Team:Penn/Notebook

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<title>University of Pennsylvania iGEM</title>
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<a href="https://2014.igem.org/Team:Penn"><li>Home</li></a>
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<p>University of Pennsylvania <span>iGEM 2014</span></p>
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  <li>Project
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  <ul>
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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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<li><a href="https://2014.igem.org/Team:Penn">Home</a></li>
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    <a href="https://2014.igem.org/Team:Penn/Magnetism"> <li>Magnetism</li> </a>
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    <li>|</li>
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    <a href="https://2014.igem.org/Team:Penn/Microbio"> <li>Microbiology</li> </a>
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<li><a href="https://2014.igem.org/Team:Penn/Project" >Project</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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<ul class="sub_menu">
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    <a href="https://2014.igem.org/Team:Penn/CdTolerance"> <li>Cadmium Tolerance</li> </a>
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<li><a href="https://2014.igem.org/Team:Penn/Overview">Overview</a></li>
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  </ul>
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<li><a href="https://2014.igem.org/Team:Penn/Motivation">Motivation</a></li>
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  </li>
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</ul>
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</li>
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  <li>Human Practices
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    <li>|</li>
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    <ul>
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<li><a href="https://2014.igem.org/Team:Penn/Project">Wet lab</a>
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      <a href="https://2014.igem.org/Team:Penn/Specsheet"><li>Spec Sheet</li></a>
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<ul class="sub_menu">
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    <a href="https://2014.igem.org/Team:Penn/Outreach"><li>Outreach</li></a>
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<li><a href="https://2014.igem.org/Team:Penn/Safety">Safety</a></li>
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    <a href="https://2014.igem.org/Team:Penn/Biomeme"><li>Biomeme</li></a>
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<li><a href="https://2014.igem.org/Team:Penn/Protocol">Protocol</a></li>
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  </ul>
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            <li><a href="https://2014.igem.org/Team:Penn/Notebook">Notebook</a></li>
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</li>
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</ul>
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  <li>Notebook
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</li>
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  <ul>
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  <li>|</li>
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      <a href="https://2014.igem.org/Team:Penn/Notebook"><li>Timeline</li></a>
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<li><a href="https://2014.igem.org/Team:Penn/HumanPractices">Human Practices</a></li>
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      <a href="https://2014.igem.org/Team:Penn/Safety"><li>Safety</li></a>
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  <li>|</li>
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    <a href="https://2014.igem.org/Team:Penn/Protocol"><li>Protocols</li></a>
-
<li><a href="https://2014.igem.org/Team:Penn/Team">About us</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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<li><a href="https://2014.igem.org/Team:Penn/Team"">Team</a></li>
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  </ul>
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            <li><a href="https://2014.igem.org/Team:Penn/Sponsors">Sponsors</a></li>
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  </li>
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</ul>
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  <li>Team
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    </li>
