The document discusses an undergraduate synthetic biology competition called iGEM where students design and build biological systems from standard DNA parts. It then describes the Cornell iGEM team's project which aims to develop a biosensor using the bacterium Shewanella oneidensis for continuous monitoring of water quality near oil and gas extraction sites. The biosensor would detect environmental toxins like arsenic and naphthalene. The document provides details on the team's prototype device, goals for genetic modifications to the organism, and plans to partner with a company called Ecovative that produces biodegradable packaging alternatives.

1. Using synthetic biology to secure a more
sustainable future

2. What is iGEM?
• iGEM is an international undergraduate synthetic biology
competition.
• Students design and build simple biological systems made from
standard interchangeable DNA parts.
• Interdisciplinary and multi-faceted!
• College, high school, entrepreneurship divisions

3. What is synthetic biology?
• The bridge between biological science and engineering
• Design and construction of novel biological functions and
systems
• Creation of synthetic components OR reassembly of pre-
existing genes

4. Who are we?

5. College Composition
Arts & Sciences
23%
Engineering
60%
CALS
10%
Human Ecology
4%
Architecture, Art &
Planning
3%

6. Year Composition
Freshmen (2017)
3%
Sophomores
(2016)
38%
Juniors (2015)
31%
Seniors (2014)
21%
Grad
(2013)
7%

7. Major Composition
Biological
Engineering
20%
Electrical &
Computer
Engineering
6% Human
Biology, Health &
Society
3%
Operations Research
3%Biological Sciences
26%
Chemistry
9%
Mechanical
Engineering
6%
History
3%
Computer Science
3%
Statistics
3%
Chemical
Engineering
18%

8. Subteams
WETLAB
Biology sector that grows and
transforms the bacteria and fungi
HUMAN PRACTICES
Analyze our project in terms of
safety and environmental impact
MODELING
Use mathematical models to
describe the biology in a
quantitative matter
DRYLAB
Create a physical object that
implements our wetlab
constructs
SPONSORSHIP
Finds the funding necessary to
complete the project

9. Cornell Resources
• Weill Hall Lab
• Professors and Grad Students
• Cornell Library
• History with Sustainability Projects
• Biotechnology Institute
– Sequencing
– 3-D Printer

10. ELECTROCHEMICAL BIOSENSING
A safe bet for safeguarding the environment

11. Our Project is a SAFE BET
Shewanella Assay for Extended
Biomonitoring of Environmental Toxins
The goal of our project was to develop a field-
deployable biosensor for continuous
monitoring of water quality in areas affected
by oil and gas extraction, using an organism
called Shewanella oneidensis.

12. Oil Sands
• Bitumen reserves found in Canada that provide an alternative
source of crude oil
• Waste from extraction is kept in tailings ponds, where it can
seep into waterways
– Tailings ponds cover more than 130 square km of northern Alberta
– Their isolation does not prevent contamination of watersheds!
• Environmental toxins (such as arsenic and naphthalene) can
thus pollute drinking water and freshwater ecosystems

13. Environmental Hazards
• Health risks to various organisms
• Threat to biodiversity and ecosystem
balance
• The EPA has set limits on levels of
several contaminants in water for these
reasons
• Arsenic and naphthalene
contamination in water is dangerous to
aquatic species and to humans

14. Application

15. Device Prototype

17. Ecovative Design is a small startup
company located in NY that has
developed a biodegradable
alternative to Styrofoam
• Uses mycelium to knit together agricultural
by-products and create a foam-like
substance
• Partnered with Dell Inc., Ford
Motors, Steelcase Inc., Puma, and a few
other companies to build alternatives to
their current Styrofoam products
• Goal of the company is to completely
replace all Styrofoam products with their
eco-friendly biodegradable product

