Tokyo/Works/Assay

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<br>[[Tokyo/Works|Works top]]　　0.[[Tokyo/Works/Hybrid promoter|Hybrid promoter]]　　1.[[Tokyo/Works/Formulation |Formulation]]　　2.[[Tokyo/Works/Assay |Assay1]]　　3.[[Tokyo/Works/Simulation |Simulation]]　　4.[[Tokyo/Works/Assay2 |Assay2]]　　5.[[Tokyo/Works/Future works |Future works]]
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<br>[[Tokyo/Works|Works top]]&nbsp;&nbsp;&nbsp;0.[[Tokyo/Works/Hybrid promoter|Hybrid promoter]]&nbsp;&nbsp;&nbsp;1.[[Tokyo/Works/Formulation |Formulation]]&nbsp;&nbsp;&nbsp;2.[[Tokyo/Works/Assay |Assay1]]&nbsp;&nbsp;&nbsp;3.[[Tokyo/Works/Simulation |Simulation]]&nbsp;&nbsp;&nbsp;4.[[Tokyo/Works/Assay2 |Assay2]]&nbsp;&nbsp;&nbsp;5.[[Tokyo/Works/Future works |Future works]]
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[[Tokyo/Hill function fitting |Purpose of this assay]]　　[[Tokyo/AHL assay|1.AHL assay]]　　[[Tokyo/IPTG assay|2.IPTG assay]]　　[[Tokyo/Preliminary assays |Preliminary assays]]
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[[Tokyo/Hill function fitting |Objective of this assay]]&nbsp;&nbsp;&nbsp;[[Tokyo/AHL assay|Effect of AHL]]&nbsp;&nbsp;&nbsp;[[Tokyo/IPTG assay|Effect of LacI-IPTG]]　　[[Tokyo/Preliminary assays |Preliminary assays]]
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==[[Tokyo/Hill function fitting |Purpose of this assay (Hill function fitting) ]] ==
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==[[Tokyo/Hill function fitting |Objective of this assay (Hill function fitting) ]] ==
<!--新しく作ったハイブリッドプロモーターに関してはデータがないので，実験によりパラメータを求める．
<!--新しく作ったハイブリッドプロモーターに関してはデータがないので，実験によりパラメータを求める．
ヒル関数をfittingさせることにより，n2,n3,K2,K3が求まる.-->
ヒル関数をfittingさせることにより，n2,n3,K2,K3が求まる.-->
We have obtained data for our newly devised hybrid promoter. By Hill function fitting, we have determined '''n2, n3, K2, and K3'''.  
We have obtained data for our newly devised hybrid promoter. By Hill function fitting, we have determined '''n2, n3, K2, and K3'''.  
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<br>[[Image:expression6-1.JPG|300px|]]
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<br>[[Image:siki1.JPG|300px|none|]]
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<br>[[Image:expression6-10-2.JPG|320px|]][[Image:expression6-11.JPG|500px|]]
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<br>[[Image:expression6-10-2.JPG|320px|left|]][[Image:siki2.JPG|400px|none|]]
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====⇒see more [[Tokyo/Hill function fitting|details]]====
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==== ==> see more [[Tokyo/Hill function fitting|details]]====
  <!--== Assays for hybrid promoter ==
  <!--== Assays for hybrid promoter ==
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== [[Tokyo/AHL assay|1.AHL assay]] ==
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== [[Tokyo/AHL assay|Effect of AHL]] ==
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<br>[[Image:hill AHL.JPG|thumb|210px|'''Fig.1 The result of AHL assay''' Fluorescence intensity (arbitrary unit, a.u.) as a function of the concentration of AHL was determined. ]]
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<br>[[Image:hill AHL.JPG|thumb|230px|'''Fig. 1 Effect of AHL on hybrid promoter''' Enhanced fluorescence intensity represents up-regulation of LuxR via AHL.|left]]
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'''Purpose'''
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'''Objective'''
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<br>check how AHL activates lux-lac hybrid promoter.
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By testing how AHL activates lux-lac hybrid promoter,  parameters(n2,K2) should be determined.
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<br>These parameters(n2,K2) is decided.
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'''Result & Conclusion'''
'''Result & Conclusion'''
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<br>As the concentration of AHL increases, GFP fluorescence increased, indicating that the hybrid promoter’s activation is strengthend with increasing concentration of AHL. From the activation graph in Fig. 1, the characteristics of the hybrid promoter expressed in Hill function, such as (n2,K2), is determined.
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<br>GFP fluorescence increased in AHL-dose dependent manner, indicating that the hybrid promoter is enhanced by LuxR via AHL. Taken together with the graph shown in Fig.1 and formulation of Hill function fitting described above , the characteristics of the hybrid promoter expressed in Hill function, such as (n2,K2), are determined.  
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====⇒see more [[Tokyo/AHL assay|details]]====
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==== ==> see more [[Tokyo/AHL assay|details]]====
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== [[Tokyo/IPTG assay|2.IPTG assay]] ==
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== [[Tokyo/IPTG assay|Effect of LacI: IPTG assay]] ==
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[[Image:hill IPTG.JPG|thumb|210px|'''Fig.2 The result of IPTG assay''' Fluorescence intensity as a function of the concentration of IPTG was determined. ]]
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'''Purpose'''
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<br>check how LacI represses this hybrid promoter.  In order to adjust LacI concentration, IPTG was added.
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<br>These parameters(n3,K3) is decided.
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<!--<br>To determine the order of the concentration of IPTG necessary for the activation of our lux-lac hybrid promoter in the LacI producing pTrc99A cells.
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<br> The order of the concentration is used for more detailed assay with narrower range of the IPTG concentration.-->
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[[Image:hill IPTG.JPG|thumb|215px|'''Fig. 2 Effect of LacI on hybrid promoter''' Enhanced fluorescence intensity represents down-regulation of LacI repression via IPTG.|left]]
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'''Objective'''
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By testing how LacI represses the lux-lac hybrid promoter, parameters(n3,K3) should be decided. In order to adjust effective concentration of LacI, IPTG was added.
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<br><br>
'''Result & Conclusion'''
'''Result & Conclusion'''
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<br><!--As the concentration of IPTG increases, GFP fluorescence increased, indicating that the hybrid promoter in the LacI expressing cell became increasingly strengthened by decreasing repression by LacI. The activation graph in Fig. 2, the characteristics of the hybrid promoter expressed in Hill function is determined.-->
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GFP fluorescence intensity was enhanced in an IPTG-dose dependent manner. It indicates that the LacI repression was getting weak by adding IPTG. Taken together with the graph shown in Fig. 2 and the formulation of Hill function fitting described above, the characteristics of the hybrid promoter expressed in Hill function was determined.
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As the concentration of IPTG increases, GFP fluorescence increased. It indicates that the hybrid promoter in the cells expressing LacI became increasingly strengthened by decline of repression by LacI. The activation graph in Fig. 2, the characteristics of the hybrid promoter expressed in Hill function is determined.  
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==== ==> see more [[Tokyo/IPTG assay|details]]====
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====⇒see more [[Tokyo/IPTG assay|details]]====
 
