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Potential of Integrating Model-Based Design of Experiments Approaches and Process Analytical Technologies for Bioprocess Scale-Down

Part of the Advances in Biochemical Engineering/Biotechnology book series (ABE,volume 177)

Abstract

Typically, bioprocesses on an industrial scale are dynamic systems with a certain degree of variability, system inhomogeneities, and even population heterogeneities. Therefore, the scaling of such processes from laboratory to industrial scale and vice versa is not a trivial task. Traditional scale-down methodologies consider several technical parameters, so that systems on the laboratory scale tend to qualitatively reflect large-scale effects, but not the dynamic situation in an industrial bioreactor over the entire process, from the perspective of a cell. Supported by the enormous increase in computing power, the latest scientific focus is on the application of dynamic models, in combination with computational fluid dynamics to quantitatively describe cell behavior. These models allow the description of possible cellular lifelines which in turn can be used to derive a regime analysis for scale-down experiments. However, the approaches described so far, which were for a very few process examples, are very labor- and time-intensive and cannot be validated easily. In parallel, alternatives have been developed based on the description of the industrial process with hybrid process models, which describe a process mechanistically as far as possible in order to determine the essential process parameters with their respective variances. On-line analytical methods allow the characterization of population heterogeneity directly in the process. This detailed information from the industrial process can be used in laboratory screening systems to select relevant conditions in which the cell and process related parameters reflect the situation in the industrial scale. In our opinion, these technologies, which are available in research for modeling biological systems, in combination with process analytical techniques are so far developed that they can be implemented in industrial routines for faster development of new processes and optimization of existing ones.

Graphical Abstract

Keywords

  • Bioprocess scale-up
  • Process analytical techniques
  • Process modeling
  • Scale-down

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References

  1. Anane E, Sawatzki A, Neubauer P, Cruz Bournazou MN (2019) Modelling concentration gradients in fed-batch cultivations of E. coli – towards the flexible design of scale-down experiments. J Chem Technol Biotechnol 94:516–526

    CAS  Google Scholar 

  2. Neubauer P, Cruz N, Glauche F, Junne S, Knepper A, Raven M (2013) Consistent development of bioprocesses from microliter cultures to the industrial scale. Eng Life Sci 13:224–238

    CAS  Google Scholar 

  3. Neubauer P, Junne S (2016) Scale-up and scale-down methodologies for bioreactors. In: Mandenius CF (ed) Bioreactors: design, operation and novel applications. Wiley-VCH Verlag GmbH, Weinheim, pp 323–354

    Google Scholar 

  4. Reitz C, Fan Q, Neubauer P (2018) Synthesis of non-canonical branched-chain amino acids in Escherichia coli and approaches to avoid their incorporation into recombinant proteins. Curr Opin Biotechnol 53:248–253

    CAS  PubMed  Google Scholar 

  5. Wang G, Haringa C, Tang W, Noorman H, Chu J, Zhuang Y, Zhang S (2020) Coupled metabolic-hydrodynamic modeling enabling rational scale-up of industrial bioprocesses. Biotechnol Bioeng 117:844–867

    CAS  PubMed  Google Scholar 

  6. Grieves M, Vickers J (2016) Digital twin: mitigating unpredictable, undesirable emergent behavior in complex systems. In: Transdisciplinary perspectives on complex systems: new findings and approaches, pp 85–113

    Google Scholar 

  7. Grossmann I (2005) Enterprise-wide optimization: a new frontier in process systems engineering. AIChE J:1846–1857

    Google Scholar 

  8. Qi Q, Tao F (2018) Digital twin and big data towards smart manufacturing and industry 4.0: 360 degree comparison. IEEE Access 6:3585–3593

    Google Scholar 

  9. Batstone DJ, Keller J, Angelidaki I, Kalyuzhnyi SV, Pavlostathis SG, Rozzi A, Sanders WTM, Siegrist H, Vavilin VA (2002) The IWA anaerobic digestion model no 1(ADM 1). Water Sci Technol 45:65–73

    CAS  PubMed  Google Scholar 

  10. Tsugawa H (2018) Advances in computational metabolomics and databases deepen the understanding of metabolisms. Curr Opin Biotechnol 54:10

    CAS  PubMed  Google Scholar 

  11. Kitano H (2002) Computational systems biology. Nature 420:206–210

    CAS  PubMed  Google Scholar 

  12. Stephanopoulos GN, Aristidou AA, Nielsen J (1998) Review of cellular metabolism. In: Metabolic engineering. Academic Press, San Diego, pp 21–79

