Team:Penn/Notebook

From 2014.igem.org

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<li>Troubleshooted AMB-1 electroporation experiment with plating at every step </li>
<li>Troubleshooted AMB-1 electroporation experiment with plating at every step </li>
<li>Began cloning successfully assembled PCRed constructs into PYMB essentials</li>
<li>Began cloning successfully assembled PCRed constructs into PYMB essentials</li>
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<img src="https://static.igem.org/mediawiki/2014/8/84/Amb1bacteria.png" width="200px">
             </ul>
             </ul>
         </li>
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<li>Week 14
<li>Week 14
             <ul>
             <ul>
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                 <li></li>
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                 <li>Make new E-MSGM media</li>
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                 <li>Re-designed construct</li>
             </ul>
             </ul>
         </li>
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             <ul>
             <ul>
                 <li>Troubleshooted cloning E. coli construct for cadmium tolerance</li>
                 <li>Troubleshooted cloning E. coli construct for cadmium tolerance</li>
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                <li>Sequence verified finished constructs on PYMB</li>
             </ul>
             </ul>
         </li>
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             <ul>
             <ul>
                 <li>Built the prototype of a portable spectrophotometer for cell recovery experiment</li>
                 <li>Built the prototype of a portable spectrophotometer for cell recovery experiment</li>
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                <li>Designed primers for Gibson Assembly of final construct</li>
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<br>
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<p>Human Practices</p>
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<li>Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers.</li>
             </ul>
             </ul>
         </li>
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             <ul>
             <ul>
                 <li>Tested AMB-1 aerobic culture and anaerobic culture with magnetometer</li>
                 <li>Tested AMB-1 aerobic culture and anaerobic culture with magnetometer</li>
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                <li>Troubleshooted and retried cloning E. coli construct</li>
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<li>PCRed up parts we received for construction of shuttle vector</li>
             </ul>
             </ul>
         </li>
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             <ul>
             <ul>
                 <li>Tested AMB-1 aerobic culture and anaerobic culture with magnetometer</li>
                 <li>Tested AMB-1 aerobic culture and anaerobic culture with magnetometer</li>
 +
                <li>Finished PCRing parts we received from IDT</li>
             </ul>
             </ul>
         </li>
         </li>

Revision as of 04:06, 16 October 2014

Notebook

  • Week 1
    • Molecular Biology Training Workshop
    • Practiced the basics of molecular cloning
  • Week 2
    • Idea Brainstorming and Generation
    • Compiled a preliminary list of potential ideas
  • Week 3
    • Settled on two main ideas: 1. quorum sensing with antibiotics 2. Heavy metal removal with Magnetotactic bacteria
    • Learned how to use Geneious to design cloning process
    • Practiced extracting biobricks and transforming NEB Turbo cells with plasmids

      • Human Practices

    • Visited Biomeme to get the portable qPCR machine
  • Week 4
    • Decided on the project idea: Heavy metal removal with Magnetotactic bacteria
    • Identified primers and promoters in AMB-1 strain
    • Identified AMB-1 transformation vector
    • Extracted smtA biobrick gene and made glycerol stock
  • Week 5
    • Developed three goals to accomplish for the project
    • Determined the constructs to clone into AMB-1
    • Designed two fast-fail experiments
    • Created a workflow for the construction of plasmid

      • Human Practices

    • Planned outreach events at high school summer programs
  • Week 6
    • Ordered chemicals for AMB-1 growth medium
    • Completed primer design
    • Obtained AMB-1 strain from Dr.Goulian
  • Week 7
    • Determined the OD600 plate reading conversion formula experimentally
    • Attempted to do E.Coli and AMB-1 cadmium tolerance test
    • Designed all construct on Geneious

      • Human Practices

    • Met with Dr.Rizk to discuss presenting to incoming bioengineering freshmen
  • Week 8
    • Ordered DNAs from Genscript and IDT
  • Week 9
    • Redid E.Coli Cadmium Tolerance Test in M9 media
    • Learned to do cell count for AMB-1
    • Attempted to make AMB-1 chemically competent

      • Human Practices

    • Presented to high school students at Penn M&T program
    • Planned a synthetic biology preceptorial
    • Contacted Schuylkill Action Network
  • Week 10
    • Completed AMB-1 growth curve under different media
    • Determined cell count and OD600 conversion formula for AMB-1 experimentally
    • Completed E.Coli Cadmium Tolerance Test in LB media

      • Human Practices

    • Volunteered at SEA Science Carnival
  • Week 11
    • Addressed EMSGM growth problem with pH
    • Make new recovery media with adjusted pH for optimal AMB-1 growth
    • Chemical Transformation with different recovery broths
    • Attempted PCR assembly with synthesized parts
  • Week 12
    • Used anaerobic chambers to grow plates
    • Troubleshooted lack of magnetism with new iron maleate solution
    • Troubleshooted AMB-1 electroporation experiment with plating at every step
    • Began cloning successfully assembled PCRed constructs into PYMB essentials
  • Week 13
    • Finished cloning flurescent protein with smtA and mCherry into PYMB essentials
    • Transform AMB-1 with this construct to test for successful transformation with fluorescence test
  • Week 14
    • Make new E-MSGM media
    • Re-designed construct
  • Week 15
    • Troubleshooted cloning E. coli construct for cadmium tolerance
    • Sequence verified finished constructs on PYMB
  • Week 16
    • Built the prototype of a portable spectrophotometer for cell recovery experiment
    • Designed primers for Gibson Assembly of final construct

      • Human Practices

    • Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers.
  • Week 17
    • Tested AMB-1 aerobic culture and anaerobic culture with magnetometer
    • Troubleshooted and retried cloning E. coli construct
    • PCRed up parts we received for construction of shuttle vector
  • Week 18
    • Tested AMB-1 aerobic culture and anaerobic culture with magnetometer
    • Finished PCRing parts we received from IDT
  • Week 19
    • Measured the magnetic strength indicator T2 for various concentration of AMB-1 culture and attempted to develop a trendline
    • Counted fully grown sample of aerobic AMB-1 and made a trendline converting OD to cell concentration
    • Cloned all biobricks into PSB1C3 backbone
  • Week 20
    • compiled all data and graphics for wiki

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