Team:Virginia/Safety Guidelines

• PROJECT
  • DESIGN
  • MODELING
  • EXPERIMENTS
  • PARTS
  • SUMMARY
• HUMAN PRACTICES
  • INTERVIEWS
  • SURVEY
  • SAFETY GUIDELINES
  • POLICY PROPOSAL
  • PUBLIC EDUCATION
  • iGEM OUTREACH
  • BUSINESS
• TEAM
  • TEAM MEMBERS
  • COLLABORATIONS
  • ATTRIBUTIONS
• DOCUMENTATION
  • NOTEBOOK
  • SAFETY
  • REFERENCES

← Survey Policy Proposal →

INTRODUCTION

Open Bio Labs currently implements the safety standards of the iGEM organization. While these are sufficient for the organization’s current purpose, we, the 2016 Virginia iGEM team, believe it is in the best interest of Open Bio Labs to publish on their website a set of safety guidelines better suited for the goals and philosophy of a biohackerspace with an emphasis on biocontainment.

In the United States, there are three primary regulatory agencies for synthetic biology: the US Environmental Protection Agency (EPA), the US Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS) and the US Food and Drug Administration (FDA). A 2014 report on Synthetic Biology and the US Biotechnology Regulatory System by J. Craig Venter Institute cites that these agencies have an adequate level of authority to address most, but not all, environmental, health and safety concerns with regard to synthetic biology (1). Because APHIS’ authority extends over engineered plants and FDA’s authority extends over foods and drugs, EPA is the only agency with broad authority to make regulatory decisions based on risks posed by genetically modified microbes to health and safety of humans, animals and ecosystems. A primary concern is that the anticipated increase in number and diversity of engineered microbes, especially those intended to be used in an open environment, will challenge EPA’s resources, expertise and authority to regulate synthetic biology. Furthermore, studies done by the NRC have concluded that genetic engineering does not present more risks than other methods of genetic modification like traditional breeding or hybridization (2). Thus, individual products could pose risks that depend on the genetic changes made to which constructs, which can only be assessed on a case-by-base basis, an additional challenge for regulation. The emergence of biohackerspaces could potentially strengthen these concerns due to the desire to fuel innovation of novel biotechnology with minimal regulation. For this reason, we believe there is significant motivation for a community biology laboratory to implement a biocontainment method that can guarantee the survival of genetically modified microorganisms only under controlled conditions, applicable in a laboratory setting and an open environment.

Additionally, while the US has pre-market approval processes established (like the completion of an Environmental Impact Statement after an environmental assessment), the system recognizes that a pre-market approval is costly for producers and impractical because manufacturers already have market incentives to sell safe products. Post-market regulatory authority allows products to move to shelves more quickly and less expensively, but with more potential for harmful products to be sold (1). However, not everybody agrees that primarily post-market approval is the right answer. Due to the difficulty of “recalling” a living GMO from an open environment should there be health or environmental concern, some organizations have called for more stringent US biotechnology regulation system (3).

To comply with this emerging sentiment and strengthen the biosafety practices of an community space that undergoes no institutional safety review, we propose the acceptance of an auxotrophic biocontainment method that confers an organism’s dependence on protected leucine, a user-supplied nutrient. This will allow creators to ensure the safety of their science, as well as quell the public’s concerns about community science spaces.

SAFETY GUIDELINES
Values

At Open Bio Labs, we are interested in protecting the safety of the members and guests using our facility, the people in our community, our local and global environment and our ability to operate as a biohackerspace.

Our goals are to drive innovation and curiosity, while implementing safety without requiring everyone to be experts or presenting a barrier to entry.

Our safety practices are designed to be commensurate with the risks of the activities taking place at OBL. Policies will be developed if and when needed.

Open Bio Labs will not exhibit judgement whether an experiment is good science. During all stages of a project, we encourage members to consider the ethics of their work. We reserve the right to disallow any project from continuing if the ethical considerations do not align with OBL rules. Additionally, we encourage the expression of opinions, as we desire to operate as a springboard for individuals to learn and explore.

Why biosafety matters (globally and in the lab)

Biosafety is an important consideration when working with all chemicals and organisms. Safe research in the lab can prevent environmental and human health harm, as well as costly mistakes. Some important consideration beyond the nature of the chemicals and organisms in use are the importance of well planned protocols, following protocols, good communication practices, thorough document management and the encouragement of open and honest reporting. Leaders must always ensure learning and not just training. By following these standard practices, an individual and her team can lower the risk that their research poses to others in the lab and in the world.

