Difference between revisions of "Team:UC San Diego/Interlab"

 
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           <div class="col-md-6 col-md-offset-3 col-xs-8 col-xs-offset-2">
 
           <div class="col-md-6 col-md-offset-3 col-xs-8 col-xs-offset-2">
 
             <h2>Interlab</h2>
 
             <h2>Interlab</h2>
−
<p>Donec dignissim, enim vitae dapibus aliquam, enim tellus dignissim purus, a interdum felis tellus vel felis.</p>
+
<p>The Interlab Measurement Study was conducted by Walter Thavarajah, Vivienne Gunadhi, and Jenny Lee on 7/18/15 - 8/23/15, with support and troubleshooting advice from Phillip Kyriakakis.</p>
 
           </div>
 
           </div>
 
         </div>
 
         </div>
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             <div class="main-post">
 
             <div class="main-post">
  
−
               <div class="post-content">
+
               <div class="image-post">
 +
                <img src="https://static.igem.org/mediawiki/2015/2/2b/UCSD_title-interexp.png" alt="post image">
 +
              </div>
 +
                <div class="post-content">  
  
−
                <div class="post-title">
 
−
                  <h1>Interlab</h1>
 
−
                </div>
 
−
 
−
                <div class="post-discription">
 
 
                    
 
                    
 +
<h3>Devices Used</h3>
 +
<p>
 +
GFP generator I13504 was expressed under promoters J23101, J23106, and J23117 to form devices 1, 2, and 3, respectively. GFP device I20270 was used as a positive control and promoter R0040 was used as a negative control. DH5-alpha <i>E. coli</i> was used as a chassis organism. All DNA samples were obtained from the Spring 2015 DNA Distribution Kit. All final constructs were contained in backbone pSB1C3.
 +
<h3>Assembly</h3>
 +
<p>
 +
After amplification, the promoter-containing plasmids were digested with SpeI and PstI, while the GFP-containing plasmid was digested with XbaI and PstI. The GFP generator was gel purified and ligated into each of the promoter-containing plasmids with NEB Quick T4 DNA ligase. The completed devices were verified by sequencing.
 +
<h3>Growth Conditions</h3>
 +
<p>
 +
For each sample, 5mL of bacterial culture in selective LB media was cultured in plastic, 14mL test tubes overnight. Antibiotic was added from a 1000x stock kept at -4&deg;C. The tubes were kept at 37&deg;C and shaken at 300 RPM. The shaker used was a New Brunswick Scientific Excella E24, with a shaking diameter of 19mm. Cultures were prepared in triplicate.
 +
<h3>Sampling</h3>
 +
<p>
 +
After measurement of sample OD600, the cells were resuspended in water to a final volume of 500&micro;L and a final OD600 of 0.5 for plate reader measurement. Fluorescence measurements were also taken in the cells’ growth phase. To do this, sample OD600 was measured, then cells were resuspended in LB media for a final volume of 3mL and final OD600 of 0.1. These cells were allowed to grow for five hours before resuspension in water to a final volume of 500&micro;L and a final OD600 of 0.5 for plate reader measurement.
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
  
 +
      <div class="container">
 +
        <div class="row">
 +
          <div class="col-md-12">
 +
            <div class="main-post">
  
−
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
+
              <div class="image-post">
 +
                <img src="https://static.igem.org/mediawiki/2015/d/d9/UCSD_title-intermeas.png" alt="post image">
 +
              </div>
  
 +
<div class="post-content">
 +
<h3>Measurement<h3>
 +
</div>
 +
<div class="post-content">
 +
<p>
 +
Three 150&micro;L technical replicates from each 500&micro;L sample were loaded into a 96-well plate. Fluorescence measurements were performed on a Tecan Infinite M200 Pro plate reader. Measurement parameters are recorded in the following table:
  
 +
<!-- STATIONARY PHASE, FLUORESCENCE -->
 +
<div class="table-title">
 +
<center><h3>Measurement Parameters</h3></center>
 +
</div>
 +
<table class="table-fill">
  
