Team:Groningen/Safety

From 2013.igem.org

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Our project is designed for use that is inside a laboratory, however accidents can occur and can cause release into the community and environment. These possible risks are discussed in 3.1 and 3.2 respectively.
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The coating GEM its swimming behavior is adapted by linking circuits of genes in another way. Thus, at that point no new genes are introduced. However to introduce the new gene circuit we use a standard laboratory technique involving resistance genes that normally not occur in B. subtilis.<br>
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The silk protein gene (<i>masp2>/i>) originating from <i>Argiope Aurantia</i> is an eukaryotic gene that is codon optimized for <i>B. subtilis</i>. 
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Our project is designed for use that is inside a laboratory, however accidents can occur and can cause release from our 'Coating GEM' into the community and environment. These possible risks are discussed in 3.1 and 3.2 respectively.
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<H3>3.1. Risk Assessments</h3>
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<h3>3.1. Community</h3>
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<h4>3.1.1. Release in Community & Enviroment</h4>
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<h3>3.2. Environmental</h3>
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<h4>3.1.2. Streptavidin coated implant</h4>
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Revision as of 10:45, 24 September 2013

Safety

On this page the safety related ethics and issues are discussed.
First with a general introduction and eventually the specific related safety of our project.



1. Introduction

In 1983 the World Health Organization (WHO) published the first edition of the laboratory biosafety manual. This manual was composed for countries over the world to accept and implement the concepts of biological safety. This gave countries a scaffold to develop their national regulations in handeling pathogenic microorganisms.

The revised version of this manual in 2004, also addresses the current biosafety issues we are facing today, e.g. the use of genetic modified organisms (GMOs)[1]. Also a more recent development is the upcoming field of synthetic biology, which brings along more biosafety and ethical issues (discussed below).

In here, we will address the biological safety issues directly on our project with detailed information described by various organisations such as the WHO and the Commission on Genetic Modification (COGEM).

Infective microorganisms are classified, for laboratory work, by four risk groups. In this iGEM project we are working with Escherichia coli and Bacillus subtilis. For E. coli it is known that it can cause irritation to skin, eyes, and respiratory tract, and could affect kidneys, however this is a low individual and community risk[2]. B. subtilis is unlikey to cause any harm to individual and community, and is also Generally Recognized as Safe (GRAS) [3].

In this case, the only relevant risk group for our project is Risk Group 1 (no or low individual and community risk). Microorganisms classified in this group are unlikely to cause human or animal diseases are classified in this group. For Risk Group 1 a Basic Biosafety Level 1 (BSL1) laboratory is required.

For our project we work on a BSL1 lab and all persons that do laboratory related work have a Good Microbiological Techniques (GMT) certificate. With this certificate we are approved to work with Risk Group 2 organisms in a BSL2 laboratory according to the advice of the Royal Dutch Society of Microbiology.


GMT commitments:
  1. All GMT related work can only be performed by those people that have permission from the Biological Safety Officer (Lolkema, J. S.). Work according to the rules, even if you believe there is no apparent risk.
  2. During GMT related work all doors and windows have to be closed. Verify that insects and other pests are not present in the lab.
  3. Wear a closed lab coat. Do not take this lab coat outside the GMT area unless it is absolutely necessary for the experiment. In case of a contamination of the lab coat, sterilize the lab coat first, with bleach or autoclaving, before washing.
  4. Clean and sterilize spills immediately. Report serious contamination immediately to the BSO.
  5. It is absolutely prohibited to eat, drink or smoke, or to have cups, plates, mugs or silverware in the GMT area.
  6. Pipetting by mouth is prohibited. Used pipets are collected in a disinfecting solution.
  7. Prevent aerosols. These may be created by: splashing drops; pouring of liquids; discharging pipettes; opening of moist plugs; using inoculating loops that are too hot. Use needles only if there is absolutely no alternative.
  8. Glassware and instruments that have been in contact with GMO's have to be sterilized or disinfected before being washed reused or discarded.
  9. Biological waste has to be collected in autoclavable plastic bags, which are autoclaved before discarding (use indicator tape to demonstrate that the bag was autoclaved). Wash hands with soap and water after work and before leaving the room. Bench surface areas have to be cleaned and disinfected daily. Keep area clean and organized.
  10. Record the general nature of the work clearly in a labjournal.


