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SYNTHETIC BIOLOGY:
IMPLEMENTATION AND IMPACT
Yale iGEM
What is Synthetic Biology?
 Modification of existing organisms…
What is Synthetic Biology?
 …with the goal of applying these novel
organisms for the betterment of mankind.
So what’s the game plan for today?
A brief history of synthetic biology
Case Study: artemisinin and synthetic biology
Biofuels and synthetic biology
Agriculture and synthetic biology
Obstacles, ethical issues, and looking to the
future
Yale’s iGEM project
1953 – Enter James Watson, Francis
Crick, and Rosalind Franklin
 Watson and Crick discovered the structure of the
DNA molecule with the invaluable help of Rosalind
Franklin
Structure of DNA
Models and Photographs
Structure of DNA
 Each DNA molecule is composed of two strands
which are made of a phosphate backbone and
are connected in the middle by nucleotides
 Four nucleotides: Adenine (A), Guanine (G),
Cytosine (C), and Thymine (T)
 Key point: each one binds
to only one other: A to T and
C to G
 One pair of A -T or C-G is called a
Base Pair
Importance of the structure of DNA
 Allows DNA to replicate
and create identical
new strands
 Demonstrated how
information is stored
and passed along in
cells
What are genes?
 A gene is simply a sequence of nucleotide base pairs,
something like AAGGATCCACTGAGATTACCA, which codes for a
protein.
How do genes code proteins?
 DNA  RNA
 Protein
Genes are constantly regulated
 Cells don’t just continually produce proteins – their genes are
always regulated and controlled by a series of genetic parts,
such as switches, promoters, and repressors.
Lac operon system
 The system works by using a protein called a “repressor”
 When there is no lactose present, the repressor binds to the
gene which codes for lactose -digesting proteins. This
prevents the proteins from being created
 When lactose is introduced to the cell, the repressor reacts
with the lactose and detaches from the DNA . As a result,
lactose-digesting proteins are created again
Lac operon system
Thus, proteins are only made when they are needed, i.e. when lactose is
present!
Well, so what? Why should we
care?
CASE STUDY: ARTEMISININ
AND SYNTHETIC BIOLOGY
The Plague of Malaria
 In 2012, malaria caused between 473,000 and
789,000 deaths worldwide, primarily in sub Saharan Africa
 Malaria accounts for one in every five children’s
deaths globally
Current treatment, quinine, and its
failure
 Currently, the most popular
treatment for Malaria is
Quinine
 Excessive usage af ter World
War II led to the Malaria
parasite developing a
resistance to the drug.
 Resistance is extremely
dangerous - people will not be
able to be cured if the
medicine doesn’t work
The advent of artemisinin
 Recently discovered potent
antimalarial drug
 Artemisinin can be used to its full
potency to fight malaria, unlike the
now almost-defunct Quinine
However…
 Artemisinin is derived from the Sweet Wormwood plant
 Cultivation is a hindrance to its cheap and easy global
distribution…
 But distribution MUST
be cheap and easy in
impoverished countries!
However pt. 2
 The supply of artemisinin is influenced heavily by farming
conditions
 Leads to fluctuations in supply and prices
 Not viable as Quinine replacement
Synthetic Biology Comes into Play
 A way to create cheap synthetic artemisinin was
pioneered by Stanford professor Jay Keasling
Cells do the work
 A simple organism was chosen to manufacture
this artemisinin:
Yeast
 Synthetic genetic circuit + natural DNA
reading/transcribing mechanism = yeast cell
which produces artemisinin
Economic Impact of
Synthetic Artemisinin
 Hundreds of thousands of farmers in
developing countries rely on sweet
wormwood farming
 Synthetic artemisinin would eliminate
need for sweet wormwood cultivation
 Puts hundreds of thousands of
farmers out of a job
Economic Impact of Synthetic Artemisinin
 Recall this graph:
 Introduction of cheap synthetic -made artemisinin would
stabilize prices (and lower them)
 More accessible to those at risk for malaria
Is it worth it?
 Which is more important?
 Stable prices and accessibility to medicine for millions at risk for
malaria
OR
 The livelihoods of hundreds of thousands of farmers
BIOFUELS AND
SYNTHETIC BIOLOGY
Fossil Fuels
 Most fuels used currently are extracted from the earth
 Unsustainable and cause pollution
An alternative: biofuels
 A fuel which is synthesized
from organic resources
 Scientists are developing
engineered cells which
consume biomass and
produce fuels
For starters, Ethanol
 Already naturally made in small quantities by cells via
anaerobic respiration
The problem
 The amount of ethanol secreted by bacteria
naturally is nowhere near enough to power a car!
