Munehiro Asally Flashcards
(16 cards)
Give examples of chemical sensors
IPTG, aTc, AHLs (QS molecules), Wastes, NO
Give examples of non-chemical sensors
Light, UV, Heat, Electricity
Give examples of high value chemical outputs
Antibiotics, Methan, Vanillin, Drugs
What parameters need to be considered for transcriptional level circuit design?
- Promoter strength (a.k.a binding/unbinding affinity)
- Promoter leakiness and basal expression (there could be an upstream promotor that’s always on)
- RNAP abundances
- Terminator
- Length
How would you tune transcription rate?
- RNAP binding affinities
- Promoter insulation
- Promoter leakiness and basal expression
What parameters need to be considered for translational level circuit design?
• RBS strength o RBS calculator • Codon optimization o tRNA abundances o Codon usages • mRNA stability (decay rate) • Riboregulators • Ribosome availability o Isocost
What parameters need to be considered for post-translational level circuit design?
- Protein stability (degradation rate)
- Protein activity
- Protein localization
- Affinities to other molecules
What is the function of biofilms?
- Adhesion
- Cohesion
- Protective barrier
- adsorption to surfaces
When coupling the sensor and actuator of different cells, what would you do?
change the amplitudes or frequencies but changing the frequency is more robust.
Most ways of communication between cells in multicellular communities are limited by:
Diffusion
What is the units of the diffusion coefficient?
µm2/s
What is time proportional to in relation to diffusion?
L^2/D
D = diffusion coefficient
How would you estimate the diffusion coefficient?
Stokes-Enstein equation.
it depends on temperature (T), media viscosity (n with long second line) and radius R
What sensor molecules enable larger scale coupling?
Volatile molecules like nitrogen monoxide, acetic acid and radicals
What causes Turing patterns?
interactions between two morphogens: slow actuator and fast inhibitor
What reaction puts Turing’s predictions into practice?
Belousov-Zhabotinsky (B-Z) reaction. It serves as a classical example of non-equilibrium thermodynamics (always changing), resulting in the establishment of a nonlinear chemical oscillator.