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==Appendix: [[Tokyo/Preliminary assays |Preliminary assays ]]==
==Appendix: [[Tokyo/Preliminary assays |Preliminary assays ]]==
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We conducted preliminary assays to practice experiments and check if the materials and methods worked properly.
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We conducted preliminary assays as practice experiments and check of materials and methods.
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====⇒See more [[Tokyo/Preliminary assays |details]]====
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==== ==> See more [[Tokyo/Preliminary assays |details]]====
== ==
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[[Tokyo/Works/Formulation |Before(Formulation)]]　<<　[[Tokyo/Works/Assay |Assay1]]　>>　[[Tokyo/Hill function fitting|Assay1 contents]]　>>>>　[[Tokyo/Works/Simulation |Simulation]]　　
[[Tokyo/Works/Formulation |Before(Formulation)]]　<<　[[Tokyo/Works/Assay |Assay1]]　>>　[[Tokyo/Hill function fitting|Assay1 contents]]　>>>>　[[Tokyo/Works/Simulation |Simulation]]　　

Latest revision as of 04:53, 27 October 2007


Works top   0.Hybrid promoter   1.Formulation   2.Assay1   3.Simulation   4.Assay2   5.Future works

Objective of this assay   Effect of AHL   Effect of LacI-IPTG　　Preliminary assays


Objective of this assay (Hill function fitting)

We have obtained data for our newly devised hybrid promoter. By Hill function fitting, we have determined n2, n3, K2, and K3.


Siki1.JPG

Expression6-10-2.JPG
Siki2.JPG



==> see more details


Effect of AHL


Fig. 1 Effect of AHL on hybrid promoter Enhanced fluorescence intensity represents up-regulation of LuxR via AHL.

Objective By testing how AHL activates lux-lac hybrid promoter, parameters(n2,K2) should be determined.

Result & Conclusion
GFP fluorescence increased in AHL-dose dependent manner, indicating that the hybrid promoter is enhanced by LuxR via AHL. Taken together with the graph shown in Fig.1 and formulation of Hill function fitting described above , the characteristics of the hybrid promoter expressed in Hill function, such as (n2,K2), are determined.


==> see more details




Effect of LacI: IPTG assay

Fig. 2 Effect of LacI on hybrid promoter Enhanced fluorescence intensity represents down-regulation of LacI repression via IPTG.

Objective By testing how LacI represses the lux-lac hybrid promoter, parameters(n3,K3) should be decided. In order to adjust effective concentration of LacI, IPTG was added.

Result & Conclusion GFP fluorescence intensity was enhanced in an IPTG-dose dependent manner. It indicates that the LacI repression was getting weak by adding IPTG. Taken together with the graph shown in Fig. 2 and the formulation of Hill function fitting described above, the characteristics of the hybrid promoter expressed in Hill function was determined.

==> see more details






Appendix: Preliminary assays

We conducted preliminary assays as practice experiments and check of materials and methods.

==> See more details

Before(Formulation)　<<　Assay1　>>　Assay1 contents　>>>>　Simulation　　

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