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Intelligent Models of the Quantitative Behavior of Microbial Systems

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Abstract

Under different environmental conditions, microbial systems display complex behavioral patterns that are difficult to express quantitatively by mechanistic methods. Therefore, two alternate approaches based on different forms of intelligence have emerged. One approach uses methods of artificial intelligence (AI) such as neural networks, expert systems, and genetic algorithms to describe cellular behavior. The second methodology, which leads to the class of cybernetic models, relies on intelligence postulated to be possessed by the cells themselves. While both AI and cybernetic methods have been effective in many applications where mechanistic models are inadequate, all three methods have strengths and weaknesses. This recognition has led to the development of hybrid systems that combine two or more approaches for different aspects of a microbial system. However, the optimum design of hybrid systems still remains heuristic. The rationale and the developments from mechanistic to hybrid models are discussed here, and it is suggested that eventually a truly intelligent system should be self-evolving to maintain itself at the optimum configuration at all times.

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References

  • Altenberg, L. (1995). The schema theorem and Price’s theorem. In D. Whitley, & M. Vose (Eds.), Foundations of genetic algorithms 3 (pp. 23–49). San Francisco, USA: Morgan Kaufmann.

    Google Scholar 

  • Babel, W., Ackerman, J. U., & Breuer, U. (2001). Physiology, regulations, and limits of the synthesis of poly (3HB). Advances in Biochemical Engineering, Biotechnology, 71, 125–157.

    CAS  Google Scholar 

  • Baeza, J. A., Ferreira, E. C., & Laufuente, J. (2000). Knowledge-based supervision and control of waste-water treatment plant: A real-time application. Water Science and Technology, 41, 129–137.

    CAS  Google Scholar 

  • Bapat, P. M., Das, D., Sohoni, S. V., & Wangikar, P. P. (2006). Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterranei S699, a case study. Microbial Cell Factories, 5, 32. doi:10.1186/1475-2859-5-32.

    Article  Google Scholar 

  • Barnett, W. M. (1992). Knowledge-based expert system applications in waste treatment operation and control. ISA Transactions, 31, 53–60. doi:10.1016/0019-0578(92)90009-8.

    Article  Google Scholar 

  • Cakmakci, M. (2007). Adaptive neuro-fuzzy modeling of anaerobic digestion of primary sedimentation sludge. Bioprocess and Biosystems Engineering, 30, 349–357. doi:10.1007/s00449–007–0131–2.

    Article  CAS  Google Scholar 

  • Chen, L. Z., Nguang, S. K., Li, X. M., & Chen, X. D. (2004). Soft sensors for on-line biomass measurements. Bioprocess and Biosystems Engineering, 26, 191–195. doi:10.1007/s00449-004-0367-z.

    Article  CAS  Google Scholar 

  • Chen, V. C. P., & Rollins, D. K. (2000). Issues regarding artificial neural network modeling for reactors and fermenters. Bioprocess and Biosystems Engineering, 22, 85–93.

    CAS  Google Scholar 

  • Chu, W. B. Z., & Constantinides, A. (1998). Modeling, optimization and computer control of the cephalosporin C fermentation process. Biotechnology and Bioengineering, 32, 277–288. doi:10.1002/bit.260320304.

    Article  Google Scholar 

  • Cybenko, G. (1989). Approximation by superpositions of a sigmoidal function. Mathematics of Control, Signals and Systems, 2, 303–314. doi:10.1007/BF02551274.

    Article  Google Scholar 

  • Deb, K., Pratap, A., Agarwal, S., & Meyarivan, T. (2002). A fast and elitist multi-objective genetic algorithm: NSGA-II. IEEE Transactions on Evolutionary Computation, 6, 182–197. doi:10.1109/4235.996017.

    Article  Google Scholar 

  • Desai, K., Badhe, Y., Tambe, S. S., & Kulkarni, B. D. (2006). Soft-sensor development for fed-batch bioreactors using support vector regression. Biochemical Engineering Journal, 27, 225–239. doi:10.1016/j.bej.2005.08.002.

    Article  CAS  Google Scholar 

  • Dhurjati, P., Ramkrishna, D., Flickinger, M. C., & Tsao, G. T. (1985). A cybernetic view of microbial growth: modeling microbes as optimal strategists. Biotechnology and Bioengineering, 27, 1–9. doi:10.1002/bit.260270102.

    Article  CAS  Google Scholar 

  • Doshi, P., Rengaswamy, R., & Venkatesh, K. V. (1997). Modelling of microbial growth for sequential utilization in a multi-substrate environment. Process Biochemistry, 32, 643–650. doi:10.1016/S0032-9592(97)00013-7.

