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Topic 1
Introduction to Synthetic Biology
Topic 2 Topic 3 Topic 4 Topic 5
Foundations for Synthetic Biology
Vincent RouillyBioengineering Department
Imperial College London
Topic 1
Introduction to Synthetic Biology
Topic 2 Topic 3 Topic 4 Topic 5
Standardfor Physical DNA Composition
Vincent RouillyBioengineering Department
Imperial College London
Topic 1
Introduction to Synthetic Biology
Topic 2 Topic 3 Topic 4 Topic 5
Standards for Functional Composition
Vincent RouillyBioengineering Department
Imperial College London
PoPS / RiPS Generators
PoPS
RiPS
Modular and re-usablePoPS devices
PoPS / RiPS Devices
PoPS
RiPS
PoPS
Modular and re-usableRiPS devices
RiPS
Transcriptional Device
CC
activator
Question 1: What does this system do ?
Question 2: Extract a modular and re-usable device from this circuit.
Transcriptional Device
A B C
Question 1: What does this system do ?
Question 2: Extract 3 modular and re-usable devices from this circuit.
Question 3:Update the design so this system can be easily plugged
into a larger system
Transcriptional Device
PoPS
PoPS
PoPSPoPS
PoPS
Question:
How to implement this device ?
To Promote Re-usability
StandardInputs
StandardOutputs
Modular Design
To Promote Re-usability
SystemDocumentation+ a great
StandardInputs
StandardOutputs
Modular Design
Topic 1 Topic 2
Introduction to Synthetic Biology
Topic 3 Topic 4 Topic 5
Characterising Standard Biological Parts
Vincent RouillyBioengineering Department
Imperial College London
What is a good Part / Device / System characterisation ?
SystemSystem
Characterisation
What is a good Part / Device / System characterisation ?
System
A good Device Characterisation is:
the minimum amount of information someone needs to reuse the part without any prior knowledge
SystemCharacterisation
What type of info do we expect ?
SystemSystem
Characterisation
What type of info do we expect ?
SystemSystem
Characterisation
Physical Characteristics Performance Characteristics
What type of info do we expect ?
SystemSystem
Characterisation
Performance Characteristics
Physical Characteristics
- Background info- Sequencing certificate- Sequence analysis- ...
What type of info do we expect ?
SystemSystem
Characterisation
Physical Characteristics Performance Characteristics
What type of info do we expect ?
SystemSystem
Characterisation
Performance Characteristics
Physical Characteristics- Functional description- Performance measurements- Environmental conditions used during testing- ...
Functional Properties Dependencies
Device
Functional Properties Dependencies
Device
Vector
Functional Properties Dependencies
Device
Vector
Vector
VectorVector
DeviceDevice
Device
Functional Properties Dependencies
Device
Vector
Vector
VectorVector
Chassis (host)
DeviceDevice
Device
Functional Properties Dependencies
Device
Vector
Vector
VectorVector
Chassis (host)
Environmental Conditions
DeviceDevice
Device
Functional Properties Dependencies
Device
Vector
Vector
VectorVector
Chassis (host)
Environmental Conditions
DeviceDevice
Device
Too high level of complexity
To obtain a reliable and reproducible characterisation we need to standardise
the way we are probing the system
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
- Media- Temperature- Cell Density (OD600)- ...
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
E.Coli (strain ?)Yeast
Cell-Free System...
- Media- Temperature- Cell Density (OD600)- ...
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
Calibration
E.Coli (strain ?)Yeast
Cell-Free System...
- Media- Temperature- Cell Density (OD600)- ...
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
How do you measure PoPS ?
RNApmRNA
RBS
Ribosome
amino-acid chain
RNAp
Protein Generator
How do you measure RiPS ?
RNApmRNA
RBS
Ribosome
amino-acid chain
RNAp
Protein Generator
Indirect Measurement
Protein Generator
d[mRNA]dt = k1 - d1[mRNA]
d[Protein]dt = k2.[mRNA] - d2[Protein]
time
concentration [Protein]
[mRNA]
GFP Measurement
time time time
OD600 GFP GFP/OD600
37C/Shacking
GFP
E.Coli + Part
Measurement Kit
Back to Basic Parts
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
S X ?
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
ConstitutivePromoter
E X S PS X
Promoter Screening Plasmid
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
S X ?
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
Ribosome Binding Site
E X S PS X
JC Anderson (MIT Registry)
RBS Screening Plasmid
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
S X ?
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
Terminator
E X S PS X
Terminator / Inverter Screening Plasmid
Inverter
E X S P
PoPS based Screening Plasmid
Jason Kelly (Endy's Lab)
PoPS based Screening Plasmid
Jason Kelly (Endy's Lab)
F2620 / T9002
Barry Canton (Endy's Lab)
LuxR GFPpLuxRpTetR
F2620 / T9002
Barry Canton (Endy's Lab)
LuxR GFPpLuxRpTetR
F2620 T9002
F2620: Description
Barry Canton (Endy's Lab)
F2620: Transfer Function
Barry Canton (Endy's Lab)
F2620: Specificity
Barry Canton (Endy's Lab)
F2620
Barry Canton (Endy's Lab)
F2620: Stability
Barry Canton (Endy's Lab)
References
> Drew Endy Talks > OpenWetWare Folks> iGEM Competition> BioBricks Foundation
Measurement
System
Mea
sure
men
t
Inputs Outputs Observations
