Team:TU-Delft/Safety

From 2012.igem.org

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<h2>Biosafety</h2>
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<h3>Question 1: Would any of your project ideas raise safety issues?</h3>
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<p><b>Inquiry</b> <b>WHO Level</b>
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Strains used
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<i>Escherichia coli</i> K-12 1<sup>[1]</sup>
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<i>Saccharomyces cerevisiae</i> S288C         1<sup>[2]</sup>
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Origin parts
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<i>Saccharomyces cerevisiae</i>         1<sup>[2]</sup>
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<i>Rattus norvegicus</i> 1
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<i>Homo sapiens</i> 1
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These organisms and parts all belong to WHO level 1, which is the minimum hazardous risk.
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The Escherichia coli K-12 strain is a less hazardous version of the more hazardous original that belongs to WHO level 2. E. coli K-12 is not considered a human or animal pathogen nor is it toxicogenic. Any concerns for E. coli K-12 in terms of health considerations are mitigated by its poor ability to colonize the colon and establish infections. However, this strain can still pose a threat to the health of a team member, if the person has a low-response immune system. Moreover, E. coli K-12 strains are very unlikely to pose a hazard to either animals, plants, or other microorganisms.<sup>[3]</sup>
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Saccharomyces cerevisiae has an extensive history of use in the area of food processing. Despite considerable use of the organism in research and the presence of S. cerevisiae in food, there are limited reports in the literature of its pathogenicity to humans or animals, and only in those cases where the human had a debilitating condition. Factors associated with the virulence of yeasts (i.e., phospholipases) indicate that this organism is nonpathogenic. The organism has not been shown to produce toxins to humans.<sup>[4]</sup>
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Before working in the laboratory, all team members where subjugated to the hand-washing test and the (bio)safety instructions of the laboratory itself, i.e. how to react if there is a fire, etc. The safety regulations of the used chemicals remained in the standard codes for safe use, i.e. use gloves, protection glasses and mask if explicitly mentioned.
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These is however a future risk when dealing with these organisms when this project will go public. The ultimate goal of this research would be to engineer a device that can actually be used in developing countries. One idea of developing this low-budget diagnostic tool, would be a petri dish that contains three different yeast strains of which each strain is related to one of the four specific tuberculosis (TB) molecules, present in the breath or saliva of a patient. Each strain has a different pigment output, and as soon as all pigments are activated, this could be a indication that the patient has TB.
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The disposal of these petri dishes, used or unused, should go according to biosafety regulation, because it contains both the novel strains of the yeast cells, and the organism that causes TB. This regulation should be supervised by experts that operate in those countries.
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<h3>Question 2: Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</h3>
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<p>There are no safety issues involved with our Biobricks.</p>
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<h3>Question 3: Is there a local biosafety group, committee, or review board at your institution?</h3>
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<p>The Ministry of Housing, Spatial Planning and the Environment (VROM) is a political organization operating under the leadership of the Minister and State Secretary. VROM is responsible for the EU directives on environmental safety of GMOs and regulation of traceability and labelling of GMOs.<sup>[5]</sup>
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To work with biological material, you should have a properly equipped laboratory, and always have permission from a biological safety officer (BVF). At present, only the Faculty of Applied Sciences of the Technical University of Delft has a biological safety officer, who is Dr. L.A. (Lesley) Robertson.<sup>[6]</sup>
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Our project has been approved by our safety officer, according by law. Additional advice included that biologists working with GMOs should never forget the seriousness of what they are doing. An extensively used organism like baker’s yeast, which seems to be very safe to work with, can still pose a threat to people with a low immune system.
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<h3>Question 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?</h3>
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<p>One concern in synthetic biology, is the possibility that a GMO would leave the laboratory – and especially the ones with an antibiotic resistance – and conquer the natural world at the expense of the wild-type organisms. Even though the GMO itself might not be harmful to humans and nature, a phenomenon like horizontal gene transfer (HGT) might cause it to become dangerous.
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Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transmission of DNA between different genomes. It is made possible in large part by the existence of mobile genetic elements, such as plasmids, transposons (“jumping genes”), and bacteria-infecting viruses (bacteriophages). These elements are transferred between organisms through different mechanisms, which in prokaryotes include transformation, conjugation, and transduction. The newly acquired DNA is incorporated into the genome of the recipient through either recombination or insertion.<sup>[7]</sup>
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A proposed solution to battle HGT in the field of synthetic biology, are Xeno Nucleic Acids (XNA).  The "X" in XNA stands for "xeno." Scientists use the xeno prefix to indicate that one of the ingredients typically found in the building blocks that make up RNA and DNA has been replaced by something different from what we find in nature – a xeno-organism.<sup>[8]</sup>
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Because natural and xeno-organisms are supposed to use a different and very specific set of nucleotide binding proteins for replication and transcription, gene flow – whether horizontal or via sexual reproduction – cannot occur between the two realms of life. DNA cannot be interpreted by the XNA replication machinery and vice versa. A piece of XNA cannot, therefore, escape to wild-type organisms and be incorporated into their DNA genomes. Also the XNA organism cannot benefit from genes “discovered” by (natural) evolution through horizontal gene flow (but only through deliberate engineering, and XNA internal evolution). An additional increase in orthogonality and thus safety would be the deployment of several orthogonal systems, such as XNA with different non-canonical bases and rearranged codon assignment.<sup>[9]</sup>
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If this orthogonal way of synthetic biology is adopted in the iGEM competition, it could lead to more (fundamental) advances in synthetic biology and biosafety.
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</p>
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<h3>References</h3>
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<p>[1] <a href="http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf">http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf</a>
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[2] <a href="http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=201388&Template=fungiYeast">http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=201388&Template=fungiYeast</a>
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[3] <a href="http://epa.gov/biotech_rule/pubs/fra/fra004.htm">http://epa.gov/biotech_rule/pubs/fra/fra004.htm</a>
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[4] <a href="http://www.epa.gov/biotech_rule/pubs/fra/fra002.htm">http://www.epa.gov/biotech_rule/pubs/fra/fra002.htm</a>
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[5] <a href="http://www.biosafety-europe.eu/d20public_300309.pdf">http://www.biosafety-europe.eu/d20public_300309.pdf</a>
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[6] <a href="https://intranet.tudelft.nl/live/pagina.jsp?id=39234121-1031-41f1-825a-636a79c41857&lang=en">https://intranet.tudelft.nl/live/pagina.jsp?id=39234121-1031-41f1-825a-636a79c41857&lang=en</a>
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[7] <a href="http://www.britannica.com/EBchecked/topic/1757605/horizontal-gene-transfer">http://www.britannica.com/EBchecked/topic/1757605/horizontal-gene-transfer</a>
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[8] <a href="http://io9.com/5903221/meet-xna-the-first-synthetic-dna-that-evolves-like-the-real-thing">http://io9.com/5903221/meet-xna-the-first-synthetic-dna-that-evolves-like-the-real-thing</a>
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[9] <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909387/">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909387/</a>
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</p>
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</div>
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Revision as of 09:24, 6 September 2012

