Optimization and scale up of industrial fermentation processes

Alves SS, Vasconcelos JMT (1996) Optimisation of agitation and aeration in fermenters. Bioprocess Biosyst Eng 14:119–123 Apostol I, Levine J, Lippincott J, Leach J, Hess E, Glascock CB, Weickert MJ, Blackmore R (1997) Incorporation of norvaline at leucine positions in recombinant human hemoglobin expressed in Escherichia coli. J Biol Chem 272:28980–28988 Amanullah A, McFarlane CM, Emery AM, Nienow AW (2001) Scale-down model to simulate spatial pH variations in large-scale bioreactors. Biotechnol Bioeng 73:390–399 Anderson RKI, Jayaraman K, Voisard D, Marison IW, von Stockar U (2002) Heat flux as an on-line indicator of metabolic activity in pilot scale bioreactor during the production of Bacillus thuringiensis var. galleriae-based pesticides. Thermochim Acta 386:127–138 Ansorge MB, Kula MR (2000) Production of recombinant l-leucine dehydrogenase from Bacillus cereus in pilot scale using the runaway replication system E. coli (pIET98). Biotechnol Bioeng 68:557–562 Arndt M, Hitzmann B (2004) Kalman filter based glucose control at small set points during fed-batch cultivation of Saccharomyces cerevisiae. Biotechnol Prog 1:377–383 Berkholz R, Guthke R (2001) Model based sequential experimental design for bioprocess optimisation—an overview. Focus Biotechnol 4:129–141 Berkholz R, Rohlig D, Guthke R (2000) Data and knowledge based experimental design for fermentation process optimization. Enzyme Microb Technol 27:784–788 Bezzo F, Macchietto S, Pantelides CC (2003) General hybrid multizonal/CFD approach for bioreactor modeling. AIChE J 49:2133–2148 Boehl D, Solle D, Hitzmann B, Scheper T (2003) Chemometric modelling with two-dimensional fluorescence data for Claviceps purpurea bioprocess characterization. J Biotechnol 105:179–188 Buchholz A, Takors R, Wandrey C (2001) Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic electrospray ionization tandem mass spectrometric techniques. Anal Biochem 295:129–137 Bylund F, Collet E, Enfors EO, Larsson G (1998) Substrate gradient formation in the large scale lowers cell yield and increases byproduct formation. Bioprocess Eng 18:171–180 Bylund F, Guillard F, Enfors SO, Trägardh C, Larsson G (1999) Scale down of recombinant production: a comparative study of scaling performance. Bioprocess Eng 20:289–377 Bylund F, Castan A, Mikkola R, Veide A, Larsson G (2000) Influence of scale-up on the quality of recombinant human growth hormone. Biotechnol Bioeng 69:119–128 Cant S (2002) High-performance computing in computational fluid dynamics: progress and challenges. Philos Trans Math Phys Eng Sci 360:1211–1225 Castan A, Enfors SO (2001) Formate accumulation due to DNA release in aerobic cultivations of Escherichia coli. Biotechnol Bioeng 77:324–328 Chen VCP, Rollins DK (2000) Issues regarding artificial neural network modeling for reactors and fermenters. Bioprocess Biosyst Eng 22:85–93 Cimander C, Bachinger T, Mandenius CF (2003) Integration of distributed multi-analyzer monitoring and control in bioprocessing based on a real-time expert system. J Biotechnol 103:237–248 Collins GE, Wu P, Lu Q, Ramsey JD, Bromund RH (2004) Compact, high voltage power supply for the lab-on-chip. Lab Chip 4:408–411 Dantigny P, Ninow JL, Lakrori M (1991) A new control strategy for yeast production based on the L/A approach. Appl Microbiol Biotechnol 36:352–357 Davidson KM, Sushil S, Eggleton