“So you’ve made a synthetic cell….”
Summer@Brown2011
Who has heard of…..
The Minimal Cell?
The Minimal Cell is …
Recipient cell: M. capricolumGenome: M. mycoides JCVI-syn1.0
• First synthetic self-replicative cell (May 2010)
• Mother: computer• Function of every gene
is known (1.8 Mbp)• 15 years• 24 scientists• ~$40 million• Chassis for biological
devices
A Living Factory!
What is synthetic biology?
Design Hierarchies
• Arteminisin Project: Anti-malaria drug• BioFene: biofuels• Terraforming Research: NASA• Sensors• Bioremediation
Applications
According to the World Health Organization, each year nearly 500 million people become infected with malaria, and nearly 3 million — mostly children — die from it.
Malaria Crisis
Drug produced from plant (14 month cycle):
$2.40/dose
Drug produced from microbe (14 days):
$0.25/doseSavings:
$2.15/dose X 500 million doses = $1 Billion
Arteminisin
• Will technology follow through on promise?• Contract with Sanofi-Aventis to begin
distribution of arteminisin therapeutic in 2012
What’s next?
Living Factories
• Farnesene – BioFene
BioFene: Biofuels
• $600 million deal– Exxon and J. Craig Venter Institute– Synthetic algae to output biofuel
Biofuels
Terra-forming Research
• Green aviation and biofuels
• Develop new technologies to provide:– Food– Medicine– Life support
Emerging technologies?
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.
Job Opportunities
Analogies
Review: Molecular Biology
Biopolymer, a long chain of small units (A,C,T,G)
Double-stranded
Complementary strands
DNA: Molecule of Life
DNA
RNA
Protein
Replication
Transcription
Translation
Central Dogma of Biology
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
Transcription
Translation
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 Y Gene X Gene Z
Note that, as pictured, this network has a feedback loop
Gene Transcription
Activation
When one gene or factor induces creation of more of another gene, denoted with an arrow () connecting the two
Gene Y Gene 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 Y Gene X Gene X is not transcribed
Gene Transcription
Genome Network Project, Nature Genetics, 2009
Engineering with Synthetic Biology
Develop initial scheme for a gene network
Test smaller circuits in the network
Create mathematical model to understand theoretical behavior
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
Rational Design
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
Standardization
http://partsregistry.org/Main_Page
Standard Registry
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
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
Gene Y Higher output of Y
Lower output of YPromoter 1
Promoter 2
Modularity
D
Y
Z
β
δ
ρ
ϒ
degradation
degradation
Β= rate of mRNA transcriptionγY= rate of mRNA degradation
δ= rate of protein translationρZ= rate of protein degradation
Modeling of Genetic Networks
Y (t t)Y(t)t Y (t)t
Y(t t) Y(t)t
Yt
Y (t)
t 0,dY
dt(t) Y(t)
Same thing for translation…..
Model Transcription
Manipulating DNA to engineer organisms
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
Bacteria expressing green fluorescent protein from jelly fish
DNA Scissors: Restriction Enzymes
GENE
EcoRI
XbaI SpeI
PstI
VectorPlasmid
GENE A
EcoRI
XbaI
SpeI
PstI
GENE B
EcoRI
XbaI
SpeI
PstI
Mixed SpeI/XbalI Site
XbaISpeI
GENE A
SpeI
PstI
GENE B
EcoRI
XbaI SpeI/Xbal
GENE A
SpeI
PstI
GENE B
EcoRI
XbaI SpeI/Xbal
Plasmid
Visualizing DNA: Agarose Gel
3.0
kbp
1.0
254 bp = MCSNo Gene Insert
969 bp = GFPGene Inserted
2.01.5
Individual Bacterial Colonies
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
Examples of Ideas• BactoBlood, UC Berkeley, 2007– Develop cost-effective RBC substitute to safely
transport O2 in the bloodstream without inducing sepsis
• E. Chromi, Cambridge, 2009– Engineer bacteria to produce different pigments in
response to different concentrations of inducer
2003 2004 2005 2006 2007 2008 2009 20100
20
40
60
80
100
120
140
Year
Num
ber o
f Tea
ms
Participation Statisitics
Where is iGEM?
http://biomod.net
• International Bio-molecular Design Competition
• Focus areas: biomolecular robotics, biomolecular logic and computing and structural bionanotechnology
DNA Origami
Link
• DNA structures bend with radius of 6 nm
• Nano-car?• Nanoantennae?• Nanoscale circuits for
drug delivery vehicles?
Lab 1: Strawberries & DNA
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 Alzheimer’s
• Genome sequenced (2011): 240 million bp of DNA