified Organisms when it is exposed to nature. After special lecture, we went to the pub and discussed a lot about the future of the world and the role of synthetic biology in designing the future! <br />
<br/><br/><br/><br/><br/><br/></p><br />
<br />
<br />
<font size="5">Elite Of Elites (Combination of Mathematicians, Physicist and Biologists)</font><br/><br/> <br />
<p style="float:right"><img src="https://static.igem.org/mediawiki/2011/e/e0/%EC%9B%8C%ED%81%AC%EC%83%BE3.png" hspace=30></p><p style="justify">On September 10th, we organized a co-seminar with EOE (Elite of Elites), Mathematics and Physics club in UNIST supported by Korean government, discussed about role of synthetic biology in future and the importance of mathematical modeling for gene regulation. We believe that a team of mathematicians, physicist and biologist would help in forming a flourishing synthetic organism. We believe that the complexity of life could be simplified with mathematical calculations and physical laws. More well-defined biological systems would also be offered a warmer welcome in the general public. <br/><br/><br/><br/><br/><br/></p><br />
<br />
<br />
<br />
<font size="5">Workshop – July 26th-27h </font></br></br><br />
<p style="float:left"><img src="https://static.igem.org/mediawiki/2011/c/cf/%EC%9B%8C%ED%81%AC%EC%83%BE4.png" hspace=30></p><p style="justify">We organized a 2-day workshop in the July 26th-27th. The majority of the participants were professors, researchers and graduate students. We discussed about our iGEM idea and current topics in synthetic biology. It was honor for we undergraduates to do presentation in front of the synthetic biology experts.</font></font></p><br />
</img><br />
</font></body><br />
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<center><font size=7><font color=cc0099><b>Biosafety</b></font></font><br/><br/></center><br/><br/><br />
<font size=4 color=maroon><br />
1. Would any of your project ideas raise safety issues in terms of:<br/><br />
• <b>Researcher Safety</b>: All genetic manipulations related to this project are made in benign, non-pathogenic lab strains of <i>E. coli</i>. Students enrolled in this project had been previously educated to follow the preliminary laboratory safety rules. <br/><br />
• <b>Public and Environmental Safety</b>: Laboratory wastes are properly decontaminated before disposal. <br/><br/><br />
2. Do any of the new BioBrick™ parts (or devices) that you made this year raise any safety issues? <br/><br />
• The new biobrick parts which we are planning to make this year would not raise any safety issues. <br/><br/><br />
3. Is there a local biosafety group, committee, or review board at your institution? <br/><br />
• Though there is no special committee dedicated for Biosafety, we do have a general laboratory safety committee. The general laboratory safety committee also handles issues related to biosafety.<br/><br/><br />
4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering? <br/><br />
• Genes could be constructed such that they require several specific prerequisites to function properly, and that these prerequisites are not attainable elsewhere but in lab. The biobrick part that we are planning for would be one best example of this kind. </font><br/><br/><br/><br />
<br />
<font size=6><font color=cc0066><b>Probability</b></font><br/><br/><br />
<font size=4 color=maroon><br />
1. Could there be an unplanned event or series of events involving your project, resulting in either death, injury, occupational illness, damage to equipment or property, or damage to the environment? How likely is that going to happen? <br/><br />
• The probability of an unexpected accident is very less as the laboratory is well-maintained and periodically checked to ensure its safety.<br/><br/><br />
2. Does your project require the exposure or release of the engineered organism to people or the environment (e.g. as medicine, for bioremediation)<br/><br />
• Our device is purely constructed for a closed system. Our biobrick device is engineered with a environmental cue triggerable suicide cassette that would kill the device on exposure to environment. </font><br/><br/><br/><br />
<br />
<br />
<font size=6><b><font color=cc0066>Hazard</b></font><br/><br/><br />
<font size=4 color=maroon><br />
1. Could your device, when working properly, represent a hazard to people or the environment? <br/><br />
• It is less likely that our device would represent a hazard to people or environment.<br/><br/><br />
2. Is your engineered organism infectious? Does it produce a toxic product? Does it interfere with human physiology or the environment? <br/><br />
• No: The organism used is a benign lab strain of <i>E. coli</i> and is not infectious, does not produce toxic products, and does not interfere with human physiology or the environment. <br/><br/><br />
3. What would happen if one or several bioparts change their function or stop working as intended (e.g. through mutation)? How would the whole device or system change its properties and what unintended effects would result thereof? <br/><br />
• In case of failure of the device, there would probably be no unintended effects.<br/><br/><br />
4. What unintended effects could you foresee after your engineered organism is released to the environment? <br/><br />
• In case of release into the environment, our engineered organism would kill itself. Hence would not pose any environmental hazard.<br/><br/><br />
5. Try to think outside the box, what is the absolute worst case scenario for human health or the environment, that you could imagine? <br/><br />
• Since, we are trying to engineer a cell lysis system, we would assure that there would be no hazard to human health or environment.<br />
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<center><font size=6><font color=cc0099><b>Biosafety</b></font></font><br/><br/></center><br/><br/><br />
<font size=4 color=maroon><br />
1. Would any of your project ideas raise safety issues in terms of:<br/><br />
• <b>Researcher Safety</b>: All genetic manipulations related to this project are made in benign, non-pathogenic lab strains of <i>E. coli</i>. Students enrolled in this project had been previously educated to follow the preliminary laboratory safety rules. <br/><br />
• <b>Public and Environmental Safety</b>: Laboratory wastes are properly decontaminated before disposal. <br/><br/><br />
2. Do any of the new BioBrick™ parts (or devices) that you made this year raise any safety issues? <br/><br />
• The new biobrick parts which we are planning to make this year would not raise any safety issues. <br/><br/><br />
3. Is there a local biosafety group, committee, or review board at your institution? <br/><br />
• Though there is no special committee dedicated for Biosafety, we do have a general laboratory safety committee. The general laboratory safety committee also handles issues related to biosafety.<br/><br/><br />
4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering? <br/><br />
• Genes could be constructed such that they require several specific prerequisites to function properly, and that these prerequisites are not attainable elsewhere but in lab. The biobrick part that we are planning for would be one best example of this kind. </font><br/><br/><br/><br />
<br />
<font size=6><font color=cc0066><b>Probability</b></font><br/><br/><br />
<font size=4 color=maroon><br />
1. Could there be an unplanned event or series of events involving your project, resulting in either death, injury, occupational illness, damage to equipment or property, or damage to the environment? How likely is that going to happen? <br/><br />
• The probability of an unexpected accident is very less as the laboratory is well-maintained and periodically checked to ensure its safety.<br/><br/><br />
2. Does your project require the exposure or release of the engineered organism to people or the environment (e.g. as medicine, for bioremediation)<br/><br />
• Our device is purely constructed for a closed system. Our biobrick device is engineered with a environmental cue triggerable suicide cassette that would kill the device on exposure to environment. </font><br/><br/><br/><br />
<br />
<br />
<font size=6><b><font color=cc0066>Hazard</b></font><br/><br/><br />
<font size=4 color=maroon><br />
1. Could your device, when working properly, represent a hazard to people or the environment? <br/><br />
• It is less likely that our device would represent a hazard to people or environment.<br/><br/><br />
2. Is your engineered organism infectious? Does it produce a toxic product? Does it interfere with human physiology or the environment? <br/><br />
• No: The organism used is a benign lab strain of <i>E. coli</i> and is not infectious, does not produce toxic products, and does not interfere with human physiology or the environment. <br/><br/><br />
3. What would happen if one or several bioparts change their function or stop working as intended (e.g. through mutation)? How would the whole device or system change its properties and what unintended effects would result thereof? <br/><br />
• In case of failure of the device, there would probably be no unintended effects.<br/><br/><br />
4. What unintended effects could you foresee after your engineered organism is released to the environment? <br/><br />
• In case of release into the environment, our engineered organism would kill itself. Hence would not pose any environmental hazard.<br/><br/><br />
5. Try to think outside the box, what is the absolute worst case scenario for human health or the environment, that you could imagine? <br/><br />
• Since, we are trying to engineer a cell lysis system, we would assure that there would be no hazard to human health or environment.<br />
</font></font><br />
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<br/><br/><br />
<b><font size="6"><font color=cc0099><center>DATA PAGE</b></font></font><br/><br/></center><br />
<p align="justify"><font color=maroon>This page lists the parts which we constructed, improved or used unmodified in our project.<br/><br/></p></font><br />
<br/><br/><br/><br/><br />
<b><font size="5"><font color=cc0066>How does our system works:</b></font></font><br/><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2a/SKL20.png" width="400" height="300"/></center><br/><br/><br />
<br />
<b><font size="5"><font color=cc0066>Data for our favorite new part</b></font></font><br/><br/><br />
<font color=maroon><br />
<p align="justify">1.<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a>- A basic bio-brick part that would help our Chop. coli to sense the temperature of the environment.Fermentor and incubators will be at 37 ⁰C and the environment will be usually 25-30⁰C. The temperature dependent ribo-switch present in this part will prevent inhibit translation at 37⁰C and favor translation at temperatures less than 30⁰C. <br/><br/></p><br />
<p align="justify">2. <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>- It is a composite biobrick part that could be used along with the light receptor, Cph8 and reporter genes expressed under fim inversion promoter systems. However, due to the higher leaky level of Pompc this system was not able to perform as expected.<br/><br/><br/><br/></p><br />
<br />
<b><font size="5"><font color=cc0066>Data for pre-existing bio-brick part</b></font></font><br/><br/><br />
<br />
<p align="justify"><a href="http://partsregistry.org/Part:BBa_K592000:Experience"><b>BBa_K592000</b></a> and <a href="http://partsregistry.org/Part:BBa_K081017:Experience"><b>BBa_K508107</b></a>- We reduced the leaky level of the light receptor by controlling the expression of the transcription repressor, cI, through light. This system would help us regulate multiple genes (that are expressed from cI regulated promoters) simultaneously with a single light input. We also report the presence of cross talk between the light receptor and the osmo-regulatory response regulator.<br/><br/><br/><br/><br />
</p><br />
<b><font size="5"><font color=cc0066>We’ve also characterized the following biobrick parts</b></font></font><br/><br/><br />
