Difference between revisions of "Team:Hong Kong HKUST/InterLab"

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<h2>OUR INTERLAB OBJECTIVES</h2>
 
<h2>OUR INTERLAB OBJECTIVES</h2>
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<p>The iGEM Interlab 2018 aims to reduce lab-to-lab variability in fluorescence measurements that was shown in previous interlab studies to originate from using optical density (O.D.) as the normalisation method of fluorescence. Since O.D. is an approximation of cell number, the interlab this year attempts to address the problem by adopting a more direct normalisation method. That is, the use of absolute cell count or colony-forming units (CPU).  </p>
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<p style="color:blue">The iGEM Interlab 2018 aims to reduce lab-to-lab variability in fluorescence measurements that was shown in previous interlab studies to originate from using optical density (O.D.) as the normalisation method of fluorescence. Since O.D. is an approximation of cell number, the interlab this year attempts to address the problem by adopting a more direct normalisation method. That is, the use of absolute cell count or colony-forming units (CPU).  </p>
  
 
<h2>Method:</h2>
 
<h2>Method:</h2>

Revision as of 12:25, 17 October 2018

iGem HKUST 2018 Hielo by TEMPLATED
...

OUR INTERLAB OBJECTIVES

The iGEM Interlab 2018 aims to reduce lab-to-lab variability in fluorescence measurements that was shown in previous interlab studies to originate from using optical density (O.D.) as the normalisation method of fluorescence. Since O.D. is an approximation of cell number, the interlab this year attempts to address the problem by adopting a more direct normalisation method. That is, the use of absolute cell count or colony-forming units (CPU).

Method:

All procedures were performed according to the protocols iGEM given. 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:


  • LUDOX CL-X: 45% colloidal silica suspension, used as single reference point for converting absorbance (Abs600) to OD600
    .
  • Silica beads: Microsphere suspension that mimics the shape and size of typical E.coli cell. With known concentration, it can be used for the conversion of absorbance measurement to the universal standard concentration of bead measurement.

  • Fluorescein: Sodium fluorescein was used for obtaining the standard fluorescence curve.

  • E.coli strain DH5αCompetent cell: used for transformation, the protocol used for making it can view in here

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
Table 2: Conversion factor calculation
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

Responsive image
Fig. 2a Particle Standard Curve

Responsive image
Fig.2b Particle Standard Curve (log scale)

Responsive image
Fig.3a Fluorescein standard curve

Responsive image
Fig.3b Fluorescein standard curve (log scale)

The non-linear fluorescence standard curve is conjectured to be a result of detector over-saturation. This could be inferred from a linear curve at low concentrations of fluorescein while reaching plateau at high concentrations.

Conversion of absorbance of cells to absorbance of a known concentration of beads.

Responsive image
Fig.4a Average uM Fluorescein / OD600 of each devices

Responsive image
Fig.4b Fluorescein standard curve (log scale)

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 normalised fluorescence values between using OD and particle count, as illustrated in Figure 4 and 5. The normalised fluorescence values of the devices are consistent with their respective promoter strengths, with device 1 (BBa_J23101) as the highest (i.e. 1791 a.u.) and device 3 (BBa_J23117) as the lowest (i.e. 162 a.u.). However, cell quantification by colony-forming units failed to reproduce the modelled cell concentration by silica beads. This may conclude that the method may not be able to reduce lab-to-lab variability.

REFERENCES:

The 2018 International Genetically Engineered Machine. (17 July, 2018). Tracks/Measurement/Interlab study/Plate Reader Protocol. Retrieved from https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf

Registry of Standard Biological Parts (2018-04-17) Retrieved from http://parts.igem.org/assembly/plates.cgi?id=5641

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