Team:Exeter/lab book/3gip/wk7

From 2012.igem.org

(Difference between revisions)
m
 
(10 intermediate revisions not shown)
Line 90: Line 90:
         </p>
         </p>
         <a href="https://2012.igem.org/Team:Exeter/lab_book/3gip/wk11"; style="color:#1d1d1b">17th - 21st September</a>
         <a href="https://2012.igem.org/Team:Exeter/lab_book/3gip/wk11"; style="color:#1d1d1b">17th - 21st September</a>
 +
        <p>
 +
        -
 +
        </p>
 +
        <a href="https://2012.igem.org/Team:Exeter/Results/inducible"; style="color:#e30614" target="_blank"><font size="3"><b>Results</b></font></a>
 +
</font>
       </font>
       </font>
     </div>
     </div>
Line 98: Line 103:
   <td width="850" height="250">
   <td width="850" height="250">
   <!------------INSERT WEEKLY IMAGE HERE------------>
   <!------------INSERT WEEKLY IMAGE HERE------------>
-
     <img src="https://static.igem.org/mediawiki/2012/a/a4/Exe2012Pipette.jpg" alt="" title="" width="850" height="250">
+
     <img src="https://static.igem.org/mediawiki/2012/e/e5/Exe2012pipetting.jpg" alt="" title="" width="850" height="250">
   </td>
   </td>
   </tr>
   </tr>
Line 105: Line 110:
   <td valign="top" width="850">
   <td valign="top" width="850">
     <div style="text-align:justify">
     <div style="text-align:justify">
-
     <font face="DokChampa" color="#1d1d1b" size="2">
+
     <font face="Verdana" color="#1d1d1b" size="2">
      
