BioWire Progress Report Week Two

1
BioWire Progress ReportWeek Two

• Orr Ashenberg, Patrick Bradley, Connie Cheng,
  Kang-Xing Jin, Paula Nunes, Danny Popper, Sasha
  Rush

2
What we did last week

• Ordered BioBricks
• Experiments
• Miniprepped the BioBricks
• Modeling
• Photolithography

3
Modeling
4
Photolithography

• Went through microprinting process for mammalian
  cells in Kits lab.
• Still checking out specific proteins to use in
  modifying process for E. Coli (mannose to adhere,
  BSA to resist adhesion)
• In process of finding out CAD rules to design our
  own masks and stamps.

5
Update on the Weiss Circuit

• They are working on the same PPG (propagating
  pulse generator) design as us.
• They have simulations done, but no experimental
  data.
• Their simulations show potential back-propagation
  and self-signaling.

6
New Ideas

• Have two signaling mechanisms to create circle or
  line oscillator
• Lux with either Las or Rh1
• Would require two routers to receive the old
  signal and begin the new one.
• Challenges Designing another signaling pathway,
  crosstalk
• Use one signaling pathway to create line
  oscillator
• Bounce the pulse through the wire with delays on
  the ends
• Use an intracellular lactonase
• Allow for faster AHL degradation to reduce noise
  and potential back-propagation.

7
Schedule (old)

• Week 1 (6/6) Project Choice and Design
• Week 2 (6/13) Test AHL receiver/sender
• Week 3 (6/20) Test senderreceiver and repressor
• Week 4 (6/27) More tests
• Week 5 (7/4) Finish testing
• Week 6 (7/11) Test cell signaling density
  photolithography done
• Week 7 (7/18) Construct IFFL (incoherent
  feed-forward loop)
• Week 8 (7/25) Test it
• Week 9 (8/1)
• Week 10 (8/8)
• Week 11 (8/15)
• Week 12 (8/22)

8
Schedule (new)

• Week 1 (6/6) Project Choice and Design
• Week 2 (6/13) Got parts and set up tests
• Week 3 (6/20) Get remaining parts Test all
• Week 4 (6/27) Tests we couldnt get to last week
• Week 5 (7/4) Finish testing
• Week 6 (7/11) Test cell signaling density
  photolithography done
• Week 7 (7/18) Construct IFFL
• Week 8 (7/25) Test it
• Week 9 (8/1)
• Week 10 (8/8)
• Week 11 (8/15)
• Week 12 (8/22)