Team:Korea U Seoul/Notebook

Meeting

- First meeting with 2014 kuas team members. Discussed about what is kuas, synthetic biology and igem.

Information

- Synthetic biology homepage : http://syntheticbiology.org

- Part legistry page : http://part.igem.org

Homework

- investigate about subject of2008, 2009 igem teams investigate about subject of 2008, 2009 igem teams

Study of igem 2008~2009 colleges

1. Minseob - cell to cell communication

- Outer membrane vesicles (OMV) : gram negative bacteria like E. coli have Outer membrane vesicles (OMV), which can transfer toxin to other bacteria or host strains. Omv is composed of bi-lipid layer with water soluble core, so it can transfer both water soluble materials and lipid soluble materials. Omv is a strong candidate in long-distance messaging.

2. Hyeyeong -sensitivity tuners, color generator

- Different color expression by density

3. Juyoung –biosensor by density

- Check the expression by density divided strong, wild, weak Lock & key, Jammer

4. Heonsong – estimating stress by promoter & microorganism which can produce materials when get some light.

- Formation of hybrid-promoter, light-sensing, biomaterial production

5. Jihee- Biothermometer using RNA, not protein

- RNA double helix come untied when increase the heat.

6. Kyugin- treat for kidney disease

- using NhaA, Urea sensor

Tips of instrutor

1. Categorize the theme.
2. Regulate the level.
3. Refer other colleges access methods.

Discussion of direction

1. Take category- one of food/energy, environment, manufacturing.
2. Investigate some ideas food & energy part until 2013.12.23

Study presentation

1. JUYOUNG

- Siderosphore : Fe3+ absorb, high reducing agent. =>use ocean microbes to greenhouse effect, pathogen control, biofuel

- Degradation Aplatoxin

2. MINSEOB

- GABA : neuro-material.

- T3SS(Type 3 secretion system) : related to plant immunity. Mechanism has been found.

- Pathogen microorganism sensor : use metabolic product as marker like enterotoxin or virulence factor

- PCN(antifungal product)

- Shiga toxin producing E. coli : can develop to cell to cell communication. Herein.

- checker of cosmetics: ex) PH sensor

3. JIHEE

- dye : E. coli producing indigo

- Pectinase+ beta-chrotin, E. coli producing 3-4 nutrients-> making juice

4. HYEYEONG

- bio-filter

- removal odors of food junks : ex)remove pathogenity.

- Soil sensor

Next week

• minseob- GABA, Shiga toxin, components of cosmetics
• jihee- effectiveness of making juice
• hyeyeong- effectiveness of removing bad smells and probability of removing pathogenity
• juyeong- about iron ion, removing ground torpedo microbes

About ideas

1. JUYOUNG

- extension of siderosphore idea

2. MINSEOB

- papers of Sigatoxin

3. JIHEE

- papers about pection production

4. HYEYEONG

- papers of streptomycetes, actinomycetes

Next week

• kyungwoo- feedback to papers
• others- get feedbacks and more study about each idea.

Schedule

Fix idea until middle of January

Accounts

Presentation of ideas

1. JUYOUNG

- Siderophore : absorb iron ion FUR system ) Ferric Uptake Regulator.

- Aflatoxin

2. MINSEOB

- Shiga toxin @ shiga toxin producing E. coli: cause hemolytic-uremic syndrome (Proprotein convertases :change proprotein to protein )

- Messages in a bubble : outer membrane vesicle (OMV)

- Collaboration : proprotein caspases (one of serine proteases, subtilisin serine proteases) , send subtilisin to STEC (destroyed shiga toxin will be sent to eukaryotic, but it won’t work. )

- Develop experiments of Paris

3. JIHEE

- pectinase production from E. coli

- Cellulase+pectinase-> more degradation of pulp

- Use residuum of fruits by pectinase

4. HYEYEONG

- Removing bad smells of food junks

- the main components of bad smells include nitrogen->regulate metabolism

5. HYUKJIN

- Cellulolytic E. coli : cellulose-> oligo-saccharides-> disaccharide -> glucose(Use ocean microbes which can degrade cellulose to disaccharides, Regulating promoter for find ultimate media.)