    Google Scholar 

  13. Varma A, Palsson BO (1994) Metabolic flux balancing: basic concepts, scientific and practical use. Bio/Technology 12:994–998

    CAS  Google Scholar 

  14. Marchisio MA, Stelling J (2009) Computational design tools for synthetic biology. Curr Opin Biotechnol 20:479–485

    CAS  PubMed  Google Scholar 

  15. Saeys Y, Inza I, Larrañaga P (2007) A review of feature selection techniques in bioinformatics. Bioinformatics 23:2507–2517

    CAS  PubMed  Google Scholar 

  16. Bailey JE (1998) Mathematical modeling and analysis in biochemical engineering: past accomplishments and future opportunities. Biotechnol Prog 14:8–20

    CAS  PubMed  Google Scholar 

  17. Koutinas M, Kiparissides A, Pistikopoulos EN, Mantalaris A (2012) Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology. Comput Struct Biotechnol J 3:e201210022

    PubMed  Google Scholar 

  18. Anane E, López CDC, Barz T, Sin G, Gernaey KV, Neubauer P, Cruz Bournazou MN (2019) Output uncertainty of dynamic growth models: effect of uncertain parameter estimates on model reliability. Biochem Eng J 150:107247

    Google Scholar 

  19. Muñoz-Tamayo R, Puillet L, Daniel JB, Sauvant D, Martin O, Taghipoor M, Blavy P (2018) Review: to be or not to be an identifiable model. Is this a relevant question in animal science modelling? Animal 12:701–712

    PubMed  Google Scholar 

  20. Villaverde AF, Barreiro A, Papachristodoulou A (2016) Structural identifiability of dynamic systems biology models. PLoS Comput Biol 12:1–22

    Google Scholar 

  21. Brubaker TA (1979) Nonlinear parameter estimation. Anal Chem 51:1385A

    Google Scholar 

  22. Brun R, Kühni M, Siegrist H, Gujer W, Reichert P (2002) Practical identifiability of ASM2d parameters – systematic selection and tuning of parameter subsets. Water Res 36:4113–4127

    CAS  PubMed  Google Scholar 

  23. Kravaris C, Hahn J, Chu Y (2013) Advances and selected recent developments in state and parameter estimation. Comput Chem Eng 51:111–123

    CAS  Google Scholar 

  24. Vajda S, Rabitz H, Walter E, Lecourtier Y (1989) Qualitative and quantitative identifiability analysis of nonlinear chemical kinetic models. Chem Eng Commun 83:191–219

    CAS  Google Scholar 

  25. Bellman R, Astrom KJ (1970) On structural identifiability. Math Biosci 7:329–339

    Google Scholar 

  26. Cobelli C, DiStefano JJ (1980) Parameter and structural identifiability concepts and ambiguities: a critical review and analysis. Am J Phys 239:R7–R24

    CAS  Google Scholar 

  27. Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingmüller U, Timmer J (2009) Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics 25:1923–1929

    CAS  PubMed  Google Scholar 

  28. Neubauer P, Cruz-Bournazou MN (2017) Continuous bioprocess development: methods for control and characterization of the biological system. In: Subramanian G (ed) Continuous biomanufacturing – innovative technologies and methods. Wiley, Hoboken, pp 1–30

    Google Scholar 

  29. Anane E, García ÁC, Haby B, Hans S, Krausch N, Krewinkel M, Hauptmann P, Neubauer P, Cruz Bournazou MN (2019) A model-based framework for parallel scale-down fed-batch cultivations in mini-bioreactors for accelerated phenotyping. Biotechnol Bioeng 116:2906–2918

    CAS  PubMed  Google Scholar 

  30. Neubauer P, Glauche F, Cruz-Bournazou MN (2017) Editorial: bioprocess development in the era of digitalization. Eng Life Sci 17:1140–1141

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Narayanan H, Luna MF, von Stosch M, Cruz Bournazou MN, Polotti G, Morbidelli M, Butté A, Sokolov M (2020) Bioprocessing in the digital age: the role of process models. Biotechnol J 15:1–10

    Google Scholar 

  32. Noorman H (2011) An industrial perspective on bioreactor scale-down: what we can learn from combined large-scale bioprocess and model fluid studies. Biotechnol J 6:934–943

