Team:Korea U Seoul/template/Notebook/Apr

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2012 Korea U Seoul iGEM team's first meeting - Apr 11. 2012

1. Introduction to iGEM

- About synthetic biology : As an automobile can be described as assembly of numerous parts, synthetic biology is a field of assembled techniques from division of biotechnology. One of benefits offered in this field is that we can use necessary parts with lack of knowledge to specifics of each technique.
- Look around 2011 iGEM teams' posters, wiki pages.

2. Briefly decided role of each member (Doesn't mean working on the role only. What to focus)

- Web design team (Wiki team) - Coding wiki pages and making video clips and flash movie. : Sanghoon Han, Byeongnam Min, Kyengwoo Jang

- Design team - Dealing with Adobe photoshop, Illustrator to design most things except video clips and flash movie. Making poster and presentation files for the jamboree. : Haerim song, Jeongmin Lee, Kyengwoo Jang, Byeongnam Min, Jihoon Jeong, Kyungjin Kim

- Human practice team - Dealing with human practice activities such as introducing synthetic biology, contact with other teams for collaboration, think of future application, and extra. : Sanghoon Han, Kyengwoo Jang, Jihoon Jeong, Jihyong Nam

- Fundraising team - Literally, fundraising. Contact with local community, bio-tech companies and etc for fundraising. : Dohoon Kwon, Wonuk Lee

3. Preparation for brainstorming

- Since it's the beginning, think of rough idea, not the specific model or design including principles of how idea works out. (e.g. drawing pictures with bacteria, bacteria extracting rare earth resources)
- Refer to iGEM website. There are some projects suggested by sponsors.

4. Communication info and decided regular meeting.

- Facebook page, Twitter, Naver cafe (Korean page. http://cafe.naver.com/2012igem )
- Regular meeting on every Monday, p.m. 8:00, lecture room 335 Life Science Division West building (except Midterm and Final exam period)

5. Consideration about making club

- This year, we are planning to make a club for Korea U Seoul iGEM team to enhance communication between former participants and future participants and to share experience.
- The club would be under Division of Life Science, Korea University if made.

6. Things we have to do until next Monday

- Bring at least one plausible ideas for brainstorming in ppt file about 1~2 slides and upload it to website.
- Look around former iGEM prize winners' projects

2012 iGEM second meeting - Apr 16. 2012

1. We had time to share our ideas for brainstorming.

I) Sanghoon Han

- Fire alarm using bacteria : Making bacteria detecting CO, H2S, other toxic gases and compounds formed during incomplete combustion. After the detecting, noticeable change occurs (e.g. color change)
- Make bacteria responds to electric field to make a display system

II) Byeongnam Min

- Empty cell : Making bacterial factory by modifying bacteria to maintain only cellular structures related to production of certain material we want.
- Walking bacteria : Literally, bacteria that show walking mechanism.
- Salt eating bacteria : Using bacteria in desalination process
- Bacterial feed : Modifying bacteria to produce materials that facilitating growth and mix them with feed.
- Beeping bacteria : Making communication system of bacteria visible to human eyes.

III) Kyeongjin Kim

- Improved photosynthesis in bacteria : By using obg gene exists in ribosome, enhances bacterial photosynthesis.
- Diagnosis of diseases using bacteria : By expressing lectin proteins on the surface of bacteria that specifically recognize certain oligosaccharides, find out mutant cells

IV) Haerim Song

- Cyclopropane fatty acids : Producing alkanes by using Brucella abortus

V) Jaeho Jang

- Fat degrading bacteria : Literally, modifying bacteria to degrade fat for a diet
- Perfume production using bacteria
- Making shaving cream with bacteria : Modifies bacteria to degrade beard.
- Jean washing : Modifying bacteria to degrade fiber of jean or indigo dye to wash jean.

VI) Jeongmin Lee

- Heating bacteria : Using bacteria to get warm. Can be used to make boiler.
- Using bacteria to change a circadian rhythm : Clone the gene related to circadian rhythm and use it to overcome jet lag.

VII) Hyunkee Kim

- Silk production using bacteria : Adopt insect-oriented gene related to silk production to bacteria
- Cellulose degrading bacteria : Literally, by using cellulase gene, make bacteria to degrade cellulose.

VIII) Jihyong Nam

- Hemoglobin in bacteria : Modify bacteria to express different phenotypes according to oxygen concentration.
- Expressing various colors using bacteria : Use luciferase. By concentration of bacteria that are coated with shells having colors, different colors of lights are emitted.

IX) Jihoon Jung

- Water quality measurement device using microorganism : Measuring DO, BOD of water by how much microorganism expressed fluorescence.
- Channel Rhodopsin photometer : literally, measure amount of light using channel rhodopsin
- Making logic circuit : Channel Rhodopsin responses to presence and absence of light. By using the phenomenon, perform simple logical operations
- Solar photovoltatic power generation using microorganisms.
- Fertilizer using Agrobacterium species.
- Development of microorganisms that attaches to organic compounds and then precipitate.