CD, Marten MR (2003) Using computational fluid dynamics software to estimate circulation time distributions in bioreactors. Biotechnol Progress 19:1480–1486 Diaz A, Acevedo F (1999) Scale-up strategy for bioreactors with Newtonian and non-Newtonian broths. Bioprocess Eng 21:21–23 Dickinson TA, White J, Kauer JS, Walt DR (1998) Current trends in artificial nose technology. TIBTECH 16:250–258 Enfors SO, Jahic M, Rozkov A, Xu B, Hecker M, Jürgen B, Krüger B, Schweder T, Hamer G, O'Beirne D, Noisommit-Rizzi N, Reuss M, Boone L, Hewitt C, McFarlane C, Nienow A, Kovacs T, Trägardh C, Fuchs L, Revstedt J, Friberg PC, Hjertager B, Blomsten G, Skogman H, Hjort S, Hoeks F, Lin HJ, Neubauer P, van der Lans R, Luyben K, Vrabel P, Manelius A (2001) Physiological responses to mixing in large scale bioreactors. J Biotechnol 85:175–185 Farinas J, Chow AW, Wada HG (2001) A microfluidic device for measuring cellular membrane potential. Anal Biochem 295:138–142 Fenton D, Lai PH, Lu H, Mann M, Tsai L (1997) Control of norleucine incorporation into recombinant proteins. US patent 5599690 Ferreira LS, de Souza MB, Folly ROM (2001) Development of an alcohol fermentation control system based on biosensor measurements interpreted by neural networks. Sens Actuators B Chem 75:166–171 Flores ER, Perez F, de la Torre M (1997) Scale-up of Bacillus thuringiensis fermentation based on oxygen transfer. J Ferm Bioeng 83:561–564 Friehs K (2004) Plasmid copy number and plasmid stability. Adv Biochem Eng Biotechnol 86:47–82 Gabig-Ciminska M, Holmgren A, Andresen H, Bundvik Barken K, Wumpelmann M, Albers J, Hintsche R, Breitenstein A, Neubauer P, Los M, Czyz A, Wegrzyn G, Silfversparre G, Juregn B, Schweder T, Enfors SO (2004) Electric chips for rapid detection and quantification of nucleic acids. Biosens Bioelectron 15:537–546 Griffths D, Hall G (1993) Biosensors—what real progress is being made. TibTech 11:122–130 Hall JW, McNeil B, Rollins MJ, Draper I, Thompson BG, Macaloney G (1996) Near-infrared spectroscopic determination of acetate, ammonium, biomass and glycerol in an industrial Escherichia coli fermentation. Appl Spectrosc 50:102–108 Hammond SV (1992) NIR analysis of antibiotic fermentation. In: Murray I, Cowe IA (eds) Making light work: advances in near infrared spectroscopy, vol 1. VCH, New York, pp 584–589 Hammond SV, Brookes IK (1992) Near infrared spectroscopy—a powerful technique for at-line and on-line analysis of fermentations. In: Ladisch MR, Bose A (eds) Harnessing biotechnology for the 21st century: proceedings of the 9th international symposium and exhibition. Am Chem Soc, Washington DC, pp 325–333 Harms P, Kostov Y, Rao G (2002) Bioprocess monitoring. Curr Opin Biotechnol 13:124–127 Hewitt CJ, Nebe-von Caron G (2001) An industrial application of multiparameter flow cytometry: assessment of cell physiological state and its application to the study of microbial fermentations. Cytometry 44:179–187 Hewitt CJ, Nebe-Von Caron G (2004) The application of multi-parameter flow cytometry to monitor individual microbial cell physiological state. Adv Biochem Eng Biotechnol 89:197–223 Hewitt CJ, Nebe-von Caron G, Axelsson B, McFarlane CM, Nienow AW (2000) Studies related to the scale-up of high-cell-density E.coli fed-batch fermentations using multiparameter flow cytometry: effect of a changing microenvironment with respect to glucose and dissolved oxygen concentration. Biotechnol Bioeng 