"
Safety/Risk Group Guide
From 2014.igem.org
| Line 79: | Line 79: | ||
<div class="underconst">This section is under construction</div> | <div class="underconst">This section is under construction</div> | ||
| - | <p> | + | <p>There is no world-wide standard list of microorganisms and their Risk Groups. To determine the Risk Group of an organism, we must consult reliable sources. Because different countries sometimes disagree about Risk Groups, we suggest that you consult multiple sources. iGEM recommends the following sources for Risk Group information:</p> |
| + | |||
| + | <h5>Canadian Pathogen Safety Data Sheets (PSDS)</h5> | ||
| + | |||
| + | <p>The Public Health Agency of Canada has published safety data sheets for a wide variety of microorganisms.</p> | ||
| + | |||
| + | <ul> | ||
| + | <li><a href="http://www.phac-aspc.gc.ca/lab-bio/res/psds-ftss/index-eng.php">PSDS in English</a></li> | ||
| + | <li><a href="http://www.phac-aspc.gc.ca/lab-bio/res/psds-ftss/index-fra.php">FTSSP (fiches techniques santé-sécurité : agents pathogènes) en Français</a></li> | ||
| + | </ul> | ||
| + | |||
| + | <p>To use the PSDS, begin by scrolling down and finding your species in the list. Click on the species name to bring up extensive safety information about that species. Scroll down to "SECTION VII". Some species will have a "RISK GROUP" explicitly listed. Other species will only have "CONTAINMENT REQUIREMENTS", which will recommend a laboratory Biosafety Level.</p> | ||
| + | |||
| + | <h5>NIH Guidelines</h5> | ||
| + | |||
| + | <p>The <a href="http://osp.od.nih.gov/office-biotechnology-activities/biosafety/nih-guidelines">NIH Guidelines</a> are a set of rules that govern research on recombinant/synthetic DNA in the United States. Appendix B of the guidelines gives a list of pathogens in Risk Groups 2, 3, and 4. It does not list Risk Group 1 organisms.</p> | ||
| + | |||
| + | <p><a href="http://osp.od.nih.gov/sites/default/files/NIH_Guidelines.html#_Toc351276291">Click here to go directly to Appendix B.</a></p> | ||
| + | |||
| + | <h5>DSMZ</h5> | ||
| + | |||
| + | <p>DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen / German Collection of Microorganisms and Cell Cultures) is a large collection that includes Risk Group information for thousands of different species, strains, and cell lines. It is more difficult to use, but it includes the most species of any source we have found.</p> | ||
| + | |||
| + | <ul> | ||
| + | <li><a href="http://www.dsmz.de/catalogues/catalogue-microorganisms.html">Catalogue Microorganisms</a> -- search bacteria. Enter your genus, species, and/or strain information in the "Search term" box, and click Search. You will receive a long list of results, which may include many different strains and species. Examine the list to find the correct strain, and click on its DSM number to view its catalogue page. The Risk Group is listed in the table.</li> | ||
| + | <li><a href="http://www.dsmz.de/catalogues/catalogue-human-and-animal-cell-lines.html">Catalogue Human and Animal Cell Lines</a> -- search this catalogue by the same method as for Catalogue Microorganisms.</li> | ||
| + | <li><a href="http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date/prokariotic-nomenclature-up-to-date.html">Prokaryotic Nomenclature Up to Date</a> is an alphabetical list of <i>all</i> bacterial and archaeal species names with standing in the literature. Find your species in the list, and click on its name to view details. In the table row "Type strain", look for a blue DSM link. If one is present, it will bring you to a DSMZ catalogue page where you can find details, including Risk Group in the table. If there is no blue DSM link, it means that the DSMZ does not offer that species. <i>Note: Prokaryotic Nomenclature Up to Date concerns wild organisms, not lab strains. Therefore, it will tell you that E. coli is Risk Group 2. That is accurate, because wild E. coli can cause disease in humans. E. coli K-12, or "lab strain" E. coli, is not the same as "wild" E. coli!</i></li> | ||
| + | </ul> | ||
| + | |||
| + | <h4>Other sources</h4> | ||
| + | |||