X) Kyeongwoo Jang

- Microorganism power generator : Using pressure of gases produced by microorganisms, generate power.
- Movement of bacteria using endospore

XI) Dohoon Kwon

- Make bacteria to sense cholesterol, and then burst to release contained enzymes that breaks down cholesterol.
- Bacterial detergent : secretion of protease clean up laundry.

2. Things to be considered during brainstorming.

- Ideas related to human body : Since projects for iGEM should be done in 3~6 months, we cannot go through clinical trial. So try to think of other ideas
- 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.

3. Brief expected schedule for our team

- Apr : Decide which topic our team's gonna proceed.
- May and June : Develope the idea, design experiment and start coding our wiki page
- During Vacation : do experiment, gathering data and analyze them.
- Sep : Get ready for wiki freeze, prepare poster and presentation files.
- Oct : Final check for Asia jamboree
- Nov : World championship

4. Next meeting

- Apr 30, p.m. 8:00, lecture room 335 Life Science Division West building. (Next week is exam period, therefore, we don't have regular meeting.)
- Develope each one's idea and read some articles related to it if needed. Share the articles by uploading pdf version of them if you searched for some.

2012 iGEM third meeting - Apr 30. 2012

1. Created Facebook page and Twitter account.

- Not only our team members but other users of facebook can also visit our 2012 iGEM team site.
- Before we finish coding frame of wiki page, the page would be used to post our notebook info and other contents.
- Facebook page address : http://www.facebook.com/2012iGEM.KU
- Twitter account : http://twitter.com/igem_ku2012

2. 2nd brainstorming.

I) Dohoon Kwon

- Nitrogen Sensor & fertilizer : Modify bacteria to measure amount of nitrogen in the soil and if the amount is not enough, nitrogen fixation occurs.

II) Hyunkee Kim

- Using aldehydes or fatty acids to produce diesel : Using Isobutyryl-CoA as a substrate, adopt enzymes such as FabH2.
- Confirming whether farm produces are organic or not : Make bacteria to detect pesticides or herbicides and if they exist, to produce fluorescence.
- Plastic degrading bacteria

III) Kyeongwoo Jang

- Developed previous logic circuit idea - Binary calculator using channel rhodopsin to detect light signal.

IV) Jihoon Jung

- Concretize previous light recognizing logic circuit idea :
-> Input : light -> Processing : deliver information by simple diffusion
-> Output : fluorescent proteins => expressed when recognized certain signals

V) Byeongnam Min

- Communication with bacteria : Sensing heat shock or starvation condition of bacteria by using various σ factors. -> making some sort of 'tamagochi'. <

VI) Sanghoon Han

- Adopting absolute configuration : In synthesis of pharmaceutical, products are usually racemic compound. Synthesizing the compound with one absolute configuration by developing in vivo pathway. (e.g. Thalidomide synthesis patent)
- Addition to display system using bacteria : Distribute bacteria in 2D plate by chemotaxis or other methods.
-> Then in response to electric field, bacteria will arrange in certain direction. Light would not pass through compartment where bacteria gathered => Black and White LCD

VII) Jihyong Nam

- Chromosome walking : Illuminated DNA molecules producing energy by certain mechanism of movement.
=> By using the idea, design an interesting research.
- Shampoo & Conditioner : Molecular structure of conditioner is similar to that of shampoo except the lack of polar parts. So, the idea is producing shampoo molecule and change it to conditioner in response to certain signal.
- CaCO3 producing bacteria : Another way to fix carbon dioxide.

VIII) Wonuk Lee

- Chitin paint : Modify microorganisms to express chitin coat outside of the cell, and use them as a paint.

3. Narrowed down candidate ideas for our project.

- During the brainstorming, we've got 38 ideas
- Narrowed down ideas from those that had more than 4 votes at last meeting and ideas from this meeting and chose 12 plausible ideas (that we can actually test in our lab, and also that have not been already tested by others).
- We'll get advise from our instructor and advisors with the chosen ideas. Later on, we'll vote for a final idea for 2012 iGEM project.

Here's the list of 12 ideas :

- Display system using bacteria (in response to electric field)
- Heat releasing bacteria
- Hemoglobin in bacteria (expressing different phenotypes to O2 concentration)
- Logic circuit adopting Channel Rhodopsin
- Method to confirm whether products are organic or not (detecting herbicide)
- Communication in bacteria (making sort of 'tamagochi')
- Nitrogen sensor & fertilizer
- Chromosome walking (to produce energy)
- Shampoo - conditioner forming bacteria
- Chitin paint
- Carbon fixation forming CaCO3