 +
<thead>
 +
<tr>
 +
<th class="text-left">Parameter</th>
 +
<th class="text-left">Value</th>
 +
</tr>
 +
</thead>
  
 +
<tbody class="table-hover">
 +
<tr>
 +
<td class="text-left">Mode</td>
 +
<td class="text-left">Fluorescence Top Reading</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Shaking Duration</td>
 +
<td class="text-left">10s</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Shaking Amplitude</td>
 +
<td class="text-left">1mm</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Excitation Wavelength</td>
 +
<td class="text-left">485nm</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Emission Wavelength</td>
 +
<td class="text-left">535nm</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Excitation Bandwidth</td>
 +
<td class="text-left">9nm</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Emission Bandwidth</td>
 +
<td class="text-left">20nm</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Gain</td>
 +
<td class="text-left">109</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Number of Flashes</td>
 +
<td class="text-left">25</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Integration Time</td>
 +
<td class="text-left">20&micro;s</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Lag Time</td>
 +
<td class="text-left">0&micro;s</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Settle Time</td>
 +
<td class="text-left">0ms</td>
 +
</tr>
 +
 +
<tr>
 +
<td class="text-left">Z-Position (Manual)</td>
 +
<td class="text-left">15000&micro;m</td>
 +
</tr>
 +
 +
</tbody>
 +
</table>
 +
<p>
 +
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
 +
 +
 +
      <div class="container">
 +
        <div class="row">
 +
          <div class="col-md-12">
 +
            <div class="main-post">
 +
 +
              <div class="image-post">
 +
                <img src="https://static.igem.org/mediawiki/2015/1/18/UCSD_title-interres.png" alt="post image">
 +
              </div>
 +
 +
                <div class="post-content">
 +
                <h3>Results</h3>
 +
                </div>
 +
<div class="post-content">
 +
<p>
 +
Data is reported in arbitrary fluorescence units normalized by OD600, giving relative fluorescence in terms of cellular density.
 +
<!-- STATIONARY PHASE, FLUORESCENCE -->
 
<div class="table-title">
 
<div class="table-title">
−
<h3>Data Table</h3>
+
<center><h3>Normalized Stationary Phase Fluorescence</h3></center>
 
</div>
 
</div>
 
<table class="table-fill">
 
<table class="table-fill">
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<thead>
 
<thead>
 
<tr>
 
<tr>
−
<th class="text-left"> </th>
+
<th class="text-left">Replicate (Bio)</th>
−
<th class="text-left" colspan="3">One</th>
+
<th class="text-left" colspan="3">1</th>
−
<th class="text-left" colspan="3">Two</th>
+
<th class="text-left" colspan="3">2</th>
−
<th class="text-left" colspan="3">Three</th>
+
<th class="text-left" colspan="3">3</th>
 
</tr>
 
</tr>
 
</thead>
 
</thead>
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<thead>
 
<thead>
 
<tr>
 
<tr>
−
<th class="text-left"></th>
+
<th class="text-left">Replicate (Tech)</th>
 
<th class="text-left">1</th>
 
<th class="text-left">1</th>
 
<th class="text-left">2</th>
 
<th class="text-left">2</th>
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<tbody class="table-hover">
 
