Team:TU Delft/Project/rbs-characterization/results

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<div id="rbs-results">
 
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<html><center><img src="https://static.igem.org/mediawiki/2010/0/00/TU_Delft_project_navigation.jpg" usemap="#projectnavigation" border="0" /></center><map id="projectnavigation" name="projectnavigation"><area shape="rect" alt="Characterization" title="" coords="309,3,591,45" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/characterization" target="" /><area shape="rect" alt="Results" title="" coords="609,3,891,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/results" target="" /><area shape="rect" alt="Parts" title="" coords="9,3,290,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/parts" target="" /></map></html>
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==The Results==
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In the plot below the RBS strengths for the five tested members of the Anderson family are given along with the deviations from the mean. The strengths are given relative to the community RBS [http://partsregistry.org/Part:BBa_B0034 BBa_B0034], which has a strength of unity (1). This relationship could be built by our characterization of the community RBS [http://partsregistry.org/Part:BBa_B0032 BBa_B0032] simultaneously, which is known to have a strength (or efficiency) of 0.3 relative to [http://partsregistry.org/Part:BBa_B0032 BBa_B0034]. Therefore in the plot below, the mean value of BBa_B0032 is set to 0.3. The values have been obtained by the experimental setup described [[Team:TU_Delft/Project/rbs-characterization/parts|here]] and using the [[Team:TU_Delft/Modeling/protein-production-model|model]] to correct for growth dilution.
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==RBS Characterization Results==
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[[Image:TUDelft_2010_RBS_strength_graph.PNG|600px|thumb|center|'''Figure 1.''' RBS strength]]
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The given relative strengths are displayed assuming B0034 as the unit (The standard as used by the partsregistry). B0032 is defined to have a strength of 0.3. Therefore in the plot below, the mean value of B0032 is fixed on 0.3.
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[[Image:TUDelft2010_Rbs_strength_boxplot.png]]
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Compared to the B0032, the tested Anderson RBS'es turned out to be surprisingly weak. All 5 of them resulted in less expression than the reference expression.
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<html><div id="rbs-results"></html>
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{|border="1"
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|RBS
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==Conclusions==
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|Mean strength
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We've succeeded in characterizing five members of the Anderson ribosome binding site family by 96 well plate cultivation and simultaneous monitoring of GFP fluorescence and biomass absorbance. Fitting the obtained data to our improved [https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/characterization protein production model] yielded RBS strengths values with negligible standard deviations. To recap the following RBS strengths (efficiencies) were found:
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|Standard deviation
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<html><!-- Original data
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J61100 0.019970|0.005119
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J61101 0.119333|0.021401
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J61107 0.077024|0.014804
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J61117 0.012552|0.004484
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J61127 0.065226|0.006604
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B0032 0.300000|0.026904
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Rounded, in percentage
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J61100 0.020|0.00512
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J61101 0.119|0.02140
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J61107 0.077|0.01480
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J61117 0.013|0.00448
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J61127 0.065|0.00660
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B0032 0.300|0.02690
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--></html>
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{|
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|<b>Ribosome binding site</b>
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|<b>Mean relative strength</b>
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|<b>Standard deviation</b>
|-
|-
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|J61100
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|[http://partsregistry.org/Part:BBa_J61100 J61100]
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|0.026560
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|0.020 (2.0%)
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|0.005126
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|0.00512
|-
|-
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|J61117
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|[http://partsregistry.org/Part:BBa_J61101 J61101]
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|0.123819
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|0.119 (11.9%)
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|0.024725
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|0.02140
|-
|-
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|J61101
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|[http://partsregistry.org/Part:BBa_J61107 J61107]
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|0.081210
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|0.077 (7.7%)
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|0.013402
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|0.01480
|-
|-
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|J61107
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|[http://partsregistry.org/Part:BBa_J61117 J61117]
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|0.019763
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|0.013 (1.3%)
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|0.003963
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|0.00448
|-
|-
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|J61127  
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|[http://partsregistry.org/Part:BBa_J61127 J61127]
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|0.069657
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|0.065 (6.5%)
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|0.007422
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|0.00660
|-
|-
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|B0032
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|[http://partsregistry.org/Part:BBa_B0032 B0032]
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|0.300000
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|0.300 (Reference, 30%)
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|0.028316
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|0.02690
|}
|}
<html></div></html>
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<html><center><img src="https://static.igem.org/mediawiki/2010/0/00/TU_Delft_project_navigation.jpg" usemap="#projectnavigation" border="0" /></center><map id="projectnavigation" name="projectnavigation"><area shape="rect" alt="Characterization" title="" coords="309,3,591,45" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/characterization" target="" /><area shape="rect" alt="Results" title="" coords="609,3,891,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/results" target="" /><area shape="rect" alt="Parts" title="" coords="9,3,290,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/parts" target="" /></map></html>

Latest revision as of 21:28, 27 October 2010

CharacterizationResultsParts

The Results

In the plot below the RBS strengths for the five tested members of the Anderson family are given along with the deviations from the mean. The strengths are given relative to the community RBS [http://partsregistry.org/Part:BBa_B0034 BBa_B0034], which has a strength of unity (1). This relationship could be built by our characterization of the community RBS [http://partsregistry.org/Part:BBa_B0032 BBa_B0032] simultaneously, which is known to have a strength (or efficiency) of 0.3 relative to [http://partsregistry.org/Part:BBa_B0032 BBa_B0034]. Therefore in the plot below, the mean value of BBa_B0032 is set to 0.3. The values have been obtained by the experimental setup described here and using the model to correct for growth dilution.

Figure 1. RBS strength

Conclusions

We've succeeded in characterizing five members of the Anderson ribosome binding site family by 96 well plate cultivation and simultaneous monitoring of GFP fluorescence and biomass absorbance. Fitting the obtained data to our improved protein production model yielded RBS strengths values with negligible standard deviations. To recap the following RBS strengths (efficiencies) were found:


Ribosome binding site Mean relative strength Standard deviation
[http://partsregistry.org/Part:BBa_J61100 J61100] 0.020 (2.0%) 0.00512
[http://partsregistry.org/Part:BBa_J61101 J61101] 0.119 (11.9%) 0.02140
[http://partsregistry.org/Part:BBa_J61107 J61107] 0.077 (7.7%) 0.01480
[http://partsregistry.org/Part:BBa_J61117 J61117] 0.013 (1.3%) 0.00448
[http://partsregistry.org/Part:BBa_J61127 J61127] 0.065 (6.5%) 0.00660
[http://partsregistry.org/Part:BBa_B0032 B0032] 0.300 (Reference, 30%) 0.02690

CharacterizationResultsParts

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