Team:Caltech/Notebook/Safety

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Revision as of 06:52, 8 September 2012

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Safety Regulations

International:

• [http://www.who.int/csr/delibepidemics/WHO_CDS_CSR_LYO_2004_11/en/ WHO]
• [http://bch.cbd.int/protocol/ Convention on Biological Diversity]

National:

• [http://oba.od.nih.gov/oba/rac/Guidelines/NIH_Guidelines.htm NIH]
• [http://www.cdc.gov/biosafety/ Center for Disease Control (CDC)]
• [http://www.absa.org/ American Biological Safety Association]
• [http://www.epa.gov/opptintr/biotech/index.htm US Environmental Protection Agency (EPA)]

Local:

• [http://safety.caltech.edu/ Caltech Safety Office]
• [http://safety.caltech.edu/committees/committees_biosafety Caltech Institute Biosafety Committee]
  • [http://safety.caltech.edu/documents/24-biosafety_manual.pdf Caltech Biosafety Manual (pdf)]
  • [http://safety.caltech.edu/documents/22-biohazardous_agent_classification.pdf Caltech Biohazardous Agent Classification (pdf)]

1. Would any of your project ideas raise safety issues in terms of:
   • researcher safety,
   • public safety, or
   • environmental safety?

We are transforming genes into laboratory strains of non-pathogenic Escherichia coli and Zymomonas mobilis using plasmids with various antibiotic resistances. Since E. coli and Z. mobilis are biological safety level 1 organisms, they pose no harm to researchers following standard safety protocols. Furthermore, we have isolated bacteria, from pond water, that are capable of degrading lignin and polystyrene. According to the Caltech Safety Office, because we immediately culture those strains in minimal media, it is unlikely that we will culture any significantly pathogenic organisms. A primary goal of our project is to produce biofuels, namely ethanol. Although high concentrations of ethanol can pose a potential health hazard, our bacterial strains will not produce enough ethanol for that to be a major concern.

The primary public safety issue is the possibility of accidentally transferring these plasmids from the bacteria we use in lab to bacteria in the wild, which may occur if we do not dispose of leftover bacteria properly. To prevent the introduction of common antibiotic resistances into the wild, we make sure to bleach all liquid cultures before disposing of them, along with used tubes, petri plates, pipette tips, and electroporation cuvettes, in biohazard waste containers.

We are using laboratory strains of E. coli and Z. mobilis, which are specifically engineered to be incapable of surviving in the environment. Since these organisms and their degradation mechanisms were originally found in the wild, transfer of these genes to other species of bacteria should not pose an environmental safety issue.

 

2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
   • did you document these issues in the Registry?
   • how did you manage to handle the safety issue?
   • How could other teams learn from your experience?

The BioBricks parts that we have so far consist of a fosmid library containing genes isolated from the environment and a gene for proteorhodopsin, a light-activated protein that generates a proton gradient, inserted in plasmids with either ampicillin or chloramphenicol resistance. These parts do not confer any pathogenic properties to bacteria and may even be useless in wild-type bacteria. Thus, our parts do not raise any safety issues.

 

3. Is there a local biosafety group, committee, or review board at your institution?
   • If yes, what does your local biosafety group think about your project?
   • If no, which specific biosafety rules or guidelines do you have to consider in your country?

Yes, Caltech has an Environment, Health, and Safety (EHS) Office. We have documented the safety guidelines for both Caltech and iGEM below. Our team completed the mandatory safety training, which includes a presentation of our institute's general safety protocols and a walkthrough of our lab with the lab safety officer before we could begin any lab work. We also spent about 3 days with our graduate student mentors learning molecular biology techniques and the safety measures associated with them.

We talked to the Caltech safety office about our project. They saw no problems with our handling of biological safety since we are working with level 1 organisms. They noted that the possibility of growing pathological bacteria from our enrichment cultures is low due to immediately diluting in minimal media rather than growing environmental samples up on LB. If we suspect any of the cultured organisms are harmful, we will work with the safety office to implement proper safety procedures. Furthermore, we talked to the safety office about possible chemical hazards in our lab. Any solid waste (tubes, etc) should be put in a container or bag designed to hold hazardous waste.

 

4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?

We believe that requiring more extensive documentation of submitted parts will help improve the safety of iGEM teams. Having more information about what we are working with allows us to design better experiments, understand interactions between parts and be aware of possible dangers to ourselves or the environment due to the BioBrick.

Some ways we think teams can help make their documentation even better:

• Cite literature referenced during the design of the BioBrick
• Provide documentation of the creation and the usage of the part either directly on the part's page or through a link to the corresponding team's notebook and/or project page
• If possible, sequence the part right before submitting it to the Parts Registry and list that sequence rather than the intended or planned sequence in the part specification. If the actual sequence is significantly different from the intended sequence, note that on the Part Design or the BioBrick's main page.
• Fill out the experience page with data showing how the part worked for a specific test or link to the team wiki about use of that part. Experience pages are useful for helping teams decide what part to use if there are multiple choices to fulfill their need for their project.

How We Comply with Institute Guidelines

Training

Before working in the lab, we were required to attend the SURF Safety Presentation, a talk given by the Caltech Safety Office that goes over general guidelines for working in any sort of lab.

• How to assemble if there is a fire
  • For Braun, outside by Wilson Ave, letting the floor warden know if everyone from your lab evacuated
• Shelter in place for earthquakes and other hazards
• Emails, phone calls and texts through the automated message system will alert everyone to threats on campus
• Wear appropriate attire to work
  • Closed toed shoes
  • Long pants if working with large amounts of dangerous chemicals
  • Avoid working alone and let someone know that you're in lab if you must work alone
• For emergencies, call security at ext 5000.

The safety officers for Braun 16 are Dr. Michael Vicic, Linda Song and Grayson Chadwick. They gave us a tour of the lab, showing us were safety equipment was before getting card access to the building and lab.

• Shower and eyewash located near the main door
• Fire extinguisher near main exit
• First aid kit at front of room
• Telephone near main exit

Our graduate student mentors, Emzo de los Santos, Nate Glasser and Gita Mahmoudabadi gave us a 2-day bootcamp before we could begin work on the project. This included how to perform sterile techniques, operation of the equipment we would need in the lab, and basic molecular biology techniques, since some team members had no previous research experience.

Concise Guidelines for iGEM Researchers

(See above in Researcher Safety for a more detailed description of endocrine disruptor hazards)

• When handling cells, DNA or chemicals, researchers are required to wear gloves and change them often. This protects us and our experiments.
• Gel imaging is still done under UV, so we minimize researcher exposure by:
  • Making sure the image box is closed before turning the UV light on, and making sure the UV light is off before opening it.
  • Performing gel extractions with a blue light box, which only requires amber glasses.
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