Team:KU Seoul/Notebook

From 2009.igem.org

Revision as of 11:21, 29 August 2009

Lab

Protocols (from elsewhere and FAQs)

• How do I test the transformation efficiency of my competent cells?
  • Please see the protocol on how to [http://www.openwetware.org/wiki/TOP10_chemically_competent_cells make competent cells] for instructions on how to calculate transformation efficiency.

Discussion

Team building

From instructors

• 10.07.09

We had a review on our two ideas from Prof.Choi. He told us the ideas are creative and good but not fit for IGEM's concept. We need more feedback and information on our ideas. We need to get more familiar with IGEM's tools. Two additional ideas about Scromboid food poisoning and lactic acid degradation were referred at the end.

• 17.07.09

Till our next meeting, we should study how systemic biology works and understand related tools. Cumulate ideas. In other words, brainstorm consistently. Hyuk-jin will help with setting up experiments. Lab note opend.

• 24.07.09

We narrowed our ideas in to two. They are "Metal Detector" and "Bactaeria Compass." Think about what parts would be used and how you would build the circuits. Visit the former iGEM teams and study how they carried on their projects.

• 31.07.09

Find out the exact mechanism of metal detection. Look up the parts that are available on iGEM home. See how various metals can be detected by using E.coli.

• 07.08.09

We decided to detect 4 metals; Cd, Hg, Pb, and Ars. They are all critical to the health if ingested. Think about what the outcome would be after detection. Because there are 4 metals, you can bring out 16 different results by combining them. It seems that the most vialbe instrument would be light.

• 14.08.09

Study what parts on the registry we can use and how you would build a circuit. Increase your knowdlege on circutis by studying former iGEM teams. Remember, imitation is the mother of creation.

• 21.08.09

Vacation is almost over. The parts that we have looked for are mostly not available in the iGEM 2009 distribution registry, except for lead. We might have to construct the parts ourselves. Once we have our parts and our circuit models, doing experiments is a piece of cake. It's time to fuel up. Look for sponsors.

Brainstroming

Ideas

- Biosurfactants

- Keratinase

- Deodorant

- Perfume-producing bacteria

- Heat absorber

- Bio pencil

Should we focus on the result, or the procedure?

Decision making

From Cheolwon Choi, 4th of July

Hi everyone. We narrowed our ideas to two subjects, which are "Morse Code" and "Bio Sticker." If you would like to share any other ideas, you are more then welcome. Let's discuss about specific models for these two subjects at the upcoming meeting. Our next meeting is on 10th of July, 3 p.m. I recommend you think about at least one of the two subjects and how they should be developed. Tell me your schedules via mail so that I can fix our meeting time to the most suitable for all. I would like to share my experience at the iGEM workshop at Dongkyung about Wiki and other stuffs that you might be interested, so bring your notebooks. As I said before, prepare a specific model for the meeting. Try to document your ideas so they could be shared with others. A specific model should include these:

1. How will the chosen subject be used?

2. What are its limits?

3. What materials would be needed?

4. What former knowledge would be required to process the subject?

5. Why did you choose the subject?

6. What contributions can you make?

7. Etc.

See you next Friday.

From Cheolwon Choi, 5th of July

This mail has a linked file that contains the lists of our team member's e-mails and contacts.

From Cheolwon Choi, 10th of July

Hi everyone. The two subjects that we thought were good turned out to be not that suitable for iGEM. We need MORE ideas!!! We also need a clearer concept on synthetic biology. These are homeworks due to our next meeting, 17th of July.

1) https://2009.igem.org/Instructional_Videos Watch the videos.

2) Study the videos on iGEM 2009 home and tell us what you learned.

3) Divide our team into groups for each subject.

4) We need to learn more about Wiki. Wiki seems to take great part in judging. Although we are not that good in English, try to post your ideas. Try to visit our team Wiki everyday.

5) Please!!! Post me if you can't come.

From Simin Kim, 15th of July

Hey people. How's an aroma producing bacteria? If we can make a bacteria that can produce fragrance by using wasted food, we might not need to buy Febreeze anymore! :)

From Cheolwon Choi, 19th of July

Gees. It poured cats and dogs during the weekends. Your ideas are due Monday. I appreciate your full participation.

From Hansung Roh, 19th of July

As I was searching the text books, I thought of making a "Bacteria Array," similar to DNA array. It can be built to sense specific substrates in a compound.

From Kina Jeon, 20th of July

There is a molecule called Geosmin produced by microbes in water. It giveas the water a dirt flavor, an important factor for drinking water. We could build a bacteira that can sense geosmin and trap it, like the one Chiva university did on iGEM 2007.