| + | <p>If you cannot find your species in any of the recommended sources, you must find another source. There may be a paper in the peer-reviewed scientific literature that describes your species. Your country's government might have a list of microorganisms and their Risk Groups. (It is always a good idea to check with your country's government. Remember that different countries may disagree about Risk Groups!)</p> | ||
| + | |||
| + | <p>For help finding a reliable source, you can consult your advisor, or speak to the biosafety authorities of your university. You can also contact <span class="email"><safety AT igem DOT org></span> for help.</p> | ||
<h4>What about animals and plants?</h4> | <h4>What about animals and plants?</h4> | ||
| Line 86: | Line 119: | ||
<p>Some multicellular organisms are very popular in molecular biology. Worms (<i>C. elegans</i>), frogs (<i>Xenopus</i>), moss (<i>Physcomitrella patens</i>), thale cress (<i>Arabidopsis</i>), and fruit flies (<i>Drosophila</i>) have all been used by iGEM teams in the past.</p> | <p>Some multicellular organisms are very popular in molecular biology. Worms (<i>C. elegans</i>), frogs (<i>Xenopus</i>), moss (<i>Physcomitrella patens</i>), thale cress (<i>Arabidopsis</i>), and fruit flies (<i>Drosophila</i>) have all been used by iGEM teams in the past.</p> | ||
| + | |||
| + | <p>If you are using a part from an animal/plant, you should consider the <strong>function</strong> of the part, and consider whether it might be dangerous to humans. For example, the gene that codes for Green Fluorescent Protein comes from the jellyfish <i>Aequorea victoria</i>. Therefore, in the strictest interpretation, GFP does not have any associated Risk Group. However, GFP is only a fluorescent protein, absorbing and emitting light, so it is completely safe for humans. If you consider a different gene from <i>A. victoria</i>, such as the gene that produces the toxin in its stinging tentacles, you might come up with a very different answer!</p> | ||
<h2>Laboratory Biosafety Levels</h2> | <h2>Laboratory Biosafety Levels</h2> | ||
Revision as of 21:56, 13 May 2014
Email safety AT igem DOT org!
This page is under construction.
To learn more about Risk Groups and BioSafety Levels, consult the WHO Biosafety Manual.
Risk Groups
Common iGEM Organisms
| Species | Risk Group |
|---|---|
| Escherichia coli K-12 (and derivatives: DH5alpha, TOP10, etc) | RG 1 |
| Bacillus subtilis | RG 1 |
| Yeast (Saccharomyces cerevisiae) | RG 1 |
| Lactobacillus spp. | RG 1 |
Long paragraph about risk groups.
Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur, from a Lorem Ipsum passage, and going through the cites of the word in classical literature, discovered the undoubtable source. Lorem Ipsum comes from sections 1.10.32 and 1.10.33 of "de Finibus Bonorum et Malorum" (The Extremes of Good and Evil) by Cicero, written in 45 BC. This book is a treatise on the theory of ethics, very popular during the Renaissance. The first line of Lorem Ipsum, "Lorem ipsum dolor sit amet..", comes from a line in section 1.10.32.
"Always check your strain!"
A note about E. coli K-12
Escherichia coli is the most commonly used bacterium in molecular biology. E. coli bacteria naturally live inside the human digestive system. We scientists are used to thinking of E. coli as "safe" and even "boring", but many strains of E. coli cause terrible diseases! Famous strains such as E. coli O157:H7 have caused many deaths. Most disease-causing strains of E. coli are considered Risk Group 2.
E. coli K-12 is a "lab strain". The K-12 strain cannot survive in the human digestive system, and does not produce toxins. Therefore, it is considered Risk Group 1, and it may be used safely in the laboratory. Similarly, the strains derived from K-12 (such as DH5alpha, TOP10, etc.) are also considered Risk Group 1. Always check your strain!
iGEM participants usually use Level 1 labs, because the most common chassis organisms are Risk Group 1. Some iGEM projects use Level 2 labs. Level 3 and Level 4 labs are not used in iGEM.
Different countries may disagree about the danger of some microorganisms, and may assign the same organism to different Risk Groups. Often, this is because the same organism is more dangerous in certain parts of the world. For example, a pathogen that is more deadly in hot climates might be rated Risk Group 3 by countries with hot weather, but the same organism might be rated Risk Group 2 in countries with very cold weather.
How can I find out the Risk Group of my organism?
