iGEM - Team Aberdeen

Main

First email sent out looking for this year's members

02/02/2014

Dear All,
I am writing to you to let you know of an exciting opportunity. This year, I and a small group of academic staff will be leading an undergraduate team entry into the International Genetically Engineered Machines Competition, or iGEM. (http://igem.org/Main_Page)

For those of you not aware, iGEM is a synthetic biology competition for undergraduate students from Universities across the world, run by the Massachusetts Institute of Technology, Boston, USA. Student teams use biological engineering principles to design, construct and test a novel synthetic biology gene circuit. Student teams will work from now, January 2014 onwards, and over the summer of 2014 to construct and test their gene circuits, before travelling to Boston in November to present their results and compete in the competition by delivering a talk and poster at the multinational iGEM symposium.

Aberdeen took part successfully in the competition in 2009 and 2010 (take a look at our team web sites on the iGEM site!), and we will be entering again this year. We will be selecting a team of enthusiastic, bright and committed students to make up a University of Aberdeen iGEM entry over the next two weeks. If you are interested, come along to Taylor Building, A21, on Wednesday afternoon 5th February at 14.00 to find out more!

Best wishes,

Prof Ian Stansfield

Team members are selected

02/27/2014

We now finally have our team ready, and now the work begins.

Brainstorming

03/05/2014 - 05/16/2014

First meeting

03/05/2014

iGEM
Meeting #1
5th March, 2014

Synthetic biology project ideas:

• Bacterial drones
Engineering bacteria to carry particular substances to specific locations via manipulation of chemotaxis

• Defrosting streets in winter
To engineer bacteria expressing anti-freeze proteins from an arctic fish in order to provide an alternative for using salt in winter to defrost streets

• Light sensor
Engineering bacteria that would sense the intensity of light in our surrounding and respond when it falls below a certain threshold by producing light (e.g. to keep optimal light levels when reading). Geobacter could be used since it can transmit an electric current

• Tetrodotoxin detector
Designing a biosensor which would be able to detect lethal concentrations of tetrodotoxin in prepared puffer fish, allowing a decision whether it is safe to consume

• Recycling nappies
A bacterium which would be able to degrade a filling used in baby nappies

• Polyester degradation
Engineering bacteria to degrade polyester and hence enable recycling of polyester based thrash, e.g. margarine packages and yoga mats

• Biological night light
Engineering plants to express luminescent luciferase in order to create a touch-activated night light for children which wouldn't require electricity

• Bacterial pen
Filling a pen with bacteria manipulated to synthesize dye. Such a pen would never run out of ink as long as we would feed it with nitrogen and sugar. A water-soluble and insoluble dyes could be synthesized.

• Supplementation of Vit.C
Engineering probiotic bacteria to synthesize vitamin C in order to produce Vit. C fortified food products

• Biofilm degradation
The idea is to engineer bacteria to synthesize an enzyme capable of degrading extracellular polymeric substances which create biofilms. This would ideally reduce biofilm-associated infections by disrupting quorum sensing, decreasing antibiotic resistance in bacteria and increasing their sensitivity to cleaning agents. Engineered bacteria could be incorporated into a toothpaste.

• Water contamination detectors
Engineered bacteria would sense a presence of one of the following in water and respond via a colour change upon detection.

a) Vibrio cholerae
b) arsenic
c) aluminium
d) fluoride
e) asbestos

• Greenhouse gas reduction bacteria
An anaerobic bacteria that uses NO2 to get Methane and then 'digests' Methane into CO2 and H20. The idea is to get the bacteria to stop at Methane and thus suck it from the atmosphere. Ask here more about it, if you have the chance.

• CO Detector bacteria
Use modified bacteria that is equipped with receptors for CO to signal a high concentration of CO in air. The bacteria could emit light, change colour or other type of signal.

• Computer Bacteria
Use bacteria that conducts electricity and modify it in a way that it will conduct or not depending on a certain environmental condition. This way, we can make the bacteria mimic a computational process.

