Difference between revisions of "Team:ShanghaiTech/Measurement"
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<p>There have been a huge amount of repressive parts available in iGEM parts registry. However, no matter how much efforts you made to create approximately the same conditions using the information given by the literature to test these parts, there is still an unignorable difference in efficiency between tested parts and the parts described in the literature, due to the inevitable difference of cultivate conditions, equipments and so on. Therefore, there is a huge need to create a global standard to normalize all the data created from different labs on the earth. </p> | <p>There have been a huge amount of repressive parts available in iGEM parts registry. However, no matter how much efforts you made to create approximately the same conditions using the information given by the literature to test these parts, there is still an unignorable difference in efficiency between tested parts and the parts described in the literature, due to the inevitable difference of cultivate conditions, equipments and so on. Therefore, there is a huge need to create a global standard to normalize all the data created from different labs on the earth. </p> | ||
<p>Especially for those repressive parts using fluorescent proteins such as GFP as expression level readout, the better the repressor performs, the weaker it is for us to observe the fluorescence strength. Hence larger experimental errors may occur. Although every team will use their own relevant control groups to test their parts, we still lack a control group as a global standardization to help us visualize the difference in the performance of these repressive parts. Simply speaking, even the smallest differentiations such as different promoters or RBS (Ribosome binding site), will have a huge affect to the result of the fluorescence detection. Considering high similarity between synthetic biology and engineering, a unified standard is of great importance to be established.</p> | <p>Especially for those repressive parts using fluorescent proteins such as GFP as expression level readout, the better the repressor performs, the weaker it is for us to observe the fluorescence strength. Hence larger experimental errors may occur. Although every team will use their own relevant control groups to test their parts, we still lack a control group as a global standardization to help us visualize the difference in the performance of these repressive parts. Simply speaking, even the smallest differentiations such as different promoters or RBS (Ribosome binding site), will have a huge affect to the result of the fluorescence detection. Considering high similarity between synthetic biology and engineering, a unified standard is of great importance to be established.</p> | ||
| − | <p>In fact, we have already had a very standard and globalized measurement instrument —— | + | <p>In fact, we have already had a very standard and globalized measurement instrument —— InterLab. iGEM has been pursuing InterLab experiment for decades, yet few teams have used InterLab data properly. The experiment plasmids offered by InterLab has provided an excellent control group for GFP, hence the expression strength of experiment plasmids under different living conditions can be roughly classified by expressing standard InterLab plasmids with different strength.Since the InterLab control system has been standardized to all iGEM labs around the world, different labs can use this system as well, to have an accurate comparison about the strength of the same or even different expression systems.</p> |
<p><img class="img-fluid d-block mx-auto rounded shadow" style="width: 80%" src="https://static.igem.org/mediawiki/2018/0/0f/T--ShanghaiTech--interlabstandardcurve.tif"></p> | <p><img class="img-fluid d-block mx-auto rounded shadow" style="width: 80%" src="https://static.igem.org/mediawiki/2018/0/0f/T--ShanghaiTech--interlabstandardcurve.tif"></p> | ||
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<p>For our optimized repressive part pT181, when we tried to compare it to the previous version submitted by team Kyoto, it was unavailable for us to learn what they had used as control group to test the inhibitory effect of their version. Hence we were unable to visualize the difference between two versions of pT181.</p> | <p>For our optimized repressive part pT181, when we tried to compare it to the previous version submitted by team Kyoto, it was unavailable for us to learn what they had used as control group to test the inhibitory effect of their version. Hence we were unable to visualize the difference between two versions of pT181.</p> | ||
| − | <p>As an alternative, we tested the inhibitory effect of these two pT181 by picking five | + | <p>As an alternative, we tested the inhibitory effect of these two pT181 by picking five InterLab plasmids with different strength as control group. Under the same cultivation environment and using same promoters and RBS, the expression efficiency of our optimized pT181 is extreamly higher than that of the Kyoto pT181. (Lack of detailed explanations) </p> |
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| − | <p>This is how | + | <p>This is how InterLab data is used in our comparison experiment. The general applicability and simplicity of our operation mode should be continued.</p> |
| − | <p>Meanwhile, the expression quantity of the | + | <p>Meanwhile, the expression quantity of the InterLab plasmids can be used as a measurement criterion to compare the performance of our repressive part to other repressive parts.</p> |
| − | <p>We strongly recommend future iGEM teams to use bacteria from | + | <p>We strongly recommend future iGEM teams to use bacteria from InterLab as a standardized control group measuring the performance of their parts, especially repressive parts. With the plasmid fluorescence strength chart as a medium for different labs testing their parts, a globalized performance classification system can be formed. </p> |
</div> | </div> | ||
Revision as of 03:16, 18 October 2018
Measurement
There have been a huge amount of repressive parts available in iGEM parts registry. However, no matter how much efforts you made to create approximately the same conditions using the information given by the literature to test these parts, there is still an unignorable difference in efficiency between tested parts and the parts described in the literature, due to the inevitable difference of cultivate conditions, equipments and so on. Therefore, there is a huge need to create a global standard to normalize all the data created from different labs on the earth.
Especially for those repressive parts using fluorescent proteins such as GFP as expression level readout, the better the repressor performs, the weaker it is for us to observe the fluorescence strength. Hence larger experimental errors may occur. Although every team will use their own relevant control groups to test their parts, we still lack a control group as a global standardization to help us visualize the difference in the performance of these repressive parts. Simply speaking, even the smallest differentiations such as different promoters or RBS (Ribosome binding site), will have a huge affect to the result of the fluorescence detection. Considering high similarity between synthetic biology and engineering, a unified standard is of great importance to be established.
In fact, we have already had a very standard and globalized measurement instrument —— InterLab. iGEM has been pursuing InterLab experiment for decades, yet few teams have used InterLab data properly. The experiment plasmids offered by InterLab has provided an excellent control group for GFP, hence the expression strength of experiment plasmids under different living conditions can be roughly classified by expressing standard InterLab plasmids with different strength.Since the InterLab control system has been standardized to all iGEM labs around the world, different labs can use this system as well, to have an accurate comparison about the strength of the same or even different expression systems.
For our optimized repressive part pT181, when we tried to compare it to the previous version submitted by team Kyoto, it was unavailable for us to learn what they had used as control group to test the inhibitory effect of their version. Hence we were unable to visualize the difference between two versions of pT181.
As an alternative, we tested the inhibitory effect of these two pT181 by picking five InterLab plasmids with different strength as control group. Under the same cultivation environment and using same promoters and RBS, the expression efficiency of our optimized pT181 is extreamly higher than that of the Kyoto pT181. (Lack of detailed explanations)
This is how InterLab data is used in our comparison experiment. The general applicability and simplicity of our operation mode should be continued.
Meanwhile, the expression quantity of the InterLab plasmids can be used as a measurement criterion to compare the performance of our repressive part to other repressive parts.
We strongly recommend future iGEM teams to use bacteria from InterLab as a standardized control group measuring the performance of their parts, especially repressive parts. With the plasmid fluorescence strength chart as a medium for different labs testing their parts, a globalized performance classification system can be formed.