70:381–390 Horiuchi JI, Kishimoto M (1998) Fuzzy-aided estimation of biological parameters based on material balances. J Ferment Bacteriol 86:111–117 Huang YL, Foellmer TJ, Ang KC, Khoo SB, Yap MGS (1995) Characterization and application of an on-line flow injection analysis/wall-jet electrode system for glucose monitoring during fermentation. Anal Chim Acta 317:223–232 Hubbard DW (1987) Scaleup strategies for bioreactors containing non-newtonian broths. Ann N Y Acad Sci 506:600–607 Junker BH, Stanik M, Barna C, Salmon P, Buckland BC (1998) Influence of impeller type on mass transfer in fermentation vessels. Bioprocess Biosyst Eng 19:403–413 Kell DB, Ryder HM, Kaprelyants AS, Westerhoff HV (1991) Quantifying heterogeneity-flow cytometry of bacterial cultures. Anton van Leeuwenhoek Int J Gen Mol Microbiol 60:145–158 Kelly WJ, Humphrey AE (1998) Computational fluid dynamics model for predicting flow of viscous fluids in large fermentor with axial flow impellers and internal cooling coils. Biotechnol Prog 14:248–258 Kiick KL, Weberskirch R, Tirell DA (2001) Identification of an expanded set of translationally active methionine analogues in E. coli. FEBS Lett 502:25–30 Kim CH, Rao KJ, Youn DJ, Rhee SK (2003) Scale-up of recombinant hirudin production from Saccharomyces cerevisiae. Biotechnol Bioprocess Eng 8:303–305 Kleist S, Miksch G, Hitzmann B, Arndt M, Friehs K, Flaschel E (2003) Optimization of the extracellular production of bacterial phytase with Escherichia coli by using different fed-batch fermentation strategies. Appl Microbiol Biotechnol 61:456–462 Klyushnichenko V (2004) Capillary electrophoresis in the analysis and monitoring of biotechnological processes. Methods Mol Biol 276:77–120 Kolehmainen M, Rönkkö P, Raatikainen O (2003) Monitoring of yeast fermentation by ion mobility spectrometry measurement and data visualization with self-organizing maps. Anal Chim Acta 484:93–100 Kwint K, Nachin L, Diez A, Nyström T (2003) The bacterial universal stress protein: function and regulation. Curr Opin Microbiol 6:140–145 Larsson G, Törnkvist M, Wernersson ES, Trägard C, Noorman H, Enfors SO (1996) Substrate gradients in bioreactors: origin and consequences. Bioprocess Eng 14:281–289 Lee SY (1996) High-cell density culture of Escherichia coli. Trends Biotechnol 14:98–105 Liden G (2002) Understanding the bioreactor. Bioprocess Biosyst Eng 24:273–279 Lin HY, Neubauer P (2000) Influence of controlled glucose oscillations on a fed-batch process of recombinant Escherichia coli. J Biotechnol 79:27–37 Lin HY, Mathiszik B, Xu B, Enfors SO, Neubauer P (2001) Determinantion of the maximum specific uptake capacities for glucose and oxygen in glucose-limited fed-batch cultivations of Escherichia coli. Biotechnol Bioeng 73:347–357 Macaloney G, Hall JW, Rollins MJ, Draper I, Thompson BG, McNeil B (1994) Monitoring biomass and glycerol in an Escherichia coli fermentation using near-infrared spectroscopy. Biotechnol Tech 8:281–286 Matz G, Lennemann F (1996) On-line monitoring of biotechnological processes by gas chromatographic-mass spectrometric analysis of fermentation suspensions. J Chromatogr 750:141–149 Mogk A, Tomoyasu T, Goloubinoff P, Rudiger S, Roder D, Langen H, Bukau B (1999) Identification of thermolabile Escherichia coli proteins: prevention and reversion of aggregation by DnaK and ClpB. EMBO J 18:6934–6949 Moser I, Jobst G, Urban GA (2002) Biosensor array for