Team:Penn/Safety

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<title>Penn iGEM Wiki 2014</title>
 
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<link href="https://98c43ce680a0761e7c3ad3c1d7ae34f6de6db886.googledrive.com/host/0B9QyOqpKYA2gdGV2aGFRMWh4aXM/safety.css" rel="stylesheet" type="text/css">
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<title>University of Pennsylvania iGEM</title>
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<ul id="nav">
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<a href="https://2014.igem.org/Team:Penn"><li>Home</li></a>
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  <li>Project
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  <ul>
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      <a href="https://2014.igem.org/Team:Penn/Overview"> <li>Overview</li> </a>
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    <a href="https://2014.igem.org/Team:Penn/Magnetism"> <li>Magnetism</li> </a>
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    <a href="https://2014.igem.org/Team:Penn/Microbio"> <li>Microbiology</li> </a>
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    <a href="https://2014.igem.org/Team:Penn/Synbio"> <li>SynBio in AMB-1</li> </a>
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    <a href="https://2014.igem.org/Team:Penn/CdTolerance"> <li>Cadmium Tolerance</li> </a>
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  </ul>
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  </li>
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  <li>Human Practices
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    <ul>
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      <a href="https://2014.igem.org/Team:Penn/Specsheet"><li>Spec Sheet</li></a>
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    <a href="https://2014.igem.org/Team:Penn/Outreach"><li>Outreach</li></a>
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    <a href="https://2014.igem.org/Team:Penn/Biomeme"><li>Biomeme</li></a>
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  </ul>
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</li>
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  <li>Notebook
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  <ul>
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      <a href="https://2014.igem.org/Team:Penn/Notebook"><li>Timeline</li></a>
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      <a href="https://2014.igem.org/Team:Penn/Safety"><li>Safety</li></a>
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    <a href="https://2014.igem.org/Team:Penn/Protocol"><li>Protocols</li></a>
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    <a href="https://2014.igem.org/Team:Penn/Supplement"><li>Supplementary Materials</li></a>
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    <a href="https://2014.igem.org/Team:Penn/Resources"><li>Resources</li></a>
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  </ul>
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  </li>
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  <li>Team
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  <ul>
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      <a href="https://2014.igem.org/Team:Penn/Team"><li>About Us</li></a>
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    <a href="https://2014.igem.org/Team:Penn/Sponsors"><li>Sponsors</li></a>
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  </ul>
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  </li>
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</ul>
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<div style = "background: url('https://static.igem.org/mediawiki/2014/2/24/JaneText.png'); position: inherited; height:350px; background-size: 80%; background-repeat: no-repeat; background-position:center top;">
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</div>
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<div id="redbox">
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<div style = "text-align: center; font-size: 24px;">Timeline</div></br>
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<h3 style= "text-align: center;">Week 1</h3>
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<ol>
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  <li>Molecolar Biology Training Workshop</li>
 +
    <li>Practiced the basics of molecular cloning</li>
 +
</ol>
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<h3 style= "text-align: center;">Week 2</h3>
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<ol>
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    <li>Idea Brainstorming and Generation</li>
 +
    <li>Compiled a preliminary list of potential ideas</li>
 +
</ol>
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<h3 style= "text-align: center;">Week 3</h3>
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<ol>
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    <li>Settled on two main ideas: 1. Quorum sensing with antibiotics 2. Heavy metal removal with Magnetotactic bacteria</li>
 +
    <li>Learned how to use Geneious to design cloning process</li>
 +
    <li>Practiced extracting biobricks and transforming NEB Turbo cells with plasmids</li>
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<body>
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    <li>Human Practices</li>
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     <li>Visited Biomeme to get the portable qPCR machine</li>
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</ol>
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<div id="school_title">
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<h3 style= "text-align: center;">Week 4</h3>
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<p><a href="http://www.upenn.edu">University of Pennsylvania</a> <span>iGEM 2014</span></p>
