Team:Korea U Seoul/template/Notebook/May

From 2012.igem.org

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<div id="Notebook May 7. 2012">
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<h2> 2012 iGEM 4th meeting - May 7, 2012 </h5>
<h2> 2012 iGEM 4th meeting - May 7, 2012 </h5>
<br>
<br>
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<h3> 1. iGEM Asia jamboree </h3>
<h3> 1. iGEM Asia jamboree </h3>
<br>
<br>
-
<p>
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<dd>
- Oct 5 ~ 7, at HKUST, Hongkong.
- Oct 5 ~ 7, at HKUST, Hongkong.
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</p>
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</dd>
<br>
<br>
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<br>
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<p>
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<dt>
I) Dohoon Kwon : will upload his on the website (cafe).  
I) Dohoon Kwon : will upload his on the website (cafe).  
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</dt>
<br>
<br>
<br>
<br>
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 +
<dt>
II) Jeongmin Lee : Heat releasing bacteria
II) Jeongmin Lee : Heat releasing bacteria
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</dt>
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<dd>
- Heat releasing bacteria used in massage were based on fermentation of bacteria. Giving sawdust as a carbon source, and adding some enzymes related to fermentation will produce heat. (enough to feel warmth)  
- Heat releasing bacteria used in massage were based on fermentation of bacteria. Giving sawdust as a carbon source, and adding some enzymes related to fermentation will produce heat. (enough to feel warmth)  
But boiler using this method is under patent, so it is required to find other applications.
But boiler using this method is under patent, so it is required to find other applications.
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</dd>
<br>
<br>
<br>
<br>
 +
 +
<dt>
III) Jihoon Jung : Logic circuit adopting channel rhodopsin
III) Jihoon Jung : Logic circuit adopting channel rhodopsin
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</dt>
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<dd>
- Searched whether the idea has been already covered by previous iGEM teams. Confirmed that no team in 2011 iGEM has dealt with the idea. Will search more in 2010, 2009 iGEM teams
- Searched whether the idea has been already covered by previous iGEM teams. Confirmed that no team in 2011 iGEM has dealt with the idea. Will search more in 2010, 2009 iGEM teams
 +
</dd>
<br>
<br>
<br>
<br>
 +
 +
<dt>
IV) Sanghoon Han : Display system using bacteria (adopting magnetosome)
IV) Sanghoon Han : Display system using bacteria (adopting magnetosome)
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</dt>
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<dd>
- 2011 iGEM Washington team already carried out a magnetosome toolkit design. More research required and will figure out how to apply their toolkit in this idea. Confirmed using magnetosome system in E.coli is possible.  
- 2011 iGEM Washington team already carried out a magnetosome toolkit design. More research required and will figure out how to apply their toolkit in this idea. Confirmed using magnetosome system in E.coli is possible.  
It is still confusing how to arrange bacteria in certain direction in response to electric field, without moving bacteria distributed in 2D plate since magnetosome is for magnetotaxis, which literally refers 'taxis'.  
It is still confusing how to arrange bacteria in certain direction in response to electric field, without moving bacteria distributed in 2D plate since magnetosome is for magnetotaxis, which literally refers 'taxis'.  
 +
</dd>
<br>
<br>
<br>
<br>
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<dt>
V) Hyunkee Kim : Bateria detecting herbicides
V) Hyunkee Kim : Bateria detecting herbicides
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</dt>
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<dd>
- Detection using tfa4 gene product. 2,4-Dichlorophenoxyacetic acid has structural similarity to IAA and therefore is used as an herbicide to a dicotyledon.  
- Detection using tfa4 gene product. 2,4-Dichlorophenoxyacetic acid has structural similarity to IAA and therefore is used as an herbicide to a dicotyledon.  
Design an operon using promoter of tfa4 gene to sense 2,4-Dichlorophenoxyacetic acid and use fluorescent gene as a reporter gene.
Design an operon using promoter of tfa4 gene to sense 2,4-Dichlorophenoxyacetic acid and use fluorescent gene as a reporter gene.
-
</p>
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</dd>
<br><br>
<br><br>
<h3> 3. Teams for further development of some ideas above and suggested idea from advisors </h3>
<h3> 3. Teams for further development of some ideas above and suggested idea from advisors </h3>
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<p>
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<dd>
<br>
<br>
- Display system team : Sanghoon Han, Kyeongwoo Jang
- Display system team : Sanghoon Han, Kyeongwoo Jang
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<br>
- Partner offer research team : Haerim Song, Byeongnam Min
- Partner offer research team : Haerim Song, Byeongnam Min
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</p>
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</dd>
<br><br>
<br><br>
<h3> 4. Next meeting.. </h3>
<h3> 4. Next meeting.. </h3>
<br>
<br>
-
<p>
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<dd>
- May 14, p.m. 8:00, 8:00, lecture room 335 Life Science Division West building.
- May 14, p.m. 8:00, 8:00, lecture room 335 Life Science Division West building.
<br>
<br>
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<br>
<br>
- We will vote for a final decision next meeting.
- We will vote for a final decision next meeting.
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</p>
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</dd>
