Introduction

Ensuring that all research conducted is both safe, and secure is crucial to synthetic biology. Mitigating risks at the personal level for workers is important, as is protecting the external world, the public and the environment, by adequately containing all organisms. We have assessed safety throughout the project, from planning experiments, to standard lab practice. To do this we approached all risks in the context of the Hierarchy of Controls. This means that in all cases, we aim to eliminate any exposure to risk above all alternatives.

Elimination

The elimination of a risk is always the best possible option, as it completely removes any risk associated with a given process

  • While Arabidopsis thaliana is a white listed organism, there are hazards associated with its pollen, as it can trigger an asthmatic response in some individuals. We eliminated this risk by destroying any Arabidopsis that showed signs of budding.
  • Another risk we were able to eliminate was the hazards associated with Northern Blotting (exposure to radioactivity), by using alternative methods to detect RNAs, such as RNA Screentape and RT-qPCR.

Substitution

If elimination is possible, the next best thing is swapping a procedure or reagent for a less/ non hazardous alternative.

  • In order to minimise risks with running gels, we opted to use Gel Red instead of Ethidium Bromide for staining, as it is far safer.
  • We used dry ice to flash freeze cells, as a substitution for liquid nitrogen, as it is far safer to handle, with lower risks of cryogenic burns or asphyxiation.
  • TRIzol alternatives:
    As we were working with RNA, we needed an extraction protocol. While TRIzol is the industry standard, it also involves the use of several hazardous reagents, such as TRIzol reagent, which is toxic if swallowed or in contact with skin, and can cause severe skin burns and eye damage (phenol, guanidium isothiocyanate and chloroform). As such we greatly limited our use of that procedure, opting for alternate extraction methods, such as isopropanol precipitation, which still has hazards associated with using a highly flammable reagent.

Engineering Controls

The purpose of this level of control is to isolate individuals from a hazard

  • We used a well characterised and domesticated E.coli strain (BL21(fhuA2 [lon] ompT gal [dcm] ΔhsdS)), with existing standard methods for containment and control, in order to minimise containment breach risks.
  • When moving from the Department of Chemistry lab to the Department of Biochemistry lab, we used a specialist van service to transport all equipment and reagents, so as to minimise containment risks, as well as risks associated with moving heavy equipment.
  • Where we performed extraction using TRIzol, we strictly limited its use to the fume hood, in order to minimise the risk to the person carrying out the protocol. This is an example of how we have tried to isolate risks, separating hazards from as many people in the lab as possible.

Administrative Controls

Established safety procedures can ensure a consistently high level of safety for all workers in a lab, as well as serving to minimise harm if something goes wrong.

  • When using flammable reagents, we made certain to carry out the experiments far away from any open flames. Conversely, when using open flames, we made sure to move anything flammable, such as ethanol spray bottles and tissue paper, far from the flame.
  • Only our supervisors were permitted to operate certain equipment, such as the large centrifuge (Avanti J-30I centrifuge), to minimise any associated risks.
  • Having worked in both the Department of Chemistry and Department of Biochemistry, we completed a safety induction for both, conducted by Gabriele Cannucciari and Dr Siolian Ball respectively. Both inductions involved watching videos on the department’s safety policies, as well as an in person induction, going over standard safety protocols in both labs.
  • Prior to beginning any wet lab work we had a training session, conducted by Gabriele Cannucciari and Anqi Yu. This involved a briefing on several useful lab techniques, ensuring that when we began our own lab work, we did not misuse any equipment.
  • We aimed to be as conscious of unavoidable risks as possible, so we wrote up COSHH forms for all hazardous reagents used, as well as risk assessments for all equipment that was used. These were consulted before using either equipment or chemicals, so that we were aware of associated hazards with a procedure, such that we could minimise the odds of a safety breach. Some examples of our COSHH forms can be found at the bottom of the page. We found that subsequently filling out the iGEM safety form allowed us to consolidate our assessment of safety in the lab as well.
  • In order to standardise experimental procedures, both for scientific integrity, and as a safety precaution, we wrote detailed standard operating procedures, such that, if necessary, anyone on the team could carry out an experiment, or use a piece of equipment as safely as possible. The SOPs are presented in our experiments page, as linked to here.
  • We compiled a document summarizing the hazardous reagents so that any team member has easy access to check the potential dangers of the chemicals they are working with, as displayed below. Although due to iterations in the protocol, the spreadsheet no longer covered all of the chemicals we used.

PPE

Personal protective equipment is the final level of the Hierarchy of Controls. Its sole purpose is to only protect the individual using it. It does not in any way protect other individuals, in or beyond the lab, and should always be used in combination with other safety measures.

  • We had hair tied back where appropriate, wore lab coats and goggles, as well as gloves when needed.

Future safety

While our project is centred around designing towards a diagnostic product, there are no genetically modified organisms being distributed beyond the lab. Additionally, while the test may be dependent on a replicating RCA probe, this is itself dependent on the presence of specific miRNAs, and has no function beyond G quadruplex formation, posing no risk to the environment. The most significant hazard associated with the final product is more likely to be the hand powered centrifuge, as it is capable of reaching high speeds, as such we have produced a short operational safety video for it. We have the protocol for performing farmer extraction to try and minimise risks for anyone using the product, as displayed below.

Other documents (example COSHH forms)