Difference between revisions of "Team:IISER-Kolkata/InterLab"

Line 39: Line 39:
 
<h1 class="subheading">interLab</h1>
 
<h1 class="subheading">interLab</h1>
 
<h3 class="subsubheading">Objectives</h3>
 
<h3 class="subsubheading">Objectives</h3>
−
<p>While bacman is gearing up to protect people from arsenic , we decided to pay a visit to the gfp expressing bacteria. It s no doubt that measuring flourescence sounds exciting but even more appealing was the opportunity to be a part of a large community and share data.<br/><br/>
+
<p>While the BacMan is gearing up to protect people from arsenic , we decided to pay a visit to the GFP expressing bacteria. It is no doubt that measuring flourescence sounds exciting but even more appealing was the opportunity to be a part of this global collaborative venture and share data that will help standardize fluorescence measurement assay techniques in general.<br/><br/>
 
So we prepared ourselves to answer the Intelab question : <i>Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?</i><br/><br/>
 
So we prepared ourselves to answer the Intelab question : <i>Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?</i><br/><br/>
 
And then we started :<br/>
 
And then we started :<br/>
Line 134: Line 134:
 
</ul>
 
</ul>
 
<h3 class="subsubheading">Conclusion</h3>
 
<h3 class="subsubheading">Conclusion</h3>
−
<p>At the end of interLab we learnt not only how difficult it might be to standardize data and yet how important this process is. We were glad to be a part of the interLab study and contribute in some way what was required in the effort to standardize data.<br/>
+
<p>At the end of InterLab we learnt not only how difficult it might be to standardize data and yet how important this process is in any experiment. We are glad to have contributed positively to this international collaborative effort by obtaining data.<br/>
 
<h3 class="subsubheading">End result</h3>
 
<h3 class="subsubheading">End result</h3>
−
<p>Team IISER Kolkata is happy and satisfied with interLab.
+
<p>Team IISER Kolkata has successfully completed the InterLab exercise and our data has been duely accepted.
 
</p>
 
</p>
 
</div>
 
</div>

Revision as of 23:26, 11 October 2018

interLab

Objectives

While the BacMan is gearing up to protect people from arsenic , we decided to pay a visit to the GFP expressing bacteria. It is no doubt that measuring flourescence sounds exciting but even more appealing was the opportunity to be a part of this global collaborative venture and share data that will help standardize fluorescence measurement assay techniques in general.

So we prepared ourselves to answer the Intelab question : Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD?

And then we started :
Day 1 : Transforming E coli DH5 alpha cells with the required biobr/icks.
Day 2 : Checking plates . Some biobr/icks didn’t give enough colonies.
Day 3 : Transforming bacteria with 1.5 uL of biobr/icks. Checking plates. We had beautiful and ample colonies this time.
Day 4 : Performing all calibr/ation protocols with ludox , silica beads , fluorescein.
Day 5 : Performed the cell measurements.
Day 6 : Repeated cell measurements.
Day 7 : Performing CFU protocol.
Day 8 : Counting colonies and updating excel files.

Results

LUDOX CL-XH2O
Replicate 10.0490.027
Replicate 20.0520.029
Replicate 30.0650.024
Replicate 40.0540.026
Arith. Mean0.0550.027
Corrected Abs600 0.029 
Reference OD600 0.063 
OD600/Abs6002.211

Fluoroscence Raw Readings

Hour 0Neg. ControlPos. ControlDevice 1Device 2Device 3Device 4Device 5Device 6LB + Chlor (blank)
Colony 1, Replicate 13172494073324129310311501959634093096
Colony 1, Replicate 230524405667241293096115121156837053093
Colony 1, Replicate 33062451382774535331313552981136123561
Colony 1, Replicate 429394559816543933302125781019835953501
Colony 2, Replicate 12694412292564855345911239726638833138
Colony 2, Replicate 22569321189334591363611017686436063429
Colony 2, Replicate 33512343190914728366810965725539813510
Colony 2, Replicate 41739362583124983360611556716036823439
Hour 6Neg. ControlPos. ControlDevice 1Device 2Device 3Device 4Device 5Device 6LB + Chlor (blank)
Colony 1, Replicate 1345252293202593305438663012919804116653751
Colony 1, Replicate 2341148522183263117336672704914295123473677
Colony 1, Replicate 3366248774187393260436462648816048119213409
Colony 1, Replicate 4364656393214543167037042876616617107203600
Colony 2, Replicate 1361835310194076703836802100120176111453641
Colony 2, Replicate 2407734070210046933742371855519423105213911
Colony 2, Replicate 3350934721208436252437231735916708110123134
Colony 2, Replicate 4346636496174506107737571833916887108663084

Abs600 Raw Readings

Hour 0Neg. ControlPos. ControlDevice 1Device 2Device 3Device 4Device 5Device 6LB + Chlor (blank)
Colony 1, Replicate 10.0850.0880.0850.0870.080.0870.0840.080.073
Colony 1, Replicate 20.0860.0820.0870.090.090.0880.0880.0880.079
Colony 1, Replicate 30.080.080.0780.0840.0830.0780.0810.0850.068
Colony 1, Replicate 40.0820.0850.0790.0780.0850.080.0770.0870.069
Colony 2, Replicate 10.0810.0820.0760.0760.080.0780.0810.0790.068
Colony 2, Replicate 20.080.0740.0760.0790.0770.0760.0760.0770.063
Colony 2, Replicate 30.0670.0750.080.0830.0760.0780.0770.0720.069
Colony 2, Replicate 40.0720.0690.0680.070.0750.0720.0740.0770.071
Hour 6Neg. ControlPos. ControlDevice 1Device 2Device 3Device 4Device 5Device 6LB + Chlor (blank)
Colony 1, Replicate 10.3250.3340.0920.3930.390.1620.0980.3520.064
Colony 1, Replicate 20.3190.3160.0910.3820.3830.1520.0810.3720.062
Colony 1, Replicate 30.3460.3290.090.3880.3820.1450.0870.3680.062
Colony 1, Replicate 40.3440.3490.0960.3860.3880.1550.0820.3410.059
Colony 2, Replicate 10.3530.3180.0760.5310.3790.1370.1290.3460.056
Colony 2, Replicate 20.3680.3110.0820.5330.4090.1330.1320.3340.059
Colony 2, Replicate 30.3380.3120.0760.5270.3850.1490.140.3550.076
Colony 2, Replicate 40.3380.3280.0840.5140.3870.1560.1370.3490.076

Observations

  • The test device 3 doesn’t show a great increase in fluorescence though its absorbance is increasing. Its expression level thus must be low.
  • The test device 2 has shown difference florescence and absorbance for the two difference colonies. This could be indication of improper growth in one colony.
  • The test device 1 has shown very low growth after 6 hrs. This could be due to slow growth of bacteria in set conditions and time.

Conclusion

At the end of InterLab we learnt not only how difficult it might be to standardize data and yet how important this process is in any experiment. We are glad to have contributed positively to this international collaborative effort by obtaining data.

End result

Team IISER Kolkata has successfully completed the InterLab exercise and our data has been duely accepted.