Team:SDU-Denmark/HumanPractices/biosafety

From 2012.igem.org

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For people working with genetic modified organisms, having biosafety as an important focus point is a must. This is because when working with organisms so small, that even the naked eye can’t see them it can still have a big impact on the researchers health, and in an even worse scenario, it can potentially affect the environment and the public safety in a negative way.</br>
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Working with genetic modified organisms requires an important focus on biosafety.  
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Because of this we have taken the biosafety questions very serious, and made a point of identifying all the dangerous situations that could occur in the laboratory. </br>
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Due to the potentially hazardous nature of genetically modified organisms we have taken necessary steps to identify the possible mistakes that can occur. This involves taking precautions, one of which is strictly working with nonpathogenic bacteria[i].  
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This involves taking necessary precautions, like only working with nonpathogenic bacteria[i]. </br>
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We have been working in a class 1 laboratory and have followed all safety rules, needed to work in such an environment. In doing this we have also abided the local Danish laws[ii] on biosafety and read the specific guidelines for our institute.
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We have been working in a class 1 laboratory and have followed all the safety rules needed to work in such an environment. In doing this we have also abided the local Danish laws[ii] on biosafety and read the specific guidelines for our institute.</br>
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One specific security guideline has been to reduce the risk of our biobrick giving the bacteria pathogenic properties, since this could pose an environmental problem.
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Another thing we found important concerning biosafety, is if our biobrick could give the bacteria pathogenic abilities. We have tried our best to prevent it from giving the bacteria any advantages, compared to naturally occurring bacteria, which could pose an environmental problem.</br>
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We also had two extra safety measures in the planning phase: </br>
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In our efforts to comply with this guideline we have done the following:
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The first safety measure we planned was a L-ramnose Kill-switch. This would be a safety measure in the completed product. The consumer would get a small bag of L-ramnose, (a sugar that the body can’t digest) with the product, that they could consume some time after drinking our yogurt with inulin producing bacteria. </br>
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The first safety measure we planned was a L-ramnose kill-switch. This would act as a safety measure in the final product. The consumer would be able to eat a small bag of L-ramnose (a sugar that the body can’t digest) which in turn would kill any genetically modified bacteria inhabiting the gut. It is relevant to note that the L-ramnose system would neither affect naturally occurring bacteria nor the human intestines.
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This would kill any of our constructed bacteria left in the gut and leave the naturally occurring bacteria unharmed, while not being toxic to humans. </br>
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Our other safety is a response to the way our construct will work, we need to have our genes in two plasmids, which will let the bacteria synthesize the inulin. Because of the two different plasmids we are able to make a paired double toxin/anti-toxin kill-switch (see the figure below). This will prevent some of the mutation that can happen in the gene, and at the same time prevent horizontal gene transfer. </br>
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We have located our genes in two different plasmids thereby allowing us to construct a dual toxin/antitoxin-system. The aim of this system is to prevent horizontal gene transfer by creating a cross-dependant toxin-antitoxin (TA) system.
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The way the kill-switch is going to work is by inserting a toxin and a non corresponding anti-toxin in both of our genes, so that the toxin and its corresponding anti-toxin are on different plasmids.</br>
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As seen in the figure above, the cell can only survive by keeping both plasmids. In the case of horizontal gene transfer the receiving bacteria will lack the needed antitoxin for survival. For the same reasons, in case of a frameshift mutation knocking out one of the plasmids, the bacteria will also die. Both of these constructs require the antitoxin to be located downstream from the toxin.
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This will hopefully prevent horizontal gene transfer by killing the new host and also prevent frameshift mutations from happening in the new host. </br>
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This will of course require that the anti-toxin is downstream from the toxin so that it won’t be able to lose the toxin without losing the anti-toxin.
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<h2>Would any of your project ideas raise safety issues in terms of researcher safety, public safety, or environmental safety?</h2> </br>
<h2>Would any of your project ideas raise safety issues in terms of researcher safety, public safety, or environmental safety?</h2> </br>
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We are working in a class 1 laboratory following all the lab rules. We are using nonpathogenic bacteria[i] and we are planning on adding different kinds of kill-switches.</br>
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As seen in the figure above, the cell can only survive by keeping both plasmids. In the case of horizontal gene transfer the receiving bacteria will lack the needed antitoxin for survival. For the same reasons, in case of a frameshift mutation knocking out one of the plasmids, the bacteria will also die. Both of these constructs require the antitoxin to be located downstream from the toxin.
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Another thing we see as safety preclusion is that the biobrick we are adding is a disadvantage for the bacteria, the biobrick makes the bacteria produce inulin out of its food source which slows down the grow rate of the bacteria giving it a disadvantage competing with other bacteria in the wild.
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<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? </h2> </br>
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? </h2> </br>
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We don’t see any safety issues in any of our biobricks. In our planning phase though, we have come up with an idea on how to prevent frameshift mutations from occurring in the plasmids and how to prevent horizontal gene transfer. </br>
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Our biobrick does not prove any obvious safety issues. As mentioned in the previous paragraph our construct has no evolutionary advantages. If any issues arise these will be documented in the registry.  
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This will be solved  through  a paired, double toxin/anti-toxin kill-switch.
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<h2>What does your local biosafety group think about your project? And is there any local laws?</h2> </br>
<h2>What does your local biosafety group think about your project? And is there any local laws?</h2> </br>
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Our local biosafety group is called “Arbejdsmiljøgruppen”, they are responsible for safety in the laboratory, both biological and work related. We talked with a representative from the group about our project, and she did not find any problems with our project, as long as we followed the safety rules of a class 1 laboratory. </br>
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Our local biosafety group is called “Arbejdsmiljøgruppen”. They are responsible for biological and practical laboratory safety. During discussions with a group representative we concluded that, as long as we followed the class 1 laboratory guidelines no safety concerns were evident. Furthermore we investigated local laws concerning working with genetically modified organisms “The Order on Gene-technology and Working Environment[ii]“, which in turn correlates with rules laid down by the European Union in the ”Directive on the Contained Use of Genetically Modified Micro-organisms”.
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We also looked into the local laws and found that the local law we had to follow is “Bekendtgørelsen om Genteknologi og Arbejdsmiljø[ii]” (eng. The Order on Gene-technology and Working Environment) of 2008, which follows the rules laid down by the European Union in 1990 in the ”Directive on the Contained Use of Genetically Modified Micro-organisms”.
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One of the safety measurements we are using it the paired, double toxin/anti-toxin kill-switch which we think should be a part of coming iGEM teams safety precautions.
One of the safety measurements we are using it the paired, double toxin/anti-toxin kill-switch which we think should be a part of coming iGEM teams safety precautions.
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<h3>Apendix </h3>
<h3>Apendix </h3>

