Difference between revisions of "Team:Marburg/InterLab"

 
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<div class="titleWrapper"><div class="titleBackground" style="background-image:url(https://static.igem.org/mediawiki/2018/3/3e/T--Marburg--header_interlab.jpg)"></div><div class="title">InterLab </div></div>
  
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<div class="m_wrapper">
 
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<div class="column full_size judges-will-not-evaluate">
 
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<h3>★  ALERT! </h3>
 
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
 
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
 
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<div class="column full_size">
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<article>
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<h1>InterLab</h1>
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<br>
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<h3>Bronze Medal Criterion #4</h3>
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<p>
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<p><b>Standard Tracks:</b> Participate in the Interlab Measurement Study and/or obtain new, high quality experimental characterization data for an existing BioBrick Part or Device and enter this information on that part's Main Page in the Registry. The part that you are characterizing must NOT be from a 2018 part number range.
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<i>Coming together is a beginning; <br>
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<br><br>
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keeping together is progress; <br>
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For teams participating in the <a href="https://2018.igem.org/Measurement/InterLab">InterLab study</a>, all work must be shown on this page.
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working together is success.</i> <br>
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<b>--Edward Everett Hale</b><br>
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<br>
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<br>
  
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</p>
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<h2>Introduction:</h2>
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</div>
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<p>
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The InterLab&rsquo;s goal is to identify and correct the sources of variability in measurements, to achieve this they created a way to reliably measure GFP expression in absolute fluorescence units. One of the problems with the InterLab&rsquo;s current model is that the number of cells in the samples very. To solve this another goal was added: normalizing to absolute cell count or colony forming units instead of to the optical density (OD). A new experiment was introduced, in which the colony forming units (CFU) per 0.1 OD<sub>600</sub> were calculated.</p>
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<p>
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We conducted the three calibrations, the cell measurement and the colony forming units per 0.1 OD<sub>600</sub> E. coli culture experiments. For the cell measurement we transformed 8 plasmids into E. coli DH5-alpha. These 6 plasmids were provided by the iGEM HQ in the iGEM InterLab Kit. These test devices contained Anderson promoters and were inserted into a pSB1C3 backbone. A plasmid containing a promoter and GFP sequence (<a href="http://parts.igem.org/Part:BBa_I20270">Bba_I20270</a>) was used as the positive control and a plasmid containing a TetR repressible promoter (<a href="http://parts.igem.org/Part:BBa_R0040">Bba_R0040</a>) was used as the negative control. The plasmids were Test Device 1 (<a href="http://parts.igem.org/Part:BBa_J364000">BBa_J364000</a>), Test Device 2 (<a href="http://parts.igem.org/Part:BBa_J364001">BBa_J364001</a>), Test Device 3 (<a href="http://parts.igem.org/Part:BBa_J364001">BBa_J364002</a>), Test Device 4 (<a href="http://parts.igem.org/Part:BBa_J364007">BBa_J364007</a>), Test Device 5 (<a href="http://parts.igem.org/Part:BBa_J364008">BBa_J364008</a>) and Test Device 6 (<a href="http://parts.igem.org/Part:BBa_J364009">BBa_J364009</a>). Overnight cultures with these plasmids are diluted to an OD<sub>600</sub>of 0.02 and their absorbance (600 nm) and fluorescence (485/520) is measured in 96 well plates after 0 and 6 hrs of incubation. The fluorescein concentration is plotted against the measured fluorescence intensity of fluorescein. With this curve we converted the fluorescence of our cell measurements to a GFP concentration. To establish the CFU we counted colonies with the positive and negative control plasmids in differently diluted cultures.</p>
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<h2>Results and Discussion:</h2>
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<p>
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All measurements were conducted with a BMG lab tech CLARIOstar platereader using bottom optics. The bandpass filter was set at 530 nm/30 nm, the emission wavelength was in between 520 nm and 530 nm and the excitation wavelength was 485 nm.</p>
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<div style="display: inline-block; align-items: center;">
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      <div style="float:left; width: 49%; text-align: justify;">
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            <figure style="width: 80%;">
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        <img src="https://static.igem.org/mediawiki/2018/thumb/e/e2/T--marburg--Flurescein_Standard_Curve.png/898px-T--marburg--Flurescein_Standard_Curve.png">
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        <figcaption>
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          <b> <strong>Figure 1: Fluorescein fluorescence calibration curve.</strong> The fluorescein concentration was plotted against its fluorescence intensity.</figcaption>
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    </figure>
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<p>
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  A higher fluorescein concentration results in a higher fluorescence, but they are not linearly dependent. After a fluorescein concentration of about 5 µM the curve is saturated, and the fluorescence doesn&rsquo;t increase as much anymore.</p>
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      </div>
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      <div style="float:right; width: 49%; text-align: justify;">
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          <figure style="width: 80%; float: right">
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        <img src="https://static.igem.org/mediawiki/2018/thumb/b/b9/T--marburg--Mean_InterLab_values.png/900px-T--marburg--Mean_InterLab_values.png">
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        <figcaption>
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          <b> <strong>Figure 2: Concentration GFP/OD<sub>600</sub>. </strong> Bar chart presenting the concentration of GFP/O<sub>600</sub> of test devices 1, 2, 3, 4, 5 and 6, positive and negative control after 6 hours of incubation.</figcaption>       
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<p>
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  Device 1 showed the strongest fluorescence, followed by 4, 5, 2, 6 and 3.</p>
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    </figure>
