1. Unveiling the mysteries of synthetic biology with
Presenters: Jonlin Chen, Grace Livermore, Tim Abbott, and Jeffrey Ly
2. WHAT IS SYNTHETIC
BIOLOGY?
Designing and constructing biological devices, networks and
pathways for useful purposes
Creating synthetic components or re-assembling pre-existing genes
Wiring biological circuitry to make:
Biological switches, oscillators, toggle switches
Logic gates, pulse generators
For: Biosensing, therapeutic treatment, biofuels…. And much more
3. WHAT IS IGEM?
• ‘International Genetically Engineered Machines”
• Global synthetic biology competition
• HS / Undergraduate / Graduate / Entrepreneurship
• Students design and build complex biological systems
made from standard, interchangeable DNA parts
“Biobricks”
4. How does one genetically modify
an organism?
Herbert Boyer Robert Swanson
5. • What is a restriction enzyme?
DNA
Restriction Enzyme
• Why do bacteria have these enzymes?
• Immunity against viruses!
• Will the enzymes cut up the bacteria’s DNA?
• Nope! The bacteria is able to protect its own DNA!
6. What Made These Two Interested
in Restriction Enzymes?
Herbert Boyer Robert Swanson
• What if you could cut open bacterial DNA, and insert DNA of
your choice in?
8. History of iGEM
• Started as a spin-off of an MIT
course in 2003
• Has grown from 5 teams in 2004 to
245 in 2013!
• Competition is run by co-founder:
Randy Rettberg
• Established the BioBrick, a
standardized biological part for
easier genetic manipulation
9. How do You Clone with BioBricks?
1. Get some DNA!
5 mL culture
Plasmid DNA
E. coli
10. How do You Clone with BioBricks?
2. Amplify target sequence through PCR
11. How do You Clone with BioBricks?
3. Double-digest backbone and PCR product
12. How do You Clone with BioBricks?
4. Gel purify your digests
13. How do You Clone with BioBricks?
5. De-phosphorylate backbone
14. How do You Clone with BioBricks?
6. Ligate your DNA
15. How do You Clone with BioBricks?
7. Transform into bacteria
16. The Team
● Award-winning
undergraduate project
team
● International Genetically
Engineered Machines
● “Biobricks” : Standardized
genetic parts
○ Ever-expanding registry
● Annual competition
19. “LEAD IT GO” 2014
HEAVY METAL SEQUESTRATION SYSTEM
• Engineering E. coli for the uptake of heavy metals
• Integrate cells into dry lab’s filtration system
• Test efficacy of filter with lab based and local water
supplies
• Building CAD portfolio of designs that allow the system to
scale to many applications
20. Water Contamination
● Heavy metals
o Mercury, lead, nickel
● Sources:
o Industrial manufacturing
o Hydraulic fracturing
o Coal mining
o Construction
● Harmful to humans, ecosystem, aquatic life
o Biomagnification
21. Project Goals
● Engineer E.coli to uptake heavy metals from
the environment
● Integrate cells into a continuous water
filtration system
● Test efficacy of biological filter with lab
based and local water samples
22. Heavy Metal Transport Proteins
● Proteins specific to heavy metals
o nixA - nickel
o merT and merP - mercury
o CBP4 - lead
● Behind the constitutive Anderson promoter
nixA
Anderson
Promoter
23. E.coli - Metal Transport
E.coli
Metal Ions
Transport
Protein
24. Metallothioneins
● Low molecular weight proteins
● High metal binding affinities
o GST-YMT, GST-PMT
● Expression causes cellular dormancy
● Arabinose inducible system
Arabinose
araBAD Promoter
Metallothionein
T7 Promoter
T7 Polymerase
27. Saturation Sensing System
● Insert mRFP gene behind metal-inducible
promoters
o Cells will fluoresce when metallothioneins are
saturated
● Metal sensitive promoters induced once MT
are saturated
29. Efficacy Analysis
● Continuous flow hollow fiber reactor
● Implementation
o Factory waste water outlet
o Contaminated bodies of water
● Testing
o Lab made waste water
o Local water samples
▪ Cayuga Lake
▪ Ithaca Gun factory
30. Fun Activity: Learn to Load Gels!
Purpose:
To determine relative lengths of pieces of DNA
Applications of DNA Electrophoresis
● murder mysteries
● paternity cases
● disease diagnosis
