Difference between revisions of "Team:Virginia/Safety Guidelines"

MOTIVATION
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 adopt a standard 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.

We understand that community labs have a tremendous amount of freedom to do what they want, which also presents a lot of opportunity for things to go wrong, so to support our project of biosafety, we have partnered with our local community lab, Open Bio Labs, to develop a comprehensive, standard, and evolvable biosafety protocol for these labs to follow, which will streamline their ability to work with their community. Through Open Bio Labs, we are reaching out to other labs below to receive a first round of feedback before we share the protocol more broadly with the rest of the labs and with other relevant groups such as the CDC and the Woodrow Wilson center.

The labs we've reached out to:

• Genspace in Brooklyn, NY
• BUGSS in Baltimore, MD
• Biologik in Norfolk, VA
• Indie Biolabs in Richmond, VA
• East Meets West in Boston, MA
• TriDIYBio in the Research Triangle, NC
• Berkeley Biolabs in Berkeley, CA
• Biocurious in Sunnyvale, CA
• Counter Culture Labs in Oakland, CA
• LA Biohackers in Los Angeles, CA
• WAAG in Amsterdam, NL
• Biohackspace in London, UK
• Syntechbio in Sao Paulo, BR

Additionally, we have posted our safety guidelineson the Open Sceince Framework, a webtool developed by the Center for Open Science in Charlottesville, VA that localizes open-source scientific research for the purposes of collaboration and reproducibility.

COMMUNITY LAB SAFETY GUIDELINES

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.

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 AND 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 and 2, HTLV (human T-lymphotropic virus) 1 and 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 equipment (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.

Chemical Expiration Guide

Peroxide hazard after prolonged storage.	Peroxide hazard if concentrated.	Peroxide hazard if polymerization is initiated.
Discard after 3 months.	Discard after 1 year (or 6 months after opening).	Discard after 1 year.
Divinyl acetylene Isopropyl ether Potassium amide Potassium metal Sodium amide Sodium ethoxyacetylidel Vinylidene chloridel	Acetal Acetaldehyde Cumene Cyclohexane Cyclopentene Diacetylene Dicyclopentadiene Diethyl etherl Dioxane Ethylene glycol dimethyl ether Furan Methyl acetylene Methyl cyclopentane Tetrahydrofuran Tetrahydroaphthalene Vinyl ethers	Acrylonitrile Butadiene Chlorobutadiene Styrene Tetrafluoroethylene Vinyl acetate Vinyl acetylene Vinyl chloride Vinyl pyridine

CHEMICALS
SDS Glossary
The United Nations adopted the Globally Harmonized System (GHS) in 1992 to standardize the classification and labelling of chemicals (GHS citation). Occupational Health and Safety Administration has modified the Hazard Communication Standard (HCS), which provides requirements for Safety Data Sheets, to comply with GHS (OSHA citation). The following is an instruction guide for reading a Safety Data Sheet (SDS). There are sixteen sections included on SDS.
Section 1: Identification
Includes product identifier, manufacturer name and contact info, recommended use, restrictions on use
Section 2: Hazard identification











































Section 3: Composition/information on ingredients
Includes chemical ingredients and trade secret claims
Section 4: First-aid measures
Includes important symptoms/effects and required treatment
Section 5: Fire-fighting measures
Includes suitable extinguishing techniques and equipment, chemical hazards from fire
Section 6: Accidental release measures
Includes emergency procedures, protective equipment, proper methods of containment and cleanup
Section 7: Handling and storage
Includes precautions for safe handling and storage, incompatibilities
Section 8: Exposure controls/personal protection
Includes OSHA’s and ACGIH’s exposure limits and any other exposure limit used or recommended by the chemical manufacturer, importer or employer preparing the SDS, appropriate engineering controls and personal protective equipment (PPE)
Section 9: Physical and chemical properties
Includes chemical characteristics
Section 10: Stability and reactivity
Includes chemical stability and possibility of hazardous reactions
Section 11: Toxicological information
Includes routes of exposure, related symptoms, acute and chronic effects, numerical measures of toxicity
Section 12: Ecological information
Section 13: Disposal considerations
Section 14: Transport information
Section 15: Regulatory information
Section 16: Other information Includes date of preparation or last revision

Storage and Handling

• Use a fume hood or stand by an open window whenever opening, pouring or handling hazardous materials.
• Order smallest amount of chemicals possible to prevent spills.
• Use bottle carriers to transport all glass bottles containing chemicals.
• Order solvents and acids in poly-coated glass safety bottles.
• Properly label all chemicals, especially hazardous ones.
• Record date of receipt on each bottle to assist with inventory management
• Label and date solutions when prepared with name of chemical or mixture and any applicable hazard warnings.
• Consider storing chemicals by hazard class. Within a hazard class, store alphabetically.
Classes:

Corrosive acids (Organic and Mineral Acids: acetic, glacial acetic, butyric; Oxidizing Acids: nitric, sulfuric, perchloric, phosphoric)

Corrosive bases (ammonium hydroxide, sodium hydroxide, calcium hydroxide)

