Difference between revisions of "Team:NAIT Edmonton/Safety"

 
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                       <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Practices">policy and practices</a></li>
 
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<center><div class="top_slogan">Under Construction!</div></center>
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<center><div class="top_slogan">Lab Safety</div></center>
  
  <div class="main_content">
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<h2>iGEM teams follow a high standard of safe and responsible biological engineering. Because we are members of the synthetic biology community, we are responsible for living up to the trust placed in us to design, build, and share biological devices safely. </h2> <br>
  
 +
<center><object width="999" height="562" data="http://www.youtube.com/embed/neQjLbdODeU" frameborder="0" allowfullscreen></object></center>
  
<div class="accordion">
 
<div class="accordion-section">
 
<a class="accordion-section-title" href="#accordion-1">Background</a>
 
<div id="accordion-1" class="accordion-section-content">
 
The structural and functional study of the proteins expressed by a genome is
 
  
called proteomics. This relatively novel science uses different methodologies in order to
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<br><br><br>
  
separate and identify specific proteins of interest. Among these techniques, SDS-PAGE
 
  
plays an essential role due to its high sensitivity, low sample volume requirement, and
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  <div class="main_content">
  
high popularity. Negatively charged proteins migrate towards the positive electrode
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<div class="accordion">
 +
<div class="accordion-section">
 +
<a class="accordion-section-title" href="#accordion-2"  style="background-color:#f96040">Safety Training</a>
 +
<div id="accordion-2" class="accordion-section-content">
 +
<p>Our institution is committed to providing a safe work environment. As such, the NAIT Biosafety program ensures that potentially biohazardous materials used for our research are used only by students and staff that have had appropriate training. All the NAIT laboratories are compliant to and certified by regulations for working with biohazardous materials. NAIT follows the regulations identified in the Human Pathogens and Toxins Act (HPTA).</p><br>
  
according to their size and charge. Smaller proteins migrate further in a given amount of  
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<p>Based on the <i>Canadian Biosafety Standards and Guidelines</i> 1st edition, NAIT only has laboratories that can handle Risk Level Group 1 and 2 pathogens and toxins. Standard operating procedures are developed for all labs and facilities within NAIT that handles said pathogens and toxins. Additionally, all staff and students who enter appropriate labs, and handle or dispose of these pathogens undergo a biosafety training session. Appropriate training records are also maintained. 
  
time. As proteins are separated in this manner, users load molecular weight standards
 
  
to estimate the size (in kDa) of the proteins present in their sample. Once the proteins of
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</p>
  
a single sample have been isolated and are embedded in the polyacrylamide (PA) gel
 
  
matrix, staining procedures are used to visualize them.</p>
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</div><!--end .accordion-section-->
  
<br>
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<div class="accordion-section">
 
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<a class="accordion-section-title" href="#accordion-3" style="background-color:#FBB252">Risks for our Project</a>
<center><img src="http://upload.wikimedia.org/wikipedia/commons/4/46/SDS-PAGE_Electrophoresis.png" width="750px"></center>
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<div id="accordion-3" class="accordion-section-content">
 
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<p><b>Risks to the Safety and Health of Team Members or Others in Lab</b></p><br>
<br>
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<p style="font-size:15;">Organic dyes, such as Coomassie blue, can be used for this purpose;
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nevertheless, their low sensitivity and a detection range that goes from 1 to 50 ng can
+
  
be a challenge for detecting low abundance proteins (Jin, Huang, Yoo, & Choi, 2006). A
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<p>In our lab, we use <i>Escherichia coli</i> as our miniature factories to produce our desired proteins. According to the <i>Canadian Biosafety Standards and Guidelines, E. coli</i> is classified as RG2 meaning that it is a pathogen that is very unlikely to cause human disease or pose a serious hazard to laboratory workers. However, some bacteria may be opportunistic pathogens and may cause harm to immunocompromised individuals. For E. coli there are effective treatments and preventative measures available. </p><br>
  
higher sensitivity can be achieved by fluorescent staining techniques (from 0.1 to 10
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<p>During agarose gel electrophoresis, we use ethidium bromide to stain and visualize the bands of DNA. Ethidium bromide is a known mutagen and contact with skin may cause genetic defects. Additionally, in SDS PAGE, TEMED is used which is harmful if inhaled or ingested by the laboratory technician. Many of our reagents must be handled carefully as to prevent skin or eye contact.</p><br>
  
ng.); however, UV instruments are necessary in order to read the data (Jin et al., 2006).
 
