Team:CLSB-UK/Safety

Safety

All lab work carries some risk - to us, to others and to the environment. In line with iGEM regulations, English law and good ethical practice, we have worked to minimize these risks wherever possible. Below are the different aspects of our project, and how we have reduced their risks. From our biological lab work, creating our hardware to building our software tools and considering the future implementations of our project, we have assessed it all.

Wetlab

We are using DH5-Alpha E. coli (by NEB), which like most strains of E. coli does not present a risk to healthy humans. It is in safety risk group 1, the lowest risk level.

Most of our work is in a cell free system, making it our main chassis. Cell free extracts will enable our diagnostic tool to be used outside the lab as they are sterile and abiotic (however, we did not take it out of the lab in line with iGEM’s ‘Do Not Release’ policy). We are using the S30 cell free extract kit from Promega.

We didn’t use real bodily fluids in our experiments - in fact, we didn’t even use simulated bodily fluids, as we just used synthetic miRNA mimics. This eliminated the risk of contracting any diseases when testing our prototype.

As a UK high school we were limited by our lab and [http://www.hse.gov.uk/pubns/priced/l29.pdf strict UK regulations] which we followed to the letter throughout our lab work. Our PI is our school’s designated biosafety officer, and has experience in molecular biology labs where he received extensive safety training on all the techniques we performed. Furthermore, Sara White, a Senior Biology Technician supported our project with her expertise in microbiology procedures and general lab safety.

All our lab work safety follows recommendations by [http://www.cleapss.org.uk/ CLEAPSS] and we consult them when doing any new activity or are unsure about it. In order to carry out our work we had to apply to the [http://www.hse.gov.uk/biosafety/gmo/index.htm Health and Safety Executive] and fill in Notification of Premises for Contained Class 1 Use. We did all our risk assessments for this in consultation with Kirsten Jensen from Imperial College, who was our ultimate advisor on any health and safety matters.

Also, regulations for the UK secondary school lab work are very strict and we make sure to follow all of them, even if they are just recommendations.

Before anyone took part in wet lab work, they received safety training from our PI. This training reinforced what we had already learned as part of our Pre-U Biology course. In our safety training we learnt about:

Sterilisation techniques.
Sterilising our equipment using a bunsen burner flame and 70% concentrated ethanol, and the safe preparation of an agar plate without contamination.
Lab safety rules
All students at school must comply with our school’s general lab safety rules[1]. They include not running, eating or drinking anything in the lab and wearing safety goggles where required. We also familiarized ourselves with the school’s policies on what to do in the event of a fire alarm or security alert.
Waste disposal
We disposed of all waste into autoclave bags to be autoclaved afterwards, including gloves, pipette tips, eppendorf tubes etc. Any areas of spilages are to be cleaned with Virkon straight away and wipes are to be autoclaved. All the plates are to be autoclaved after finished work. No plate with any culture is to be cultured after opening. If the colonies are needed in the future they are to be restreaked onto a fresh plate that can be closed and stored. As a school in the UK we are not allowed to store any plates under anaerobic conditions.
Chemical Safety
We learnt about the safe use of chemicals in the lab, how to deal with any spillages and were taught that if any glassware smashes we should immediately report it to a teacher and were aware of the location of the glass disposal bin. Several members of our team were also equipped with first aid knowledge - although luckily we didn’t have to use their skills!
Practical technique
We were taught about other practical techniques such as micropipetting and minipreps, and how to use the lab equipment safely and in a way that avoided contamination.
Lab access
All school labs are locked with school issued smart-cards that restrict access to only those qualified to supervise in the lab. Students are not allowed in the lab without a teacher. All biological materials were securely locked in the lab technicians storeroom when not being worked on.

When transporting biological materials we made sure they were stored safely in a securely closed box, and were clearly labeled as to what they had in them. We certainly got some strange looks on the London underground carrying a box marked ‘non-hazardous biological material’ around! When collaborating with university labs we followed both our and their safety procedures.

Hardware

We built a cheap, portable and effective combined fluorometer and densitometer. In doing so, we encountered several risks, especially around soldering.

We did the following to reduce risks:

  • Before we started, we were taught soldering technique, the risks associated with soldering and basic first aid for burns. We also followed the physics department’s risk assessment controls for soldering in the lab.[2]
  • We (the hardware team) all take A-level physics which includes a large section on electricity so we had a good understanding of what circuits would do. We also looked up the datasheets for all the components we used to ensure we were using them properly.
  • Ensuring electronics were isolated before soldering or modifying any of the components
  • Appropriately masking conductive areas both to avoid electric shock on contact but also to reduce the risk of accidental short circuits due to wires crossing, which could cause an electrical fire.
  • Developed off an Arduino and a Digispark USB development board, which have maximum output voltages of 5V, so are unlikely to present a significant risk. Furthermore, as they are both powered off USB sockets we used computers that had overcurrent protection built-in to further reduce the risk.

Luckily, no-one burned themselves or experienced any electric shock. (although we did kill a few of our light sensors!)

Software

Cybersecurity is vital to building trust, and we wanted our software tools to be as secure as possible so people could depend on them. Furthermore products like Google Assistant and Amazon Alexa bring up privacy and data protection as important issues that we needed to address.

Our student leader in charge of software, Adam, has undertaken a certification in Data Science Ethics, and our software team visited several tech events to learn best practices for secure software development. Our software has a truly gripping privacy policy, and many safeguards are in place to keep user data safe.

We have tried to minimize the data sent from the app, and all requests are encrypted. Using IAM roles in both AWS and Google Cloud Platform we ensured that only designated individuals could view or edit the code. IAM roles also made sure that the program could only act as we intended i.e. talk with the Alexa service, but not be able to edit itself.

In line with iGEM’s goals we released all our code for the SynBioBot, Toehold Switch Tools and Fluorometer so you take a look, and if you still don’t trust us, run your own version.

Of our test

As our genetic circuits are implemented in a cell free system, the biosensor can be used outside the laboratory as the system is sterile and abiotic. Doctors all over the world could benefit from our biosensor as it provides a cheap and safe way of screening for different sorts of cancer. The risks of blood tests are minimal (bruising or dizziness being the worst possible side-effects[3]) and the additional information provided by our sensor could decrease the time it takes to reach a diagnosis of cancer and increase survival accordingly. In addition, our test provides a safer alternative to using CT and PET scans to rule out cancer in patients as it does not present a health risk. Currently, patients must have a scan to rule out cancer but using our sensor, a blood test could rule out cancer in the vast majority of patients. Both PET and CT scans subject patients to ionising radiation and therefore increasing the risk of developing cancer slightly. The radioactive tracer used in PET scans may also cause an allergic reaction. However, our system is completely radiation free; only a blood sample is required which presents a much lower risk to patients.

In ideal circumstances, we would like to be able to work with saliva, making the completely non-intrusive and hence presenting no risk to patients.

Ethical Considerations as Screening Tool

There is of course the possibility of misdiagnosis due false positives or negatives when using our sensor - but the same applies to all screening techniques and our sensor would be used in conjunction with other diagnostic techniques to ensure an accurate diagnosis. See our page on silver human practices page for more information.

References

  1. ↑ Created by our school’s science departments, not our team
  2. ↑ Created by our school’s physics department, not our team
  3. ↑ NHS.UK (2016). Blood tests - NHS Choices. Retrieved September 25, 2017, from http://www.nhs.uk/conditions/Blood-tests/Pages/Introduction.aspx