    CAS  PubMed  Google Scholar 

  33. Petsagkourakis P, Sandoval IO, Bradford E, Zhang D, del Rio-Chanona EA (2020) Reinforcement learning for batch bioprocess optimization. Comput Chem Eng 133:106649

    CAS  Google Scholar 

  34. Mandenius CF, Brundin A (2008) Bioprocess optimization using design-of-experiments methodology. Biotechnol Prog 24:1191–1203

    CAS  PubMed  Google Scholar 

  35. Wechselberger P, Sagmeister P, Herwig C (2013) Model-based analysis on the extractability of information from data in dynamic fed-batch experiments. Biotechnol Prog 29:285–296

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Covert MW, Xiao N, Chen TJ, Karr JR (2008) Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24:2044–2050

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Haringa C, Deshmukh AT, Mudde RF, Noorman HJ (2017) Euler-Lagrange analysis towards representative down-scaling of a 22 m3 aerobic S. cerevisiae fermentation. Chem Eng Sci 170:653–669

    CAS  Google Scholar 

  38. Delvigne F, Goffin P (2014) Microbial heterogeneity affects bioprocess robustness: dynamic single-cell analysis contributes to understanding of microbial populations. Biotechnol J 9:61–72

    CAS  PubMed  Google Scholar 

  39. Barz T, Lopez Cardenas DC, Cruz Bournazou MN, Körkel S, Walter SF (2016) Real-time adaptive input design for the determination of competitive adsorption isotherms in liquid chromatography. Comput Chem Eng 94:104–116

    CAS  Google Scholar 

  40. Cruz Bournazou MN, Barz T, Nickel DB, Lopez Cárdenas DC, Glauche F, Knepper A, Neubauer P (2017) Online optimal experimental re-design in robotic parallel fed-batch cultivation facilities. Biotechnol Bioeng 114:610–619

    CAS  PubMed  Google Scholar 

  41. Dörr M, Fibinger MPC, Last D, Schmidt S, Santos-Aberturas J, Böttcher D, Hummel A, Vickers C, Voss M, Bornscheuer UT (2016) Fully automatized high-throughput enzyme library screening using a robotic platform. Biotechnol Bioeng 113:1421–1432

    PubMed  Google Scholar 

  42. Haby B, Hans S, Anane E, Sawatzki A, Krausch N, Neubauer P, Cruz Bournazou MN (2019) Integrated robotic mini bioreactor platform for automated, parallel microbial cultivation with online data handling and process control. SLAS Technol 24:569–582

    CAS  PubMed  Google Scholar 

  43. Unthan S, Radek A, Wiechert W, Oldiges M, Noack S (2015) Bioprocess automation on a mini pilot plant enables fast quantitative microbial phenotyping. Microb Cell Factories 14:32

    Google Scholar 

  44. Lattermann C, Büchs J (2015) Microscale and miniscale fermentation and screening. Curr Opin Biotechnol 35:1–6

    CAS  PubMed  Google Scholar 

  45. Hemmerich J, Noack S, Wiechert W, Oldiges M (2018) Microbioreactor systems for accelerated bioprocess development. Biotechnol J 13:1–9

    Google Scholar 

  46. Lara AR, Galindo E, Ramírez OT, Palomares LA (2006) Living with heterogeneities in bioreactors: understanding the effects of environmental gradients on cells. Mol Biotechnol 34:355–382

    CAS  PubMed  Google Scholar 

  47. Oldshue JY (1966) Fermentation mixing scale-up techniques. Biotechnol Bioeng 8:3–24

    Google Scholar 

  48. Oosterhuis NMG (1984) Scale-up of bioreactors. TU Delft 162

    Google Scholar 

  49. Enfors SO, Jahic M, Rozkov A, Xu B, Hecker M, Jürgen B, Krüger E, Schweder T, Hamer G, O’Beirne D, Noisommit-Rizzi N, Reuss M, Boone L, Hewitt C, McFarlane C, Nienow A, Kovacs T, Trägårdh C, Fuchs L, Revstedt J, Friberg PC, Hjertager B, Blomsten G, Skogman H, Hjort S, Hoeks F, Lin HY, Neubauer P, Van der Lans R, Luyben K, Vrabel P, Manelius A, Manelius Å (2001) Physiological responses to mixing in large scale bioreactors. J Biotechnol 85:175–185