18. Styrofoam Market
Common Uses of Styrofoam

19. Industry Revenue is Falling
Cost is Increasing
• Production companies spent an average of
61% of their income on purchasing raw
materials
• Over 200 US cities (including Seattle) no
longer tolerate polystyrene packaging
• California is considering a polystyrene ban
– State is the home of 12.1% of industry
establishments
• Bloomberg proposed a city-wide ban on
plastic foam food containers
– New York City has the highest net
consumption of Styrofoam of any city
in the US
Demand for Styrofoam is Decreasing
• Price of Styrofoam is expected to steadily
increase over then next 10 years
– Price difference between Styrofoam and Ecovative
product will shrink
• Number of polystyrene foam
manufacturers is expected to drop due to
mergers and acquisitions
• Consumers are slowly switching over to
aluminum containers and are now looking
for more substitutes for polystyrene
containers

20. Potential Alternatives
Recycling
• Alliance of Foam Packaging Recyclers
– www.epspackaging.org
– Testing all possible ways to remold /
reuse Styrofoam
– Supported by Dart Container
Corporation, Dunkin
Donuts, McDonalds, and Jamba Juice
Styrofoam Replacement
• Cow Milk Packaging
– Uses casein found in cheese and cow
milk
– Blends the protein with clay and
glyceraldehydes so casein is stronger
and less susceptible to water damage
– Still in developmental stage

21. 3
2
1
Methods of Cloning
Current
Progress
Goals
Promoter Problems

22. Goals
• Improve product via introduction of several biological
plasmid constructs.
• Antifungal constructs to eliminate
fungal contaminants
– Provide fungal species
opportunity to outcompete
fungal contaminants
• Carotenoid pigment pathways to make product more
appealing
• Develop fungal toolkit

23. Chassis
• Ganoderma lucidum
• Higher order
basidiomycete
• Sequenced in 2012
• Reported to have
medicinal properties

24. Homologous Recombination
• Integrate linearized plasmids via natural homologous
recombination
Figure from Gene Bridges

25. Gibson Assembly
• Used for cloning in genes
with internal cut sites
• Uses polymerase,
5’ exonuclease, and
ligase in simultaneous
reaction
Photo from Integrated
DNA Technologies

26. Site-Directed Mutagenesis
• Introduce silent mutations
• Used on genes with internal restriction sites
Image from Agilent Technologies
Thermal
Cycling
DpnI
Digestion
Transformation

27. Promoter Problems
• Fungal promoters are very long
– E.coli has a check system where it splices out
potential duplications
• Very few identified Ganoderma promoters
• Potential solution: use T7 bacteriophage
promoter/polymerase
Image credit: Thomas Splettstoesser

28. 3
2
1
Partnering with Ecovative
and
Future Plans
Antifungals
Living Materials
Applications

29. Antifungals
Application
Constructing and transform genetic parts that could help
improve Ecovative’s materials
Problem
During the growing phase, the Ganoderma fungi becomes
contaminated by other fungal strains.
This slows or inhibits growth of Ganoderma we want.
Resolution
Search for and transforms antifungal protein constructs that
allow the our Ganoderma strain to fend off other fungal
contamination.

30. Partnering with Ecovative
Application
Test our genetically modified strain of Gandoderma as a
prototype foam.
Problem
Unsure of the viability of our strain in the final product.
This includes the structural and thermal strains of our
genetically modified Ganoderma lucidum.
Resolution
Send our completed Ganoderma strain to Ecovative to grow
and test the viability.
Model the structural and thermal properties of our
prototype foam.

31. Living Materials
Application
Create a bio-active material that can self-heal or "repair"
itself when physically damaged.
Problem
Fungal species form spores when stressed (or damaged)
rather than forming mycelium.
Resolution
Learn how sporulation is regulated so it can be controlled.
Control the growth of the fungal strain so only mycelium
grows.
Shutting down the pathway that induces fungal spores.

32. Thank you for your time!
Contact Info
Email: infocornelligem@gmail.com
Website: igem.engineering.cornell.edu
Facebook: www.facebook.com/cornelligem
Twitter: www.twitter.com/CUGEM
Questions?