Dynamic models of metabolism: Review of the cybernetic approach

The cybernetic approach to metabolic modeling tracing its progress from its early beginnings to its current state with regard to its relationship to other modeling approaches, applications to bioprocess modeling, metabolic engineering, and future prospects are described. The framework is shown to handle large metabolic networks in making dynamic predictions from limited data with looming prospects of extending to genome scale networks. © 2012 American Institute of Chemical Engineers AIChE J, 2012

[1]  Doraiswami Ramkrishna,et al.  Unveiling steady‐state multiplicity in hybridoma cultures: The cybernetic approach , 2003, Biotechnology and bioengineering.

[2]  D. Ramkrishna,et al.  Systematic development of hybrid cybernetic models: Application to recombinant yeast co‐consuming glucose and xylose , 2009, Biotechnology and bioengineering.

[3]  F. Srienc,et al.  Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism , 2009, Applied Microbiology and Biotechnology.

[4]  Doraiswami Ramkrishna,et al.  On modeling of bioreactors for control , 2001 .

[5]  J. Varner,et al.  Large-scale prediction of phenotype: concept. , 2000, Biotechnology and bioengineering.

[6]  M L Alexander,et al.  Cybernetic modeling of iron‐limited growth and siderophore production , 1991, Biotechnology and bioengineering.

[7]  D. Fell,et al.  Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism , 2002, Journal of mathematical biology.

[8]  D. Fell,et al.  A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks , 2000, Nature Biotechnology.

[9]  D. Ramkrishna,et al.  Revised enzyme synthesis rate expression in cybernetic models of bacterial growth , 1988, Biotechnology and bioengineering.

[10]  B. Palsson,et al.  Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli , 2003, Journal of bacteriology.

[11]  Robert Urbanczik,et al.  The geometry of the flux cone of a metabolic network. , 2005, Biophysical journal.

[12]  Matthew Lucian Alexander Cybernetic modeling of bacterial metabolite production , 1990 .

[13]  D. Ramkrishna,et al.  Synergistic Optimal Integration of Continuous and Fed-Batch Reactors for Enhanced Productivity of Lignocellulosic Bioethanol , 2012 .

[14]  D. Ramkrishna,et al.  A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables , 2008, Biotechnology progress.

[15]  D. Ramkrishna,et al.  Metabolic Engineering from a Cybernetic Perspective. 1. Theoretical Preliminaries , 1999, Biotechnology progress.

[16]  D. Fell,et al.  Is maximization of molar yield in metabolic networks favoured by evolution? , 2008, Journal of theoretical biology.

[17]  G Stephanopoulos,et al.  Metabolic flux analysis of hybridoma continuous culture steady state multiplicity. , 1999, Biotechnology and bioengineering.

[18]  Y. Schneider,et al.  Metabolic design of macroscopic bioreaction models: application to Chinese hamster ovary cells , 2006, Bioprocess and biosystems engineering.

[19]  Doraiswami Ramkrishna,et al.  Modeling of Bacterial Growth under Multiply‐Limiting Conditions. Experiments under Carbon‐ or/and Nitrogen‐Limiting Conditions , 1994 .

[20]  D. Ramkrishna,et al.  Metabolic regulation in bacterial continuous cultures: I. , 1991, Biotechnology and bioengineering.

[21]  G. Church,et al.  Analysis of optimality in natural and perturbed metabolic networks , 2002 .

[22]  G. T. Tsao,et al.  A cybernetic view of microbial growth: Modeling of cells as optimal strategists , 1985, Biotechnology and bioengineering.

[23]  Steffen Klamt,et al.  Two approaches for metabolic pathway analysis? , 2003, Trends in biotechnology.

[24]  D. Ramkrishna,et al.  Cybernetic models based on lumped elementary modes accurately predict strain‐specific metabolic function , 2011, Biotechnology and bioengineering.

[25]  J. Bailey,et al.  Toward a science of metabolic engineering , 1991, Science.

[26]  A. Narang,et al.  New patterns of mixed-substrate utilization during batch growth of Escherichia coli K12. , 1997, Biotechnology and bioengineering.

[27]  D Ramkrishna,et al.  Cybernetic modeling of bacteriol cultures at low growth rates: Single‐substrate systems , 1989, Biotechnology and bioengineering.