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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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    <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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    <a href="https://2014.igem.org/Team:Penn/Sponsors"><li>Sponsors</li></a>
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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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<!--start of content block -->
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<h3 style= "text-align: center;">Week 1</h3>
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<div id="wrapper">
+
<ol>
-
<p id="title">Notebook</p>
+
  <li>Molecolar Biology Training Workshop</li>
-
<ul id="weeklist">
+
    <li>Practiced the basics of molecolar cloning</li>
-
        <li>Week 1
+
</ol>
-
            <ul>
+
<h3 style= "text-align: center;">Week 2</h3>
-
                <li>Molecular Biology Training Workshop</li>
+
<ol>
-
                <li>Practiced the basics of molecular cloning</li>
+
    <li>Idea Brainstorming and Generation</li>
-
            </ul>
+
    <li>Compiled a preliminary list of potential ideas</li>
-
        </li>
+
</ol>
-
        <li>Week 2
+
<h3 style= "text-align: center;">Week 3</h3>
-
<ul>
+
<ol>
-
                <li>Idea Brainstorming and Generation</li>
+
    <li>Settled on two main ideas: 1. quorum sensing with antibiotics 2. Heavy metal removal with Magnetotactic bacteria</li>
-
                <li>Compiled a preliminary list of potential ideas</li>
+
    <li>Learned how to use Geneious to design cloning process</li>
-
            </ul>
+
    <li>Practiced extracting biobricks and transforming NEB Turbo cells with plasmids</li>
-
</li>
+
-
        <li>Week 3
+
-
<ul>
+
-
                <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>
+
-
<br>
+
-
<p>Human Practices</p>
+
-
<li>Visited Biomeme to get the portable qPCR machine</li>
+
-
            </ul>
+
-
</li>
+
-
        <li>Week 4
+
-
            <ul>
+
-
                <li>Decided on the project idea: Heavy metal removal with Magnetotactic bacteria</li>
+
-
                <li>Identified primers and promoters in AMB-1 strain</li>
+
-
<li>Identified AMB-1 transformation vector</li>
+
-
<li>Extracted smtA biobrick gene and made glycerol stock</li>
+
-
            </ul>
+
-
        </li>
+
-
        <li>Week 5
+
-
            <ul>
+
-
                <li>Developed three goals to accomplish for the project</li>
+
-
                <li>Determined the constructs to clone into AMB-1</li>
+
-
<li>Designed two fast-fail experiments</li>
+
-
<li>Created a workflow for the construction of plasmid</li>
+
-
<br>
+
-
<p>Human Practices</p>
+
-
<li>Planned outreach events at high school summer programs</li>
+
-
            </ul>
+
-
        </li>
+
-
        <li>Week 6
+
-
            <ul>
+
-
                <li>Ordered chemicals for AMB-1 growth medium</li>
+
-
                <li>Completed primer design</li>
+
-
<li>Obtained AMB-1 strain from Dr.Goulian</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 7
+
-
            <ul>
+
-
                <li>Determined the OD600 plate reading conversion formula experimentally</li>
+
-
                <li>Attempted to do E.Coli and AMB-1 cadmium tolerance test</li>
+
-
<li>Designed all construct on Geneious</li>
+
-
<br>
+
-
<p>Human Practices</p>
+
-
<li>Met with Dr.Rizk to discuss presenting to incoming bioengineering freshmen</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 8
+
-
            <ul>
+
-
                <li>Ordered DNAs from Genscript and IDT</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 9
+
-
            <ul>
+
-
                <li>Redid E.Coli Cadmium Tolerance Test in M9 media</li>
+
-
                <li>Learned to do cell count for AMB-1</li>
+
-
<li>Attempted to make AMB-1 chemically competent</li>
+
-
<br>
+
-
<p>Human Practices</p>
+
-
<li>Presented to high school students at Penn M&T program</li>
+
-
<li>Planned a synthetic biology preceptorial</li>
+
-
<li>Contacted Schuylkill Action Network</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 10
+
-
            <ul>
+
-
                <li>Completed AMB-1 growth curve under different media</li>
+
-
                <li>Determined cell count and OD600 conversion formula for AMB-1 experimentally</li>
+
-
<li>Completed E.Coli Cadmium Tolerance Test in LB media</li>
+
-
<br>
+
-
<p>Human Practices</p>
+
-
<li>Volunteered at SEA Science Carnival </li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 11
+
-
            <ul>
+
-
                <li>Addressed EMSGM growth problem with pH</li>
+
-
                <li>Make new recovery media with adjusted pH for optimal AMB-1 growth</li>
+
-
<li>Chemical Transformation with different recovery broths</li>
+
-
<li>Attempted PCR assembly with synthesized parts</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 12
+
-
            <ul>
+
-
