Team:UCL London/Safety

1. Would any of your project ideas raise safety issues in terms of:
- researcher safety,
- public safety, or
- environmental safety?

Safety issues have been considered throughout our project design, experimental work plan and thorough risk assessment to achieve quality by design. Furthermore, all the participants of the project have completed a safety induction given by the Departmental Biological Safety Officer, during which fire evacuation procedure, accident reporting and general safety practices have been detailed and all team members have a copy of the departmental safety book. E. coli strains that are non-pathogenic and therefore low-risk have been chosen, so there is no great safety issue with regards to the host organism as long as Safe Microbiological Technique (SMicT) is adhered to. The major hazard identified in our project is the use of Ethidium Bromide (EtBr) for staining of agarose gels. EtBr is a mutagen and moderately toxic after an acute exposure due to its ability to intercalate with DNA bases, causing mutations such as “frameshift” and deletion, leading to oncogenic development. It should be treated as a possible carcinogen and teratogen. The following control measures will be adopted:

• Nitrile gloves will be used for all EtBr handling
• EtBr preparations are to be carried out in a dedicated fume hood
• All EtBr-containing materials will be disposed of in dedicated bins
• Work surfaces must be thoroughly cleaned after each experiment

In addition, attention should be paid when operating the centrifuge, autoclave as well as microwave. For instance, weight distribution should be even in the centrifuge to prevent the rotor blade from dislodging and shredding the machine. Also, heatproof gloves should be worn when handling the autoclave to prevent first to second degree burns. Last but not least, when melting agar we must make sure the bottle cap is loosened to prevent pressure buildup.

Our project poses some risk in terms of public and environmental safety. As mentioned before, the organism we are going to use is a non-pathogenic lab strain of E. coli. However, one paper suggested that highly supercoiled plasmids which is our final product will enable a higher transfection efficiency. The potential environmental damage which may occur is the higher probability of a successful unintended transfer of antibiotic resistant genes to other bacteria in the ecosystem, thus potentially resulting in the development of multiresistant pathogens[1]. Henceforth, proper chemical waste disposal and Genetically Modified Organism containment are essential. There is also a possible risk to security through malicious misuse by individuals, groups or states. Whilst our strain of E. coli is non pathogenic, the supercoiled plasmids produced from it can be used as a disease inducing vector. Precaution steps include:

• Liquids containing E. coli, other living organisms and equipment with biological contamination must be autoclaved before disposal
• EtBr waste and contaminated materials (gloves, tissues, etc.) must be put in the dedicated bin for collection by Estates. Work surfaces must be thoroughly cleaned after each experiment.

2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
- did you document these issues in the Registry?
- how did you manage to handle the safety issue?
- how could other teams learn from your experience?

The BioBrick parts we are going to make this year are related to DNA gyrase, gyrase binding site. DNA gyrase is an essential bacterial enzyme that catalyzes the ATP-dependent negative supercoiling of double-stranded, closed-circular DNA[2]. Gyrase binding site facilitates supercoiling of specific plasmids. To date there is no research showing that DNA gyrase and its binding site could be toxic or harmful, therefore, it has little or no potential risk to human health or the environment.

3. Is there a local biosafety group, committee, or review board at your institution?
- If yes, what does your local biosafety group think about your project?
- If no, which specific biosafety rules or guidelines do you have to consider in your country?

At UCL all work with genetic modification techniques and with genetically modified organisms must first be discussed with the Departmental Genetic Modification Safety Officer (DGMSO) and approved by the College Genetic Modification Safety Committee. All work must conform to the UCL Local Rules[3][4]. A risk assessment must be performed and agreed with the DGMSO before work begins. Our project has been approved to proceed. All the participants have gone through supervised training[5], encompassing areas such as:

• What is biosafety
• Routes of infection
• The legal framework governing the work
• Hazard identification and controlling the risks
• Principles of control – physical and procedural
• Containment levels
• Correct use of safety control measures
• Good laboratory practice
• Correct disposal of laboratory wastes
• Administrative and safety information resources

These all align with national as well as international biosafety regulations and guidelines[6][7] to ensure we have a fully comprehensive biosafety approach, incorporating risk assessment, safety and civic responsibility to scientific research.

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

Antibiotic resistance has become one of the world's most pressing public health problems[8]. There are safety issues associated with using an antibiotic resistant gene as a selectable marker[9]. By using antibiotic resistant genes in research and particularly in the production of therapeutics raises the potential for horizontal gene transfer to environmental organisms and subsequent expansion of the population of antibiotic-resistant pathogens. With regards to this concern, the FDA is encouraging the use of alternative plasmid selection mechanisms.

The control of gene expression could potentially be helpful in improving the safety of engineered genes by building in complex control circuits to induce expression of the cassette only under certain conditions.

We also suggest the establishment of a branch-off discipline from synthetic biology, called biosafety engineering – where consolidation of all biosafety provisions and protocols into a single specialized field can help to efficiently make parts, devices and systems even safer for industry and consumerism. This opens up a window of opportunity for government watchdogs (consumer protection) and regulatory bodies to assert greater authority in the growing biosciences sector.

References
[1]Cupillard, L. et al., 2005. Impact of plasmid supercoiling on the efficacy of a rabies DNA vaccines to protect cats. Vaccine 23: 1910-1916.
[2]Reece, R.J. and Maxwell, A., 1991. DNA Gyrase: Structure and Function. Critical Reviews in Biochemistry and Molecular Biology. 26 (3/4):335-375.
[3]Safety Handbook, 2010/2011. Department of Biochemical Engineering, UCL.
[4]Institute of Child Health Flow Cytometry Core Facility, UCL Biosafety: Important health and safety documents, [online] Available from: http://www.ucl.ac.uk/ich/services/lab-services/FCCF/biosafety (Accessed on 25 August 2011)
[5]UCL Principles and Practice of Biosafety Course, [online] Available from: http://www.ucl.ac.uk/estates/safetynet/training/biosafety_pp.pdf (Accessed on 25 August 2011)
[6]Health and Safety Executive: Guidance from the Scientific Advisory Committee on Genetic Modification, [online] Available from: http://www.hse.gov.uk/biosafety/gmo/acgm/acgmcomp/ (Accessed on 25 August 2011)
[7]World Health Organization , Laboratory Biosafety Manual - Third Edition, [online] Available from: http://www.who.int/csr/resources/publications/biosafety/en/Biosafety7.pdf (Accessed on 25 August 2011)
[8]U.S. Department of Health and Human Services, Food and Drug Administration, 2011. Antibiotics and Antibiotic Resistance
[9]U.S. Department of Health and Human Services, Food and Drug Administration, 1998. Guidance for Industry Use of Antibiotic Resistance Marker Genes in Transgenic Plants.

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