    CAS  PubMed  Google Scholar 

  50. Larsson G, Törnkvist M, Ståhl Wernersson E, Trägårdh C, Noorman H, Enfors SO (1996) Substrate gradients in bioreactors: origin and consequences. Bioprocess Eng 14:281–289

    CAS  Google Scholar 

  51. Brand E, Junne S, Anane E, Cruz-Bournazou MN, Neubauer P (2018) Importance of the cultivation history for the response of Escherichia coli to oscillations in scale-down experiments. Bioprocess Biosyst Eng 41:1305–1313

    CAS  PubMed  Google Scholar 

  52. Sweere APJ, Luyben KCAM, Kossen NWF (1987) Regime analysis and scale-down: tools to investigate the performance of bioreactors. Enzym Microb Technol 9:386–398

    CAS  Google Scholar 

  53. Lin HY, Mathiszik B, Xu B, Enfors SO, Neubauer P (2001) Determination of the maximum specific uptake capacities for glucose and oxygen in glucose-limited fed-batch cultivations of Escherichia coli. Biotechnol Bioeng 73:347–357

    CAS  PubMed  Google Scholar 

  54. Bylund F, Collet E, Larsson G, Enfors SO, Larsson G (1998) Substrate gradient formation in the large-scale bioreactor lowers cell yield and increases by-product formation. Bioprocess Eng 18:171–180

    CAS  Google Scholar 

  55. Neubauer P, Häggström L, Enfors SO (1995) Influence of substrate oscillations on acetate formation and growth yield in Escherichia coli glucose limited fed-batch cultivations. Biotechnol Bioeng 47:139–146

    CAS  PubMed  Google Scholar 

  56. Xu B, Jahic M, Blomsten G, Enfors SO (1999) Glucose overflow metabolism and mixed-acid fermentation in aerobic large-scale fed-batch processes with Escherichia coli. Appl Microbiol Biotechnol 51:564–571

    PubMed  Google Scholar 

  57. Nienow AW (2006) Reactor engineering in large scale animal cell culture. Cytotechnology 50:9–33

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Simen JD, Löffler M, Jäger G, Schäferhoff K, Freund A, Matthes J, Müller J, Takors R, Feuer R, von Wulffen J, Lischke J, Ederer M, Knies D, Kunz S, Sawodny O, Riess O, Sprenger G, Trachtmann N, Nieß A, Broicher A (2017) Transcriptional response of Escherichia coli to ammonia and glucose fluctuations. Microb Biotechnol 10:858–872

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Spann R, Glibstrup J, Pellicer-Alborch K, Junne S, Neubauer P, Roca C, Kold D, Lantz AE, Sin G, Gernaey KV, Krühne U (2019) CFD predicted pH gradients in lactic acid bacteria cultivations. Biotechnol Bioeng 116:769–780

    CAS  PubMed  Google Scholar 

  60. Paul K, Böttinger K, Mitic BM, Scherfler G, Posch C, Behrens D, Huber CG, Herwig C (2020) Development, characterization, and application of a 2-compartment system to investigate the impact of pH inhomogeneities in large-scale CHO-based processes. Eng Life Sci 20:368–378

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Paul K, Hartmann T, Posch C, Behrens D, Herwig C (2020) Investigation of cell line specific responses to pH inhomogeneity and consequences for process design. Eng Life Sci 20:412–421

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Buchholz J, Graf M, Freund A, Busche T, Kalinowski J, Blombach B, Takors R (2014) CO 2/HCO 3− perturbations of simulated large scale gradients in a scale-down device cause fast transcriptional responses in Corynebacterium glutamicum. Appl Microbiol Biotechnol 98:8563–8572

    CAS  PubMed  Google Scholar 

  63. Spadiut O, Rittmann S, Dietzsch C, Herwig C (2013) Dynamic process conditions in bioprocess development. Eng Life Sci 13:88–101

    CAS  Google Scholar 

  64. Limberg MH, Joachim M, Klein B, Wiechert W, Oldiges M (2017) pH fluctuations imperil the robustness of C. glutamicum to short term oxygen limitation. J Biotechnol 259:248–260

    CAS  PubMed  Google Scholar 

  65. Xu S, Jiang R, Mueller R, Hoesli N, Kretz T, Bowers J, Chen H (2018) Probing lactate metabolism variations in large-scale bioreactors. Biotechnol Prog 34:756–766