From Cheolwon Choi, 20th of July

If there is a way, I want to develop a way to increase the survival rates of diesel producing bacterias. This idea is also good for raising funds if we succeed! Can we also make bio gasolines?

From Young Byun, 20th of July

Scrombroid food poisoning is the 2nd prevalent food posioning among fish and its main cause is histamine. Histidine which exists in all fish turns into histamine by histidine decarboxylase at temperature above 16 degrees celcius. Histmine is also noteworthy as a substrate for the expression of alergic reactions.

The basic mechanism is using "Band defect network" that was introduced in 'Towards Logical Designs in Biology.' GFP expression is repressed at low levels of histamine but strongly expressed at above threshold level. By this way, we can tell if the fish is edible or not. We are using a well known circuit here, so it might be a nice try.

I thought about the ideas our team produced. I think Bacteria Array is fascinating. But as for the aroma producing bacteria, can the small amount of fragrance produced overwhelm the stink of rotting food?

From Cheolwon Choi, 21st of July

There are people still confused about how to use Google groups. It is extremely SIMPLE. Send your mail to synbiogroup@googlegroups.com and all the team members recieve your mail. Yeap, that's all you need to do.

From Cheolwon Choi, 22nd of July

Hey guys. I wish there were more exchange of ideas by Google. Don't keep your ideas to yourself. Share them with others and discuss freely. Don't think that your ideas are not worth it.

From Hanseung Roh, 22nd of July http://parts.mit.edu/igem07/jam07media/Jam07_Glasgow.pdf Check it out.

From Professor Ingeol Choi, 25th of July

To team members. I have read all the mails and they are great. Try to develop more ideas on the environment part.

- Make a list of ideas and categorize them.

- Do not think about if they would work or not, yet. That's not brainstorming.

- If you want to be more specific, think about what parts or circuits you could use for the idea.

Have you all studied what synthetic biology is? Check out http://partsregistry.org/Catalog. It might help you out. The file included contains my suggestions about your ideas. Have a nice day everyone.

From Yeonjin Kong, 26th of July

As I was looking through some papers, I read about mussels. A Korean science team devloped bio-glue from mussels that live attatched to rocks in the ocean. The problem is that the amount produced is scarce, which we can solve by using microbiology. Bioglue seems attractive.

From Cheolwoo Lee, 26th of July

Remember Kina's idea about geosmin? This is an article about geosmin determined as a criteria for choosing drinkable water. http://www.iipc.co.kr/notice/notice1_view.asp?id=notice&bbsid=notice1&board_id=notice&ref=111&step=1&RefLevel=0&current_page=

From Cheolwon Choi, 28th of July

I made a list of our ideas accumulated till now. You have two votes. Choose two subjects that you think are feasible, interesting, and suitable for synthetic biology. Have your votes sent by Wednesday.

From Hansung Roh, 26th of July

I have my votes for "Bacteria Array."

I also read an interesting article on Bacillus pasteruii which concretes sand into cement using calcium carbonate. It was first invented to solidify bedrocks along beaches but is now planned to build sand walls around deserts to prevent its growth.

These are the links:

http://cedb.asce.org/cgi/WWWdisplay.cgi?0611182

http://www.popularmechanics.co.za/content/news/singlepage.asp?key=229

http://www.news.ucdavis.edu/search/news_detail.lasso?id=8040

http://www.environmentalgraffiti.com/featured/bacteria-sahara-desertification/11121

From Cheolwon Choi, 31st of July

Okay, guys. Here is a sum up of our votes, though I don't understand why you sent your votes through private mails. Our focus would be "Bacteria Array" and "Bacteria Compass."

Mascot Design : Yeonjin Kong, Yoonji Kim, Kina Jeon

Parts Study : Young Byun, Hansung Roh

Circuit Design : Hyukjin Ko, Cheolwon Choi

Brocheure : Cheolwon CHoi

Those who couldn't attend our meeting, help out any groups you would like lend a hand on. As for the parts study, make a list with Excel or whatever you would like to use, and explain how they work. Biobrick numbers registered on iGEM is also crucial.

I am planning of a party? to encourage our team. Post me your convenient time.

P.S. I almost forgot. Use Google group unless it's something VERY private !!! Don't send your mails directly to me. :)

Korean stuffs

• [http://openwetware.org/wiki/IGEM:KU_Seoul/2009/Notebook/iGEM2009 Lab Notebook@Openwetware (한글)]

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