Team:Alberta/Safety

From 2011.igem.org

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            METHODOLOGY
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    </div>
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[[Image:TeamAlberta labelledflasks.jpg|220px|thumb|left|Neurospora is stored in clearly
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labelled flasks with sponge tops to prevent contamination]]
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<h2>Team Alberta iGEM Safety Proposal</h2>
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<div id=waste>
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[[Image:Alberta_Waste.jpg|280px|thumb|left|Clearly labelled waste disposal containers ensure
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proper removal of potentially hazardous materials]]
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</div>
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<div id=manual>
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[[Image:Manual.jpg|220px|thumb|right|Information about reagents and safety protocols
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are all found in an easily accessible binder]]
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</div>
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<html><div id="center-content" style="margin-top:150px;" class="</html>{{{class|}}}<html>"></html>
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<h1>Team Alberta iGEM Safety Proposal</h1>
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<div id="horiz-line"></div>
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Team Alberta recognizes the important role that safety plays in the
Team Alberta recognizes the important role that safety plays in the
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greater community.
greater community.
-
Please find below Team Alberta’s answers to the new, required iGEM
+
<br>
 +
 
 +
Please find below Team Alberta's answers to the new, required iGEM
safety questions.
safety questions.
-
<h1>1. Would the materials used in your project and/or your final
+
<h3 id=Section_1>1. Would the materials used in your project and/or your final
-
product pose:</h1>
+
product pose:</h3>
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<div id="horiz-line"></div>
+
-
<h2>a. Risks to the safety and health of team members or others in
+
<h4>a. Risks to the safety and health of team members or others in
-
the lab?</h2>
+
the lab?</h4>
-
The materials used in our project pose little to no risks to the
+
<div class=safety-img id=labelledflask>
 +
<img src="https://static.igem.org/mediawiki/2011/8/8a/TeamAlberta_labelledflasks.jpg">
 +
Neurospora is stored in clearly labelled flasks with sponge tops to prevent contamination
 +
</div>
 +
 
 +
<p>The materials used in our project pose little to no risks to the
safety and health of our team members or others in the lab and our
safety and health of our team members or others in the lab and our
-
final product poses no risk to these individuals.
+
final product poses no risk to these individuals.</p>
-
The organism that our group has genetically manipulated,
+
<br>
-
Neurospora crassa, is well-documented as being safe1. N. crassa is
+
 
 +
<p>The organism that our group has genetically manipulated,
 +
<i>Neurospora crassa</i>, is well-documented as being safe<sup>1</sup>. N. crassa is
a biosafety level 1 organism. Since 1941 the species has been used
a biosafety level 1 organism. Since 1941 the species has been used
extensively in laboratories resulting in the publication of thousands
extensively in laboratories resulting in the publication of thousands
of research papers. In none of these numerous publications has the
of research papers. In none of these numerous publications has the
-
Neurospora genus been implicated in causing disease in either animals
+
<i>Neurospora</i> genus been implicated in causing disease in either animals
-
or plants1-4.
+
or plants<sup>1-4</sup>.</p>
 +
 
 +
<br>
-
Neurospora’s minimal threat can largely be attributed to it being
+
<p><i>Neurospora's</i> minimal threat can largely be attributed to it being
-
an obligate aerobe. Unlike other species such as yeasts, Neurospora
+
an obligate aerobe. Unlike other species such as yeasts, <i>Neurospora</i>
is unable to grow in organs such as the gut or bladder, tissues, or
is unable to grow in organs such as the gut or bladder, tissues, or
-
systemically within an organism1. Furthermore, despite Neurospora
+
systemically within an organism<sup>1</sup>. Furthermore, despite <i>Neurospora</i>
being regarded by some as an allergen, medical literature generally
being regarded by some as an allergen, medical literature generally
-
fails to mention the genus5-8.
+
fails to mention the genus<sup>5-8</sup>.</p>
-
Our team acknowledges that though certain fungal species
+
<br>
 +
 
 +
<p>Our team acknowledges that though certain fungal species
themselves may not be pathogenic, they may produce dangerous
themselves may not be pathogenic, they may produce dangerous
toxins. Throughout our research into Neurospora our group has
toxins. Throughout our research into Neurospora our group has
not found any documentation of the species producing dangerous
not found any documentation of the species producing dangerous
-
mycotoxins or any dangerous secondary metabolites1. Given that
+
mycotoxins or any dangerous secondary metabolites<sup>1</sup>. Given that
Neurospora has had such a long history of living in close association
Neurospora has had such a long history of living in close association
with humans (please see below), it is a generally regarded as being
with humans (please see below), it is a generally regarded as being
 +
harmless.</p>
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harmless.
+
<div class=safety-img id=waste>
 +
<img src="https://static.igem.org/mediawiki/2011/2/25/Alberta_Waste.jpg">
 +
Clearly labelled waste disposal containers ensure proper removal of potentially hazardous materials
 +
<br>
-
It should be noted that there are still materials used in our
+
</div>
 +
 
 +
<p>It should be noted that there are still materials used in our
project that may potentially be hazardous. Our esterification procedure
project that may potentially be hazardous. Our esterification procedure
involves the use of strong chemicals and reagents, some of which have
involves the use of strong chemicals and reagents, some of which have
the potential to cause harm. These reagents are primarily volatile and
the potential to cause harm. These reagents are primarily volatile and
-
require careful handling and storage.
+
require careful handling and storage.</p>
 +
 
 +
<br>
-
As well, Hygromycin b, an antibiotic and antifungal agent that
+
<p>As well, Hygromycin b, an antibiotic and antifungal agent that
is used for selection, is toxic if inhaled. Care must be taken around
is used for selection, is toxic if inhaled. Care must be taken around
powdered or lyophilized Hygromycin B, and precaution should be taken
powdered or lyophilized Hygromycin B, and precaution should be taken
to cover up respiratory passageways, skin, and the eyes. However,
to cover up respiratory passageways, skin, and the eyes. However,
Hygromycin B is most commonly purchased in liquid form, and in liquid
Hygromycin B is most commonly purchased in liquid form, and in liquid
-
carries with it significantly less potential for accidental inhalation.
+
carries with it significantly less potential for accidental inhalation.</p>
-
<h2>b. Risks to the safety and health of the general public if
+
<h4>b. Risks to the safety and health of the general public if
-
released by design or accident?</h2>
+
released by design or accident?</h4>
-
Our organism poses no threat to the safety and health of the
+
<p>Our organism poses no threat to the safety and health of the
general public. Neurospora has a well-documented history of living in
general public. Neurospora has a well-documented history of living in
close association with humans. It has historically resided in a variety of
close association with humans. It has historically resided in a variety of
-
businesses including bakeries, lumber yards and plywood factories1;9-
+
businesses including bakeries, lumber yards and plywood factories<sup>1;9-
-
11. Growth has also been observed on the stubble of burnt sugar cane
+
11</sup>. Growth has also been observed on the stubble of burnt sugar cane
-
fields and along burnt railway tracks13. Thus, it poses no threat to the
+
fields and along burnt railway tracks<sup>13</sup>. Thus, it poses no threat to the
-
health and safety of those in its surroundings.
+
health and safety of those in its surroundings.</p>
-
<h2>c. Risks to environmental quality if released by design or
+
<h4>c. Risks to environmental quality if released by design or
-
accident?</h2>
+
accident?</h4>
-
As mentioned, N. crassa has a long history of living in close
+
<p>As mentioned, N. crassa has a long history of living in close
association with humans; however, these instances are largely
association with humans; however, these instances are largely
documented as having occurred in moist tropical or subtropical
documented as having occurred in moist tropical or subtropical
environments. Like many fungi, warm and moist is the favored climate
environments. Like many fungi, warm and moist is the favored climate
-
for Neurospora growth1. Thus, if our organism, WT or manipulated,
+
for Neurospora growth<sup>1</sup>. Thus, if our organism, WT or manipulated,
were to be released in our dry, temperate environment of Edmonton,
were to be released in our dry, temperate environment of Edmonton,
Alberta, Canada, with its bitterly harsh winters, we would expect its
Alberta, Canada, with its bitterly harsh winters, we would expect its
survival and environmental impact to be minimal. Even if it were to
survival and environmental impact to be minimal. Even if it were to
survive, we cannot see it affecting local ecosystems by any appreciable
survive, we cannot see it affecting local ecosystems by any appreciable
-
amount.
+
amount.</p>
-
Nonetheless, our alternative biodiesel has the potential to
+
<br>
 +
 