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      </div>
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  </div>
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<div id="tableview">
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<table
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style="width=100%">
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<caption>
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Table 1: List of devices used and their respective promotors.</caption>
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<tr>
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<td width="60">
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<p><strong>Device</strong></p>
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</td>
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<td width="60">
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<p><strong>Negative control</strong></p>
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</td>
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<td width="60">
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<p><strong>Positive control</strong></p>
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</td>
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<td width="60">
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<p><strong>Test Device 1</strong></p>
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</td>
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<td width="60">
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<p><strong>Test Device 2</strong></p>
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</td>
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<td width="60">
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<p><strong>Test Device 3</strong></p>
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</td>
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<td width="60">
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<p><strong>Test Device 4</strong></p>
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</td>
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<td width="60">
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<p><strong>Test Device 5</strong></p>
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</td>
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<td width="60">
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<p><strong>Test Device 6</strong></p>
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</td>
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</tr>
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<tr>
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<td width="60">
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<p><strong>Part number</strong></p>
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</td>
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<td width="60">
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<p>BBa_R0040</p>
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</td>
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<td width="60">
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<p>BBa_I20270</p>
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</td>
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<td width="60">
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<p>BBa_J364000</p>
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</td>
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<td width="60">
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<p>BBa_J364001</p>
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</td>
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<td width="60">
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<p>BBa_J364002 B</p>
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</td>
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<td width="60">
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<p>Ba_J364007</p>
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</td>
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<td width="60">
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<p>BBa_J364008</p>
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</td>
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<td width="60">
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<p>BBa_J364009</p>
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</td>
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</tr>
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<tr>
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<td width="60">
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<p><strong>Promoter</strong></p>
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</td>
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<td width="60">
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<p>&nbsp;</p>
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</td>
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<td width="60">
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<p>J23151</p>
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</td>
 +
<td width="60">
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<p>J23101</p>
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</td>
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<td width="60">
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<p>J23106</p>
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</td>
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<td width="60">
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<p>J23117</p>
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</td>
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<td width="60">
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<p>J23100</p>
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</td>
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<td width="60">
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<p>J23104</p>
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</td>
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<td width="60">
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<p>J23116</p>
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</td>
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</tr>
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</table>
 
</div>
 
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</section>
 
  
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<p></p>
  
  
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</main>
 
  
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<h2>Conclusion:</h2>
 +
<p>
 +
Device 1 showed the strongest fluorescence followed closely by 4. The devices 5 and 2 were a lot weaker then 1 and 4. Device s6 was even weaker and almost no signal was detected.</p>
 +
<p>
 +
We encountered some problems with test device 1. The OD<sub>600</sub> didn&rsquo;t change much in 6 hours of incubation, which suggest it didn&rsquo;t grow much. All the samples were incubated together and the others all grew during this time. The negative control showed double the fluorescence as the positive control. This could have happened trough contamination or a pipetting error, where cells with a GFP expressing plasmids were inserted into the well.</p>
 +
<p>
 +
We used two iGEM protocols for these experiments, one for the general <a href="https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf">InterLab</a> experiments and calibrations and another for <a href="http://parts.igem.org/Help:Protocols/Transformation">transforming</a>.</p>
 +
</article>
 
