Team:Wash U/Biological Parts

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Revision as of 23:19, 6 July 2009

Parts

Component	Description	Part/Accession #	Base Pairs	Plasmid	Resistance	Well
RBS	Ribosomal Binding Site	[http://partsregistry.org/Part:BBa_B0034 BBa_B0034]	12	pSB1A2	Ampicillin	plate 1, 2M
Red Light Sensor	description	[http://partsregistry.org/Part:BBa_I15010 BBa_I15010]	2,238	pSB2K3	Kanamycin	N/A
OmpR (E. coli)	description	[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=947913&log$=databasead&logdbfrom=protein NP_417864.1]	720	pSB1T3	Tetracycline	N/A
Terminator	description	[http://partsregistry.org/Part:BBa_B0015 BBa_B0015]	129	pSB1AK3	Ampicillin and Kanamycin	plate 1, 23L
OmpR + Terminator	description	sequence	916	pany-amp	Ampicillin	synthesized
OmpC promoter	description	[http://partsregistry.org/Part:BBa_R0082 BBa_R0082]	108	pSB1A2	Ampicillin	plate 1, 16K
puc B/A	description	sequence	375	pSB1A3	Ampicillin	N/A
puc B	description	[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=3719170&log$=databasead&logdbfrom=nuccore YP_353390]	156	?	?	N/A
puc A	description	[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=3719171&log$=databasead&logdbfrom=nuccore YP_353391]	165	?	?	N/A
OmpC promoter+BA	description	sequence	539	pany-kana	Kanamycin	synthesized
Light Response System	description	[http://partsregistry.org/Part:BBa_M30109 BBa_M30109]	4,333	?	Ampicillin	N/A
TetR repressible	description	[http://partsregistry.org/Part:BBa_J13002 BBa_J13002]	74	pSB1A2	Ampicillin	plate 1, 13B
Green Flourescent Protein	description	[http://partsregistry.org/Part:BBa_E0240 BBa_E0240]	976	pSB1A2	Ampicillin	plate 1, 12M

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Characterization

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Modeling

Modeling the Gene Regulatory Network

Our group seeks to assess the optimality of the synthetic system that modulates pucB/A gene expression and LH2 complex assembly in Rhodobacter sphaeroides. Here we employ a mathematical model of this system to generate predictions about the behavior of the active system in response to light input. Features of the system that the model may help investigate include the time scale of response to light signals, the robustness of the system in response to fluctuations in light intensity, and the translation between changes in gene expression and the absorbance spectrum of the engineered cells.

Though the context of the model can extend back to the transcription of PrrA/B genes involved in integration oxygen and light signals, a preliminary testing model was developed using assumptions of certain initial conditions to isolate the light signal's effect. Since Cph8 and OmpR are located on the same transcript downstream of the puc promoter region, it was assumed that their associated protein and mRNA had already reached steady state concentrations. Moreover, the concentrations of the factors were assumed to be equal at this state. The model whose diagram was constructed in the Simbiology Toolbox distributed by MathWorks details key reactions leading to the translation of the pucB/A genes. The reaction rate equation used for the phosphorylation of OmpR as a consequence of the light signal reaching Cph8 bound to OmpR is capture in a modified form of Michaelis-Menten kinetics. A logic function that corresponds to light ON/OFF (1/0) multiplies the maximum reaction rate in the numerator. Thus, the model assumes that no phosphorylation occurs by this mechanism in the absence of light. The OmpC promoter binding equation was based on the Hill Equation for a Repressor (1).

pucBA Expression Model Diagram

pucBA Model Equations

pucBA Model Reactions

References

1. Alon, Uri. Introduction to systems biology and the design principles of biological networks. Boca Raton, FL: Chapman & Hall, 2006.
2. Bower, James M. Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology). New York: M.I.T. PRESS, 2001.
3. System modeling in cellular biology from concepts to nuts and bolts. Cambridge, MA: MIT P, 2006.
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@@ Line 140: / Line 140: @@
 :Our group seeks to assess the optimality of the synthetic system that modulates pucB/A gene expression and LH2 complex assembly in ''Rhodobacter sphaeroides''.  Here we employ a mathematical model of this system to generate predictions about the behavior of the active system in response to light input. Features of the system that the model may help investigate include the time scale of response to light signals, the robustness of the system in response to fluctuations in light intensity, and the translation between changes in gene expression and the absorbance spectrum of the engineered cells.
 <br>
-:Though the context of the model can extend back to the transcription of PrrA/B genes involved in integration oxygen and light signals, a preliminary testing model was developed using assumptions of certain initial conditions to isolate the light signal's effect.  Since Cph8 and OmpR are located on the same transcript downstream of the puc promoter region, it was assumed that their associated protein and mRNA had already reached steady state concentrations.  Moreover, the concentrations of the factors were assumed to be equal at this state.  The model whose diagram was constructed in the Simbiology Toolbox distributed by MathWorks details key reactions leading to the translation of the pucB/A genes.  The reaction rate equation used for the phosphorylation of OmpR as a consequence of the light signal reaching Cph8 bound to OmpR is capture in a modified form of Michaelis-Menten kinetics.  A logic function that corresponds to light ON/OFF (1/0) multiplies the maximum reaction rate in the numerator.  Thus, the model assumes that no phosphorylation occurs by this mechanism in the absence of light.
+:Though the context of the model can extend back to the transcription of PrrA/B genes involved in integration oxygen and light signals, a preliminary testing model was developed using assumptions of certain initial conditions to isolate the light signal's effect.  Since Cph8 and OmpR are located on the same transcript downstream of the puc promoter region, it was assumed that their associated protein and mRNA had already reached steady state concentrations.  Moreover, the concentrations of the factors were assumed to be equal at this state.  The model whose diagram was constructed in the Simbiology Toolbox distributed by MathWorks details key reactions leading to the translation of the pucB/A genes.  The reaction rate equation used for the phosphorylation of OmpR as a consequence of the light signal reaching Cph8 bound to OmpR is capture in a modified form of Michaelis-Menten kinetics.  A logic function that corresponds to light ON/OFF (1/0) multiplies the maximum reaction rate in the numerator.  Thus, the model assumes that no phosphorylation occurs by this mechanism in the absence of light.  The OmpC promoter binding equation was based on the Hill Equation for a Repressor (1).
-<br>
-:The OmpC promoter binding equation was based on the Hill Equation for a Repressor (1).
 <br>
 [[Image:pucBAModelDiagram.jpg|thumb|450px|pucBA Expression Model Diagram]]
 <br>
+[[Image:pucBAModelEq.jpg|thumb|450px|pucBA Model Equations]]
-[[Image:pucBAModelEq.jpg|450px]]
 <br>
 [[Image:pucBAModelRxn.jpg|thumb|450px|pucBA Model Reactions]]
 <br>