Lecture 10. Mathematical and computational modelling in synth. and eng. biol. Flashcards
What is synthetic biology?
Synthetic Biology is the combination of engineering principles and molecular biology techniques to produce novel biological solutions
What is a CAD tool?
Computer-aided design software suites that let the engineer explore ideas before prototyping
What are the benefits of CAD tools?
Saves time: increases productivity
Increased accuracy: automated checks/verification
Ease of “versioning”: enables rapid diversification of products/generation of new products
Ease of sharing: enhances collaboration
Links to manufacture (for CAD-CAM): automated production of manufacturing drawings
Link to Enterprise Resource Planning: automated construction of parts lists and/or costs
How are CAD tools used in structural modelling tools?
3D models of D/RNA or protein structures either predicted or experimentally (X-ray/NMR) determined
Based on biophysical laws temperature and molecular dynamics simulations
RNA tools can simulate RNA structure based on
sequences, some can also do ligand interactions
Protein tools can simulate the impact of ligand
docking or structural changes based on amino acid
substructions
What are examples of CAD tools used in structural modelling?
RNAfold and PyMol
How are CAD tools used in sequence design tools?
Calculators based on biophysical thermodynamic
calculations (first principles) or machine
learning (large datasets needed)
Predict promoter or ribosome binding site DNA
sequences based on a desired initiation rate or vice versa
Analysis tools to identify repeat DNA sequences, increase evolutionary stability
Now some tools to identify complex secondary
structures in mRNAs or mRNA decay rates
What is an example of a CAD tool used in sequence design?
De Novo DNA
How are CAD tools used in sequence engineering tools?
DNA plasmid maps: “ATGCs lists”
[Automated] annotation of promoters, RBSs,
coding sequences and RE sites
Extended tools may enable prediction of primer
sequences (with optimal PCR temperatures and off
target effects), restriction digests
Use common exchange formats for sharing sequences and sequence information
What are examples of CAD tools used in sequence engineering?
Snap Gene
OpenVectorEditor
Benchling
How are CAD tools used in circuit simulation tools?
Chemistry/Physics or engineering informed models
Capture how chemical/gene expression/population changes over the course of the circuits function
Still a new area of research: many bespoke tools available but often still requires specialist knowledge
What is the DBTL cycle of synthetic biology?
Design
Build
Test
Learn
What are examples of computational modelling in synthetic biology?
Boolean networks: Composed of a set of logical interactions which captures how different molecules activate each other
Petri nets: Takes the form of a network graph of interactions or decision points. The graph is initialised with a set of tokens which then move between the nodes
Interacting state machines: Composed of submodels/“machines” which relate inputs-to -outputs and are connected in a hierarchical network
What are examples of mathematical modelling in synthetic biology?
Genome scale metabolic modelling for metabolic engineering
Dynamic modelling for gene circuit engineering
How to do mathematical modelling in synthetic biology
Choose the circuit topology (i.e. the synthetic gene regulatory network) you want to test.
Derive the mathematical model:can create an ordinary differential equation model based on the Law of Mass action and/or Hill functions
Analysis
If not promising, change the topology and compare models
In a toggle switch, where do equilibrium points occur?
When the nullclines cross
How can you see if the equilibrium points are stable?
We can draw the phase plane gradients/direction of each point section is plotted to guide trajectories
Now test stability, Choose some starting points and see where you end up
When does noise become important when designing a model?
Molecule populations are small
The solution is not homogenous
Time scales are very short
What type of simulations let us quantify noise?
Stochastic simulations
η = σ/μ
How can we construct genome-scale/whole metabolic models of metabolism?
From annotated genomes
This involves constructing the stichometry matrix, S
The rate of change of metabolites, x, within the network is dx/dt = S*v(x) where v is a vector of the reaction fluxes
How can dx/dt be accurately predicted when constructing metabolic models?
You need to know all of the parameters for all of the enzymes
But if we assume the cells are at mid exponential phase then their metabolism isn’t changing so dx/dt = 0, solve for v
What can genome scale metabolic modelling be used for?
Identifying relationships between product synthesis and growth rates. Multiple algorithms exist to identify production routes which maximise product synthesis and/or growth
Why would whole cell models be ideal CAD tools?
Capture all host-circuit interactions so enable most accurate predictions
What problems are there in generate whole cell models?
What biology do we not know?
How do we parameterise the models? 1000s of parameters with sparse data
How do we mix modelling formalisms
First WCMs run slowly
