Biological Pathways Analysis and Engineering




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E coli metabolic capabilities E coli metabolic capabilities Desired Phenotype E coli metabolic capabilities Desired Phenotype E coli metabolic capabilities How can we systematically select the appropriate set of pathways genes to recombine into existing production systems How can we identify gene knockouts that will force biochemical overproduction by coupling it with cell growth How can we identify multiple metabolic manipulations for producing a desired product and also computationally evaluate of the consequences of potential network modifications GLC PEP PYR G6P D6PGL D6PGC F6P F16P DHAP GAP RL5P X5P R5P S7P GAP E4P F6P 13P2DG FUM 3PDGL 2PDGL PEP OA PYR ACCOA LAC ETH SUCC MAL CIT ACTP SUCCOA AKG ICIT AC Escherichia coli Chemical Process Plant DNA Sequence Proteins Enzymes Genes Metabolic Pathways Cellular Physiology Increasing Complexity DNA Sequence Automated Sequencing Genomics Genes DNA Microarrays Transcriptomics Enzymes Gene Products 2 D Protein Arrays Proteomics Metabolism and Cellular Physiology Genome Annotation Genome Database DNA sequence ORFs identification Genes ORFs assignment Genes Products Function ORF open reading frame a short fragment of DNA that is translated into RNA message Metabolic Reconstruction List of reactions Pathway Database Organism Specific Model Construction Organism s metabolism Literature Review Wet Lab Manual curation Metabolism of Complex Carbohydrates Biodegradation of Xenobiotics Nucleotide Metabolism Metabolism of Complex Lipids Glucose Glc 6 P Carbohydrate Metabolism Lipid Metabolism Metabolism of Other Amino Acids Amino Acid Metabolism Energy Metabolism Metabolism of Cofactors and Vitamins Biosynthesis of Secondary Metabolites Fru 6 P Glucose G6P Central Metabolism in E coli 0 1 Reaction network v1 A Stoichiometric matrix B v2 2B Mass balance C d B v1 2 v2 dt v1 v2 A 1 0 B 1 C Steady state assumption v mmol B gDW hr 2 0 0 Metabolic Flux 1 S ij v j j i set of metabolites chemical species j set of reactions Given






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