</html>
 
</html>
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{{Marburg/footer}}

Latest revision as of 02:48, 18 October 2018

InterLab

Coming together is a beginning;
keeping together is progress;
working together is success.
--Edward Everett Hale


Introduction:

The InterLab’s goal is to identify and correct the sources of variability in measurements, to achieve this they created a way to reliably measure GFP expression in absolute fluorescence units. One of the problems with the InterLab’s current model is that the number of cells in the samples very. To solve this another goal was added: normalizing to absolute cell count or colony forming units instead of to the optical density (OD). A new experiment was introduced, in which the colony forming units (CFU) per 0.1 OD600 were calculated.

We conducted the three calibrations, the cell measurement and the colony forming units per 0.1 OD600 E. coli culture experiments. For the cell measurement we transformed 8 plasmids into E. coli DH5-alpha. These 6 plasmids were provided by the iGEM HQ in the iGEM InterLab Kit. These test devices contained Anderson promoters and were inserted into a pSB1C3 backbone. A plasmid containing a promoter and GFP sequence (Bba_I20270) was used as the positive control and a plasmid containing a TetR repressible promoter (Bba_R0040) was used as the negative control. The plasmids were Test Device 1 (BBa_J364000), Test Device 2 (BBa_J364001), Test Device 3 (BBa_J364002), Test Device 4 (BBa_J364007), Test Device 5 (BBa_J364008) and Test Device 6 (BBa_J364009). Overnight cultures with these plasmids are diluted to an OD600of 0.02 and their absorbance (600 nm) and fluorescence (485/520) is measured in 96 well plates after 0 and 6 hrs of incubation. The fluorescein concentration is plotted against the measured fluorescence intensity of fluorescein. With this curve we converted the fluorescence of our cell measurements to a GFP concentration. To establish the CFU we counted colonies with the positive and negative control plasmids in differently diluted cultures.

Results and Discussion:

All measurements were conducted with a BMG lab tech CLARIOstar platereader using bottom optics. The bandpass filter was set at 530 nm/30 nm, the emission wavelength was in between 520 nm and 530 nm and the excitation wavelength was 485 nm.

Figure 1: Fluorescein fluorescence calibration curve. The fluorescein concentration was plotted against its fluorescence intensity.

A higher fluorescein concentration results in a higher fluorescence, but they are not linearly dependent. After a fluorescein concentration of about 5 µM the curve is saturated, and the fluorescence doesn’t increase as much anymore.

Figure 2: Concentration GFP/OD600. Bar chart presenting the concentration of GFP/O600 of test devices 1, 2, 3, 4, 5 and 6, positive and negative control after 6 hours of incubation.

Device 1 showed the strongest fluorescence, followed by 4, 5, 2, 6 and 3.

Table 1: List of devices used and their respective promotors.

Device

Negative control

Positive control

Test Device 1

Test Device 2

Test Device 3

Test Device 4

Test Device 5

Test Device 6

Part number

BBa_R0040

BBa_I20270

BBa_J364000

BBa_J364001

BBa_J364002 B

Ba_J364007

BBa_J364008

BBa_J364009

Promoter

 

J23151

J23101

J23106

J23117

J23100

J23104

J23116

Conclusion:

Device 1 showed the strongest fluorescence followed closely by 4. The devices 5 and 2 were a lot weaker then 1 and 4. Device s6 was even weaker and almost no signal was detected.

We encountered some problems with test device 1. The OD600 didn’t change much in 6 hours of incubation, which suggest it didn’t grow much. All the samples were incubated together and the others all grew during this time. The negative control showed double the fluorescence as the positive control. This could have happened trough contamination or a pipetting error, where cells with a GFP expressing plasmids were inserted into the well.

We used two iGEM protocols for these experiments, one for the general InterLab experiments and calibrations and another for transforming.

B. Marchal