<br />
<p align="justify"> <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>- It is the last segment of a composite biobrick composed of the light receptors, Cph8 and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>. The reporter gene expressed from this biobrick is the genes for DpnI enzymes (originally belongs to <i>Streptococcus pneumonia</i>). However, we could not see the complete digestion of the DNA in darkness. We suspect that the expression level might not sufficient to digest the entire DNA. We are trying to optimize the RBS of these genes to favor higher expression and complete digestion of the genomic DNA. <br />
Biobricks parts under construction</p><br />
<p align="justify">We are trying to clone the DpnI enzymes under PBAD promoter in order to optimize its RBS and the expression level. But we could not accomplish this on time.</p><br />
</font><br />
</body><br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/experiment/data_sheetTeam:UNIST Korea/experiment/data sheet2011-10-04T17:13:43Z<p>Lyl: </p>
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<br/><br/><br />
<b><font size="6"><font color=cc0099><center>DATA PAGE</b></font></font><br/><br/></center><br />
<p align="justify">This page lists the parts which we constructed, improved or used unmodified in our project.<br/><br/></p><br />
<br/><br/><br/><br/><br />
<b><font size="5"><font color=cc0066>How does our system works:</b></font></font><br/><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2a/SKL20.png" width="400" height="300"/></center><br/><br/><br />
<br />
<b><font size="5"><font color=cc0066>Data for our favorite new part</b></font></font><br/><br/><br />
<font color=maroon><br />
<p align="justify">1.<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a>- A basic bio-brick part that would help our Chop. coli to sense the temperature of the environment.Fermentor and incubators will be at 37 ⁰C and the environment will be usually 25-30⁰C. The temperature dependent ribo-switch present in this part will prevent inhibit translation at 37⁰C and favor translation at temperatures less than 30⁰C. <br/><br/></p><br />
<p align="justify">2. <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>- It is a composite biobrick part that could be used along with the light receptor, Cph8 and reporter genes expressed under fim inversion promoter systems. However, due to the higher leaky level of Pompc this system was not able to perform as expected.<br/><br/><br/><br/></p><br />
<br />
<b><font size="5"><font color=cc0066>Data for pre-existing bio-brick part</b></font></font><br/><br/><br />
<br />
<p align="justify"><a href="http://partsregistry.org/Part:BBa_K592000:Experience"><b>BBa_K592000</b></a> and <a href="http://partsregistry.org/Part:BBa_K081017:Experience"><b>BBa_K508107</b></a>- We reduced the leaky level of the light receptor by controlling the expression of the transcription repressor, cI, through light. This system would help us regulate multiple genes (that are expressed from cI regulated promoters) simultaneously with a single light input. We also report the presence of cross talk between the light receptor and the osmo-regulatory response regulator.<br/><br/><br/><br/><br />
</p><br />
<b><font size="5"><font color=cc0066>We’ve also characterized the following biobrick parts</b></font></font><br/><br/><br />
<br />
<p align="justify"> <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>- It is the last segment of a composite biobrick composed of the light receptors, Cph8 and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>. The reporter gene expressed from this biobrick is the genes for DpnI enzymes (originally belongs to <i>Streptococcus pneumonia</i>). However, we could not see the complete digestion of the DNA in darkness. We suspect that the expression level might not sufficient to digest the entire DNA. We are trying to optimize the RBS of these genes to favor higher expression and complete digestion of the genomic DNA. <br />
Biobricks parts under construction</p><br />
<p align="justify">We are trying to clone the DpnI enzymes under PBAD promoter in order to optimize its RBS and the expression level. But we could not accomplish this on time.</p><br />
</font><br />
</body><br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/experiment/data_sheetTeam:UNIST Korea/experiment/data sheet2011-10-04T17:11:39Z<p>Lyl: </p>
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<b><font size="6"><font color=cc0099>DATA PAGE</b></font></font><br/><br/><br />
<p align="justify">This page lists the parts which we constructed, improved or used unmodified in our project.<br/><br/></p><br />
<br/><br/><br />
<b><font size="5"><font color=cc0066>How does our system works:</b></font></font><br/><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2a/SKL20.png" width="400" height="300"/></center><br/><br/><br />
<br />
<b><font size="5"><font color=cc0066>Data for our favorite new part</b></font></font><br/><br/><br />
<font color=maroon><br />
<p align="justify">1.<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a>- A basic bio-brick part that would help our Chop. coli to sense the temperature of the environment.Fermentor and incubators will be at 37 ⁰C and the environment will be usually 25-30⁰C. The temperature dependent ribo-switch present in this part will prevent inhibit translation at 37⁰C and favor translation at temperatures less than 30⁰C. <br/><br/></p><br />
<p align="justify">2. <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>- It is a composite biobrick part that could be used along with the light receptor, Cph8 and reporter genes expressed under fim inversion promoter systems. However, due to the higher leaky level of Pompc this system was not able to perform as expected.<br/><br/></p><br />
<b><font size="5"><font color=cc0066>Data for pre-existing bio-brick part</b></font></font><br/><br/><br />
<br />
<p align="justify"><a href="http://partsregistry.org/Part:BBa_K592000:Experience"><b>BBa_K592000</b></a> and <a href="http://partsregistry.org/Part:BBa_K081017:Experience"><b>BBa_K508107</b></a>- We reduced the leaky level of the light receptor by controlling the expression of the transcription repressor, cI, through light. This system would help us regulate multiple genes (that are expressed from cI regulated promoters) simultaneously with a single light input. We also report the presence of cross talk between the light receptor and the osmo-regulatory response regulator.<br/><br/> </p><br />
<b><font size="5"><font color=cc0066>We’ve also characterized the following biobrick parts</b></font></font><br/><br/><br />
<br />
<p align="justify"> <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>- It is the last segment of a composite biobrick composed of the light receptors, Cph8 and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>. The reporter gene expressed from this biobrick is the genes for DpnI enzymes (originally belongs to <i>Streptococcus pneumonia</i>). However, we could not see the complete digestion of the DNA in darkness. We suspect that the expression level might not sufficient to digest the entire DNA. We are trying to optimize the RBS of these genes to favor higher expression and complete digestion of the genomic DNA. <br />
Biobricks parts under construction</p><br />
<p align="justify">We are trying to clone the DpnI enzymes under PBAD promoter in order to optimize its RBS and the expression level. But we could not accomplish this on time.</p><br />
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July 5- We took a tour of the lab, learnt basic laboratory safety rule and learnt basic techniques like how to prepare LB-Medium, how to use the autoclave.<br/><br />
We inoculated <i>E. coli</i> strain SCS110 so that we will make competent cell tomorrow. We also prepared ice coldwater and glycerol for tomorrow’s experiment.<br/><br/><br/><br />
July 6- We learnt how to make Electro Competent Cell. <br/> While JaeSung and Eeseul were busy making Comp cell, Bokeun and YuLim were busy setting PCR and recovering Biobrick Parts<br/>. We made a list of the biobrick parts we would use in our experiment and we tried to recover those plasmids from the DNA kit box we obtained from iGEM. <br/><br/><br/><br />
July 7- We saw pretty colonies on our plates we made yesterday. We failed to recover all of the biobrick parts we aimed for. So, we tried to recover them once again. We also have transformed the pSIM5 plasmid carrying the lambda red system into SCS110 to perform gene knockout. <br/><br />
Then our instructor, Vinu tried to explain us the use of lambda red system for gene knockouts. We were excited with the function of exo, gamma and beta proteins. We inoculated SCS110 pSIM5 cells for tomorrow’s experiment. Eeseul made a PCR product that is to be used to knockout our target gene. <br/><br/><br/><br />
July 8- We tried to knock out gene. SCS110 is a comparatively slow growing cell. It was funny to induce cells at 42⁰C and immediately cooling them and making electrocompetent for transformation. <br/><br/><br/><br />
July 9- We were excited to see tiny small colonies on our Kanamycin plates. We went ahead to do a colony PCR to check for the true deletion. At the end of the day, we confirmed that we have deleted our gene, EnvZ. We were so excited because now we can make our <i>E. coli</i> to sense light. Our instructor advised us to remove the kanamycin cassette before we proceed to check the light sensing ability. <br/><br/><br/><br />
July 11- We inoculated the SCS110 ∆envZ strains to make competent cell and transform pCP20 plasmid, which would help us to remove the kanamycin cassette. <br/><br/><br/><br />
July 12, we failed to remove the kanamycin cassette. Our instructor advised us to try it again.<br />
We tried again. Eeseul got a lot of stress in removing the kanamycin cassette. So YuLim tried to remove the kanamycin cassette. <br/><br/><br/><br />
July 13, YuLim also failed to remove the kanamycin cassette. Vinu advised us to give up this strain, as the plasmid pCP20 may not be compatible with SCS110 host strain. So we decided to use MG1655. We inoculated MG1655 pSIM5 strain to delete kanamycin cassette. <br/><br/><br/><br />
July 14, Eeseul tried to delete envZ gene in MG1655. JaeSung and Bokeun were busy writing Safety rule and Abstract which is due for tomorrow. YuLim and Vinu tried to isolate the genomic DNA from Streptococcus which they will use it to amplify the Dpn cassette. It was little hard and a long boring procedure as it is a gram-positive bacterium. But, finally they got a good yield. <br/><br/><br/><br />
July 16, We were busy learning the Vector NTI program in order to design our primers. It was little hard at the beginning but we started mastering it soon. <br/><br/><br/><br />
July 18, We were still busy designing primers for our future experiments. Primers for Gibson’s Assembly was little difficult. We took care of adding RBS and additional bases for restriction sites. Finally at the end of the day almost all of our primers were being designed. Now, our instructor will check our primers and place an order for our primers. <br/><br/><br/><br />
July 21- Our primers have come. Our instructor explained us the ways to process our primers. JaeSung went crazy about the calculation and finally Bokeun helped him fix his problem. <br />
Everybody rushed to set our PCRs. YuLim got all of her holin genes successfully. But she failed to get her Dpn PCR product. Vinu suggested that she should try a gradient PCR. So, she went ahead to set a gradient PCR. <br/><br/><br/><br />
July 22, YuLim still failed to get her PCR product. Vinu suggested Dpn digestion of the genomic DNA itself to confirm if Streptococcus DNA we had really has a Dpn gene. To our suspicion, Streptococcus DNA was digested by Dpn suggesting it has no Dpn. Vinu tried to place order for another Streptococcus strain from KCTC. Bokeun went ahead to clone his fimE gene into a plasmid pACYC. <br/><br/><br/><br />
July 23, Bokeun and JaeSung are done with their cloning, they luckily got one colony, and that had their target gene inserted. <br />