 +
<p>Nonetheless, our alternative biodiesel has the potential to
revolutionize economies throughout the world, as discussed in our
revolutionize economies throughout the world, as discussed in our
human practices component, and we must therefore regard the effects
human practices component, and we must therefore regard the effects
of environmental exposure to Neurospora in other climates. Were
of environmental exposure to Neurospora in other climates. Were
Neurospora to be released in other warmer climates it may readily
Neurospora to be released in other warmer climates it may readily
-
 
survive, creating its own niche within the environment. However, the
survive, creating its own niche within the environment. However, the
aforementioned nonpathogenicity of the genus results in this not being
aforementioned nonpathogenicity of the genus results in this not being
-
a source of alarm1-4.
+
a source of alarm<sup>1-4</sup>.</p>
-
Further, Team Alberta predicts that our manipulated strain
+
<br>
 +
 
 +
<p>Further, Team Alberta predicts that our manipulated strain
of Neurospora crassa would be disadvantaged to survive relative
of Neurospora crassa would be disadvantaged to survive relative
to WT in any environment; our genetic manipulation results in the
to WT in any environment; our genetic manipulation results in the
-
organism’s energy being diverted away from essential metabolic
+
organism's energy being diverted away from essential metabolic
functions, inhibiting organismal growth and manipulation. This puts it
functions, inhibiting organismal growth and manipulation. This puts it
-
at a disadvantage against natural competing fungi.
+
at a disadvantage against natural competing fungi.</p>
-
<h2>d. Risks to security through malicious misuse by individuals,
+
<h4>d. Risks to security through malicious misuse by individuals,
-
groups or states?</h2>
+
groups or states?</h4>
-
Unforeseen alteration of biopart functions may represent issues
+
<p>Unforeseen alteration of biopart functions may represent issues
of concern. However, in our case if one or several of our bioparts were
of concern. However, in our case if one or several of our bioparts were
changed to alter their function or stop working as intended, limited to
changed to alter their function or stop working as intended, limited to
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our organism would likely die or have a limited existence; if further
our organism would likely die or have a limited existence; if further
alterations to thioesterase genes were to prevent their function, then
alterations to thioesterase genes were to prevent their function, then
-
the organism may return to a more WT phenotype12.
+
the organism may return to a more WT phenotype<sup>12</sup>.</p>
 +
 
 +
<br>
-
The misuse of our bioconverter represents a potential threat
+
<p>The misuse of our bioconverter represents a potential threat
to safety. The esterification process requires heat and flammable
to safety. The esterification process requires heat and flammable
chemicals contained within a sealed vessel and thus the potential for
chemicals contained within a sealed vessel and thus the potential for
-
serious injury exists.
+
serious injury exists.</p>
-
<h1>2. If your response to any of the questions above is yes:</h1>
+
<h3 id=Section_2>2. If your response to any of the questions above is yes:</h3>
-
<div id="horiz-line"></div>
+
<h4>a. Explain how you addressed these issues in project design
-
<h2>a. Explain how you addressed these issues in project design
+
and while conducting laboratory work.</h4>
-
and while conducting laboratory work.</h2>
+
-
To deal with such issues our team greatly scrutinized all
+
<p>To deal with such issues our team greatly scrutinized all
steps within our procedure for potential hazards and subsequently
steps within our procedure for potential hazards and subsequently
collectively addressed all areas of concern. Please see the outline
collectively addressed all areas of concern. Please see the outline
-
below.
+
below.</p>
-
(esterification diagram goes here)
+
<br>
 +
 
 +
<img width=650px src="https://static.igem.org/mediawiki/2011/7/74/TeamAlbertaReagentsAndChemicals.png">
 +
 
 +
<br>
-
Our careful consideration of the potential safety concerns
+
<p>Our careful consideration of the potential safety concerns
associated with the completion of our project and our careful
associated with the completion of our project and our careful
documentation and safety training have allowed us to work both
documentation and safety training have allowed us to work both
 +
responsibly and cautiously, limiting the probability of injuries.</p>
-
responsibly and cautiously, limiting the probability of injuries.
+
<br>
-
All MSDS data sheets were followed in working with strong acids,
+
<p>All MSDS data sheets were followed in working with strong acids,
bases, volatile chemicals, or otherwise potentially harmful reagents. All
bases, volatile chemicals, or otherwise potentially harmful reagents. All
antibiotics and antifungals were stored cold and in sealed containers,
antibiotics and antifungals were stored cold and in sealed containers,
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and were designed to eliminate all possibility of heating closed
and were designed to eliminate all possibility of heating closed
containers. (For details on the safe handling of Hygromycin b, please
containers. (For details on the safe handling of Hygromycin b, please
-
see question 3).
+
see question 3).</p>
-
Safety issues arising from the completion of our bioreactor were
+
<br>
 +
 
 +
<p>Safety issues arising from the completion of our bioreactor were
addressed in the stages of its design. Several important safeguards
addressed in the stages of its design. Several important safeguards
were incorporated. For example, our bioconverter is designed to
were incorporated. For example, our bioconverter is designed to
automatically turn off upon exceeding the recommended temperature
automatically turn off upon exceeding the recommended temperature
-
and pressure past specific margins.
+
and pressure past specific margins.</p>
-
<h2>b. Describe and document safety, security, health and/or
+
<h4>b. Describe and document safety, security, health and/or
-
environmental issues as you submit your parts to the Registry.</h2>
+
environmental issues as you submit your parts to the Registry.</h4>
-
In submitting parts to the registry, Team Alberta has actively
+
<p>In submitting parts to the registry, Team Alberta has actively
undertaken the practice of describing and documenting any safety,
undertaken the practice of describing and documenting any safety,
security, health and/or environmental issues of our parts as they are
security, health and/or environmental issues of our parts as they are
submitted to the registry. None of our parts confer any pathogenicity
submitted to the registry. None of our parts confer any pathogenicity
or otherwise harmful effects upon either Neurospora crassa or
or otherwise harmful effects upon either Neurospora crassa or
-
Escherichia coli.
+
Escherichia coli.</p>
-
One of our parts will confer Hygromycin B resistance to
+
<br>
 +
 