    CAS  PubMed  Google Scholar 

  66. Brunner M, Doppler P, Klein T, Herwig C, Fricke J (2018) Elevated pCO2 affects the lactate metabolic shift in CHO cell culture processes. Eng Life Sci 18:204–214

    CAS  PubMed  Google Scholar 

  67. Delvigne F, Noorman H (2017) Scale-up/scale-down of microbial bioprocesses: a modern light on an old issue. Microb Biotechnol 10:685–687

    PubMed  PubMed Central  Google Scholar 

  68. Cortés JT, Flores N, Bolívar F, Lara AR, Ramírez OT (2016) Physiological effects of pH gradients on Escherichia coli during plasmid DNA production. Biotechnol Bioeng 113:598–611

    PubMed  Google Scholar 

  69. Junne S, Klingner A, Kabisch J, Schweder T, Neubauer P (2011) A two-compartment bioreactor system made of commercial parts for bioprocess scale-down studies: impact of oscillations on Bacillus subtilis fed-batch cultivations. Biotechnol J 6:1009–1017

    CAS  PubMed  Google Scholar 

  70. Käß F, Hariskos I, Michel A, Brandt HJ, Spann R, Junne S, Wiechert W, Neubauer P, Oldiges M (2014) Assessment of robustness against dissolved oxygen/substrate oscillations for C. glutamicum DM1933 in two-compartment bioreactor. Bioprocess Biosyst Eng 37:1151–1162

    PubMed  Google Scholar 

  71. Schilling BM, Pfefferle W, Bachmann B, Leuchtenberger W, Deckwer W-DD (1999) A special reactor design for investigations of mixing time effects in a scaled-down industrial L-lysine fed-batch fermentation process. Biotechnol Bioeng 64:599–606

    CAS  PubMed  Google Scholar 

  72. Delvigne F, Boxus M, Ingels S, Thonart P (2009) Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli. Microb Cell Fact 8:15

    PubMed  PubMed Central  Google Scholar 

  73. Junne S, Neubauer P (2018) How scalable and suitable are single-use bioreactors? Curr Opin Biotechnol 53:240–247

    CAS  PubMed  Google Scholar 

  74. Löffler M, Simen JD, Jäger G, Schäferhoff K, Freund A, Takors R (2016) Engineering E. coli for large-scale production – strategies considering ATP expenses and transcriptional responses. Metab Eng 38:73–85

    PubMed  Google Scholar 

  75. Delvigne F, Baert J, Sassi H, Fickers P, Grünberger A, Dusny C (2017) Taking control over microbial populations: current approaches for exploiting biological noise in bioprocesses. Biotechnol J 12:1600549

    Google Scholar 

  76. Lemoine A, Delvigne F, Bockisch A, Neubauer P, Junne S (2017) Tools for the determination of population heterogeneity caused by inhomogeneous cultivation conditions. J Biotechnol 251:84–93

    CAS  PubMed  Google Scholar 

  77. Avery SV (2006) Microbial cell individuality and the underlying sources of heterogeneity. Nat Rev Microbiol 4:577–587

    CAS  PubMed  Google Scholar 

  78. Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A (2017) Homogenizing bacterial cell factories: analysis and engineering of phenotypic heterogeneity. Metab Eng 42:145–156

    CAS  PubMed  Google Scholar 

  79. Lieder S, Jahn M, Seifert J, von Bergen M, Müller S, Takors R (2014) Subpopulation-proteomics reveal growth rate, but not cell cycling, as a major impact on protein composition in Pseudomonas putida KT2440. AMB Express 4:1–10

    CAS  Google Scholar 

  80. Delvigne F, Zune Q, Lara AR, Al-Soud W, Sørensen SJ (2014) Metabolic variability in bioprocessing: implications of microbial phenotypic heterogeneity. Trends Biotechnol 32:608–616

    CAS  PubMed  Google Scholar 

  81. Van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJM, Planqué R, Hulshof J, O’Toole TG, Wahl SA, Teusink B (2014) Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science 343:1245114

    PubMed  Google Scholar 

  82. Brognaux A, Han S, Sørensen SJ, Lebeau F, Thonart P, Delvigne F (2013) A low-cost, multiplexable, automated flow cytometry procedure for the characterization of microbial stress dynamics in bioreactors. Microb Cell Fact 12

    Google Scholar 

  83. Lieder S, Jahn M, Koepff J, Muller S, Takors R (2016) Environmental stress speeds up DNA replication in Pseudomonas putida in chemostat cultivations. Biotechnol J 11:155–163