    Article  CAS  Google Scholar 

  • Fuzzy logic toolbox. User’s guide. MathWorks: Natick, MD, USA. Ch.2.

  • Gadkar, K. G., Doyle III, I. J., Crowley, T. J., & Varner, J. D. (2003). Cybernetic model predictive control of a continuous bioreactor with cell recycle. Biotechnology Progress, 19, 1487–1497. doi:10.1021/bp025776d.

    Article  CAS  Google Scholar 

  • Gadkar, K. G., Mehra, S., & Gomes, J. (2005). On-line adaptation of neural networks for bioprocess control. Computers & Chemical Engineering, 29, 1047–1057. doi:10.1016/j.compchemeng.2004.11.004.

    Article  CAS  Google Scholar 

  • Gall, R. A. B., & Patry, G. (1989). Knowledge-based system for the diagnosis of an activated sludge plant. In G. Patry, & D. Chapman (Eds.), Dynamic modeling and expert systems in wastewater engineering (pp. 193–240). London: Lewis.

    Google Scholar 

  • Galvanauskas, V., Simutis, R., & Lubbert, A. (2004). Hybrid process models for process optimization, monitoring and control. Bioprocess and Biosystems Engineering, 26, 393–400. doi:10.1007/s00449-004-0385-x.

    Article  CAS  Google Scholar 

  • Giordano, R. C., Bertini, J. R., Nicoletti, M., & Giordano, R. L. C. (2008). On-line filtering of CO2 signals from a bioreactor gas outflow using a committee of constructive neural networks. Bioprocess and Biosystems Engineering, 31, 101–109. doi:10.1007/s00449-007-0152-x.

    Article  CAS  Google Scholar 

  • Goldberg, D. E. (1989). Genetic algorithms in search, optimization and machine learning. Addison-Wesley: New York.

    Google Scholar 

  • Guardia, M. J., Gambhir, A., Europa, A. F., Ramkrishna, D., & Hu, W. S. (2000). Cybernetic modeling and regulation of metabolic pathways in multiple steady states of hybridoma cells. Biotechnology Progress, 16, 847–853. doi:10.1021/bp000069a.

    Article  CAS  Google Scholar 

  • Hanai, T., Katayama, A., Honda, H., & Kobayashi, T. (1997). Automatic fuzzy modeling for Ginjo sake brewing process using fuzzy neural networks. Journal of Chemical Engineering of Japan, 30, 94–100. doi:10.1252/jcej.30.94.

    Article  CAS  Google Scholar 

  • Hanai, T., Nishida, T., Ohkusu, E., Honda, H., & Kobayashi, T. (1995). Experimental fermentation of Ginjo sake with two fuzzy controls. Seibutsu-kogaku Jpn, 73, 283–289.

    CAS  Google Scholar 

  • Hartley, S. J. (1998). Concurrent programming: The java programming language. Oxford University Press: New York.

    Google Scholar 

  • Hassoun, M. H. (1995). Fundamentals of artificial neural networks. MIT: Cambridge, U.S.A.

    Google Scholar 

  • Hodgson, B. J., Taylor, C. N., Ushio, M., Leigh, J. R., Kalganova, T., & Baganz, F. (2004). Intelligent monitoring of bioprocesses: a comparison of structured and unstructured approaches. Bioprocess and Biosystems Engineering, 26, 353–359. doi:10.1007/s00449-004-0382-0.

    Article  CAS  Google Scholar 

  • Holland, J. H. (1975). Adaptation in natural and artificial systems. University of Michigan: Ann Arbor, MI, USA.

    Google Scholar 

  • Horiuchi, J. I. (2002). Fuzzy modeling and control of biological processes. Journal of Bioscience and Bioengineering, 94, 574–578.

    CAS  Google Scholar 

  • Hornik, K., Stinchcombe, M., & White, H. (1990). Multilayer feedforward networks are universal approximators. Neural Networks, 2, 359–366. doi:10.1016/0893-6080(89)90020-8.

    Article  Google Scholar 

  • Huong, V. L., Votruba, J., & Stuchl, I. (1994). Bioengineering analysis of incomplete data for waste water treatment by fuzzy expert system. Collection of Czechoslovak Chemical Communications, 59, 595–602.

    Article  CAS  Google Scholar 

  • Isidori, A. (1999). Nonlinear control systems. Springer: New York.

