NTHU 共 21 頁，第 1 頁 Modeling and Simulating the Biological Pathway - case study - 第六組 Systems Biology Presentation

NTHU 共 21 頁，第 2 頁Outline Information gathering –KEGG web service –Ontology-based knowledge extraction Modeling environment –Stoichiometric matrix Simulating environment –Kinetics model Results and discussion

NTHU 共 21 頁，第 3 頁 Global 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 molecular interactions and Chemical coefficients According to the Quality of Service and use’s goal to make the Biological plan Measure the chemical values by calculating the coefficients and pathway structure

NTHU 共 21 頁，第 4 頁Architecture Pathway database Kinetics database chemical database Biological database 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

NTHU 共 21 頁，第 5 頁Benefit Relational database system for managing kinetic data, chemical structure, pathway, chemical reaction Provide stoichiometric information and parameters for kinetics equations to the model

NTHU 共 21 頁，第 6 頁 Web 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 ….etc The 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.

NTHU 共 21 頁，第 7 頁 Ontology-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 is 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.

NTHU 共 21 頁，第 8 頁Glycolysis

NTHU 共 21 頁，第 9 頁 Enzyme 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 and p and q the concentrations of the products.

NTHU 共 21 頁，第 10 頁Example DEMO

NTHU 共 21 頁，第 11 頁Results

NTHU 共 21 頁，第 12 頁 Results (II)

NTHU 共 21 頁，第 13 頁 Future 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.

NTHU 共 21 頁，第 14 頁 Biosynthesis of Ethanol by E.coli Systems Biology Presentation

NTHU 共 21 頁，第 15 頁Glycolysis

NTHU 共 21 頁，第 16 頁Problem

NTHU 共 21 頁，第 17 頁 Pyruvate Decarboxylase Reference –Saccharomyces cerevisiae pyruvate decarboxylase 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.

NTHU 共 21 頁，第 18 頁 Alcohol Dehydrogenase Only strain K-12 definitely have alcohol dehydrogenase (adhP) alcohol dehydrogenase (EC )

NTHU 共 21 頁，第 19 頁 Escherichia 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, adhB) –and the cat gene (acetyltransferase) have been integrated into the E. coli B chromosom.

NTHU 共 21 頁，第 20 頁 Two strain used for this! 1.Strain K-12 definitely have alcohol dehydrogenase (adhP) Saccharomyces cerevisiae pyruvate decarboxylase (pdc1) recombinant 2.Escherichia coli strain KO11 Z. mobilis genes for ethanol production (pdc, adhB) recombinant

NTHU 共 21 頁，第 21 頁Reference 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,