Team:KU Seoul/Notebook

Discussion

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

- Bacteria Array

Should we focus on the result, or the procedure?

Decision making

From Ingeol Choi, 22th of September

From Hansung Roh, 24th of September

The prices are really good.

From Ingeol Choi, 24th of September

The plane tickets seem nice. Go make the reservations.

From Hyukjin Ko, 23rd of September

The PCR results came out well, except for the vectors.

I will rerun the vector PCRs in different conditions.

The PCR results will be attatched.

From Young Byun, 23rd of September

http://air.interpark.com/lts/jsp/discountCity.jsp?SaleType=M&areaCode=U1&CityCode=LAX&aNationCode=US&mbn=tourair&mln=air_country04&tdOpen=Y#f_air

It's a discount ticket from Incheon -> Narita -> New York -> Boston for only $1000!!!

It might be annoying to wait for planes during intervals, but I think the cheap price beats it.

We will depart on 29th of October and arrive on 3rd of November.

There are not that many seats left, so I think we should make reservation till this weekend.

From Young Byun, 23rd of September

I am terribly sorry for the delay.

I am not trying to make excuses, but I had severe fever and almost forgot about the abstract.

I sent it today.

I just wish it's not too late.

From Ingeol Choi, 22th of September

[Fwd: Missed iGEM deadline: Project abstract and title]

What's going on guys?

From Hyukjin Ko, 21st of September

There's a Korean Synthetic Biology conference this week.

If you have anything to present, send them to me.

Those who are interested are welcome to join me.

From Young Byun, 21st of September

I will look over your abstract, Cheolwon. I think it's great.

From Hyukjin Ko, 19th of September

I thank those who came to the meeting today.

We finished plasmid extraction.

The attatched file is its result.

We will run PCR when the ordered primers arrive on Tuesday.

I will post the ppt file for today's meeting tomorrow.

From Cheolwon Choi, 19th of September

I made our team abstract. My poor English fails me.

Our team project is related to the detection system for heavy metals which are harmful for environment, such as arsenic, mercury, and cadmium. The purpose of this project is to detect the concentration of heavy metals in the waste water with mixed color system. We use several flurosence proteins GFP RFP and amd gene as detection markers. Each heavy metal promoter produce matched flurosence protein. For examples, High concentration of Arsenic could induce the green flurosence with GFP proteins. Such system works very well as accurate as ppb (parts per billion concentration) Finely, the mixed heavy metals produce gradient and mixed colors according to light mixed rules. This system is more effective than previous circuits because of integrated analysis.

From Ingeol Choi, 18th of September

Make sure Jamboree registration is done.

Update wiki, Young and Hansung.

Design Team T-shirts.

From Hyukjin Ko, 17th of September

We transformed our parts to E. coli DH5a and ccdB survival strain in the morning.

We wll work on plasmid mini prep. and agarose gel electrophoresis after supper.

I think we should meet on Saturday (19th), 2p.m.

The meeting will include:

1. primer design & cloning method

2. discussion for refined design

It's not compulsory, so those who are not interested don't have to come.

http://ginkgobioworks.com/support/

I am sure most of the members know this, but reviewing is always a good idea :)

From Ingeol Choi, 17th of September

Register the Jamboree members, Hansung.

From Hyukjin Ko, 17th of September

The ppt file is from the presentation I made on Tuesday.

It includes all the explanation.

As I have mentioned on Tuesday, we will be using degradation tag to remove already expressed proteins.

We are going to transform the parts from the distribution plate.

Members expected to come at the scheduled hour should be here on time.

I am planning to give detailed explanation on the primers on Saturday.

From Ingeol Choi, 17th of September

The hotels have been reserved.

Hyatt Regency 10/30(Fri)~11/2(Mon) (3 nights)

Check out the flight plans also.

There is no direct flight from Incheon to Boston.

Progress is slow, but I think we are on track.

Burn your fuels.

