Safety | Stony-Brook

Lab Safety Trainings

Our team performed our work in a BSL-1 laboratory at Stony Brook University, in Stony Brook, NY, USA. In this context, before any member of our team could perform any work, we completed required safety training. These included specific required courses from the Stony Brook University Environmental Health and Safety (EHS), and the Collaborative Institutional Training Initiative (CITI) Responsible Conduct in Research (RCR) Program. The courses we took are described in the following two tables below (scroll down)

Stony Brook University Environmental Health and Safety Courses

Safety Training	Description
ENV 001 - Hazardous Waste Management	Instructs researchers in appropriate management, storage, and disposal practices for hazardous waste.
ELS 002 - Laboratory Safety - Chemical Hazards	Instructs researchers in risk assessment and safe handling for chemicals in the laboratory.
IELS 003 - Laboratory Safety - Safe Handling of Biological Hazards.	Instructs researchers in the basics of biological lab safety, including the different requirements for the Biosafety Levels, biohazard risk management and handling, and hazard communication.

Collaborative Institutional Training Initiative (CITI) Responsible Conduct in Research (RCR) Courses

Safety Training	Description
Responsible Conduct of Research in The Biomedical Sciences	Instructs researchers in administrative, authorial, and ethical requirements in biological research.

Further information about the Responsible Conduct of Research in The Biomedical Sciences course in particular is available upon request, though is not publicly available through either SBU or CITI.

Experimental Design and Conduct Considerations

We took several additional measures to ensure the safety of our team members and our colleagues throughout our work. This included measures during the experimental design and also during the actual performance of tasks in the laboratory. These measures aligned with the requirements for responsible conduct of research in a BSL-1 lab, per the writeup of Nathanson et al. of UCLA, which can be accessed in the references below for further information. The following is a sampling of the measures we took.

Non-Pathogenic E. Coli

When we designed our experiments, we never considered using pathogenic E. coli strains for any purpose, as they were not only not necessary for our work but also because of the risks inherent in using such strains. We deliberately ensured that all strains of E. coli used were known to be non-pathogenic. The non-pathogenic strains we used included MRE600 (Jiang et al., 2019) and BL21* for gene expression, and DH5ɑ (Chart et al., 2000)and DH10β for cloning(Durfee et al., 2008).

Risk Communication

When preparing to undertake protocols, we discussed the risks associated with the use of specific potentially dangerous materials we were unfamiliar with and reiterated basic safety precautions for more common materials.

Wearing PPE

No work was completed in our lab without the proper PPE being worn by those undertaking the work. Depending on the experiments being performed, this could have included (but is not limited to) gloves, lab coats, goggles, UV glasses, and face shields. Before leaving the lab and after the completion of relevant work, team members removed their PPE so as to potential exposure to biohazards for our colleagues in the Centers for Molecular Medicine building at Stony Brook University.

Waste Management and Disposal

All surfaces we worked on with biological material were immediately cleaned with ethanol. All containers, whether being reused or disposed of, were bleached with Germicidal Ultra Bleach at a 1:10 dilution with water. Biological waste, and any other material, container, or surface that interacted with biological waste, that was to be disposed was disposed into the biohazard waste bin. No outside waste or possible contaminants, including food and external liquids, were permitted in the lab space.

Consultations with Advisors

Any time we had questions about the necessary safety precautions for a given protocol, experiment, or task, we consulted with our advisors to clarify. We consulted with our Primary PI John Peter Gergen, our Secondary PIs Gabor Balazsi, Kathryn Gunn, and Joshua Rest, and Head Curator Mary Bernero, we discussed with members of the 2023 Stony Brook University iGEM Team including Michelle Yang and Bushra Islam, graduate students at Stony Brook Melanie Cragan and Andrew Sillato, and others.

Future Implementation - FDA Regulations

Our proposed implementation is in a cell-free system in combination with a microfluidic assay for the filtration of microRNA out of the blood. As such, we have had to consider, in consultation with our advisors and stakeholders, the safety implications that come along with such an implementation.

As we hope to detect microRNA concentrations in patients' bloodstream, we have to consider pertinent regulations regarding handling of blood. The United States Food and Drug Administration (FDA) maintains several pertinent regulations with regards to blood collection, preparation, storage, transportation, and testing. Upon review of these regulations, we found that outside of the blood handling, storage, transportation, and disposal performed by clinicians, our system will need to conform with FDA regulations regarding In Vitro Diagnostic products. This includes both for our actual cell-free system once it receives microRNA, as well as the microfluidic assay from which the miRNA will be extracted from the blood.

The FDA maintains regulations for In Vitro Diagnostic products. These and other regulations are described in further detail in Code of Federal Regulations Title 21 (21 CFR), referenced below. Regulations potentially relevant to our system, if it were to be further developed, are the following:
(1). 21 CFR Part 11 - Electronic Records; Electronic Signatures
- Part 11 covers proper handling of records and signatures for subjects/patients in the event such handling occurs electronically, which would likely apply in our case.
(2). 21 CFR Part 50: Protection of Human Subjects
- With regard to clinical trials, Part 50 requires that those conducting studies acquire informed consent from all subjects prior to any tests.

(3). 21 CFR Part 56: Institutional Review Boards
- With regard to clinical studies, Part 56 requires that any and all experiments be approved by an Institutional Review Board. This is to ensure that, in addition to the acquisition of informed consent as covered in part 50, that tests are carried out ethically in accordance with relevant institutional, state, and federal standards.
(4). 21 CFR Part 58: Good Laboratory Practice For Nonclinical Laboratory Studies
- Part 58 is concerned with blood handling by IVDs during nonclinical/preclinical studies. It ensures that proper handling of samples occurs such that data produced on the pathway to full clinical approval is accurately and ethically gathered.
(5). 21 CFR Part 809: In Vitro Diagnostic Products for Human Use
- Part 809's primary purpose, with regard to devices that handle blood, is to emphasize and ensure that IVDs can utilize and extract from blood without compromising the integrity of the sample.

(6). 21 CFR Part 812: Investigational Device Exemptions
As the device could impact patients'/subjects' treatment decisions/outcomes, it is likely that Part 812 would require us to apply for an Investigational Device Exemption, which allows devices of this nature to be used in clinical study settings even though it is still in the process of actually receiving full clinical approval.
(7). 21 CFR Part 820: Quality System Regulation
Part 820 concerns safety and performance requirements for IVDs. For devices that handle blood, this means being able to process blood in such a way that the blood is not subject to external contamination and produces the intended results efficiently and replicably (positive or negative depending on miRNA concentration, in our case). For devices that handle DNA, this means that the sample must be sufficiently extracted, that it must not be contaminated in the process, and that our system must accurately report its concentration.
(8). 21 CFR Part 862: Clinical Chemistry and Clinical Toxicology Devices
Part 862 sets out detailed performance criteria for devices for the proper handling and analysis of blood, though our IVD deals primarily with one specific product in the blood.