Using synthetic biology to secure a more sustainable future

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

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

Who are we?

College Composition

Arts & Sciences23%

Engineering60%

CALS10%

Human Ecology3%

Architecture, Art & Planning3%

Year CompositionFreshmen (2017)

3%

Sophomores (2016)38%

Juniors (2015)31%

Seniors (2014)21%

Grad (2013)7%

Major CompositionBiological Engineer-

ing21%

Electrical & Computer Engineering

6%

Human Biology, Health & Society

3%

Operations Research3%Biological Sciences

26%Chemistry9%

Mechanical Engineer-ing6%

History3%

Computer Science3%

Statistics3%

Chemical Engineering18%

SubteamsWETLAB

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

Cornell Resources

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

ELECTROCHEMICAL BIOSENSINGA safe bet for safeguarding the environment

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.

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

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

Application

Device Prototype

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

Styrofoam Market

Common Uses of Styrofoam

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

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

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Methods of Cloning

CurrentProgress

GoalsPromoter Problems

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

Chassis

• Ganoderma lucidum• Higher order

basidiomycete• Sequenced in 2012• Reported to have

medicinal properties

Homologous Recombination• Integrate linearized plasmids via natural homologous

recombination

Figure from Gene Bridges

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

Site-Directed Mutagenesis• Introduce silent mutations• Used on genes with internal restriction sites

Image from Agilent Technologies

Thermal Cycling

DpnI Digestion

Transformation

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

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Partnering with Ecovative

andFuture Plans

Antifungals

Living Materials

Applications

AntifungalsApplication

Constructing and transform genetic parts that could help improve Ecovative’s materials

ProblemDuring the growing phase, the Ganoderma fungi becomes contaminated by other fungal strains.This slows or inhibits growth of Ganoderma we want.

ResolutionSearch for and transforms antifungal protein constructs that allow the our Ganoderma strain to fend off other fungal contamination.

Partnering with EcovativeApplication

Test our genetically modified strain of Gandoderma as a prototype foam.

ProblemUnsure of the viability of our strain in the final product.This includes the structural and thermal strains of our genetically modified Ganoderma lucidum.

ResolutionSend our completed Ganoderma strain to Ecovative to grow and test the viability.Model the structural and thermal properties of our prototype foam.

Living MaterialsApplication

Create a bio-active material that can self-heal or "repair" itself when physically damaged.

ProblemFungal species form spores when stressed (or damaged) rather than forming mycelium.

ResolutionLearn 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.

Thank you for your time!

Contact Info

Email: infocornelligem@gmail.comWebsite: igem.engineering.cornell.eduFacebook: www.facebook.com/cornelligemTwitter: www.twitter.com/CUGEM

Questions?