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<ol>
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</div>
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     <li>Decided on the project idea: Heavy metal removal with Magnetotactic bacteria
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<ul>
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    <li>Identified primers and promoters in AMB-1 strain
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<li><a href="https://2014.igem.org/Team:Penn"><span class="menu_item">Home</span></a></li>
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    <li>Identified AMB-1 transformation vector
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     <li>|</li>
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    <li>Extracted smtA biobrick gene and made glycerol stock
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<li><a href="https://2014.igem.org/Team:Penn/Overview" ><span class="menu_item">Project</span></a>
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</ol>
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<ul class="sub_menu">
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<h3 style= "text-align: center;">Week 5</h3>
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<li><a href="https://2014.igem.org/Team:Penn/Overview">Overview</a></li>
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<ol>
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<li><a href="https://2014.igem.org/Team:Penn/Motivation">Motivation</a></li>
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    <li>Developed three goals to accomplish for the project
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</ul>
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    <li>Determined the constructs to clone into AMB-1
-
</li>
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    <li>Designed two fast-fail experiments
-
     <li>|</li>
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  <li> Created a workflow for the construction of plasmid
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<li><a href="https://2014.igem.org/Team:Penn/Protocol"><span class="menu_item">Wet lab</span></a>
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<ul class="sub_menu">
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                        <li><a href="https://2014.igem.org/Team:Penn/Protocol">Protocol</a></li>
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                        <li><a href="https://2014.igem.org/Team:Penn/Safety">Safety</a></li>
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                        <li><a href="https://2014.igem.org/Team:Penn/Notebook">Notebook</a></li>
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</ul>
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</li>
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  <li>|</li>
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<li><a href="https://2014.igem.org/Team:Penn/Outreach"><span class="menu_item">Human Practices</span></a>
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              <ul class="sub_menu">
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                        <li><a href="https://2014.igem.org/Team:Penn/Outreach">Outreach</a></li>
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                        <li><a href="https://2014.igem.org/Team:Penn/Biomeme">Biomeme</a></li>
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</ul>
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        </li>
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  <li>|</li>
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<li><a href="https://2014.igem.org/Team:Penn/Team"><span class="menu_item">About us</span></a>
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    <ul class="sub_menu">
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<li><a href="https://2014.igem.org/Team:Penn/Team">Team</a></li>
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<li><a href="https://2014.igem.org/Team:Penn/Sponsors">Sponsors</a></li>
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</ul>
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    <div id="igem_logo"><a href="https://igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="50px"></a>
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  <li> Human Practices
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<div id="wrapper">
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    <li>Planned outreach events at high school summer programs
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<h2>Biological Safety</h2>
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</ol>
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<p>
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<h3 style= "text-align: center;">Week 6</h3>
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    Our work throughout iGEM has been split between using both three different E. coli strains (DH5 alpha, W3110, and MG 1655) and Magnetospirillum Magneticum AMB-1. All four of these strains pose minimal risk inside the lab. We use strict biosafety laboratory techniques when handling these organisms and any piece of labware that comes in contact with them.
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<ol>
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</p>
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    <li>Ordered chemicals for AMB-1 growth medium
-
<p style="border-bottom:1px black solid; margin-bottom:50px">
+
    <li>Completed primer design
-
</p>
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    <li>Obtained AMB-1 strain from Dr.Goolian
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<h3>E.coli</h3>
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</ol>