 +
<p>One of our parts will confer Hygromycin B resistance to
Neurospora crassa, and such strains that contain this part should be
Neurospora crassa, and such strains that contain this part should be
-
noted as being resistant to that particular antifungal agent.
+
noted as being resistant to that particular antifungal agent.</p>
-
<h1>3. Under what biosafety provisions will / do you operate?</h1>
+
<h3 id=Section_3>3. Under what biosafety provisions will / do you operate?</h3>
-
<div id="horiz-line"></div>
+
-
<h2>a. Does your institution have its own biosafety rules and if so
+
<h4>a. Does your institution have its own biosafety rules and if so
-
what are they? Provide a link to them online if possible.</h2>
+
what are they? Provide a link to them online if possible.</h4>
-
Yes, the University of Alberta contains a specified set of
+
<p>Yes, the University of Alberta contains a specified set of
Biosafety Rules that are outlined within the Biosafety Manual that is
Biosafety Rules that are outlined within the Biosafety Manual that is
published by the Office of Environmental Health and Safety. A link to
published by the Office of Environmental Health and Safety. A link to
-
this valuable resource can be found here:
+
his valuable resource can be found here:
-
http://www.ehs.ualberta.ca/en/EHSDivisions/~/media/
+
<a href="http://www.ehs.ualberta.ca/en/EHSDivisions/~/media/8C72A3F626FB47B6BD70EC79C94CD1CE.ashx">
-
8C72A3F626FB47B6BD70EC79C94CD1CE.ashx
+
http://www.ehs.ualberta.ca/en/EHSDivisions/~/media/8C72A3F626FB47B6BD70EC79C94CD1CE.ashx</a></p>
-
<h2>b. Does your institution have an Institutional Biosafety
+
<h4>b. Does your institution have an Institutional Biosafety
Committee or equivalent group? If yes, have you discussed
Committee or equivalent group? If yes, have you discussed
your project with them? Describe any concerns or changes
your project with them? Describe any concerns or changes
-
that were made based on this review.</h2>
+
that were made based on this review.</h4>
-
Team Alberta consulted the University of Alberta’s Office of
+
<p>Team Alberta consulted the University of Alberta's Office of
Environmental Health and Safety throughout the planning of our
Environmental Health and Safety throughout the planning of our
project. The Biosafety Division of this office provides both technical
project. The Biosafety Division of this office provides both technical
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a safe working and learning environment for both staff and students.
a safe working and learning environment for both staff and students.
In addition, the division also monitors compliance with federal and
In addition, the division also monitors compliance with federal and
-
provincial legislation16.
+
provincial legislation<sup>16</sup>.</p>
 +
 
 +
<br>
-
Our team submitted a written overview of the relevant safety
+
<p>Our team submitted a written overview of the relevant safety
considerations associated with our project to this office. Upon
considerations associated with our project to this office. Upon
perusal of this document, the Biosafety Officer provided us with
perusal of this document, the Biosafety Officer provided us with
recommendations to fully ensure that our project met all biosafety
recommendations to fully ensure that our project met all biosafety
-
requirements. Please see the Biosafety Officer’s recommendations
+
requirements. Please see the Biosafety Officer's recommendations
-
below and how we met each of them:
+
below and how we met each of them:</p>
-
i) It was recommended that if our lab were to grow N. Crassa beyond
+
<ol style="list-style-type:lower-roman">
 +
<li>
 +
    <p>It was recommended that if our lab were to grow N. Crassa beyond
a 10L culture volume that we would have to obtain permission from
a 10L culture volume that we would have to obtain permission from
the federal government, as such a culture would be considered large
the federal government, as such a culture would be considered large
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production of cultures beyond a 9.5L volume. In addition, it was
production of cultures beyond a 9.5L volume. In addition, it was
recommended that our lab prepare a Biological Spill Remediation kit
recommended that our lab prepare a Biological Spill Remediation kit
-
according to the Standard Operating Protocols (SOP) of the university.
+
according to the Standard Operating Protocols (SOP) of the university.</p>
-
To avoid having to proceed with a lengthy governmental registration
+
<p>To avoid having to proceed with a lengthy governmental registration
process in the relatively short timeframe of the iGEM competition, our
process in the relatively short timeframe of the iGEM competition, our
lab will ensure that no culture we prepare will be larger than 9.5L.
lab will ensure that no culture we prepare will be larger than 9.5L.
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than 1.5L. As well, the members of our lab assembled the materials
than 1.5L. As well, the members of our lab assembled the materials
required for a Biological Spill Remediation kit, which will allow for the
required for a Biological Spill Remediation kit, which will allow for the
-
safe and efficient cleanup of any potential spills.
+
safe and efficient cleanup of any potential spills.</p>
-
ii) The Biosafety officer recommended that our lab ensure all cultures
+
</li>
-
of N. crassa be rendered inert prior to disposal.
+
<li>
 +
<p>The Biosafety officer recommended that our lab ensure all cultures
 +
of N. crassa be rendered inert prior to disposal.</p>
-
The members of our lab have already been adhering to this practice
+
<p>The members of our lab have already been adhering to this practice
by treating all cultures of N. crassa with a household bleach mixture
by treating all cultures of N. crassa with a household bleach mixture
for a minimum of one hour prior to disposal. Our bleach mixture
for a minimum of one hour prior to disposal. Our bleach mixture
contains a minimum of one part bleach to three parts culture, which is
contains a minimum of one part bleach to three parts culture, which is
consistent with the guidelines outlined by the Biosafety Division of the
consistent with the guidelines outlined by the Biosafety Division of the
 +
Environmental Health and Safety Office.</p>
 +
</li>
-
Environmental Health and Safety Office.
+
<li>
-
 
+
<p>The Biosafety Officer recommended that all individuals working
-
iii) The Biosafety Officer recommended that all individuals working
+
within our lab should wear personal protective equipment (PPE),
within our lab should wear personal protective equipment (PPE),
comprised of fully-fastened laboratory coats or gowns, disposable
comprised of fully-fastened laboratory coats or gowns, disposable
-
gloves, safety glasses, closed-toe shoes and floor-length pants.
+
gloves, safety glasses, closed-toe shoes and floor-length pants.</p>
-
The members of our lab have been adhering to this common
+
<p>The members of our lab have been adhering to this common
-
laboratory practice since the very beginning.
+
laboratory practice since the very beginning.</p>
 +
</li>
-
iv) Due to the use of the antibiotic and antifungal Hygromycin b, the
+
<li>
 +
<p>Due to the use of the antibiotic and antifungal Hygromycin b, the
Biosafety Officer recommended that all work with this antibiotic be
Biosafety Officer recommended that all work with this antibiotic be
carried out in a fume hood. He further recommended that members
carried out in a fume hood. He further recommended that members
of our team coming in contact with this antibiotic be fit-tested for N95
of our team coming in contact with this antibiotic be fit-tested for N95
respirators in the event that this antibiotic cannot be handled within
respirators in the event that this antibiotic cannot be handled within
-
the fume hood.
+
the fume hood.</p>
-
The members of our team who are not fit-tested for N95 respirators
+
<p>The members of our team who are not fit-tested for N95 respirators
will not work with Hygromycin b. The two members of our team that
will not work with Hygromycin b. The two members of our team that
will work with this antibiotic have been fit-tested with N95 respirators
will work with this antibiotic have been fit-tested with N95 respirators
so that they may safely handle this compound, regardless of its form.
so that they may safely handle this compound, regardless of its form.
-
All work with Hygromycin b will be carried out within a fumehood.
+
All work with Hygromycin b will be carried out within a fumehood.</p>
 +
</li>
 +
</ol>
-
<h2>c. Will / did you receive any biosafety and/or lab training
+
<h4>c. Will / did you receive any biosafety and/or lab training
-
before beginning your project? If so, describe this training.</h2>
+
before beginning your project? If so, describe this training.</h4>
 +
 
