Difference between revisions of "Team:UChicago/Experiments"

 
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{{UChicago/Header}}
 
{{UChicago/Header}}
  
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  <w:LsdException Locked="false" Priority="60" Name="Light Shading"/>
+
  <w:LsdException Locked="false" Priority="61" Name="Light List"/>
+
  <w:LsdException Locked="false" Priority="62" Name="Light Grid"/>
+
  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/>
+
  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/>
+
  <w:LsdException Locked="false" Priority="65" Name="Medium List 1"/>
+
  <w:LsdException Locked="false" Priority="66" Name="Medium List 2"/>
+
  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1"/>
+
  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/>
+
  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/>
+
  <w:LsdException Locked="false" Priority="70" Name="Dark List"/>
+
  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading"/>
+
  <w:LsdException Locked="false" Priority="72" Name="Colorful List"/>
+
  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
+
  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
+
  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
+
  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
+
  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
+
  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
+
  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
+
  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
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  <w:LsdException Locked="false" Priority="34" QFormat="true"
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  Name="List Paragraph"/>
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  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
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  <w:LsdException Locked="false" Priority="30" QFormat="true"
+
  Name="Intense Quote"/>
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  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
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  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
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  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
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  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
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  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
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  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
+
  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
+
  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
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  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
+
  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
+
  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
+
  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
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  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
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  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
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  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
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  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
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  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
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  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
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  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
+
  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
+
  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
+
  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
+
  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
+
  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
+
  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
+
  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
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  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
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  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
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  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
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  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
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  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
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  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
+
  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
+
  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
+
  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
+
  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
+
  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
+
  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
+
  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
+
  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
+
  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
+
  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
+
  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
+
  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
+
  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
+
  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
+
  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
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  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
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  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
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  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
+
  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
+
  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
+
  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
+
  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
+
  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
+
  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
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  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
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  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
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  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
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  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
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  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
+
  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
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  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
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  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
+
  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
+
  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
+
  <w:LsdException Locked="false" Priority="19" QFormat="true"
+
  Name="Subtle Emphasis"/>
+
  <w:LsdException Locked="false" Priority="21" QFormat="true"
+
  Name="Intense Emphasis"/>
+
  <w:LsdException Locked="false" Priority="31" QFormat="true"
+
  Name="Subtle Reference"/>
+
  <w:LsdException Locked="false" Priority="32" QFormat="true"
+
  Name="Intense Reference"/>
+
  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
+
  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
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  UnhideWhenUsed="true" Name="Bibliography"/>
+
  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
+
  UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
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  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
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  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
+
  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
+
  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
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  <w:LsdException Locked="false" Priority="46"
+
  Name="Grid Table 1 Light Accent 1"/>
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  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
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  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
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  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
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  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
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  <w:LsdException Locked="false" Priority="51"
+
  Name="Grid Table 6 Colorful Accent 1"/>
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  <w:LsdException Locked="false" Priority="52"
+
  Name="Grid Table 7 Colorful Accent 1"/>
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  <w:LsdException Locked="false" Priority="46"
+
  Name="Grid Table 1 Light Accent 2"/>
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  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
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  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
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  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
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  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
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  <w:LsdException Locked="false" Priority="51"
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  Name="Grid Table 6 Colorful Accent 2"/>
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  <w:LsdException Locked="false" Priority="52"
+
  Name="Grid Table 7 Colorful Accent 2"/>
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  <w:LsdException Locked="false" Priority="46"
+
  Name="Grid Table 1 Light Accent 3"/>
+
  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
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  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
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  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
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  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
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  <w:LsdException Locked="false" Priority="51"
+
  Name="Grid Table 6 Colorful Accent 3"/>
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  <w:LsdException Locked="false" Priority="52"
+
  Name="Grid Table 7 Colorful Accent 3"/>
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  <w:LsdException Locked="false" Priority="46"
+
  Name="Grid Table 1 Light Accent 4"/>
+
  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
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  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
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  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
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  <w:LsdException Locked="false" Priority="51"
+
  Name="Grid Table 6 Colorful Accent 4"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="Grid Table 7 Colorful Accent 4"/>
+
  <w:LsdException Locked="false" Priority="46"
+
  Name="Grid Table 1 Light Accent 5"/>
+
  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
+
  <w:LsdException Locked="false" Priority="51"
+
  Name="Grid Table 6 Colorful Accent 5"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="Grid Table 7 Colorful Accent 5"/>
+
  <w:LsdException Locked="false" Priority="46"
+
  Name="Grid Table 1 Light Accent 6"/>
+
  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
+
  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
+
  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
+
  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
+
  <w:LsdException Locked="false" Priority="51"
+
  Name="Grid Table 6 Colorful Accent 6"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="Grid Table 7 Colorful Accent 6"/>
+
  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
+
  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
+
  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
+
  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
+
  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
+
  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
+
  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
+
  <w:LsdException Locked="false" Priority="46"
+
  Name="List Table 1 Light Accent 1"/>
+
  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
+
  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
+
  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
+
  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
+
  <w:LsdException Locked="false" Priority="51"
+
  Name="List Table 6 Colorful Accent 1"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="List Table 7 Colorful Accent 1"/>
+
  <w:LsdException Locked="false" Priority="46"
+
  Name="List Table 1 Light Accent 2"/>
+
  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
+
  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
+
  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
+
  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
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  <w:LsdException Locked="false" Priority="51"
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  Name="List Table 6 Colorful Accent 2"/>
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  <w:LsdException Locked="false" Priority="52"
+
  Name="List Table 7 Colorful Accent 2"/>
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  <w:LsdException Locked="false" Priority="46"
+
  Name="List Table 1 Light Accent 3"/>
+
  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
+
  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
+
  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
+
  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
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  <w:LsdException Locked="false" Priority="51"
+
  Name="List Table 6 Colorful Accent 3"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="List Table 7 Colorful Accent 3"/>
+
  <w:LsdException Locked="false" Priority="46"
+
  Name="List Table 1 Light Accent 4"/>
+
  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
+
  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
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  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
+
  <w:LsdException Locked="false" Priority="51"
+
  Name="List Table 6 Colorful Accent 4"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="List Table 7 Colorful Accent 4"/>
+
  <w:LsdException Locked="false" Priority="46"
+
  Name="List Table 1 Light Accent 5"/>
+
  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
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  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
+
  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
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  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
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  <w:LsdException Locked="false" Priority="51"
+
  Name="List Table 6 Colorful Accent 5"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="List Table 7 Colorful Accent 5"/>
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  <w:LsdException Locked="false" Priority="46"
+
  Name="List Table 1 Light Accent 6"/>
+
  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
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  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
+
  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
+
  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
+
  <w:LsdException Locked="false" Priority="51"
+
  Name="List Table 6 Colorful Accent 6"/>
+
  <w:LsdException Locked="false" Priority="52"
+
  Name="List Table 7 Colorful Accent 6"/>
+
</w:LatentStyles>
+
</xml><![endif]-->
+
 
