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Brewing-up the technologies of tomorrow with synthetic biology
Dr Tom Ellis
Centre for Synthetic Biology and InnovationDepartment of Bioengineering
Imperial College London
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Sedimentation of yeast by flocculation genes
Because flocculation is unpredictable, brewers use isinglass or mechanical purification using huge centrifuges and big filters
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Design & build a DNA-coded timer from parts
PARTS:GENES and GENETIC SWITCHES
SOURCE DNA:BACTERIA, PLANTS, JELLYFISH
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Timer ‘networks’ that can be tuned predictablymutate,
select, measure
input datapredictive model
3 promoter ‘nodes’, 20 promoters per library = 8000 possible networksPredictable custom gene networks with diverse reset times
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Modular timer networks ‘wired in’ to control flocculation rather than GFP
Timer networks control yeast sedimentation
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Synthetic Biology
Synthetic biology is the engineering of biology: the synthesis of complex, biologically based (or inspired) systems which display functions that do not exist in nature.
Source: High-level Expert Group European Commission
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Engineering Biology
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Synthetic biology is ‘hacking’ the code books for life: DNA genomes
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There’s almost a limitless amount of DNA to play with
• Biology is now an information science based on DNA code• Custom DNA sequence can ordered to be written chemically
Feb 2012: 137,384,889,783 bp
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Re-wiring microbiology for new applications
Synthetic Biology The Cell
Microbes respond and make decisions using networks of interacting genes
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Next-generation synthetic gene networks Timothy K Lu, Ahmad S Khalil & James J Collins
Nature Biotechnology 27, 1139 - 1150 (2009)
Adaptive Learning Networks: e.g. associated memory
Intelligent Biosensors: e.g. navigating bacteria
Example synthetic biology Apps
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Rewriting whole Operating Systems
2010: J. Craig Venter Institute
Complete synthesis of a 1 million base pair bacterial genome from electronic code
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Sc2.0 – A Human-made Yeast Genome
Project = Synthetic Yeast 2.0 http://biostudio.bme.jhu.edu/sc2/
A major international project now in 4 countries: USA, China, UK and India
Complete synthesis and assembly of a modified synthetic yeast genome of 11 million base pairs
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Swapping natural DNA sequence for synthetic in yeast
ReiterativeRecombinationMethod
Requires two selectable markers
Makes use of yeast’s ability to recombine matching sequences
SERIAL process
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Sc2.0 – A global projectDec 2012 statusMADE INT
20% 0%
48% 8%
100% 100%
0% 0%
90% 8%
100% 70%
0% 0%
20% 0%
100% 95%
0% 0%
13% 0%
75% 22%
0% 0%
0% 0%
0% 0%
0% 0%
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Synthetic Yeast to Brew beyond beer
Penicillin Biosynthesis encoded into synthetic yeast chromosomes
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Amazing Apps have been built by students
E.coliE.coli V.fischerilambdaphage
cyanobacter
Following an abstraction similar to electronic engineering
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2005 – Students at a summer school
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iGEM is a synthetic biology competition
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iGEM uses BioBricks – modular DNA parts
Standard Modular AssemblyRegistry of Standard Parts
Open source distributed parts kit
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What could synthetic biology give us?
With James King and Daisy Ginsberg
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What could synthetic biology give us?
With Nicola Morgan (RCA Fashion)
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What could synthetic biology give us?• Biofuels and hydrogen to replace petrol and oil, made from sunlight and CO2
• Cheaper, faster production of anti-malarials and rare or new antibiotics
• Bacteria that enrich soil with natural fertilisers
• Plants that detect explosives from landmines
• Rapid ‘printing’ of new vaccines
• Microbes or viruses to detect and kill cancers
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What could synthetic biology give us?
• Cell-based computers and hard-drives
• Buildings that grow and change
• Yoghurt that makes your farts smell like mint
• Microbes to colonise Mars
• Targeted bio-weapons such as personalised viruses or crop-spoiling pests
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Is this safe?
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Bringing together disciplines
Cell Biology
MicrobiologyBiochemistry
Genomics
BiotechnologyEcology
Bioinformatics
Mathematical Modelling
Software
CAD/EDA
Simulation
Control Theory
Chaos Theory
Ethics
Philanthropy
Patenting
Environment
Social Science
Medicine
SustainabilityEnergy
Mining
Pollution
Computing
Nanotech Electronics
EducationOpen Source
Industry
Start-upsArt & Design
Fashion
Synthetic Biology
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High School iGEMiGEM HS runs from August to May, with finals in June. Allows leaders to work with students schedules and allow school students to experience synthetic biology.
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Mini-iGEM and Work-Experience iGEM
Two weeks to:• brainstorm and develop a project idea• write-up a description of the project• consider the implications of it• code a simulation of how it works• present the project to the class
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Further InformationSynthetic Biology at Imperial College Londonhttp://www3.imperial.ac.uk/syntheticbiology
The Ellis Labhttp://openwetware.org/wiki/Ellis_Lab
Synthetic Biology: A Primer Textbook
http://www.amazon.co.uk/Synthetic-Biology-Paul-S-Freemont/dp/1848168632
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Further InformationThe iGEM competition and Schools iGEM
http://igem.org/Main_Page
The BioBricks Parts Registryhttp://partsregistry.org/Main_Page
The BioBricks Foundationhttp://biobricks.org/
The Woodrow Wilson Project: synthetic biology 101http://www.synbioproject.org/topics/synbio101/
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Further InformationShort excellent video describing synthetic biologyhttp://www.youtube.com/watch?v=rD5uNAMbDaQ
David Shukman visits Imperial’s Synthetic Biology Centrehttp://www.bbc.co.uk/news/science-environment-17511081
BBC News article by David Shukmanhttp://www.bbc.co.uk/news/science-environment-17436365
Horizon 1 hour special on Synthetic Biology with Adam Rutherfordhttp://www.bbc.co.uk/programmes/b01b45zh