Bokeun was extremely excited with it. We transformed 3 plasmids (light receptors, fimE and GFP) into one strain.<br />
JaeSung went on to check the expression of mRNA at different temperatures. The preliminary result was promising and he was able to see some difference based on the temperature. <br/><br/><br/><br />
July 25- JaeSung went on to screen for the cells Bokeun made to find one cell, which carries all 3 plasmids. He used TECAN microplate reader to screen for the cell. Finally he got one colony that contains all 3 plasmids. So, he streaked it on a plate. <br/><br/><br/><br />
July 26, JaeSung’s plate was completely green the next day. Then we realized that TECAN is dark. So, in our cell darkness lead to fimE expression which in turn inverted all of the promoters of GFP making GFP expression constitutive. So, we learnt that we should take care of darkness when we use fimE system. <br/><br/><br/><br />
July 27-29- We went for a workshop on Climate Change. We explained the audience about iGEM and our goal. We were explaining our project for the first time to a group of people. We were excited with that. We celebrated the day with alcohol. <br/><br/><br/><br />
August 1- We deleted the envZ gene and integrated cI gene into the chromosome of MG1655 using lambda red system. <br/><br/><br/><br />
August 3, We tried to transform the light sensing biobricks and the reporter gene into the envZ deleted strain<br/><br/><br/><br />
August 10, Our strain containing the light plasmid and reporter plasmids are ready. We made a quick check of its functionality in the presence and absence of light. <br/><br/><br/><br />
August 13, We got the new Streptococcus DNA and successfully amplified the Dpn genes. Gibson’s assembly works very well. <br/><br/><br/><br />
August 16, YuLim completed cloning Holin and Dpn into a plasmid without the prmoter. <br/><br/><br/><br />
August 17, YuLim went on to put the promoters in front of Holin and Dpn. She has two kinds of promoter one is a inversion promoter, ptrc* and another is a Constitutive Promoter. She is aware that it is not as easy to clone the promoters, as it was to clone the genes. She was causing in using specific strains for each promoters. (pL promoter into ECNR2; Dpn into SCS110). <br/><br/><br/><br />
September 4- Eeseul repeated the mRNA-GFP. However, she had difficulty in understanding the GFP expression as she made a temperature shift at the early log phase. She had to deal with a slow growing and fast growing strain. So, she gave up the experiment as she could not predict her output and even the control was not as expected. Bokeun tried to check the effect of different concentration of glucose on the light receptor. He could see a good cross talk of the light and the osmo-regulator. <br/><br/><br/><br />
September 5- JaeSung repeated the mRNA experiment even when his control gave good result. He could not see any difference in GFP expression with temperature dependent riboswitch. <br/><br/><br/><br />
September 7- JaeSung tried to check the effect of light on cI expression by following GFP expression every one hour. After one day of tiresome experiment, he got a very good result. <br/><br/><br/><br />
September 8, We had a deep discussion on Synthetic Biology and iGEM to Science Specialized High Schools in Korea and in Singapore. <br/><br/><br/><br />
September 11, Eeseul tried to check the effect of cross-talk between the osmo-regulator and the light receptor using salt. She found no cross-talk with salt. YuLim was almost done with her cloning of Holin and Dpn cassette. Now she is ready to check their functionality. <br/><br/><br/><br />
September 18- Bokeun and Eeseul tried to prove the cross-talk using various sugars such as Arabinose and Glucose. They found a similar pattern even when they used arabinose or glucose. <br/><br/><br/><br />
September 21- We had a group presentation with all members of our department. It was our first official presentation. We were excited and we got many good feed backs. <br/><br/><br/><br />
September 22- We were busy making our websites and documenting the results. We were aware that the wiki would freeze soon. <br/><br/><br/><br />
September 23- We went on to clone Holin and Dpn under the control of pBAD promoter as the light promoter did not work<br/><br/><br/><br />
September 28 We cloned the riboswitch regulated GFP into pTrc promoter to check for a significant change in GFP with temperature. We still could not see any significant changes in GFP. <br/><br/><br/><br />
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<font size=6><font color=cc0099><center>Future work & Application</center></font></font><br/><br/><br />
<font size=3 color=maroon><br />
<p align="justify">In the future our first effort will be to optimize the lysis module such that the Dpn enzymes are efficiently exploited by the synthetic microbes to eradicate its genetic material in a non-native environment. <br/> <br/><br />
On top of this, UNIST team will also introduce more controlled system into <i>E.coli</i> so that it can be more safe to the environment and easy to be handled in the laboratory. <br/> <br/></p><br />
<br />
<p align="justify">We would like to introduce the following components into our <i>Chop. coli</i> in order to achieve our goal<br/><br />
<center><b><font color=cc0066><font size=5>Second light receptor&nbsp;&nbsp;&&nbsp;&nbsp;Quorum Sensing System</font></b></font></center><br/><br/></p><br />
<br />
<br />
<p align="justify">Two light signals before lysis would help in providing a more tight control and ensure that the device would still work even when one of them is mutated.Our team will also introduce a fourth sensing module to the <i>Chop. coli</i> using the <b><font size=4><font color=brown>quorum sensing system</font></b></font>. In case of fermentor <i>E. coli</i> will experience its native original quorum sensing molecule, AI2 <br />
UNIST team is going to make that engineer <i>E.coli</i> to recognize different quorum sensing molecules such as AHL to differentiate between the fermentor and the real world.<br />
This system will also help achieve an effective and tight control of lysis device. </br><br />
<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/d/d5/SKL30.png" width="500" height="500"/><br />
</center><br/><br />
<center><b>Figure explaining the future appearance of <i>Chop. coli</i></b></center><br />
<br />
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<font size=3 color=maroon><br />
<p align="justify">In the future our first effort will be to optimize the lysis module such that the Dpn enzymes are efficiently exploited by the synthetic microbes to eradicate its genetic material in a non-native environment. <br/> <br/><br />
On top of this, UNIST team will also introduce more controlled system into <i>E.coli</i> so that it can be more safe to the environment and easy to be handled in the laboratory. <br/> <br/></p><br />
<br />
<p align="justify">We would like to introduce the following components into our <i>Chop. coli</i> in order to achieve our goal<br/><br/><br />
<center><b><font color=cc0066><font size=5>Second light receptor&nbsp;&nbsp;&&nbsp;&nbsp;Quorum Sensing System</font></b></font></center><br/><br/></p><br />
<br />
<br />
<p align="justify">Two light signals before lysis would help in providing a more tight control and ensure that the device would still work even when one of them is mutated.Our team will also introduce a fourth sensing module to the <i>Chop. coli</i> using the <b><font size=4><font color=brown>quorum sensing system</font></b></font>. In case of fermentor <i>E. coli</i> will experience its native original quorum sensing molecule, AI2 <br />
UNIST team is going to make that engineer <i>E.coli</i> to recognize different quorum sensing molecules such as AHL to differentiate between the fermentor and the real world.<br />
This system will also help achieve an effective and tight control of lysis device. </br><br />
<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/d/d5/SKL30.png" width="500" height="500"/><br />
</center><br/><br />
<center><b>Figure explaining the future appearance of <i>Chop. coli</i></b></center><br />
<br />
</font><br />
<br />
<br />
</body><br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/project/future_workTeam:UNIST Korea/project/future work2011-10-04T17:04:03Z<p>Lyl: </p>
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<font size=6><font color=cc0099>Future work & Application</font></font><br/><br/><br />
<font size=3 color-maroon><br />
<p align="justify">In the future our first effort will be to optimize the lysis module such that the Dpn enzymes are efficiently exploited by the synthetic microbes to eradicate its genetic material in a non-native environment. <br/> <br/><br />
On top of this, UNIST team will also introduce more controlled system into <i>E.coli</i> so that it can be more safe to the environment and easy to be handled in the laboratory. <br/> <br/></p><br />
<br />
<p align="justify">We would like to introduce the following components into our <i>Chop. coli</i> in order to achieve our goal<br/><br/><br />
<center><b><font color=cc0066><font size=6>Second light receptor</font></font></b></center><br/><br/><br />
<center><b><font color=cc0066><font size=5>Quorum Sensing System</font></b></font></center><br/><br/></p><br />
<br />
<br />
<p align="justify">Two light signals before lysis would help in providing a more tight control and ensure that the device would still work even when one of them is mutated.Our team will also introduce a fourth sensing module to the <i>Chop. coli</i> using the <b><font size=4><font color=brown>quorum sensing system</font></b></font>. In case of fermentor <i>E. coli</i> will experience its native original quorum sensing molecule, AI2 <br />
UNIST team is going to make that engineer <i>E.coli</i> to recognize different quorum sensing molecules such as AHL to differentiate between the fermentor and the real world.<br />
This system will also help achieve an effective and tight control of lysis device. </br><br />
<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/d/d5/SKL30.png" width="500" height="500"/><br />
</center><br/><br />
<center><b>Figure explaining the future appearance of <i>Chop. coli</i></b></center><br />
<br />
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</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/project/Judging_FormTeam:UNIST Korea/project/Judging Form2011-10-04T17:02:32Z<p>Lyl: </p>
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<font size="6"><font color="cc0066"><center>JUDGING FORM</font></font><br/><br/><br />
<p align="left"><font color=maroon> We believe our team deserves a <font color="red"><font size="4"><b> GOLD </font></b></font>medal <br />
<br />
because we met the following criteria <br/><br/><br/><br/><br />
<br />
<font size="5" font color="red"><b>Requirements for a Bronze Medal: </b><br/></font><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Register the team, have a great summer, and plan to have fun at the Regional Jamboree. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Successfully complete and submit this iGEM 2011 Judging form. <br/><br/><br />
<br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Create and share a Description of the team's project using the iGEM wiki and the team's parts using the Registry of Standard Biological Parts. <br/><br/> <br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/> Plan to present a Poster and Talk at the iGEM Jamboree. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Standard Biological Parts. <br/><br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Submit DNA for at least one new BioBrick Part or Device to the Registry. <br/><br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br/><br/><br />
<br />
<br />
