Team:York UK/Project.html

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iGEM York

iGEM York Team

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The University of York

The University of York is Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi in sem sodales, viverra nunc id, interdum tortor. Sed urna augue, dictum eget justo ut, dictum elementum massa. Nunc eu metus nunc. Aenean tempor sit amet quam accumsan vulputate. Curabitur nec tempus quam, quis fermentum leo. In laoreet venenatis arcu, sit amet elementum leo dignissim ut. Aenean id elementum nulla. Ut velit neque, lobortis id mollis quis, luctus sed tortor. Nam aliquam vitae orci et pharetra. Nunc ut metus in orci venenatis fermentum. Suspendisse placerat est purus, sagittis vehicula elit fermentum vitae. Aenean eleifend, odio sit amet semper dictum, dolor tortor feugiat nisl, ac ornare enim nisi sit amet purus. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Pellentesque sed turpis pretium, feugiat eros sit amet, consequat ligula.

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Safety

Safe Practices in the Lab

Our team conducted the research at the University of York, in the teaching laboratories of the Biology Department. All work was conducted in a biosafety level (BSL) 1 laboratory. We used Escherichia coli DH5a, BL21 and K12 wild type, which are well characterised and do not constitute a threat to the environment. Shewanella oneidensis and Salmonella enterica typhimurium serovar 14208s were not used (as we had the genes synthesised, instead of amplifying them from the genome). Before gaining access to the lab space, team members were required to:

Complete chemical waste disposal training
Attend an orientation with Dr Jen Lee and Nikki Begg, part of the technical staff of the labs, regarding the University of York Health & Safety Regulations
Receive specific training from Dr Jen Lee and from Dr James Chong, our main supervisor, for the equipment in the lab
Complete a risk assessment form provided by Biological Safety Advisor (David Nelson)
Sign after-hours access agreements with the University, after having been instructed on the regulations and procedures which apply for working in the lab at weekends and between 18:00-08:00

Our standard lab practices were in compliance with the World Health Organization’s Biosafety Level 1 guidelines. Safety forms were approved on September 22, 2013, by Evan Appleton of behalf of iGEM. Many of our basic lab practices are described below. [PLEASE INSERT THE TWO PDFs WITH THE SAFETY FORMS, THAT YOU GUYS SENT TO iGEM. JUST MAKE THEM AVAILABLE AS A DOCUMENT WHICH CAN BE DOWNLOADED OR SMTH LIKE THIS]

Researchers were required to wear gloves while in the lab space, and to remove both gloves and wash their hands when going into the write-up area or in other lab common areas;
No gloves were allowed to leave the lab space, and no food or drink was allowed into the lab space, including the computer room;
Within the Department of Biology, microbiological samples were transported only via the internal service elevator and on lab-associated stairs which were accessed by card, to avoid contamination of public areas;
All flammable liquids were kept in a flammable storage cabinet;
The lab contained distinct waste containers for general waste, biohazard waste, biohazard sharps, and non-biohazard broken glassware;
Liquid bacterial waste was always autoclaved before being discharged into sanitary sewage;
Benchtops were decontaminated with ethanol before and after lab work was conducted;
Tools that came into contact with bacteria were soaked in ethanol and flame-treated before and after use;
An autoclave was used to decontaminate growth media, glassware, tubes, pipette tips, etc. All lab members were trained in preparing waste and media for being autoclaved. The actual autoclaving programs were run for us by the staff of the teaching labs, to avoid dangers to researcher safety;
An emergency shower, eyewash, and first aid kit were available within the lab space in case of emergency.
Dry ice was carried in iceboxes and thick gloves were used to take samples from them. Dry ice was left in the room to evaporate instead of disposing anywhere.
Microwave was used for melting agarose for agarose gels and LB agar for making LB agar plates. Thick gloves were used to take hot samples after heating.
Gel electrophoresis tanks were kept separately to avoid any electric shock.
All the unused isolated DNA was autoclaved in order to shear the genetic material that would not be used by bacteria in environment.
While using Bunsen burners no gloves were worn in order to prevent melting the gloves and causing high level of damage to the skin.
For adjusting the pH highly corrosive 1M NaOH was used. Thus gloves and protective glasses were worn in order to avoid any skin burning.
Phenol/Chloroform extraction of S. oneidensis genome was performed in the fume hood as both of the compounds are volatile and toxic.
β-mercaptoethanol was used during the beta galactosidase activity assay. All the procedures performed in the fume hood to avoid intoxication of highly volatile compound.
As gold ions are toxic to most of the living organisms after each experiment we treated them with the excess of HEPES to form gold aggregates as well as washed with excess of water to dilute to non-toxic concentrations.

To minimise the risk one might be exposed to when working with Ethidium Bromide (which is a carcinogen) we used its safer alternative, SYBR Safe, for our gel electrophoresis. Team members were protected from exposure to UV rays during gel reading with a UV shield. Facial shields were also available for use when needed.

Safety Concerns for Our Project:

There are no serious safety concerns, as the genes or their products that we work on have no identified risk to human health, do not influence the environment and are specific for only our project.

Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?

The only safety issue associated with our new BioBrick parts is researcher safety in testing the parts. We have documented our standard operating procedures above, which other teams can reference if they want to use our parts, or test other parts using arsenic or naphthalene. We are also conducting extensive tests to assess the functionality of our BioBrick parts, to ensure that they behave as expected under different conditions.

Safety Concerns for iGEM Competition:

Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?

use other selection forms like auxotrophic mutants for amino acids, not antibiotic resistance, to prevent release of resistant strains into the environment. However, because we wanted to try MFC with wastewater, this method would not be useful as in addition we would need to add amino acid, which would affect the metabolism.
usually the antibiotics that are used in the lab are different from medically common antibiotics and would potentially cause no influence towards MRSA and similar
make standard iGEM safety guidelines to be followed by all the teams