Difference between revisions of "Team:Lethbridge/InterLab"

 
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<h1>INTERLAB STUDY</h1>
 
<h1>INTERLAB STUDY</h1>
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<p class="f14">Synthetic biology interconnects the principles of biology and engineering. Reliable and repeatable measurement is one of the fundamentals of engineering, which synthetic biology must also aspire to achieve. However, replicability of fluorescence measurements between labs presents a unique challenge because of differences in how the data are acquired and processed, and other sources of systematic variability that are not accounted for (such as the number of cells in a sample). By using “relative expression” comparisons, users from different labs cannot directly compare results. <br><br>
+
<p class="f12">Synthetic biology interconnects the principles of biology and engineering. Reliable and repeatable measurement is one of the fundamentals of engineering, which synthetic biology must also aspire to achieve. However, replicability of fluorescence measurements between labs presents a unique challenge because of differences in how the data are acquired and processed, and other sources of systematic variability that are not accounted for (such as the number of cells in a sample). By using “relative expression” comparisons, users from different labs cannot directly compare results. <br><br>
 
The purpose of the 2018 InterLab Study was to attempt to reduce lab-to-lab variability by standardizing green fluorescent protein (GFP) fluorescence measurements. This was done by normalizing GFP fluorescence to absolute cell count or colony-forming units (CFUs) instead of optical density (OD).</p>
 
The purpose of the 2018 InterLab Study was to attempt to reduce lab-to-lab variability by standardizing green fluorescent protein (GFP) fluorescence measurements. This was done by normalizing GFP fluorescence to absolute cell count or colony-forming units (CFUs) instead of optical density (OD).</p>
 
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<h3>Overview</h3>
 
<h3>Overview</h3>
<p class="f14"> Two approaches were used:<br><br>
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<p class="f12"> Two approaches were used:<br><br>
  
 
<b>1. Converting between absorbance of cells to absorbance of a known concentration of beads.</b><br>
 
<b>1. Converting between absorbance of cells to absorbance of a known concentration of beads.</b><br>
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<h3>Our Equipment</h3>
 
<h3>Our Equipment</h3>
  
<p class="f14">A Molecular Devices Spectramax i3x plate reader was used to measure sample absorbance and fluorescence. This device has variable temperature settings, top optics, and pathlength correction, which can be disabled. All GFP measurements were taken at wavelengths of 535/25nm for emission and 485/20nm for excitation. We used clear-bottomed 96-well plates for all measurements.</p><br><br>
+
<p class="f12">A Molecular Devices Spectramax i3x plate reader was used to measure sample absorbance and fluorescence. This device has variable temperature settings, top optics, and pathlength correction, which can be disabled. All GFP measurements were taken at wavelengths of 535/25nm for emission and 485/20nm for excitation. We used clear-bottomed 96-well plates for all measurements.</p><br><br>
  
  
 
<h3> Calibration </h3>
 
<h3> Calibration </h3>
  
<p class="f14">1. LUDOX CL-X (45% colloidal silica suspension) was used as a single point reference to obtain a
+
<p class="f12">1. LUDOX CL-X (45% colloidal silica suspension) was used as a single point reference to obtain a
 
conversion factor to transform absorbance data into a comparable OD measurement.<br><br>
 
conversion factor to transform absorbance data into a comparable OD measurement.<br><br>
  
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<h3> Cell Measurement Protocol </h3>
 
<h3> Cell Measurement Protocol </h3>
  
<p class="f14">Briefly, we measured the raw absorbance and fluorescence of diluted cells (transformed with the below testing devices) at 0 hours and after 6 hours of incubation at 37°C.</p><br></br>
+
<p class="f12">Briefly, we measured the raw absorbance and fluorescence of diluted cells (transformed with the below testing devices) at 0 hours and after 6 hours of incubation at 37°C.</p><br></br>
  
  
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     <th font-weight: bold;">Location</th>
 
     <th font-weight: bold;">Location</th>
 
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     <td>Negative Control</td>
 
     <td>Negative Control</td>
 
     <td>BBa_R0040</td>
 
     <td>BBa_R0040</td>
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     <td>Well 2D</td>
 
     <td>Well 2D</td>
 
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     <td>Positive Control</td>
 
     <td>Positive Control</td>
 
     <td>BBa_I20270</td>
 
     <td>BBa_I20270</td>
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     <td>Well 2B</td>
 
     <td>Well 2B</td>
 
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<tr class="f10">
 
     <td>Test Device 1 </td>
 
     <td>Test Device 1 </td>
 
     <td>BBa_J364000</td>
 
     <td>BBa_J364000</td>
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     <td>Well 2F</td>
 
     <td>Well 2F</td>
 
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   </tr>
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     <td>Test Device 2</td>
 