A few solutions
 Insertion of a gene which increases the amount
of ATP and NADH (energy -providing molecules) in
a cell. More energy, more ethanol naturally
produced
 Knocking out all chemical processes except the
fermentation of ethanol using chemical means
The yeast of biofuels
 There is one organism on which companies are focusing their
time, ef fort, and hundreds of millions of dollars:
algae
Advantages of using algae as a biofuel
producer
Uses of
Corn
 Single Functionality
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Alcohol
Livestock feed
Human feed
Cooking oil
Bakery Products
Soap
Insecticides
Ethanol
Ceramics
Adhesives
Flour
Uses of
Algae
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Green Stuff
in Fancy
Drinks
Ethanol
Per-acre production: Algae can produce between
9,000 and 61,000 liters of fuel per hectare per year,
compared to corn’s maximum of 5,000 liters
Infinite energy - photosynthesizing
Example: land required to displace all
gasoline in the united states, by method
Current obstacles
 Algae live in water – large water tanks required
 Maintenance, storage, etc
 Expensive
 Processing
 Transport
In-Progress Solutions
 Insertion of a gene which makes algae communal – they don’t
hoard sunlight from other cells. Sharing is caring!
Get Humans involved
 Insertion of a human gene into algae:
The gene that codes carbonic anhydrase ( CA)II
 CAII regulates CO2 levels in human
red blood cells by combining CO2 and
H20 into bicarbonate and protons
 In algae, CAII converts excess C
atoms into CO2, which is used during
photosynthesis to produce energy
 More naturally -produced energy =
more energy for production of
biofuels = cheaper fuels =
commercial viability
Episode IV: A New Hope
 In the United States alone, there are 1 .3 Billion tons of
unused biomass
 Biomass is used to feed microbes which manufacture
biofuels;
 With this much biomass, we have the potential to
replace the domestic production of oil
OBSTACLES AND LOOKING
TO THE FUTURE
Ethical Considerations
 How to asses emerging tech
 Public Beneficence
 Is the technology helpful for people?
 Responsible Stewardship
 Humans responsible for human safety and for earth’s safety
 Intellectual freedom and responsibility
 Pursuing science safely and without harm to others
 Democratic deliberation
 Civil, public exchange of opinions and ideas
 Justice and fairness
 Commitment to all groups sharing benefits and burdens equally
Applying these considerations to
Synthetic Biology
 Public beneficence
 How will synthetic biology benefit humanity?
 Medicine
 Biofuels
 Energy
 Agriculture
 Responsible Stewardship
 Ethics education
 Collaboration between government and scientists
Applying these considerations to
Synthetic Biology
 Intellectual freedom and responsibility
 Garage Engineering
 Uncontrolled Release
 Bioterrorism
 Democratic Deliberation
 Improving scientific literacy
 Validating scientific claims about genetic engineering
 Justice and Fairness
 Managing risks of pathogens
 Applications of Synthetic Biology
benefiting all
PORTING MULTIPLEX
AUTOMATED GENOME
ENGINEERING INTO
OTHER EUBACTERIA
Yale iGEM
2015
MULTIPLEX AUTOMATED GENOME
ENGINEERING (MAGE)
MAGE PROCESS
Subject matter experts: George Church, Ph.D., Frederic Vigneault, Ph.D., M.Sc.
Producer/writer: Rick Groleau
Graphic design and technical development: Lenni Armstrong, Jamie Ciocco
RHIZOBIA ARE NITROGEN-FIXING BACTERIA
Rhizobia fix nitrogen in root
nodules of legumes
Symbiotic relationship
Rhizobia fix
Nitrogen
Legumes
provide essential
molecules
NITROGEN-POOR SOIL:
AN ISSUE IN AGRICULTURE
Relative yield losses in corn crops in Sub-Saharan Africa.
Fischer et al. 2014.
© Punchstock
CYANOBACTERIA: PHOTOSYNTHETIC BACTERIA
Cyanobacteria
 Photosynthetic aquatic bacteria
 Can grow off of light and trace metals – net gain in
energy production when harvesting
PORTING MAGE INTO OTHER
EUBACTERIA
Challenges
to
Overcome
Finding betahomologues
Transforming
plasmid into
cells
MutS
Knockout
Selecting for
transformants
IDENTIFYING BETA HOMOLOGS
 Lambda-red beta protein is specific to E. Coli
 Tools for comparing nucleotide sequences
 NCBI Blast
 HMMER
VECTOR DESIGN FOR
EXPRESSION OF RECOMBINASE
Broad-host range plasmid
pKT230
TRANSFORMATION AND SELECTION
KanR
ELECTROPORATION
PROOF OF CONCEPT:
CITRINE AS A SCREEN FOR MAGE
Wang and Isaacs et. al 2009
THANK YOU, EVERYONE!
MORE ABOUT IGEM
 Want to know more about iGEM?
 (http://igem.org/About)
 Want to start a team?
 http://2015.igem.org/Starting_a_Team