  
The most sensitive method up to date is radiolabeling, but the requirement of hazardous
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<b><p>Risks to the Safety and Health of the General Public or Environment</p><br></b>
  
isotopes and their complex management makes it a complicated procedure (Jin et al.,
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<p>
  
2006). Silver staining is a method that offers great sensitivity and an easy to handle
+
The novel proteins we are creating have never been studied and thus we are not sure about how they will affect our environment.  
 +
There is no direct contact of our strains of E. coli with the environment outside the laboratory and therefore, our project provides no remarkable risk to the general public. Any equipment that is exposed to bacteria is sterilized properly either by an autoclave or bactericides. </p><br>
  
protocol, thus making it one of the most commonly used staining methods. </p>
 
  
<br>
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<p>In staining, our silver solutions (a heavy metal) have the potential to bioaccumulate. Heavy metals can enter our water supply if not disposed of properly.
  
<center><img src="http://www.bio-rad.com/webroot/web/images/lsr/products/electrophoresis/product_overlay_content/global/lsr_biosafe_coomasie_gel.jpg"></center>
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</p>
  
 
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<div class="accordion-section">
 
<div class="accordion-section">
<a class="accordion-section-title" href="#accordion-2">The Problem</a>
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<a class="accordion-section-title" href="#accordion-4" style="background-color: #f7e133">Measures to Reduce Risk</a>
<div id="accordion-2" class="accordion-section-content">
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<div id="accordion-4" class="accordion-section-content">
<p>Difficulties with silver staining arise when the molecular weight markers are re-
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<p>
  
colored golden-brown in the staining process. Markers offer evenly distributed proteins
 
  
that show bands of equal intensity and known size. Researchers can compare these
+
<p><b>Reducing Risk for Team Members</b></p><br>
  
bands with their sample and identify the protein they are looking for based on its size. A
+
<p>To reduce the risk of contamination or exposure to E. coli, our team works in a certified BioSafety Cabinet. Additionally, we take appropriate precautions when handling the organisms including wearing proper PPE (see figures below). We always wear our PPE when handling our reagents or conducting any experiments. </p><br>
  
subset of these markers has color-coded standard proteins to facilitate the identification
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of each band. Post-silver staining, the users lose the ability to use the color code as a
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reference.</p>
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<br>
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  <div class="section_one_three">
 
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        <div class="roundimg"><img src="https://static.igem.org/mediawiki/2015/8/80/NAIT_Gloves.png" alt="" title="" /></a></div>
<center><img src="http://labs.mmg.pitt.edu/gjoerup/silver_stain.jpg" width="750px"></center>
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        <p class="centered_text">
 
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Gloves
</div><!--end .accordion-section-content-->
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        </p>
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        </div>
 
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<div class="accordion-section">
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  <div class="section_one_three">
<a class="accordion-section-title" href="#accordion-3">Our Goal</a>
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        <div class="roundimg"><img src="https://static.igem.org/mediawiki/2015/3/37/NAIT_SafetyGoggles.png" alt="" title="" /></a></div>
<div id="accordion-3" class="accordion-section-content">
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        <p class="centered_text">
<p>Our goal is to develop a marker that, when interacting with the reagents used in
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Safety Glasses
 +
        </p>
 +
        </div>
  
the staining protocol, will develop colour bands in specific positions so as to help in the
+
  <div class="section_one_three">
 +
        <div class="roundimg"><img src="https://static.igem.org/mediawiki/2015/2/25/NAIT_Smoc.png" alt="" title="" /></a></div>
 +
        <p class="centered_text">
 +
Lab Coat
 +
        </p>
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        </div>
  
identification of the protein(s) of interest post-staining. In order to do so, investigation of
+
<p><b>Reducing Risk for the General Public and Environment</b></p><br>
  
how specific amino acids react with silver staining reagents is underway by our team.  
+
<p>The health of the general public and the environment is very important to our team. Although the novel proteins we are constructing have unknown functions and effects, our entire project requires us to denature and essentially de-activate them. Therefore, we are certain that the denatured proteins will not have any downstream effects on our environment. </p><br>
  
This will have as an outcome the creation of novel proteins that contain an excess of a
+
<p>When disposing our reagents after an experiment, we follow the guidelines specified in NAIT’s Bio Safety program. Specifically, our silver solutions are placed into heavy metal disposal buckets and disposed of carefully as to not affect our environment</p>
  
particular amino acid and/or chemical modifications that will generate a specific colour
 
  
after treating it with silver staining reagents. To obtain such proteins, the introduction of
 
  
novel nucleotide sequences into a plasmid would be done first by in vitro transcription
 
  
translation and later by transforming E. coli cells with expression vectors.</p>
+
</p>
  
