Team:Korea U Seoul/Notebook/Jul

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      <h4><p id="title">Notebook : June</p></h4>
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    <dt>
 +
<b> A. June, 4, 2012 </b>
 +
</dt>
 +
            <p style="padding-left:30px;">Today, we discussed about main topic and preliminary topic which are bacterial logic gate and carbon fixation using carbonic anhydras</p>
 +
            <br>
 +
            <dd>
 +
<b> 1) Idea development </b>
 +
                <br>
 +
               
 +
                <b>&nbsp;&nbsp;Jeongmin Lee, Kyeongjin Kim: DNA logic gate</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;reviewed a paper on DNA gate by KAIST 2012
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Possible to make logic gate (XOR, NOR, AND, OR) based on DNA
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mechanism: DNA hairpin: input DNA is complementary to output DNA which releases florescence.
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Half adder possible, but requires further research on full adder
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Hyunkee Kim</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Deoxyribozyme based logic gate
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Jang Kyeongwoo Jang</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Progress on XOR logic gate
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Possible candidate for XOR logic gate is .Lux R operon and Las R operon which is orthologous to each other
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Promoter design<br>
 +
                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;① las - lux - output<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;② lux - las – output
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;output is the same protein. When two signals are simultaneously given, each operon inhibits transcription. In effect, this results in no transcription at all
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Jihoon Jung</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;researched on output-input chemicals
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;One was substance that uses quorum sensing
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For example, AHL(Acyl-homoserine lectone)
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Since each bacteria uses different AHL, signal won’t mix up
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Sanghoon Han</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;researched on output-input chemicals
 +
</p>
 +
         
 +
                <br>
 +
               
 +
                <b> 2) Next meeting </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Carbonic anhydrase : Byeongnam Min, Haerim Song, Ji Hyoung Nam
 +
</p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;DNA logic gate : Jeongmin Lee, Kyeongjin Kim, Wonuk Lee
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Plasmid logic gate : Hyunkee Kim, Jang Kyeongwoo Jang, Jihoon Jung, Sanghoon Han
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Half adder, full adder completion: everyone
 +
                </p>
 +
           
 +
            <br><br><br>
 +
                <dt>
 +
<b> B. June 25, 2012 </b>
 +
</dt>
 +
            <p style="padding-left:30px;">Today, we discussed about main topic and preliminary topic which are bacterial logic gate, Molecular Beacon, and carbon fixation using carbonic anhydrase.</p>
 +
            <br>
 +
            <dd>
 +
<b> 1) Idea development </b>
 +
                <br>
 +
                <b>&nbsp;&nbsp;Jeongmin Lee, Kyeongjin Kim: DNA logic gate</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Possible to make logic gate (XOR, NOR, AND, OR) based on DNA
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Nearly impossible if more than half adder is used. (Note: longer DNA is required).
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  As DNA gets longer, price for synthesis is getting higher and even more when protein is attached to DNA.
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Hyunkee Kim, Kyeongwoo Jang, Sanghoon Han, Jihoon Jung</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  need to unify input signal and output signal
 +
</p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Improvement on modeling of full gate.
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If input and output are the same, these can interfere in signal transfer.
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;That is to say, input chemical must be destroyed once it gives signal to adjacent promoter..
 +
                </p>             
 +
               
 +
                <b>&nbsp;&nbsp;Back up idea team ( Jihyong Nam, Byeongnam Min,  Haerim Song, Dohoon Kwon)</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Haerim Song: Inhibition of virulence of bacteria on plant – type 3 secretion
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Sponsor (Dohoon Kwon, Wonuk Lee)</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;in order to get funding, we need to have presentation on our research or submit a report.
 +
</p>
 +
             
 +
                <br>
 +
             
 +
                <b> 2) Next meeting </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;From next week, we will have our regular meeting on Wednesday 8p.m
 +
</p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Before next meeting, research the problems and limitations that we discussed during our regular meeting
 +
                </p>
 +
            </dd>
 +
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 +
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Revision as of 07:31, 26 September 2012

Notebook : June

A. June, 4, 2012

Today, we discussed about main topic and preliminary topic which are bacterial logic gate and carbon fixation using carbonic anhydras


1) Idea development
  Jeongmin Lee, Kyeongjin Kim: DNA logic gate

     reviewed a paper on DNA gate by KAIST 2012

     Possible to make logic gate (XOR, NOR, AND, OR) based on DNA

     Mechanism: DNA hairpin: input DNA is complementary to output DNA which releases florescence.

     Half adder possible, but requires further research on full adder

  Hyunkee Kim

      Deoxyribozyme based logic gate

  Jang Kyeongwoo Jang

     Progress on XOR logic gate

     Possible candidate for XOR logic gate is .Lux R operon and Las R operon which is orthologous to each other

     Promoter design
      ① las - lux - output
      ② lux - las – output

     output is the same protein. When two signals are simultaneously given, each operon inhibits transcription. In effect, this results in no transcription at all

  Jihoon Jung

     researched on output-input chemicals

     One was substance that uses quorum sensing

     For example, AHL(Acyl-homoserine lectone)

     Since each bacteria uses different AHL, signal won’t mix up

  Sanghoon Han

     researched on output-input chemicals


2) Next meeting

     Carbonic anhydrase : Byeongnam Min, Haerim Song, Ji Hyoung Nam

     DNA logic gate : Jeongmin Lee, Kyeongjin Kim, Wonuk Lee

     Plasmid logic gate : Hyunkee Kim, Jang Kyeongwoo Jang, Jihoon Jung, Sanghoon Han

     Half adder, full adder completion: everyone




B. June 25, 2012

Today, we discussed about main topic and preliminary topic which are bacterial logic gate, Molecular Beacon, and carbon fixation using carbonic anhydrase.


1) Idea development
  Jeongmin Lee, Kyeongjin Kim: DNA logic gate

      Possible to make logic gate (XOR, NOR, AND, OR) based on DNA

      Nearly impossible if more than half adder is used. (Note: longer DNA is required).

      As DNA gets longer, price for synthesis is getting higher and even more when protein is attached to DNA.

  Hyunkee Kim, Kyeongwoo Jang, Sanghoon Han, Jihoon Jung

      need to unify input signal and output signal

     Improvement on modeling of full gate.

     If input and output are the same, these can interfere in signal transfer.

     That is to say, input chemical must be destroyed once it gives signal to adjacent promoter..

  Back up idea team ( Jihyong Nam, Byeongnam Min, Haerim Song, Dohoon Kwon)

     Haerim Song: Inhibition of virulence of bacteria on plant – type 3 secretion

  Sponsor (Dohoon Kwon, Wonuk Lee)

     in order to get funding, we need to have presentation on our research or submit a report.


2) Next meeting

     From next week, we will have our regular meeting on Wednesday 8p.m

     Before next meeting, research the problems and limitations that we discussed during our regular meeting

Retrieved from "http://2012.igem.org/Team:Korea_U_Seoul/Notebook/Jul"