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Sunday 19th July 2009

Project phases

Phase 1- Compound/threshold/detection

  • Chassis?
  • List of specifications


  • 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


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
- 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!