<tbody class="table-hover">
 
<tr>
 
<tr>
−
<td class="text-left">Dev1</td>
+
<td class="text-left">J23101+I13504</td>
−
<td class="text-left">#</td>
+
<td class="text-left">212661</td>
−
<td class="text-left">#</td>
+
<td class="text-left">218069</td>
−
<td class="text-left">#</td>
+
<td class="text-left">224560</td>
−
<td class="text-left">#</td>
+
<td class="text-left">87324</td>
−
<td class="text-left">#</td>
+
<td class="text-left">83817</td>
−
<td class="text-left">#</td>
+
<td class="text-left">85638</td>
−
<td class="text-left">#</td>
+
<td class="text-left">99780</td>
−
<td class="text-left">#</td>
+
<td class="text-left">104666</td>
−
<td class="text-left">#</td>
+
<td class="text-left">96564</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
−
<td class="text-left">Dev2</td>
+
<td class="text-left">J23106+I13504</td>
−
<td class="text-left">#</td>
+
<td class="text-left">91142</td>
−
<td class="text-left">#</td>
+
<td class="text-left">90870</td>
−
<td class="text-left">#</td>
+
<td class="text-left">91374</td>
−
<td class="text-left">#</td>
+
<td class="text-left">138854</td>
−
<td class="text-left">#</td>
+
<td class="text-left">135266</td>
−
<td class="text-left">#</td>
+
<td class="text-left">138449</td>
−
<td class="text-left">#</td>
+
<td class="text-left">78490</td>
−
<td class="text-left">#</td>
+
<td class="text-left">76435</td>
−
<td class="text-left">#</td>
+
<td class="text-left">76820</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
−
<td class="text-left">Dev3</td>
+
<td class="text-left">J23117+I13504</td>
−
<td class="text-left">#</td>
+
<td class="text-left">196742</td>
−
<td class="text-left">#</td>
+
<td class="text-left">189264</td>
−
<td class="text-left">#</td>
+
<td class="text-left">189532</td>
−
<td class="text-left">#</td>
+
<td class="text-left">177459</td>
−
<td class="text-left">#</td>
+
<td class="text-left">173740</td>
−
<td class="text-left">#</td>
+
<td class="text-left">180933</td>
−
<td class="text-left">#</td>
+
<td class="text-left">255947</td>
−
<td class="text-left">#</td>
+
<td class="text-left">235695</td>
−
<td class="text-left">#</td>
+
<td class="text-left">240583</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
−
<td class="text-left">Neg</td>
+
<td class="text-left">I20270</td>
−
<td class="text-left">#</td>
+
<td class="text-left">59086</td>
−
<td class="text-left">#</td>
+
<td class="text-left">58353</td>
−
<td class="text-left">#</td>
+
<td class="text-left">58899</td>
−
<td class="text-left">#</td>
+
<td class="text-left">66048</td>
−
<td class="text-left">#</td>
+
<td class="text-left">66005</td>
−
<td class="text-left">#</td>
+
<td class="text-left">65974</td>
−
<td class="text-left">#</td>
+
<td class="text-left">23207</td>
−
<td class="text-left">#</td>
+
<td class="text-left">23189</td>
−
<td class="text-left">#</td>
+
<td class="text-left">22479</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
−
<td class="text-left">Pos</td>
+
<td class="text-left">R0040</td>
−
<td class="text-left">#</td>
+
<td class="text-left">7841</td>
−
<td class="text-left">#</td>
+
<td class="text-left">8595</td>
−
<td class="text-left">#</td>
+
<td class="text-left">8823</td>
−
<td class="text-left">#</td>
+
<td class="text-left">9514</td>
−
<td class="text-left">#</td>
+
<td class="text-left">9610</td>
−
<td class="text-left">#</td>
+
<td class="text-left">9661</td>
−
<td class="text-left">#</td>
+
<td class="text-left">8611</td>
−
<td class="text-left">#</td>
+
<td class="text-left">8411</td>
−
<td class="text-left">#</td>
+
<td class="text-left">11601</td>
 
</tr>
 
</tr>
 
</tbody>
 
</tbody>
 
</table>
 
</table>
 +
<p>
  
 +
<center><img src="https://static.igem.org/mediawiki/2015/4/41/UCSD_Normalized_Stationary_Phase_Flourescence-8-23.jpg"></center>
 +
<p>
 +
<!-- GROWTH PHASE, FLUORESCENCE -->
 +
<div class="table-title">
 +
<center><h3>Normalized Growth Phase Fluorescence</h3></center>
 +
</div>
 +
<table class="table-fill">
  