<font size="5" font color="red"><b>Requirements for a Silver Medal: </b><br/></font><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected; characterize the operation of your new part/device. <br/><br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Enter this information and other documentation on the part's 'Main Page' section of the Registry <br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br/><br/><br />
<br />
<br />
<font size="5" font color="red"><b>Requirements for a Gold Medal:</b> <br/></font><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Improve an existing BioBrick Part or Device and enter this information back on the Experience Page of the Registry. <br/> <br/><br />
Part Number(s): <a href="http://partsregistry.org/Part:BBa_K592000:Experience"><b>BBa_K592000</b></a>,<br />
,<a href="http://partsregistry.org/Part:BBa_K081017:Experience"><b>BBa_K508107</b></a><br />
<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system. <br/><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation. <br/><br/></font></p><br />
<br />
<br />
<br />
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<body style="background:#F5F5DC"><br />
<p style="color:black;background-color:#F5F5DC;"><br/><br/><br />
<font size="6"><font color="cc0066"><center>JUDGING FORM</font></font><br/><br/><br />
<p align="left"><font color=maroon> We believe our team deserves a <font color="red"><font size="4"><b> GOLD </font></b></font>medal <br />
<br />
because we met the following criteria <br/><br/><br/><br/><br />
<br />
<font color="red"><b>Requirements for a Bronze Medal: </b><br/></font><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Register the team, have a great summer, and plan to have fun at the Regional Jamboree. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Successfully complete and submit this iGEM 2011 Judging form. <br/><br/><br />
<br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Create and share a Description of the team's project using the iGEM wiki and the team's parts using the Registry of Standard Biological Parts. <br/><br/> <br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/> Plan to present a Poster and Talk at the iGEM Jamboree. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Standard Biological Parts. <br/><br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Submit DNA for at least one new BioBrick Part or Device to the Registry. <br/><br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br/><br/><br />
<br />
<br />
<font color="red"><b>Requirements for a Silver Medal: </b><br/></font><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected; characterize the operation of your new part/device. <br/><br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Enter this information and other documentation on the part's 'Main Page' section of the Registry <br/><br />
Part Number(s): <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>,<br />
,<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a><br />
<br/><br/><br/><br/><br />
<br />
<br />
<font color="red"><b>Requirements for a Gold Medal:</b> <br/></font><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Improve an existing BioBrick Part or Device and enter this information back on the Experience Page of the Registry. <br/> <br/><br />
Part Number(s): <a href="http://partsregistry.org/Part:BBa_K592000:Experience"><b>BBa_K592000</b></a>,<br />
,<a href="http://partsregistry.org/Part:BBa_K081017:Experience"><b>BBa_K508107</b></a><br />
<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system. <br/><br/><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="27" height="27"/>Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation. <br/><br/></font></p><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
</body><br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/project/abstractTeam:UNIST Korea/project/abstract2011-10-04T16:56:51Z<p>Lyl: </p>
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<font face=calibri color=cc0066 size="6">CHOp-Coli-LATE</font><br/><br/><br />
<p align="justify"><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/><br />
<font face=calibri color=maroon size="4"><br />
Recently, microbe-driven fermentation products are gaining increased importance. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/><br />
However, release of these microbes to the open environment would pose increasing threat to the society due to the possibility of changes expected in the indigenous microbial population and <b>horizontal gene transfer</b>.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Hence, we have engineered a synthetic self-killing system for the famous industrial workhorse, <i>Escherichia coli</i>. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>High temperature (37⁰C), native quorum sensing molecule (AI-2) and the darkness present in the fermentor will keep the self-killing system turned off.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Environmental signals such as low temperature (25 ⁰C), foreign quorum sensing molecules and light encountered by the <i>E. coli</i> outside of the fermentor would trigger the self-killing device. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Unlike other lysis device, we have introduced a novel self-killing device that chops up the DNA. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Thus, this system would not only favor cell death but also ensure that all the genetic materials are destroyed and guarantee that there would be no horizontal gene transfer</font><br/><br/><br />
</p><br />
<br />
<p><br />
<center><iframe width="520" height="415" src="http://www.youtube.com/embed/obMNlytEvBU" frameborder="0" allowfullscreen></iframe></center><br />
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<font size="6"><font color=cc0066><center>Synthetic Microbes</p></font></font><br/><br />
<p align="justify"><font size=4 color=maroon>Synthetic Microbes are gaining increased importance in 21 st century. Synthetic Microbes are more promising hosts for fuel production, bioremediation and many other potential processes. There is an increased dependence on the synthetic microbes even for certain basic needs such as medicine and fuels. However, synthetic microbes do not experience a warm welcome from the general public because they are believed to endanger the environment.Synthetic Microbes: <br/><br/></P><br />
<p align="left"><br />
<font size="5"><font color="Red">C</font></font>an escape from its restricted area and can<br />
<br/> <font size="5"><font color="Red">H</font></font>orizontally tranfer its genetic materials to pathogens leading to super bugs that can go <br/><br />
<font size="5"><font color="Red">O</font></font>ut of control of human and<br/><br />
<font size="5"><font color="Red">C</font></font>ause epidemics; can <br/><br />
<br />
<font size="5"><font color="Red">O</font></font>bdurately occupy the universe and can be a<br/><br />
<br />
<font size="5"><font color="Red">L</font></font>ethal biological weapon hence synthetic microbes are being <br/><br />
<font size="5"><font color="Red">A</font></font>bjured by the world as they<br/><br />
<font size="5"><font color="Red">T</font></font>hreaten the existing biodiversity and are believed to be <br/><br />
<font size="5"><font color="Red">E</font></font>nvironmentally damaging <font size="5"><font color="Red">ELYZIANS</font></font> <br/><br/></p><br/><br />
<br />
<br />
<font size="6"><font color="cc0066">DNA is two sides of the same coin</font></font><br/><br/><br />
<font size="4" color=maroon><br />
<p align="justify">All advances in synthetic biology is because of the tiny double helical molecule called <font size="5"><font color="Red">DNA</font></font>. All threats of synthetic biology is again because of these tiny molecules called <font size="5"><font color="Red">DNA</font></font>. Thus, DNA forms two sides of the same coin. <br /></font><br/><br/></font></p><br />
<br />
<br />
<font size="6"><font color=cc0066> Overview of CHOCOLATE</font></font><br/><br/><br />
<font size="4" color=maroon><br />
<p align="justify">CHOCOLATE project aims at eradicating the negative aspects of synthetic biology by exploiting the defence mechanism used by natural microbes to differentiate its genome from that of the foreign DNA. Natural microbes utilize a group of restriction enzymes like dam, dcm and dpn to diferentiate its DNA from that of the foreign DNA. We simply modified the host defence machanism such that the synthetic microbe would identify its genome as its native when it stays in its desired environment and the host defence will be switched OFF. However, when the synthetic microbe senses that it is in a non-native environment it would turn ON its host defence to destroy its own DNA and kill itself. Thus, this system would not only favor cell death but also ensure that all the genetic materials are destroyed and guarantee that there would be no horizontal gene transfer. </font></font><br />
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<font size="6"><font color=cc0066><center>Synthetic Microbes</p></font></font><br/><br />
<p align="justify"><font size=4 color=maroon>Synthetic Microbes are gaining increased importance in 21 st century. Synthetic Microbes are more promising hosts for fuel production, bioremediation and many other potential processes. There is an increased dependence on the synthetic microbes even for certain basic needs such as medicine and fuels. However, synthetic microbes do not experience a warm welcome from the general public because they are believed to endanger the environment.Synthetic Microbes: <br/><br/></P><br />
<p align="left"><br />
<font size="5"><font color="Red">C</font></font>an escape from its restricted area and can<br />
<br/> <font size="5"><font color="Red">H</font></font>orizontally tranfer its genetic materials to pathogens leading to super bugs that can go <br/><br />
<font size="5"><font color="Red">O</font></font>ut of control of human and<br/><br />
<font size="5"><font color="Red">C</font></font>ause epidemics; can <br/><br />
<br />
<font size="5"><font color="Red">O</font></font>bdurately occupy the universe and can be a<br/><br />
<br />
<font size="5"><font color="Red">L</font></font>ethal biological weapon hence synthetic microbes are being <br/><br />
<font size="5"><font color="Red">A</font></font>bjured by the world as they<br/><br />
<font size="5"><font color="Red">T</font></font>hreaten the existing biodiversity and are believed to be <br/><br />
<font size="5"><font color="Red">E</font></font>nvironmentally damaging <font size="5"><font color="Red">ELYZIANS</font></font> <br/><br/></p><br/><br />
<br />
<br />
<font size="6"><font color="cc0066">DNA is two sides of the same coin</font></font><br/><br/><br />
<font size="4" color=maroon><br />
<p align="justify">All advances in synthetic biology is because of the tiny double helical molecule called <font size="5"><font color="Red">DNA</font></font>. All threats of synthetic biology is again because of these tiny molecules called <font size="5"><font color="Red">DNA</font></font>. Thus, DNA forms two sides of the same coin. <br /></font><br/><br/></font></p><br />
<br />
<br />
<font size="6"><font color=cc0066> Overview of CHOCOLATE</font></font><br/><br/><br />
<font size="4" color=maroon><br />
<p align="justify">CHOCOLATE project aims at eradicating the negative aspects of synthetic biology by exploiting the defence mechanism used by natural microbes to differentiate its genome from that of the foreign DNA. Natural microbes utilize a group of restriction enzymes like dam, dcm and dpn to diferentiate its DNA from that of the foreign DNA. We simply modified the host defence machanism such that the synthetic microbe would identify its genome as its native when it stays in its desired environment and the host defence will be switched OFF. However, when the synthetic microbe senses that it is in a non-native environment it would turn ON its host defence to destroy its own DNA and kill itself. Thus, this system would not only favor cell death but also ensure that all the genetic materials are destroyed and guarantee that there would be no horizontal gene transfer. </font></font><br />
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<font size="6"><font color=cc3333><center>Synthetic Microbes</p></font></font><br/><br />
