Dynamic modeling of microbial cell populations

Current Opinion in Biotechnology

Volumn 14, Issue 5, 2003, Pages 460-467

  Henson, Michael A ^a  

^a University of Massachusetts   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOANALYSIS; BACTERIUM CULTURE; CELL CYCLE; CELL DIFFERENTIATION; CELL POPULATION; CELL SYNCHRONIZATION; CONTINUOUS CULTURE; ESCHERICHIA COLI; FERMENTATION; FLOW CYTOMETRY; GLYCOLYSIS; INTERMETHOD COMPARISON; MATHEMATICAL MODEL; MICROBIAL POPULATION DYNAMICS; NONHUMAN; NONLINEAR SYSTEM; ONLINE ANALYSIS; PRIORITY JOURNAL; REVIEW; SACCHAROMYCES CEREVISIAE; YEAST;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0142122311     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(03)00104-6     Document Type: Review

References (45)

1. Zamamiri A.M., Birol G., Hjortso M.A. Multiple steady states and hysteresis in continuous, oscillating cultures of budding yeast. Biotechnol. Bioeng. 75:2001;305-312.
2. Futcher B. Cell cycle synchronization. Methods Cell Sci. 21:1999;79-86.
3. Dano S., Sorensen P., Hynne G.F. Sustained oscillations in living cells. Nature. 402:1999;320-322.
4. Dano S., Hynee F., De Monte S., d'Ovidio F., Sorensen P.G., Westerhoff H. Synchronization of glycolytic oscillations in a yeast cell population. Faraday Discuss. 120:2001;261-276 An approximate cell model systematically derived from a detailed single-cell model of yeast glycolytic oscillations is used to construct a cell ensemble consisting of 1000 individual cells.
5. Birol G., Zamamiri A.M., Hjortso M.A. Frequency analysis of autonomously oscillating yeast cultures. Process Biochem. 35:2000;1085-1091.
6. Uchiyama K., Morimoto M., Yokoyama Y., Shioya S. Cell cycle dependency of rice α-amylase production in a recombinant yeast. Biotechnol. Bioeng. 54:1997;262-271.
7. Frykman S., Srienc F. Cell cycle dependent protein secretion by Saccharomyces cerevisiae. Biotechnol. Bioeng. 76:2001;259-268.
8. Rieseberg M., Kaspar C., Reardon K.F., Scheper T. Flow cytometry in biotechnology. Appl. Microbiol. Biotechnol. 56:2001;350-360.
9. Abu-Absi N.R., Zamamiri A., Kacmar J., Balough S.J., Srienc F. Automated flow cytometry for acquisition of time-dependent population data. Cytometry. 51:2003;87-96.
10. Duboc P., von Stockar U. Modeling of oscillating cultivations of Saccharomyces cerevisiae: identification of population structure and expansion kinetics based on on-line measurements. Chem. Eng. Sci. 55:2000;149-160.
11. Yin K.K., Yang H., Daoutidis P., Yin G.G. Simulation of population dynamics using continuous-time finite-state Markov chains. Comput. Chem. Eng. 27:2001;235-249.
12. Tsuchiya H.M., Fredrickson A.G., Aris R. Dynamics of microbial cell populations. Adv. Chem. Eng. 6:1966;125-206.
13. Hjortso M.A., Nielsen J. Population balance models of autonomous microbial oscillations. J. Biotechnol. 42:1995;255-269.
14. Nishimura Y., Bailey J.E. Bacterial population dynamics in batch and continuous-flow microbial reactors. AIChE J. 27:1981;73-81.
15. Mantzaris N.V., Liou J.-J., Daoutidis P., Srienc F. Numerical solution of a mass structured cell population balance model in an environment of changing substrate concentration. J. Biotechnol. 71:1999;157-174.
16. Hatzis C., Srienc F., Fredrickson A.G. Multistaged corpuscular models of microbial growth: Monte Carlo simulations. Biosystems. 36:1995;19-35.
17. Ramkrishna D: Population Balances: Theory and Applications to Particulate Processes in Engineering. New York: Academic Press; 2000.
18. Srienc F. Cytometric data as the basis for rigorous models of cell population dynamics. J. Biotechnol. 71:1999;233-238.
19. Villadsen J. On the use of population balances. J. Biotechnol. 71:1999;251-253.
20. Fredrickson A.G., Mantzaris N.V. A new set of population balance equations for microbial and cell populations. Chem. Eng. Sci. 57:2002;2265-2278.
21. Mhaskar P., Hjortso M.A., Henson M.A. Cell population modeling and parameter estimation for continuous cultures of Saccharomyces cerevisiae. Biotechnol. Prog. 18:2002;1010-1026 A systematic methodology for estimating key parameters of PBE physiological functions from readily available extracellular measurements is presented.