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<p>All three strains of E. coli are highly conserved and pose minor risks when handeled carefully in the lab. All three strains of E. coli are rod shaped, gram negative bacteria. While E. coli resides in the intestinal tract of many organisms, all three straisn used in the lab are safe to work with as they lack the adaptability and capability to cause infection. ATCC has assigned all strains a biosafety level of 1.</p>
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<h3 style= "text-align: center;">Week 7</h3>
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<h3>Magnetospirillum Magneticum AMB-1</h3>
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<ol>
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<p>Magnetospirillum Magneticum AMB-1 is a strain of magnetic bacteria that poses minimal health risk to humans in a lab environment. This strain of bacteria is too sensitive to environmental conditions to cause infections to humans. At the same time all procedures used to handle E. coli are used with Magnetospirillum Magneticum AMB-1 as well. This includes bleaching old cultures and disposing old tubes according to biohazard protocols.
+
    <li>Determined the OD600 plate reading conversion formola experimentally
-
</p>
+
    <li>Attempted to do E.Coli and AMB-1 cadmium tolerance test
-
<h3>Public Safety</h3>
+
    <li>Designed all construct on Geneious
-
<p>Since some of our bacteria may have antibiotic resistance and could theoretically pose a health risk, we use biohazard protocols to prevent any release of our bacteria from the lab. This includes bleaching cultures before disposing of them and disposing of any old tubes in biohazard containers. This eliminates the risk of any bacteria escaping our lab or making their way into any adjacent labs.
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    </p>
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<h3>Handling and disposal of Cadmium and other Inorganic Toxic Substances</h3>
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<p>
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We took cautinous measures when handling cadmium and other toxic substances. <span style="font-style:italic">Lab coats, masks, gloves, and goggles</span> are worn all time. The handling is done in a fume hood to prevent inhalation of toxic substances.
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<br>
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<br>
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We followed protocols established by Environmental Health &amp; Radiation Safety at the University of Pennsylvania to dispose any toxic substances. We disposed the waste in designated containers and trained specialists will pick up the containers from lab and dispose of the waste properly.</p>
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<!-- end of content-->
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 +
    <li>Human Practices
 +
    <li>Met with Dr.Rizk to discuss presenting to incoming bioengineering freshmen
 +
</ol>
 +
<h3 style= "text-align: center;">Week 8</h3>
 +
<ol>
 +
    <li>Ordered DNAs from Genscript and IDT
 +
</ol>
 +
<h3 style= "text-align: center;">Week 9</h3>
 +
<ol>
 +
    <li>Redid E.Coli Cadmium Tolerance Test in M9 media
 +
    <li>Learned to do cell count for AMB-1
 +
    <li>Attempted to make AMB-1 chemically competent
-
<!-- start of footer-->
+
    <li>Human Practices
-
<div id="footer">
+
    <li>Presented to high school students at Penn M&T program
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<object id="follow_me" width='101' height='48'><embed src='http://www.socialbuttonmaker.com/Swfs/45da3933-8326-4170-89c0-10dea0659e98/button.swf' type='application/x-shockwave-flash' width='101' height='48' loop='false' wmode='transparent'><noscript><a href='http://soccerisland.info/'>island soccer news</a></noscript></embed><img src='' width=0 height=0 id='flashbutton'/><script type='text/javascript' src='http://www.socialbuttonmaker.com/Scripts/FlashButton.js'></script></object>
+
    <li>Planned a synthetic biology preceptorial
-
<p>Penn iGEM  &copy; 2014</p>
+
    <li>Contacted Schuylkill Action Network
-
</div>
+
</ol>
-
<!-- end of footer -->
+
<h3 style= "text-align: center;">Week 10</h3>
 +
<ol>
 +
    <li>Completed AMB-1 growth curve under different media
 +
    <li>Determined cell count and OD600 conversion formola for AMB-1 experimentally
 +
    <li>Completed E.Coli Cadmium Tolerance Test in LB media
-
</body>
+
    <li>Human Practices
 +
  <li> Volunteered at SEA Science Carnival
 +
</ol>
 +
<h3 style= "text-align: center;">Week 11</h3>
 +
<ol>
 +
    <li>Addressed EMSGM growth problem with pH
 +
    <li>Make new recovery media with adjusted pH for optimal AMB-1 growth
 +
    <li>Chemical Transformation with different recovery broths
 +
    <li>Attempted PCR assembly with synthesized parts
 +
</ol>
 +
<h3 style= "text-align: center;">Week 12</h3>
 +
<ol>
 +
    <li>Used anaerobic chambers to grow plates
 +
    <li>Troubleshooted lack of magnetism with new iron maleate solution
 +
    <li>Troubleshooted AMB-1 electroporation experiment with plating at every step
 +
    <li>Began cloning successfolly assembled PCRed constructs into PYMB essentials
 +
</ol>
 +
<h3 style= "text-align: center;">Week 13</h3>
 +
<ol>
 +
    <li>Finished cloning flurescent protein with smtA and mCherry into PYMB essentials
 +
    <li>Transform AMB-1 with this construct to test for successfol transformation with fluorescence test
 +
</ol>
 +
<h3 style= "text-align: center;">Week 14</h3>
 +
<ol>
 +
    <li>Make new E-MSGM media
 +
    <li>Re-designed construct
 +
</ol>
 +
<h3 style= "text-align: center;">Week 15</h3>
 +
<ol>
 +
    <li>Troubleshooted cloning E. coli construct for cadmium tolerance
 +
    <li>Sequence verified finished constructs on PYMB
 +
</ol>
 +
<h3 style= "text-align: center;">Week 16</h3>
 +
<ol>
 +
    <li>Built the prototype of a portable spectrophotometer for cell recovery experiment
 +
    <li>Designed primers for Gibson Assembly of final construct
 +
 