<p align="justify"><font size=4 color=maroon>Synthetic Microbes are gaining increased importance in 21 st century. Synthetic Microbes are more promising hosts for fuel production, bioremediation and many other potential processes. There is an increased dependence on the synthetic microbes even for certain basic needs such as medicine and fuels. However, synthetic microbes do not experience a warm welcome from the general public because they are believed to endanger the environment.Synthetic Microbes: <br/><br/></P><br />
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<font size="5"><font color="Red">C</font></font>an escape from its restricted area and can<br />
<br/> <font size="5"><font color="Red">H</font></font>orizontally tranfer its genetic materials to pathogens leading to super bugs that can go <br/><br />
<font size="5"><font color="Red">O</font></font>ut of control of human and<br/><br />
<font size="5"><font color="Red">C</font></font>ause epidemics; can <br/><br />
<br />
<font size="5"><font color="Red">O</font></font>bdurately occupy the universe and can be a<br/><br />
<br />
<font size="5"><font color="Red">L</font></font>ethal biological weapon hence synthetic microbes are being <br/><br />
<font size="5"><font color="Red">A</font></font>bjured by the world as they<br/><br />
<font size="5"><font color="Red">T</font></font>hreaten the existing biodiversity and are believed to be <br/><br />
<font size="5"><font color="Red">E</font></font>nvironmentally damaging <font size="5"><font color="Red">ELYZIANS</font></font> <br/><br/></p><br/><br />
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<br />
<font size="6"><font color="cc3333">DNA is two sides of the same coin</font></font><br/><br/><br />
<font size="4" color=maroon><br />
<p align="justify">All advances in synthetic biology is because of the tiny double helical molecule called <font size="5"><font color="Red">DNA</font></font>. All threats of synthetic biology is again because of these tiny molecules called <font size="5"><font color="Red">DNA</font></font>. Thus, DNA forms two sides of the same coin. <br /></font><br/><br/></font></p><br />
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<br />
<font size="6"><font color=cc3333> Overview of CHOCOLATE</font></font><br/><br/><br />
<font size="4" color=maroon><br />
<p align="justify">CHOCOLATE project aims at eradicating the negative aspects of synthetic biology by exploiting the defence mechanism used by natural microbes to differentiate its genome from that of the foreign DNA. Natural microbes utilize a group of restriction enzymes like dam, dcm and dpn to diferentiate its DNA from that of the foreign DNA. We simply modified the host defence machanism such that the synthetic microbe would identify its genome as its native when it stays in its desired environment and the host defence will be switched OFF. However, when the synthetic microbe senses that it is in a non-native environment it would turn ON its host defence to destroy its own DNA and kill itself. Thus, this system would not only favor cell death but also ensure that all the genetic materials are destroyed and guarantee that there would be no horizontal gene transfer. </font></font><br />
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<br/><br/><b><font size="7"><font color=cc0066><Center>RESULTS</font></b></font><br/><br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
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<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
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<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br/><br />
<b><font size="6"><font color=cc0066><center>SENSORY MODULE</b></font></font><br/><br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><font face=calibri color=red size="5"><center>Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br/><br />
<b><font size="6"><font color=cc0066><center>INFORMATION PROCESSING MODULE</b></font></font><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=cc0066><center>LYSIS MODULE</b></font></font><br/></p><br />
<p align="left">•We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
•Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
•However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
•Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
•Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
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<br/><br/><b><font size="6"><font color=cc0066><Center>RESULTS</font></b></font><br/><br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=cc0066><center>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><font face=calibri color=red size="5"><center>Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=cc0066><center>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=cc0066><center>LYSIS MODULE</b></font></font><br/><br/></p><br />
<p align="left">•We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
•Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
•However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
•Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
•Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
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<br/><br/><b><font size="6"><font color=sienna><Center>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna><center>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><font face=calibri color=red size="5"><center>Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna><center>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna><center>LYSIS MODULE</b></font></font><br/><br/></p><br />
<p align="left">•We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
•Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
•However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
•Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
•Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
<br />
</body><br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna><Center>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna><center>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><font face=calibri color=red size="5"><center>Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna><center>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna><center>LYSIS MODULE</b></font></font><br/><br/></p><br />
<p align="left">•We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
•Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
•However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
•Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
•Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
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</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/project/modulesTeam:UNIST Korea/project/modules2011-10-04T16:37:11Z<p>Lyl: </p>
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<br/><br/><br/><br/><b><font size="6"><font color=sienna><Center>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna><center>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><font face=calibri color=red size="5"><center>Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna><center>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna><center>LYSIS MODULE</b></font></font><br/><br/><br />
<left>•We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
•Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
•However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
•Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
•Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna><Center>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna><center>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><font face=calibri color=red size="5"><center>Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna><center>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna><center>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
<br />
</body><br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/project/modulesTeam:UNIST Korea/project/modules2011-10-04T16:34:03Z<p>Lyl: </p>
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
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<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><font face=calibri color=red size="5"><center>Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br/><br />
<br />
<font face=calibri color=red size="5"><center> Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
<br />
</body><br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br/><br />
<br />
<font face=calibri color=red size="5">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
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</body><br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna>Conclusion of sensory module: <i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br/><br />
<br />
<font face=calibri color=red size="5">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality</font><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna>Conclusion of processor module : <i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
<br />
</body><br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/project/modulesTeam:UNIST Korea/project/modules2011-10-04T16:29:09Z<p>Lyl: </p>
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna>Conclusion of sensory module: <i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br/><br />
<br />
<font face=calibri color=red size="5">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Light &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Osmolality<font/><br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna>Conclusion of processor module : <i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
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</body><br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna>Conclusion of sensory module: <i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br/><br />
<br />
<font face=calibri color=red size="5">&nbsp;&nbsp;&nbsp; Light &nbsp;&nbsp;&nbsp; Temperature &nbsp;&nbsp;&nbsp; Osmolality<br />
<br/><br/><br/><br/><br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna>Conclusion of processor module : <i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
<br />
</body><br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="5"><font color=sienna>Conclusion of sensory module: <i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br />
<br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="5"><font color=Sienna>Conclusion of processor module : <i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
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</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/project/modulesTeam:UNIST Korea/project/modules2011-10-04T16:17:40Z<p>Lyl: </p>
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
</img><br />
<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="6"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br />
<table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b><font size="4"><font color="red">Temperature</font></font></th><br />
<th><font size="5"><font color="red">Light</font></font></th><br />
<th><font size="5"><font color="red">Osmolality</font></font></th><br />
</tr></table><br/><br/><br />
<b><font size="6"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="4"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="6"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
<br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
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<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="6"><font color=sienna><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br />
<table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b><font size="4"><font color="red">Temperature</font></font></th><br />
<th><font size="5"><font color="red">Light</font></font></th><br />
<th><font size="5"><font color="red">Osmolality</font></font></th><br />
</tr></table><br/><br/><br />
