According to the terms in The Health and Safety at Work Act (1974) of the United Kingdom government, the employer has duties towards its employees regarding their safety, and the employees, in turn, have the responsibility to comply with the employer’s safety measures for the safety of both themselves and others who may be affected. The fact that these terms are written in the United Kingdom legislation means that any violations can be charged as criminal offences and penalised by fines, imprisonment, etc, highlighting the importance of ensuring a safe and healthy working environment and processes. We also feel extra compelled in making safe and responsible research our bottom line as we represent our university on the global stage and aim to positively impact the world, thus taking a combination of approaches to realise our commitment as a team.
Laboratory All the relevant laboratory work for our project is done in a working space of Biosafety level II.
Regulations and Guidelines We strictly and meticulously followed all the national laws and regulations and institutional guidelines that govern biosafety or biosecurity in research laboratories, particularly for those involved in synthetic biology. These include The Genetically Modified Organisms (Contained Use) Regulations 2014 [link: https://www.hse.gov.uk/pubns/books/l29.htm], The Control of Substances Hazardous to Health Regulations 2002 [link: https://www.legislation.gov.uk/uksi/2002/2677/contents/made], and the University of Oxford Safety Office Biorisk Management regulations [link: https://safety.admin.ox.ac.uk/biorisk-management].
Extensive Training Prior to entering the lab and beginning any lab work, every team member went through two safety induction sessions. The first induction session was with the Department of Biology, covering topics including Safety Organisation and Responsibilities, Required Health & Safety Forms/Documents, Incidents & Accidents & Prevention & Reporting, Hazards and Risks, Risk Assessment, Laboratory Compliance Policy, General Laboratory Rules, etc. The second induction session was with the specific lab group, covering the details of safety practices inside the lab and its surroundings (e.g. Responsible individuals, Disinfection and sterilization, Emergency procedures, Personnel & Physical & Chemical & Fire & Electrical safety, etc). Additionally, all of the members have taken the courses and obtained certificates for the Biological Safety and Genetic Modification Part I and II, which is a fundamental module in the Health and Safety training programme provided by the University Safety Office.
Safety and Security Measures Many actions were practised in order to manage the risks throughout different stages of the project. On the most basic level, everyone in the wet lab always dressed appropriately, wore standard Personal Protective Equipment correctly, and followed good occupational hygiene. Proper and sufficient decontamination and containment measures are always taken. Benchtop and other working areas were always kept tidy. Moreover, controls on inventory and data access were applied with Benching and maintained daily. Protocols were optimised and readily available in both paper and electronic formats. Out-of-hours working was prohibited unless a risk assessment form was submitted and special permission was granted by the PIs and the Department. Constant surveillance of bacterial cultures also allowed early detection if the containment strategies were ineffective.
Monitoring and Report Before we formally began the experiment, we held conversations with our PIs and researchers in the field (e.g. Baker Lab) to get better insight into the safe handling of our chosen protein, bacteria, and experimental procedures. To ensure maximum safety inside the lab in the later stages, we worked closely with our PIs and several appointed PhD students and postdocs, and a lab manager, with whom we consulted before moving to the next stage of our project. All of them were also responsible for helping to take immediate measures when they are aware of any issue that may be a hazard to the health or safety of any team members or others around. We would then together notify the Departmental Safety Officers, and the PIs would take the responsibility of reporting these issues to the University and to any members in charge of safety supervision.
Before we embark on the journey of the project, we made sure that we understood the Safe Rules and Policies of iGEM competition and read over the relevant sections in iGEM Responsibility, including Guidance and Safety Policies.
We made sure that all the organisms, parts, and activities we chose to be involved in our project are within the realm of permission of the White List and emailed the iGEM Safety Committee to check if there is any level of uncertainty.
Throughout the entire experiment, we only utilised the Risk Group / Safety Level 1 microorganism as the platform for cloning and expression. Different E. Coli strains were used in different stages of the process. We used Stellar E.coli for plasmid cloning and amplification and BL21 and Omp8 for protein expression. All the cells have been altered to be safely used in the BSL II lab where our experiments took place. All GMO-based lab work done on bacteria was registered with the Departmental Safety Office and approved by the Safety Officer and Head of the Department prior to the experiment by completing GM risk assessment forms. These forms were completed and submitted under the supervision of our PI, and each covered a specific GM bacteria strain we worked with.