Revision as of 16:15, 7 September 2012

iGEM TEAM ::: SDU-DENMARK courtesy of NIAID

Biosafety

Working with genetic modified organisms requires an important focus on biosafety. Due to the potentially hazardous nature of genetically modified organisms we have taken necessary steps to identify the possible mistakes that can occur. This involves taking precautions, one of which is strictly working with nonpathogenic bacteria[i]. We have been working in a class 1 laboratory and have followed all safety rules, needed to work in such an environment. In doing this we have also abided the local Danish laws[ii] on biosafety and read the specific guidelines for our institute. One specific security guideline has been to reduce the risk of our biobrick giving the bacteria pathogenic properties, since this could pose an environmental problem. In our efforts to comply with this guideline we have done the following: The first safety measure we planned was a L-ramnose kill-switch. This would act as a safety measure in the final product. The consumer would be able to eat a small bag of L-ramnose (a sugar that the body can’t digest) which in turn would kill any genetically modified bacteria inhabiting the gut. It is relevant to note that the L-ramnose system would neither affect naturally occurring bacteria nor the human intestines. We have located our genes in two different plasmids thereby allowing us to construct a dual toxin/antitoxin-system. The aim of this system is to prevent horizontal gene transfer by creating a cross-dependant toxin-antitoxin (TA) system. As seen in the figure above, the cell can only survive by keeping both plasmids. In the case of horizontal gene transfer the receiving bacteria will lack the needed antitoxin for survival. For the same reasons, in case of a frameshift mutation knocking out one of the plasmids, the bacteria will also die. Both of these constructs require the antitoxin to be located downstream from the toxin.

Would any of your project ideas raise safety issues in terms of researcher safety, public safety, or environmental safety?


As seen in the figure above, the cell can only survive by keeping both plasmids. In the case of horizontal gene transfer the receiving bacteria will lack the needed antitoxin for survival. For the same reasons, in case of a frameshift mutation knocking out one of the plasmids, the bacteria will also die. Both of these constructs require the antitoxin to be located downstream from the toxin.

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


Our biobrick does not prove any obvious safety issues. As mentioned in the previous paragraph our construct has no evolutionary advantages. If any issues arise these will be documented in the registry.

What does your local biosafety group think about your project? And is there any local laws?


Our local biosafety group is called “Arbejdsmiljøgruppen”. They are responsible for biological and practical laboratory safety. During discussions with a group representative we concluded that, as long as we followed the class 1 laboratory guidelines no safety concerns were evident. Furthermore we investigated local laws concerning working with genetically modified organisms “The Order on Gene-technology and Working Environment[ii]“, which in turn correlates with rules laid down by the European Union in the ”Directive on the Contained Use of Genetically Modified Micro-organisms”.

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 of the safety measurements we are using it the paired, double toxin/anti-toxin kill-switch which we think should be a part of coming iGEM teams safety precautions.

Apendix

Bacteria: E. coli Strains: TOP10 and XL gold
[i] link til apendix
[ii]link til https://www.retsinformation.dk/Forms/R0710.aspx?id=12325)

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