Team:Yale/Notebook/Week3

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== Notebook: Week 3 ==
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week1">Week 1</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week2">Week 2</a></li>
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<li><a id="page" href="https://2011.igem.org/Team:Yale/Notebook/Week3">Week 3</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week4">Week 4</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week5">Week 5</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week6">Week 6</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week7">Week 7</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week8">Week 8</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week9">Week 9</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week10">Week 10</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week11">Week 11</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week12">Week 12</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week13">Week 13</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week14">Week 14</a></li>
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<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week15">Week 15</a></li>
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</ul>
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<div id="entry">
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<h1>Week 3: May 29-June 5</h1>
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<ul>
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<li>Monday:<ul>
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<li>Prepared LB media and cultures</li>
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</ul></li><li>
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Tuesday:<ul>
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<li>Additional research on Rhagium inquisitor antifreeze protein and gene synthesis options</li>
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</ul></li><li>
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Wednesday:<ul>
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<li>Tokyo Tech iGEM BioBrick <a href="http://partsregistry.org/Part:BBa_K193209:Experience#Applications_of_BBa_K193209">BBa_K193209</a> arrives, Davies Lab type III AFP (Zoarces elongatus) arrives, transform and streak plates with respective genes</li>
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<li>Completed modelling/homology studies for RiAFP, but failed to determine any sort of homologous secondary protein structure</li>
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<li>Meeting with faculty adviser Prof Farren Isaacs about project and RiAFP gene synthesis design.</li>
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<li>Emailed various companies for sponsorship for gene synthesis</li>
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<li>Emailed various professors for suggestions for AFP extracellular export mechanism</li>
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<li>Emailed other iGEM teams for sponsorship suggestions</li>
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</ul></li><li>
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Thursday:<ul>
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<li>Retrieved Origami cell lines (for better disulfide bond formation in cytoplasm, allowing better protein folding) from Yong Xiong lab
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''Monday''
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</li>
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- Food
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<li>Began designing various permutations of RiAFP gene, with possible His-tag, GFP fusion, pelB/OmpA export leader sequence, etc on IDT website after securing sponsorship</li>
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</ul></li><li>
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''Tuesday''
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Friday:<ul>
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- Darren arrives
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<li>Decided on IDT construct with pelB-eGFP-TEV-RiAFP-His and ordered gene from website </li>
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<li>Contacted Fass Lab of the Weizmann Institute about various TmAFP plasmids to compare against Tokyo Tech BioBrick</li>
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- Discussion of R. inquisitor
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</ul></li><li>
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Saturday:<ul>
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''Wednesday''
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<li>Miniprepped Tokyo Tech plasmid and Canadian ZeAFP Type III plasmids and nanodropped for concentration</li>
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- Tokyo Tech iGEM Plasmid (TmAFP) and Canada, Davies Lab Plasmid (ZeAFP) arrived, streaked 1 plate for each plasmid
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<li>Subcultured 2 colonies for Canadian ZeAFP-transformed BL21s in 100 mL flasks</li>
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<li>Designed primers with BioBrick prefix/suffix overhang for PCR amplification of RiAFP synthetic gene</li>
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- Modelling/homology study for RiAFP
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</ul></li><li>
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Sunday:<ul>
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- Afternoon meeting with Prof. Farren Isaacs about project and gene we're looking to synthesize
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<li>1 in 40 dilution of previous day's overnight subculture</li>
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</ul></li>
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- Emailed companies for sponsorship for gene synthesis
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</ul>
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</div>
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- Emailed other iGEM teams for suggestion
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<div style="clear:both"></div>
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</div>
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''Thursday''
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- Found protocol for Origami cell lines at Xiong lab
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- Designed gene on IDT website
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''Friday''
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- Asking about TEV, GFP, His
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- Ordered gene
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- Contacted Israeli lab about Plasmids
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''Saturday''
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- Miniprep, Nanodrop
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- Cultured 2 colonies in 100 mL flasks
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- Warren worked on primer design
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''Sunday''
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- 1/40 dilution in 1 liter
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[[Team:Yale/Notebook|Back to Notebook]]
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Latest revision as of 18:53, 27 September 2011

iGEM Yale

Week 3: May 29-June 5

  • Monday:
    • Prepared LB media and cultures
  • Tuesday:
    • Additional research on Rhagium inquisitor antifreeze protein and gene synthesis options
  • Wednesday:
    • Tokyo Tech iGEM BioBrick BBa_K193209 arrives, Davies Lab type III AFP (Zoarces elongatus) arrives, transform and streak plates with respective genes
    • Completed modelling/homology studies for RiAFP, but failed to determine any sort of homologous secondary protein structure
    • Meeting with faculty adviser Prof Farren Isaacs about project and RiAFP gene synthesis design.
    • Emailed various companies for sponsorship for gene synthesis
    • Emailed various professors for suggestions for AFP extracellular export mechanism
    • Emailed other iGEM teams for sponsorship suggestions
  • Thursday:
    • Retrieved Origami cell lines (for better disulfide bond formation in cytoplasm, allowing better protein folding) from Yong Xiong lab
    • Began designing various permutations of RiAFP gene, with possible His-tag, GFP fusion, pelB/OmpA export leader sequence, etc on IDT website after securing sponsorship
  • Friday:
    • Decided on IDT construct with pelB-eGFP-TEV-RiAFP-His and ordered gene from website
    • Contacted Fass Lab of the Weizmann Institute about various TmAFP plasmids to compare against Tokyo Tech BioBrick
  • Saturday:
    • Miniprepped Tokyo Tech plasmid and Canadian ZeAFP Type III plasmids and nanodropped for concentration
    • Subcultured 2 colonies for Canadian ZeAFP-transformed BL21s in 100 mL flasks
    • Designed primers with BioBrick prefix/suffix overhang for PCR amplification of RiAFP synthetic gene
  • Sunday:
    • 1 in 40 dilution of previous day's overnight subculture

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