simultaneous measurement of glucose, lactate, glutamate, and glutamine. Biosens Bioelectron 17:297–302 Muramatsu R, Negishi T, Mimoto T, Miura A, Miosawa S, Hayashi H (2002) Existence of β-methylnorleucine in recombinant hirudin produced by Escherichia coli. J Biotechnol 93:131–142 Neils C, Tyree Z, Finlayson B, Folch A (2004) Combinatorial mixing of microfluidic streams. Lab Chip 4:342–350 Neubauer P, Lin HY, Mathiszik B (2003) Metabolic load of recombinant protein production: inhibition of cellular capacities for glucose uptake and respiration after induction of a heterologous gene in Escherichia coli. Biotechnol Bioeng 83:53–64 Nishi H, Tsumagari N, Kakimoto T, Terabe S (1989) Separation of β-lactam antibiotics by micellar electrokinetic chromatography. J Chromatogr 477:259–270 Nishi H, Fukuyama T, Matsuo M (1990) Separation and determination of aspoxicillin in human plasma by micellar electrokinetic chromatography with direct sample injection. J Chromatogr 515:245–255 Nordstrom K, Uhlin BE (1992) Runaway-replication plasmids as tools to produce large quantities of proteins from cloned genes in bacteria. Biotechnology 6:661–666 Oniscu C, Galaction AI, Cascaval D, Ungureanu F (2001) Modelling of mixing in stirred bioreactors 1. Mixing time for non-aerated simulated broths. Roum Biotechnol Lett 6:119–129 Onyeaka H, Nienow A, Hewitt CJ (2003) Further studies related to the scale-up of high cell density Escherichia coli fed-batch fermentations: the additional effect of changing microenvironment when using aqueous ammonia to control pH. Biotechnol Bioeng 84:474–484 Pollard D, Buccino R, Connors N, Kirschner T, Olewinski R, Saini K, Slamon P (2001) Real-time analyte monitoring of a fungal fermentation, at a pilot scale, using in mid-infrared spectroscopy. Bioprocess Biosyst Eng 24:13–24 Reischer H, Schotola I, Striedner G, Pötschacher F, Bayer K (2004) Evaluation of the GFP signal and its aptitude for novel on-line monitoring strategies of recombinant fermentation processes. J Biotechnol 115–125 Riesenberg D, Menzel K, Schulz V, Schumann K, Veith G, Zuber G, Knorre WA (1990) High cell density fermentation of recombinant Escherichia coli expressing human interferon alpha 1. Appl Microbiol Biotechnol 34:77–82 Rocha I, Ferreira EC (2002) On-line simultaneous monitoring of glucose and acetate with FIA during high cell density fermentation of recombinant E. coli. Bioelectrochem 56:127–129 Russel AB, Thomas CR, Lilly MD (1995) Oxygen transfer measurements during yeast fermentations in a pilot scale airlift fermenter. Bioprocess Biosyst Eng 12:71–79 Schaefer U, Boos W, Takors R, Weuster-Bootz D (1999) Automated sample device for monitoring intracellular metabolite dynamics. Anal Biochem 270:88–96 Schmalzriedt S, Jenne M, Mauch K, Reuss M (2003) Integration of physiology and fluid dynamics. Adv Biochem Eng Biotechnol 80:19–68 Schügerl K, Brandes T, Dullau K, Holzhauer-Rieger K, Hotop S, Hübner U, Wu X, Zhou W (1991) Fermentation monitoring and control by on-line flow injection and liquid chromatography. Anal Chim Acta 249:87–100 Schweder T, Krüger E, Xu B, Jürgen B, Blomsten G, Enfors SO, Hecker M (1999) Monitoring genes that respond to process-related stress in large-scale bioprocesses. Biotechnol Bioeng 65:151–159 Solle D, Geissler D, Stark E, Scheper T, Hitzmann B (2003) Chemometric modelling based on 2D-fluorescence spectra without a calibration measurement. Bioinformatics 