BioWire Progress Report Week Two Orr Ashenberg, Patrick Bradley, Connie Cheng, Kang-Xing Jin, Paula Nunes, Danny Popper, Sasha Rush

What we did last week Ordered BioBricks Experiments – Miniprepped the BioBricks Modeling Photolithography

Modeling

Photolithography Went through microprinting process for mammalian cells in Kit’s 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.

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.

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.

Schedule (old) Week 1 (6/6): Project Choice and Design Week 2 (6/13): Test AHL receiver/sender Week 3 (6/20): Test sender+receiver 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): “

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 couldn’t 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): “