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− | <img src="https://static.igem.org/mediawiki/2018/ | + | <img src="https://static.igem.org/mediawiki/2018/3/32/T--Hong_Kong_HKUST--Interlabbanner.png" class="rounded mx-auto d-block" alt="..." width="100%" height="100%"> |
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<h2>OUR INTERLAB OBJECTIVES</h2> | <h2>OUR INTERLAB OBJECTIVES</h2> | ||
− | <p>The | + | <p>The iGEM Interlab 2018 aims to reduce lab-to-lab variability in fluorescence measurements that were shown in previous interlab studies which use an optical density (O.D.) as the normalization method of fluorescence. Since O.D. is an approximation of cell number, the interlab this year attempts to address the problem by two orthogonal approaches. Hypothesized that silica beads have similar light scattering properties as the cells due to their similarities in size and shape, one of the approaches is to convert the absorbance of cells to the absorbance of a known concentration of silica beads <sup>[1]</sup>. Adopting a more direct normalization method, the other approach is to normalize the absorbance of cells by absolute cell counts or colony-forming units (CFU). </p> |
<h2>Method:</h2> | <h2>Method:</h2> | ||
− | <p>All procedures | + | <p>All procedures were performed according to the given iGEM protocol <sup>[2]</sup>, except that the O.D. measurement setting was changed from OD<sub>600</sub> to OD<sub>595</sub>, due to the limited options of plate reader in HKUST. After further discussion with the iGEM headquarter, we retained the data to be OD<sub>595</sub>. |
</p> | </p> | ||
<h2>Machines, materials and parts:</h2> | <h2>Machines, materials and parts:</h2> | ||
− | |||
<h3><i>Machines:</i></h3><br/> | <h3><i>Machines:</i></h3><br/> | ||
− | <li>Envision Multilabel Reader</li> | + | <ul style="color:black; |
+ | font-size:13pt; | ||
+ | font-family:arial;"> | ||
+ | <li><p>Envision Multilabel Reader (Model: EnVision Xcite)</p></li> <br/> | ||
</ul> | </ul> | ||
<p> | <p> | ||
− | *To know more about the setting of EnVision multilabel reader, please <a href="">click</a> | + | *To know more about the setting of EnVision multilabel reader, please <a href="">click</a> <br/> |
</p> | </p> | ||
<p> | <p> | ||
− | <ul> | + | <!--<ul style="color:black; |
− | <li><b>LUDOX CL-X | + | font-size:13pt; |
− | </ | + | font-family:arial;">--> |
− | + | <h3><i>Materials:</i></h3><br/> | |
− | + | <li><b>LUDOX CL-X</b>: 45% colloidal silica suspension, used as single reference point for converting absorbance (Abs<sub>600</sub>) to OD<sub>600</sub> <br/>. | |
− | + | ||
</li> | </li> | ||
− | <li>E.coli strain DH5αCompetent cell: | + | <li><b>Silica beads</b>: Microsphere suspension that mimics the shape and size of typical <i>E.coli</i> cell. With known concentration, it can be used for the conversion of absorbance measurement to the universal standard concentration of bead measurement. |
− | </li> | + | |
− | </ul> | + | </li> <br/> |
+ | <li><b>Fluorescein</b>: Sodium fluorescein was used for obtaining the standard fluorescence curve.</b> | ||
+ | </li> <br/> | ||
+ | <li><i>E.coli</i> strain DH5αCompetent cell: used for transformation, the protocol used for making it can view in <a href="http://www.unc.edu/depts/marzluff/Marzluff/Protocols_files/Inoue%20Method%20for%20Preparation%20of%20Ultracompetent%20cells.pdf">here</a> | ||
+ | </li> <br/> | ||
+ | |||
+ | <!--</ul>--> | ||
</p> | </p> | ||
− | < | + | <h3><i>Parts:</i></h3><br/> |
− | <table style="width:100%"> | + | <table style="width:100% ;color:black; |