    Google Scholar 

  • James, S., Legge, R., & Budman, H. (2000). On-line estimation in bioreactors: a review. Reviews in Chemical Engineering, 14, 311–340.

    Google Scholar 

  • James, S., Legge, R., & Budman, H. (2002). Comparative study of black box and hybrid estimation methods in fed-batch fermentation. Journal of Process Control, 12, 113–121.

    Article  CAS  Google Scholar 

  • Jang, J. S. R. (1993). ANFIS: adaptive-network-based fuzzy inference systems. IEEE Transactions on Man and Cybernetics, 23, 665–685.

    Article  Google Scholar 

  • Jang, J. S. R., Sun, C. T., & Mizutani, E. (1997). Neuro-fuzzy and soft computing: A computational approach to learning and machine intelligence. Prentice-Hall: London.

    Google Scholar 

  • Khanna, S., & Srivastava, A. K. (2005). A simple structured mathematical model for biopolymer (PHB) production. Biotechnology Progress, 21, 830–838.

    Article  CAS  Google Scholar 

  • Kim, B. M., Kim, S. W., & Yang, D. R. (2003). Cybernetic modeling of the cephalosporin C fermentation process by Cephalosporium acremomiun. Biotechnology Letters, 25, 611–616.

    Article  CAS  Google Scholar 

  • Kishimoto, M., Omasa, T., Katakura, Y., Suga, K., & Okumura, K. (2000). Efficient production of desulfurizing cells with the aid of an expert system. Biochemical Engineering Journal, 5, 143–147.

    Article  CAS  Google Scholar 

  • Kompala, D. S., Ramkrishna, D., Jansen, J. B., & Tsao, G. T. (1986). Investigation of bacterial growth on multiple substrates: experimental evaluation of cybernetic models. Biotechnology and Bioengineering, 28, 1044–1055.

    Article  CAS  Google Scholar 

  • Korb, K. B., & Nicholson, A. E. (2004). Bayesian artificial intelligence. CRC: Baton Rouge.

    Google Scholar 

  • Lee, S. Y., Lim, H. C., & Hong, J. J. (1997). Application of nonsingular transformation to on-line optimal control of poly-β-hydroxybutyrate fermentation. Journal of Biotechnology, 55, 135–150.

    Article  CAS  Google Scholar 

  • Lee, F. C., Rangaiah, G. P., & Ray, A. K. (2007). Multi-objective optimization of an industrial penicillin V bioreactor train using non-dominated sorting genetic algorithm. Biotechnology and Bioengineering, 98, 586–598.

    Article  CAS  Google Scholar 

  • Leib, T. M., Pereira, C. J., & Villadsen, J. (2001). Bioreactors: a chemical engineering perspective. Chemical Engineering Science, 56, 5485–5497.

    Article  CAS  Google Scholar 

  • Lendenmann, U., & Egli, T. (1998). Kinetic models for the growth of Escherichia coli with mixtures of sugars under carbon-limited conditions. Biotechnology and Bioengineering, 59, 98–107.

    Article  Google Scholar 

  • Liden, G. (2001). Understanding the bioreactor. Bioprocess and Biosystems Engineering, 24, 273–279.

    Google Scholar 

  • Mandenius, C. -F. (2004). Recent developments in the monitoring, modeling and control of biological production systems. Bioprocess and Biosystems Engineering, 26, 347–351.

    Article  CAS  Google Scholar 

  • MathWorks (1995–1998). Matlab 5.3. MathWorks: Natick, MD, USA.

    Google Scholar 

  • Matsumara, M., Imanaka, T., Yoshida, T., & Taguchi, H. (1981). Modeling of cephalosporin C production and application to fed-batch culture. Journal of Fermentation Technology, 59, 115–123.

    Google Scholar 

  • Modak, J. M., & Lim, H. C. (1989). Feedback optimization of fed-batch fermentation. Biotechnology and Bioengineering, 30, 528–540.

    Article  Google Scholar 

  • Monod, J. (1949). The growth of bacterial cultures. Annual Reviews of Microbiology, 3, 371–394.

    Article  CAS  Google Scholar 

  • Na, J. -G., Chang, Y. K., Chung, B. H., & Lim, H. C. (2002). Adaptive optimization of fed-batch culture of yeast by using genetic algorithms. Bioprocess and Biosystems Engineering, 24, 299–308.

    Article  CAS  Google Scholar 

  • Nakano, K., Katsu, R., Tada, K., & Matsumara, M. (2000). Production of highly concentrated xylitol by Candida magnoliae under microaerobic condition by simple fuzzy control. Journal of Bioscience and Bioengineering, 89, 372–376.

