Difference between revisions of "Team:Manchester/Notebook"

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         <b>Table 3. Master mix </b>
 
         <b>Table 3. Master mix </b>
 
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       </center>
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      <br /><br />
  
 
         <br />
 
         <br />
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         </center>
 
         </center>
 
         <center>
 
         <center>
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       <p class="width25">Figure 1: Colour change observed following absorbance of oxidised ABTS. Master mix containing: glucose oxidase, HRP and ABTS was added to 6 different concentrations of glucose. </p>
+
       <b>Figure 1: Colour change observed following absorbance of oxidised ABTS. Master mix containing: glucose oxidase, HRP and ABTS was added to 6 different concentrations of glucose. </b>
 
         </center>
 
         </center>
 +
 +
      <br /><br />
  
 
         <li>Based on results from yesterday, further increases in in reagents concentration that make up the master mix were tested. We tested the same glucose concentration as on 22/07/2016. The same parameters for the absorbance reading were used (i.e. every 2 sec for 5 min). The only parameter that was changed this time was master mix reagent concentration (table 4)</li>
 
         <li>Based on results from yesterday, further increases in in reagents concentration that make up the master mix were tested. We tested the same glucose concentration as on 22/07/2016. The same parameters for the absorbance reading were used (i.e. every 2 sec for 5 min). The only parameter that was changed this time was master mix reagent concentration (table 4)</li>
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         <b>Table 4. Master mix </b>
 
         <b>Table 4. Master mix </b>
 
       </center>
 
       </center>
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 +
      <br /><br />
  
 
       <h2 style="text-align:center">Result</h2>
 
       <h2 style="text-align:center">Result</h2>
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         <b>Table 5. Glucose Concentration </b>
 
         <b>Table 5. Glucose Concentration </b>
  
 +
      <br /><br />
  
 
       <h2 style="text-align:center">Result</h2>
 
       <h2 style="text-align:center">Result</h2>
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           </center>
 
           </center>
 
           <center>
 
           <center>
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         <p class="width25">Figure 2: Colour intensity following addition of master mix (ABTS,  HRP and H2O2)</p>
+
         <b>Figure 2: Colour intensity following addition of master mix (ABTS,  HRP and H2O2)</b>
 
           </center>
 
           </center>
 
       </ul>
 
       </ul>
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      <br /><br />
 
     </div>
 
     </div>
  
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<!------------------------------------------------------Week 6----------------------------------------------------->
  
  
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<button type="button" class="week6button">Week 6 (1<sup>st</sup> to 5<sup>th</sup> of August)</button>
  
