Difference between revisions of "Team:Pasteur Paris/Measurement"

 
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<img src="https://static.igem.org/mediawiki/2015/7/78/Measurement_pasteur2015.jpg" style="width: 100%;"/>
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<h2> Measurement</h2>
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<br/><br/><div class="carregris">
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<center><h3><i>Esterase pNP Assay in BAP 1</i></h3></center>
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<p align="justify" style="text-indent:3em;">In order to make a strain that combines PET degradation pathway and erythromycin synthesis pathway we investigated the activity of the Esterase (Est13) in the BAP 1 <i>E. coli</i> strain, used for Ery production in Pfeifer’s laboratory. <b>Esterase is the first enzyme in PET degradation pathway</b>, unfortunately the reaction between PET and esterase is very slow, it takes approximately 2 weeks to accumulate detectable degradation products. To bypass this technical difficulty we chose a different substrate of Esterase: the <b>4-Nitrophenyl butyrate</b>, also called para-Nitrophenylbutyrate. The 4-Nitrophenyl butyrate have a similar chemical structure with the PET, but is a way smaller.</p></br>
  
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<p style="text-indent:3em;" align="justify"><span style="color: #004864; font-size: 1.2em;"><b>&rarr; Protocol:</b></span></p>
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<p align="justify">In a P96 plate, we had in each well 100 µl of our bacterial suspension OD(600nm)=0.5 or OD(600nm)=0.1.
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In the appropriates wells, 10 µL of susbtrate 10mM, 50mM, or 0mM was added. The plate was put incubating at 34°C in the spectrophotometer for 30 minutes. We use a spectrophotometer TECAN for this experiment: we took the respective suspension's absorptions (405 nm) every 2 minutes.
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The difference of substrate's concentration or OD(600 nm) help us to know which conditions are optimal for this enzymatic activity.</p>
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<br/>
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<p style="text-indent:3em;" align="justify"><span style="color: #004864; font-size: 1.2em;"><b>&rarr; Our Controls:</b></span></p>
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<p>We did 3 controls for this experiment:</p>
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<ul><li>With only the medium and the substrate, to see if there are a reaction between this 2 products;</li>
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<li>With the unmodified BAP 1 bacteria in presence of the substrate, to see if the bacteria degrade the 4-Nitrophenyl butyrate without our construct;</li>
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<li>With the modified bacteria or unmodified bacteria without substrat, too see that our results come really from the esterase enzymatic activity;</li>
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</ul>
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<p>We realized this experiment 3 times for more precision, and with 3 different clones of our construction.</p>
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<br/><br/>
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<center><p><i><b>pNP-Assay</b></i></p></center>
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<p>Due to the technical problems we successfully performed Esterase test on BAP1 strain only 1 time. The result is present as the average value of triplicates +/- standard deviation.</p>
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<center><img src="https://static.igem.org/mediawiki/2015/f/f9/PNBPasteur.png" style="width: 50%;">
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<h4>Note</h4>
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<p style="text-indent:3em;" align="justify"><span style="color: #004864; font-size: 1.2em;"><b>&rarr; Conclusion</b></span></p>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Measurement Approach award</a>, you must fill out this page.</p>
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<p align="justify" style="text-indent:3em;">Presence of the plasmid containing the gene of Esterase allows BAP 1 strain to degrade the substrate 4-Nitrophenyl Butyrate. The negative control shows that BAP 1 itself doesn't degrade 4-Nitrophenyl butyrate naturally. The observed accumulation of 4-Nitrophenol Butyrate most likely depends on the Esterase plasmid.</p>
 
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<p>There are a lot of exciting Parts in the Registry, but many Parts have still not been characterized. Synthetic Biology needs great measurement approaches for characterizing new parts, and efficient new methods for characterizing many parts at once. If you've done something exciting in the area of Measurement, describe it here!</p>
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<br/><br/><div class="carregris">
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<center><h3><i>Impact of the ethylene glycol and of the terephthalate acid on the strain BAP 1 of E.coli</i></h3></center>
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<br/>
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<p style="text-indent:3em;" align="justify"><span style="color: #004864; font-size: 1.2em;"><b>&rarr; Experiments:</b></span></p>
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<center>
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<a href="https://static.igem.org/mediawiki/2015/0/0d/Measurements.pdf" target="_blank">
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<img src="https://static.igem.org/mediawiki/2015/d/d3/Measurementdss.jpg" title="FRENCH" width="175" height="250"/></a>
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<h4>Inspiration</h4>
 
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<p>You can look at what other teams did to get some inspiration! <br />
 
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Here are a few examples:</p>
 
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<ul>
 
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<li><a href="https://2014.igem.org/Team:Aachen">2014 Aachen  </a></li>
 
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<li><a href="https://2014.igem.org/Team:Valencia_Biocampus">2014 Valencia Biocampus</a></li>
 
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Latest revision as of 21:55, 19 November 2015







Esterase pNP Assay in BAP 1


In order to make a strain that combines PET degradation pathway and erythromycin synthesis pathway we investigated the activity of the Esterase (Est13) in the BAP 1 E. coli strain, used for Ery production in Pfeifer’s laboratory. Esterase is the first enzyme in PET degradation pathway, unfortunately the reaction between PET and esterase is very slow, it takes approximately 2 weeks to accumulate detectable degradation products. To bypass this technical difficulty we chose a different substrate of Esterase: the 4-Nitrophenyl butyrate, also called para-Nitrophenylbutyrate. The 4-Nitrophenyl butyrate have a similar chemical structure with the PET, but is a way smaller.


→ Protocol:

In a P96 plate, we had in each well 100 µl of our bacterial suspension OD(600nm)=0.5 or OD(600nm)=0.1. In the appropriates wells, 10 µL of susbtrate 10mM, 50mM, or 0mM was added. The plate was put incubating at 34°C in the spectrophotometer for 30 minutes. We use a spectrophotometer TECAN for this experiment: we took the respective suspension's absorptions (405 nm) every 2 minutes. The difference of substrate's concentration or OD(600 nm) help us to know which conditions are optimal for this enzymatic activity.


→ Our Controls:

We did 3 controls for this experiment:

  • With only the medium and the substrate, to see if there are a reaction between this 2 products;
  • With the unmodified BAP 1 bacteria in presence of the substrate, to see if the bacteria degrade the 4-Nitrophenyl butyrate without our construct;
  • With the modified bacteria or unmodified bacteria without substrat, too see that our results come really from the esterase enzymatic activity;

We realized this experiment 3 times for more precision, and with 3 different clones of our construction.



pNP-Assay

Due to the technical problems we successfully performed Esterase test on BAP1 strain only 1 time. The result is present as the average value of triplicates +/- standard deviation.




→ Conclusion

Presence of the plasmid containing the gene of Esterase allows BAP 1 strain to degrade the substrate 4-Nitrophenyl Butyrate. The negative control shows that BAP 1 itself doesn't degrade 4-Nitrophenyl butyrate naturally. The observed accumulation of 4-Nitrophenol Butyrate most likely depends on the Esterase plasmid.



Impact of the ethylene glycol and of the terephthalate acid on the strain BAP 1 of E.coli


→ Experiments:



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