    Article  CAS  Google Scholar 

  • Namjoshi, A., Kienle, A., & Ramkrishna, D. (2003). Steady-state multiplicity in bioreactors: bifurcation analysis of cybernetic models. Chemical Engineering Science, 58, 793–800.

    Article  CAS  Google Scholar 

  • Narang, A., Konopka, A., & Ramkrishna, D. (1997). The dynamics of microbial growth on mixtures of substrates in batch reactors. Journal of Theoretical Biology, 184, 301–317.

    Article  CAS  Google Scholar 

  • Nucci, E. R., Silva, R. G., Gomes, T. C., Giordano, R. C., & Cruz, A. J. G. (2005). A fuzzy logic algorithm for identification of the harvesting threshold during PGA production by Bacillus megaterium. Brazilian Journal of Chemical Engineering, 22, 521–527.

    Article  CAS  Google Scholar 

  • Ohshiro, T., & Izumi, Y. (1999). Microbial desulfurization of organic sulfur compounds in petroleum. Bioscience, Biotechnology and Biochemistry, 63, 1–9.

    Article  CAS  Google Scholar 

  • Paraskevas, P. A., Pantelakis, I. S., & Lekkas, T. D. (1999). An advanced integrated expert system for wastewater treatment plants control. Knowledge-Based Systems, 12, 355–361.

    Article  Google Scholar 

  • Park, Y. S., Shi, Z. P., Shiba, S., Cayuela, C., Iijima, S., & Kobayashi, T. (1993). Application of fuzzy reasoning on control of glucose and ethanol concentrations in baker’s yeast culture. Applied Microbiology and Biotechnology, 38, 649–655.

    CAS  Google Scholar 

  • Patnaik, P. R. (1998). Neural network applications to fermentation processes. In G. Subramanian (Ed.), Bioseparation and Bioprocessing, Vol. I, Ch.14. Wiley-VCH: Weinheim, Germany.

    Google Scholar 

  • Patnaik, P. R. (2000). Are microbes intelligent beings? An assessment of cybernetic modeling. Biotechnology Advances, 18, 267–288.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2001a). A simulation study of dynamic neural filtering and control of a fed-batch bioreactor under nonideal conditions. Chemical Engineering Journal, 84, 533–541.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2001b). Microbial metabolism as an evolutionary response: the cybernetic approach to modeling. Critical Reviews in Biotechnology, 21, 155–175.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2001c). Further enhancement of fed-batch strepokinase yield in the presence of inflow noise by coupled neural networks. Process Biochemistry, 37, 145–151.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2002). Can imperfections help to improve bioreactor performance? Trends in Biotechnology, 20, 135–137.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2003a). Oscillatory metabolism of Saccharomyces cerevisiae: an overview of mechanisms and models. Biotechnology Advances, 21, 183–192.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2003b). Effect of fluid dispersion on cybernetic control of microbial growth on substitutable substrates. Bioprocess and Biosystems Engineering, 25, 315–321.

    CAS  Google Scholar 

  • Patnaik, P. R. (2003c). An integrated hybrid neural system for noise filtering, simulation and control of a fed-batch recombinant fermentation. Biochemical Engineering Journal, 15, 165–175.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2005a). Process analysis in a disturbed environment during oscillatory metabolism of Saccharomyces ceresiae. Indian Journal of Biotechnology, 4, 201–208.

    CAS  Google Scholar 

  • Patnaik, P. R. (2005b). Neural network designs for poly-β-hydroxybutyrate production optimization under simulated industrial conditions. Biotechnology Letters, 27, 409–415.

    Article  CAS  Google Scholar 

  • Patnaik, P. R. (2006a). External, extrinsic and intrinsic noise in cellular systems: analogies and implications for protein synthesis. Biotechnology and Molecular Biology Reviews, 1, 123–129.

    Google Scholar 

  • Patnaik, P. R. (2006b). Hybrid filtering to rescue stable oscillations from noise-induced chaos in continuous cultures of budding yeast. FEMS Yeast Research, 6, 129–138.

    Article  CAS  Google Scholar 

  • Punal, A., Rodriguez, J., Franco, A., Carrasco, E. F., Roca, E., & Lema, J. M. (2001). Advanced monitoring and control of anaerobic wastewater treatment plants: diagnosis and supervision by a fuzzy-based expert system. Water Science and Technology, 43, 191–198.