<style>
 
<style>
 
<!--
 
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Line 652: Line 11:
 
  @font-face
 
  @font-face
 
{font-family:"MS Mincho";
 
{font-family:"MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;
+
panose-1:2 2 6 9 4 2 5 8 3 4;}
mso-font-alt:"Arial Unicode MS";
+
mso-font-charset:128;
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mso-generic-font-family:roman;
+
mso-font-format:other;
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mso-font-pitch:fixed;
+
mso-font-signature:0 134676480 16 0 131072 0;}
+
 
@font-face
 
@font-face
 
{font-family:"Cambria Math";
 
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;
+
panose-1:2 4 5 3 5 4 6 3 2 4;}
mso-font-charset:0;
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mso-generic-font-family:roman;
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mso-font-pitch:variable;
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mso-font-signature:-536870145 1107305727 0 0 415 0;}
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@font-face
 
@font-face
 
{font-family:Calibri;
 
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;
+
panose-1:2 15 5 2 2 2 4 3 2 4;}
mso-font-charset:0;
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mso-generic-font-family:swiss;
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mso-font-pitch:variable;
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mso-font-signature:-536870145 1073786111 1 0 415 0;}
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@font-face
 
@font-face
 
{font-family:Cambria;
 
{font-family:Cambria;
panose-1:2 4 5 3 5 4 6 3 2 4;
+
panose-1:2 4 5 3 5 4 6 3 2 4;}
mso-font-charset:0;
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mso-generic-font-family:roman;
+
mso-font-pitch:variable;
+
mso-font-signature:-536870145 1073743103 0 0 415 0;}
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@font-face
 
@font-face
 
{font-family:Times;
 
{font-family:Times;
panose-1:2 2 6 3 5 4 5 2 3 4;
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panose-1:2 2 6 3 5 4 5 2 3 4;}
mso-font-charset:0;
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mso-generic-font-family:roman;
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mso-font-pitch:variable;
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mso-font-signature:-536858881 -1073711037 9 0 511 0;}
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@font-face
 
@font-face
{font-family:"Lucida Grande";
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{font-family:"Lucida Grande";}
mso-font-charset:0;
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mso-generic-font-family:auto;
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mso-font-pitch:variable;
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mso-font-signature:-520090897 1342218751 0 0 447 0;}
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@font-face
 
@font-face
 
{font-family:"Comic Sans MS";
 
{font-family:"Comic Sans MS";
panose-1:3 15 7 2 3 3 2 2 2 4;
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panose-1:3 15 7 2 3 3 2 2 2 4;}
mso-font-charset:0;
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mso-generic-font-family:script;
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mso-font-pitch:variable;
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mso-font-signature:647 1073741843 0 0 159 0;}
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@font-face
 
@font-face
 
{font-family:Garamond;
 
{font-family:Garamond;
panose-1:2 2 4 4 3 3 1 1 8 3;
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panose-1:2 2 4 4 3 3 1 1 8 3;}
mso-font-charset:0;
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mso-generic-font-family:roman;
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mso-font-pitch:variable;
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mso-font-signature:647 0 0 0 159 0;}
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@font-face
 
@font-face
 
{font-family:"\@MS Mincho";
 
{font-family:"\@MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;
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panose-1:2 2 6 9 4 2 5 8 3 4;}
mso-font-charset:128;
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mso-generic-font-family:roman;
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mso-font-format:other;
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mso-font-pitch:fixed;
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mso-font-signature:0 134676480 16 0 131072 0;}
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  /* Style Definitions */
 