 
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</div><!--end .accordion-section-content-->
 
</div><!--end .accordion-section-->
 
</div><!--end .accordion-section-->
  
<div class="accordion-section">
 
<a class="accordion-section-title" href="#accordion-4">Our Solution</a>
 
<div id="accordion-4" class="accordion-section-content">
 
<p>Design novel protein sequences that will stain in colour.</p>
 
 
</div><!--end .accordion-section-content-->
 
</div><!--end .accordion-section-->
 
 
<div class="accordion-section">
 
<a class="accordion-section-title" href="#accordion-5">Why Does this Matter?</a>
 
<div id="accordion-5" class="accordion-section-content">
 
<p>With the current technique used today, researchers poke holes into the PA gel so that they can retain their molecular weight ladder reference points. Not only does this take time to do, but it also ruins the integrity of the gel making the staining process much more likely to damage the fragile gel.</p>
 
 
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<input class="modal-state" id="reagents" type="checkbox" />
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<div class="modal">
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 +
    <center><h1>Reagents Used</h1></center>
 +
    <p>Silver Staining</p><br>
 +
    <p>Cloning and Transforming Cells </p><br>
 +
    <p>Making Agarose and PA Gels</p><br>
 
   </div>
 
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Latest revision as of 04:15, 16 September 2015

Team NAIT 2015

Lab Safety

iGEM teams follow a high standard of safe and responsible biological engineering. Because we are members of the synthetic biology community, we are responsible for living up to the trust placed in us to design, build, and share biological devices safely.





Safety Training

Our institution is committed to providing a safe work environment. As such, the NAIT Biosafety program ensures that potentially biohazardous materials used for our research are used only by students and staff that have had appropriate training. All the NAIT laboratories are compliant to and certified by regulations for working with biohazardous materials. NAIT follows the regulations identified in the Human Pathogens and Toxins Act (HPTA).


Based on the Canadian Biosafety Standards and Guidelines 1st edition, NAIT only has laboratories that can handle Risk Level Group 1 and 2 pathogens and toxins. Standard operating procedures are developed for all labs and facilities within NAIT that handles said pathogens and toxins. Additionally, all staff and students who enter appropriate labs, and handle or dispose of these pathogens undergo a biosafety training session. Appropriate training records are also maintained.

Risks for our Project

Risks to the Safety and Health of Team Members or Others in Lab


In our lab, we use Escherichia coli as our miniature factories to produce our desired proteins. According to the Canadian Biosafety Standards and Guidelines, E. coli is classified as RG2 meaning that it is a pathogen that is very unlikely to cause human disease or pose a serious hazard to laboratory workers. However, some bacteria may be opportunistic pathogens and may cause harm to immunocompromised individuals. For E. coli there are effective treatments and preventative measures available.


During agarose gel electrophoresis, we use ethidium bromide to stain and visualize the bands of DNA. Ethidium bromide is a known mutagen and contact with skin may cause genetic defects. Additionally, in SDS PAGE, TEMED is used which is harmful if inhaled or ingested by the laboratory technician. Many of our reagents must be handled carefully as to prevent skin or eye contact.


Risks to the Safety and Health of the General Public or Environment


The novel proteins we are creating have never been studied and thus we are not sure about how they will affect our environment. There is no direct contact of our strains of E. coli with the environment outside the laboratory and therefore, our project provides no remarkable risk to the general public. Any equipment that is exposed to bacteria is sterilized properly either by an autoclave or bactericides.


In staining, our silver solutions (a heavy metal) have the potential to bioaccumulate. Heavy metals can enter our water supply if not disposed of properly.

Measures to Reduce Risk

Reducing Risk for Team Members


To reduce the risk of contamination or exposure to E. coli, our team works in a certified BioSafety Cabinet. Additionally, we take appropriate precautions when handling the organisms including wearing proper PPE (see figures below). We always wear our PPE when handling our reagents or conducting any experiments.


Gloves

Safety Glasses

Lab Coat

Reducing Risk for the General Public and Environment


The health of the general public and the environment is very important to our team. Although the novel proteins we are constructing have unknown functions and effects, our entire project requires us to denature and essentially de-activate them. Therefore, we are certain that the denatured proteins will not have any downstream effects on our environment.


When disposing our reagents after an experiment, we follow the guidelines specified in NAIT’s Bio Safety program. Specifically, our silver solutions are placed into heavy metal disposal buckets and disposed of carefully as to not affect our environment