- Filamentus bacteria phage

- C. glutamioum: agarose fili designing: new microbes, not E. coli

Next week

• Proteins which can attach to filamentus bacteria phage

Dine together: Le’guette 60500 korean dollars

discussion

1. OMV
2. Agarose
3. Bio informatics
4. Micro Dynamics

discussion

1. OMV dynamics
2. Reappearance experiment -OMV
3. Targeting -OMV
4. Agarase + other enzyme metabolic pathway
5. Cellulose degradation –agarose degradation

Ideas

1. OMV reservation
2. Circular per-mutation protein

- advantage : high effectiveness

- high tolerance enzyme : endothermic

- new substrate-specificity expression

Human practice

Apply Univ-expo

Next week

1. minseob –study the structure, what kind of protein we will attach

NGS

Hyukjjin’s presentation

Enzyme fuel cell

reference

1. http://www.sony.net/SonyInfo/csr/SonyEnvironment/technology/bio_battery2.html
2. http://www.nature.com/ncomms/2014/140121/ncomms4026/full/ncomms4026.html
3. https://2013.igem.org/Team:Bielefeld-Germany

Apply Univ-expo

Human practice

1. Waiting contact from Univ EXPO.

Ideas

1. Kyungwoo - Microbial behavior control

Next week

1. Evolutionary dynamics study

Dynamics

1. Game theory : what does other man thinks what I do
2. Future is the reason of the past.

Two prey diet choice program.

Two resource diet choice program.

Calorie restriction

Agarose + glucose media : showing calorie restriction

Rock scissor paper theory

1. (p : secrete toxin, low metabolism ability, r : having toxin resistance , reasonable metabolism ability , s : best metabolism ability among three)
2. The system make balance between P, r, s

Circular GFP

Use various microbes

Parasitic microbes

When the circumstance changes, changing itself will have low effectiveness than living in the nature.

Subject

1. Enzyme whip
2. Sortase application
3. How to design?
4. Agar-metabolic fuel cells
5. Microbial behavior control; popular

JI HEE-DNA SEQUENCING

1. What is DNA sequencing?
2. Basic Method

- Maxam-Gilbert sequencing

- Sanger sequencing : chain terminating->Dye-terminator sequencing

3. Advanced method

- Shotgun sequencing

- Bridge PCR

- Emulsion PCR : DNA fragments are amplified upon primers attached to beads

4. Next generation method

- 454pyrosequencing

- Illumine sequencing : use bridge PCR

5. Next next generation sequencing
6. Next next next generation sequencing

Sponsor

1. crowdfunding –research sponsoring site , happybean
2. The Korean Federation of science and technology society
3. apply for ERA synbio
4. CCP-(not settled)

Todo List

1. airplane& accommodation reservation

- airplane ; H.Y.Choi

- accommodation ; J.H.Park

2. group t-shirt
3. novel human practices ; each person should propose at least one idea.
4. we should get better results than high school iGEM.
5. wiki design ; D.H.Kim -complete within August
6. poster design ; J.H.Park-complete within August

Todo List

1. iGEM safety form
2. human practice) poster display, facebook, reports
3. experiment designing
4. new application part !
5. group t-shirt
6. way to earn money

Todo List

1. Attention fee for Giant jamboree
2. inquiry of speech in CSIA
3. preparing wiki materials
4. making material for public relations
5. Measurement interlab study
6. making projet proposal - microbiology lab of CSBL for high school students

Todo List

1. fill in wiki
2. making materials for public relations
3. CSIA speech
4. measurement interlab study-x
5. feedback from professor
6. present condition of experiment

Todo List

1. fill in wiki
2. making film for crowd funding
3. present condition of experiment

Todo List

1. making film for public relations
2. speech in CSIA on August 20th 4p.m.
3. present condition of experiment

Todo List

1. present condition of wiki, public relations, experiment
2. approvement of ‘check in’
3. human practice-CCP
4. resetting timetable
5. payment of attention fee in Giant Jamboree
6. plan for boston

Todo List

1. Present condition of Wiki
2. Present condition of the Tumblbug
3. Present condition of experiments
4. apllication of ccp

Todo List

1. Present condition of Wiki
2. Present condition of the Tumblbug
3. Present condition of experiments
4. delay of ccp
5. visa

Todo List

1. Present condition of Wiki
2. Present condition of the Tumblbug
3. Present condition of experiments
4. delay of ccp
5. judging form : https://igem.org/2014_Judging_Form
6. poster guide line : https://2014.igem.org/Poster_Guidelines

Todo List

1. data roaming : egg
2. visa : HJY, JKJ
3. Wiki page-part check

- judging form

- who did experiment, sponsor, advisor

- safety questions

- team collaborations

4. present condition of the tumblbug
5. present condition of experiments