Lecture 8. Principles of Gene Circuit Design 2 Flashcards
What is a chassis?
The biological host for plugging in synthetic biology circuits (eg DNA)
What are examples of chassis?
E. coli
B. subtilis
P. putida
S. cerevisiae
What are the uses of an oscillator?
Automate recurring tasks
Navigation
Spatial patterning (temporal dynamics)
Sensor
Communication
Encoding
What is a repressilator?
Ring oscillator where three inputs inhibit each other (think rock paper scissors)
What equation is used to tell you when a system will oscillate?
y = (β / (1+x^n)) - x
β = promoter strength
n = sensitivity
What do you want in a repressilator model?
Strong promoter (high β)
Ultrasensitve repression curve (high n)
Low leakiness (ideally zero)
Similar protein and mRNA decay rate
When does a ring oscillator produce oscillation?
When n>2, oscillations sustain when β (promoter strength) is n sufficiently high
When ring oscillator has an odd number of nodes
What is the role of a repressor sponge?
Repressor has an additional site to bind, causing threshold level to shift
What improvements have been made to the ring oscillator?
Integration of reporter system
Degradation machinery (minimise protease competition)
Repressor sponges
Culture condition
The threshold was so low, which caused a lot of noise in the system
In a colony, what can oscillations be translated as?
The growth of a colony is driven by the replication of the cells at the leading edge. Interior cells reduce its metabolic activity, which result in locking their oscillation state –giving rise to a spatial pattern.
What is key to oscillator design?
Delayed negative feedback can produce self-sustaining oscillations
The precision of repressilator can be improved by
simplification
Combining negative and positive feedback loops enables relaxation oscillators
Negative feedback can be improved by simplification
What is an open-loop control?
Set the desired action and then series of action
What is an closed-loop control?
Constant feedback of output to input
Is there any difference in open and closed-loop controlled circuits when the environment is stable?
Nope
What can closed-loop control systems do in cell cultures?
Closed-loop control system can reject the disturbances to the cell culture
Medium shift: Changes in metabolism, cell size Doubling time changes from ~38 min to ~25 min
Temperature shift: Doubling time changes from ~38 min to >1 hour. Cell shrunk in size
Reduction in input signal
How can cell-cell heterogeneity be reduced?
By individualised closed-loop control
How can individualised control of gene expression be enabled?
By integrating closed-loop control system via a computer program
What is a hybrid oscillator?
Oscillator that involves a computer program
What can a hybrid oscillator do?
Can implement the delayed negative feedback loop within a computer without the use of enzymes
Computer increases the amount of GFP when it detects low levels