Though originally thinking of using SARS-COVID-19 spike proteins for the initial test of our biosensor – as the sensor proteins to which we had immediate access -- we decided to avoid any unnecessary risks and maximise the safety level of our project. Thus, we reoriented the plan, expressing our own HER2 sensor proteins and using HER2 proteins for the same purpose. For our experiment, only commonly used vectors for cloning and protein expression in E.coli were used: pET21b+, pET29b+ and pRSET A. These vectors carry only the common non-protein-coding parts including LacI promoter, resistance, T7 promoter and its RBS. Our sensor proteins, LucCage and LucKey, were de novo-designed biosensors with proven specificity to the intended target, and our test proteins, were from Risk Group / Safety Level 2 microorganisms – all on the White List. No other proteins/protein-coding genes under the dangerous category were used.
All the activities done in our project could be viewed as fundamental biochemistry experiments like cloning, transformation, protein expression, His-tag protein purification, and in vitro chemiluminescence measurements, etc. Nothing was done that could potentially increase the risk to human/animal health and environmental safety.
Though we designed our biosensor to be used in testing environmentally collected water samples, considering the high risk of pathogen contamination in the water samples we need, we judged that it would be the most responsible action for us to use lab-produced protein solutions instead, which still sufficed the purpose in this proof-of-concept stage. Thus, no environmental samples were used in our project.
During the iGEM Competition timeline, we were very aware of the proper containment of our genetically-modified bacterial strains and their protein products. Though the eventual aim of our biosensor is to be released inside a containing device, we adopted the suggestion by iGEM and focused on producing the best laboratory results instead.
Our project does not require the use of any new antimicrobial resistance factors or the conferring of antimicrobial resistance to new species. The only antimicrobial resistance genes for plasmid selections we used were Ampicilin or Kanamycin resistance, with additional Kanamycin resistance in Omp8 competent cells (always paired with pRSET A ampicillin-resistant plasmid), all of which are widely used in the institution and worldwide.
Human Experimentation and Animal Use Our project does not require the use of any human samples, animals, and/or animal samples. Gene Drive Our project does not require the implementation of a gene drive. SARS-CoV-2 Our project does not require the use of live SARS-CoV-2 or parts from SARS-CoV-2.
Our project does not require conducting laboratory experiments involving humans. For the forms of social science research we have conducted as a part of our Integrated Human Practice [link: https://2023.igem.wiki/oxford/human-practices], including interviews and public engagement, we can confidently attest that they were done in accordance with relevant United Kingdom laws and regulations, as well as institutional rules or guidance of the University of Oxford. Our commitments and actions towards responsible and ethical conduct of the human subject research we have done are described in detail in the Ethical and Responsible Considerations.
We have worked with several commercial reagent/biological parts/service suppliers during the course of the project, including oligos from IDT, DNA dyes from Vazyme, miniprep kits from Promega and Beckman, etc. We were once notified that one of the plasmid purification kits we were trying to order would be classified as dangerous materials and could involve custom clearance, but we eventually did not choose to go forward with the particular order to avoid unnecessary risks. None of the other shipments was dangerous or caused safety and security concerns at any level.
Cell-Free Extraction
In an optimal scenario, our final product should have the cell-free biosensor released as a part of a containing device beyond the laboratory environment into low-resource field testing settings, we have to make sure that no genetically-modified microorganisms exist in the final product, thus minimising the risk of accidental exposure to users, other organisms, and the environment. Even though we ended up not carrying out the experiment due to time constraints, we had planned to modify and employ the procedures developed by NUS-Singapore iGEM 2018 team [link: https://2018.igem.org/Team:NUS_Singapore-A], demonstrating the absence of our GM bacteria in the final biosensor solution.
De Novo Proteins
De novo proteins, like our biosensor in the project, are proteins that are designed and engineered from scratch rather than naturally occurring. They have the potential to be used in various applications, including therapeutics, industrial enzymes, and more and are anticipated to show an exponential growth rate with the enhancement of AI in biotechnology research. However, as of now, there isn't a specific regulatory framework solely dedicated to the safe application of de novo proteins. Seeing the blank in the regulatory space on de novo proteins, we decided to explore the diverse opinions and establish preliminary guidelines to help ensure that the development and application of these proteins are conducted responsibly and safely, with due consideration for potential risks and benefits. This safety and responsibility investigation on de novo proteins is described in detail in the Ethical and Responsible Considerations.