There is no world-wide standard list of microorganisms and their Risk Groups. To determine the Risk Group of an organism, we must consult reliable sources. Because different countries sometimes disagree about Risk Groups, we suggest that you consult multiple sources. iGEM recommends the following sources for Risk Group information:
Canadian Pathogen Safety Data Sheets (PSDS)
The Public Health Agency of Canada has published safety data sheets for a wide variety of microorganisms.
To use the PSDS, begin by scrolling down and finding your species in the list. Click on the species name to bring up extensive safety information about that species. Scroll down to "SECTION VII". Some species will have a "RISK GROUP" explicitly listed. Other species will only have "CONTAINMENT REQUIREMENTS", which will recommend a laboratory Biosafety Level.
NIH Guidelines
The NIH Guidelines are a set of rules that govern research on recombinant/synthetic DNA in the United States. Appendix B of the guidelines gives a list of pathogens in Risk Groups 2, 3, and 4. It does not list Risk Group 1 organisms.
Click here to go directly to Appendix B.
DSMZ
DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen / German Collection of Microorganisms and Cell Cultures) is a large collection that includes Risk Group information for thousands of different species, strains, and cell lines. It is more difficult to use, but it includes the most species of any source we have found.
- Catalogue Microorganisms -- search bacteria. Enter your genus, species, and/or strain information in the "Search term" box, and click Search. You will receive a long list of results, which may include many different strains and species. Examine the list to find the correct strain, and click on its DSM number to view its catalogue page. The Risk Group is listed in the table.
- Catalogue Human and Animal Cell Lines -- search this catalogue by the same method as for Catalogue Microorganisms.
- Prokaryotic Nomenclature Up to Date is an alphabetical list of all bacterial and archaeal species names with standing in the literature. Find your species in the list, and click on its name to view details. In the table row "Type strain", look for a blue DSM link. If one is present, it will bring you to a DSMZ catalogue page where you can find details, including Risk Group in the table. If there is no blue DSM link, it means that the DSMZ does not offer that species. Note: Prokaryotic Nomenclature Up to Date concerns wild organisms, not lab strains. Therefore, it will tell you that E. coli is Risk Group 2. That is accurate, because wild E. coli can cause disease in humans. E. coli K-12, or "lab strain" E. coli, is not the same as "wild" E. coli!
Other sources
If you cannot find your species in any of the recommended sources, you must find another source. There may be a paper in the peer-reviewed scientific literature that describes your species. Your country's government might have a list of microorganisms and their Risk Groups. (It is always a good idea to check with your country's government. Remember that different countries may disagree about Risk Groups!)
For help finding a reliable source, you can consult your advisor, or speak to the biosafety authorities of your university. You can also contact <safety AT igem DOT org> for help.
What about animals and plants?
The four Risk Groups only apply to microorganisms (bacteria, fungi, and viruses), with very few exceptions. For animals, plants, and other multicellular organisms, there are different safety guidelines. Your country and your university will have their own set of guidelines governing experiments on animals and plants. You should consult your advisor, your lab manager, or the authorities at your university.
Some multicellular organisms are very popular in molecular biology. Worms (C. elegans), frogs (Xenopus), moss (Physcomitrella patens), thale cress (Arabidopsis), and fruit flies (Drosophila) have all been used by iGEM teams in the past.
If you are using a part from an animal/plant, you should consider the function of the part, and consider whether it might be dangerous to humans. For example, the gene that codes for Green Fluorescent Protein comes from the jellyfish Aequorea victoria. Therefore, in the strictest interpretation, GFP does not have any associated Risk Group. However, GFP is only a fluorescent protein, absorbing and emitting light, so it is completely safe for humans. If you consider a different gene from A. victoria, such as the gene that produces the toxin in its stinging tentacles, you might come up with a very different answer!
Laboratory Biosafety Levels
Quick Lesson on Biosafety Levels
This "Quick Learn Lesson" will give you a general idea of what the four BioSafety Levels look like. It is prepared by the U.S. Government, so it uses U.S. definitions for each Level. Most countries will use a very similar system, but some details may vary.
Most countries divide biological laboratories into four levels, based on their ability to contain increasingly dangerous pathogens.
The World Health Organization defines Level 1 as the most safe, and Level 4 as the most dangerous. Most countries in the world follow this system, and iGEM follows this system as well.
Note: A smaller number of countries, mostly those that were formerly part of the Soviet Union, use a different system where the numbers are reversed (with Level 1 being the most dangerous). Make sure you know which system your country uses!
