IGEM:IMPERIAL/2009/Feedback

Sunday 19th July 2009

Project phases

Phase 1- Compound/threshold/detection

• Chassis?
  
• List of specifications
  

Phase2-Encapsulation

• List spec
  
• Pros and cons of each method
  
• Polyglu
  

Phase 3- Killing strategy/gene deletion

• List spec
• Mechanism:Double mechanism-fail safe
• Sensing environment vs. timer
  

Phase 4- Storage

• Short term vs. longterm
  
• Application
  
• Viability/stability
  

Phase 5- Delivery

• Application
  
• Pros and cons
  

Research strategy suggestions

• What is your interest?
  
• Main stream press
  
• Motivation: Search for current problems?
  
• Find genes and compounds they code for
  
• Interesting molecules
  
• Recent
  
• Exciting
  

Deadlines

Sunday 19th July

• Shortlist
• Apply to framework

Monday 20th July 10am

• Go through everything
• Assign key roles
• Get details of what we are doing by the end of the day

Tuesday 21st July 2009

Presentation Session Feedback

• Prof:
  

Need a project overview
Presentation does not follow the engineering process
- need 2-3 slides focusing on this
PKU
- there is a real problem/real emotional message to get across
- is a novel application!
Focus on one application with the method being compatible to other applications

• Advisor:
  

Need details of the enzyme
- where it works
- where the conversion occurs etc.
What is the recommendation per module?!
- Need a summary after each

• Prof:
  

More modelling
- Have the PKU pathway

• Prof:
  

How to trigger encapsulation process?
How feasible is the killing strategy?

• Prof:
  

Which track are we aiming to enter?
How close is this to previous projects?
Need something that actually works with results
- killing strategy
- encapsulation

• Prof:
  

Match the thresholds and sensitivities
- can be done
- use GFP reporter with an optical read out?

• Advisor:
  

Produce 2 chassis/cells?
Explore module, get genes, find existing bacillus/E.coli chassis, one with a good coat formation and one that can produce the drug.

• Prof:
  

Create new self encapsulation module
Take out the biological pathway and place in Bacillus
Drill down
Make sure it’s quality controlled before consumption

• Prof:
  

Be brutal in testing the risk for each module
Try to order parts ASAP
- waiting time should not be a limiting factor
Come on a lot since Friday
- got bones of a good project
- like idea of modules

• Advisor:
  

Write a high level specification page (case study almost?!)
Look at an E.coli apoptotic mechanism
- there is one

• Prof:
  

What about the proteases?!
- Use protein deficient strain?
Still a lot of yes/no points we need to sort out

Deadline for BioBrick design: Friday

• Prof & Advisor:
  

What is the critical path in the project?

• Prof:
  

Amalyse, protease, lipase deficiency?
Enzyme deficiencies in the gut
Need the pros and cons of different applications
- where are they on they wiki?
- convince what you want to pick is feasible/efficient
- what are the mechanisms (existing)
- why do we need the enzyme?
- regulation, control, how does it know what/how much to make?
- give details, details, details!