 +
<div class=safety-img id=manual>
 +
<img src="https://static.igem.org/mediawiki/2011/c/c7/Manual.jpg">
 +
Information about reagents and safety protocols are all found in an easily accessible binder
 +
</div>
-
The members of our lab have all had variable levels of laboratory
+
<p>The members of our lab have all had variable levels of laboratory
experience upon beginning the summer. Though most members
experience upon beginning the summer. Though most members
had some level of biosafety training from previous lab experiences,
had some level of biosafety training from previous lab experiences,
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on new safety procedures as our project developed. For example, upon
on new safety procedures as our project developed. For example, upon
beginning work with our organism, N. crassa, all lab members were
beginning work with our organism, N. crassa, all lab members were
-
briefed on its safe disposal.
+
briefed on its safe disposal.</p>
-
<h2>d. Does your country have national biosafety regulations or
+
<h4>d. Does your country have national biosafety regulations or
-
guidelines? If so, provide a link to them online if possible.</h2>
+
guidelines? If so, provide a link to them online if possible.</h4>
-
Yes, the Public Health Agency of Canada outlines national
+
<p>Yes, the Public Health Agency of Canada outlines national
biosafety guidelines. Specifically, the Laboratory Biosafety and
biosafety guidelines. Specifically, the Laboratory Biosafety and
Biosecurity Division of this agency is responsible for publishing
Biosecurity Division of this agency is responsible for publishing
-
 
biosafety regulations. A quick synopsis of these guidelines may be
biosafety regulations. A quick synopsis of these guidelines may be
found here:
found here:
-
http://www.phac-aspc.gc.ca/lab-bio/regul/index-eng.php.
+
<a href="http://www.phac-aspc.gc.ca/lab-bio/regul/index-eng.php">http://www.phac-aspc.gc.ca/lab-bio/regul/index-eng.php</a></p>
-
<h1>4.Optional Question: Do you have other ideas on how to deal
+
<h3 id=Section_4>4.Optional Question: Do you have other ideas on how to deal
with safety or security issues that could be useful for future
with safety or security issues that could be useful for future
iGEM competitions? How could parts, devices and systems be
iGEM competitions? How could parts, devices and systems be
-
made even safer through biosafety engineering?</h1>
+
made even safer through biosafety engineering?</h3>
-
<div id="horiz-line"></div>
+
-
In order to motivate future iGEM teams to further emphasize
+
<p>In order to motivate future iGEM teams to further emphasize
safety in their daily laboratory practices, we propose that each team
safety in their daily laboratory practices, we propose that each team
completes a detailed safety report for a minimal medal requirement.
completes a detailed safety report for a minimal medal requirement.
Line 330: Line 360:
immense rewards in their future work, iGEM or otherwise. Moreover,
immense rewards in their future work, iGEM or otherwise. Moreover,
this would encourage teams to be more creative with respects to
this would encourage teams to be more creative with respects to
-
synthetic biology and genetic engineering.
+
synthetic biology and genetic engineering.</p>
 +
 
 +
<br>
-
Our team recognizes that biosafety engineering has the potential
+
<p>Our team recognizes that biosafety engineering has the potential
to make many devices and systems safer. For example, essential
to make many devices and systems safer. For example, essential
gene knockouts can be created through partial or full amino acid
gene knockouts can be created through partial or full amino acid
Line 342: Line 374:
or negatively respond to varying wavelengths of light and electrical
or negatively respond to varying wavelengths of light and electrical
stimuli. All this and more should be taken into account when designing
stimuli. All this and more should be taken into account when designing
-
any organic circuit.
+
any organic circuit.</p>
-
References
+
-
     <h1>References</h1>
+
     <h3 id=References>References</h3>
-
    <div id="horiz-line"></div>
+
-
1. Perkins DD and Davis RH: <b>Evidence for Safety of Neurospora
+
<ol>
 +
    <li>
 +
Perkins DD and Davis RH: <b>Evidence for Safety of Neurospora
Species for Academic and Commercial Use.</b><i> Applied and
Species for Academic and Commercial Use.</b><i> Applied and
Environmental Microbiology </i>2006, 66 (12): 5107-5109.
Environmental Microbiology </i>2006, 66 (12): 5107-5109.
 +
    </li>
-
2. Davis RH: <b>Neurospora: contributions of a model organism. </b><i>Oxford
+
    <li>
 +
Davis RH: <b>Neurospora: contributions of a model organism. </b><i>Oxford
University Press</i> US; 2000.
University Press</i> US; 2000.
 +
    </li>
-
3. Perkins DD: Neurospora: <b>the organism behind the molecular
+
    <li>
 +
Perkins DD: Neurospora: <b>the organism behind the molecular
revolution. </b><i>Genetics </i>1992, 130: 687-701.
revolution. </b><i>Genetics </i>1992, 130: 687-701.
 +
    </li>
-
4. Perkins DD: <b> Neurospora genetics at the turn of the century.
+
    <li>
 +
Perkins DD: <b> Neurospora genetics at the turn of the century.
</b><i>Fungal Genetics Newsletter</i> 2000, 47: 83-88.
</b><i>Fungal Genetics Newsletter</i> 2000, 47: 83-88.
 +
    </li>
-
5. Frank MM, Austen KF, Claman HN, Unanue ER: <b>Samter’s
+
    <li>
 +
Frank MM, Austen KF, Claman HN, Unanue ER: <b>Samterâs
immunological diseases, 5th ed. </b><i> Little, Brown & Co</i> US; 1995.
immunological diseases, 5th ed. </b><i> Little, Brown & Co</i> US; 1995.
 +
    </li>
-
6. Kay AB: <b>Allergy and allergic diseases. </b><i> Blackwell</i> US; 1997.
+
    <li>
 +
Kay AB: <b>Allergy and allergic diseases. </b><i> Blackwell</i> US; 1997.
 +
    </li>
-
7. Middleton E, Reed CE, Ellis EF, Adkinson, NF, Yunginger, Busse,
+
    <li>
 +
Middleton E, Reed CE, Ellis EF, Adkinson, NF, Yunginger, Busse,
WW: <b>Allergy: principles and practice, 5th ed. </b><i> Mosby </i>US; 1998.
WW: <b>Allergy: principles and practice, 5th ed. </b><i> Mosby </i>US; 1998.
 +
    </li>
-
8. Patterson R, Grammer LC, Greenberger PA: <b>Allergic diseases:
+
    <li>
 +
Patterson R, Grammer LC, Greenberger PA: <b>Allergic diseases:
diagnosis and management, 5th ed. </b><i> Lippncott-Raven </i> US; 1997.
diagnosis and management, 5th ed. </b><i> Lippncott-Raven </i> US; 1997.
 +
    </li>
-
9. Shear CL, Dodge BO: <b>Life histories and heterothallism of the
+
    <li>
 +
Shear CL, Dodge BO: <b>Life histories and heterothallism of the
red bread-mold fungi of the Monilia sitophila group. </b><i>Journal
red bread-mold fungi of the Monilia sitophila group. </b><i>Journal
Agricultural Research </i>1927, 34: 1019-1042.
Agricultural Research </i>1927, 34: 1019-1042.
 +
    </li>
-
10. Yassin S, Wheals A: <b>Neurospora species in bakeries. </b><i>Journal
+
    <li>
 +
Yassin S, Wheals A: <b>Neurospora species in bakeries. </b><i>Journal
Applied Bacteriology </i>1992, 72: 337-380.
Applied Bacteriology </i>1992, 72: 337-380.
 +
    </li>
-
11. Shaw DE: <b>Honeybees collecting Neurospora spores from
+
    <li>
 +
Shaw DE: <b>Honeybees collecting Neurospora spores from
steam Pinus logs in Queensland. </b><i> Mycologist </i>1993, 7: 182-185.
steam Pinus logs in Queensland. </b><i> Mycologist </i>1993, 7: 182-185.
 +
    </li>
-
12. Nelson DL, Cox MM: <b>Lehninger Principles of Biochemistry.</b><i> W.H
+
    <li>
 +
Nelson DL, Cox MM: <b>Lehninger Principles of Biochemistry.</b><i> W.H
Freeman </i>US; 2009.
Freeman </i>US; 2009.
 +
    </li>
-
13. <b>iGEM website:</b><i> https://2011.igem.org/Safety </i>
+
    <li>
 +
<b>iGEM website:</b><i> https://2011.igem.org/Safety </i>
 +
    </li>
-
14.
+
    <li>
-
<b>Hygromycin
+
<b>Hygromycin material and safety data sheet: </b><br><i>
-
material
+
-
and
+
-
safety
+
-
data
+
-
sheet: </b><i>
+
http://www.invivogen.com/MSDS/HygromycinB_solution_v4_MSDS.pdf</i>
http://www.invivogen.com/MSDS/HygromycinB_solution_v4_MSDS.pdf</i>
 +
    </li>
-
15. Kafer E, Luk D: <b>Sensitivity of bleomycin and hydrogen
+
    <li>
 +
Kafer E, Luk D: <b>Sensitivity of bleomycin and hydrogen
peroxide of DNA repair-defective mutants in Neurospora
peroxide of DNA repair-defective mutants in Neurospora
crassa. </b><i>Mutant Research</i> 1989, 217(1): 75-81.
crassa. </b><i>Mutant Research</i> 1989, 217(1): 75-81.
 +
    </li>
-
16. <b>University of Alberta Environmental Health and Safety website:</b><i>
+
    <li>
 +
<b>University of Alberta Environmental Health and Safety website:</b><i>
http://www.ehs.ualberta.ca/ </i>
http://www.ehs.ualberta.ca/ </i>
 +
    </li>
 +
</ol>
 +
    </div>
 +
</div>
-
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+
</html>
-
%
+
-
%
+
-
%
+
-
%
+
-
%
+
-
%
+
-
%
+
-
%
+
-
 