From Hyukjin Ko, 16th of September

Graduates stay in the lab most of the day, so don't worry about our schedules.

Drop by any time. :)

I will try to post our actual plans tonight.

From Jihee Jang, 15th of September

I will make an excel file that shows everyone's available time.

Send me your free time schedule that you are willing to spend for our experiments.

From Hyukjin Ko, 14th of September

I will visit Professor Choi on Monday and discuss final decisions.

We need to amplify the required genes, and grow cells to extract genomic DNA. Additional plates are also needed.

I will explain more about the details on Tuesday, 5 p.m.

It is mandatory that all members attend.

From Hyukjin Ko, 11th of September

Now that's what I call useful information.

Way to go, Young.

From Young Byun, 1oth of September

I just read a paper on YodA protein!!!

It's a cadmium specific protein.

It is normally kept at a low level, but when Cadmium is induced to the cell, the concentration goes up 50 times.

The beautiful aspect is that it is very specific for cadmium and no other metals.

School festival is coming up.

From Young Byun, 10th of September

I found this paper using LazZ and lux to detect mercury by attatching them to mercury promoter PmerTPAD and

Cu promotoer PcoE.

Cu showed gradual response to concentration, but mercury only showed threshold response.

I think Lux is a good tool for detection we could try out on our experiment.

Fund raising is not going well.

The big companies are not cooperative either.

Sigh.

From Cheolwon Choi, 10th of September

I think cadmium sensing protein CadC could be used.

I think they are not included in the iGEM distribution, but it works in E.coli.

Part:BBa_K112406

From Cheolwon Choi, 10th of September

Our final brochure.

From Hyukjin Ko, 9th of September

The papers Keena presented were completely irrelevant.

We need to use microbes that detect heavy metals using a specific system.

These papers seem to explain human related genes and their relationship with heavy metals.

To make it short, I need more information on Pb and Lead.

Ars, the information Young sent me was quite useful.

I know school started, but why do I always see the same people trying really hard while others do nothing?

Professor and other students are not working on the project because they got plenty of time left.

It's your iGEM. Work on it.

I want to order the primers till this weekend so we can start our experiments on Monday.

See you all.

From Keena Jeon, 8th of September

I am not sure if these are useful, but I think it contains some information.

Give me feedback.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2535653

From Ingeol Choi, 7th of September

1. What about circuits for other metals?

2. How will you use AMD as a reporter?

3. Any simulations?

From Cheolwon Choi, 7th of September

The meeting held on Friday was great.

Almost all members attended the meeting: Hansung, Hyukjin, Jihee, Jihae, Young, Simin, Cheolwoo, Yeonjin, and me.

Sadly, Yeonjin, Keena and Yoonjoo is quitting iGEM project due to personal reasons.

Young, Jihee, Jihae, Hansung, and I am going to attend the Jamboree.

We decided to separate the members for our experiment.

The problem at hand is what parts we are going to use.

We will be also looking for sponsors next week.

Have a great week all !

From Hyukjin Ko, 7th of September

I tried to post it on the weekends, but something came up.

It's a simple draft of the circuit.

Explanations are included in the files attatched.

Good night everyone.

From Ingeol Choi, 2nd of September

[Fwd: Team KU_Seoul: Check In 2]

It's a letter from HQ.

I won't be able to attend the meeting on Friday due to work, but have a great time.

Have the bill sent to my lab.

Find out who is joining the Jamboree.

I need to make reservations for the hotel.

As for the fund raising, try to estimate the total amount of cost.

We can try to receive supports based on that.

From Cheolwon Choi, 2nd of September

As I have announced before, we will meet on this Friday and have dinner together.

I wish all the members come.

6 p.m. West Department 1st floor.

From Young Byun, 2nd of September

I have tried various corporates and associations, but they are not that willing to support us.

I do understand that it might be waste of money for them, but it is really disappointing.

The attatched file includes addresses to few places that gave relatively positive response.

I am planning to visit them next week.

