BioWire Preliminary Thoughts
From FreeBio
BioWire Preliminary Thoughts
Things we need to look into:
- Signalling molecules, senders, receivers. (orr)
- Circuit design (FFLs, etc.). (connie and kang-xing)
- Photolithography feasibility. (danny)
- Microscopy/visualization methods. (table for now)
- Modelling. (sasha and kang-xing)
Signalling molecules
How is HSL? Is the part available, can we order it, etc.?
Desirable properties of molecule "A":
- Short range
- Speed of diffusion fine-tuned to model
- Must have receptor for A
- Must be synthesizable biologically
Want a low-latency receiver.
Can we have multiple signalling molecules/pathways at the same time?
Cool patterns- many pulses or waves.
Circuit design
- Incoherent feed-forward loop. Fast excitation. Slow but strong inhibition. Repression needs to dominate over HSL.
- Need a timing diagram.
- Known examples of FFL in E. coli?
- Danny's idea: maybe we can have all of the wire be on while the input is on?
Photolithography feasiblity
- Read up on photolithography.
- Will bacteria stick and to what?
- Talk to Kit. Are there bacteria experts we can talk to? Berg, Losick.
Visualization methods
- GFP-lite?
- mCherry as Chris mentions on possible reporter systems, supposedly this cuts down a lot of the time necessary to see the fluorescent reporter. Has been done in yeast but not bacteria.
Modelling
Two levels of modelling--global and cellular. Do we need to combine the two?
Stochastirator
Moleculizer
Need to find out concentrations of particles to see if we need to model particles individually or if can make the continuous assumption.
Parameters:
- Diffusion coefficient m^2/s
- Degradation coefficient 1/s
Cellular level modelling:
Replicated Mangan and Alon simulation. Incoherent Type 1 FFL. Problem: our circuit isn't exactly incoherent type 1, since it's kind of autoregulatory (not X->Y-|Z, it's more X->Y-|X). So far unable to get pulse-like behavior in X->Y-|X in simulation, but haven't put that much time into it...