+
-
 
+
-
<h1>Team Alberta iGEM Safety Proposal</h1>
+
-
<div id="horiz-line"></div>
+
-
 
+
-
<p> Team Alberta recognizes the important role that safety plays in the completion of any scientific undertaking. Our
+
-
team members are fully committed to not only ensuring the safety of those within our lab but also addressing any potential risks that our project may pose to the greater community. </p>
+
-
 
+
-
 
+
-
<h1>1. Safety</h1>
+
-
<div id="horiz-line"></div>
+
-
 
+
-
<h2>1.1 Neurospora crassa</h2>
+
-
 
+
-
<p> It is well documented that the organism that our group plans to genetically manipulate, [[Neurospora crassa]], is safe<sup>1</sup>. Since 1941 the species has been used extensively in laboratories resulting in the publishing of thousands of research papers. In none of these numerous publications has the <i>Neurospora</i> genus been implicated in causing disease in either animals or plants<sup>1-4</sup>. </p>
+
-
 
+
-
<p><i>Neurospora’s</i> minimal threat can largely be attributed to it being an obligate aerobe. Resultantly, unlike other species such as yeasts, <i>Neurospora</i> is unable to grow in organs such as the gut or bladder, tissues, or systemically within an organism<sup>1</sup>. Furthermore, despite <i>Neurospora</i> being regarded by some as an allergen, medical literature generally fails to mention the genus<sup>5-8</sup>. </p>
+
-
 
+
-
<p>Our team acknowledges that though certain fungal species themselves may not be pathogenic, they may produce dangerous toxins. Throughout our extensive research into <i>Neurospora</i> our group has not found documentation of the species producing dangerous mycotoxins or any dangerous secondary metabolites<sup>1</sup>. Given the <i>Neurospora</i> has had such a long history of living in close association with humans (please see below) the aforementioned facts are even moreso compelling<sup>1</sup>.</p>
+
-
 
+
-
<h2>1.2 Reagents and Chemicals</h2>
+
-
 
+
-
 
+
-
<p>In light of our procedure involving the use of many reagents and chemicals, each of our team members has received safety training (ex. WHMIS, etc.) on each of the materials we will be using. Moreover, data sheets for each of these materials are stored in an organized binder that is readily accessible to each team member. </p>
+
-
 
+
-
<p>Our overall experimental procedure involves many steps. Most notably, the esterification portion of our procedure involves the greatest use of chemicals and reagents. We have therefore greatly scrutinized all steps within this procedure for potential hazards and have appropriately addressed all concerns (<i>please see the outline below</i>). </p>
+
-
 
+
-
<br>
+
-
[[Image:TeamAlbertaReagentsAndChemicals.png|500px]]
+
-
 
+
-
 
+
-
<h2>1.3 Environmental Exposure</h2>
+
-
 
+
-
<p>Effects of unforeseen release of <i>Neurospora crassa</i> into the environment
+
-
must be considered. We asked ourselves what would happen if either our WT or
+
-
manipulated organism were to be released into the environment. </p>
+
-
 
+
-
<p><i>Neurospora</i> has a well-documented history of living in close association
+
-
with humans. It is commonly regarded as having resided in a variety of
+
-
businesses including bakeries, lumber yards and plywood factories1;<sup>9-11</sup>. Growth
+
-
has also been observed on the stuble of burnt sugar cane fields and along burnt
+
-
railway tracks<sup>13</sup>. However, these instances are largely documented as having
+
-
occurred in moist tropical or subtropical environments, the favored climate for
+
-
<i>Neurospora</i> growth<sup>1</sup>. Thus, if our organism, WT or manipulated, were to be
+
-
released in our dry, temperate environment, [[Edmonton, Alberta, Canada]], with its
+
-
bitterly harsh winters, we would expect its survival and therefore impact to be
+
-
minimal. </p>
+
-
 
+
-
<p>Nonetheless, as we discussed in the [[human practices]] component of our
+
-
project, our alternative biodiesel has the potential to revolutionize economies
+
-
throughout the world and we must therefore regard the effects of environmental
+
-
exposure to <i>Neurospora</i> in other climates. Were <i>Neurospora</i> to be released in
+
-
other warmer climates it may readily survive, creating its own niche within the
+
-
environment. The aforementioned nonpathogenicity of the genus results in this not being a source of alarm<sup>1-4</sup>. </p>
+
-
 
+
-
<p>Team Alberta further predicts that our manipulated strain of <i>Neurospora
+
-
crassa</i> would be disadvantaged to survive relative to WT in any environment: our
+
-
[[genetic manipulation]] results in the organism’s energy being diverted away from
+
-
other essential functions, inhibiting organismal growth and manipulation. </p>
+
-
 
+
-
<h2>1.4 Biopart Malfunction</h2>
+
-
 
+
-
<p>Unforeseen alteration of biopart functions may represent issues of
+
-
concern. However, in our case if one or several of our bioparts were to change
+
-
their function or stop working as intended, limited safety issues would arise.
+
-
Our knockout of the FAD gene results in there being limited potential for its
+
-
mutation and subsequent alteration of function. Further, our manipulation of
+
-
thioesterases similarly represents limited safety concerns due to their prevalence
+
-
in all organisms. If mutations were to occur in thioesterase genes and result
+
-
in overproduction, our organism would likely die or have a limited existence; if
+
-
mutation to thioesterase genes were to prevent its function, then the organism
+
-
may return to a more WT phenotype<sup>12</sup>.</p>
+
-
 
+
-
<h2>1.5 Device Malfunction</h2>
+
-
 
+
-
<p>The malfunction of our [[bioconverter]] represents a potential threat to safety.
+
-
The esterification process requires heat and flammable chemicals contained
+
-
within a sealed vessel and thus the potential for serious injury undoubtedly
+
-
exists. We addressed these areas of concern in our [[product design]] by
+
-
incorporating various safeguards. For example, our bioconverter is designed to
+
-
automatically turn off upon exceeding the recommended temperature and
+
-
pressure past specific margins.</p>
+
-
 