+ | font-size:13pt; | ||
+ | font-family:arial;"> | ||
<tr> | <tr> | ||
<th>Parts</th> | <th>Parts</th> | ||
Line 97: | Line 128: | ||
<td>BBa_R0040 (nil)</td> | <td>BBa_R0040 (nil)</td> | ||
<td>nil</td> | <td>nil</td> | ||
+ | <td>GFP</td> | ||
+ | <td>BBa_B0010, BBa_B0012</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>BBa_J23101 (1791au)</td> | <td>BBa_J23101 (1791au)</td> | ||
<td>BBa_B0034 (1.0)</td> | <td>BBa_B0034 (1.0)</td> | ||
+ | <td>GFP</td> | ||
+ | <td>BBa_B0010, BBa_B0012</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>Plate 7 Well 2H</td> | <td>Plate 7 Well 2H</td> | ||
<td>BBa_J23106 (1185au)</td> | <td>BBa_J23106 (1185au)</td> | ||
+ | <td>BBa_B0034 (1.0)</td> | ||
+ | <td>GFP</td> | ||
+ | <td>BBa_B0010, BBa_B0012</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>Plate 7 Well 2J</td> | <td>Plate 7 Well 2J</td> | ||
<td>BBa_J23117 (162au)</td> | <td>BBa_J23117 (162au)</td> | ||
+ | <td>BBa_B0034 (1.0)</td> | ||
+ | <td>GFP</td> | ||
+ | <td>BBa_B0010, BBa_B0012</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>Plate 7 Well 2L</td> | <td>Plate 7 Well 2L</td> | ||
<td>BBa_J23100(2547au)</td> | <td>BBa_J23100(2547au)</td> | ||
− | <td>BBa_B0034* (nil)</td> | + | <td>BBa_B0034* (nil)</td> |
+ | <td>GFP</td> | ||
+ | <td>BBa_B0010, BBa_B0012</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>BBa_J23100(2547au)</td> | <td>BBa_J23100(2547au)</td> | ||
<td>BBa_B0034* (nil)</td> | <td>BBa_B0034* (nil)</td> | ||
+ | <td>GFP</td> | ||
+ | <td>BBa_B0010, BBa_B0012</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
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<h2>Result:</h2> | <h2>Result:</h2> | ||
<p> | <p> | ||
− | < | + | <h3><i>Calibrations:</i></h3> |
+ | </p> | ||
+ | <p> | ||
Conversion factor of OD<sub>600</sub>(OD<sub>600</sub>/Abs<sub>600</sub>) = 3.036 | Conversion factor of OD<sub>600</sub>(OD<sub>600</sub>/Abs<sub>600</sub>) = 3.036 | ||
− | <table style="width:100%"> | + | |
+ | <br> | ||
+ | <caption style="text-align:center;color:black; | ||
+ | font-size:13pt; | ||
+ | font-family:arial;">Table 2: Conversion factor calculation</caption> </p> | ||
+ | <table style="width:100%;color:black; | ||
+ | font-size:13pt; | ||
+ | font-family:arial;"> | ||
<tr> | <tr> | ||
<th> </th> | <th> </th> | ||
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</tr> | </tr> | ||
</table> | </table> | ||
− | |||
</p> | </p> | ||
<figure> | <figure> | ||
− | <img src="https://static.igem.org/mediawiki/2018/ | + | <center><img src="https://static.igem.org/mediawiki/2018/1/1f/T--Hong_Kong_HKUST--Particlestandardnew.png" class="img-fluid" alt="Responsive image" width="500px" height="500px" ></center> |
− | <figcaption>Fig. 2a Particle Standard Curve</figcaption> | + | <center><figcaption style="color:black; |
+ | font-size:13pt; | ||
+ | font-family:arial;"><b>Fig. 2a</b> Particle Standard Curve</figcaption></center> | ||
+ | <br> | ||
</figure> | </figure> | ||
+ | |||
<figure> | <figure> | ||
− | <img src="https://static.igem.org/mediawiki/2018/2/23/T--Hong_Kong_HKUST--Particlestandardcurvelog.png" class="img-fluid" alt="Responsive image"> | + | <center><img src="https://static.igem.org/mediawiki/2018/2/23/T--Hong_Kong_HKUST--Particlestandardcurvelog.png" class="img-fluid" alt="Responsive image" width="500px" height="500px"></center> |
− | <figcaption>Fig.2b Particle Standard Curve (log scale) | + | <center><figcaption style="color:black; |
− | </figcaption> | + | font-size:13pt; |
+ | font-family:arial;"><b>Fig.2b</b> Particle Standard Curve (log scale) | ||