Anyone who wants to go, text me.

From Ingeol Choi, 31stof August

https://2009.igem.org/Team:KU_Seoul

Color selections are fine, but try to make them brighter.

They are kind of dark.

From Young Byun, 31stof August

I have changed the design and colors of our main page.

See if it's okay and give me comments so I can fix it.

I will apply it to every other sections.

From Cheolwon Choi, 30th of August

The vacation is almost over, and 2nd semester is coming up.

I am planning to have a meeting next Friday, 4th of September.

We will be using the lab after class, so approximate time for our experiments would be around 5 p.m.

Have a nice weekend.

From Hansung Roh, 30th of August

Nice job, Young.

I will help you.

From Young Byun, 29th of August

I have updated the Notebook section of our wiki.

The discussion we had during July has been updated.

I have a hard time figuring out how to link pictures with other sites.

Someone help me out.

From Ingeol Choi, 26th of August

Nice work, Young.

Try to update wiki as well.

From Young Byun, 25th of August

I have sent the Preliminary team track selection.

I considered it urgent.

We need to visit iGEM home more often.

From Ingeol Choi, 25th of August

1. Most metal detectors can be used in E.coli. I think we can make them with PCR.

2. Look for parts for other metals. If they are not registered, let us do the job.

The brochure is fine, but try to make it look more professional.

Remind yourself that it's not to introduce me, but to introduce Team_KU.

The Samsung sponsoring did not work out well.

They say their budget plan is full.

Our preliminary team track selection should be environment.

I don't remember sending preliminary team track selection, which probably means nobody did.

From Hyukjin Ko, 24th of August

Sorry for the late letter.

Mercury detecting part BBa_I728456 and other parts are all not included in the 2009 distribution plate,

which means we would not be able to use them.

You can check available parts here.

http://partsregistry.org/Help:IGEM_09_DNA_distribution

I am currently on vacation, but I will try to build a circuit using AMD.

Have a nice vacation!!!

From Cheolwon Choi, 23rd of August

Here's our brochure.

Comments are welcome.

From Young Byun, 22nd of August

What do you mean by Preliminary team track selection?

Have we sent it?

Are we on the right track?

From Ingeol Choi, 19th of August

Visit me on Monday.

[Fwd: [iGEM Interest] The MathWorks offer deadline and Preliminary track selections]

Check the letter.

From Cheolwon Choi, 19th of August

Yes, I will have the brochure done by 23rd.

We will discuss about the participants of CCP on Friday.

I also need your approval of our team.

May I visit your office on Monday?

From Ingeol Choi, 18th of August

Seems like a good chance.

Try to make a brochure as well.

I am planning to visit Samsung next Tuesday, and I need it.

From Cheolwon Choi, 18th of August

CCP stands for Creative Challenger Program.

It supports teams like us, but we need to register and compete to be selected.

Let's give it a try.

From Ingeol Choi, 18th of August

The metal promoters registered do not seem to work.

http://partsregistry.org/Promoters/Catalog/Metal_sensitive

From Young Byun, 18th of August

This is an Arsenite part I found on the web.

There is no Arsenite part registered on iGEM currently.

Let us register it.

http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00239

From Ingeol Choi, 17th of August

If we are thinking three inputs, we can use the tri-stable switch.

http://openwetware.org/wiki/IGEM:Brown/2007/Tri-Stable_Switch

Professor Kwangil Ko is working on something similar.

You might want to visit his lab.

Update your wiki!

From Cheolwon Choi, 17th of August

I think we have found all the sensors for lead, arsenic, and mercury.

We should now focus on how to express them.

For example, if we mix up GFP, YFP, RFP, would the results come out as a mixed fluorescence?

We can also use pigments, but we must look for them.

The amd gene professor recommended seems like a good candidate.

However, if we are to express them differently, we need two more pigments.

Let's look for them.

From Ingeol Choi, 15th of August

1. You can sense and bind mercury with MerR ( However, it might bind other metals as well.)

2. It would be great if we bind all four different metals simultaneously( which should be hard).

3. Talk with Hyukjin for experiment planning.

4. Synthetic Biology team is going on a trip for three days. We won't be able to make it on Friday meeting.

From Simin Kim, 14th of August

IGEM 2007 team has already tried mercury metal sensor, but they failed to make it work. (http://parts.mit.edu/igem07/index.php/MIT) I think this is due to lack of appropriate biobricks registered. I am looking through other teams to study. Hope we can all meet on Friday. See you all.

From Ingeol Choi, 15th of August

1. Signal in: Mercury detection: MerR - mercury binding protein regulator

2. Signal out: amd gene cloned by Hyukjin (Able to detect with Tyrenol)

References

http://mic.sgmjournals.org/cgi/content/abstract/152/3/709

http://www.ncbi.nlm.nih.gov/pubmed/10503547

http://www.sciencemag.org/cgi/content/abstract/301/5638/1383 (copper?)

From Young Byun, 14th of August

I designed our mascot as I mentioned. I will put it up on wiki. See how it looks.

From Ingeol Choi, 13th of August

https://2009.igem.org/Judging has been posted. See what is needed. Confirm who's going to the Jamboree.

From Cheolwon Choi, 8th of August

I finished our brocheure. Let's make a list of places to visit for our fund raising.

From Hansung Roh, 8th of August

Participants : Youngseol Byun, Hansung Roh, Hyukjin Ko, Cheolwoo Lee

Discussion 1 : We need to study the mechanisms for our parts. Understand how they work.

Discussion 2 : We are going to have our detector show the difference in concentration. Check out the former iGEM team that worked on Vanillin.

Conclusion : Study circuits and how to build them.

From Ingeol Choi, 7th of August

Jamboree registration starts at last. Get excited!!!

From Young Byun, 7th of August

How is creating our mascot a bacteria holding a metal detctor? I will work on it.

From Cheolwon Choi, 6th of August

Thanks for the feedbacks. Can you guys send me your thoughts about iGEM to put them in our brocheure. Slogans for the brocheure are also welcome.

From Hansung Roh, 6th of August

We need a decent title for the brocheure. How's 'We design life!!! - Metal detecting cell' ? We need something strong!

From Cheolwon Choi, 5th of August

I agree with Young.

I made a brocheure for our fund raising. I need feedback.

From Young Byun, 5th of August

I think the logo should contain something to do with our project. Nice work, though.

From Yoonji Kim, 5th of August

I made our logo for iGEM. They come in two different colors. See and how you like it. Give me suggestions.

From Ingeol Choi, 3rd of August

Don't worry. Team Gronigen's project and ours is quite different. Update our project discription for wiki.

From Cheolwon Choi, 4th of August

Thanks everyone for your participation inspite of vacation. I refined my ideas and made some fixes with the diagram I sent before. See what changed.

From Young Byun, 4th of August

Team Gronigen seems to do something similar with us. https://2009.igem.org/Team:Groningen Check it out.

From Young Byun, 3rd of August

Among the teams of iGEM 2007, there's a device that compares A and B's concentration. I think we can use this to figure out which metal is contained more.

I have looked up the parts for Lead, Cadmium, Mercury as Cheolwon had suggested. As for lead, it is confirmed that it works well but for cadmium and mercury we have to try them ourselves.

I added an excel file that shows the parts I looked up.

From Hansung Roh, 3rd of August

I looked up some parts in the registry with the keyword Metal. It seems like there are not many that we can use. How is everyone else going?

From Cheolwon Choi, 3rd of August

Here is a schematic diagram of biosensor. Your opinions are very welcome.

From Young Byun, 1st of August

Send me your photos and a short description of yourself by this weekend. Mottos and your message to iGEM are very welcome. Have a terrific weekend !!!

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. :)

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

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 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 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, 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 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 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 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 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, 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 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, 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.

Korean stuffs

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