                <li>Used anaerobic chambers to grow plates </li>
+
-
                <li>Troubleshooted lack of magnetism with new iron maleate solution</li>
+
-
<li>Troubleshooted AMB-1 electroporation experiment with plating at every step </li>
+
-
<li>Began cloning successfully assembled PCRed constructs into PYMB essentials</li>
+
-
<img src="https://static.igem.org/mediawiki/2014/8/84/Amb1bacteria.png" width="200px">
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 13
+
-
            <ul>
+
-
                <li>Finished cloning flurescent protein with smtA and mCherry into PYMB essentials </li>
+
-
                <li>Transform AMB-1 with this construct to test for successful transformation with fluorescence test</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 14
+
-
            <ul>
+
-
                <li>Make new E-MSGM media</li>
+
-
                <li>Re-designed construct</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 15
+
-
            <ul>
+
-
                <li>Troubleshooted cloning E. coli construct for cadmium tolerance</li>
+
-
                <li>Sequence verified finished constructs on PYMB</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 16
+
-
            <ul>
+
-
                <li>Built the prototype of a portable spectrophotometer for cell recovery experiment</li>
+
-
                <li>Designed primers for Gibson Assembly of final construct</li>
+
-
<br>
+
-
<p>Human Practices</p>
+
-
<li>Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers.</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 17
+
-
            <ul>
+
-
                <li>Tested AMB-1 aerobic culture and anaerobic culture with magnetometer</li>
+
-
                <li>Troubleshooted and retried cloning E. coli construct</li>
+
-
<li>PCRed up parts we received for construction of shuttle vector</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 18
+
-
            <ul>
+
-
                <li>Tested AMB-1 aerobic culture and anaerobic culture with magnetometer</li>
+
-
                <li>Finished PCRing parts we received from IDT</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 19
+
-
            <ul>
+
-
                <li>Measured the magnetic strength indicator T2 for various concentration of AMB-1 culture and attempted to develop a trendline</li>
+
-
                <li>Counted fully grown sample of aerobic AMB-1 and made a trendline converting OD to cell concentration</li>
+
-
<li>Cloned all biobricks into PSB1C3 backbone</li>
+
-
            </ul>
+
-
        </li>
+
-
<li>Week 20
+
-
            <ul>
+
-
                <li>compiled all data and graphics for wiki</li>
+
-
            </ul>
+
-
        </li>
+
-
    </ul>
+
-
</div>
+
-
<!-- end of content block -->
+
-
<!-- start of footer-->
+
    <li>Human Practices</li>
-
<div id="footer">
+
    <li>Visited Biomeme to get the portable qPCR machine</li>
-
<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>
+
</ol>
-
<p>Penn iGEM  &copy; 2014</p>
+
<h3 style= "text-align: center;">Week 4</h3>
-
</div>
+
<ol>
-
<!-- end of footer -->
+
    <li>Decided on the project idea: Heavy metal removal with Magnetotactic bacteria
-
</body>
+
    <li>Identified primers and promoters in AMB-1 strain
 +
    <li>Identified AMB-1 transformation vector
 +
    <li>Extracted smtA biobrick gene and made glycerol stock
 +
</ol>
 +
<h3 style= "text-align: center;">Week 5</h3>
 +
<ol>
 +
    <li>Developed three goals to accomplish for the project
 +
    <li>Determined the constructs to clone into AMB-1
 +
    <li>Designed two fast-fail experiments
 +
  <li> Created a workflow for the construction of plasmid
 +
 
 +
  <li> Human Practices
 +
    <li>Planned outreach events at high school summer programs
 +
</ol>
 +
<h3 style= "text-align: center;">Week 6</h3>
 +
<ol>
 +
    <li>Ordered chemicals for AMB-1 growth medium
 +
    <li>Completed primer design
 +
    <li>Obtained AMB-1 strain from Dr.Goolian
 +
</ol>
 +
<h3 style= "text-align: center;">Week 7</h3>
 +
<ol>
 +
    <li>Determined the OD600 plate reading conversion formola experimentally
 +
    <li>Attempted to do E.Coli and AMB-1 cadmium tolerance test
 +
    <li>Designed all construct on Geneious
 +
 
 +
    <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
 +
 
 +
    <li>Human Practices
 +
    <li>Presented to high school students at Penn M&T program
 +
    <li>Planned a synthetic biology preceptorial
 +
    <li>Contacted Schuylkill Action Network
 +
</ol>
 +
<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
 +
 
 +
    <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>
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Revision as of 07:24, 17 October 2014

University of Pennsylvania iGEM

Timeline

Week 1

  1. Molecolar Biology Training Workshop
  2. Practiced the basics of molecolar 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/Notebook"