22. Mantzaris N.V., Daoutidis P., Srienc F. Numerical solution of multi-variable cell population balance models: I. Finite difference methods. Comput. Chem. Eng. 25:2001;1411-1440 A comprehensive study of finite difference discretization methods for numerical solution of PBE models is presented.
23. Mantzaris N.V., Daoutidis P., Srienc F. Numerical solution of multi-variable cell population balance models: II. Spectral methods. Comput. Chem. Eng. 25:2001;1441-1462.
24. Mantzaris N.V., Daoutidis P., Srienc F. Numerical solution of multi-variable cell population balance models: III. Finite element methods. Comput. Chem. Eng. 25:2001;1463-1481.
25. Zhu G.-Y., Zamamiri A.M., Henson M.A., Hjortso M.A. Model predictive control of continuous yeast bioreactors using cell population models. Chem. Eng. Sci. 55:2000;6155-6167.
26. Zamamiri A.M., Zhang Y., Henson M.A., Hjortso M.A. Dynamics analysis of an age distribution model of oscillating yeast cultures. Chem. Eng. Sci. 57:2002;2168-2181.
27. Zhang Y., Zamamiri A.M., Henson M.A., Hjortso M.A. Cell population models for bifurcation analysis and nonlinear control of continuous yeast bioreactors. J. Process Contr. 12:2002;721-734 Bifurcation analysis is used to compare PBE model predictions to experimentally observed behavior associated with yeast cell-cycle dependent oscillations.
28. Zhang Y., Henson M.A., Kevrekidis Y.G. Nonlinear model reduction for dynamic analysis of cell population models. Chem. Eng. Sci. 58:2003;429-445.
29. Mantzaris N.V., Srienc F., Daoutidis P. Nonlinear productivity control using a multi-staged cell population balance model. Chem. Eng. Sci. 57: 2002;1-14 A PBE model is used to design feedback controllers that optimize the production of a metabolite secreted only during one cell-cycle phase.
30. Ganusov V.V., Bril'kov A.V., Pechurkin N.S. Mathematical modeling of population dynamics of unstable plasmid-bearing bacterial strains under continuous cultivation in a chemostat. Biophysics. 45:2000;881-887.
31. Nielsen J, Villadsen J: Bioreaction engineering principles. New York: Plenum Press; 1994.
32. Birol G., Undey C., Parulekar S.J., Cinar A. A morphologically structured model for penicillin production. Biotechnol. Bioeng. 77:2002;538-552.
33. Ward J.P., King J.R., Koerber A.J., Williams P., Croft J.M., Sockett R.E. Mathematical modeling of quorum sensing in bacteria. IMA J. Math Appl. Med. Biol. 18:2001;263-292.
34. Shuler M.L. Single-cell models: promise and limitations. J. Biotechnol. 71:1999;225-228.
35. Domach M.M., Shuler M.L. A finite representation model for an asynchronous culture of E. coli. Biotechnol. Bioeng. 26:1984;877-884.
36. Ataai M.M., Shuler M.L. Simulation of CFSTR through development of a mathematical model for anaerobic growth of Escherichia coli cell population. Biotechnol. Bioeng. 27:1985;1051-1055.
37. Bier M., Bakker B.M., Westerhoff H.V. How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment. Biophys. J. 78:2000;1087-1093.
38. Wolf J., Heinrich R. Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation. Biochem. J. 345:2000;321-334.
39. Wolf J., Passarge J., Somsen O.J.G., Snoep J.L., Heinrich R., Westerhoff H.V. Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. Biophys. J. 78:2000;1145-1153.
40. Hynne F., Dano S., Sorenson P.G. Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys. Chem. 94:2001;121-163.
41. Henson M.A., Muller D., Reuss M. Cell population modeling of yeast glycolytic oscillations. Biochem. J. 368:2002;433-446 Ensemble models consisting of 1000 individual cells are used to investigate the effects of random cellular variations on cell population synchronization and to compute dynamic NADH distributions.
42. Gujer W. Microscopic versus macroscopic biomass models in activated sludge processes. Water Sci. Technol. 45:2002;1-11.
43. Ginovart M., Lopez D., Valls J. INDSIM, an individual-based discrete simulation model to study bacterial cultures. J. Theor. Biol. 214:2002;305-319.
44. Daoutidis P., Henson M.A. Dynamics and control of cell populations in continuous bioreactors. AIChE Symp. Ser. 326:2002;274-289.
45. Henson M.A. Dynamic modeling and control of yeast cell populations in continuous biochemical reactors. Comput. Chem. Eng. 27:2003;1185-1199.