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Basic Safety Questions for Lethbridge iGEM 2013

  1. a. Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:
    • Species: Escherichia coli
    • Strain no/name: DHα and BL21 DE3
    • Risk Group: 1
    • Risk group source link:
    • Disease risk to humans? If so, which disease? Very low risk, not associated with causing disease in humans
  2. Highest Risk Group listed: 1
  3. List and describe all new or modified coding regions you will be using in your project. (If you use parts from the 2013 iGEM Distribution without modifying them, you do not need to list those parts.)
    1. Part number: BBa_K1210000
      • Where did you get the physical DNA for this part (which lab, synthesis company, etc) : Synthesized, GENEWIZ
      • What species does this part originally come from?: Virus
      • What is the Risk Group of the species?: 2
      • What is the function of this part, in its parent species?: Programmed -1 ribosomal frameshifting
    2. Part number: BBa_K1210001
      • Where did you get the physical DNA for this part (which lab, synthesis company, etc) : Synthesized, GENEWIZ
      • What species does this part originally come from?: IBV- Infectious bronchitis virus
      • What is the Risk Group of the species?: 2
      • What is the function of this part, in its parent species?: Programmed -1 ribosomal frameshifting
  4. Do the biological materials used in your lab work pose any of the following risks? Please describe.
    • a. Risks to the safety and health of team members or others working in the lab?

      There is very minimal risk to safety as we only work with laboratory strains of Escherichia coli, and all team members have previously undergone laboratory safety training.

    • b. Risks to the safety and health of the general public, if released by design or by accident?

      None of the parts that we have made raise any safety issues.

    • c. Risks to the environment, if released by design or by accident?

      There are no direct risks to the environment if the parts are released by design or by accident. The organisms containing these parts are not currently designed for environmental applications. Therefore, risk of environmental contamination is very low.

    • d. Risks to security through malicious misuse by individuals, groups, or countries?

      Our project only poses safety issues if it was to be used to aid in the expression of dangerous sequences making harmful proteins. However, we intend to create software to help genes synthesis companies detect harmful sequences hidden in another frame, preventing the synthesis of dangerous sequences.

  5. If your project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise? (Consider the different categories of risks that are listed in parts a-d of the previous question.) Also, what risks might arise if the knowledge you generate or the methods you develop became widely available? (Note: This is meant to be a somewhat open-ended discussion question.)

    The parts do not cause any harm for the lab worker, public, or the environment. If individuals make use of the frameshifting parts, with the intent of hiding dangerous sequences, synthesis companies may have to modify or develop new screening methods for detecting these dangerous sequences.

  6. Does your project include any design features to address safety risks? (For example: kill switches, auxotrophic chassis, etc.) Note that including such features is not mandatory to participate in iGEM, but many groups choose to include them.

    Our parts do not include any design features to address safety risks. However, we are creating software which will help gene synthesis companies prevent the misuse of our parts for malicious intent.

  7. What safety training have you received (or plan to receive in the future)? Provide a brief description, and a link to your institution’s safety training requirements, if available.

    All iGEM team members have been fully trained in WHMIS as well as an introduction to biosafety basics.

  8. Under what biosafety provisions will / do you work?
    • a. Please provide a link to your institution biosafety guidelines

    • b. Does your institution have an Institutional Biosafety Committee, or an equivalent group? If yes, have you discussed your project with them? Describe any concerns they raised with your project, and any changes you made to your project plan based on their review.

      The University of Lethbridge Risk and Safety Services department has appointed a committee for biosafety. This committee ensures that biological materials are used safely on campus. We have discussed our project with them and they forsee no problems with the Lethbridge 2013 iGEM project.

    • c. Does your country have national biosafety regulations or guidelines? If so, please provide a link to these regulations or guidelines if possible.


    • d. According to the WHO Biosafety Manual, what is the BioSafety Level rating of your lab? (Check the summary table on page 3, and the fuller description that starts on page 9.) If your lab does not fit neatly into category 1, 2, 3, or 4, please describe its safety features [see for help].

      BSL1, we are using a RNA sequence that is from a risk group 2 organism, however, we do not require the use of the actual organism to utilize this element.

    • e. What is the Risk Group of your chassis organism(s), as you stated in question 1? If it does not match the BSL rating of your laboratory, please explain what additional safety measures you are taking.

      Risk Group 1

Safety Form 2 Questions for Lethbridge iGEM 2013

  1. Organism name and strain name or number: Infectious bronchitis virus
  2. Organism Risk Group: Group 2
  3. If you are using this organism as a chassis, write "chassis". If you are using a genetic part from the organism, give the name of the part and a brief description of what it does and why you are using it.

    BBa_K120001: includes the sequence for a pseudoknot secondary structural RNA element that can cause programmed -1 frameshifting during translation. We plan to characterize the frameshifting frequency of this pseudoknot and create a library of frameshifting elements.

    BBa_K120000: includes reporter genes upstream and downstream of the pseudoknot, as a construct for testing the frameshift frequency.

  4. How did you physically acquire the organism or part?

    The part was synthesized by GENEWIZ.

  5. What potential safety/health risks to team members, other people at your institution, or the general public could arise from your use of this organism/part?

    The part itself is innocuous and not infectious. Since it is just a short sequence of DNA that, when transcribed into RNA, folds into a specific secondary structure, it does not pose a safety threat to our team members, the university, or the general public.

  6. What measures do you intend to take to ensure that your project is safe for team members, other people at your institution, and the general public?

    Since the part itself does not pose a safety threat, standard laboratory safety procedures will be followed, including ensuring that the part or the chassis containing the part does not leave the laboratory space. Proper personal protective equipment will be worn at all times when working with the part and all team members are fully trained in WHMIS and biosafety before being allowed to work in the laboratory.

  7. If you are using only a part from the organism, and you believe the part by itself is not dangerous, explain why you believe it is not dangerous.

    Use of the part does not require handling of the virus from which it comes. Therefore, the part itself is not dangerous. Pseudoknots are common RNA elements found in organisms besides viruses, and are not dangerous outside of the context of their host.

  8. Why do you need to use this organism/part? Is there an organism/part from a less dangerous Risk Group that would accomplish the same purpose?

    We use standard E. coli strains as our chassis for the expression of our constructs. The pseudoknot from infectious bronchitis virus (IBV) has been shown to cause frameshifting in E. coli cells. Therefore, the sequence of the IBV pseudoknot was used. Most pseudoknot sequences that have been characterized for frameshifting activity originate from viruses, so the pseudoknot sequence could not be retrieved from a Risk Level 1 organism.

  9. Is the organism/part listed under the Australia Group guidelines, or otherwise restricted for transport? If so, how will your team ship this part to iGEM and the Jamborees?

    The organism that the part originates from is not listed under the Australia Group guidelines, and therefore no additional measures are needed for transport of the BioBrick part.

  10. Please describe the BioSafety Level of the lab in which the team works, or description of safety features of lab (Refer to Basic Safety form, question 8. d.). If you are using organisms with a BSL level greater than you lab, please explain any additional safety precautions you are taking.

    The lab in which the team works is rated as a BioSafety Level 1 laboratory. Prior to starting lab work, all members must complete WHMIS and Biosafety Training. Since use of the part does not require handling of the Risk Level 2 organism that it comes from, no additional safety precautions are necessary.