Explosives (ammonium nitrate, nitro urea, picric acid, trinitroaniline, trinitrobenzene, trinitrobenzoic acid, trinitrotoluene, urea nitrate)

Flammable liquids (acetone, benzene, diethyl ether, methanol, ethanol, toluene, glacial acetic acid)

Flammable solids (phosphorus, magnesium, ethyl acetate)

Oxidizers (sodium hypochlorite, ethyl acetate, benzoyl peroxide, potassium permanganate, potassium chlorate, potassium dichromate, peroxides, perchlorates, chlorates, nitrates)

Poisons (cyanides, cadmium, mercury, osmium, acrylamide, ethidium bromide, sodium azide)

Water reactives (sodium metal, potassium metal, lithium metal, lithium aluminum hydride)

Flammable compressed gases (methane, acetylene, propane, hydrogen)

Oxidizing compressed gases (oxygen, chlorine)

Poisonous compressed gases (carbon monoxide, hydrogen sulfide, hydrogen chloride)

• Store flammable and combustible materials in an approved storage cabinet.
• Do not store chemicals on the floor.
• Store hazardous chemicals no higher than eye level.
• Liquids should be stored on shelves with a lipped edge and in spill trays in case of breaks or leaks.
• Store acids in a cabinet by themselves, preferably in the ventilated storage area beneath chemical fume hood. Nitric, perchloric, chromic and sulfuric acids are strong oxidizers and must be kept isolated from organic acids.
• Store bases in a corrosives cabinet.
• Store highly toxic materials in a closed, dedicated poison cabinet.
• Do not store chemicals in fume hood, as this prevents proper airflow, reduces available work space and may increase fire or spill hazards.
• Do not store hazardous chemicals under a sink.
• Store chemicals away from heat and direct sunlight.
• Keep a chemical inventory.

Compressed gases
All compressed gases must be stored in a cylinder secure to a wall, bench or fixed support using a chain or strap placed at ⅔ the height of the cylinder. Do not store full and empty cylinders together. Minimize number of cylinders in lab and be sure to label contents of every cylinder.

PERSONAL PROTECTIVE EQUIPMENT

• Do not wear PPE outside the laboratory.
• Wear closed-toed shoes.
• If handling hazardous chemicals, wear safety glasses with side shields.
• If wearing a lab coat, choose tightly-weaved, heavy-weight cotton and tightly-fitted sleeves.
• Polyethylene lab coats are liquid resistant.

When choosing gloves, consider duration of chemical contact, concentration of chemical, temperature of chemical, compatibility of chemical, dexterity requirements, grip requirements, size and comfort. Gloves come in many materials for different purposes. Consult the table below.

Glove Guidelines: Types and Uses

Fabric Type	Uses
Disposable: vinyl, latex, nitrile	Dry powders, aqueous solutions
Reusable: neoprene	Corrosives, solvents and alcohols Resists oils
Reusable: nitrile	Organic solvents (non-halogenated) Puncture and abrasion resistant
Reusable: Nomex or Zetex	Temperature extremes
Reusable: Butyl	Aldehydes, ketones and esters
Reusable: Viton	Chlorinated and aromatic solvents

Latex is a natural material made from rubber. They pose the possibility of allergic reactions. Latex has a slight advantage over nitrile with comfort and dexterity. They are good for wearing for an extended amount of time and for high-risk situations involving infectious material. Additionally, they are lightly-powdered for easy application, elastic, strong and biodegradable. Nitrile gloves are made from synthetic rubber. They are the most puncture resistant, often referred to as “medical grade”. They have a high level of sensitivity, mold to the hand, good for an extended amount of time, work well for high-risk situations involving infectious material, resist many chemicals, have a long shelf life and are colored to help identify if the glove has been punctured. Vinyl gloves are less durable, less expensive, looser, good for short-term, low-risk tasks, have anti-static properties, are best used for non-hazardous materials and are lightly powdered. Butyl rubber gloves are good for extended contact with ketones and esters. They are poor for gasoline and aliphatic, aromatic and halogenated hydrocarbons. Neoprene gloves are good for extended contact of acids, bases, alcohols, fuels, peroxides, hydrocarbons and phenols. They are not good for halogenated and aromatic hydrocarbons. Norfoil gloves are good for most hazardous chemicals, but usually a poor fit. Viton gloves are good for extended contact with chlorinated and aromatic solvents. They have good resistance to cuts and abrasions. They are poor for ketones and expensive.

BIOCONTAINMENT
Engineering genetically modified microbes requires special precautions to prevent escape or environmental release. To promote innovation at community laboratories, a standard biocontainment method should be available for interested parties that develop a genetically engineered organism to solve a problem. A biocontainment method robust enough to allow a scientist to take a genetically engineered microbe from Open Bio Labs to another facility for further testing should be implemented, effectively securing this community lab as a launchpad for innovation. Additionally, due to the self-governed nature of a community laboratory, there is likely to be more risk for an engineered organism from a laboratory to get released into the environment by accident. A biocontainment method can also serve as a layer of protection for a researcher at a community lab that a large flux of people through its doors. This objective needs further investigation.