Team:Yale/Notebook/Week3

From 2011.igem.org

(Difference between revisions)
 
(4 intermediate revisions not shown)
Line 1: Line 1:
-
== Notebook: Week 3 ==
+
{{:Team:Yale/Templates/Yale_Header_Else}}
 +
<html>
 +
<div id="text">
 +
      <div id="container">
 +
<div id="left-col">
 +
<ul id="nb">
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week1">Week 1</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week2">Week 2</a></li>
 +
<li><a id="page" href="https://2011.igem.org/Team:Yale/Notebook/Week3">Week 3</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week4">Week 4</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week5">Week 5</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week6">Week 6</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week7">Week 7</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week8">Week 8</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week9">Week 9</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week10">Week 10</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week11">Week 11</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week12">Week 12</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week13">Week 13</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week14">Week 14</a></li>
 +
<li><a href="https://2011.igem.org/Team:Yale/Notebook/Week15">Week 15</a></li>
 +
</ul>
 +
</div>
 +
<div id="entry">
 +
<h1>Week 3: May 29-June 5</h1>
 +
<ul>
 +
<li>Monday:<ul>
 +
<li>Prepared LB media and cultures</li>
 +
</ul></li><li>
 +
Tuesday:<ul>
 +
<li>Additional research on Rhagium inquisitor antifreeze protein and gene synthesis options</li>
 +
</ul></li><li>
 +
Wednesday:<ul>
 +
<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>
 +
<li>Completed modelling/homology studies for RiAFP, but failed to determine any sort of homologous secondary protein structure</li>
 +
<li>Meeting with faculty adviser Prof Farren Isaacs about project and RiAFP gene synthesis design.</li>
 +
<li>Emailed various companies for sponsorship for gene synthesis</li>
 +
<li>Emailed various professors for suggestions for AFP extracellular export mechanism</li>
 +
<li>Emailed other iGEM teams for sponsorship suggestions</li>
 +
</ul></li><li>
 +
Thursday:<ul>
 +
<li>Retrieved Origami cell lines (for better disulfide bond formation in cytoplasm, allowing better protein folding) from Yong Xiong lab
-
''Monday''
+
</li>
-
- Food
+
<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>
-
 
+
</ul></li><li>
-
''Tuesday''
+
Friday:<ul>
-
- Darren arrives
+
<li>Decided on IDT construct with pelB-eGFP-TEV-RiAFP-His and ordered gene from website </li>
-
- Discussion of R. inquisitor
+
<li>Contacted Fass Lab of the Weizmann Institute about various TmAFP plasmids to compare against Tokyo Tech BioBrick</li>
-
 
+
</ul></li><li>
-
''Wednesday''
+
Saturday:<ul>
-
- Tokyo Tech iGEM Plasmid (TmAFP) and Canada, Davies Lab Plasmid (ZeAFP) arrived, streaked 1 plate for each plasmid
+
<li>Miniprepped Tokyo Tech plasmid and Canadian ZeAFP Type III plasmids and nanodropped for concentration</li>
-
- Modelling/homology study for RiAFP
+
<li>Subcultured 2 colonies for Canadian ZeAFP-transformed BL21s in 100 mL flasks</li>
-
- Afternoon meeting with Prof. Farren Isaacs about project and gene we're looking to synthesize
+
<li>Designed primers with BioBrick prefix/suffix overhang for PCR amplification of RiAFP synthetic gene</li>
-
- Emailed companies for sponsorship for gene synthesis
+
</ul></li><li>
-
- Emailed other iGEM teams for suggestion
+
Sunday:<ul>
-
 
+
<li>1 in 40 dilution of previous day's overnight subculture</li>
-
''Thursday''
+
</ul></li>
-
- Found protocol for Origami cell lines at Xiong lab
+
</ul>
-
- Designed gene on IDT website
+
</div>
-
 
+
<div style="clear:both"></div>
-
''Friday''
+
</div>
-
- Asking about TEV, GFP, His
+
-
- Ordered gene
+
-
- Contacted Israeli lab about Plasmids
+
-
 
+
-
''Saturday''
+
-
- Miniprep, Nanodrop
+
-
- Cultured 2 colonies in 100 mL flasks
+
-
- Warren worked on primer design
+
-
 
+
-
''Sunday''
+
-
- 1/40 dilution in 1 liter
+
-
 
+
-
 
+
-
----
+
-
 
+
-
 
+
-
 
+
-
[[Team:Yale/Notebook|Back to Notebook]]
+

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

Retrieved from "http://2011.igem.org/Team:Yale/Notebook/Week3"