  /* Style Definitions */
 
  p.MsoNormal, li.MsoNormal, div.MsoNormal
 
  p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
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{margin:0in;
mso-style-qformat:yes;
+
mso-style-parent:"";
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margin:0in;
+
 
margin-bottom:.0001pt;
 
margin-bottom:.0001pt;
mso-pagination:widow-orphan;
 
 
font-size:12.0pt;
 
font-size:12.0pt;
font-family:"Cambria",serif;
+
font-family:"Cambria",serif;}
mso-ascii-font-family:Cambria;
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mso-ascii-theme-font:minor-latin;
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mso-fareast-font-family:"MS Mincho";
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mso-fareast-theme-font:minor-fareast;
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mso-hansi-font-family:Cambria;
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mso-hansi-theme-font:minor-latin;
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</head>
 
</head>
  
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+
<body lang=EN-US link=blue vlink=purple>
  
 
<div class=WordSection1>
 
<div class=WordSection1>
  
<p class=MsoNormal align=center style='text-align:center;line-height:150%'><b
+
<p class=MsoNormal align=center style='text-align:center;line-height:150%'><b><span
style='mso-bidi-font-weight:normal'><span style='font-size:26.0pt;line-height:
+
style='font-size:32.0pt;line-height:150%;font-family:"Calibri",sans-serif;
150%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
+
color:#C00000'>Methods</span></b></p>
mso-hansi-theme-font:major-latin;mso-bidi-font-family:Arial;color:#C00000;
+
mso-bidi-font-style:italic'>Experiments and Protocols</span></b><b
+
style='mso-bidi-font-weight:normal'><span style='font-size:26.0pt;line-height:
+
150%;font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
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mso-hansi-theme-font:major-latin;mso-bidi-font-family:Arial;color:black;
+
mso-bidi-font-style:italic'><o:p></o:p></span></b></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><i><span style='font-size:11.0pt;
 
<p class=MsoNormal style='line-height:150%'><i><span style='font-size:11.0pt;
line-height:150%;font-family:"Arial",sans-serif;color:black'><o:p>&nbsp;</o:p></span></i></p>
+
line-height:150%;font-family:"Arial",sans-serif;color:black'>&nbsp;</span></i></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Oscillator System</span></p>
color:black;mso-bidi-font-style:italic'>Oscillator System</span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Garamond",serif;color:black'>We plan oscillations
color:black'>We plan oscillations using western blots and densitometry analysis
+
using western blots and densitometry analysis to track the different
to track the different phosphorylation states of <span class=SpellE>KaiC</span>.
+
phosphorylation states of KaiC. In order to synchronize a population of cells,
In order to synchronize a population of cells, we used M9 minimal media with no
+
we used M9 minimal media with no carbon supplements in order to limit the ATP
carbon supplements in order to limit the ATP provided to the E.coli cells. This
+
provided to the E.coli cells. This shock was conducted for both one and six
shock was conducted for both one and six hours (See results). </span><span
+
hours (See results). </span></p>
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif'>&nbsp;</span></p>
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Garamond",serif;color:black'>In addition to
color:black'>In addition to examining oscillations of our <span class=SpellE>KaiABC</span>
+
examining oscillations of our KaiABC biobrick, we also aimed to optimize these
<span class=SpellE>biobrick</span>, we also aimed to optimize these
+
oscillations by altering the concentrations of KaiA, which is driven under an
oscillations by altering the concentrations of <span class=SpellE>KaiA</span>,
+
L-rhamnose inducible promoter. The input to output ratio of KaiA was first
which is driven under an L-<span class=SpellE>rhamnose</span> inducible
+
investigated using a 10 fold gradient of L-rhamnose concentrations. We assayed
promoter. The input to output ratio of <span class=SpellE>KaiA</span> was first
+
the amount of KaiA produced using Bradford assay and western blots. We
investigated using a 10 fold gradient of L-<span class=SpellE>rhamnose</span>
+
estimated the correct concentrations of L-rhamnose as well as the time of
concentrations. We assayed the amount of <span class=SpellE>KaiA</span>
+
produced using Bradford assay and western blots. We estimated the correct
+
concentrations of L-<span class=SpellE>rhamnose</span> as well as the time of
+
 
