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Costas D. Maranas

Costas D. Maranas. Penn State University. Publications. 10.0. 2.9. 2.9. 2.9. 7.1. Flux Elucidation. Isotopomer analysis using GC/MS (Christensen & Neilsen, 1999;Fischer & Sauer, 2003). 0.9. 8.5. 0.9. 0.6. 8.5. Isotopomer analysis using NMR spectra (Schmidt et.al. , 1999). 17.5.

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Costas D. Maranas

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  1. Costas D. Maranas Penn State University

  2. Publications 10.0 2.9 2.9 2.9 7.1 Flux Elucidation • Isotopomer analysis using GC/MS (Christensen & Neilsen, 1999;Fischer & Sauer, 2003) 0.9 8.5 0.9 0.6 8.5 • Isotopomer analysis using NMR spectra (Schmidt et.al., 1999) 17.5 17.5 • Computational models for flux elucidation (Zupke at al. , 1994;Wiechert & Graff, 1996; Wiechert et.al. 1996;Mollney et.al. 1999 ) 8.0 16.5 8.0 7.2 8.0 16.5 8.9 12.7 10.9 8.0 • Optimization algorithms (Phalakornkule et.al., 2001 ;Ghosh et.al., 2004; Riascos et.al., 2005, Zamboni et al., 2005) 8.9 8.0 4. Development of experimental and computational tools to evaluate metabolic flux C13 destinations Observations Labeled Isotopes e.g. C13 glucose GC-MS . . . E.Coli cell NMR

  3. Tyrosine Phenyl alanine Pran Prpp Tyrphtophan Phpyr pphn 34hpp Arginine Methionine 2dda7p Acglu Proline Pro-L Glu-L Leucine Valine Alac-S Gln-L 4pasp Asp-L Phom Glx Hom-L Threonine Aspsa Asn-L Lysine co2 Pser-L Serine Glycine Cystenine 3php Acser Limitations • Employed metabolic models are of limited scope (i.e. 30-50 rxns) • For genome-scale models (~1,000 rxns), measurables do not always elucidate unique flux distributions Many relevant pathways are absent…

  4. Elucidating Fluxes in Genome-Scale Models using Isotopomer Labeling Experiments(Poster no: 92) • Enable flux elucidation for genome-scale models Isotopomer mapping matrices (IMM) have been constructed genome-scale models of E coli (Burgard & Van Dien) Large-scale non-linear programming problem Minimize s.t. Isotopomer balance Mass balance Isotopomer fraction balance

  5. Computational Approaches Elucidation of Metabolic Fluxes Environmental and/or Genetic Perturbations Question 1: What are the bottlenecks in broadening the use of HT data for the quantitative estimation of metabolic fluxes ? Glucose Microarrays GC-MS NMR Regulatory interactions High Throughput Data

  6. Microarrays GC-MS Regulatory interactions NMR High Throughput Data Computational Approaches Elucidation of Metabolic Fluxes Environmental and/or Genetic Perturbations Question 2: Given HT data, how can we use computations to reliably elucidate fluxes in metabolic networks ? Glucose

  7. Microrarrays GC-MS Regulatory interactions NMR Acetate High Throughput Data Computational Approaches Elucidation of Metabolic Fluxes Environmental and/or Genetic Perturbations Question 3: How can we anticipate the effect of environmental and/or genetic manipulations on metabolic fluxes ?

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