Difference between revisions of "Team:IISc Bangalore/Measurement"

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<h3>★  ALERT! </h3>
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<div class="column full_size">
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<li class="dropdown"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Project </a>
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          <li><a href="https://2016.igem.org/Team:IISc_Bangalore/Description">Description</a></li>
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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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<h5>Inspiration</h5>
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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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<li><a href="https://2015.igem.org/Team:William_and_Mary">2015 William and Mary</a></li>
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<h3>Summary</h3>
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<p>Currently, there are no methods of quantifying Ag43 aggregation quantitatively in unsaturated cultures. In theory, the average sedimentation coefficient is an excellent parameter to quantify the degree of aggregation as larger aggregates sink faster, but its estimation involves the use of an expensive analytical ultracentrifuge.</p>
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<p>We developed a protocol to estimate the cluster size distribution (cluster size in units of rpm to settle down the cluster in a given time) in a culture expressing Ag43 that by sedimentation experiments that use only a normal laboratory centrifuge. The data obtained was also in agreement with our expectation of the cluster size distribution and also agreed with our model describing the effect of centrifugation.</p>
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<p>To summarize, we developed a parameter to estimate aggregation - average cluster size and estimated this parameter experimentally. This provides a more precise, quantitative method for characterizing the biobricks expressing proteins that cause aggregation like Ag43 and INP.
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<p><a href="https://static.igem.org/mediawiki/2016/1/10/Ag43-Aggregation-Profile-Model.pdf">Link to the PDF file of the aggregation profile model</a>.</p>
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Latest revision as of 03:11, 20 October 2016


Team IISc iGem

Summary

Currently, there are no methods of quantifying Ag43 aggregation quantitatively in unsaturated cultures. In theory, the average sedimentation coefficient is an excellent parameter to quantify the degree of aggregation as larger aggregates sink faster, but its estimation involves the use of an expensive analytical ultracentrifuge.

We developed a protocol to estimate the cluster size distribution (cluster size in units of rpm to settle down the cluster in a given time) in a culture expressing Ag43 that by sedimentation experiments that use only a normal laboratory centrifuge. The data obtained was also in agreement with our expectation of the cluster size distribution and also agreed with our model describing the effect of centrifugation.

To summarize, we developed a parameter to estimate aggregation - average cluster size and estimated this parameter experimentally. This provides a more precise, quantitative method for characterizing the biobricks expressing proteins that cause aggregation like Ag43 and INP.

Link to the PDF file of the aggregation profile model.

Sponsors



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