    CAS  PubMed  Google Scholar 

  84. Hewitt CJ, von Caron GN, 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

    CAS  PubMed  Google Scholar 

  85. Patel A, Antonopoulou I, Enman J, Rova U, Christakopoulos P, Matsakas L (2019) Lipids detection and quantification in oleaginous microorganisms: an overview of the current state of the art. BMC Chem Eng 1

    Google Scholar 

  86. Marbà-Ardébol AM, Emmerich J, Neubauer P, Junne S (2017) Single-cell-based monitoring of fatty acid accumulation in Crypthecodinium cohnii with three-dimensional holographic and in situ microscopy. Process Biochem 52:223–232

    Google Scholar 

  87. Marbà-Ardébol AM, Bockisch A, Neubauer P, Junne S (2018) Sterol synthesis and cell size distribution under oscillatory growth conditions in Saccharomyces cerevisiae scale-down cultivations. Yeast 35:213–223

    PubMed  Google Scholar 

  88. Lemoine A, Limberg MHMH, Kästner S, Oldiges M, Neubauer P, Junne S (2016) Performance loss of Corynebacterium glutamicum cultivations under scale-down conditions using complex media. Eng Life Sci 16:620–632

    CAS  Google Scholar 

  89. Nachin L, Nannmark U, Nyström T (2005) Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol 187:6265–6272

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Trivedi A, Mavi PS, Bhatt D, Kumar A (2016) Thiol reductive stress induces cellulose-anchored biofilm formation in Mycobacterium tuberculosis. Nat Commun 7

    Google Scholar 

  91. Kurt T, Marbà-Ardébol AM, Turan Z, Neubauer P, Junne S, Meyer V (2018) Rocking Aspergillus: morphology-controlled cultivation of Aspergillus niger in a wave-mixed bioreactor for the production of secondary metabolites. Microb Cell Factories 17:128

    Google Scholar 

  92. Lin PJ, Scholz A, Krull R (2010) Effect of volumetric power input by aeration and agitation on pellet morphology and product formation of Aspergillus niger. Biochem Eng J 49:213–220

    CAS  Google Scholar 

  93. Gómez-Ríos D, Junne S, Neubauer P, Ochoa S, Ríos-Estepa R, Ramírez-Malule H (2019) Characterization of the metabolic response of Streptomyces clavuligerus to shear stress in stirred tanks and single-use 2D rocking motion bioreactors for clavulanic acid production. Antibiotics 8

    Google Scholar 

  94. Hardy N, Moreaud M, Guillaume D, Augier F, Nienow A, Béal C, Chaabane FB (2017) Advanced digital image analysis method dedicated to the characterization of the morphology of filamentous fungus. J Microsc 266:126–140

    CAS  PubMed  Google Scholar 

  95. Kuschel M, Siebler F, Takors R (2017) Lagrangian trajectories to predict the formation of population heterogeneity in large-scale bioreactors. Bioengineering 4:27

    PubMed Central  Google Scholar 

  96. Ladner T, Grünberger A, Probst C, Kohlheyer D, Büchs J, Delvigne F (2017) Application of mini- and micro-bioreactors for microbial bioprocesses. In: Current developments in biotechnology and bioengineering: bioprocesses, bioreactors and controls. Elsevier, Amsterdam, pp 433–461

    Google Scholar 

  97. Morchain J, Gabelle J-C, Cockx A (2013) Coupling of biokinetic and population balance models to account for biological heterogeneity in bioreactors. AICHE J 59:369–379

    CAS  Google Scholar 

  98. Pigou M, Morchain J (2015) Investigating the interactions between physical and biological heterogeneities in bioreactors using compartment, population balance and metabolic models. Chem Eng Sci 126:267–282

    CAS  Google Scholar 

  99. Lapin A, Müller D, Reuss M (2004) Dynamic behavior of microbial populations in stirred bioreactors simulated with Euler−Lagrange methods: traveling along the lifelines of single cells. Ind Eng Chem Res 43:4647–4656

    CAS  Google Scholar 

  100. Lapin A, Klann M, Reuss M (2010) Multi-scale spatio-temporal modeling: lifelines of microorganisms in bioreactors and tracking molecules in cells. Adv Biochem Eng Biotechnol 121:23–43

    CAS  PubMed  Google Scholar 

  101. Anane E, López DC, Neubauer P, Cruz Bournazou MN (2017) Modelling overflow metabolism in Escherichia coli by acetate cycling. Biochem Eng J 125:23–30