      
-
       <font face="DokChampa" color="#57b947" size="4">
+
       <font face="Verdana" color="#57b947" size="4">
       <p><b><u>The 3-Gene Inducible Plasmid: 20th - 24th August 2012</u></b></p>
       <p><b><u>The 3-Gene Inducible Plasmid: 20th - 24th August 2012</u></b></p>
       </font>
       </font>
Line 114: Line 119:
<p><i><b>Morning</b></i></p>
<p><i><b>Morning</b></i></p>
<p>•<u>Gel Electrophoresis</u></p>  
<p>•<u>Gel Electrophoresis</u></p>  
-
<p>Last weeks 3A assembly was run to check fragment sizes after digestion using the EcoR1 and Pst1 enzymes</p>
+
<p>The 3A assembly from last week was run to check fragment sizes after digestion using the EcoR1 and Pst1 enzymes</p>
<p><i>wfcA</i> + BBa_B0014</p>  
<p><i>wfcA</i> + BBa_B0014</p>  
<p><i>wbnJ</i> + BBa_B0014</p>  
<p><i>wbnJ</i> + BBa_B0014</p>  
Line 121: Line 126:
<p><i><b>Afternoon</b></i></p>
<p><i><b>Afternoon</b></i></p>
-
<p>•<u>Two step Phusion PCR</u></p>
+
<p>•<a href="https://2012.igem.org/Team:Exeter/lab_book/proto/7" style="color:#57b947"><u>Two Step Phusion PCR</u></a></p>
-
<p>The reaction was set up using the Biolabs Phusion PCR protocol. </p><br>
+
<p>The reaction was set up using the Biolabs Phusion PCR protocol.</p><br>
<p>Two reactions were set up: </p>
<p>Two reactions were set up: </p>
Line 130: Line 135:
<p>Reaction 2: genomic DNA hopefully containing the <i>wbbC</i> gene</p>  
<p>Reaction 2: genomic DNA hopefully containing the <i>wbbC</i> gene</p>  
-
<p>The PCR mix was stored at -20°C over night so a gel could be run the next morning. </p><br>
+
<p>The PCR mix was stored at -20°C overnight so a gel could be run in the morning. </p><br>
<p><b><u>Wednesday 22nd August</u></b></p>
<p><b><u>Wednesday 22nd August</u></b></p>
Line 138: Line 143:
The <i>fadR</i> control showed a strong band but the <i>wbbC</i> gene showed nothing. </p><br>
The <i>fadR</i> control showed a strong band but the <i>wbbC</i> gene showed nothing. </p><br>
-
<p>•<u>Two step Phusion PCR using an initial lower annealing temperature</u></p>
+
<p>•<a href="https://2012.igem.org/Team:Exeter/lab_book/proto/7" style="color:#57b947"><u>Two Step Phusion PCR</u></a> using an initial lower annealing temperature</p>
-
<p>The reaction was set up using the Biolabs Phusion PCR protocol. </p><br>
+
<p>The reaction was set up using the Biolabs Phusion PCR <a href="https://2012.igem.org/Team:Exeter/lab_book/proto/7" style="color:#57b947"><u>protocol</u></a>. </p><br>
<p>Two reactions were set up: </p>
<p>Two reactions were set up: </p>
Line 151: Line 156:
<p><i><b>Afternoon</b></i></p>
<p><i><b>Afternoon</b></i></p>
-
<p>•<u> Transformation:</u></p>  
+
<p>•<a href="https://2012.igem.org/Team:Exeter/lab_book/proto/1" style="color:#57b947"><u>Transformation</u></a></p>  
<p><i>hasA</i> + BBa_B0014 in pSB1T3</p>
<p><i>hasA</i> + BBa_B0014 in pSB1T3</p>
<p><i>amyA</i> (cyclodextran gene) + BBa_B0014 in pSB1T3</p>
<p><i>amyA</i> (cyclodextran gene) + BBa_B0014 in pSB1T3</p>
Line 158: Line 163:
<p>Spread on two tetracycline plates for each transformation using 20μl and 150μls respectively. </p><br>
<p>Spread on two tetracycline plates for each transformation using 20μl and 150μls respectively. </p><br>
-
<p>Transformed for Becca. See Showcasing Polysaccharide Production: 20th - 24th August 2012, Thursday 23/08/12</p><br>
+
<p>Transformed for Becca. See <a href="https://2012.igem.org/Team:Exeter/lab_book/novpol/wk7" style="color:#57b947" target="_blank"><u>Showcasing Polysaccharide Production:</u></a> 20th - 24th August 2012, Thursday 23/08/12</p><br>
<p><b><u>Thursday 23rd August</u></b></p>
<p><b><u>Thursday 23rd August</u></b></p>
<p><i><b>Morning</b></i></p>
<p><i><b>Morning</b></i></p>
-
<p>• <u>Two step Phusion PCR using serial dilution of genomic DNA</u></p>
+
<p>• <a href="https://2012.igem.org/Team:Exeter/lab_book/proto/7" style="color:#57b947"><u>Two Step Phusion PCR</u></a> using serial dilution of genomic DNA</p>
-
<p>The reaction was set up using the Biolabs Phusion PCR protocol. </p><br>
+
<p>The reaction was set up using the Biolabs Phusion PCR <a href="https://2012.igem.org/Team:Exeter/lab_book/proto/7" style="color:#57b947"><u>Protocol</u></a>. </p><br>
<p>Two reactions were set up: </p>
<p>Two reactions were set up: </p>
Line 171: Line 176:
<p>Reaction 1: <i>wbbC</i> (sequenced with mutation) control</p>
<p>Reaction 1: <i>wbbC</i> (sequenced with mutation) control</p>
<p>Reaction 2: genomic DNA hopefully containing the WbbC gene</p>  
<p>Reaction 2: genomic DNA hopefully containing the WbbC gene</p>  
-
<p>The genomic DNA was nanodropped and from this four different</p> concentraitons prepared. Four reaction tubes containing 1μl, 0.8μl, 0.5μl and 0.1μl were used for this PCR reaction. </p>
+
<p>The genomic DNA was nanodropped and from this four different concentrations prepared. Four reaction tubes containing 1μl, 0.8μl, 0.5μl and 0.1μl were used for this PCR reaction. </p>
<p>A 1% agarose gel was prepared. 1μl of loading buffer was added to 5μl of the PCR mix and this was loaded onto the gel and run for 20 minutes. </p>
<p>A 1% agarose gel was prepared. 1μl of loading buffer was added to 5μl of the PCR mix and this was loaded onto the gel and run for 20 minutes. </p>
<p>The <i>wbbC</i> control showed a strong band but the <i>wbbC</i> gene showed nothing. We know that the primers work with <i>wbbC</i>. </p><br>
<p>The <i>wbbC</i> control showed a strong band but the <i>wbbC</i> gene showed nothing. We know that the primers work with <i>wbbC</i>. </p><br>
Line 180: Line 185:
<p><b><u>Friday 24th August</u></b></p>
<p><b><u>Friday 24th August</u></b></p>
<p><i><b>Morning</b></i></p>
<p><i><b>Morning</b></i></p>
-
<p>•<u>Three step Phusion PCR using a 10 fold dilution</u></p>
+
<p>•<a href="https://2012.igem.org/Team:Exeter/lab_book/proto/12" style="color:#57b947"><u>Three Step Phusion PCR</u></a> using a 10 fold dilution</p>
-
<p>The reaction was set up using the Biolabs Phusion PCR protocol and using a three step PCR. </p><br>
+
<p>The reaction was set up using the Biolabs Phusion PCR Three Step <a href="https://2012.igem.org/Team:Exeter/lab_book/proto/12" style="color:#57b947"><u>protocol</u></a>. </p><br>
-
<p>28 reactions were set up reactions were set up: </p>
+
<p>28 reactions were set up: </p>
-
<p><i>wbbC</i> (sequenced with mutation) control as a positive control at either end of the PCR gradient</p>
+
<p><i>wbbC</i> (sequenced with mutation) control as a positive control at either end of the PCR gradient.</p>
<p>Mastermix as a negative control at either side of the PCR gradient
<p>Mastermix as a negative control at either side of the PCR gradient
genomic DNA hopefully containing the <i>wbbC</i> gene across the PCR gradient using the 10 fold dilution. </p>
genomic DNA hopefully containing the <i>wbbC</i> gene across the PCR gradient using the 10 fold dilution. </p>
<p>A 1% agarose gel was prepared. 1ul of loading buffer was added to 5ul of the PCR mix and this was loaded onto the gel and run for 20 minutes.</p>
<p>A 1% agarose gel was prepared. 1ul of loading buffer was added to 5ul of the PCR mix and this was loaded onto the gel and run for 20 minutes.</p>
-
<p>The <i>wbbC</i> control showed a strong band, the negative control showed nothing and the <i>wbbC</i> gene from genomic DNA showed nothing. The genomic DNA may not hold the <i>wbbC</i> gene. </p><br>
+
<p>The <i>wbbC</i> control showed a strong band, the negative control showed nothing as did the <i>wbbC</i> gene from genomic DNA. The genomic DNA may not hold the <i>wbbC</i> gene. </p><br>
<p><i><b>Afternoon</b></i></p>
<p><i><b>Afternoon</b></i></p>
-
<p>Made competent cells in the afternoon following the protocol exactly. </p>  
+
<p><u>Made competent cells. </u></p>
 +
 