induction data from the Paris-Bettencourt 2014 team. Induction was completed
 
induction data from the Paris-Bettencourt 2014 team. Induction was completed
 
for 10 hours. We additionally conducted a time-course of induction for 16 hours
 
for 10 hours. We additionally conducted a time-course of induction for 16 hours
in order to determine the saturation point of <span class=SpellE>KaiA</span>,
+
in order to determine the saturation point of KaiA, and to examine the
and to examine the degradation rate of <span class=SpellE>KaiA</span> after
+
degradation rate of KaiA after removal of the inducer from the
removal of the inducer from the synchronization/shock in M9 minimal media. </span><span
+
synchronization/shock in M9 minimal media. </span></p>
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Read-Out System</span></p>
color:black;mso-bidi-font-style:italic'>Read-Out System</span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Garamond",serif;color:black'>We plan to assay the
color:black'>We plan to assay the read-out system by putting together pMC002 or
+
read-out system by putting together pMC002 or pMC003 with the KaiC
pMC003 with the <span class=SpellE>KaiC</span> <span class=SpellE>phosphomimetics</span>
+
phosphomimetics pMC004-7. pMC004-7 exhibit different phosphorylation states of
pMC004-7. <span class=GramE>pMC004-7</span> exhibit different phosphorylation
+
KaiC, essentially portraying a snapshot of KaiC throughout its oscillations in
states of <span class=SpellE>KaiC</span>, essentially portraying a snapshot of <span
+
the KaiABC system. We will pair each of these phosphomimetics with pMC002,
class=SpellE>KaiC</span> throughout its oscillations in the <span class=SpellE>KaiABC</span>
+
containing the master regulator RpaA, its activator SasA, and a response
system. We will pair each of these <span class=SpellE>phosphomimetics</span>
+
regulator RpaB (the function of this has not been clearly characterized yet).
with pMC002, containing the master regulator <span class=SpellE>RpaA</span>,
+
We will also pair each of the phosphomimetics with pMC003, exhibiting the same
its activator <span class=SpellE>SasA</span>, and a response regulator <span
+
factors RpaA, RpaB, and SasA with the addition of CikA, a negative regulator of
class=SpellE>RpaB</span> (the function of this has not been clearly
+
RpaA. We will assay the activation and deactivation of RpaA by measuring the
characterized yet). We will also pair each of the <span class=SpellE>phosphomimetics</span>
+
fluorescence of GFP under a plate reader. Given that the LVA-Stop tagged GFP is
with pMC003, exhibiting the same factors <span class=SpellE>RpaA</span>, <span
+
directly downstream the circadian kaibc promoter, we expect differences in
class=SpellE>RpaB</span>, and <span class=SpellE>SasA</span> with the addition
+
activation/deactivation of RpaA to directly impact the amount of GFP expressed.
of <span class=SpellE>CikA</span>, a negative regulator of <span class=SpellE>RpaA</span>.
+
As such, we expect different fluorescence readings for each of the
We will assay the activation and deactivation of <span class=SpellE>RpaA</span>
+
phosphomimetics. Furthemore, we hypothesize that pMC003 will yield a greater
by measuring the fluorescence of GFP under a plate reader. Given that the
+
contrast in fluorescence readings between each phosphomimetic, given that it is
LVA-Stop tagged GFP is directly downstream the circadian <span class=SpellE>kaibc</span>
+
a negative regulator of RpaA.</span><span style='font-size:16.0pt;line-height:
promoter, we expect differences in activation/deactivation of <span
+
150%;font-family:"Arial",sans-serif;color:black'> </span></p>
class=SpellE>RpaA</span> to directly impact the amount of GFP expressed. As
+
such, we expect different fluorescence readings for each of the <span
+
class=SpellE>phosphomimetics</span>. <span class=SpellE>Furthemore</span>, we
+
hypothesize that pMC003 will yield a greater contrast in fluorescence readings
+
between each <span class=SpellE>phosphomimetic</span>, given that it is a
+
negative regulator of <span class=SpellE>RpaA</span>.</span><span
+
style='font-size:11.0pt;line-height:150%;font-family:"Arial",sans-serif;
+
color:black'> </span><span style='font-size:10.0pt;line-height:150%;font-family:
+
"Times",serif;mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><o:p></o:p></span></p>
+
  