• Fire detector bacteria
Fire detectors work by constantly checking for contamination in the air from smoke particles. They achieve this by flowing a current through a radioactive emitter, which decreases/stops emitting radiation when surrounded by smoke particles. This fall in current, triggers the detector. We could try imitating this behaviour with the electricity conducting bacteria, by making it not able to conduct electricity when smoke particles are with high concentration.

• Bio-deodorant
James' idea. We really liked this one and it doesn't seem so far-fetched.

• Contaminated water detector
Use E.coli (or sth.) to secrete colour in reaction to certain toxins in water. Problematic as in pure water witn only toxin diluted, there is no energy source for the bacteria.

• Break down of oil spills
Make a bacteria break down oil into non-harmful matter in order to clean up oil spills.

• Reduce saturated fat intake in humans
Use a similar idea to the previous one, but in this case, bacteria will extract saturated fat from food intake and make it indigestible or the bacteria itself could break it down to something less harmful.

Project selected

06/02/2014 - 06/06/2014

Ag43+Quorum sensing for a surface marker detection system

SDM, In-Fusion and Sequencing Primers designed

Approx. 06/02/2014 - 06/10/2014

Additional BioBricks ordered

06/06/2014

Scottish Teams Liaison at Edinburgh

06/09/2014 - 06/10/2014

Poster and Presentation

06/09/2014

#‎iGEM2014ABDN

06/10/2014

Wetlab

06/23/2014 - 08/29/2014

Ag43 BioBrick has Pst1 sites!

06/30/2014

Our fate is uncertain, Ag43 contains Pst1 sites. Rescued INP plasmids from 2014 distribution (523008, 523013)as a fallback plan.

Ana & Martyna are team Ag43

06/30/2014 - 08/15/2014

James Mc analyses E.coli growth

Approx. 06/30/2014 - Approx. 07/12/2014

Jamie and Joseph are team INP

06/30/2014 - 08/15/2014

James Mc analyses Quorum Fluoresence

07/07/2014 - 08/15/2014

Dr Rey Carabeo offers us the use of his FluoSTAR OPTIMA automated fluoresence plate reader, enabling us easy analysis of fluoresence in response to quorum over time.

Team joins forces

08/15/2014 - Approx. 08/27/2014

The INP(-)His, INP-YFP-His, and Ag43-FLAG are doubly-transformed with Sender and Receiver constructs

End of wetlab

08/29/2014

iGEM 2014 Calendar

iGEM 2014 registration

02/14/2014 - 03/31/2014

Opens February 14th
Closes March 31st, Team registration fee due

DNA Distribution Plate Kits received

Approx. 05/01/2014 - Approx. 05/31/2014

ESTA applications

Approx. 06/02/2014 - Approx. 08/20/2014

For travelling to USA

Open Office Hours

06/19/2014

Ask safety questions, meet other iGEMers! (More office hours will be scheduled later in summer.)

'About our Lab' form due

06/23/2014

'Measurement Interlab Study' Signup Deadline

07/01/2014

11.59PM EDT

Giant Jamboree Registration

07/18/2014 - Approx. 09/19/2014

Preliminary Safety forms due

07/21/2014

Track Selection due

07/25/2014

Team project descriptions due

08/15/2014

Team rosters due

08/15/2014

Project titles and abstracts due

08/30/2014

Final Safety forms due

09/01/2014

Giant Jamboree fee & Interlab Data

09/19/2014

11.59PM EDT
-September 19 Giant Jamboree attendance fee due at 11:59PM EDT
-September 19 Measurement Interlab Study Data due at 11:59PM EDT

BioBrick Part DNA due at the Registry

Approx. 10/01/2014 - 10/10/2014

Parts should be received by this date
Project and Part documentation due, including documentation for all medal criteria

Wikis FREEZE and Judging form

10/17/2014

-Judging form due
-Giant Jamboree wiki FREEZE at 11:59PM EDT
-Parts.igem.org wiki FREEZE at 11:59PM EDT
-Additional Part DNA due to the Registry (not a requirement)
-Judges Assignments distributed