 +
<p>40ml of LB was inoculates in a 250ml Monod flask with 0.4ml of the overnight culture. Growth at 37°C and 200rpm until A650=0.4-0.5. </p>
 +
<p>The culture was transferred to a 40ml Falcon sterile tube and harvested by centrifugation at 8,000rpm for 8 minutes at 4°C. </p>
 +
<p>The pellet was drained and resuspended in 4ml of TF-2 solution. </p>
 +
<p>This was then placed on ice for 15 minutes and then spun again as above. </p>
 +
<p>The pellets were drained and resuspended in 4ml of TF-2. </p>
 +
<p>The competent cells were then spit into 0.2ml aliquots and frozen at -70°C immediately. </p>
 +
 
      
      
     </font>
     </font>
Line 203: Line 216:
   
   
  </table>
  </table>
 +
 +
<table width="980" align="center" cellspacing="20">
 +
<tr align="center">
 +
  <td>
 +
  <font color="#57B947" size="1" face="Verdana">
 +
    <p><u>Website Designed and Built by: Ryan Edginton, James Lynch & Alex Clowsley</u> &nbsp;&nbsp;|&nbsp;&nbsp;
 +
    <a href="https://igem.org/Team.cgi?id=764" style="color:#57B947" target="_blank"><u>Contact Us</u></a>  &nbsp;&nbsp;|&nbsp;&nbsp;
 +
    <a href="https://2012.igem.org/Team:Exeter/site_map" style="color:#57B947"><u>Site Map</u></a></p>
 +
  </font>
 +
  </td>
 +
</tr>
 +
</table>
</body>
</body>
</html>
</html>

Latest revision as of 00:06, 27 September 2012

ExiGEM2012 Lab Book 3GP wk7

The 3-Gene Inducible Plasmid: 20th - 24th August 2012

Tuesday 21st August

Morning

Gel Electrophoresis

The 3A assembly from last week was run to check fragment sizes after digestion using the EcoR1 and Pst1 enzymes

wfcA + BBa_B0014

wbnJ + BBa_B0014

BBa_B0034 wbbC + BBa_B0014


Afternoon

Two Step Phusion PCR

The reaction was set up using the Biolabs Phusion PCR protocol.


