The NYUAD iGEM 2018 team took special measures to ensure that all experiments were conducted safely and that all risks were assessed and managed in advance. Our project complies with the safety and requirements of iGEM as outlined below. Chuck, senior instructor of our Biology lab, demonstrates how we followed safety protocol.
#ChuckSays Wear a lab coat, gloves and safety goggles at all times in the lab
#ChuckSays Turn off equipment after use and dispose off all wastes safely
All experiments that were conducted at NYU Abu Dhabi complied with the university’s safety protocol. Hussain Mir Nawaz (hussain@nyu.edu) is the Biosafety Officer working for the EHS (Environmental Health and Safety) department overseeing the biosafety program at NYUAD. The guidelines include Laboratory Biosafety Manual, Bloodborne Pathogen Exposure Control Plan, Institutional Biosafety Committee (IBC), Institutional Animal Care & Use Committee (IACUC). Our PIs and instructors, Ibrahim Chehade and Ashley Isaac, have conducted biosafety training for all of the team members and supervised lab sessions.
Rules and guidelines included wearing appropriate PPE in the laboratory, and ensuring appropriate supervision is present from PIs or instructors when working in the laboratory. Other measures that were taken include appropriate waste disposal of biohazardous materials to ensure the safety of all laboratory individuals and the environment in accordance with NYUAD Environmental Health and Safety Policy.
This year’s iGEM project at NYUAD involves the use of E. coli DH5-Alpha cells, which were transformed with non-toxic, non-pathogenic genes present in Listeria monocytogenes (lmo0733), Salmonella spp. (invA), Vibrio cholera (gbpA) and Campylobacter jejuni (hipO gene). These cells, according to the manufacturer Safety Data Sheets, present a minimal potential hazard to laboratory personnel and the environment. E. coli DH5-Alpha cells were also transformed with Shiga Toxin producing gene, which is a non-pathogenic and non-toxic gene used by the 2017 NYUAD iGEM team, in order to validate the previous year’s project. These transformed bacteria were amplified using two techniques: loop-mediated isothermal amplification (LAMP) and Recombinase Polymerase Amplification (RPA) to detect the presence of food-borne pathogens by using these genes as markers. However, these genes were not translated and do not code for any functional proteins when the bacteria are transformed with these genes. Our primer design was based on these gene sequences for use in the LAMP and RPA experiments, and the samples with amplified DNA were visualized using a colorimetric assay and SYBR green fluorescent dye. The experiments were validated by running native gels.
A common strain that causes no known harm, E. coli DH5-Alpha cells pose minimal potential hazard to laboratory personnel and the environment. The only biological model used to test our concept, E. coli DH5-Alpha cells are in risk group 1. The other organisms on the list of potentially dangerous biological agents were not used. Simply a gene marker of those organisms were synthesized and used to transform the E. coli DH5-Alpha cells, as explained above. We ordered specific highly conserved gene markers found in our pathogens of interest from IDT, noting that these genes will not produce any functional proteins when used. These genes were ligated into a backbone plasmid and the E. coli DH5-Alpha cells were transformed with this plasmid. The transformed bacteria was used as a model for detection of these pathogens by amplifying the DNA of the specific gene using the techniques mentioned above.
Additionally, prior to ligation, a smaller segment of the gene was amplified using PCR; thus, the team did not work with the full length of the sequence, ensuring an additional measurement of safety.
Our pathogen detection device will not involve the use of transformed E. coli cells or plasmids. Users will need to be careful while handling the food that will be sampled as it may contain food-borne pathogens that will be detected using our device. For this reason, our food sample collector minimizes direct human contact with the food. We will provide resources to send the waste back to us to be disposed off safely after detecting the presence of any food-borne pathogens, ensuring our consumers’ safety.