+
-
 
+
-
<h2>1.6 Cumulative Risk Assessment</h2>
+
-
 
+
-
<center><b>Risk = Hazards x Probability<sup>13</sup> </b></center>
+
-
 
+
-
<h2>Hazards</h2>
+
-
 
+
-
<p>Any of the above mentioned areas of concern represent potential hazards
+
-
that may be associated with our project. Throughout our project’s design and
+
-
continued development, these were continually addressed and limited, where
+
-
possible.</p>
+
-
 
+
-
<h2>Probability</h2>
+
-
 
+
-
<p>The probability of our project resulting in any harm to members of our lab,
+
-
    the community, or the environment is very low. This minimal probability can be
+
-
    attributed to our team’s careful consideration of the potential safety concerns
+
-
    associated with the completion of our project; our careful documentation and
+
-
    safety training have allowed us to work both responsibly and cautiously thus
+
-
    limiting the probability of injuries. Of course, if these practices were to subside,
+
-
    the probability of injury would proportionally increase. </p>
+
-
 
+
-
    <p>As mentioned before, our team plans to develop a contained [[bioconverter]]
+
-
    within which all the processes needed to carry out the production of our
+
-
    alternative biodiesel are to be carried out; our team further aspires to scale-up
+
-
    this device for industrial production. Therefore, our project does not require the
+
-
    exposure or release of our engineered organism to people or the environment
+
-
    further limiting the probability of unfavorable events.</p>
+
-
 
+
-
    <h1>2. Documentation and management of safety issues</h1>
+
-
    <div id="horiz-line"></div>
+
-
 
+
-
    <h2>2.1 Safe Handling of Biobrick Parts and Devices</h2>
+
-
 
+
-
 
+
-
    <p>None of the [[genetic parts]] or devices that we have used or made this year
+
-
    raise any safety issues with the exception of our inserting a [[Hygromycin b resistance]] gene. The most predominant threat that this component possesses
+
-
    stems from our daily use of Hygromycin b in selection procedures. Hygromycin b
+
-
    is listed as potentially being fatal if absorbed through the skin or if swallowed. In
+
-
    addition, it is listed as being a hazard for birth defects, eye irritation, and
+
-
    respiratory tract irritation<sup>14</sup>. Our team diligently handled this area of concern by
+
-
    always wearing lab coats, safety goggles, and surgical masks when working with
+
-
    this potent antibiotic. Further, when our genetic parts are assembled into
+
-
    devices, no additional areas of concern arise. </p>
+
-
 
+
-
    <p>It should also be noted environmental exposure of our Hygromycin b
+
-
    resistant strain does not pose a significant threat as our organism remains
+
-
    sensitize to other antifungal treatments such as Bleomycin<sup>15</sup>.</p>
+
-
 
+
-
    <h2>2.2 Registry Documentation</h2>
+
-
 
+
-
    <p>The potential safety issues arising from inserting a [[Hygromycin b
+
-
    resistance]] gene will be carefully documented when our created part is submitted
+
-
    to the registry. We plan to outline the aforementioned hazards and proper
+
-
    handling procedures in our submission.</p>
+
-
 
+
-
    <h2>2.3 Application to other teams</h2>
+
-
 
+
-
    <p>Team Alberta feels that the best way that other teams can learn from our
+
-
    experiences with Hygromycin b and engineering Hygromycin b resistance is from
+
-
    the careful documentation of our work. As previously mentioned, Team Alberta
+
-
    intends to outline the potential hazards associated with Hygromycin b exposure
+
-
    and procedures for its proper handling in our registry submission. This will afford
+
-
    future iGEM teams ease of access to information in determining how to safely
+
-
    handle the potent antibiotic and subsequently resistant strains.</p>
+
-
 
+
-
    <h1>3. Project Evaluation by University of Alberta Environmental Health and Safety</h1>
+
-
    <div id="horiz-line"></div>
+
-
 
+
-
    <p>Team Alberta consulted the University of Alberta’s Office of Environmental
+
-
    Health and Safety throughout the planning of our project. The Biosafety Division
+
-
    of this office provides both technical expertise and support to labs throughout
+
-
    campus and thus ensures a safe working and learning environment for both staff
+
-
    and students. In addition, the division also monitors compliance with federal and
+
-
    provincial legislation<sup>16</sup>. </p>
+
-
 
+
-
    <p>We have currently submitted a written overview of the relevant safety
+
-
    considerations associated with our project and we are patiently awaiting any final
+
-
    feedback that the Biosafety Officer may provide us with. Please check back
+
-
    shortly for an update.</p>
+
-
 
+
-
    <h1>4. Safety Considerations for Future iGEM Competitions</h1>
+
-
    <div id="horiz-line"></div>
+
-
 
+
-
    <p>In order to motivate future iGEM teams to increasingly emphasize safety
+
-
    in their daily laboratory practices, we propose that each team completes a
+
-
    detailed safety report for a minimal medal requirement. </p>
+
-
 
+
-
    <p>Our team recognizes that biosafety engineering has the potential to make
+
-
    many devices and systems safer. For example, knockouts may be created
+
-
    through partial or full deletions as oppose to single nucleotide alterations that
+
-
    are susceptible to mutation, auxtotrophic stains may be created, or antibiotic
+
-
    resistance may be removed. In our project, we are crossing out extraneous
+
-
    basta resistance found in mus strains from our final organism. </p>
+
-
 
+
-
    <p>Bearing in mind the increasing importance of safety engineering, Team
+
-
    Alberta further proposes that future iGEM competitions require teams to engineer
+
-
    their parts to have several safeguards in order to achieve a gold medal. Such
+
-
    components being medal requirements, we feel that it would increasingly
+
-
    motivate iGEM participants to more actively address potential safety issues in
+
-
    their future work, iGEM or otherwise. Moreover, this would encourage teams to
+
-
    be more creative with respects to organismal engineering.</p>
+
-
 
+
-
    <h1>References</h1>
+
-
    <div id="horiz-line"></div>
+
-
1. Perkins DD and Davis RH:  <b>Evidence for Safety of Neurospora Species for Academic and Commercial Use.</b> <i>Applied and Environmental Microbiology</i> 2006, <b>66</b> (12): 5107-5109.
+
-
 
+
-
2. Davis RH: <i>Neurospora: contributions of a model organism.</i> Oxford University Press US; 2000.
+
-
 
+
-
3. Perkins DD: <b>Neurospora: the organism behind the molecular revolution.</b> <i>Genetics</i> 1992, <b>130</b>: 687-701.
+
-
 
+
-
4. Perkins DD: <b>Neurospora genetics at the turn of the century</b>. <i>Fungal Genetics Newsletter</i> 2000, <b>47</b>: 83-88.
+
-
 
+
-
5. Frank MM, Austen KF, Claman HN, Unanue ER: <i>Samter’s immunological diseases, 5<sup>th</sup> ed.</i> Little, Brown & Co US; 1995.
+
-
 
+
-
6. Kay AB: <i>Allergy and allergic diseases.</i> Blackwell US; 1997.
+
-
 
+
-
7. Middleton E, Reed CE, Ellis EF, Adkinson, NF, Yunginger, Busse, WW: <i>Allergy: principles and practice, 5<sup>th</sup> ed.</i> Mosby US; 1998.
+
-
 
+
-
8. Patterson R, Grammer LC, Greenberger PA: <i>Allergic diseases: diagnosis and management, 5<sup>th</sup> ed.</i> Lippncott-Raven US; 1997.
+
-
 
