Synthetic Biology: A New Engineering Discipline? Summer@Brown
2011
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Announcements MONDAY: Holiday! TUESDAY: Boston Science Museum
Meet at 8:30 am at Thayer and Charlesfield WEDNESDAY: Wear closed
gym clothes/toe shoes to class! THURSDAY: Class time will be from 1
4 pm. FRIDAY: Class time will be from 9 12 pm.
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Overview What is synthetic biology? Where are the applications?
Lab 1: Strawberries & DNA How to create a synthetic organism?
Lab 2: Restriction enzyme mapping Undergraduate Design
Competitions
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What is synthetic biology? A Living Factory!
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Design Hierarchies
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What is Synthetic Biology? The design and construction of new
biological parts, devices and systems AND The re-design of
existing, natural biological systems for a useful purpose Schubert,
C. Nature, 2006(441), 277-279
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Review: Molecular Biology
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DNA Biopolymer, a long chain of small units (A,C,T,G)
Double-stranded Complementary strands
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Central Dogma of Biology DNA RNA Protein Replication
Transcription Translation
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Gene Transcription A gene is a region of DNA, corresponding to
a unit of inheritance. DNA Protein Many genes produce proteins. RNA
Ribosome Binding Site Gene Y Promoter Ribosome Binding Site Gene Y
Y Y Transcription Translation
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Gene Transcription Some genes have the ability to regulate
other genes. When placed in the same organism, these genes interact
with one another to form a gene network. Gene YGene XGene Z Note
that, as pictured, this network has a feedback loop
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Activation Gene Transcription When one gene or factor induces
creation of more of another gene, denoted with an arrow ( )
connecting the two Gene YGene X Gene X is transcribed Repression
When one gene or factor prohibits creation of another gene, denoted
with a perpendicular symbol (--|) connecting the two Gene YGene X
Gene X is not transcribed
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Genome Network Project, Nature Genetics, 2009
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Engineering with Synthetic Biology
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Rational Design Develop initial scheme for a gene network Test
smaller circuits in the network Create mathematical model to
understand theoretical behavior
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Rational Design If indicated, modify theory based upon
experimental results Construct and test larger network As with
other engineering disciplines, this process requires
standardization, modularity, and modeling Tweak as
needed/desired
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Standardization US Standard Screw Thread In this country, no
organized attempt has as yet been made to establish any system,
each manufacturer having adopted whatever his judgment may have
dictated as best, or as most convenient for himself William
Sellers, Franklin Institute, April 21, 1864
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Standard Parts Registry http://partsregistry.org/Main_Page
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Modularity Enabled by standardization Swap interchangeable
parts or units in a particular category to achieve new function
Groups of parts define a unique functional unit New unit, new
function
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Modularity Analogy: Upgrading the processor on your computer -
All other parts of the computer remain the same, but the computer
functions differently. Example: Modular promoters Gene Y Higher
output of Y Lower output of Y Promoter 1 Promoter 2
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Mathematical Modeling D Y Z degradation = rate of mRNA
transcription Y= rate of mRNA degradation = rate of protein
translation Z= rate of protein degradation
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Modeling Transcription Same thing for translation..
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Where are the applications? Pharmaceuticals and new vaccines
(shorten flu vaccine process by 99%) Biofuels Terraforming
Research, NASA
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According to the World Health Organization, each year nearly
500 million people become infected with malaria, and nearly three
million mostly children die from it. Example 1: Anti-malaria
Drug
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Artemisinin Drug produced from plant (14 month cycle):
$2.40/dose Drug produced from microbe (14 days): $0.25/dose
Savings: $2.15/dose X 500 million doses = $1 Billion
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Whats next? Will technology follow through on promise? Contract
with Sanofi-Aventis to begin distribution of arteminisin
therapeutic in 2012
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Living Factories
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Example 2: Biofuels Farnesene BioFene
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Biofuels $600 million deal Exxon and J. Craig Venter Institute
Synthetic algae to output biofuel Pitfall: Require massive amount
of plant material Land space?
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Craig Venter One of the first to sequence human genome 3
billion base pairs of DNA Created the first synthetic cell (2010)
Founder of the J. Craig Venter Institute
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Example 3: Terraforming
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Where synthetic biology can help in space? Green aviation and
biofuels Develop new technologies to provide: Food Medicine Life
support
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The Past: We took familiar biological organisms into space, and
engineered environments to suit them. The Future: We will engineer
biological systems to make them suited to extraterrestrial
environments, and employ these systems in new kinds of
missions.
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Job Opportunities
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Lab 1: Strawberries & DNA
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All you wanted to know about.Strawberries Fruit of the Fragaria
genus of flowering plants from rose family An octoploid = 8
complete sets of chromosome in a single cell Contains fiestin an
antioxidant linked to prevention of Alzheimers Genome sequenced
(2011): 240 million bp of DNA
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How to create a synthetic organism?
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Tools of the trade: Plasmids Antibiotic Selection Marker -used
to select bacteria containing gene of interest Promoter -enables
controlled expression of gene Gene -encodes protein of interest
Multiple Cloning Sites -allows other genes to be introduced into
the plasmid Units of DNA for controlled transfer of genes between
organisms
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Bacteria expressing green fluorescent protein from jelly
fish
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DNA Scissors: Restriction Enzymes GENE EcoRI XbaI SpeI PstI
Vector
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GENE A EcoRI XbaI SpeI PstI GENE B EcoRI XbaI SpeI PstI Mixed
SpeI/XbalI Site XbaISpeI GENE A SpeI PstI GENE B EcoRI
XbaISpeI/Xbal
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GENE A SpeI PstI GENE B EcoRI XbaISpeI/X bal
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Visualizing DNA: Agarose Gel 969 bp 3.0 kbp 1.0 254 bp 2.0
1.5
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Lab 2: Restriction enzyme mapping on DNA plasmid
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http://ung.igem.org/Main_Page International Genetically
Engineered Machine competition (for undergraduates) Given a kit of
biological parts Goal: design and build new biological systems and
operate them in living cells
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Examples of Ideas BactoBlood, UC Berkeley, 2007 Develop
cost-effective RBC substitute to safely transport O 2 in the
bloodstream without inducing sepsis E. Chromi, Cambridge, 2009
Engineer bacteria to produce different pigments in response to
different concentrations of inducer
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Participation Statisitics
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Where is iGEM?
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http://biomod.net International Bio-molecular Design
Competition Focus areas: biomolecular robotics, biomolecular logic
and computing and structural bionanotechnology
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DNA Origami Link DNA structures bend with radius of 6 nm
Nano-car? Nanoantennae? Nanoscale circuits for drug delivery
vehicles?