Team:Wash U/Biological Parts

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3. <u>System modeling in cellular biology from concepts to nuts and bolts.</u> Cambridge, MA: MIT P, 2006.
3. <u>System modeling in cellular biology from concepts to nuts and bolts.</u> Cambridge, MA: MIT P, 2006.
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Revision as of 22:42, 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

Slide2.jpg Slide3.jpg

Slide4.jpg Slide5.jpg

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Modeling

Modeling the Gene Regulatory Network

Our group seeks to assess the optimality of the synthetic system that modulates pucBA 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.


pucBA Expression Model Diagram


PucBAModelEq.jpg

pucBA Model Reactions


PucBAModelTestSim.jpg


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. Back To Top


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