+
-
9. Shear CL, Dodge BO: <b>Life histories and heterothallism of the red bread-mold fungi of the Monilia sitophila group.</b> <i>Journal Agricultural Research</i> 1927, <b>34</b>: 1019-1042.
+
-
 
+
-
10. Yassin S, Wheals A: <b>Neurospora species in bakeries.</b> <i>Journal Applied Bacteriology</i> 1992, <b>72</b>: 337-380.
+
-
 
+
-
11. Shaw DE: <b>Honeybees collecting Neurospora spores from steam Pinus logs in Queensland.</b> <i>Mycologist</i> 1993, <b>7</b>: 182-185.
+
-
 
+
-
12.  Nelson DL, Cox MM: <i>Lehninger Principles of Biochemistry.</i> W.H Freeman US; 2009.
+
-
 
+
-
13. iGEM website: https://2011.igem.org/Safety
+
-
 
+
-
14. Hygromycin material and safety data sheet: http://www.invivogen.com/MSDS/
+
-
HygromycinB_solution_v4_MSDS.pdf
+
-
 
+
-
15. Kafer E, Luk D: <b>Sensitivity of bleomycin and hydrogen peroxide of DNA repair-defective mutants in Neurospora crassa.</b> <i>Mutant Research</i> 1989, <b>217</b>(1): 75-81.
+
-
 
+
-
16. University of Alberta Environmental Health and Safety website: http://www.ehs.ualberta.ca/
+
-
{{Team:Alberta/endMainContent}}
+
{{Team:Alberta/footer|achievements=selected}}

Latest revision as of 16:41, 26 September 2011

METHODOLOGY

Team Alberta iGEM Safety Proposal

Team Alberta recognizes the important role that safety plays in the completion of any scientific undertaking. Our team members are fully committed to not only ensuring the safety of those within our lab but also addressing any potential risks that our project may pose to the greater community.
Please find below Team Alberta's answers to the new, required iGEM safety questions.

1. Would the materials used in your project and/or your final product pose:

a. Risks to the safety and health of team members or others in the lab?

Neurospora is stored in clearly labelled flasks with sponge tops to prevent contamination

The materials used in our project pose little to no risks to the safety and health of our team members or others in the lab and our final product poses no risk to these individuals.


The organism that our group has genetically manipulated, Neurospora crassa, is well-documented as being safe1. N. crassa is a biosafety level 1 organism. Since 1941 the species has been used extensively in laboratories resulting in the publication of thousands of research papers. In none of these numerous publications has the Neurospora genus been implicated in causing disease in either animals or plants1-4.


Neurospora's minimal threat can largely be attributed to it being an obligate aerobe. Unlike other species such as yeasts, Neurospora is unable to grow in organs such as the gut or bladder, tissues, or systemically within an organism1. Furthermore, despite Neurospora being regarded by some as an allergen, medical literature generally fails to mention the genus5-8.


Our team acknowledges that though certain fungal species themselves may not be pathogenic, they may produce dangerous toxins. Throughout our research into Neurospora our group has not found any documentation of the species producing dangerous mycotoxins or any dangerous secondary metabolites1. Given that Neurospora has had such a long history of living in close association with humans (please see below), it is a generally regarded as being harmless.

Clearly labelled waste disposal containers ensure proper removal of potentially hazardous materials

It should be noted that there are still materials used in our project that may potentially be hazardous. Our esterification procedure involves the use of strong chemicals and reagents, some of which have the potential to cause harm. These reagents are primarily volatile and require careful handling and storage.


As well, Hygromycin b, an antibiotic and antifungal agent that is used for selection, is toxic if inhaled. Care must be taken around powdered or lyophilized Hygromycin B, and precaution should be taken to cover up respiratory passageways, skin, and the eyes. However, Hygromycin B is most commonly purchased in liquid form, and in liquid carries with it significantly less potential for accidental inhalation.

b. Risks to the safety and health of the general public if released by design or accident?

Our organism poses no threat to the safety and health of the general public. Neurospora has a well-documented history of living in close association with humans. It has historically resided in a variety of businesses including bakeries, lumber yards and plywood factories1;9- 11. Growth has also been observed on the stubble of burnt sugar cane fields and along burnt railway tracks13. Thus, it poses no threat to the health and safety of those in its surroundings.

c. Risks to environmental quality if released by design or accident?

As mentioned, N. crassa has a long history of living in close association with humans; however, these instances are largely documented as having occurred in moist tropical or subtropical environments. Like many fungi, warm and moist is the favored climate for Neurospora growth1. Thus, if our organism, WT or manipulated, were to be released in our dry, temperate environment of Edmonton, Alberta, Canada, with its bitterly harsh winters, we would expect its survival and environmental impact to be minimal. Even if it were to survive, we cannot see it affecting local ecosystems by any appreciable amount.


Nonetheless, our alternative biodiesel has the potential to revolutionize economies throughout the world, as discussed in our human practices component, and we must therefore regard the effects of environmental exposure to Neurospora in other climates. Were Neurospora to be released in other warmer climates it may readily survive, creating its own niche within the environment. However, the aforementioned nonpathogenicity of the genus results in this not being a source of alarm1-4.


Further, Team Alberta predicts that our manipulated strain of Neurospora crassa would be disadvantaged to survive relative to WT in any environment; our genetic manipulation results in the organism's energy being diverted away from essential metabolic functions, inhibiting organismal growth and manipulation. This puts it at a disadvantage against natural competing fungi.

d. Risks to security through malicious misuse by individuals, groups or states?

Unforeseen alteration of biopart functions may represent issues of concern. However, in our case if one or several of our bioparts were changed to alter their function or stop working as intended, limited to no safety issues would arise. Our knockout of the FadD gene results in there being limited potential for its alteration of function. Further, our manipulation of thioesterases similarly represents limited safety concerns due to their prevalence in all organisms. If further alterations were to be made to thioesterase genes and resulted in overproduction, our organism would likely die or have a limited existence; if further alterations to thioesterase genes were to prevent their function, then the organism may return to a more WT phenotype12.


The misuse of our bioconverter represents a potential threat to safety. The esterification process requires heat and flammable chemicals contained within a sealed vessel and thus the potential for serious injury exists.

2. If your response to any of the questions above is yes:

a. Explain how you addressed these issues in project design and while conducting laboratory work.

To deal with such issues our team greatly scrutinized all steps within our procedure for potential hazards and subsequently collectively addressed all areas of concern. Please see the outline below.



Our careful consideration of the potential safety concerns associated with the completion of our project and our careful documentation and safety training have allowed us to work both responsibly and cautiously, limiting the probability of injuries.


All MSDS data sheets were followed in working with strong acids, bases, volatile chemicals, or otherwise potentially harmful reagents. All antibiotics and antifungals were stored cold and in sealed containers, and any reacting chemicals were kept in separate storage areas. All experiments done involving the use of open flame, electrical power sources, or flammable substances were treated with the utmost caution. All experiments with distillation used properly fitted apparatus and were designed to eliminate all possibility of heating closed containers. (For details on the safe handling of Hygromycin b, please see question 3).


Safety issues arising from the completion of our bioreactor were addressed in the stages of its design. Several important safeguards were incorporated. For example, our bioconverter is designed to automatically turn off upon exceeding the recommended temperature and pressure past specific margins.

b. Describe and document safety, security, health and/or environmental issues as you submit your parts to the Registry.

In submitting parts to the registry, Team Alberta has actively undertaken the practice of describing and documenting any safety, security, health and/or environmental issues of our parts as they are submitted to the registry. None of our parts confer any pathogenicity or otherwise harmful effects upon either Neurospora crassa or Escherichia coli.