[28]  Doraiswami Ramkrishna,et al.  Cybernetic Modeling and Regulation of Metabolic Pathways. Growth on Complementary Nutrients , 1994 .

[29]  F. H. Adler Cybernetics, or Control and Communication in the Animal and the Machine. , 1949 .

[30]  D. Ramkrishna,et al.  Complex growth dynamics in batch cultures: Experiments and cybernetic models , 1991, Biotechnology and bioengineering.

[31]  D. Ramkrishna,et al.  Cybernetic modeling of bacterial cultures at low growth rates: Mixed‐substrate systems , 1988, Biotechnology and bioengineering.

[32]  Abhijit Anand Namjoshi,et al.  Multiplicity and stability of steady states in continuous bioreactors: dissection of cybernetic models , 2001 .

[33]  G. T. Tsao,et al.  Cybernetic modeling of microbial growth on multiple substrates , 1984, Biotechnology and bioengineering.

[34]  D. Kompala,et al.  Cybernetic model of the growth dynamics of Saccharomyces cerevisiae in batch and continuous cultures. , 1999, Journal of biotechnology.

[35]  G. T. Tsao,et al.  Investigation of bacterial growth on mixed substrates: Experimental evaluation of cybernetic models , 1986, Biotechnology and bioengineering.

[36]  Jamey D. Young,et al.  Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis. , 2011, Metabolic engineering.

[37]  Doraiswami Ramkrishna,et al.  Prediction of metabolic function from limited data: Lumped hybrid cybernetic modeling (L‐HCM) , 2010, Biotechnology and bioengineering.

[38]  W. Wiechert 13C metabolic flux analysis. , 2001, Metabolic engineering.

[39]  B. C. Baltzis,et al.  Limitation of growth rate by two complementary nutrients: Some elementary but neglected considerations , 1988, Biotechnology and bioengineering.

[40]  May C. Chen Toward a New Philosophy of Biology: Observations of an Evolutionist , 1990, The Yale Journal of Biology and Medicine.

[41]  G. T. Tsao,et al.  Fuel ethanol production from lignocellulosic sugars: studies using a genetically engineered Saccharomyces yeast , 1997 .

[42]  D. Ramkrishna A Cybernetic Perspective of Microbial Growth , 1983 .

[43]  D. Ramkrishna,et al.  Reduction of a set of elementary modes using yield analysis , 2009, Biotechnology and bioengineering.

[44]  R Ramakrishna,et al.  Cybernetic modeling of growth in mixed, substitutable substrate environments: Preferential and simultaneous utilization. , 1996, Biotechnology and bioengineering.

[45]  Doraiswami Ramkrishna,et al.  When is the Quasi-Steady-State Approximation Admissible in Metabolic Modeling? When Admissible, What Models are Desirable? , 2009 .

[46]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[47]  J. Monod,et al.  Recherches sur la croissance des cultures bactériennes , 1942 .

[48]  Jamey D. Young,et al.  Integrating cybernetic modeling with pathway analysis provides a dynamic, systems‐level description of metabolic control , 2008, Biotechnology and bioengineering.

[49]  Jamey D. Young,et al.  An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis , 2008, Biotechnology and bioengineering.

[50]  J. Varner,et al.  Metabolic Engineering from a Cybernetic Perspective. 2. Qualitative Investigation of Nodal Architechtures and Their Response to Genetic Perturbation , 1999, Biotechnology progress.

[51]  A. Gambhir,et al.  Multiple steady states with distinct cellular metabolism in continuous culture of mammalian cells. , 2000, Biotechnology and bioengineering.

[52]  A. Kienle,et al.  Experimental and theoretical analysis of poly (β-hydroxybutyrate) formation and consumption in Ralstonia eutropha , 2011 .

[53]  D. Ramkrishna,et al.  Towards Increasing the Productivity of Lignocellulosic Bioethanol: Rational Strategies Fueled by Modeling , 2012 .

[54]  Jamey Dale Young A system-level mathematical description of metabolic regulation combining aspects of elementary mode analysis with cybernetic control laws , 2005 .

[55]  Doraiswami Ramkrishna,et al.  On the Matching and Proportional Laws of Cybernetic Models , 2007, Biotechnology progress.

[56]  Jin Il Kim A hybrid cybernetic modeling for the growth of Escherichia coli in glucose-pyruvate mixtures , 2008 .