 +
<thead>
 +
<tr>
 +
<th class="text-left">Replicate (Bio)</th>
 +
<th class="text-left" colspan="3">1</th>
 +
<th class="text-left" colspan="3">2</th>
 +
<th class="text-left" colspan="3">3</th>
 +
</tr>
 +
</thead>
  
 +
<thead>
 +
<tr>
 +
<th class="text-left">Replicate (Tech)</th>
 +
<th class="text-left">1</th>
 +
<th class="text-left">2</th>
 +
<th class="text-left">3</th>
 +
<th class="text-left">1</th>
 +
<th class="text-left">2</th>
 +
<th class="text-left">3</th>
 +
<th class="text-left">1</th>
 +
<th class="text-left">2</th>
 +
<th class="text-left">3</th>
 +
</tr>
 +
</thead>
  
−
<center><img src="images/image-post.jpg" alt="image here"></center>
+
<tbody class="table-hover">
−
 
+
<tr>
−
<p>[Plasmid Diagram]</p>
+
<td class="text-left">J23101+I13504</td>
−
 
+
<td class="text-left">228630</td>
−
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
+
<td class="text-left">220402</td>
−
 
+
<td class="text-left">215458</td>
−
<blockquote>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</blockquote>
+
<td class="text-left">250390</td>
−
 
+
<td class="text-left">260929</td>
−
                <center><img src="images/image-post.jpg" alt="image here?"></center>
+
<td class="text-left">251502</td>
−
 
+
<td class="text-left">223796</td>
−
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
+
<td class="text-left">244465</td>
−
 
+
<td class="text-left">239753</td>
−
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>
+
</tr>
−
 
+
<tr>
−
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris eu suscipit lectus. Pellentesque ut risus rhoncus, congue tortor at, aliquam augue. Vestibulum ex mi, varius quis sollicitudin at, blandit ac lorem. Vivamus mattis sapien turpis, in fringilla nulla cursus id. Vestibulum vestibulum velit et accumsan aliquet. Aenean nulla justo, scelerisque id pulvinar eu, fringilla et nisl. Cras sapien magna, tincidunt in sapien et, sagittis sodales lacus. Praesent a ex ut augue fringilla interdum.</p>  
+
<td class="text-left">J23106+I13504</td>
−
 
+
<td class="text-left">137338</td>
 +
<td class="text-left">136645</td>
 +
<td class="text-left">138662</td>
 +
<td class="text-left">152553</td>
 +
<td class="text-left">152022</td>
 +
<td class="text-left">151875</td>
 +
<td class="text-left">155750</td>
 +
<td class="text-left">154273</td>
 +
<td class="text-left">156722</td>
 +
</tr>
 +
<tr>
 +
<td class="text-left">J23117+I13504</td>
 +
<td class="text-left">213819</td>
 +
<td class="text-left">199649</td>
 +
<td class="text-left">202460</td>
 +
<td class="text-left">206332</td>
 +
<td class="text-left">209273</td>
 +
<td class="text-left">209787</td>
 +
<td class="text-left">201584</td>
 +
<td class="text-left">204465</td>
 +
<td class="text-left">170296</td>
 +
</tr>
 +
<tr>
 +
<td class="text-left">I20270</td>
 +
<td class="text-left">132783</td>
 +
<td class="text-left">133059</td>
 +
<td class="text-left">135514</td>
 +
<td class="text-left">111394</td>
 +
<td class="text-left">113750</td>
 +
<td class="text-left">117485</td>
 +
<td class="text-left">138890</td>
 +
<td class="text-left">126284</td>
 +
<td class="text-left">128169</td>
 +
</tr>
 +
<tr>
 +
<td class="text-left">R0040</td>
 +
<td class="text-left">18327</td>
 +
<td class="text-left">17437</td>
 +
<td class="text-left">18190</td>
 +
<td class="text-left">18767</td>
 +
<td class="text-left">17509</td>
 +
<td class="text-left">17658</td>
 +
<td class="text-left">16599</td>
 +
<td class="text-left">16547</td>
 +
<td class="text-left">15929</td>
 +
</tr>
 +
</tbody>
 +
</table>
 +
<p>
  