<b><font size="4"><font color=sienna>INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color=sienna>fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color=sienna>cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="6"><font color=Sienna><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="4"><font color=Sienna>LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
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<br/><br/><br/><br/><b><font size="6"><font color=sienna>RESULTS</font></b></font><br/><br/><br />
<br />
<p align="justify"><font face=calibri color=maroon size="4">Our project aims at designing <i>E. coli</i> to sense its environment and act accordingly. In order to achieve this, we have categorized our projects into three main groups.<font/><br/> <br/></p><br />
<img src="https://static.igem.org/mediawiki/2011/2/2e/Siganl_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/8/8c/Process_module.png" width="250" height="300"><br />
<img src="https://static.igem.org/mediawiki/2011/6/6b/Lysis_module.png" width="250" height="300"><br />
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<br/><table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
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<th><b>Sensory Module</th><br />
<th>Processing Module</th><th>Lysis Module</th><br />
</tr></table><br/><br/><br/><br />
<b><font size="6"><font color=Sienna>SENSORY MODULE</b></font></font><br/><br/><br />
<br />
<p align="justify">We have engineered two different sensors into <i>E. coli</i>. The first sensor is an <font color="blue"><b>optical sensor</b></font> that detects the light present in the environment. We used Cph8, hybrid light receptor, as a optical sensor (Fig 1) [1]. The second sensor is to a <font color="blue"><b>physical sensor</b></font> that would sense the temperature of the environment. We used the temperature dependent ribo-switch as a physical sensor to detect the temperature of the environment (Fig 2) [2].<br/></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/1/1b/Picture1.png" width="400" height="300"/></center><br />
<p align="justify"><b>Figure 1 – Efficiency of the optical sensor was evaluated by following GFP expression in the presence and absence of light.</b></p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/c/c8/Picture2.jpg" width="700" height="300"/></center><br/><br />
<p align="justify"><b>Figure 2: The physical sensor engineered in <i>Chop. coli</i> helps it to differentiate between 30⁰C and 37⁰C when GFP was fused with the temperature dependent ribo-switch. </b><br/><br/></p><br />
<br />
<p align="justify">Being aware that fermentor is always maintained at 37⁰C, we assumed that the physical sensor would help <i>Chop. coli</i> to differentiate its environment. However, one cannot guarantee the presence of complete darkness in the fermentor. We hypothesized if the hybrid light receptor (hybrid of light receptor and osmo regulator) could also help determine the osmolarity. The fermentor is supposed to contain sugar at a higher concentration than the environment. As expected, the light receptor could sense high sugar concentration and behave similar to darkness in the presence of high sugar concentration. This would be an advantageous feature in <i>Chop. coli</i>. </p><br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2c/SKL12.png" width="800" height="300"/></center><br/><br />
<p align="justify"><b>Figure 3. The hybrid light receptor and osmo-regulator suffers from cross talk. Response to darkness was similar to its response to high concentration of sugar. This would be advantageous for <i>Chop. coli</i> as either high sugar concentration or darkness present in the fermentor will keep the cells from lysis.</b><br/><br/></p><br />
<center><b><font size="6"><font color="blue"><i>Chop. coli</i> can efficiently sense its environment</center></b></font></font><br/><br />
<table style="background-color:#F5F5DC;"><table width="75%" border="0"><br />
<tr><br />
<th><b><font size="4"><font color="red">Temperature</font></font></th><br />
<th><font size="5"><font color="red">Light</font></font></th><br />
<th><font size="5"><font color="red">Osmolality</font></font></th><br />
</tr></table><br/><br/><br />
<b><font size="4"><font color="blue">INFORMATION PROCESSING MODULE</b></font></font><br/><br/><br />
<p align="justify">After sensing the environment through optical and physical sensor, <i>Chop. coli </i>should process the information. We introduced two different processor system: fim inversion system and cI control system.<br/><br />
• <b><font color="blue">fim inversion system</font><br/></b><br />
Even though we were able to successfully construct and regulate fim inversion system using light, we were not able to control the basal fimE expression leading to the failure of this construct.<br/><br />
• <b><font color="blue">cI control system</font><br/></b><br />
As expected, the cI system was able to provide an efficient control of gene expression with light despite a background expression. To reduce the background further we integrated the cI expressed from Pompc into the chromosome of E. coli. Chromosomally encoded cI reduced the background expression further (Figure 4).<br/> <br/> </p><br />
<center><b><font size="6"><font color="blue"><i>Chop. coli</i> can efficiently process its signal</center></b></font></font><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/6/60/SKL13.png" width="500" height="300"/></center><br/><br />
<p align="justify"><b>Figure 4: The cI processor system was able to work efficiently independent of the phase at which the gene expression was induced.</b><br />
<br/><br/></p><br />
<p align="justify"><b><font size="4"><font color="blue">LYSIS MODULE</b></font></font><br/><br/><br />
• We used two different lysis module to in order to compare the efficiency of lysis module to eradicate the genetically modified organisms: Holin mediated cell lysis and DpnI mediated DNA damage.<br/><br />
• Initially we had problems in cloning both the holin and Dpn genes under PL promoter as it is a constitutive promoter and lead to rapid cell death. We finally accomplished cloning the lytic cassette using ECNR2 strain which expresses cI constitutively. <br/><br />
• However, neither of our lysis module was able to give us the expected result. We have already characterized individual components of our signal processing system such as the light receptor, temperature sensor and the cI processor using GFP output. <br/><br />
• Hence, we believe that the expression of the lysis system was not sufficient to demonstrate the expected outcome. We would like to optimize the expression of the lysis device by changing the strength of the RBS in order to prove the efficiency of our system.<br/><br />
• Currently, we are trying to express the lytic cassette genes from PBAD promoter. But we could not accomplish this on time. <br/></p><br />
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<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/><br />
<font face=calibri color=maroon size="4"><br />
Recently, microbe-driven fermentation products are gaining increased importance. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/><br />
However, release of these microbes to the open environment would pose increasing threat to the society due to the possibility of changes expected in the indigenous microbial population and <b>horizontal gene transfer</b>.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Hence, we have engineered a synthetic self-killing system for the famous industrial workhorse, <i>Escherichia coli</i>. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>High temperature (37⁰C), native quorum sensing molecule (AI-2) and the darkness present in the fermentor will keep the self-killing system turned off.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Environmental signals such as low temperature (25 ⁰C), foreign quorum sensing molecules and light encountered by the <i>E. coli</i> outside of the fermentor would trigger the self-killing device. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Unlike other lysis device, we have introduced a novel self-killing device that chops up the DNA. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Thus, this system would not only favor cell death but also ensure that all the genetic materials are destroyed and guarantee that there would be no horizontal gene transfer</font><br/><br/><br />
</p><br />
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<font face=calibri color=brown size="6">CHOp-Coli-LATE</font><br/><br/><br />
<p align="justify"><br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/><br />
<font face=calibri color=maroon size="5"><br />
Recently, microbe-driven fermentation products are gaining increased importance. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/><br />
However, release of these microbes to the open environment would pose increasing threat to the society due to the possibility of changes expected in the indigenous microbial population and <b>horizontal gene transfer</b>.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Hence, we have engineered a synthetic self-killing system for the famous industrial workhorse, <i>Escherichia coli</i>. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>High temperature (37⁰C), native quorum sensing molecule (AI-2) and the darkness present in the fermentor will keep the self-killing system turned off.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Environmental signals such as low temperature (25 ⁰C), foreign quorum sensing molecules and light encountered by the <i>E. coli</i> outside of the fermentor would trigger the self-killing device. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Unlike other lysis device, we have introduced a novel self-killing device that chops up the DNA. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Thus, this system would not only favor cell death but also ensure that all the genetic materials are destroyed and guarantee that there would be no horizontal gene transfer</font><br/><br/><br />
</p><br />
<br />
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Recently, microbe-driven fermentation products are gaining increased importance. <br/><br/><br />
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<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/><br />
However, release of these microbes to the open environment would pose increasing threat to the society due to the possibility of changes expected in the indigenous microbial population and <b>horizontal gene transfer</b>.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Hence, we have engineered a synthetic self-killing system for the famous industrial workhorse, <i>Escherichia coli</i>. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>High temperature (37⁰C), native quorum sensing molecule (AI-2) and the darkness present in the fermentor will keep the self-killing system turned off.<br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/> Environmental signals such as low temperature (25 ⁰C), foreign quorum sensing molecules and light encountered by the <i>E. coli</i> outside of the fermentor would trigger the self-killing device. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Unlike other lysis device, we have introduced a novel self-killing device that chops up the DNA. <br/><br/><br />
<br />
<img src="http://lornapblog.files.wordpress.com/2011/05/big-tick.jpg" width="32" height="32"/>Thus, this system would not only favor cell death but also ensure that all the genetic materials are destroyed and guarantee that there would be no horizontal gene transfer</font><br/><br/><br />
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<center><font face=calibri color=darkred size="6">UNIST_Korea Team Members<font/><br/><br/><br/><br />
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<center><img src="https://static.igem.org/mediawiki/2011/1/12/Songbogeon.jpg"width="200" height="200"><br/></center><br/><br/><br />
<br/><center>Ee Seul, Shin<br/><br />
<center><img src="https://static.igem.org/mediawiki/2011/b/b6/Shin.jpg"width="200" height="200"><br/><br/><br />