 +
 +
  <div class="week6">
 +
 +
    <div class="pilot">
 +
 +
    <h1 class="subnote">Pilot Experiment</h1>
 +
 +
      <ul class="list">
 +
        <li>Performed the following reaction where ABTS is oxidised in the presence of H2O2 (final concentration 250 μg/ml ) and HRP  (final concentration 250 μg/ml </li>
 +
 +
      <center>
 +
        <table>
 +
          <tr>
 +
            <th>Concentration of ABTS (μg/ml)</th>
 +
          </tr>
 +
          <tr>
 +
            <td>1</td>
 +
          </tr>
 +
          <tr>
 +
            <td>5</td>
 +
          </tr>
 +
          <tr>
 +
            <td>10</td>
 +
          </tr>
 +
          <tr>
 +
            <td>15</td>
 +
          </tr>
 +
          <tr>
 +
            <td>20</td>
 +
          </tr>
 +
        </table>
 +
      </center>
 +
 +
        <li>Just measured absorbance of water  at 420 nm</li>
 +
 +
      <center>
 +
        <table>
 +
          <tr>
 +
            <th></th>
 +
            <th>Concentration (μg/ml)</th>
 +
          </tr>
 +
          <tr>
 +
            <th>HRP</th>
 +
            <td>0.25</td>
 +
          </tr>
 +
          <tr>
 +
            <th>HRP</th>
 +
            <td>2.50</td>
 +
          </tr>
 +
          <tr>
 +
            <th>H<sub>2</sub>O<sub>2</sub></th>
 +
            <td>5.08</td>
 +
          </tr>
 +
        </table>
 +
 +
        <b>Measured absorbance of each of the reagents at 420 nm</b>
 +
      </center>
 +
 +
      <br /><br />
 +
 +
        <li>Set up the reaction with all 4 reagents. Measured absorbance every 25 sec for 900 sec. Run samples in triplicates</li>
 +
 +
    <center>
 +
      <table>
 +
<tr>
 +
<th>&nbsp;</th>
 +
<th>ABTS (μl)</th>
 +
<th>H2O2 (μl)</th>
 +
<th>HRP (μl)</th>
 +
<th>PBS (μl)</th>
 +
</tr>
 +
<tr>
 +
<th>Sample 1</th>
 +
<td>10</td>
 +
<td>5</td>
 +
<td>5</td>
 +
<td>180</td>
 +
</tr>
 +
<tr>
 +
<td>Sample 2</td>
 +
<td>15</td>
 +
<td>7.5</td>
 +
<td>5</td>
 +
<td>172.5</td>
 +
</tr>
 +
<tr>
 +
<td>Sample 3</td>
 +
<td>20</td>
 +
<td>10</td>
 +
<td>5</td>
 +
<td>165</td>
 +
</tr>
 +
<tr>
 +
<td>Sample 4</td>
 +
<td>25</td>
 +
<td>12.5</td>
 +
<td>5</td>
 +
<td>157.5</td>
 +
</tr>
 +
<tr>
 +
<td>Sample 5</td>
 +
<td>30</td>
 +
<td>15</td>
 +
<td>5</td>
 +
<td>150</td>
 +
</tr>
 +
<tr>
 +
<td>Sample 6;</td>
 +
<td>35</td>
 +
<td>17.5</td>
 +
<td>5</td>
 +
<td>142.5</td>
 +
</tr>
 +
      </table>
 +
 +
      <b>Volume of reagents to add per well</b>
 +
 +
      <br /><br />
 +
 +
    <center>
 +
      <table>
 +
        <tr>
 +
          <th></th>
 +
          <th>Stocks</th>
 +
        </tr>
 +
        <tr>
 +
          <th>H<sub>2</sub>O<sub>2</sub></th>
 +
          <td>0.05g/ml</td>
 +
        </tr>
 +
        <tr>
 +
          <th>ABTS</th>
 +
          <td>0.0025g/ml</td>
 +
        </tr>
 +
        <tr>
 +
          <th>HRP</th>
 +
          <td>0.00025g/ml</td>
 +
        </tr>
 +
      </table>
 +
    </center>
 +
 +
    <b>Concentration of stocks used</b>
 +
      <br /><br />
 +
 +
      </ul>
 +
 +
    </div>
 +
 +
 +
    <div class="geneswitch">
 +
 +
    <h1 class="subnote">Inducible Gene Switch</h1>
 +
 +
      <ul class="list">
 +
        <li></li>
 +
        <li></li>
 +
        <li></li>
 +
      </ul>
 +
 
 +
    </div>
 +
 +
  </div>
  
  

Revision as of 17:49, 14 October 2016

Manchester iGEM 2016

Notebook

Inducible Gene Switch

  • Re-suspended DNA (constitutive promoters) from iGEM Distribution kit and transformed them into DH5α strain.
  • Growth was found on the negative control plates so re-transformed DNA
  • Inoculated of transformed cells.

Pilot Experiment

  • Made stocks of our reagents Glucose Stock for 0.005 g/mL, Glucose Oxidase Stock for 0.0025 g/mL, HRP Stock for 250 μL/mL, ABTS for 0.0025 g/mL

Inducible Gene Switch

  • Performed miniprep for overnight cultures
  • Prepared fresh batch of DH5α chemical competent cells
  • Restriction enzyme digest of constitutive promoters and control(pUC19) for validation with EcoRI and PstI
figure 1 figure 1

Pilot Experiment

  • Still awaiting the arrival of the BMG spectrophotometer

Inducible Gene Switch

  • Prepared DH5α chemical competent cells
  • Prepared Chloramphenicol antibiotic stock
  • Restreaked alcA 1 (BBa_K678001) and spispink(BBa_K1033923 pink chromoprotein)

Pilot Experiment

  • We began by preparing master mix containing three reagents glucose oxidase, HRP and ABTS (table 1)
    • Final reagent (μg/ml)
    Glucose oxidase 60
    HRP 60
    ABTS 100
    Table 1. Master mix