     <td>Test Device 2</td>
 
     <td>BBa_J364001</td>
 
     <td>BBa_J364001</td>
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     <td>Well 2H</td>
 
     <td>Well 2H</td>
 
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   </tr>
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     <td>Test Device 3</td>
 
     <td>Test Device 3</td>
 
     <td>BBa_J364002</td>
 
     <td>BBa_J364002</td>
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     <td>Well 2J</td>
 
     <td>Well 2J</td>
 
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     <td>Test Device 4</td>
 
     <td>Test Device 4</td>
 
     <td>BBa_J364007</td>
 
     <td>BBa_J364007</td>
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     <td>Well 2L</td>
 
     <td>Well 2L</td>
 
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   </tr>
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     <td>Test Device 5</td>
 
     <td>Test Device 5</td>
 
     <td>BBa_J364008</td>
 
     <td>BBa_J364008</td>
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     <td>Well 2N</td>
 
     <td>Well 2N</td>
 
   </tr>
 
   </tr>
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     <td>Test Device 6</td>
 
     <td>Test Device 6</td>
 
     <td>BBa_J364009</td>
 
     <td>BBa_J364009</td>
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<h1>Results</h1>
 
<h1>Results</h1>
  
<p class="f14">We expected a linear relationship between concentration and fluorescence/absorbance. However, the log-scale particle standard curve (Figure 2B) does not exhibit a linear relationship. Possible sources of error include pipetting error or oversaturation of the detector.<br><br>
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<div class="oneText-Wrapper">
The conversion of average fluorescence to reference unit was designed to reduce the impact of unorganized unit system.
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<br>For fluorescence to OD conversion, fluorescence was converted to absorbance and to OD.
+
<p class="f12">In our standard curves, we expected a linear relationship between concentration and fluorescence/absorbance. However, the log-scale particle standard curve (Figure 2B) does not exhibit a linear relationship. Possible sources of error include pipetting error or oversaturation of the detector.</p><br><br>
<br>For fluorescence to particle conversion, Molecules of Equivalent of Fluorescence (MEFL) was converted to absorbance and to particles.
+
<br>The trend showed that except device 3, all other devices contained fluorescence part and the device 2 and 5 had increased fluorescence part after 6 hours, but device 1,4, and 6 had decreased fluorescence part after 6 hours. </p>
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<h3>Fluorescein Standard Curve</h3>
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<img src="https://static.igem.org/mediawiki/2018/c/c4/T--Lethbridge--Fluorescein_Standard_Curve_V2.png" alt="">
        <center><img src="https://static.igem.org/mediawiki/2018/c/c4/T--Lethbridge--Fluorescein_Standard_Curve_V2.png" width = 400 px; height=250px; padding: 30px;></center>
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        <p>Fluorescein standard curve</p>
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<img src="https://static.igem.org/mediawiki/2018/9/9c/T--Lethbridge--Fluorescein_Standard_Curve_log_scale_V2.png" alt="">
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      <center><img src="https://static.igem.org/mediawiki/2018/9/9c/T--Lethbridge--Fluorescein_Standard_Curve_log_scale_V2.png" width = 400 px; height=250px; padding: 30px;></center>
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    <p>Fluorescein standard curve (log scale)</p>
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<br><br>
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<h3>Particle Standard Curve</h3>
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        <center><img src="https://static.igem.org/mediawiki/2018/6/6a/T--Lethbridge--Particle_Standard_Curve_V2.png" width = 400 px; height=250px; padding: 30px;></center>
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<p class="f10"><b>Figure 1:</b> A) Fluorescein standard curve. B) Fluorescein standard curve (log-scale).</p>
        <p>Standard curve of particles</p>
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      <center><img src="https://static.igem.org/mediawiki/2018/9/9d/T--Lethbridge--Particle_Standard_Curve_log_scale_V2.png"width = 400 px; height=250px; padding: 30px;></center>
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    <p>Standard curve of particles (log scale)</p>
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</div>
 
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<div style="clear: both"></div><br><br>
<br><br>
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<h3>Average Fluorescence</h3>
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        <center><img src="https://static.igem.org/mediawiki/2018/9/99/T--Lethbridge--Average_Fluorescence_vs_OD.png" width = 400 px; height=250px; padding: 30px;></center>
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        <p>Average fluorescence per OD</p>
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<img src="https://static.igem.org/mediawiki/2018/6/6a/T--Lethbridge--Particle_Standard_Curve_V2.png" alt="">
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      <center><img src="https://static.igem.org/mediawiki/2018/2/2f/T--Lethbridge--Average_Fluorescence_vs_particle.png" width = 400 px; height=250px; padding: 30px;></center>
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<div class="twoImage-Image">
    <p>Average fluorescence per particle  </p>
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<img src="https://static.igem.org/mediawiki/2018/9/9d/T--Lethbridge--Particle_Standard_Curve_log_scale_V2.png" alt="">
    </div>
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</div>
 