<br/><center>Yu-Lim, Lee<br />
<br/></center><br />
<center><img src="https://static.igem.org/mediawiki/2011/6/6e/Leeyoolim.jpg"width="200" height="200"><br/><br/><br/><br />
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<br/><center>Jae Sung, Yoo<br/><br />
<center><img src="https://static.igem.org/mediawiki/2011/b/b4/Leejaesung.png"width="200" height="200"><br/><br/><br/></center></font><br />
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<center><img src="https://static.igem.org/mediawiki/2011/b/b6/Shin.jpg"width="200" height="200"><br/><br/><br />
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<br/><center>Jae Sung, Yoo<br/><br />
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<br/><center><font face=calibri size="3">Professor Sung Kuk, Lee<br/><br />
<center><img src="https://static.igem.org/mediawiki/2011/7/7d/Sung-pic-1.jpg"width="200" height="200"><br/></center> <br/><br/><br />
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<center><img src="https://static.igem.org/mediawiki/2011/1/12/Songbogeon.jpg"width="200" height="200"><br/></center><br/><br/><br />
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<center><img src="https://static.igem.org/mediawiki/2011/b/b6/Shin.jpg"width="200" height="200"><br/><br/><br />
<br/><center>Yu-Lim, Lee<br/><br />
<br/></center><br />
<center><img src="https://static.igem.org/mediawiki/2011/6/6e/Leeyoolim.jpg"width="200" height="200"><br/><br/><br/><br />
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<br><br />
Dr. --- Y.K Cho<br/><br />
Associate Professor<br/><br />
School of NanoBiochemical Science<br/><br />
UNIST , Korea<br/><br />
Special Thanks to <br/><br />
<br />
1. Ryu, Young Shin<br/><br />
<br />
2. Euna<br/><br />
<br />
3. GooHee Kim<br/><br />
<br />
4. JMP<br/><br />
<br />
5. SH<br/><br />
<br />
6. Mo<br/><br />
<br />
7. Vinu<br/><br/><br />
<br />
<br />
<br />
We also thank all members of NBC for their kind support and solid encouragement<br />
<br />
<br />
</HTML></div>Lylhttp://2011.igem.org/Team:UNIST_Korea/human_practice/human_practiceTeam:UNIST Korea/human practice/human practice2011-10-04T13:38:06Z<p>Lyl: </p>
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<font face=calibri><font size="6">Human Practice</font><br />
<br/><br/><br />
<br />
Media Attention: We published an article in Korean language to introduce synthetic biology and iGEM competition to all universities in Korea. To do this we gathered a simple description of the projects of all 4 iGEM teams from South Korea (KAIST , KOREA UNIV. , CBNU, UNIST) and finally summarized it. We believe that this article would reach all universities of Korea and would motivate few other undergraduates to join hands for Synthetic Biology. Visit http://www.ksbb.or.kr/home/kor/ for more details.<br />
Attachment :iGEM_BT_news-v1.pdf</br></br></br><br />
<br />
<center><br />
<table border="1"><br />
<tr><br />
<th><img src="https://static.igem.org/mediawiki/2011/5/5f/%EC%B9%B4%EC%9D%B4%EC%8A%A4%ED%8A%B8.png"></th><br />
<th><img src="https://static.igem.org/mediawiki/2011/3/34/%EA%B3%A0%EB%A0%A4%EB%8C%80.png"></th></tr><br />
<tr><th>KAIST</th><th>KOREA</th></tr><br />
<tr><th><img src="https://static.igem.org/mediawiki/2011/9/99/%EC%B6%A9%EB%B6%81%EB%8C%80.png"></th><br />
<th><img src="https://static.igem.org/mediawiki/2011/e/e3/UNIST.png"></th></tr><br />
<tr><th>CBNU</th><th>UNIST</th></tr></table></center><br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br/><br/><br />
<br />
<font size="5">Sowing Synthetic Seeds in the Young Minds of High School Students</font><br/><br/><br />
On September 3rd, we organized a small symposium with high school students from Korea Science Academy and National University of Singapore. The students belonged to mathematics and science departments. We discussed future aspects of synthetic biology and its detailed applications for bio-fuel production. We believe that the seeds to harvest synthetic fruits should be laid even from the very young age. <br />
<br/><br/><br/><br/><br/><br/><br />
<br />
<br />
<font size="5">Special lecture on synthetic biology – August 24th </font><br/><br/><br />
We organized a special lecture on synthetic biology (Synthetic Biology : Advances and Threats) to non-biologists in UNIST Students from different departments like Electrical Engineering Department, Chemical Engineering Department, Technology management and Physics department were present at the session. We discussed the possible strategies we have to control the Genetically Modified Organisms when it is exposed to nature. After special lecture, we went to the pub and discussed a lot about the future of the world and the role of synthetic biology in designing the future! <br />
<br/><br/><br/><br/><br/><br/><br />
<br />
<br />
<font size="5">Elite Of Elites (Combination of Mathematicians, Physicist and Biologists)</font><br/><br/> <br />
On September 10th, we organized a co-seminar with EOE (Elite of Elites), Mathematics and Physics club in UNIST supported by Korean government, discussed about role of synthetic biology in future and the importance of mathematical modeling for gene regulation. We believe that a team of mathematicians, physicist and biologist would help in forming a flourishing synthetic organism. We believe that the complexity of life could be simplified with mathematical calculations and physical laws. More well-defined biological systems would also be offered a warmer welcome in the general public. <br/><br/><br/><br/><br/><br/><br />
<br />
<br />
<br />
<font size="5">Workshop – July 26th-27h </font></br></br><br />
We organized a 2-day workshop in the July 26th-27th. The majority of the participants were professors, researchers and graduate students. We discussed about our iGEM idea and current topics in synthetic biology. It was honor for we undergraduates to do presentation in front of the synthetic biology experts.</font></font><br />
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<font size=6><b>Biosafety</b></font><br/><br/><br />
<font size=4><br />
1. Would any of your project ideas raise safety issues in terms of:<br/><br />
• <b>Researcher Safety</b>: All genetic manipulations related to this project are made in benign, non-pathogenic lab strains of <i>E. coli</i>. Students enrolled in this project had been previously educated to follow the preliminary laboratory safety rules. <br/><br />
• <b>Public and Environmental Safety</b>: Laboratory wastes are properly decontaminated before disposal. <br/><br/><br />
2. Do any of the new BioBrick™ parts (or devices) that you made this year raise any safety issues? <br/><br />
• The new biobrick parts which we are planning to make this year would not raise any safety issues. <br/><br/><br />
3. Is there a local biosafety group, committee, or review board at your institution? <br/><br />
• Though there is no special committee dedicated for Biosafety, we do have a general laboratory safety committee. The general laboratory safety committee also handles issues related to biosafety.<br/><br/><br />
4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering? <br/><br />
• Genes could be constructed such that they require several specific prerequisites to function properly, and that these prerequisites are not attainable elsewhere but in lab. The biobrick part that we are planning for would be one best example of this kind. </font><br/><br/><br/><br />
<br />
<font size=6><b>Probability</b></font><br/><br/><br />
<font size=4><br />
1. Could there be an unplanned event or series of events involving your project, resulting in either death, injury, occupational illness, damage to equipment or property, or damage to the environment? How likely is that going to happen? <br/><br />
• The probability of an unexpected accident is very less as the laboratory is well-maintained and periodically checked to ensure its safety.<br/><br/><br />
2. Does your project require the exposure or release of the engineered organism to people or the environment (e.g. as medicine, for bioremediation)<br/><br />
• Our device is purely constructed for a closed system. Our biobrick device is engineered with a environmental cue triggerable suicide cassette that would kill the device on exposure to environment. </font><br/><br/><br/><br />
<br />
<br />
<font size=6><b>Hazard</b></font><br/><br/><br />
<font size=4><br />
1. Could your device, when working properly, represent a hazard to people or the environment? <br/><br />
• It is less likely that our device would represent a hazard to people or environment.<br/><br/><br />
2. Is your engineered organism infectious? Does it produce a toxic product? Does it interfere with human physiology or the environment? <br/><br />
• No: The organism used is a benign lab strain of <i>E. coli</i> and is not infectious, does not produce toxic products, and does not interfere with human physiology or the environment. <br/><br/><br />
3. What would happen if one or several bioparts change their function or stop working as intended (e.g. through mutation)? How would the whole device or system change its properties and what unintended effects would result thereof? <br/><br />
• In case of failure of the device, there would probably be no unintended effects.<br/><br/><br />
4. What unintended effects could you foresee after your engineered organism is released to the environment? <br/><br />
• In case of release into the environment, our engineered organism would kill itself. Hence would not pose any environmental hazard.<br/><br/><br />
5. Try to think outside the box, what is the absolute worst case scenario for human health or the environment, that you could imagine? <br/><br />
• Since, we are trying to engineer a cell lysis system, we would assure that there would be no hazard to human health or environment.<br />
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<b><font size="6"><font color="blue">DATA PAGE</b></font></font><br/><br/><br />
<p align="justify">This page lists the parts which we constructed, improved or used unmodified in our project.<br/><br/></p><br />
<br/><br/><br />
<b><font size="5"><font color="blue">How does our system works:</b></font></font><br/><br/><br />
<br />
<center> <img src="https://static.igem.org/mediawiki/2011/2/2a/SKL20.png" width="400" height="300"/></center><br/><br/><br />
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<b><font size="5"><font color="blue">Data for our favorite new part</b></font></font><br/><br/><br />
<br />
<p align="justify">1.<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526002"><b>BBa_K526002</b></a>- A basic bio-brick part that would help our Chop. coli to sense the temperature of the environment.Fermentor and incubators will be at 37 ⁰C and the environment will be usually 25-30⁰C. The temperature dependent ribo-switch present in this part will prevent inhibit translation at 37⁰C and favor translation at temperatures less than 30⁰C. <br/><br/></p><br />
<p align="justify">2. <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>- It is a composite biobrick part that could be used along with the light receptor, Cph8 and reporter genes expressed under fim inversion promoter systems. However, due to the higher leaky level of Pompc this system was not able to perform as expected.<br/><br/></p><br />
<b><font size="5"><font color="blue">Data for pre-existing bio-brick part</b></font></font><br/><br/><br />
<br />
<p align="justify"><a href="http://partsregistry.org/Part:BBa_K592000:Experience"><b>BBa_K592000</b></a> and <a href="http://partsregistry.org/Part:BBa_K081017:Experience"><b>BBa_K508107</b></a>- We reduced the leaky level of the light receptor by controlling the expression of the transcription repressor, cI, through light. This system would help us regulate multiple genes (that are expressed from cI regulated promoters) simultaneously with a single light input. We also report the presence of cross talk between the light receptor and the osmo-regulatory response regulator.<br/><br/> </p><br />