    CAS  Google Scholar 

  • Ramkrishna, D. (1982). A cybernetic perspective of microbial growth. In E. Papoutsakis, G. N. Stephanopoulos, & H. W. Blanch (Eds.), Foundations of Biochemical Engineering. Kinetics and Thermodynamics in Biological Systems (pp. 161–178), , American Chemical Society: Washington DC.

    Google Scholar 

  • Ramkrishna, D. (2003). On modeling of bioreactors for control. Journal of Process Control, 13, 581–589.

    Article  CAS  Google Scholar 

  • Roeva, O., Pencheva, T., Hitzmann, B., & Tzonkov, S. (2004). A genetic algorithms based approach for identification of Escherichia coli fed-batch fermentation. Bioautomation, 1, 30–41.

    Google Scholar 

  • Russell, S., & Norvig, P. (2002). Artificial intelligence: A modern approach. NJ: Prentice-Hall.

    Google Scholar 

  • San, K., & Stephanopoulos, G. (1989). Optimization of fed-batch penicillin fermentation: a case of singular optimal control with state constraints. Biotechnology and Bioengineering, 34, 72–78.

    Article  CAS  Google Scholar 

  • Sarkar, D., & Modak, J. M. (2003). Optimization of fed-batch bioreactors using genetic algorithms. Chemical Engineering Science, 58, 2283–2296.

    Article  CAS  Google Scholar 

  • Shi, Z., & Shimizu, K. (1992). Neuro-fuzzy control of bioreactor systems with pattern recognition. Journal of Fermentation and Bioengineering, 74, 39–45.

    Article  CAS  Google Scholar 

  • Shiba, S., Nishida, Y., Park, Y. S., Iijima, S., & Kobayashi, T. (1994). Improvement of clone α-amylase gene expression in fed-batch culture of recombinant Saccharomyces cerevisiae by regulating both glucose and ethanol concentrations using a fuzzy contoller. Biotechnology and Bioengineering, 44, 1055–1063.

    Article  CAS  Google Scholar 

  • Shioya, S., Shimizu, K., & Yoshida, T. (1999). Knowledge-based design and operation of bioprocess systems. Journal of Bioscience and Bioengineering, 87, 261–266.

    Article  CAS  Google Scholar 

  • Sonnleiter, B. (2000). Instrumentation of biotechnological processes. Advances in Biochemical Engineering Biotechnology, 66, 1–64.

    Google Scholar 

  • Straight, J. V., & Ramkrishna, D. (1994). Cybernetic modeling and regulation of metabolic pathways. Growth on complementary nutrients. Biotechnology Progress, 10, 574–587.

    Article  CAS  Google Scholar 

  • Suenari, K., Tsuchiya, Y., Teshima, Y., Koizumi, J., & Nagai, S. (1990). Performance of sake mash brewing with fuzzy control. Hakkokogaku (Japanese), 68, 131–136.

    Google Scholar 

  • Tsuchiya, Y., Koizumi, J., Suenari, K., Teshima, Y., & Nagai, S. (1990). Concentrations of fuzzy rules and a fuzzy simulation based on the control technique of Hiroshima Toji (experts). Hakkokogaku (Japanese), 68, 123–129.

    Google Scholar 

  • ul-Haq, I., & Mukhtar, H. (2006). Fuzzy logic control of bioreactor for enhanced biosynthesis of alkaline protease by an alkalophilic strain of Bacillus subtilis. Current Microbiology, 52, 149–152.

    Article  CAS  Google Scholar 

  • Varner, J., & Ramkrishna, D. (1998). Application of cybernetic models to metabolic engineering: Investigation of storage pathways. Biotechnology and Bioengineering, 58, 282–291.

    Article  CAS  Google Scholar 

  • Zangirolami, T. C., Johansen, C. L., Nielsen, J., & Jorgensen, S. B. (1997). Simulation of penicillin production in fed-batch cultivations using a morphologically structured model. Biotechnology and Bioengineering, 56, 593–604.

    Article  CAS  Google Scholar 

  • Zuo, K., Cheng, H. -P., Wu, S. -C., & Wu, T. (2006). A hybrid model combining hydrodynamic and biological effects for production of bacterial cellulose with a pilot plant airlift reactor. Biochemical Engineering Journal, 29, 81–90.

    Article  CAS  Google Scholar 

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IMTECH communication no.017/2008

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Patnaik, P.R. Intelligent Models of the Quantitative Behavior of Microbial Systems. Food Bioprocess Technol 2, 122–137 (2009). https://doi.org/10.1007/s11947-008-0112-8

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