 +
<center><img src="https://static.igem.org/mediawiki/2015/2/2c/UCSD_Normalized_Growth_Phase_Flourescence-8-23.jpg"></center>
 +
<p>
 
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Latest revision as of 21:32, 20 November 2015

Interlab

The Interlab Measurement Study was conducted by Walter Thavarajah, Vivienne Gunadhi, and Jenny Lee on 7/18/15 - 8/23/15, with support and troubleshooting advice from Phillip Kyriakakis.

post image

Devices Used

GFP generator I13504 was expressed under promoters J23101, J23106, and J23117 to form devices 1, 2, and 3, respectively. GFP device I20270 was used as a positive control and promoter R0040 was used as a negative control. DH5-alpha E. coli was used as a chassis organism. All DNA samples were obtained from the Spring 2015 DNA Distribution Kit. All final constructs were contained in backbone pSB1C3.

Assembly

After amplification, the promoter-containing plasmids were digested with SpeI and PstI, while the GFP-containing plasmid was digested with XbaI and PstI. The GFP generator was gel purified and ligated into each of the promoter-containing plasmids with NEB Quick T4 DNA ligase. The completed devices were verified by sequencing.

Growth Conditions

For each sample, 5mL of bacterial culture in selective LB media was cultured in plastic, 14mL test tubes overnight. Antibiotic was added from a 1000x stock kept at -4°C. The tubes were kept at 37°C and shaken at 300 RPM. The shaker used was a New Brunswick Scientific Excella E24, with a shaking diameter of 19mm. Cultures were prepared in triplicate.

Sampling

After measurement of sample OD600, the cells were resuspended in water to a final volume of 500µL and a final OD600 of 0.5 for plate reader measurement. Fluorescence measurements were also taken in the cells’ growth phase. To do this, sample OD600 was measured, then cells were resuspended in LB media for a final volume of 3mL and final OD600 of 0.1. These cells were allowed to grow for five hours before resuspension in water to a final volume of 500µL and a final OD600 of 0.5 for plate reader measurement.

post image

Measurement

Three 150µL technical replicates from each 500µL sample were loaded into a 96-well plate. Fluorescence measurements were performed on a Tecan Infinite M200 Pro plate reader. Measurement parameters are recorded in the following table:

Measurement Parameters

Parameter Value
Mode Fluorescence Top Reading
Shaking Duration 10s
Shaking Amplitude 1mm
Excitation Wavelength 485nm
Emission Wavelength 535nm
Excitation Bandwidth 9nm
Emission Bandwidth 20nm
Gain 109
Number of Flashes 25
Integration Time 20µs
Lag Time 0µs
Settle Time 0ms
Z-Position (Manual) 15000µm

post image

Results

Data is reported in arbitrary fluorescence units normalized by OD600, giving relative fluorescence in terms of cellular density.

Normalized Stationary Phase Fluorescence

Replicate (Bio) 1 2 3
Replicate (Tech) 1 2 3 1 2 3 1 2 3
J23101+I13504 212661 218069 224560 87324 83817 85638 99780 104666 96564
J23106+I13504 91142 90870 91374 138854 135266 138449 78490 76435 76820
J23117+I13504 196742 189264 189532 177459 173740 180933 255947 235695 240583
I20270 59086 58353 58899 66048 66005 65974 23207 23189 22479
R0040 7841 8595 8823 9514 9610 9661 8611 8411 11601

Normalized Growth Phase Fluorescence

Replicate (Bio) 1 2 3
Replicate (Tech) 1 2 3 1 2 3 1 2 3
J23101+I13504 228630 220402 215458 250390 260929 251502 223796 244465 239753
J23106+I13504 137338 136645 138662 152553 152022 151875 155750 154273 156722
J23117+I13504 213819 199649 202460 206332 209273 209787 201584 204465 170296
I20270 132783 133059 135514 111394 113750 117485 138890 126284 128169
R0040 18327 17437 18190 18767 17509 17658 16599 16547 15929