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<br><br>
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<p class="f10"><b>Figure 2:</b> A) Particle standard curve. B) Particle standard curve (log-scale).</p>
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<img src="https://static.igem.org/mediawiki/2018/9/99/T--Lethbridge--Average_Fluorescence_vs_OD.png" alt="">
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<div class="twoImage-Image">
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<img src="https://static.igem.org/mediawiki/2018/2/2f/T--Lethbridge--Average_Fluorescence_vs_particle.png" alt="">
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 +
 
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<p class="f10"><b>Figure 3:</b> A) Average fluorescence per optical density. B) Average fluorescence per particle.</p>
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<div style="clear: both"></div><br><br>
  
  

Latest revision as of 23:33, 17 October 2018



Interlab Banner Image

INTERLAB STUDY

Synthetic biology interconnects the principles of biology and engineering. Reliable and repeatable measurement is one of the fundamentals of engineering, which synthetic biology must also aspire to achieve. However, replicability of fluorescence measurements between labs presents a unique challenge because of differences in how the data are acquired and processed, and other sources of systematic variability that are not accounted for (such as the number of cells in a sample). By using “relative expression” comparisons, users from different labs cannot directly compare results.

The purpose of the 2018 InterLab Study was to attempt to reduce lab-to-lab variability by standardizing green fluorescent protein (GFP) fluorescence measurements. This was done by normalizing GFP fluorescence to absolute cell count or colony-forming units (CFUs) instead of optical density (OD).



Methods

Overview

Two approaches were used:

1. Converting between absorbance of cells to absorbance of a known concentration of beads.
Absorbance is a measure of how light is scattered by cells in liquid, which can be used to estimate the concentration of cells in the sample. Assuming that silica beads approximately the same size and shape of E. coli cells would have similar optical properties, we can use the absorbance measurement of a known concentration of beads to produce a standardized “equivalent concentration of beads” measurement.

2. Counting colony-forming units (CFUs) from the sample.
We can estimate the number of individual cells in a volume of liquid media by plating a sample and quantifying colonies (which are each clones of a single cell). The number of colonies in positive and negative control samples can be used to calculate a conversion factor from absorbance to CFU.

For complete methods, refer to: https://2018.igem.org/Measurement/InterLab/Plate_Reader



Our Equipment

A Molecular Devices Spectramax i3x plate reader was used to measure sample absorbance and fluorescence. This device has variable temperature settings, top optics, and pathlength correction, which can be disabled. All GFP measurements were taken at wavelengths of 535/25nm for emission and 485/20nm for excitation. We used clear-bottomed 96-well plates for all measurements.



Calibration

1. LUDOX CL-X (45% colloidal silica suspension) was used as a single point reference to obtain a conversion factor to transform absorbance data into a comparable OD measurement.

2. A dilution series of monodisperse silica microspheres was used to measure absorbance and produce a standard curve of particle concentration. This standard curve was later used to convert absorbance measurements to an estimated number of cells.

3. A dilution series of fluorescein, which has similar excitation and emission properties to GFP, was used to generate a fluorescein standard curve. This standard curve was later used to convert cell-based readings to an equivalent fluorescein concentration.



Cell Measurement Protocol

Briefly, we measured the raw absorbance and fluorescence of diluted cells (transformed with the below testing devices) at 0 hours and after 6 hours of incubation at 37°C.



Device Part number Plate Location
Negative Control BBa_R0040 Kit Plate 7 Well 2D
Positive Control BBa_I20270 Kit Plate 7 Well 2B
Test Device 1 BBa_J364000 Kit Plate 7 Well 2F
Test Device 2 BBa_J364001 Kit Plate 7 Well 2H
Test Device 3 BBa_J364002 Kit Plate 7 Well 2J
Test Device 4 BBa_J364007 Kit Plate 7 Well 2L
Test Device 5 BBa_J364008 Kit Plate 7 Well 2N
Test Device 6 BBa_J364009 Kit Plate 7 Well 2P


Results

In our standard curves, we expected a linear relationship between concentration and fluorescence/absorbance. However, the log-scale particle standard curve (Figure 2B) does not exhibit a linear relationship. Possible sources of error include pipetting error or oversaturation of the detector.



Figure 1: A) Fluorescein standard curve. B) Fluorescein standard curve (log-scale).



Figure 2: A) Particle standard curve. B) Particle standard curve (log-scale).



Figure 3: A) Average fluorescence per optical density. B) Average fluorescence per particle.