+ | </figcaption></center> | ||
+ | <br> | ||
</figure> | </figure> | ||
+ | |||
<figure> | <figure> | ||
− | <img src="https://static.igem.org/mediawiki/2018/ | + | <center><img src="https://static.igem.org/mediawiki/2018/b/b7/T--Hong_Kong_HKUST--FLuorescein_standard_curve%28new%29.png" class="img-fluid" alt="Responsive image" width="500px" height="500px"></center> |
− | <figcaption>Fig.3a Fluorescein standard curve</figcaption> | + | <center><figcaption style="color:black; |
+ | font-size:13pt; | ||
+ | font-family:arial;"><b>Fig.3a</b> Fluorescein standard curve</figcaption></center> | ||
</figure> | </figure> | ||
+ | <br> | ||
+ | |||
<figure> | <figure> | ||
− | <img src="https://static.igem.org/mediawiki/2018/0/0a/T--Hong_Kong_HKUST--Fluoresceinlog.png" class="img-fluid" alt="Responsive image"> | + | <center><img src="https://static.igem.org/mediawiki/2018/0/0a/T--Hong_Kong_HKUST--Fluoresceinlog.png" class="img-fluid" alt="Responsive image" width="500px" height="500px"></center> |
− | <figcaption>Fig. | + | <center><figcaption style="color:black; |
− | </figcaption> | + | font-size:13pt; |
+ | font-family:arial;"><b>Fig.3b</b> Fluorescein standard curve (log scale) | ||
+ | </br> | ||
+ | The non-linear fluorescence standard curve is conjectured to be a result of detector over-saturation. </br>This could be inferred from a linear curve at low concentrations of fluorescein while reaching plateau at high concentrations. | ||
+ | </figcaption></center> | ||
</figure> | </figure> | ||
<br> | <br> | ||
− | < | + | <p> </p> |
+ | |||
+ | <h2>Conversion of absorbance of cells to absorbance of a known concentration of beads.</h2> | ||
+ | <br/> | ||
<figure> | <figure> | ||
− | <img src="https://static.igem.org/mediawiki/2018/ | + | <center><img src="https://static.igem.org/mediawiki/2018/d/d2/T--Hong_Kong_HKUST--AverageuMInterlabwiki%28new%29.png" class="img-fluid" alt="Responsive image" width="500px" height="500px"></center> |
− | <figcaption>Fig. | + | <center><figcaption style="color:black; |
− | </figcaption> | + | font-size:13pt; |
+ | font-family:arial;"><b>Fig.4a</b> Average <sub>u</sub>M Fluorescein / OD<sub>600</sub> of each devices | ||
+ | </figcaption></center> | ||
</figure> | </figure> | ||
+ | <br> | ||
+ | |||
<figure> | <figure> | ||
− | <img src="https://static.igem.org/mediawiki/2018/2/ | + | <center><img src="https://static.igem.org/mediawiki/2018/2/27/T--Hong_Kong_HKUST--AverageMEFLInterlabwiki.png" class="img-fluid" alt="Responsive image" width="500px" height="500px"></center> |
− | <figcaption>Fig. | + | <center><figcaption style="color:black; |
− | </figcaption> | + | font-size:13pt; |
+ | font-family:arial;"><b>Fig.4b</b> Fluorescein standard curve (log scale) | ||
+ | </figcaption></center> | ||
</figure> | </figure> | ||
+ | <br> | ||
<h2>Counting colony-forming units (CFUs) from the sample | <h2>Counting colony-forming units (CFUs) from the sample | ||
</h2><br/> | </h2><br/> | ||
Line 217: | Line 296: | ||
Colonies count: <br/> | Colonies count: <br/> | ||
Negative control (BBa_R0040): | Negative control (BBa_R0040): | ||
− | + | </p> | |
− | <table> | + | <table style="color:black; |
+ | font-size:13pt; | ||
+ | font-family:arial;"> | ||
<tr> | <tr> | ||
<th></th> | <th></th> | ||
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</tr> | </tr> | ||
</table> | </table> | ||
− | + | <p> | |
Positive control ((BBa_I120270): | Positive control ((BBa_I120270): | ||
− | + | </p> | |
− | <table> | + | <table style="color:black; |
+ | font-size:13pt; | ||
+ | font-family:arial;"> | ||
<tr> | <tr> | ||