<b><font size="5"><font color="blue">We’ve also characterized the following biobrick parts</b></font></font><br/><br/><br />
<br />
<p align="justify"> <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526001"><b>BBa_K526001</b></a>- It is the last segment of a composite biobrick composed of the light receptors, Cph8 and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K526000"><b>BBa_K526000</b></a>. The reporter gene expressed from this biobrick is the genes for DpnI enzymes (originally belongs to <i>Streptococcus pneumonia</i>). However, we could not see the complete digestion of the DNA in darkness. We suspect that the expression level might not sufficient to digest the entire DNA. We are trying to optimize the RBS of these genes to favor higher expression and complete digestion of the genomic DNA. <br />
Biobricks parts under construction</p><br />
<p align="justify">We are trying to clone the DpnI enzymes under PBAD promoter in order to optimize its RBS and the expression level. But we could not accomplish this on time.</p><br />
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July 5- We took a tour of the lab, learnt basic laboratory safety rule and learnt basic techniques like how to prepare LB-Medium, how to use the autoclave.<br/><br />
We inoculated E. coli strain SCS110 so that we will make competent cell tomorrow. We also prepared ice coldwater and glycerol for tomorrow’s experiment.<br/><br/><br/><br />
July 6- We learnt how to make Electro Competent Cell. <br/> While JaeSung and Eeseul were busy making Comp cell, Bokeun and YuLim were busy setting PCR and recovering Biobrick Parts<br/>. We made a list of the biobrick parts we would use in our experiment and we tried to recover those plasmids from the DNA kit box we obtained from iGEM. <br/><br/><br/><br />
July 7- We saw pretty colonies on our plates we made yesterday. We failed to recover all of the biobrick parts we aimed for. So, we tried to recover them once again. We also have transformed the pSIM5 plasmid carrying the lambda red system into SCS110 to perform gene knockout. <br/><br />
Then our instructor, Vinu tried to explain us the use of lambda red system for gene knockouts. We were excited with the function of exo, gamma and beta proteins. We inoculated SCS110 pSIM5 cells for tomorrow’s experiment. Eeseul made a PCR product that is to be used to knockout our target gene. <br/><br/><br/><br />
July 8- We tried to knock out gene. SCS110 is a comparatively slow growing cell. It was funny to induce cells at 42⁰C and immediately cooling them and making electrocompetent for transformation. <br/><br/><br/><br />
July 9- We were excited to see tiny small colonies on our Kanamycin plates. We went ahead to do a colony PCR to check for the true deletion. At the end of the day, we confirmed that we have deleted our gene, EnvZ. We were so excited because now we can make our Chop. coli to sense light. Our instructor advised us to remove the kanamycin cassette before we proceed to check the light sensing ability. <br/><br/><br/><br />
July 11- We inoculated the SCS110 ∆envZ strains to make competent cell and transform pCP20 plasmid, which would help us to remove the kanamycin cassette. <br/><br/><br/><br />
July 12, we failed to remove the kanamycin cassette. Our instructor advised us to try it again.<br />
We tried again. Eeseul got a lot of stress in removing the kanamycin cassette. So YuLim tried to remove the kanamycin cassette. <br/><br/><br/><br />
July 13, YuLim also failed to remove the kanamycin cassette. Vinu advised us to give up this strain, as the plasmid pCP20 may not be compatible with SCS110 host strain. So we decided to use MG1655. We inoculated MG1655 pSIM5 strain to delete kanamycin cassette. <br/><br/><br/><br />
July 14, Eeseul tried to delete envZ gene in MG1655. JaeSung and Bokeun were busy writing Safety rule and Abstract which is due for tomorrow. YuLim and Vinu tried to isolate the genomic DNA from Streptococcus which they will use it to amplify the Dpn cassette. It was little hard and a long boring procedure as it is a gram-positive bacterium. But, finally they got a good yield. <br/><br/><br/><br />
July 16, We were busy learning the Vector NTI program in order to design our primers. It was little hard at the beginning but we started mastering it soon. <br/><br/><br/><br />
July 18, We were still busy designing primers for our future experiments. Primers for Gibson’s Assembly was little difficult. We took care of adding RBS and additional bases for restriction sites. Finally at the end of the day almost all of our primers were being designed. Now, our instructor will check our primers and place an order for our primers. <br/><br/><br/><br />
July 21- Our primers have come. Our instructor explained us the ways to process our primers. JaeSung went crazy about the calculation and finally Bokeun helped him fix his problem. <br />
Everybody rushed to set our PCRs. YuLim got all of her holin genes successfully. But she failed to get her Dpn PCR product. Vinu suggested that she should try a gradient PCR. So, she went ahead to set a gradient PCR. <br/><br/><br/><br />
July 22, YuLim still failed to get her PCR product. Vinu suggested Dpn digestion of the genomic DNA itself to confirm if Streptococcus DNA we had really has a Dpn gene. To our suspicion, Streptococcus DNA was digested by Dpn suggesting it has no Dpn. Vinu tried to place order for another Streptococcus strain from KCTC. Bokeun went ahead to clone his fimE gene into a plasmid pACYC. <br/><br/><br/><br />
July 23, Bokeun and JaeSung are done with their cloning, they luckily got one colony, and that had their target gene inserted. <br />
Bokeun was extremely excited with it. We transformed 3 plasmids (light receptors, fimE and GFP) into one strain.<br />
JaeSung went on to check the expression of mRNA at different temperatures. The preliminary result was promising and he was able to see some difference based on the temperature. <br/><br/><br/><br />
July 25- JaeSung went on to screen for the cells Bokeun made to find one cell, which carries all 3 plasmids. He used TECAN microplate reader to screen for the cell. Finally he got one colony that contains all 3 plasmids. So, he streaked it on a plate. <br/><br/><br/><br />
July 26, JaeSung’s plate was completely green the next day. Then we realized that TECAN is dark. So, in our cell darkness lead to fimE expression which in turn inverted all of the promoters of GFP making GFP expression constitutive. So, we learnt that we should take care of darkness when we use fimE system. <br/><br/><br/><br />
July 27-29- We went for a workshop on Climate Change. We explained the audience about iGEM and our goal. We were explaining our project for the first time to a group of people. We were excited with that. We celebrated the day with alcohol. <br/><br/><br/><br />
August 1- We deleted the envZ gene and integrated cI gene into the chromosome of MG1655 using lambda red system. <br/><br/><br/><br />
August 3, We tried to transform the light sensing biobricks and the reporter gene into the envZ deleted strain<br/><br/><br/><br />
August 10, Our strain containing the light plasmid and reporter plasmids are ready. We made a quick check of its functionality in the presence and absence of light. <br/><br/><br/><br />
August 13, We got the new Streptococcus DNA and successfully amplified the Dpn genes. Gibson’s assembly works very well. <br/><br/><br/><br />
August 16, YuLim completed cloning Holin and Dpn into a plasmid without the prmoter. <br/><br/><br/><br />
August 17, YuLim went on to put the promoters in front of Holin and Dpn. She has two kinds of promoter one is a inversion promoter, ptrc* and another is a Constitutive Promoter. She is aware that it is not as easy to clone the promoters, as it was to clone the genes. She was causing in using specific strains for each promoters. (pL promoter into ECNR2; Dpn into SCS110). <br/><br/><br/><br />
September 4- Eeseul repeated the mRNA-GFP. However, she had difficulty in understanding the GFP expression as she made a temperature shift at the early log phase. She had to deal with a slow growing and fast growing strain. So, she gave up the experiment as she could not predict her output and even the control was not as expected. Bokeun tried to check the effect of different concentration of glucose on the light receptor. He could see a good cross talk of the light and the osmo-regulator. <br/><br/><br/><br />
September 5- JaeSung repeated the mRNA experiment even when his control gave good result. He could not see any difference in GFP expression with temperature dependent riboswitch. <br/><br/><br/><br />
September 7- JaeSung tried to check the effect of light on cI expression by following GFP expression every one hour. After one day of tiresome experiment, he got a very good result. <br/><br/><br/><br />
September 8, We had a deep discussion on Synthetic Biology and iGEM to Science Specialized High Schools in Korea and in Singapore. <br/><br/><br/><br />
September 11, Eeseul tried to check the effect of cross-talk between the osmo-regulator and the light receptor using salt. She found no cross-talk with salt. YuLim was almost done with her cloning of Holin and Dpn cassette. Now she is ready to check their functionality. <br/><br/><br/><br />
September 18- Bokeun and Eeseul tried to prove the cross-talk using various sugars such as Arabinose and Glucose. They found a similar pattern even when they used arabinose or glucose. <br/><br/><br/><br />
September 21- We had a group presentation with all members of our department. It was our first official presentation. We were excited and we got many good feed backs. <br/><br/><br/><br />
September 22- We were busy making our websites and documenting the results. We were aware that the wiki would freeze soon. <br/><br/><br/><br />
September 23- We went on to clone Holin and Dpn under the control of pBAD promoter as the light promoter did not work<br/><br/><br/><br />
August 28 We cloned the riboswitch regulated GFP into pTrc promoter to check for a significant change in GFP with temperature. We still could not see any significant changes in GFP. <br/><br/><br/><br />
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<font size=6><font color=Brown>Future work & Application</font></font><br/><br/><br />
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<p align="justify">In the future our first effort will be to optimize the lysis module such that the Dpn enzymes are efficiently exploited by the synthetic microbes to eradicate its genetic material in a non-native environment. <br/> <br/><br />
On top of this, UNIST team will also introduce more controlled system into <i>E.coli</i> so that it can be more safe to the environment and easy to be handled in the laboratory. <br/> <br/></p><br />
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<p align="justify">We would like to introduce the following components into our <i>Chop. coli</i> in order to achieve our goal<br/><br/><br />
<center><b><font color=Red>Second light receptor</font></b></center><br/><br/><br />
<center><b><font color=Red>Quorum Sensing System</font></b></center><br/><br/></p><br />
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<p align="justify">Two light signals before lysis would help in providing a more tight control and ensure that the device would still work even when one of them is mutated.Our team will also introduce a fourth sensing module to the <i>Chop. coli</i> using the <b><font size=4><font color=brown>quorum sensing system</font></b></font>. In case of fermentor <i>E. coli</i> will experience its native original quorum sensing molecule, AI2 <br />
UNIST team is going to make that engineer <i>E.coli</i> to recognize different quorum sensing molecules such as AHL to differentiate between the fermentor and the real world.<br />
This system will also help achieve an effective and tight control of lysis device. </br><br />
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<center><b>Figure explaining the future appearance of <i>Chop. coli</i></b></center><br />
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