    CAS  Google Scholar 

  102. Lara AR, Taymaz-Nikerel H, Mashego MR, Van Gulik WM, Heijnen JJ, Ramirez OT, van Winden WA, Van Gulik WM, Heijnen JJ, Van Winden WA, Ramírez OT, van Winden WA (2009) Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses. Biotechnol Bioeng 104:1153–1161

    CAS  PubMed  Google Scholar 

  103. Soini J, Ukkonen K, Neubauer P (2011) Accumulation of amino acids deriving from pyruvate in Escherichia coli W3110 during fed-batch cultivation in a two-compartment scale-down bioreactor. Adv Biosci Biotechnol 02:336–339

    CAS  Google Scholar 

  104. Barz T, Sommer A, Wilms T, Neubauer P, Cruz Bournazou MN (2018) Adaptive optimal operation of a parallel robotic liquid handling station. IFAC-PapersOnLine 51:765–770

    Google Scholar 

  105. Lemoine A, Martnez-Iturralde NM, Spann R, Neubauer P, Junne S (2015) Response of Corynebacterium glutamicum exposed to oscillating cultivation conditions in a two- and a novel three-compartment scale-down bioreactor. Biotechnol Bioeng 112:1220–1231

    CAS  PubMed  Google Scholar 

  106. Korneli C, Bolten CJ, Godard T, Franco-Lara E, Wittmann C, Universita T (2012) Debottlenecking recombinant protein production in Bacillus megaterium under large-scale conditions—targeted precursor feeding designed from metabolomics. Biotechnol Bioeng 109:1538–1550

    CAS  PubMed  Google Scholar 

  107. Janakiraman V, Kwiatkowski C, Kshirsagar R, Ryll T, Huang YM (2015) Application of high-throughput mini-bioreactor system for systematic scale-down modeling, process characterization, and control strategy development. Biotechnol Prog 31:1623–1632

    CAS  PubMed  Google Scholar 

  108. Gábor A, Banga JR (2015) Robust and efficient parameter estimation in dynamic models of biological systems. BMC Syst Biol 9:74

    PubMed  PubMed Central  Google Scholar 

  109. Rollié S, Mangold M, Sundmacher K (2012) Designing biological systems: systems engineering meets synthetic biology. Chem Eng Sci 69:1–29

    Google Scholar 

  110. Bareither R, Pollard D (2011) A review of advanced small-scale parallel bioreactor technology for accelerated process development: current state and future need. Biotechnol Prog 27:2–14

    CAS  PubMed  Google Scholar 

  111. Rameez S, Mostafa SS, Miller C, Shukla AA (2014) High-throughput miniaturized bioreactors for cell culture process development: reproducibility, scalability, and control. Biotechnol Prog 30:718–727

    CAS  PubMed  Google Scholar 

  112. Herwig C, Garcia-Aponte OF, Golabgir A, Rathore AS (2015) Knowledge management in the QbD paradigm: manufacturing of biotech therapeutics. Trends Biotechnol 33:381–387

    CAS  PubMed  Google Scholar 

  113. Rathore AS (2009) Roadmap for implementation of quality by design (QbD) for biotechnology products. Trends Biotechnol 27:546–553

    CAS  PubMed  Google Scholar 

  114. Velez-Suberbie ML, Betts JPJ, Walker KL, Robinson C, Zoro B, Keshavarz-Moore E (2017) High-throughput automated microbial bioreactor system used for clone selection and rapid scale-down process optimization. Biotechnol Prog 15:1–11

    Google Scholar 

  115. de Lorenzo V, Schmidt M (2018) Biological standards for the knowledge-based BioEconomy: what is at stake. New Biotechnol 40:170–180

    Google Scholar 

  116. Schallmey M, Frunzke J, Eggeling L, Marienhagen J (2014) Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. Curr Opin Biotechnol 26:148–154

    CAS  PubMed  Google Scholar 

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Neubauer, P., Anane, E., Junne, S., Cruz Bournazou, M.N. (2020). Potential of Integrating Model-Based Design of Experiments Approaches and Process Analytical Technologies for Bioprocess Scale-Down. In: Herwig, C., Pörtner, R., Möller, J. (eds) Digital Twins. Advances in Biochemical Engineering/Biotechnology, vol 177. Springer, Cham. https://doi.org/10.1007/10_2020_154

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