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From 2011.igem.org

Contents 1 2/11 - Orientation(1st meeting) 2 2/16 - The basics 3 2/18 - Parts registry 4 2/21 - Q & A session 5 2/23 - Groups formed 6 2/25 - 2010 iGEM posters (Slovenia, Peking, Bristol)

2/11 - Orientation(1st meeting)

• 2010 KU iGEM team member's presentation
• Advisor's presentation
• 2011 KU iGEM team member introduction

2/16 - The basics

We had a second meeting to study about iGEM registry.

• We learned about:

1. A reason for using low # in plasmid backbone's operation, and its merits and demerits.
2. How to express parts of plasmid such as RBS, promoter, ...etc.
3. Types of restriction enzymes
4. Why a scar occurs and how to prevent it (Silver's method, application of Berkley's method, Lim standard)
5. How to construct a backbone having desired origins and antibiotic resistance based on Reshma method.
6. Practical usage in companies.
7. Both parts and plasmids can be archived (recording, saving, storing)

• What we didn't understand were:

1. Why scars occur, and preventing shift caused from it, and a relationship between mixed and scar.
2. What the meaning of 'shuffling protein domain' and 'overhanging of 4 base pair' in Lims standard are.
3. Relationship between restriction sites E, S, N.

2/18 - Parts registry

• We continued studying about parts registry.

http://partsregistry.org/Part_Names

http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix

http://partsregistry.org/Assembly:Composable

http://partsregistry.org/Help:BioBrick_Assembly

http://partsregistry.org/Assembly:Standard_assembly

http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly

http://partsregistry.org/Assembly:Rolling_assembly

http://partsregistry.org/Assembly:RBS-CDS_issues

http://partsregistry.org/Help:Ribosome_Binding_Sites

http://partsregistry.org/Ribosome_Binding_Sites/Catalog

http://partsregistry.org/Ribosome_Binding_Sites/Further_Reading

http://partsregistry.org/Ribosome_Binding_Sites/Glossary

http://partsregistry.org/Help:Ribosome_Binding_Sites/Mechanism

http://partsregistry.org/Ribosome_Binding_Sites/Design

http://partsregistry.org/Ribosome_Binding_Sites/Construction

http://partsregistry.org/Help:Ribosome_Binding_Sites/Standard_Assembly

http://partsregistry.org/Help:Ribosome_Binding_Sites/Mechanism#The_Shine-Dalgarno_Sequence

• We studied about part's prefix and suffix and how to assemble it. We went further to find out what an RBS is, and studied glossaries and composition of them. Then we asked concepts we didn't understand to advisors.

2/21 - Q & A session

Today’s meeting was canceled due to an unexpected problem with school’s Wi-Fi. We therefore had a question-and-answer session.

• The questions were:

1. Aligned space.
2. Orthogonal RBS
3. Meaning of 'various purposes of origin of replication'.

2/23 - Groups formed

We finished studying the 'Help' section of registry.

• What we learned and did:

1. Termination, rho-dependent/independent pathway, types of RNA polymerase.
2. Design, components, construction, efficiency of terminator.
3. There are forward, reverse, and bidirectional terminators.
4. How to differentiate between natural parts and synthesized parts using barcode.
5. Parts symbols.
6. Read dissertations related to the above topics.

• Questions

1. The relationship between poly (A) tract, poly (T) tract and bidirectional terminator
   • (http://partsregistry.org/Help:Terminators/Design)
2. What is a reverse primer and why we need to design it in oligo terminator construction
   • (http://partsregistry.org/Help:Terminators/Construction)
3. The meaning of forward/bidirectional/reverse terminator
4. The Existence of forward/bidirectional/reverse terminator in eukaryotic cell
5. The meaning of barcode in forward/bidirectional/reverse terminator
6. The meaning of stop/start/binding symbols

• Conference

- We decided to see previous years’ finalists' research for brain-storming.

- Kyengwoo Jang will be editor-in-chief of wiki, and Min-jeong Lee will manage tweeter. Other members will also play a part in managing them.

- We divided the team into three groups for effective drawing of ideas.

• Group 1 : MinGyu Kim, Seungwan Chae, Haerim Song, YunHyung Choi, Sooyoung Yoon, JinSick Choi.
• Group 2 : JeongWan Chae, Kyengwoo Jang, Ji-hyong Nam, Jong woo Hong, Min-jeong Lee, Songa Jung, Areum Go.
• Group 3 : Seong Min Pak, Yeji Chae, Seungbo Ryu, Hanon Lee, Beomgyo O, Heuiseop Jung.

- Once first semester begins in March, we will have meetings once a week.

- Until the end of March, we need to gather/organize our ideas and make overall outline of our research procedure.

2/25 - 2010 iGEM posters (Slovenia, Peking, Bristol)

We studied using 2010 iGEM teams’ posters. We focused on coming up with ideas and observing how the posters were made, rather than trying to understand the overall mechanism.

1. Slovenia
   • Zinc finger; viewing it methodologically: SPR, EMSA, beta-galactosidase activity
   • Explanation of oscillators based on ZNFs
2. Peking
   • Heavy metal decontamination kit; detection of mercury and its coagulation.
3. BCCS-Bristol
   • Measuring of nitrogen concentration using microorganism to measure soil fertility level.

• Conference

- We decided to receive additional applications to join the KU-iGEM team until 28/2/2011.

- After first semester begins, meetings will be held every Friday at 7PM

- Leader of each group

• Group 1 : MinGyu Kim
• Group 2 : JeongWan Chae
• Group 3 : Seong Min Pak