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Safety

Biosafety



Question 1: Would any of your project ideas raise safety issues?



Inquiry WHO Level

Strains used

Escherichia coli K-12 1[1] Saccharomyces cerevisiae S288C 1[2]

Origin parts

Saccharomyces cerevisiae 1[2] Rattus norvegicus 1 Homo sapiens 1

These organisms and parts all belong to WHO level 1, which is the minimum hazardous risk.

The Escherichia coli K-12 strain is a less hazardous version of the more hazardous original that belongs to WHO level 2. E. coli K-12 is not considered a human or animal pathogen nor is it toxicogenic. Any concerns for E. coli K-12 in terms of health considerations are mitigated by its poor ability to colonize the colon and establish infections. However, this strain can still pose a threat to the health of a team member, if the person has a low-response immune system. Moreover, E. coli K-12 strains are very unlikely to pose a hazard to either animals, plants, or other microorganisms.[3]

Saccharomyces cerevisiae has an extensive history of use in the area of food processing. Despite considerable use of the organism in research and the presence of S. cerevisiae in food, there are limited reports in the literature of its pathogenicity to humans or animals, and only in those cases where the human had a debilitating condition. Factors associated with the virulence of yeasts (i.e., phospholipases) indicate that this organism is nonpathogenic. The organism has not been shown to produce toxins to humans.[4]

Before working in the laboratory, all team members where subjugated to the hand-washing test and the (bio)safety instructions of the laboratory itself, i.e. how to react if there is a fire, etc. The safety regulations of the used chemicals remained in the standard codes for safe use, i.e. use gloves, protection glasses and mask if explicitly mentioned.

