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Modeling and Simulating the Modeling and Simulating the Biological PathwayBiological Pathway
- case study -- case study -
第六組
Systems Biology Presentation
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OutlineOutline
• Information gathering – KEGG web service– Ontology-based knowledge extraction
• Modeling environment– Stoichiometric matrix
• Simulating environment– Kinetics model
• Results and discussion
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Global agent ArchitectureGlobal agent Architecture
Database (KEGG, NCBI, Micro-array)、 Bioinformatics Toolkit
Web service Matchmaker (Broker Agent)
Information wrapper Agent
Connect the service
Information Gathering
Bio-ontology& thesauri
Pathway modeling agent
Literature extraction agent
Quantitative Simulation agent
Workflow Planning agent
Model the pathway according to
the promoter and
molecular interactions
Extract the
molecularinteractions
and Chemical
coefficients
According tothe
Quality of Serviceand use’s goal
to make theBiological plan
Measure the chemical valuesby calculating the coefficients
and pathway
structure
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ArchitectureArchitecture
Pathwaydatabase
Kineticsdatabase
chemicaldatabase
Biologicaldatabase
Stoichiometric model
Dynamic model
Get the kinetics coefficient from the experiments
or literature
Get the gene name,chemical compound and its physical information
Get the chemical reaction
Get the biological pathway
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BenefitBenefit
• Relational database system for managing kinetic data, chemical structure, pathway, chemical reaction
• Provide stoichiometric information and parameters for kinetics equations to the model
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Web service-KEGGWeb service-KEGG
KEGG API provides valuable means for accessing the KEGG system, such as for searching and computing biochemical pathways in cellular processes or analyzing the universe of genes in the completely sequenced genomes. get_genes_by_pathway,get_enzymes_by_pathway,get_compounds_by_pathway,get_reactions_by_pathway….etcThe users can access the KEGG API server by the SOAP technology over the HTTP protocol. The SOAP server also comes with the WSDL, which makes it easy to build a client library for a specific computer language.
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Ontology-based knowledge extractionOntology-based knowledge extraction
• Concentration (mM), Volume (m),Flux (mM/s),PH,…etc
• C-mol/min*L-cytosol – where C-mol is a mol of carbon and L-cytosol i
s a litre of cytosolic water
• Sentence: – The pyruvate concentration that is required to
accommodate a flux of 0.48 C-mol/min*L-cytosol, is 8 mM.
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GlycolysisGlycolysis
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Enzyme KineticsEnzyme Kinetics
One substrate, one product reversible Michaelis-Menten kinetics was used to describe the enzymes PGI, PGM and ENO:
where a and p represent the concentrations of the corresponding substrate and product, respectively. G is the mass-action ratio, p/a, Keq is the equilibrium constant, peq/aeq. Ka and Kp are the Michaelis-Menten constants for a and p.Reversible Michaelis-Menten kinetics for two noncompeting substrate-product couples was used for HK, GraPDH, PGK and PYK:
where a and b represent the concentrations of the substrates andp and q the concentrations of the products.
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ExampleExample
DEMO
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ResultsResults
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Results (II)Results (II)
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Future workFuture work
• The combination of flux based static modeling with dynamic modeling based on kinetic equations
• The model can be initiated as a stoichiometric model that is gradually converted into a dynamic model by adding dynamic equations.
• Flux distribution analysis as a method for calculating each flux in stoichiometric models.
• Substances at the boundary between dynamic models and stoichiometric model are influenced by both flux.
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Biosynthesis of EthanolBiosynthesis of Ethanolby by E.coliE.coli
Systems Biology Presentation
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GlycolysisGlycolysis
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ProblemProblem
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Pyruvate DecarboxylasePyruvate Decarboxylase
• Reference– Saccharomyces cerevisiae pyruvate decarb
oxylase PDC1 has been isolated and fused to the indicator gene Escherichia coli lacZ.
– T7 RNA polymerase promoter phi 10, that a cloned Saccharomyces cerevisiae pyruvate decarboxylase gene ( pdc1) can be expressed in Escherichia coli.
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Alcohol DehydrogenaseAlcohol Dehydrogenase
• Only strain K-12 definitely have alcohol dehydrogenase (adhP)
• alcohol dehydrogenase (EC 1.1.1.1)
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Escherichia coli strain KO11Escherichia coli strain KO11
• E. coli KO11 and three ethanol-resistant mutants of this strain (LY01-LY03).
• Strain KO11 is an ethanol-producing recombinant in which the – Z. mobilis genes for ethanol production (pdc, a
dhB) – and the cat gene (acetyltransferase) have bee
n integrated into the E. coli B chromosom.
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Two strain used for this!Two strain used for this!
1. Strain K-12• definitely have alcohol dehydrogenase (adh
P)• Saccharomyces cerevisiae pyruvate decarb
oxylase (pdc1) recombinant
2. Escherichia coli strain KO11• Z. mobilis genes for ethanol production (pdc,
adhB) recombinant
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ReferenceReference
• Karp, P.D.; Riley, M.; Saier, M.; Paulsen, I.T.; Collado-Vides, J.; Paley, S.; Pellegrini-Toole, A.; Bonavides, C.; Gama-Castro, S. The Ecocyc database. Nucleic Acids Res. 2002, 30,56-58
• Yomano, L.P.; York, S.W.; Ingram, L.O. Journal of Industrial Microbiology & Biotechnology. Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. 1998, 20, 132-138