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<br><br><br><br>
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<h3> 1. Final development sharing and discussion </h3>
<h3> 1. Final development sharing and discussion </h3>
<br>
<br>
-
<p>
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<dt>
I) Sanghoon Han, Kyeongwoo Jang
I) Sanghoon Han, Kyeongwoo Jang
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</dt>
<br>
<br>
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<dd>
- Display system using bacteria
- Display system using bacteria
<br>
<br>
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<br>
<br>
- The concern mentioned last meeting was not solved and for that, changed point of view with magnetosome to use it in distribution of bacteria, not to arrange in direction. Also decided to focus on displaying, not to build polaroid using bacteria.
- The concern mentioned last meeting was not solved and for that, changed point of view with magnetosome to use it in distribution of bacteria, not to arrange in direction. Also decided to focus on displaying, not to build polaroid using bacteria.
 +
</dd>
<br><br>
<br><br>
 +
 +
<dt>
II) Haerim Song, Byeongnam Min
II) Haerim Song, Byeongnam Min
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</dt>
<br>
<br>
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<dd>
- Partner offer research
- Partner offer research
<br>
<br>
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<br>
- Whether to use this species directly or clone genes and transform them into E.coli would be decided after enough searches done about the species.
- Whether to use this species directly or clone genes and transform them into E.coli would be decided after enough searches done about the species.
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</dd>
<br><br>
<br><br>
 +
 +
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<dt>
III) Jihoon Jung, Jeongmin Lee
III) Jihoon Jung, Jeongmin Lee
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</dt>
<br>
<br>
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<dd>
- Logic circuit
- Logic circuit
<br>
<br>
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<br>
- Use filter or other methods to prevent leakage of the molecules when they bound.
- Use filter or other methods to prevent leakage of the molecules when they bound.
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</dd>
<br><br>
<br><br>
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 +
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<dt>
IV) Wonuk Lee, Jihyong Nam, Kyeongjin Kim
IV) Wonuk Lee, Jihyong Nam, Kyeongjin Kim
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</dt>
<br>
<br>
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<dd>
- Pearl producing bacteria
- Pearl producing bacteria
<br>
<br>
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<br>
<br>
- Crystal nucleus to catalyze crystal formation (pearl) inside the microorganism's cells is crystals of actin filaments.
- Crystal nucleus to catalyze crystal formation (pearl) inside the microorganism's cells is crystals of actin filaments.
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</dd>
<br><br>
<br><br>
 +
 +
<dt>
V) Hyunkee Kim
V) Hyunkee Kim
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</dt>
<br>
<br>
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<dd>
- Herbicides detecting bacteria
- Herbicides detecting bacteria
<br>
<br>
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<br>
<br>
- Fluorescent genes would be used as a reporter genes.  
- Fluorescent genes would be used as a reporter genes.  
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</dd>
<br><br>
<br><br>
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<dt>
VI) Dohoon Kwon
VI) Dohoon Kwon
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</dt>
<br>
<br>
 +
<dd>
- Nitrogen fixing bacteria is already commercialized.
- Nitrogen fixing bacteria is already commercialized.
<br>
<br>
- Bacteria degrading cholesterol molecules to prevent or cure atherosclerosis are  already under research from other well-funded institutions.  
- Bacteria degrading cholesterol molecules to prevent or cure atherosclerosis are  already under research from other well-funded institutions.  
-
</p>
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</dd>
<br><br>
<br><br>
 +
<h3> 2. Final call </h3>
<h3> 2. Final call </h3>
<br>
<br>
-
<p>
+
<dt>
Decided the idea for our project by a show of hands.
Decided the idea for our project by a show of hands.
 +
</dt>
<br>
<br>
 +
<dd>
- The final call was 'Logic circuit design using bacteria'.
- The final call was 'Logic circuit design using bacteria'.
<br>
<br>
- A partner offer research will be carried as well since we can still submit the proposal due to May 30.
- A partner offer research will be carried as well since we can still submit the proposal due to May 30.
-
</p>
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</dd>
<br><br>
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<dt>
Partner offer research : Byeongnam Min, Dohoon Kwon, Jihyong Nam, Haerim Song
Partner offer research : Byeongnam Min, Dohoon Kwon, Jihyong Nam, Haerim Song
 +
</dt>
<br>
<br>
 +
<dd>
- How to make a physical platform for diffusion roote : Sanghoon Han, Wonuk Lee
- How to make a physical platform for diffusion roote : Sanghoon Han, Wonuk Lee
<br>
<br>
- Further research about possible promoters and molecules for AND, OR, XOR gates, half adder circuit and design brief overall circuit for a binary calculator (only addition) : Kyeongwoo Jang, Jihoon Jung, Hyunkee Kim, Jeongmin Lee, Kyeongjin Kim
- Further research about possible promoters and molecules for AND, OR, XOR gates, half adder circuit and design brief overall circuit for a binary calculator (only addition) : Kyeongwoo Jang, Jihoon Jung, Hyunkee Kim, Jeongmin Lee, Kyeongjin Kim
 +
</dd>
<br><br>
<br><br>
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</div>
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Latest revision as of 08:17, 8 August 2012