Two reactions were set up:

Reaction 1: fadR control

Reaction 2: genomic DNA hopefully containing the wbbC gene

The PCR mix was stored at -20°C overnight so a gel could be run in the morning.


Wednesday 22nd August

Morning

A 1% agarose gel was prepared. 1μl of loading buffer was added to 5μl of the PCR mix and this was loaded onto the gel and run for 20 minutes. The fadR control showed a strong band but the wbbC gene showed nothing.


Two Step Phusion PCR using an initial lower annealing temperature

The reaction was set up using the Biolabs Phusion PCR protocol.


Two reactions were set up:

Reaction 1: wbbC (sequenced with mutation) control

Reaction 2: genomic DNA hopefully containing the wbbC gene

A 1% agarose gel was prepared. 1uμl of loading buffer was added to 5μl of the PCR mix and this was loaded onto the gel and run for 20 minutes. The wbbC control showed a strong band but the wbbC genomic gene showed nothing. We know that the primers work with wbbC.


Afternoon

Transformation

hasA + BBa_B0014 in pSB1T3

amyA (cyclodextran gene) + BBa_B0014 in pSB1T3

sacB + BBa_B0014 in pSB1T3

Using Invitrogen TOP10 competent cells split into 2 eppendorfs containing 25μl each.

Spread on two tetracycline plates for each transformation using 20μl and 150μls respectively.


Transformed for Becca. See Showcasing Polysaccharide Production: 20th - 24th August 2012, Thursday 23/08/12


Thursday 23rd August

Morning

Two Step Phusion PCR using serial dilution of genomic DNA

The reaction was set up using the Biolabs Phusion PCR Protocol.


Two reactions were set up:

Reaction 1: wbbC (sequenced with mutation) control

Reaction 2: genomic DNA hopefully containing the WbbC gene

The genomic DNA was nanodropped and from this four different concentrations prepared. Four reaction tubes containing 1μl, 0.8μl, 0.5μl and 0.1μl were used for this PCR reaction.

A 1% agarose gel was prepared. 1μl of loading buffer was added to 5μl of the PCR mix and this was loaded onto the gel and run for 20 minutes.

The wbbC control showed a strong band but the wbbC gene showed nothing. We know that the primers work with wbbC.


Afternoon

Competent Cells

Before the transformation started, 1μl of cells from two tubes were pipetted onto agar plates containing no antibiotic and incubated overnight at 37°C.


Friday 24th August

Morning

Three Step Phusion PCR using a 10 fold dilution

The reaction was set up using the Biolabs Phusion PCR Three Step protocol.


28 reactions were set up:

wbbC (sequenced with mutation) control as a positive control at either end of the PCR gradient.

Mastermix as a negative control at either side of the PCR gradient genomic DNA hopefully containing the wbbC gene across the PCR gradient using the 10 fold dilution.

A 1% agarose gel was prepared. 1ul of loading buffer was added to 5ul of the PCR mix and this was loaded onto the gel and run for 20 minutes.

The wbbC control showed a strong band, the negative control showed nothing as did the wbbC gene from genomic DNA. The genomic DNA may not hold the wbbC gene.


Afternoon

Made competent cells.

40ml of LB was inoculates in a 250ml Monod flask with 0.4ml of the overnight culture. Growth at 37°C and 200rpm until A650=0.4-0.5.

The culture was transferred to a 40ml Falcon sterile tube and harvested by centrifugation at 8,000rpm for 8 minutes at 4°C.

The pellet was drained and resuspended in 4ml of TF-2 solution.

This was then placed on ice for 15 minutes and then spun again as above.

The pellets were drained and resuspended in 4ml of TF-2.

The competent cells were then spit into 0.2ml aliquots and frozen at -70°C immediately.

Website Designed and Built by: Ryan Edginton, James Lynch & Alex Clowsley   |   Contact Us   |   Site Map