  • Six different glucose concentrations were then made as depicted in table 2
    • Final glucose concentration (μg/ml)
    0.50
    1.00
    .25
    1.50
    1.75
    2.00
    Table 2. Glucose concentration



  • Protocol
    1. 50 μl of glucose solution was added into each well. Samples were run in triplicates
    2. Tube containing master mix was placed into spectrophotometer.
    3. Spectrophotometer was then used to measure absorbance of our green coloured product-oxidised ABTS at 420 nm. Absorbance values were taken every 2 sec for 3 min once 150 ul of master mix was added into each well.
  • Results
    1. The rate of reaction did not level off and poor colour intensity was observed.
    2. We repeated the same experiment we did earlier this week. However instead of measuring absorbance for 3 min absorbance was measured every 2 sec for a 5 min period.
    3. Results - Reaction rate did level off after measuring absorbance for 5 min. However, colour intensity was still very poor.

Inducible Gene Switch

  • Resuspended DNA(RBS, amilCP(blue chromoprotein) and amilGFP(yellow chromoprotein)) from iGEM Distribution kit and transformed them into DH5α strain.
  • Inoculated alcA 1 and spispink for miniprep
  • Important event:
    18th July - Resurrected DNA from iGEM DNA distribution kit

Pilot Experiment

  • To increase the brightness of the colour change we repeated the experiment we performed on 22/07/2016. However this time we doubled the concentration of each reagent that made up the master mix (table 3).
    • Final reagent concentration (μg/ml)
    Glucose oxidase 120
    HRP 20
    ABTS 200
    Table 3. Master mix



    Result

    Increasing the concentration of master mix reagent did not yield intense colour changes (figure 1)

    figure 1
    Figure 1: Colour change observed following absorbance of oxidised ABTS. Master mix containing: glucose oxidase, HRP and ABTS was added to 6 different concentrations of glucose.


  • Based on results from yesterday, further increases in in reagents concentration that make up the master mix were tested. We tested the same glucose concentration as on 22/07/2016. The same parameters for the absorbance reading were used (i.e. every 2 sec for 5 min). The only parameter that was changed this time was master mix reagent concentration (table 4)
    • Final reagent concentration (μg/ml)
    Glucose oxidase 625
    HRP 62.5
    ABTS 625
    Table 4. Master mix


    Result

    Strongly visible green colour was not observed following today’s experiment

  • Today it was decided to increase glucose concentration (table 5) following previous experimental conditions that did not result in appearance of intense green colour. Concentration of master mix reagents and absorbance time window was kept the same as on 22/07/2016. Samples were run in triplicates
    • Final glucose concentration (μg/ml)
    0.50
    1.00
    .25
    1.50
    1.75
    2.00
    Table 5. Glucose Concentration

    Result

    At the end of our experiment we noticed very intense colour change as shown in figure 2.

    figure 2
    Figure 2: Colour intensity following addition of master mix (ABTS, HRP and H2O2)


Inducible Gene Switch

  • Ordered genes from IDT: alcA2 and alcR
  • Inoculated CP1 and CP3

Pilot Experiment

  • Performed the following reaction where ABTS is oxidised in the presence of H2O2 (final concentration 250 μg/ml ) and HRP (final concentration 250 μg/ml
    • Concentration of ABTS (μg/ml)
    1
    5
    10
    15
    20
  • Just measured absorbance of water at 420 nm
    • Concentration (μg/ml)
    HRP 0.25
    HRP 2.50
    H2O2 5.08
    Measured absorbance of each of the reagents at 420 nm


  • Set up the reaction with all 4 reagents. Measured absorbance every 25 sec for 900 sec. Run samples in triplicates
    •   ABTS (μl) H2O2 (μl) HRP (μl) PBS (μl)
    Sample 1 10 5 5 180
    Sample 2 15 7.5 5 172.5
    Sample 3 20 10 5 165
    Sample 4 25 12.5 5 157.5
    Sample 5 30 15 5 150
    Sample 6; 35 17.5 5 142.5
    Volume of reagents to add per well

    Stocks
    H2O2 0.05g/ml
    ABTS 0.0025g/ml
    HRP 0.00025g/ml
    Concentration of stocks used

Inducible Gene Switch

Pilot Experiment

Inducible Gene Switch

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