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Q. Are you planning to do any of the following activities, which are prohibited in the competition?
No, we are not planning to do any prohibited activities
Q. Please read over iGEM’s White List. Will your team use any organisms or parts not on the whitelist, or do any activities not on the whitelist?
No, all our work is covered by the White List
Q. Are you planning to do any of the following activities that require advance permission from iGEM?
No, we are not doing any of the kinds of work outlined above
Q. Are you collecting any data about people, such as their opinions, quotations, medical history, gender, behavior, attitudes, or concerns?
No, we are not doing surveys, interviews, or other human subjects research
Q. Please upload a photo or two of your lab showing the relevant safety features.
Q. What is the biosafety level of your work space?
Level 1 – standard microbiological lab
Q. Which work areas will you use / are you using to handle biological materials?
Open bench
Q. Which work areas will you use / are you using to handle biological materials?
Open bench
Chemical fume hood
Q. Describe the goal of your project: what is your engineered organism (or other synthetic biology product, system, or tool) supposed to do?
By modifying E. coli bacteria to be able to detect cancerous RNA, we would hope to design a non-invasive, inexpensive test kit to detect cancer. We plan to do this by using conditionally active guide RNAs (gRNAs) to direct the Cas12a to a reporter construct.
Q. Which whole organisms, including viruses and cell lines, will you engineer in your project?
Escherichia coli
Q. As part of your project, are you planning to make / have made new parts or substantively changed existing parts in the Registry?
Yes
Q. Could any of your parts be hazardous on their own and/or in the context of your project?
None of our parts could be hazardous
Q. What experiments will you do with your organisms and parts?
Detect endogenous synthetic RNA: Repeat the experiments from a paper in which RNA is transcribed from a plasmid in E.coli which switches on a gRNA and directs Cas12a to cut or bind a reporter plasmid. Detect exogenous synthetic RNA: Repeat the experiment above, but by adding exogenous synthetic trigger RNA to the E. coli. Detect endogenous cancerous RNA: Modify the plasmids in E. coli to transcribe sections of the human c-Myc RNA, as well as new switchable gRNAs which are activated by it. Detect RNA with positive selection plates: Modify the reporter plasmid to allow E. coli growth on selective media only upon Cas12a targeting.
Q. What kinds of chemicals are you using in your project?
Carcinogens, Highly Flammable Chemicals, Acids and corrosive chemicals (Gel Stain (SYBR Safe dye), 70% Ethanol, Acetic Acid)
Q. What hazards are presented by the organisms, parts, chemicals, or experiments you described in Part 2?
Human health or safety hazards, Environmental hazards, Engineered E. Coli, may have some human health risks. Strong acids, organic solvents, and DNA dyes are hazardous to human health.
Q. For each of the hazards you identified in the previous question, please give 1-3 sentences describing how harm could occur.
Human health or safety hazards: The chemicals that we will be using could harm us if they are ingested or injected in any manner. Environmental hazards: The chemicals used in this project may pose harmful conditions if improperly disposed of (drain, etc.)
Q. Imagine that, in the future, your project was fully developed into a real product that real people could use. How would people use it?.
Only in the lab - The project has applications in the real world in a diagnostics lab. Blood serum and other human samples will be used as a method of detecting cancer.
Q. If you were permitted, would the continued development of your project require release beyond containment?
No, the future development of my project would not require release beyond containment
Q. Have people on your team had a conversation (within your team or with someone outside the team) about how any of the bad outcomes below might relate to your project?
Harm to human health and safety, Harm to materials, equipment, and infrastructure, Harm to the environment, including wild plants and animals, Creating or reinforcing of social inequities, Breaking norms about engineering biology
Q. Considering the future use(s) and conversations from the previous questions, do you think your project could potentially lead to any of the bad outcomes listed below? Check all the appropriate boxes and expand in the comments section.
Harm to human health and safety, Creating or reinforcing of social inequities
Q. How might the bad outcomes that you identified in the previous question come to pass? Check all that apply.
Our goal is to create a potentially inexpensive product to detect cancer in its early stages. This product, if successful, could be used for malicious purposes. For example, if health insurance or financial institutions find a way to acquire the data used from a tool like this, they could use this data acquired from our tool to hike up health insurance cost rates for people at risk for cancer. Additionally, if this project does succeed in creating a product that can detect cancer in its early stages, but fails to prove to be a cost effective device, this could increase social inequities by creating a new, expensive device to detect cancer that only few members of society can access.
Q. If your project were fully developed, could any of your engineered organisms or parts spread autonomously in the environment?
Yes the plasmids and/or E. Coli could spread, however unlikely. None provide a fitness advantage.
Q. Who are the experts, other than your supervisor(s), supporting you in managing risks? If you discover a hazard or risk in your project, who would you go to for help?
Rowan Callahan
Q. What safety and security rules or guidance cover your work?
OSHA has created standards for the handling and disposal of biohazard wastes for worker protection. Our lab must follow these guidelines. In addition to this, our institution, the OHSU, has additional safety and security rules that we as interns must abide by. For example, as interns we are primarily limited to BSL-1 lab work unless otherwise specified, in which case, we will be supervised and given plenty of instruction. We will also be taught where safety tools are in case we need to access them.
Q. Will your project need extra support or review to manage the risks you have identified above?
No, the project does not need additional support or review.
Q. Have your team members received any safety and/or security training?
Yes, we have already received safety and/or security training (May 2022).
Q. Please select the topics that you learned about (or will learn about) in your safety and security training.
Lab access and rules (e.g. appropriate clothing, eating and drinking), Responsible individuals (e.g. lab or departmental specialist or institutional biosafety officer),Differences between biosafety levels,Biosafety equipment (e.g. biosafety cabinets),Good microbial technique,Disinfection and sterilization,Emergency procedures,Rules for transporting samples between labs or shipping between institutions,Physical biosecurity (e.g. tracking materials, access controls),Personnel biosecurity (e.g. watching for unusual behaviour),Dual-use research and/or experiments of concern,Chemical, fire and electrical safety
Q. What laboratory biosafety and biosecurity measures are you using to manage the risks in your project?
Accident reporting (system to record any lab accidents), Personal Protective Equipment / PPE (wearing lab coats, gloves, eye protection, etc.), Inventory controls (tracking who has what physical materials and where the materials are), Physical access controls (controlling who can access your lab or storage spaces), Data access controls (controlling who can access computers or databases), Lone Worker or Out of Hours policy (procedures for working alone or at times when normal support is unavailable), Medical surveillance (finding out if you get sick because of an organism or chemical you used), Waste management system (such as decontaminating waste before it leaves your institution)
Q. What other actions have you taken to manage the risks in your project?
Participating in a safety workshop hosted by iGEM (e.g. the Values and Risks workshop), Crafting a responsible communication plan (e.g. redacting specific information, highlighting the biosafety measures used), Deciding not to do an activity (e.g. deciding against animal use experiments, avoiding infection experiments with a plant native to your country)
Q. Overall, how will the actions you’ve taken, expert support, rules, training, and other procedures and practices you described help you to manage the risks in your project?
Through the elaborate electronic trainings offered from our experienced program directors for our internship, we were taught effective methods to prevent risks in the laboratory. This has helped us to instill confidence in our abilities to be safe and not induce injury. We have also discussed with mentors and others about project safety risks.