One of our parts will confer Hygromycin B resistance to Neurospora crassa, and such strains that contain this part should be noted as being resistant to that particular antifungal agent.

3. Under what biosafety provisions will / do you operate?

a. Does your institution have its own biosafety rules and if so what are they? Provide a link to them online if possible.

Yes, the University of Alberta contains a specified set of Biosafety Rules that are outlined within the Biosafety Manual that is published by the Office of Environmental Health and Safety. A link to his valuable resource can be found here: http://www.ehs.ualberta.ca/en/EHSDivisions/~/media/8C72A3F626FB47B6BD70EC79C94CD1CE.ashx

b. Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them? Describe any concerns or changes that were made based on this review.

Team Alberta consulted the University of Alberta's Office of Environmental Health and Safety throughout the planning of our project. The Biosafety Division of this office provides both technical expertise and support to labs throughout campus and thus ensures a safe working and learning environment for both staff and students. In addition, the division also monitors compliance with federal and provincial legislation16.


Our team submitted a written overview of the relevant safety considerations associated with our project to this office. Upon perusal of this document, the Biosafety Officer provided us with recommendations to fully ensure that our project met all biosafety requirements. Please see the Biosafety Officer's recommendations below and how we met each of them:

  1. It was recommended that if our lab were to grow N. Crassa beyond a 10L culture volume that we would have to obtain permission from the federal government, as such a culture would be considered large scale production. The Biosafety Officer therefore recommends avoiding production of cultures beyond a 9.5L volume. In addition, it was recommended that our lab prepare a Biological Spill Remediation kit according to the Standard Operating Protocols (SOP) of the university.

    To avoid having to proceed with a lengthy governmental registration process in the relatively short timeframe of the iGEM competition, our lab will ensure that no culture we prepare will be larger than 9.5L. To date, the largest culture that we have prepared has been less than 1.5L. As well, the members of our lab assembled the materials required for a Biological Spill Remediation kit, which will allow for the safe and efficient cleanup of any potential spills.

  2. The Biosafety officer recommended that our lab ensure all cultures of N. crassa be rendered inert prior to disposal.

    The members of our lab have already been adhering to this practice by treating all cultures of N. crassa with a household bleach mixture for a minimum of one hour prior to disposal. Our bleach mixture contains a minimum of one part bleach to three parts culture, which is consistent with the guidelines outlined by the Biosafety Division of the Environmental Health and Safety Office.

  3. The Biosafety Officer recommended that all individuals working within our lab should wear personal protective equipment (PPE), comprised of fully-fastened laboratory coats or gowns, disposable gloves, safety glasses, closed-toe shoes and floor-length pants.

    The members of our lab have been adhering to this common laboratory practice since the very beginning.

  4. Due to the use of the antibiotic and antifungal Hygromycin b, the Biosafety Officer recommended that all work with this antibiotic be carried out in a fume hood. He further recommended that members of our team coming in contact with this antibiotic be fit-tested for N95 respirators in the event that this antibiotic cannot be handled within the fume hood.

    The members of our team who are not fit-tested for N95 respirators will not work with Hygromycin b. The two members of our team that will work with this antibiotic have been fit-tested with N95 respirators so that they may safely handle this compound, regardless of its form. All work with Hygromycin b will be carried out within a fumehood.

c. Will / did you receive any biosafety and/or lab training before beginning your project? If so, describe this training.

Information about reagents and safety protocols are all found in an easily accessible binder

The members of our lab have all had variable levels of laboratory experience upon beginning the summer. Though most members had some level of biosafety training from previous lab experiences, including WHMIS certification, some members did not have any previous safety training. Because of this uneven experience, all members of our team received a laboratory tour at the beginning of the project. This included an overview of general laboratory safety procedures and protocols. Additionally, all team members were briefed on new safety procedures as our project developed. For example, upon beginning work with our organism, N. crassa, all lab members were briefed on its safe disposal.

d. Does your country have national biosafety regulations or guidelines? If so, provide a link to them online if possible.

Yes, the Public Health Agency of Canada outlines national biosafety guidelines. Specifically, the Laboratory Biosafety and Biosecurity Division of this agency is responsible for publishing biosafety regulations. A quick synopsis of these guidelines may be found here: http://www.phac-aspc.gc.ca/lab-bio/regul/index-eng.php

4.Optional Question: Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?

In order to motivate future iGEM teams to further emphasize safety in their daily laboratory practices, we propose that each team completes a detailed safety report for a minimal medal requirement. Bearing in mind the increasing importance of safety in the rapidly expanding synthetic biology field, Team Alberta further proposes that future iGEM competitions require teams to engineer their parts and organisms with several safeguards in place in order to achieve a gold medal. If these components were medal requirements, we feel that it would greatly motivate iGEM participants to address potential safety issues, and not just obvious ones, far ahead of time. This attention towards possible problems, and the solutions around them, will pay immense rewards in their future work, iGEM or otherwise. Moreover, this would encourage teams to be more creative with respects to synthetic biology and genetic engineering.


Our team recognizes that biosafety engineering has the potential to make many devices and systems safer. For example, essential gene knockouts can be created through partial or full amino acid deletions instead of single nucleotide alterations that are susceptible to mutation. Auxotrophic (or nutrient-deficient) strains can be created to ensure that an organism has no chance to exist outside of the laboratory environment, ensuring a minimal chance of contaminating the outside world. Organisms can even be designed to positively or negatively respond to varying wavelengths of light and electrical stimuli. All this and more should be taken into account when designing any organic circuit.

References

  1. Perkins DD and Davis RH: Evidence for Safety of Neurospora Species for Academic and Commercial Use. Applied and Environmental Microbiology 2006, 66 (12): 5107-5109.
  2. Davis RH: Neurospora: contributions of a model organism. Oxford University Press US; 2000.
  3. Perkins DD: Neurospora: the organism behind the molecular revolution. Genetics 1992, 130: 687-701.
  4. Perkins DD: Neurospora genetics at the turn of the century. Fungal Genetics Newsletter 2000, 47: 83-88.
  5. Frank MM, Austen KF, Claman HN, Unanue ER: Samterâs immunological diseases, 5th ed. Little, Brown & Co US; 1995.
  6. Kay AB: Allergy and allergic diseases. Blackwell US; 1997.
  7. Middleton E, Reed CE, Ellis EF, Adkinson, NF, Yunginger, Busse, WW: Allergy: principles and practice, 5th ed. Mosby US; 1998.
  8. Patterson R, Grammer LC, Greenberger PA: Allergic diseases: diagnosis and management, 5th ed. Lippncott-Raven US; 1997.
  9. Shear CL, Dodge BO: Life histories and heterothallism of the red bread-mold fungi of the Monilia sitophila group. Journal Agricultural Research 1927, 34: 1019-1042.
  10. Yassin S, Wheals A: Neurospora species in bakeries. Journal Applied Bacteriology 1992, 72: 337-380.
  11. Shaw DE: Honeybees collecting Neurospora spores from steam Pinus logs in Queensland. Mycologist 1993, 7: 182-185.
  12. Nelson DL, Cox MM: Lehninger Principles of Biochemistry. W.H Freeman US; 2009.
  13. iGEM website: https://2011.igem.org/Safety
  14. Hygromycin material and safety data sheet:
    http://www.invivogen.com/MSDS/HygromycinB_solution_v4_MSDS.pdf
  15. Kafer E, Luk D: Sensitivity of bleomycin and hydrogen peroxide of DNA repair-defective mutants in Neurospora crassa. Mutant Research 1989, 217(1): 75-81.
  16. University of Alberta Environmental Health and Safety website: http://www.ehs.ualberta.ca/