ORGANISMS & PARTS
Allowed organisms (including viral genomes)

• Risk Group 1 organisms (for example E. coli K-12, S. cerevisiae, B. subtilis, Lactobacillus spp., etc.). Each country has the ability to classify organisms by risk group according to the pathogenicity of the organism, modes of transmission and host range, as well as availability of preventive measures and availability of effective treatment. As defined by the National Institute of Health (NIH), Risk Group 1 organisms are “agents that are not associated with disease in healthy adult humans.” (2). This database (https://my.absa.org/tiki-index.php?page=Riskgroups) maintained by the ABSA is the best place to find out what risk group certain organisms belong to.
• Bacteriophages T2, T4, T7, M13, P1, Phi X 174 and Lambda (unless containing a virulence factor)
• Phagemids
• Human and primate cells lines that have been tested and certified free of known pathogens
• Cells lines from plants, fungi or animals that are not primates
• Nematodes
• Physcomitrella patens, Arabidopsis spp., and Nicotiana spp.

Allowed parts (1)

• All Registry parts from the BioBrick registry (http://parts.igem.org/Main_Page) except those with a Red Flag
• Non-protein-coding parts that are promoters, RBSs, terminators, binding sites for transcriptional regulators, endonucleases, other proteins that bind to DNA, aptamers and catalytic RNAs, CRISPR guide RNAs, microRNAs, small interfering RNAs, and short hairpin RNAs that do not target human genes Cas9 and other CRISPR-associated nucleases (when integrated into an asexually reproducing organism)
• Prions from non-mammalian organisms
• Proteins or protein-coding genes from animals, plants or Risk Group 1 and 2 microorganisms except those in the following dangerous categories: virulence factors, factors that help pathogens evade or shut down the immune system, factors that help pathogens halt the host’s DNA/RNA replication, transcription or translation, factors that regulate the immune system such as cytokines and interferons, proteins that are toxic to humans and enzymes that produce a molecule that is toxic to humans.

FAQ
What is a virulence factor?

Virulence factors refer to the properties that enable an organism to live on or within a host of a particular species and increase its potential to cause disease. Virulence factors include bacterial toxins, cell surface proteins that mediate bacterial attachment, cell surface carbohydrates and proteins that protect a bacterium, and hydrolytic enzymes that may contribute to the pathogenicity of the bacterium (3). This definition was taken from the Virulence Factor Database, a good resource for information about virulence factors of bacterial pathogens (http://www.mgc.ac.cn/VFs/main.htm).

How do I know if my cell line is pathogen-free? What pathogens should I be concerned about?

If you bought cells from a vendor or culture collection, consult the catalog. If you cannot find safety and pathogen information in the catalog, contact the vendor. If you received cells from another lab, find out where they originally came from. The viral genome could be integrated into the cell’s genome. Most viruses have a limited host range, meaning they can only infect closely related species. Viruses have Risk Group numbers, so if your cell line contains any viruses, you must handle it at the appropriate laboratory Safety Level. Some dangerous viruses that infect human cell lines: HBV (hepatitis B virus), HCV (hepatitis C virus), HIV (human immunodeficiency virus) 1 & 2, HTLV (human T-lymphotropic virus) 1 & 2, CMV (cytomegalovirus) (1).

LAB SETUP

• Access to safety showers, eyewash stations and exit pathways should be unimpeded.
• An open window may substitute for ventilation of work with non-hazardous chemicals.
• As an alternative to expensive autoclave gloves, a community lab can use tightly-weaved cotton heat-resistant oven mitts.

CLEANING
Spills Major Spills Call 911 if:

• The spill is likely to result in uncontrolled release of hazardous substances into drains, the air, etc.
• Response to a release poses a safety or health hazard to the responder.
• The researcher is uncomfortable.

What to do:

• Leave the area, closing all doors behind you.
• Prevent others from entering the area.
• Initiate first aid if necessary.
• Notify someone in charge.

Minor Spills

• Only attempt to clean if it is a non-volatile liquid with which you are familiar.
• Wear personal protective equipments (goggles, gloves and lab coat).
• Use absorbent material to contain spill.
• Choose correct disposal container (or bag) to collect and dispose as chemical waste.
• Always let the fire department handle spills of the following chemicals: Aromatic amines, nitro compounds, organic halides, bromine carbon, disulfide ethers, cyanides, hydrazines and nitriles.

Broken glass

Currently, Open Bio Labs is working on establishing a partnership with the University of Virginia to dispose of sharps and broken glass safely. In the meantime, it is feasible to completely wrap broken glass in newspaper, tape it shut and dispose of it in the regular trash. When using this method, one must be sure that broken glass is wrapped thick enough so that it will not poke through the paper to cut someone.

Waste Chemical Waste

• Keep chemical waste containers closed at all times.
• Don’t discard chemicals in sinks, waste boxes or chemical trash.
• Check chemical expiration dates frequently and discard expired reagents.