These is however a future risk when dealing with these organisms when this project will go public. The ultimate goal of this research would be to engineer a device that can actually be used in developing countries. One idea of developing this low-budget diagnostic tool, would be a petri dish that contains three different yeast strains of which each strain is related to one of the four specific tuberculosis (TB) molecules, present in the breath or saliva of a patient. Each strain has a different pigment output, and as soon as all pigments are activated, this could be a indication that the patient has TB.

The disposal of these petri dishes, used or unused, should go according to biosafety regulation, because it contains both the novel strains of the yeast cells, and the organism that causes TB. This regulation should be supervised by experts that operate in those countries.



Question 2: Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?



There are no safety issues involved with our Biobricks.




Question 3: Is there a local biosafety group, committee, or review board at your institution?



The Ministry of Housing, Spatial Planning and the Environment (VROM) is a political organization operating under the leadership of the Minister and State Secretary. VROM is responsible for the EU directives on environmental safety of GMOs and regulation of traceability and labelling of GMOs.[5]

To work with biological material, you should have a properly equipped laboratory, and always have permission from a biological safety officer (BVF). At present, only the Faculty of Applied Sciences of the Technical University of Delft has a biological safety officer, who is Dr. L.A. (Lesley) Robertson.[6]

Our project has been approved by our safety officer, according by law. Additional advice included that biologists working with GMOs should never forget the seriousness of what they are doing. An extensively used organism like baker’s yeast, which seems to be very safe to work with, can still pose a threat to people with a low immune system.




Question 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?



One concern in synthetic biology, is the possibility that a GMO would leave the laboratory – and especially the ones with an antibiotic resistance – and conquer the natural world at the expense of the wild-type organisms. Even though the GMO itself might not be harmful to humans and nature, a phenomenon like horizontal gene transfer (HGT) might cause it to become dangerous.

Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transmission of DNA between different genomes. It is made possible in large part by the existence of mobile genetic elements, such as plasmids, transposons (“jumping genes”), and bacteria-infecting viruses (bacteriophages). These elements are transferred between organisms through different mechanisms, which in prokaryotes include transformation, conjugation, and transduction. The newly acquired DNA is incorporated into the genome of the recipient through either recombination or insertion.[7]

A proposed solution to battle HGT in the field of synthetic biology, are Xeno Nucleic Acids (XNA). The "X" in XNA stands for "xeno." Scientists use the xeno prefix to indicate that one of the ingredients typically found in the building blocks that make up RNA and DNA has been replaced by something different from what we find in nature – a xeno-organism.[8]

Because natural and xeno-organisms are supposed to use a different and very specific set of nucleotide binding proteins for replication and transcription, gene flow – whether horizontal or via sexual reproduction – cannot occur between the two realms of life. DNA cannot be interpreted by the XNA replication machinery and vice versa. A piece of XNA cannot, therefore, escape to wild-type organisms and be incorporated into their DNA genomes. Also the XNA organism cannot benefit from genes “discovered” by (natural) evolution through horizontal gene flow (but only through deliberate engineering, and XNA internal evolution). An additional increase in orthogonality and thus safety would be the deployment of several orthogonal systems, such as XNA with different non-canonical bases and rearranged codon assignment.[9]

If this orthogonal way of synthetic biology is adopted in the iGEM competition, it could lead to more (fundamental) advances in synthetic biology and biosafety.



References



[1] http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf
[2] http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=201388&Template=fungiYeast
[3] http://epa.gov/biotech_rule/pubs/fra/fra004.htm
[4] http://www.epa.gov/biotech_rule/pubs/fra/fra002.htm
[5] http://www.biosafety-europe.eu/d20public_300309.pdf
[6] https://intranet.tudelft.nl/live/pagina.jsp?id=39234121-1031-41f1-825a-636a79c41857&lang=en
[7] http://www.britannica.com/EBchecked/topic/1757605/horizontal-gene-transfer
[8] http://io9.com/5903221/meet-xna-the-first-synthetic-dna-that-evolves-like-the-real-thing
[9] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909387/