UCC iGEM 2014

iGEM 2013 Jamboree

What is iGEM?

iGEM (International Genetically Engineered

Machine) is a synthetic biology competition for

third level students. The iGEM competition

began in 2004 and has grown exponentially with

over 245 participating universities from across

the globe. iGEM involves teams of

undergraduate students undertaking research

projects in the area of synthetic biology over the

summer months. The teams then present their

work at the iGEM Jamboree and compete for

prizes in a variety of categories. This year’s

iGEM Jamboree is being held in Boston at the

Hynes Convention Center in November and is

expected to attract more than 2500 participants. It

is being billed as “the largest single event in the

history of iGEM and synthetic biology”, and this

year UCC will be entering the competition with

Ireland’s first ever team.

Russell working in the lab

Our Projects

Operation Hagfish: Create cell “factories” that mass-produce a

biopolymer that is found naturally in the slime of

the hagfish. The exciting properties of this

biopolymer indicate that it will have many

potential applications in the food, medical

devices, and textile industries.

Biagnostics: Development of a novel method for DNA-based

diagnostics using bacterial detection of target

DNA sequences from two different strains of the

Human Papillomavirus. We foresee applications

for this in healthcare settings in resource-poor,

developing countries.

Filaments and threads produced by our team from natural hagfish slime; Top, Left to Right: Natural Hagfish Slime; Filaments imaged at

20x and 100X magnification by UV microscopy; Bottom, Left to Right: Filaments imaged by atomic force microscopy; scanning electron

microscopy; a thread generated from hagfish slime

Operation Hagfish

Our first project involves the production of a new

polymer using filaments made naturally by the

hagfish.

The hagfish is a fish which lives at the bottom of

the ocean, and when agitated produces copious

amounts of slime to clog the gills of predators.

What’s interesting is that within the slime there are

long filaments, which have fascinating properties.

These filaments are 100x thinner than a human hair

and stronger than nylon, steel and possibly Kevlar.

The hagfish cannot be farmed, and we proposed to

synthesize the filament in bacteria to create this

biological material. This material will be

lightweight, strong and completely biodegradable.

We are currently inserting the DNA sequence into

a plasmid and for the proteins to be expressed in

E.coli. Since the filament is made of two proteins

we will be looking at various methods of obtaining

the final filament- ideally they will be co-

expressed, and we will be able to secrete it using a

secretory pathway.

We have acquired samples of the hagfish slime and

extracted the protein from it. So far we have

produced threads and films from the natural slime.

A suite of tests including, scanning electron

microscopy, powder x-ray diffraction, atomic force

microscopy, water contact angle tests were

completed in order to characterise the physical

characteristics of the protein at a molecular level.

Left: Cian, Leanne, Gavin, Ian and Timothy in the lab; Top-Middle: Colonies

Top-Right: Agarose Gel-loading; Bottom-Right: Dan and Ian on the board

Biagnostics

Our second project involves the production of a

DNA detector using a modified DNA plasmid.

Molecular diagnostics is a growing area of

diagnostics and analysing genetic material has now

become the norm for disease diagnosis and

treatment. Genetic abnormalities, cancer diagnosis

and detection of viral infections all rely on these new

methods of analysis as they are accurate, highly

reliable and reveal more information than traditional

tests.

Using genetically modified organisms to detect a

specific sequence of DNA overcomes many

obstacles in molecular biology. Firstly, no expensive

equipment is required. With just a few reagents and

the time it takes to grow cells overnight, a result can

be achieved. This avoids costly machines and

expensive chemicals required in current methods. In

addition, no special training is required to carry out

this test.

Where could we see Biagnostics? Applications

include, on the farm to test animal infections, GP

office to reduce time for tests and in medical

laboratories as a low cost diagnostic solution.

The model of our DNA detector is currently in the

design phase. Construction of our plasmid probe is

underway. The first DNA sequence to be detected

will belong to HPV (Human Papilloma Virus) 16,

which causes the majority of cervical cancer cases

worldwide. Screening for HPV infection, although

commonplace in Ireland, is not often carried out in

under-resourced countries where the infection is

most prevelant. Biagnostics HPV-16 detector could

be a solution to these populations as it is simple,

cheap and requires no specialist equipment.

The most exciting feature of Biagnostics is its ability

to be customised. Our DNA detector could easily be

modified to detect virtually any DNA sequence,

making it’s applications in diagnosis endless!

Our Team

Russell Banta 3rd Year Chemistry

Cian Scannell 2nd Year Mathematics

Cian O' Donnell 1st Year Biochemistry

Patrick Xie 4th Year Engineering

Shama Chilakwad 3rd Year Genetics

Timothy O' Flynn 3rd Year Genetics

Leanne O’ Sullivan 2nd Year Biomed

Dan Collins 3rd Year Genetics

Gavin King 3rd Year Biochemistry

Ian McDermott 3rd Year Biochemistry

Academic Mentors

Dr. Paul Young Biochemistry & Cell Biology, UCC

Prof. Tommie McCarthy Biochemistry & Cell Biology, UCC

iGEM 2013 Teams from around the World

How can you help?

By being our sponsors! We have already raised €27,000 of our €50,000 target. The remaining €23,000 will go

towards attending the Jamboree held in M.I.T. We will be representing Ireland in the single largest synthetic

biology event.

Sponsorship level €10,000 €5,000 €2,000 €1,000

Logo on T-shirt ✓ ✓ ✓ ✓

Logo on banner ✓ ✓ ✓ ✓

Logo on iGEM wiki ✓ ✓ ✓

Main Logo on back of T-shirt ✓

Media coverage (Facebook, Twitter, Papers) ✓ ✓

Main logo on front of T-shirt ✓

Mentioned at the Boston Jamboree Presentation ✓

Contact Us:

E-mail: uccigem2014@gmail.com Address: College of SEFS, UCC, Co. Cork, Ireland Phone No: Russell Banta: +353 (0)83 180 0102 Dr. Paul Young: +353 (0)21 420 5994