 +
    <li>Human Practices
 +
    <li>Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers.
 +
</ol>
 +
<h3 style= "text-align: center;">Week 17</h3>
 +
<ol>
 +
    <li>Tested AMB-1 aerobic colture and anaerobic colture with magnetometer
 +
    <li>Troubleshooted and retried cloning E. coli construct
 +
    <li>PCRed up parts we received for construction of shuttle vector
 +
</ol>
 +
<h3 style= "text-align: center;">Week 18</h3>
 +
<ol>
 +
    <li>Tested AMB-1 aerobic colture and anaerobic colture with magnetometer
 +
    <li>Finished PCRing parts we received from IDT
 +
</ol>
 +
<h3 style= "text-align: center;">Week 19</h3>
 +
<ol>
 +
  <li> Measured the magnetic strength indicator T2 for various concentration of AMB-1 colture and attempted to develop a trendline
 +
  <li> Counted folly grown sample of aerobic AMB-1 and made a trendline converting OD to cell concentration
 +
    <li>Cloned all biobricks into PSB1C3 backbone
 +
</ol>
 +
<h3 style= "text-align: center;">Week 20</h3>
 +
<ol>
 +
    <li>compiled all data and graphics for wiki
 +
 
 +
 
 +
</ol>
 +
</body>
</html>
</html>

Revision as of 12:44, 17 October 2014

University of Pennsylvania iGEM

Timeline

Week 1

  1. Molecolar Biology Training Workshop
  2. Practiced the basics of molecular cloning

Week 2

  1. Idea Brainstorming and Generation
  2. Compiled a preliminary list of potential ideas

Week 3

  1. Settled on two main ideas: 1. Quorum sensing with antibiotics 2. Heavy metal removal with Magnetotactic bacteria
  2. Learned how to use Geneious to design cloning process
  3. Practiced extracting biobricks and transforming NEB Turbo cells with plasmids
  4. Human Practices
  5. Visited Biomeme to get the portable qPCR machine

Week 4

  1. Decided on the project idea: Heavy metal removal with Magnetotactic bacteria
  2. Identified primers and promoters in AMB-1 strain
  3. Identified AMB-1 transformation vector
  4. Extracted smtA biobrick gene and made glycerol stock

Week 5

  1. Developed three goals to accomplish for the project
  2. Determined the constructs to clone into AMB-1
  3. Designed two fast-fail experiments
  4. Created a workflow for the construction of plasmid
  5. Human Practices
  6. Planned outreach events at high school summer programs

Week 6

  1. Ordered chemicals for AMB-1 growth medium
  2. Completed primer design
  3. Obtained AMB-1 strain from Dr.Goolian

Week 7

  1. Determined the OD600 plate reading conversion formola experimentally
  2. Attempted to do E.Coli and AMB-1 cadmium tolerance test
  3. Designed all construct on Geneious
  4. Human Practices
  5. Met with Dr.Rizk to discuss presenting to incoming bioengineering freshmen

Week 8

  1. Ordered DNAs from Genscript and IDT

Week 9

  1. Redid E.Coli Cadmium Tolerance Test in M9 media
  2. Learned to do cell count for AMB-1
  3. Attempted to make AMB-1 chemically competent
  4. Human Practices
  5. Presented to high school students at Penn M&T program
  6. Planned a synthetic biology preceptorial
  7. Contacted Schuylkill Action Network

Week 10

  1. Completed AMB-1 growth curve under different media
  2. Determined cell count and OD600 conversion formola for AMB-1 experimentally
  3. Completed E.Coli Cadmium Tolerance Test in LB media
  4. Human Practices
  5. Volunteered at SEA Science Carnival

Week 11

  1. Addressed EMSGM growth problem with pH
  2. Make new recovery media with adjusted pH for optimal AMB-1 growth
  3. Chemical Transformation with different recovery broths
  4. Attempted PCR assembly with synthesized parts

Week 12

  1. Used anaerobic chambers to grow plates
  2. Troubleshooted lack of magnetism with new iron maleate solution
  3. Troubleshooted AMB-1 electroporation experiment with plating at every step
  4. Began cloning successfolly assembled PCRed constructs into PYMB essentials

Week 13

  1. Finished cloning flurescent protein with smtA and mCherry into PYMB essentials
  2. Transform AMB-1 with this construct to test for successfol transformation with fluorescence test

Week 14

  1. Make new E-MSGM media
  2. Re-designed construct

Week 15

  1. Troubleshooted cloning E. coli construct for cadmium tolerance
  2. Sequence verified finished constructs on PYMB

Week 16

  1. Built the prototype of a portable spectrophotometer for cell recovery experiment
  2. Designed primers for Gibson Assembly of final construct
  3. Human Practices
  4. Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers.

Week 17

  1. Tested AMB-1 aerobic colture and anaerobic colture with magnetometer
  2. Troubleshooted and retried cloning E. coli construct
  3. PCRed up parts we received for construction of shuttle vector

Week 18

  1. Tested AMB-1 aerobic colture and anaerobic colture with magnetometer
  2. Finished PCRing parts we received from IDT

Week 19

  1. Measured the magnetic strength indicator T2 for various concentration of AMB-1 colture and attempted to develop a trendline
  2. Counted folly grown sample of aerobic AMB-1 and made a trendline converting OD to cell concentration
  3. Cloned all biobricks into PSB1C3 backbone

Week 20

  1. compiled all data and graphics for wiki

Retrieved from "http://2014.igem.org/Team:Penn/Safety"