<th></th> | <th></th> | ||
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</table> | </table> | ||
+ | <p> | ||
Colony-forming unit (CFU): | Colony-forming unit (CFU): | ||
Negative control (BBa_R0040): | Negative control (BBa_R0040): | ||
− | + | </p> | |
− | <table> | + | <table style="color:black; |
+ | font-size:13pt; | ||
+ | font-family:arial;"> | ||
<tr> | <tr> | ||
<th></th> | <th></th> | ||
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</tr> | </tr> | ||
</table> | </table> | ||
− | Average < | + | <h2> |
− | <ul> | + | Average </h2> |
+ | <ul style="color:black; | ||
+ | font-size:13pt; | ||
+ | font-family:arial;"> | ||
<li>Colony 1: 1.69E+07 CFU/ml/0.1OD</li> | <li>Colony 1: 1.69E+07 CFU/ml/0.1OD</li> | ||
<li>Colony 2: 1.88E+07 CFU/ml/0.1OD</li> | <li>Colony 2: 1.88E+07 CFU/ml/0.1OD</li> | ||
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<h2>Conclusion:</h2> | <h2>Conclusion:</h2> | ||
<p> | <p> | ||
− | + | There is no significant difference in the pattern of normalized fluorescence values between using O.D. and particle count, as illustrated in Figure 4 and 5. The normalized fluorescence values of the devices are consistent with their respective promoter strengths, with device 1 (BBa_J23101) as the highest fluorescence value (i.e. 1791 a.u.) and device 3 (BBa_J23117) as the lowest fluorescence value (i.e. 162 a.u.). However, cell quantification by colony-forming units failed to reproduce the modeled cell concentration by silica beads. This may conclude that the two methods, CFU cell count and silica beads, may not be able to produce a consistent value of cell concentration. | |
+ | </p> | ||
+ | <section id="One" class="wrapper style3"> | ||
+ | <div class="inner"> | ||
+ | <header class="align-center"> | ||
+ | |||
+ | <h2>REFERENCES:</h2> | ||
+ | |||
+ | </header> | ||
+ | </div> | ||
+ | </section> | ||
+ | <p>1. Measurement/InterLab - 2018.igem.org", 2018.igem.org, 2018. Available: https://2018.igem.org/Measurement/InterLab | ||
+ | </p> | ||
+ | <p>2. InterLab Plate Reader Protocol. The 2018 International Genetically Engineered Machine. Available:https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf | ||
</p> | </p> | ||
</div> | </div> | ||
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Latest revision as of 18:23, 17 October 2018
OUR INTERLAB OBJECTIVES
The iGEM Interlab 2018 aims to reduce lab-to-lab variability in fluorescence measurements that were shown in previous interlab studies which use an optical density (O.D.) as the normalization method of fluorescence. Since O.D. is an approximation of cell number, the interlab this year attempts to address the problem by two orthogonal approaches. Hypothesized that silica beads have similar light scattering properties as the cells due to their similarities in size and shape, one of the approaches is to convert the absorbance of cells to the absorbance of a known concentration of silica beads [1]. Adopting a more direct normalization method, the other approach is to normalize the absorbance of cells by absolute cell counts or colony-forming units (CFU).
Method:
All procedures were performed according to the given iGEM protocol [2], except that the O.D. measurement setting was changed from OD600 to OD595, due to the limited options of plate reader in HKUST. After further discussion with the iGEM headquarter, we retained the data to be OD595.
Machines, materials and parts:
Machines:
Envision Multilabel Reader (Model: EnVision Xcite)
*To know more about the setting of EnVision multilabel reader, please click
Materials:
.