 
<p class=MsoNormal align=center style='text-align:center;line-height:150%'><span
 
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line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>&nbsp;</span></p>
color:black;mso-bidi-font-weight:bold'>Specific Assays:</span><span
+
style='font-size:10.0pt;line-height:150%;font-family:"Times",serif;mso-fareast-font-family:
+
"Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Comic Sans MS";color:black'>&nbsp;</span></p>
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Gibson Assembly </span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>&nbsp;</span></p>
color:black'>Gibson assembly was conducted using NEBs 2x <span class=SpellE>HiFi</span>
+
Assembly Master Mix. Volume of Gibson was halved in order to save reagent. 50
+
ng of the longest fragment in each reaction was added, and other fragments were
+
added in ratio relative to the longest fragment. 5uL of the master mix was
+
used, and H2O was added to bring whole volume of reaction to 10 <span
+
class=SpellE>uL</span>. Reaction was incubated at 50C for 1 hour. </span><span
+
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Specific Assays:</span></p>
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>PCR </span><span style='font-size:16.0pt;
+
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span class=SpellE><span
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Gibson Assembly </span></p>
mso-bidi-font-family:Arial;color:black'>Phusion</span></span><span
+
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:Arial;color:black'> DNAP from <span class=SpellE>Thermo</span>
+
Fisher with HF buffer used for reactions. Each reaction was supplemented with
+
DMSO. Gradient PCRs, <span class=SpellE>miniprep</span> PCRs, and colony PCRs
+
were conducted with 10uL as the final reaction volume. Samples that would be
+
gel extracted were conducted with 50 <span class=SpellE>uL</span> as the final
+
reaction volume. 10 <span class=SpellE>uM</span> primers were added. 30 cycles
+
of PCR were conducted. See Notebook for details on cycle temperatures. </span><span
+
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif;color:black'>Gibson assembly was
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
conducted using NEBs 2x HiFi Assembly Master Mix. Volume of Gibson was halved
 +
in order to save reagent. 50 ng of the longest fragment in each reaction was
 +
added, and other fragments were added in ratio relative to the longest fragment.
 +
5uL of the master mix was used, and H2O was added to bring whole volume of
 +
reaction to 10 uL. Reaction was incubated at 50C for 1 hour. </span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Gel Electrophoresis</span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>PCR </span></p>
color:black'>Gel set up in TAE buffer. 1% agarose gel used for standard
+
electrophoresis. 0.8% gel used for smaller fragments. 0.7 <span class=SpellE>uL</span>
+
of EtBr added for imaging. Gels run for 30 mins at 120V. Invitrogen 1 kB ladder
+
used for standard protocols. </span><span style='font-size:14.0pt;line-height:
+
150%;font-family:"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif;color:black'>Phusion DNAP from
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
Thermo Fisher with HF buffer used for reactions. Each reaction was supplemented
 +
with DMSO. Gradient PCRs, miniprep PCRs, and colony PCRs were conducted with
 +
10uL as the final reaction volume. Samples that would be gel extracted were
 +
conducted with 50 uL as the final reaction volume. 10 uM primers were added. 30
 +
cycles of PCR were conducted. See Notebook for details on cycle temperatures. </span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Gel Extraction </span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span class=SpellE><span
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Gel Electrophoresis</span></p>
mso-bidi-font-family:Arial;color:black'>Machery</span></span><span
+
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:Arial;color:black'>-Nagel gel extraction kit used. See
+
notebook for complete protocol. Samples eluted in 15 <span class=SpellE>uL</span>
+
of elution buffer. </span><span style='font-size:14.0pt;line-height:150%;
+
font-family:"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif;color:black'>Gel set up in TAE
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
buffer. 1% agarose gel used for standard electrophoresis. 0.8% gel used for
 +
smaller fragments. 0.7 uL of EtBr added for imaging. Gels run for 30 mins at
 +
120V. Invitrogen 1 kB ladder used for standard protocols. </span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Transformation </span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Gel Extraction </span></p>
color:black'>Competent cells made by team using RbCl2 and CaCl2 chemically
+
competent protocols. </span><span style='font-size:14.0pt;line-height:150%;
+
font-family:"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Garamond",serif;color:black'>Machery-Nagel gel
color:black'>Efficiencies of competent cells were <u>4.00 x 10^5 <span
+
extraction kit used. See notebook for complete protocol. Samples eluted in 15
class=SpellE>transformants</span>/<span class=GramE>ng <span style='text-decoration:
+
uL of elution buffer. </span></p>
none;text-underline:none'>&nbsp;and</span></span></u> &nbsp;<u>1.15 x 10^6 <span
+
class=SpellE>transformants</span>/ng </u>respectively. Transformation was
+
conducted by incubating on ice for 30 mins and conducting a heat shock at 42 C
+
for 1 min. Colonies plated using glass beads method. Incubation at 37C
+
overnight. </span><span style='font-size:14.0pt;line-height:150%;font-family:
+
"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Transformation </span></p>
color:black;mso-bidi-font-style:italic'>Sequencing </span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Garamond",serif;color:black'>Competent cells made
color:black'>Sequencing conducted by the University of Chicago’s sequencing
+
by team using RbCl2 and CaCl2 chemically competent protocols. </span></p>
centers. </span><span style='font-size:14.0pt;line-height:150%;font-family:
+
"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif;color:black'>Efficiencies of
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
competent cells were <u>4.00 x 10^5 transformants/ng </u>&nbsp;and &nbsp;<u>1.15
 +
x 10^6 transformants/ng </u>respectively. Transformation was conducted by
 +
incubating on ice for 30 mins and conducting a heat shock at 42 C for 1 min.
 +
Colonies plated using glass beads method. Incubation at 37C overnight. </span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Growing cultures</span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Sequencing </span></p>
color:black'>Cultures grown for induction were incubated at 37C. OD600 for
+
initial assays were measured to be around 1.5. In latter assays, cells were
+
diluted to be OD 600 ~0.6-0.7. Initial cultures were always grown in LB. </span><span
+
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif;color:black'>Sequencing conducted
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
by the University of Chicago Comprehensive Cancer Center’s sequencing centers. </span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Induction </span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Growing cultures</span></p>
color:black'>Induction of <span class=SpellE>rhamnose</span> to drive <span
+
class=SpellE>KaiA</span> expression conducted in M9 minimal media with
+
supplements: 0.4% glycerol and 0.1% <span class=SpellE>casamino</span> acids.
+
Induction solutions made with varying concentrations of <span class=SpellE>rhamnose</span>
+
in order to characterize the input-output ratio of <span class=SpellE>rhamnose</span>
+
to <span class=SpellE>KaiA</span>. This was significant for us to be able to
+
vary the concentrations of <span class=SpellE>KaiA</span> and to develop more
+
robust oscillations. Induction conducted for 10 hours at 30C. Induction
+
protocol followed from Silver Lab (Chen, A. H., <span class=SpellE>Lubkowicz</span>,
+
D., <span class=SpellE><span class=GramE>Yeong</span></span>, V., Chang, R. L.,
+
&amp; Silver, P. a. (2015a). <span class=SpellE>Transplantability</span> of a
+
circadian clock to a <span class=SpellE>noncircadian</span> organism. Science
+
Advance, 1(5), 1–6. </span><a href="http://doi.org/10.1126/sciadv.1500358"><span
+
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:Arial;color:#1155CC'>http://doi.org/10.1126/sciadv.1500358</span></a><span
+
class=GramE><span style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:Arial;color:black'>) .</span></span><span
+
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
mso-bidi-font-family:Arial;color:black'> </span><span style='font-size:14.0pt;
+
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif;color:black'>Cultures grown for
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
induction were incubated at 37C. OD600 for initial assays were measured to be
 +
around 1.5. In latter assays, cells were diluted to be OD 600 ~0.6-0.7. Initial
 +
cultures were always grown in LB. </span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Synchronization </span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Induction </span></p>
color:black'>Synchronization to synchronize the <span class=SpellE>KaiABC</span>
+
clock was conducted by incubating induced cells in M9 minimal media only (no
+
supplements). Synchronization conducted for both 1 hour and 6 hours. Silver lab
+
reported 1 hour synchronization while Rust lab has seen 6 hours to be adequate
+
for cyanobacteria. </span><span style='font-size:14.0pt;line-height:150%;
+
font-family:"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Garamond",serif;color:black'>Induction of
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
rhamnose to drive KaiA expression conducted in M9 minimal media with
 +
supplements: 0.4% glycerol and 0.1% casamino acids. Induction solutions made
 +
with varying concentrations of rhamnose in order to characterize the
 +
input-output ratio of rhamnose to KaiA. This was significant for us to be able
 +
to vary the concentrations of KaiA and to develop more robust oscillations.
 +
Induction conducted for 10 hours at 30C. Induction protocol followed from
 +
Silver Lab (Chen, A. H., Lubkowicz, D., Yeong, V., Chang, R. L., &amp; Silver,
 +
P. a. (2015a). Transplantability of a circadian clock to a noncircadian
 +
organism. Science Advance, 1(5), 1–6. </span><a
 +
href="http://doi.org/10.1126/sciadv.1500358"><span style='font-size:16.0pt;
 +
line-height:150%;font-family:"Garamond",serif;color:#1155CC'>http://doi.org/10.1126/sciadv.1500358</span></a><span
 +
style='font-size:16.0pt;line-height:150%;font-family:"Garamond",serif;
 +
color:black'>) . </span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
color:black;mso-bidi-font-style:italic'>Oscillation Time Course </span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Synchronization </span></p>
color:black'>Following synchronization, cells were reintroduced in M9 media
+
 
with 1mM leucine and 0.5% succinate supplements to allow for slow growth. Oscillations
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
were tracked by freezing 2 mL cell samples every 6 hours in a -80C freezer. The
+
line-height:150%;font-family:"Garamond",serif;color:black'>Synchronization to
time duration for tracking oscillations was set at 3 days. </span><span
+
synchronize the KaiABC clock was conducted by incubating induced cells in M9
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
minimal media only (no supplements or inducer). Synchronization conducted for
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
both 1 hour and 6 hours. Silver lab reported 1 hour synchronization while Rust
 +
lab has seen 6 hours to be adequate for cyanobacteria. </span></p>
 +
 
 +
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 +
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
 +
 
 +
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 +
line-height:150%;font-family:"Comic Sans MS";color:black'>Oscillation Time
 +
Course </span></p>
 +
 
 +
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 +
line-height:150%;font-family:"Garamond",serif;color:black'>Following
 +
synchronization, cells were reintroduced in M9 media with 1mM leucine and 0.5%
 +
succinate supplements to allow for slow growth. Oscillations were tracked by
 +
freezing 2 mL cell samples every 6 hours in a -80C freezer. The time duration
 +
for tracking oscillations was set at 3 days. No rhamnose was added back, due to
 +
Silver lab’s reports of desynchronization of oscillations attributed to reintroduction
 +
of inducer with their construct.</span></p>
  
 
<p class=MsoNormal style='margin-bottom:12.0pt;line-height:150%'><span
 
<p class=MsoNormal style='margin-bottom:12.0pt;line-height:150%'><span
style='font-size:10.0pt;line-height:150%;font-family:"Times",serif;mso-fareast-font-family:
+
style='font-size:16.0pt;line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
"Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Western Blot</span></p>
color:black;mso-bidi-font-style:italic'>Western Blot</span><span
+
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Garamond",serif;color:black'>In order to track
color:black'>In order to track expression of <span class=SpellE>KaiA<span
+
expression of KaiA,B,C, and phosphorylation states of KaiC western blots were
class=GramE>,B,C</span></span>, and phosphorylation states of <span
+
conducted. For simple expression assays, such as when characterizing the pRha
class=SpellE>KaiC</span> western blots were conducted. For simple expression
+
promoter and quantifying KaiA expression, a 14-20% BioRad precast protein gel
assays, such as when characterizing the <span class=SpellE>pRha</span> promoter
+
was used during SDS page gel run. For tracking different phoshphorylation
and quantifying <span class=SpellE>KaiA</span> expression, a 14-20% <span
+
states of KaiC, a 4-7% BioRad precast protein gel was used. Bradford assays
class=SpellE>BioRad</span> precast protein gel was used during SDS page gel
+
were conducted before SDS-page in order to standardize the amount of protein
run. For tracking different <span class=SpellE>phoshphorylation</span> states
+
added per sample. A positive control of cyanobacterial lysate, and a negative
of <span class=SpellE>KaiC</span>, a 4-7% <span class=SpellE>BioRad</span>
+
control of E.coli cells containing an empty Cam circular backbone were run.
precast protein gel was used. Bradford assays were conducted before SDS-page in
+
Purified protein samples provided by the Rust lab were run to quantify amount
order to standardize the amount of protein added per sample. A positive control
+
of KaiA, B, and C expressed by transformed E.coli cells. Transfer accomplished
of cyanobacterial lysate, and a negative control of E.coli cells containing an
+
using PVDF membranes. Membrane sandwich apparatus was prepared under Towbin
empty Cam circular backbone were run. Purified protein samples provided by the
+
Rust lab were run to quantify amount of <span class=SpellE>KaiA</span>, B, and
+
C expressed by transformed E.coli cells. Transfer accomplished using PVDF
+
membranes. Membrane sandwich apparatus was prepared under <span class=SpellE>Towbin</span>
+
 
transfer buffer. Blocking to prevent non-specific binding of antibodies was
 
transfer buffer. Blocking to prevent non-specific binding of antibodies was
 
conducted using TBST+2% dry milk. This was followed by a stain of primary
 
conducted using TBST+2% dry milk. This was followed by a stain of primary
Line 1,222: Line 325:
 
membranes were washed using wash buffer then stained with anti-goat HRP
 
membranes were washed using wash buffer then stained with anti-goat HRP
 
secondary antibody allowing us to visualize the primary antibody stain. The
 
secondary antibody allowing us to visualize the primary antibody stain. The
membranes were washed then imaged using <span class=SpellE>chemilumenescnece</span>
+
membranes were washed then imaged using chemilumenescnece imaging systems. </span></p>
imaging systems. </span><span style='font-size:14.0pt;line-height:150%;
+
font-family:"Garamond",serif;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Comic Sans MS";color:black'>Imaging and
color:black;mso-bidi-font-style:italic'>Imaging and Quantification</span><span
+
Quantification</span></p>
style='font-size:16.0pt;line-height:150%;font-family:"Comic Sans MS";
+
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt;
+
<p class=MsoNormal style='line-height:150%'><span style='font-size:16.0pt;
line-height:150%;font-family:"Garamond",serif;mso-bidi-font-family:Arial;
+
line-height:150%;font-family:"Garamond",serif;color:black'>Densitometry of
color:black'>Densitometry of images was conducted in ImageJ. <i>&nbsp;</i></span><span
+
images was conducted in ImageJ. For the induction time course and the oscillation
style='font-size:14.0pt;line-height:150%;font-family:"Garamond",serif;
+
assays (oscillation data not up on wiki, but to be presented at the Jamboree),
mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p>
+
the nanogram amount of each protein was determined by calibrating to a
 +
logarithm curve of purified standards of known concentration ran on the same
 +
Western blot. This allowed for determination of accurate stoichiometric ratios
 +
between KaiA on the rhamnose inducible promoter and KaiB and KaiC, both on the
 +
constitutive promoter. Normalization for OD was performed for post-shock time
 +
points, including oscillation time points, to control for changes in cell
 +
density and protein degradation after induction of KaiA was turned off.</span></p>
  
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
 
<p class=MsoNormal style='line-height:150%'><span style='font-size:10.0pt;
line-height:150%;font-family:"Times",serif;mso-fareast-font-family:"Times New Roman";
+
line-height:150%;font-family:"Times",serif'>&nbsp;</span></p>
mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
+
  
<p class=MsoNormal style='line-height:150%'><o:p>&nbsp;</o:p></p>
+
<p class=MsoNormal style='line-height:150%'>&nbsp;</p>
  
 
</div>
 
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{{UChicago/Footer}}
 
{{UChicago/Footer}}

Latest revision as of 03:55, 9 October 2015

Team UChicago banner.jpg

Methods

 

Oscillator System

We plan oscillations using western blots and densitometry analysis to track the different phosphorylation states of KaiC. In order to synchronize a population of cells, we used M9 minimal media with no carbon supplements in order to limit the ATP provided to the E.coli cells. This shock was conducted for both one and six hours (See results).

 

In addition to examining oscillations of our KaiABC biobrick, we also aimed to optimize these oscillations by altering the concentrations of KaiA, which is driven under an L-rhamnose inducible promoter. The input to output ratio of KaiA was first investigated using a 10 fold gradient of L-rhamnose concentrations. We assayed the amount of KaiA produced using Bradford assay and western blots. We estimated the correct concentrations of L-rhamnose as well as the time of induction data from the Paris-Bettencourt 2014 team. Induction was completed for 10 hours. We additionally conducted a time-course of induction for 16 hours in order to determine the saturation point of KaiA, and to examine the degradation rate of KaiA after removal of the inducer from the synchronization/shock in M9 minimal media.

 

Read-Out System

We plan to assay the read-out system by putting together pMC002 or pMC003 with the KaiC phosphomimetics pMC004-7. pMC004-7 exhibit different phosphorylation states of KaiC, essentially portraying a snapshot of KaiC throughout its oscillations in the KaiABC system. We will pair each of these phosphomimetics with pMC002, containing the master regulator RpaA, its activator SasA, and a response regulator RpaB (the function of this has not been clearly characterized yet). We will also pair each of the phosphomimetics with pMC003, exhibiting the same factors RpaA, RpaB, and SasA with the addition of CikA, a negative regulator of RpaA. We will assay the activation and deactivation of RpaA by measuring the fluorescence of GFP under a plate reader. Given that the LVA-Stop tagged GFP is directly downstream the circadian kaibc promoter, we expect differences in activation/deactivation of RpaA to directly impact the amount of GFP expressed. As such, we expect different fluorescence readings for each of the phosphomimetics. Furthemore, we hypothesize that pMC003 will yield a greater contrast in fluorescence readings between each phosphomimetic, given that it is a negative regulator of RpaA.

https://lh4.googleusercontent.com/pWda2PyQ3OVkertP1WQ3IpbHbnRP2oYVYTWA9rbP6devD_5FxIpJpZVUHp6FyFAtENPb5vqx58NKiR6baFdfQn9WyoOgfShLyk99QO6w4r0zQiCTjOtAeyltVK2WBOf5pok=s1600

 

 

 

 

Specific Assays:

 

Gibson Assembly

Gibson assembly was conducted using NEBs 2x HiFi Assembly Master Mix. Volume of Gibson was halved in order to save reagent. 50 ng of the longest fragment in each reaction was added, and other fragments were added in ratio relative to the longest fragment. 5uL of the master mix was used, and H2O was added to bring whole volume of reaction to 10 uL. Reaction was incubated at 50C for 1 hour.

 

PCR

Phusion DNAP from Thermo Fisher with HF buffer used for reactions. Each reaction was supplemented with DMSO. Gradient PCRs, miniprep PCRs, and colony PCRs were conducted with 10uL as the final reaction volume. Samples that would be gel extracted were conducted with 50 uL as the final reaction volume. 10 uM primers were added. 30 cycles of PCR were conducted. See Notebook for details on cycle temperatures.

 

Gel Electrophoresis

Gel set up in TAE buffer. 1% agarose gel used for standard electrophoresis. 0.8% gel used for smaller fragments. 0.7 uL of EtBr added for imaging. Gels run for 30 mins at 120V. Invitrogen 1 kB ladder used for standard protocols.

 

Gel Extraction

Machery-Nagel gel extraction kit used. See notebook for complete protocol. Samples eluted in 15 uL of elution buffer.

 

Transformation

Competent cells made by team using RbCl2 and CaCl2 chemically competent protocols.

Efficiencies of competent cells were 4.00 x 10^5 transformants/ng  and  1.15 x 10^6 transformants/ng respectively. Transformation was conducted by incubating on ice for 30 mins and conducting a heat shock at 42 C for 1 min. Colonies plated using glass beads method. Incubation at 37C overnight.

 

Sequencing

Sequencing conducted by the University of Chicago Comprehensive Cancer Center’s sequencing centers.

 

Growing cultures

Cultures grown for induction were incubated at 37C. OD600 for initial assays were measured to be around 1.5. In latter assays, cells were diluted to be OD 600 ~0.6-0.7. Initial cultures were always grown in LB.

 

Induction

Induction of rhamnose to drive KaiA expression conducted in M9 minimal media with supplements: 0.4% glycerol and 0.1% casamino acids. Induction solutions made with varying concentrations of rhamnose in order to characterize the input-output ratio of rhamnose to KaiA. This was significant for us to be able to vary the concentrations of KaiA and to develop more robust oscillations. Induction conducted for 10 hours at 30C. Induction protocol followed from Silver Lab (Chen, A. H., Lubkowicz, D., Yeong, V., Chang, R. L., & Silver, P. a. (2015a). Transplantability of a circadian clock to a noncircadian organism. Science Advance, 1(5), 1–6. http://doi.org/10.1126/sciadv.1500358) .

 

Synchronization

Synchronization to synchronize the KaiABC clock was conducted by incubating induced cells in M9 minimal media only (no supplements or inducer). Synchronization conducted for both 1 hour and 6 hours. Silver lab reported 1 hour synchronization while Rust lab has seen 6 hours to be adequate for cyanobacteria.

 

Oscillation Time Course

Following synchronization, cells were reintroduced in M9 media with 1mM leucine and 0.5% succinate supplements to allow for slow growth. Oscillations were tracked by freezing 2 mL cell samples every 6 hours in a -80C freezer. The time duration for tracking oscillations was set at 3 days. No rhamnose was added back, due to Silver lab’s reports of desynchronization of oscillations attributed to reintroduction of inducer with their construct.

 

Western Blot

In order to track expression of KaiA,B,C, and phosphorylation states of KaiC western blots were conducted. For simple expression assays, such as when characterizing the pRha promoter and quantifying KaiA expression, a 14-20% BioRad precast protein gel was used during SDS page gel run. For tracking different phoshphorylation states of KaiC, a 4-7% BioRad precast protein gel was used. Bradford assays were conducted before SDS-page in order to standardize the amount of protein added per sample. A positive control of cyanobacterial lysate, and a negative control of E.coli cells containing an empty Cam circular backbone were run. Purified protein samples provided by the Rust lab were run to quantify amount of KaiA, B, and C expressed by transformed E.coli cells. Transfer accomplished using PVDF membranes. Membrane sandwich apparatus was prepared under Towbin transfer buffer. Blocking to prevent non-specific binding of antibodies was conducted using TBST+2% dry milk. This was followed by a stain of primary anti-rabbit antibodies for the Kai proteins provided by the Rust Lab. The membranes were washed using wash buffer then stained with anti-goat HRP secondary antibody allowing us to visualize the primary antibody stain. The membranes were washed then imaged using chemilumenescnece imaging systems.

 

Imaging and Quantification

Densitometry of images was conducted in ImageJ. For the induction time course and the oscillation assays (oscillation data not up on wiki, but to be presented at the Jamboree), the nanogram amount of each protein was determined by calibrating to a logarithm curve of purified standards of known concentration ran on the same Western blot. This allowed for determination of accurate stoichiometric ratios between KaiA on the rhamnose inducible promoter and KaiB and KaiC, both on the constitutive promoter. Normalization for OD was performed for post-shock time points, including oscillation time points, to control for changes in cell density and protein degradation after induction of KaiA was turned off.

 

 



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