19:173–177 Spichiger-Keller UE (1997) Ion- and substrate specific optode membranes and optical detection modes. Sens Actuators B Chem B38:68–77 Stark E, Hitzmann B, Schügerl K, Scheper T, Fuchs C, Koster D, Märkl H (2002) In-situ-fluorescence probes: a useful tool for non-invasive bioprocess monitoring. Adv Biochem Eng Biotechnol 74:21–38 Thiry M, Cingolani D (2002) Optimizing scale-up fermentation processes. Trends Biotechnol 20:103–105 Tothill IE, Newman JD, White SF, Turner APF (1997) Monitoring of the glucose concentration during microbial fermentation using a novel mass-producible biosensor suitable for on-line use. Enzyme Microb Technol 20:590–596 Trelea IC, Titica M, Landaud S, Latrille E, Corrieu G, Cheruy A (2001) Predictive modelling of brewing fermentation: from knowledge-based to black box models. Math Comput Simul 56:405–424 Türker M (2004) Development of biocalorimetry as a technique for process monitoring and control in technical scale fermentations. Thermochim Acta (in press) Turner AP (1994) Biosensors. Curr Opin Biotechnol 5:49–53 Turner C, Rudnitskaya A, Legin A (2003) Monitoring batch fermentations with an electronic tongue. J Biotechnol 103:87–91 Umakoshi H, Kuboi R, Komaswa I, Tsuchido T, Matsumura Y (1998) Heat-induced translocation of cytoplasmic beta-galactosidase across inner membrane of Escherichia coli. Biotechnol Prog 14:210–217 Vaccari G, Dosi E, Campi AL, Gonzalez-Vara A, Matteuzi D, Mantovani G (1994) A near infrared spectroscopy technique for the control of fermentation processes: an application to lactic acid fermentation. Biotechnol Bioeng 43:913–917 Vaidyanathan S, Macaloney G, Vaughan J, McNeil B, Harvey LM (1999) Monitoring of submerged bioprocesses. Crit Rev Biotechnol 19:277–316 van de Merbel NC (1997) The use of ultrafiltration and column liquid chromatography for an on-line fermentation monitoring. Trends Anal Chem 16:162–173 van de Merbel NC, Lingemann H, Brinkmann UAT (1993) Automated monitoring of biotechnological processes using on-line ultrafiltration and column liquid chromatography. Anal Chim Acta 279:39–50 Wang DIC, Cooney CL (1997) Translation of laboratory, pilot, and plant scale data. In: Wang DIC et al (eds) Fermentation and enzyme technology. Wiley, New York, pp 194–211 Weickert MJ, Apostol I (1998) High-fidelity translation of recombinant human hemoglobin in Escherichia coli. Appl Environ Microbial 64:1589–1593 Williams KA, Saini S, Wick TM (2002) Computational fluid dynamics modeling of steady-state momentum and mass transport in a bioreactor for cartilage tissue engineering. Biotechnol Progress 18:951–963 Wolfbeis OS (2002) Fiber-optic chemical sensors and biosensors. Anal Chem 74:2663–2678 Wong I, Hernandez A, Garcia MA, Segura R, Rodriguez I (2002) Fermentation scale up for recombinant K99 antigen production cloned in Escherichia coli MC1061. Proc Biochem 37:1195–1199 Xu B, Jahic M, Bomsten G, Enfors SO (1999) Glucose overflow metabolism and mixed acid fermentation in aerobic large-scale fed-batch processes with Echerichia coli. Appl Microbiol Biotechnol 51:564–571 Yawalkar AA, Heesink ABM, Versteeg GF, Vishwas GP (2002) Gas–liquid mass transfer coefficient in stirred tank reactors. Can J Chem Eng 80:840–848 Yim SC, Jeong KJ, Chang HN, Lee SY (2001) High-level secretory production of human granulocyte-colony stimulating factor by fed-batch culture of recombinant E.coli. Bioprocess Biosyst Eng 24:249–254