Team:Korea U Seoul/Notebook/May

     will upload his on the website (cafe).

      EHeat 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.

     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

     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'.

     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.

     Oct 5 ~ 7, at HKUST, Hongkong.

     For the experiment, we would use prokaryotic cells and yeast cells. Also we can use eukaryote's gene. But since our lab does not deal with eukaryotic cells, try to think of ideas in this boundary.

     Ideas already done by previous iGEMers cannot be used again but it is possible to improve the ideas and they would be approved to use.

     - 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

     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.

      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.

      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.

     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.

     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.

     Herbicides detecting bacteria.

     Introduced an article referring promoter for 2,4-Dichlorophenoxyacetic acid

     Fluorescent genes would be used as a reporter genes.

     Nitrogen fixing bacteria is already commercialized.

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

     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.

     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