Lecture 7. Principles of Gene Circuit Design 1 Flashcards
What is the fundamental design of a circuit?
Sensor → Controller (processor) → Actuator
What did the operon model imply in 1965?
Analogous mechanisms may be conserved across the domains of life
The elements are modular, meaning that operators and regulators can be decoupled from downstream operons
The elements can be composed to form gene regulatory networks with complex emergent behaviours
Why are mathematical models used to predict and perfect design?
Don’t have to do experiments, cheaper and faster
In a simple circuit, how much is there to consider?
10 reactions and 28 parameters to consider
What is the ordinary differential equation and what is it used for?
(ODE) is a powerful way of modelling biochemical reactions
[A] + [B] ⇌ [AB]
What is the basic form of ODE for gene expression?
dR/dt = leak + f(R) - γR
What is a model in the context of synthetic biology?
A model is something we want to simulate and something we want to make predictions with
What are the characteristics of a good model?
Accuracy: Is it realistic? (depends what you are measuring against)
Predictability: Can it predict the behaviours?
Reusability: Can it be reused in similar cases
Parsimony: Is it simple?
What is SBOL?
Synthetic Biology Open Language
Simulates genetic circuit design and their reactions
What parameters must be considered for transcription-level design?
Promoter strength
Promoter leakiness and basal expression
RNAP abundances
Terminator
Length (Gene length and distance)
How can the parameters for transciption-level design be tuned by?
RNAP binding affinities
Promoter insulation: tight regulation by adding terminator before promoter to prevent leakage
Promoter leakiness and basal expression
Why is codon optimisation tricky?
Some rare codons are necessary for protein structure
What parameters must be considered for post-transcription-level design?
Protein stability (degradation rate)
Protein activity
Protein localisation
Affinities to other molecules
What are the advantages of post-translational level regulations?
Post-translational level regulations can offer many advantages including fast dynamics
What are the disadvantages of post-translational level regulations?
This area is the least explored due to complexity and difficulties of protein engineering
Which is faster, positive auto-regulation or negative auto-regulation?
NAR
What are the common challenges associated with engineering synthetic biology circuits?
Design: Limited quantitative measurement/analysis, cahssis, metabolic burden, cell physiology
Evolution: Mutation and Selection
Gene expression noise and cell-cell heterogeneity
