Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question...
Transcript of Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question...
![Page 1: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/1.jpg)
Topic 1
Introduction to Synthetic Biology
Topic 2 Topic 3 Topic 4 Topic 5
Foundations for Synthetic Biology
Vincent RouillyBioengineering Department
Imperial College London
![Page 2: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/2.jpg)
Topic 1
Introduction to Synthetic Biology
Topic 2 Topic 3 Topic 4 Topic 5
Standardfor Physical DNA Composition
Vincent RouillyBioengineering Department
Imperial College London
![Page 3: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/3.jpg)
Topic 1
Introduction to Synthetic Biology
Topic 2 Topic 3 Topic 4 Topic 5
Standards for Functional Composition
Vincent RouillyBioengineering Department
Imperial College London
![Page 4: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/4.jpg)
PoPS / RiPS Generators
PoPS
RiPS
![Page 5: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/5.jpg)
Modular and re-usablePoPS devices
PoPS / RiPS Devices
PoPS
RiPS
PoPS
Modular and re-usableRiPS devices
RiPS
![Page 6: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/6.jpg)
Transcriptional Device
CC
activator
Question 1: What does this system do ?
Question 2: Extract a modular and re-usable device from this circuit.
![Page 7: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/7.jpg)
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
![Page 8: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/8.jpg)
Transcriptional Device
PoPS
PoPS
PoPSPoPS
PoPS
Question:
How to implement this device ?
![Page 9: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/9.jpg)
To Promote Re-usability
StandardInputs
StandardOutputs
Modular Design
![Page 10: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/10.jpg)
To Promote Re-usability
SystemDocumentation+ a great
StandardInputs
StandardOutputs
Modular Design
![Page 11: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/11.jpg)
Topic 1 Topic 2
Introduction to Synthetic Biology
Topic 3 Topic 4 Topic 5
Characterising Standard Biological Parts
Vincent RouillyBioengineering Department
Imperial College London
![Page 12: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/12.jpg)
What is a good Part / Device / System characterisation ?
SystemSystem
Characterisation
![Page 13: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/13.jpg)
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
![Page 14: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/14.jpg)
What type of info do we expect ?
SystemSystem
Characterisation
![Page 15: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/15.jpg)
What type of info do we expect ?
SystemSystem
Characterisation
Physical Characteristics Performance Characteristics
![Page 16: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/16.jpg)
What type of info do we expect ?
SystemSystem
Characterisation
Performance Characteristics
Physical Characteristics
- Background info- Sequencing certificate- Sequence analysis- ...
![Page 17: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/17.jpg)
What type of info do we expect ?
SystemSystem
Characterisation
Physical Characteristics Performance Characteristics
![Page 18: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/18.jpg)
What type of info do we expect ?
SystemSystem
Characterisation
Performance Characteristics
Physical Characteristics- Functional description- Performance measurements- Environmental conditions used during testing- ...
![Page 19: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/19.jpg)
Functional Properties Dependencies
Device
![Page 20: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/20.jpg)
Functional Properties Dependencies
Device
Vector
![Page 21: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/21.jpg)
Functional Properties Dependencies
Device
Vector
Vector
VectorVector
DeviceDevice
Device
![Page 22: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/22.jpg)
Functional Properties Dependencies
Device
Vector
Vector
VectorVector
Chassis (host)
DeviceDevice
Device
![Page 23: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/23.jpg)
Functional Properties Dependencies
Device
Vector
Vector
VectorVector
Chassis (host)
Environmental Conditions
DeviceDevice
Device
![Page 24: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/24.jpg)
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
![Page 25: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/25.jpg)
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
![Page 26: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/26.jpg)
- Media- Temperature- Cell Density (OD600)- ...
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
![Page 27: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/27.jpg)
E.Coli (strain ?)Yeast
Cell-Free System...
- Media- Temperature- Cell Density (OD600)- ...
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
![Page 28: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/28.jpg)
Calibration
E.Coli (strain ?)Yeast
Cell-Free System...
- Media- Temperature- Cell Density (OD600)- ...
Characterisation and Standards
Characterisation
StandardConditions
StandardChassis(host)
StandardMeasurement
![Page 29: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/29.jpg)
How do you measure PoPS ?
RNApmRNA
RBS
Ribosome
amino-acid chain
RNAp
Protein Generator
![Page 30: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/30.jpg)
How do you measure RiPS ?
RNApmRNA
RBS
Ribosome
amino-acid chain
RNAp
Protein Generator
![Page 31: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/31.jpg)
Indirect Measurement
Protein Generator
d[mRNA]dt = k1 - d1[mRNA]
d[Protein]dt = k2.[mRNA] - d2[Protein]
time
concentration [Protein]
[mRNA]
![Page 32: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/32.jpg)
GFP Measurement
time time time
OD600 GFP GFP/OD600
37C/Shacking
GFP
E.Coli + Part
![Page 33: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/33.jpg)
Measurement Kit
Back to Basic Parts
![Page 34: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/34.jpg)
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
S X ?
![Page 35: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/35.jpg)
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
ConstitutivePromoter
E X S PS X
Promoter Screening Plasmid
![Page 36: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/36.jpg)
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
S X ?
![Page 37: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/37.jpg)
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
Ribosome Binding Site
E X S PS X
JC Anderson (MIT Registry)
RBS Screening Plasmid
![Page 38: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/38.jpg)
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
S X ?
![Page 39: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/39.jpg)
Measurement Kit
Jason Kelly (Endy's Lab)
GFP
Terminator
E X S PS X
Terminator / Inverter Screening Plasmid
Inverter
E X S P
![Page 40: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/40.jpg)
PoPS based Screening Plasmid
Jason Kelly (Endy's Lab)
![Page 41: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/41.jpg)
PoPS based Screening Plasmid
Jason Kelly (Endy's Lab)
![Page 42: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/42.jpg)
F2620 / T9002
Barry Canton (Endy's Lab)
LuxR GFPpLuxRpTetR
![Page 43: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/43.jpg)
F2620 / T9002
Barry Canton (Endy's Lab)
LuxR GFPpLuxRpTetR
F2620 T9002
![Page 44: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/44.jpg)
F2620: Description
Barry Canton (Endy's Lab)
![Page 45: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/45.jpg)
F2620: Transfer Function
Barry Canton (Endy's Lab)
![Page 46: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/46.jpg)
F2620: Specificity
Barry Canton (Endy's Lab)
![Page 47: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/47.jpg)
F2620
Barry Canton (Endy's Lab)
![Page 48: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/48.jpg)
F2620: Stability
Barry Canton (Endy's Lab)
![Page 49: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/49.jpg)
References
> Drew Endy Talks > OpenWetWare Folks> iGEM Competition> BioBricks Foundation
![Page 50: Foundations for Synthetic Biology · 2017-01-26 · Question 1: What does this system do ? Question 2: Extract 3 modular and re-usable devices from this circuit. ... characterisation](https://reader033.fdocuments.us/reader033/viewer/2022050313/5f75b9d5740ee6476709fbc8/html5/thumbnails/50.jpg)
Measurement
System
Mea
sure
men
t
Inputs Outputs Observations