Yale iGEM SYNTHETIC BIOLOGY: IMPLEMENTATION AND IMPACT
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Modification of existing organisms What is Synthetic
Biology?
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with the goal of applying these novel organisms for the
betterment of mankind. What is Synthetic Biology?
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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 Yales iGEM project So whats the game plan for today?
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Watson and Crick discovered the structure of the DNA molecule
with the invaluable help of Rosalind Franklin 1953 Enter James
Watson, Francis Crick, and Rosalind Franklin
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Models and Photographs Structure of DNA
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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 Structure of
DNA
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Allows DNA to replicate and create identical new strands
Demonstrated how information is stored and passed along in cells
Importance of the structure of DNA
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A gene is simply a sequence of nucleotide base pairs, something
like AAGGATCCACTGAGATTACCA, which codes for a protein. What are
genes?
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DNA RNA Protein How do genes code proteins?
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Cells dont just continually produce proteins their genes are
always regulated and controlled by a series of genetic parts, such
as switches, promoters, and repressors. Genes are constantly
regulated
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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
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Thus, proteins are only made when they are needed, i.e. when
lactose is present!
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Well, so what? Why should we care?
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CASE STUDY: ARTEMISININ AND SYNTHETIC BIOLOGY
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In 2012, malaria caused between 473,000 and 789,000 deaths
worldwide, primarily in sub- Saharan Africa Malaria accounts for
one in every five childrens deaths globally The Plague of
Malaria
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Currently, the most popular treatment for Malaria is Quinine
Excessive usage after 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
doesnt work Current treatment, quinine, and its failure
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Recently discovered potent antimalarial drug Artemisinin can be
used to its full potency to fight malaria, unlike the now
almost-defunct Quinine The advent of artemisinin
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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
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The supply of artemisinin is influenced heavily by farming
conditions Leads to fluctuations in supply and prices Not viable as
Quinine replacement However pt. 2
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A way to create cheap synthetic artemisinin was pioneered by
Stanford professor Jay Keasling Synthetic Biology Comes into
Play
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A simple organism was chosen to manufacture this artemisinin:
Yeast Synthetic genetic circuit + natural DNA reading/transcribing
mechanism = yeast cell which produces artemisinin Cells do the
work
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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
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Recall this graph: Introduction of cheap synthetic-made
artemisinin would stabilize prices (and lower them) More accessible
to those at risk for malaria Economic Impact of Synthetic
Artemisinin
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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 Is it worth it?
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BIOFUELS AND SYNTHETIC BIOLOGY
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Most fuels used currently are extracted from the earth
Unsustainable and cause pollution Fossil Fuels
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A fuel which is synthesized from organic resources Scientists
are developing engineered cells which consume biomass and produce
fuels An alternative: biofuels
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Already naturally made in small quantities by cells via
anaerobic respiration For starters, Ethanol
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The amount of ethanol secreted by bacteria naturally is nowhere
near enough to power a car! The problem
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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 A few solutions
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There is one organism on which companies are focusing their
time, effort, and hundreds of millions of dollars: algae The yeast
of biofuels
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Single Functionality Advantages of using algae as a biofuel
producer Uses of Corn Uses of Algae Alcohol Livestock feed Human
feed Cooking oil Bakery Products Soap Insecticides Ethanol Ceramics
Adhesives Flour 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 corns maximum of 5,000
liters Infinite energy - photosynthesizing
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Example: land required to displace all gasoline in the united
states, by method
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Algae live in water large water tanks required Maintenance,
storage, etc Expensive Processing Transport Current obstacles
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Insertion of a gene which makes algae communal they dont hoard
sunlight from other cells. Sharing is caring! In-Progress
Solutions
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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 Get Humans involved
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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 Episode IV: A New Hope
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OBSTACLES AND LOOKING TO THE FUTURE
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How to asses emerging tech Public Beneficence Is the technology
helpful for people? Responsible Stewardship Humans responsible for
human safety and for earths 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 Ethical Considerations
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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
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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 Applying these
considerations to Synthetic Biology
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PORTING MULTIPLEX AUTOMATED GENOME ENGINEERING INTO OTHER
EUBACTERIA Yale iGEM 2015
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MULTIPLEX AUTOMATED GENOME ENGINEERING (MAGE)
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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
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RHIZOBIA ARE NITROGEN-FIXING BACTERIA Rhizobia fix nitrogen in
root nodules of legumes Symbiotic relationship Rhizobia fix
Nitrogen Legumes provide essential molecules
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NITROGEN-POOR SOIL: AN ISSUE IN AGRICULTURE Relative yield
losses in corn crops in Sub-Saharan Africa. Fischer et al. 2014.
Punchstock
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Cyanobacteria Photosynthetic aquatic bacteria Can grow off of
light and trace metals net gain in energy production when
harvesting CYANOBACTERIA: PHOTOSYNTHETIC BACTERIA
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Challenges to Overcome Finding beta- homologues Transforming
plasmid into cells Selecting for transformants MutS Knockout
PORTING MAGE INTO OTHER EUBACTERIA
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IDENTIFYING BETA HOMOLOGS Lambda-red beta protein is specific
to E. Coli Tools for comparing nucleotide sequences NCBI Blast
HMMER
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VECTOR DESIGN FOR EXPRESSION OF RECOMBINASE Broad-host range
plasmid pKT230
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TRANSFORMATION AND SELECTION ELECTROPORATION Kan R
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PROOF OF CONCEPT: CITRINE AS A SCREEN FOR MAGE Wang and Isaacs
et. al 2009
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THANK YOU, EVERYONE!
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