Parts:
Parts | Parts location on the kits plate | Parts used as the promoter(strength) | Parts used as the RBS(Efficiency) | Reporter Gene | Parts used as the Terminator |
---|---|---|---|---|---|
Positive Control(BBa_I20270) | Plate 7 Well 2B | BBa_J23151 (nil) | BBa_B0032 (0.3) | GFP | BBa_B0010, BBa_B0012 |
Negative Control (BBa_R0040) | Plate 7 Well 2D | BBa_R0040 (nil) | nil | GFP | BBa_B0010, BBa_B0012 |
Test Device 1 (BBa_J364000) | Plate 7 Well 2F | BBa_J23101 (1791au) | BBa_B0034 (1.0) | GFP | BBa_B0010, BBa_B0012 |
Test Device 2 (BBa_J364001) | Plate 7 Well 2H | BBa_J23106 (1185au) | BBa_B0034 (1.0) | GFP | BBa_B0010, BBa_B0012 |
Test Device 3 (BBa_J364002) | Plate 7 Well 2J | BBa_J23117 (162au) | BBa_B0034 (1.0) | GFP | BBa_B0010, BBa_B0012 |
Test Device 4 (BBa_J364007) | Plate 7 Well 2L | BBa_J23100(2547au) | BBa_B0034* (nil) | GFP | BBa_B0010, BBa_B0012 |
Test Device 4 (BBa_J364007) | Plate 7 Well 2L | BBa_J23100(2547au) | BBa_B0034* (nil) | GFP | BBa_B0010, BBa_B0012 |
Result:
Calibrations:
Conversion factor of OD600(OD600/Abs600) = 3.036
LUDOX CL-X | H20 | |
---|---|---|
Replicate 1 | 0.045 | 0.024 |
Replicate 2 | 0.045 | 0.025 |
Replicate 3 | 0.044 | 0.024 |
Replicate 4 | 0.049 | 0.027 |
Arithmethic mean | 0.046 | 0.025 |
Corrected Abs600 | 0.021 | |
Reference OD600 | 0.063 | |
OD600/Abs600 | 3.036 |
Conversion of absorbance of cells to absorbance of a known concentration of beads.
Counting colony-forming units (CFUs) from the sample
Colonies count:
Negative control (BBa_R0040):
Dillution 3 | Dillution 4 | Dillution 5 | |
---|---|---|---|
Colony 1, Replicate 1 | 180 | 13 | 3 |
Colony 1, Replicate 2 | 120 | 14 | 3 |
Colony 1, Replicate 3 | 197 | 33 | 2 |
Colony 2, Replicate 1 | 283 | 33 | 2 |
Colony 2, Replicate 2 | 214 | 28 | 3 |
Colony 2, Replicate 3 | 218 | 29 | 1 |
Positive control ((BBa_I120270):
Dillution 3 | Dillution 4 | Dillution 5 | |
---|---|---|---|
Colony 1, Replicate 1 | 228 | 29 | 1 |
Colony 1, Replicate 2 | 184 | 25 | 1 |
Colony 1, Replicate 3 | 153 | 25 | 1 |
Colony 2, Replicate 1 | 254 | 19 | 3 |
Colony 2, Replicate 2 | 168 | 27 | 2 |
Colony 2, Replicate 3 | 213 | 24 | 3 |
Colony-forming unit (CFU): Negative control (BBa_R0040):
Dillution 3 | Dillution 4 | Dillution 5 | |
---|---|---|---|
Colony 1, Replicate 1 | 1.44E+07 | 1.04E+07 | 2.40E+07 |
Colony 1, Replicate 2 | 9.60E+06 | 1.12E+07 | 2.40E+07 |
Colony 1, Replicate 3 | 1.58E+07 | 2.64E+07 | 1.60E+07 |
Colony 2, Replicate 1 | 2.26E+07 | 1.84E+07 | 1.60E+07 |
Colony 2, Replicate 2 | 1.71E+07 | 2.24E+07 | 2.40E+07 |
Colony 2, Replicate 3 | 1.74E+07 | 2.32E+07 | 8.00E+06 |
Average
- Colony 1: 1.69E+07 CFU/ml/0.1OD
- Colony 2: 1.88E+07 CFU/ml/0.1OD
- Average: 1.785E+07 CFU/ml/0.1OD
- Using conversion factor OD/Abs= 3.036
- Conversion factor: CFU/Abs/ml= 54.34 CFU/Abs/ml
Conclusion:
There is no significant difference in the pattern of normalized fluorescence values between using O.D. and particle count, as illustrated in Figure 4 and 5. The normalized fluorescence values of the devices are consistent with their respective promoter strengths, with device 1 (BBa_J23101) as the highest fluorescence value (i.e. 1791 a.u.) and device 3 (BBa_J23117) as the lowest fluorescence value (i.e. 162 a.u.). However, cell quantification by colony-forming units failed to reproduce the modeled cell concentration by silica beads. This may conclude that the two methods, CFU cell count and silica beads, may not be able to produce a consistent value of cell concentration.
REFERENCES:
1. Measurement/InterLab - 2018.igem.org", 2018.igem.org, 2018. Available: https://2018.igem.org/Measurement/InterLab
2. InterLab Plate Reader Protocol. The 2018 International Genetically Engineered Machine. Available:https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf