Team:KAIST-Korea/Notebook/Diary/June

June 1

1. Contact List
   • S.B. Yang> keep contacting the guys (sponsors).
   • HNMT

   Ajou Univ.: S.H. Kim, H.J. Yun

   Database: H.S. Kim, J.B. Jung

   • Spike Proteins

   Seoul Asan Hospital: N.B. Lim, E.S. Kim

   Foreign institute: S.J. Kim, K.K. Kim

   Seoul Nat. Univ.: Y.W. Yang, D.C. Yang

   • contact by tomorrow (tel., e-mail)
2. Homepage - work on it
3. project name
   • SARS
   • Corona Secretion Vesicle
   • V- Carpet boming
   • SCV
   • Smart Vesicle
   • At the end> AVRI 1 (everyone Auto-targeting Vesicle Releasing Instrument)
4. LT
5. GenoCon
6. assignment due
   • Contact by tomorrow
   • Group photo tomorrow 17:30
   • stanford (K.K. Kim, H.W. Yang, S.J. Kim), E.coli exporting system (E.S. Kim, J.B. Jung, D.C. Yang), Yeast(H.S. Kim, S.W. Kim, S.B. Yang, N.B. Lim, H.J. Yun), Mammal cell()
   • ppt by Thursday 16:00
   • ppt : N.B. Lim, J.B. Jung

Meet at 4 o'clock from now on.

June 3

Discuss on HNMT, Secretion system - Some E.coli has secretion system which secretes materials without vesicle. There are vesicle that is made in outer membrane not in cytoplasm. And we don't know which makes vesicle to be formed. So we can't regulate its behavior. But fortunately there are vesicle formating bacteria in some studies. But their main purpose is to deliver the antigen and ours is delivering drugs with spike protein. But we haven found a way to do this. Therefore we decided to look for that information.

June 7

1. HNMT - find a way to acquire it.
2. Signal Peptide
   • We found signal peptide that works on human cell. Since we will use e.coli, found signal peptide should replace e.coli's one. E.coli's signal peptide is short, so we just synthesize it. Cutting human's signal peptide is problematic: appropriate restriction enzyme is needed, which may not exist - Thorough search is required.
3. Homepage
   • Use Namo web editor. Get designs ready. Design logo, 'AVRI 1'
4. Fine (meeting)
   • Unannounced: \5,000 (should be addressed with proper reason at least an hour ago)
   • Late: \1,000 per 10 min.
5. Contact: N.B. Lim, D.C. Yang, H.W. Yang, H.J. Yun

• Assignment

- Find HNMT - Way to replace signal protein

June 8

Other ideas idea 1

There are some micro organism that transform ammonia to nitrous acid. Maybe we can use this to make some kind of water purification system or using it for removing bad smell.

idea 2

Making a filter system that can kill other bacteria for air conditioning system. Or we can extend this idea to make a water conditioning system.

idea 3

In 2007 iGEM competition there are study that is about curing cancer. They made a system that can detect and cure cancer. They used a spike protein to target specific cancer. And maybe we can extend this idea for our own project.

idea 4

Since there are bacteria timer and we can control it. If we use this idea, we can make a system that make corrosion of iron. Then we can make a timer that make a some kind of structure in iron.

idea 5

There are sensor that detect 4 components on cancer tissue. If we can put antibody and get a signal from it then we can make a bacteria that has antibody which can detect cancer. We can make pH to be the output or some kind of chemicals or GFP.

idea 6

There are some people in america who eat cyano bacteria. Since one of the good point of bacteria is their rate of reproduction, if we make a bacteria that alternates food than it will be very useful.

idea 7

There are many people who suffer from gas poisoning and explosion. So we thought of a sensor that can detect harmful gas. Since gas poisoning occur because affinity of harmful gas with hemoglobin than oxygen, we can make a system with hemoglobin to detect harmful gas.

idea 8

There are many project that made a experimental protocols or simple version of its systems. So maybe we can look for difficulties in experimental life and give an improvement.

June 10

1. Call Prof. Park.
2. Upload layout: S.J. Kim (referred wikis)
   • mediawiki Extension

   flash show

   cite

   Image map

   Get administer's e-mail (N.B. Lim)

3. Rough copy of self-introduction
4. Topic: Let's stick with current topic. If there is new idea, proceed it as a subtopic. Put priority on the main topic. Design and architecture of homepage will be based on the current topic.

June 12&13

We talked about logo design.

1. Meet Prof. Park (Monday) (K.K. Kim , N.B. Lim, D.C. Yang)
2. 바이오니아 (Wednesday)
3. Photo at 2 o'clock on Tuesday
4. Hoping gene delivered during this week. (Potential request to Bioneer)
5. Experiment starts next week. Contact professor.
6. Construct homepage on Monday. The front page's design is complete.

--- Monday --- Meet Prof. Park Design of homepage's main page Team introduction --- Tuesday --- Take photos at 14:00 --- Wednesday --- Contact Bioneer

June 15

Fusion Antibody: Illinois team does not show what they did. We got to investigate 'fusion antibody' ourselves. http://www.springerlink.com/content/16lv45623117qj15/fulltext.pdf http://www.cbcrp.org/research/PageGrant.asp?grant_id=163

1. Study Illinois team
2. Search 'fusion antibody'

misc. - photo time is moved to 3 o'clock on Wednesday

June 16

Making Team intro., abstract in wiki

June 21

We decided to visit 바이오니아 at Wednesday 10AM We are making improvement on media wiki menu. We did the diary design. We need to research if we can do this on yeast.

• Assignments

1. Individual photo
2. Self comment

June 22

Decided a final idea -Our final idea is using cytokine receptor. This will be acting like kinase. There will be JAK1 attached to cytokine receptor. Then STAT1 will be attached later if the receptor gets signal. After that two STAT1 will be combined to turn on the GAS promotor. Then we can activate GFP. We also can use STAT1, STAT2, and IRF6 promotor in the same way. And we will be using YAC since plasmid will be in large scale.

we decided wiki menu design.

June 23

We had a meeting with professor in Bioprocess engineering Research Center, Tae Jung Park. He said that we can't use yeast as our host because it is very hard to express GFP and it will take a long time to detect cancer. Therefore there will be no advantage in using yeast as our host. So we have to use e.coli as our host. And we assign each one in separated parts for efficient processing.

1) management : NB, HU. 2) cloning : SB, JB, HJ, ES 3) culture : DC, GG, SJ 4）checking protein expression : SH, HS

June 24

We searched for the protocols of our experiment and materials that we need.

June 25

1. Listing experiment materials by Sunday
2. Plasmid design
3. Looking for the host of our system.

We decided to design 2 plasmid. One has two promotor and behind each promotor it has GFP and fusion antibody sequence. Other one has one promotor with two RBS to separate STAT1 and JAK1.

June 28

We decided what to put on our main wiki menu. We listed the materials for our experiments that we need to buy.

Sub-Menu