Introduction to Synthetic Biology - OpenWetWare

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Introduction to Synthetic Biology - OpenWetWare

Introduction to Synthetic Biology

Topic 1

Topic 2 Topic 3 Topic 4 Topic 5

Foundations for Synthetic Biology

Vincent Rouilly

Bioengineering Department

Imperial College London


Introduction to Synthetic Biology

Topic 1

Topic 2 Topic 3 Topic 4 Topic 5

Standard

for Physical DNA Composition

Vincent Rouilly

Bioengineering Department

Imperial College London


Introduction to Synthetic Biology

Topic 1

Topic 2 Topic 3 Topic 4 Topic 5

Standards

for Functional Composition

Vincent Rouilly

Bioengineering Department

Imperial College London


PoPS / RiPS Generators

PoPS

RiPS


PoPS

RiPS

PoPS / RiPS Devices

Modular and re-usable

PoPS devices

Modular and re-usable

RiPS devices

PoPS

RiPS


activator

Transcriptional Device

C

Question 1:

What does this system do ?

Question 2:

Extract a modular and re-usable device from this circuit.

C


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


PoPS

Transcriptional Device

PoPS

PoPS

Question:

How to implement this device ?

PoPS

PoPS


Standard

Inputs

To Promote Re-usability

Modular

Design

Standard

Outputs


Standard

Inputs

To Promote Re-usability

Modular

Design

+ a great

Standard

Outputs

System

Documentation


Introduction to Synthetic Biology

Topic 1 Topic 2

Topic 3 Topic 4 Topic 5

Characterising

Standard Biological Parts

Vincent Rouilly

Bioengineering Department

Imperial College London


What is a good Part / Device / System

characterisation ?

System

System

Characterisation


What is a good Part / Device / System

characterisation ?

System

System

Characterisation

A good Device Characterisation is:

the minimum amount of information someone needs

to reuse the part without any prior knowledge


What type of info do we expect ?

System

System

Characterisation


What type of info do we expect ?

System

System

Characterisation

Physical Characteristics Performance Characteristics


What type of info do we expect ?

System

Physical Characteristics

- Background info

- Sequencing certificate

- Sequence analysis

- ...

System

Characterisation

Performance Characteristics


What type of info do we expect ?

System

System

Characterisation

Physical Characteristics Performance Characteristics


What type of info do we expect ?

System

Physical Characteristics

System

Characterisation

Performance Characteristics

- Functional description

- Performance measurements

- Environmental conditions

used during testing

- ...


Functional Properties Dependencies

Device


Functional Properties Dependencies

Device

Vector


Functional Properties Dependencies

Device

Vector

Device

Vector

Device

Vector

Device

Vector


Functional Properties Dependencies

Device

Vector

Device

Vector

Chassis (host)

Device

Vector

Device

Vector


Functional Properties Dependencies

Device

Vector

Environmental Conditions

Device

Vector

Chassis (host)

Device

Vector

Device

Vector


Functional Properties Dependencies

Too high level Device of complexity

Vector

Device

Vector

Environmental Conditions

Chassis (host)

Device

To obtain a reliable and reproducible

Vector Device

characterisation we need to standardise

the way we are probing the system

Vector


Characterisation and Standards

Standard

Conditions

Standard

Chassis

(host)

Characterisation

Standard

Measurement


- Media

- Temperature

- Cell Density (OD600)

- ...

Characterisation and Standards

Standard

Conditions

Standard

Chassis

(host)

Characterisation

Standard

Measurement


- Media

- Temperature

- Cell Density (OD600)

- ...

Characterisation and Standards

Standard

Conditions

Characterisation

Standard

Measurement

Standard

Chassis

(host)

E.Coli (strain ?)

Yeast

Cell-Free System

...


- Media

- Temperature

- Cell Density (OD600)

- ...

Characterisation and Standards

Standard

Conditions

Characterisation

Standard

Measurement

Standard

Chassis

(host)

E.Coli (strain ?)

Yeast

Cell-Free System

...

Calibration


How do you measure PoPS ?

RBS

RNAp

amino-acid chain

Ribosome

mRNA

Protein Generator

RNAp


How do you measure RiPS ?

RBS

RNAp

amino-acid chain

Ribosome

mRNA

Protein Generator

RNAp


concentration

d[mRNA]

dt

d[Protein]

dt

Indirect Measurement

= k1 - d1[mRNA]

= k2.[mRNA] - d2[Protein]

Protein Generator

[Protein]

[mRNA]

time


37C/Shacking

OD600 GFP

GFP Measurement

GFP

E.Coli + Part

GFP/OD600

time time time


Measurement Kit

Back to Basic Parts


Measurement Kit

GFP

?

S X

Jason Kelly (Endy's Lab)


S X

Measurement Kit

Promoter Screening Plasmid

GFP

E X S P

Constitutive

Promoter

Jason Kelly (Endy's Lab)


Measurement Kit

GFP

?

S X

Jason Kelly (Endy's Lab)


S X

Measurement Kit

RBS Screening Plasmid

GFP

JC Anderson (MIT Registry)

E X S P

Ribosome

Binding Site

Jason Kelly (Endy's Lab)


Measurement Kit

GFP

?

S X

Jason Kelly (Endy's Lab)


Measurement Kit

Terminator / Inverter Screening Plasmid

S X

GFP

E X S P

Terminator

E X S P

Inverter

Jason Kelly (Endy's Lab)


PoPS based Screening Plasmid

Jason Kelly (Endy's Lab)


PoPS based Screening Plasmid

Jason Kelly (Endy's Lab)


F2620 / T9002

pTetR

LuxR pLuxR GFP

Barry Canton (Endy's Lab)


F2620 / T9002

pTetR

LuxR pLuxR GFP

F2620 T9002

Barry Canton (Endy's Lab)


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)


Drew Endy Talks

> OpenWetWare Folks

> iGEM Competition

> BioBricks Foundation

References


System

Measurement

Inputs Outputs Observations

Measurement

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