2012 iGEM 4th meeting - May 7, 2012


1. iGEM Asia jamboree


- Oct 5 ~ 7, at HKUST, Hongkong.

2. Shared research info done about previous ideas and discussed about it


I) Dohoon Kwon : will upload his on the website (cafe).


II) Jeongmin Lee : Heat releasing bacteria
- Heat releasing bacteria used in massage were based on fermentation of bacteria. Giving sawdust as a carbon source, and adding some enzymes related to fermentation will produce heat. (enough to feel warmth) But boiler using this method is under patent, so it is required to find other applications.


III) Jihoon Jung : Logic circuit adopting channel rhodopsin
- Searched whether the idea has been already covered by previous iGEM teams. Confirmed that no team in 2011 iGEM has dealt with the idea. Will search more in 2010, 2009 iGEM teams


IV) Sanghoon Han : Display system using bacteria (adopting magnetosome)
- 2011 iGEM Washington team already carried out a magnetosome toolkit design. More research required and will figure out how to apply their toolkit in this idea. Confirmed using magnetosome system in E.coli is possible. It is still confusing how to arrange bacteria in certain direction in response to electric field, without moving bacteria distributed in 2D plate since magnetosome is for magnetotaxis, which literally refers 'taxis'.


V) Hyunkee Kim : Bateria detecting herbicides
- Detection using tfa4 gene product. 2,4-Dichlorophenoxyacetic acid has structural similarity to IAA and therefore is used as an herbicide to a dicotyledon. Design an operon using promoter of tfa4 gene to sense 2,4-Dichlorophenoxyacetic acid and use fluorescent gene as a reporter gene.