1.1. Synthetic Biology

The synthetic biology is an emerging discipline in biology with possible great potential, however it brings along new biosafety and ethical questions[4]. Nowadays, the risk assessment framework is still applicable of the developments in synthetic biology, however, eventually when new developments in synthetic biology will arise the current risk assessments will not be adequate anymore[5].

The International Risk Governance Council (IRSC) stated risks that arose from reports of various organisations[4] :

  1. Insufficient basic knowledge about the potential risks posed by designed and synthetic organisms.

  2. Uncontrolled release of novel genetically modified organisms with potential environmental or human health implications, either arising from accidental release into the environment or from applications entailing deliberate release.

  3. Bio-terrorism, biological warfare and the construction of novel organisms designed to be hostile to human interests.

  4. The possible emergence of a ‘bio-hacker’ culture in which lone individuals develop dangerous organisms much as they currently create computer viruses.

  5. Patenting and the creation of monopolies, inhibiting basic research and restricting product development to large companies.


Many of those safety and ethical questions have been discussed in Schmidt, M. 2009[6].




Our Project: The Coating GEMs

2. Safety Precautions on the lab

2.1. DNA stain

Ethidium Bromide (EB) is a fluorescent nucleic acid stain that is commonly used in agarose gel electrophoresis. However, EB is a hazardous chemical in case of ingestion, skin contact (irritant), eye contact (irritant), and inhalation [7]. It was observed that EB concentrations of 0.1-5µg/ml inhibit cell growth and the mitochondrial DNA synthesis of cultured L and BHK cells. EB treatment to these cell lines showed a structural alternation of covalently closed mitochondrial DNA. Also an increased degree of supercoiling and breakage of circular DNA was observed. These changes occurred in the pre-existing as in the newly synthesized DNA. The caused changes in the DNA by EB were reversible by growth of cells in EB-free medium [8].

On the carcinogenic effects of EB no data is available, however it is highly plausible that, because of its interaction with DNA, it may cause mutations and may lead to carcinogen effects.

Therefore, we choose to use SERVA DNA Stain G. This stain is non-carcinogenic and according to the AMES test it causes significantly fewer mutations than EB according to SERVA (see safety test results).


3. Safety Aspects of Our Project

In our projected we created a Coating Genetically Engineered Machine.
The machine is an engineered B. subtilis strain that can swim to the heated implant and secrete silk. We visualized our idea in the movie shown below.
The coating of the implant will be performed in vitro in a laboratory and can be scaled up to industrial levels easily. A possible setup is shown below in the picture right.

The Coating GEMs: Possible Experimental Setup:

The coating GEM its swimming behavior is adapted by linking circuits of genes in another way. Thus, at that point no new genes are introduced. However to introduce the new gene circuit we use a standard laboratory technique involving resistance genes that normally not occur in B. subtilis.
The silk protein gene (masp2>/i>) originating from Argiope Aurantia is an eukaryotic gene that is codon optimized for B. subtilis. Our project is designed for use that is inside a laboratory, however accidents can occur and can cause release from our 'Coating GEM' into the community and environment. These possible risks are discussed in 3.1 and 3.2 respectively.

3.1. Risk Assessments

3.1.1. Release in Community & Enviroment

3.1.2. Streptavidin coated implant



4. References

[1]     Laboratory biosafety manual 3rd revision, WHO
[2]     Website from American Biological Safety Association (ABSA):  www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli
[3]     Singh, M et al. Microbial Cell Factories 2009, 8:38
[4]     Policy Brief: Guidelines for the Appropriate Risk Governance of Synthetic Biology from the International Risk Governance Council (IRGC) 2010
[5]     Synthetic Biology – Update 2013: Anticipating developments in synthetic biology, COGEM Topic Report, CGM/130117-01
[6]     Schmidt, M. Systems and Synthetic Biology 3, 1-4, Special Issue: Societal Aspects of Synthetic Biology
[7]     Material Safety Data Sheet: Ethidium Bromide
[8]     Margit M.K. Nass, Differential effects of ethidium bromide on mitochondrial and nuclear DNA synthesis in vivo in cultured mammalian cells, Experimental Cell
         Research, Volume 72, Issue 1, May 1972, Pages 211-222, ISSN 0014-4827

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