3. Teams for further development of some ideas above and suggested idea from advisors


- Display system team : Sanghoon Han, Kyeongwoo Jang
- Logic circuit team : Jihoon Jung, Jeongmin Lee
- herbicide team : Hyunkee Kim, Dohoon Kwon
- Producing pearl : Jihyong Nam, Kyeongjin Kim, Wonuk Lee
- Partner offer research team : Haerim Song, Byeongnam Min


4. Next meeting..


- May 14, p.m. 8:00, 8:00, lecture room 335 Life Science Division West building.
- Each team is going to search for more background info and articles about the ideas and develop them further until next meeting.
- We will vote for a final decision next meeting.




2012 iGEM 5th meeting - May 14, 2012


1. Final development sharing and discussion


I) Sanghoon Han, Kyeongwoo Jang

- Display system using bacteria
- Further researched about 2011 Washington team's magnetosome toolkit, how to adopt magnetosome formation system into E.coli.
- Searched about 2009 Valencia team's project, Light Cell Display. Refered their modeling.
- Found some reference papers about 2D distribution of bacteria and arrangement of bateria in certain direction using light (not electric field).
- The concern mentioned last meeting was not solved and for that, changed point of view with magnetosome to use it in distribution of bacteria, not to arrange in direction. Also decided to focus on displaying, not to build polaroid using bacteria.


II) Haerim Song, Byeongnam Min

- Partner offer research
- Among 6 questions suggested by OSLI, they gave brief solution about producing hydrogen gas from carbon dioxide.
- Purple non-sulfur bacteria Rhodopseudomonas palustris applies protein from fixABCX operon for the nitrogen fixation and when it faces environment with insufficient nitrogen, it produces hydrogen gas instead of producing ammonia gas.
- Same gene exists in E.coli as well, but doesn't work, as known.
- Whether to use this species directly or clone genes and transform them into E.coli would be decided after enough searches done about the species.


III) Jihoon Jung, Jeongmin Lee

- Logic circuit
- Found out that 2011 Peking team already did the idea, but was just simple, AND/OR circuit design.
- Additional XOR gate design and building full adder circuit to make binary calculator (only processing addition) would be much advanced form compare to previous iGEM team
- Possible molecules for XOR gate : proteinA - Fc region of IgG, (His)6-nickel ion(II), etc..
- Two molecules used in XOR gate should be small enough to easily diffuse, able to bind one another, and promoter recognizing the molecules should exist.
- Use filter or other methods to prevent leakage of the molecules when they bound.


IV) Wonuk Lee, Jihyong Nam, Kyeongjin Kim

- Pearl producing bacteria
- Searched the principle of pearl formation, introducing the article "Self-assembly of amorphous calcium carbonate microlens arrays".
- Facing global warming, to reduce CO2 level, use microorganisms to fix carbon in form of calcium carbonate. This idea is already under patent -using enzymes to fix carbon- so it is required to think of another way.
- Crystal nucleus to catalyze crystal formation (pearl) inside the microorganism's cells is crystals of actin filaments.


V) Hyunkee Kim

- Herbicides detecting bacteria
- Introduced an article referring promoter for 2,4-Dichlorophenoxyacetic acid
- Fluorescent genes would be used as a reporter genes.


VI) Dohoon Kwon

- Nitrogen fixing bacteria is already commercialized.
- Bacteria degrading cholesterol molecules to prevent or cure atherosclerosis are already under research from other well-funded institutions.


2. Final call


Decided the idea for our project by a show of hands.

- The final call was 'Logic circuit design using bacteria'.
- A partner offer research will be carried as well since we can still submit the proposal due to May 30.


3. Distribution of work for our '2012 project' and a partner offer research until next meeting


Partner offer research : Byeongnam Min, Dohoon Kwon, Jihyong Nam, Haerim Song

- How to make a physical platform for diffusion roote : Sanghoon Han, Wonuk Lee
- Further research about possible promoters and molecules for AND, OR, XOR gates, half adder circuit and design brief overall circuit for a binary calculator (only addition) : Kyeongwoo Jang, Jihoon Jung, Hyunkee Kim, Jeongmin Lee, Kyeongjin Kim


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