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Rydal T, Frandsen J, Nadal-Rey G, Albæk MO, Ramin P. Bringing a scalable adaptive hybrid modeling framework closer to industrial use: Application on a multiscale fungal fermentation. Biotechnol Bioeng 2024; 121:1609-1625. [PMID: 38454575 DOI: 10.1002/bit.28670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024]
Abstract
Digitalization has paved the way for new paradigms such as digital shadows and digital twins for fermentation processes, opening the door for real-time process monitoring, control, and optimization. With a digital shadow, real-time model adaptation to accommodate complex metabolic phenomena such as metabolic shifts of a process can be monitored. Despite the many benefits of digitalization, the potential has not been fully reached in the industry. This study investigates the development of a digital shadow for a very complex fungal fermentation process in terms of microbial physiology and fermentation operation on pilot-scale at Novonesis and the challenges thereof. The process has historically been difficult to optimize and control due to a lack of offline measurements and an absence of biomass measurements. Pilot-scale and lab-scale fermentations were conducted for model development and validation. With all available pilot-scale data, a data-driven soft sensor was developed to estimate the main substrate concentration (glucose) with a normalized root mean squared error (N-RMSE) of 2%. This robust data-driven soft sensor was able to estimate accurately in lab-scale (volume < 20× pilot) with a N-RMSE of 7.8%. A hybrid soft sensor was developed by combining the data-driven soft sensor with a mass balance to estimate the glycerol and biomass concentrations on pilot-scale data with N-RMSEs of 11% and 21%, respectively. A digital shadow modeling framework was developed by coupling a mechanistic model (MM) with the hybrid soft sensor. The digital shadow modeling framework significantly improved the predictability compared with the MM. The contribution of this study brings the application of digital shadows closer to industrial implementation. It demonstrates the high potential of using this type of modeling framework for scale-up and leads the way to a new generation of in silico-based process development.
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Affiliation(s)
- Thomas Rydal
- Fermentation Pilot Plant, Novonesis A/S, Bagsværd, Denmark
| | - Jesper Frandsen
- Department of Chemical and Biochemical Engineering, Process and Systems Engineering Centre (PROSYS), Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Pedram Ramin
- Department of Chemical and Biochemical Engineering, Process and Systems Engineering Centre (PROSYS), Technical University of Denmark, Kongens Lyngby, Denmark
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2
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Modeling of Bioprocesses via MINLP-based Symbolic Regression of S-system Formalisms. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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3
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A general deep hybrid model for bioreactor systems: Combining first principles with deep neural networks. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Urniezius R, Kemesis B, Simutis R. Bridging Offline Functional Model Carrying Aging-Specific Growth Rate Information and Recombinant Protein Expression: Entropic Extension of Akaike Information Criterion. ENTROPY 2021; 23:e23081057. [PMID: 34441197 PMCID: PMC8393800 DOI: 10.3390/e23081057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/03/2022]
Abstract
This study presents a mathematical model of recombinant protein expression, including its development, selection, and fitting results based on seventy fed-batch cultivation experiments from two independent biopharmaceutical sites. To resolve the overfitting feature of the Akaike information criterion, we proposed an entropic extension, which behaves asymptotically like the classical criteria. Estimation of recombinant protein concentration was performed with pseudo-global optimization processes while processing offline recombinant protein concentration samples. We show that functional models including the average age of the cells and the specific growth at induction or the start of product biosynthesis are the best descriptors for datasets. We also proposed introducing a tuning coefficient that would force the modified Akaike information criterion to avoid overfitting when the designer requires fewer model parameters. We expect that a lower number of coefficients would allow the efficient maximization of target microbial products in the upstream section of contract development and manufacturing organization services in the future. Experimental model fitting was accomplished simultaneously for 46 experiments at the first site and 24 fed-batch experiments at the second site. Both locations contained 196 and 131 protein samples, thus giving a total of 327 target product concentration samples derived from the bioreactor medium.
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Fuzzy Logic-Based Adaptive Control of Specific Growth Rate in Fed-Batch Biotechnological Processes. A Simulation Study. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article presents the development and application of a distinct adaptive control algorithm that is based on fuzzy logic and was used to control the specific growth rate (SGR) in a fed-batch biotechnological process. The developed control algorithm was compared with two adaptive control systems that were based on a model-free adaptive technique and gain scheduling technique. A typical mathematical model of recombinant Escherichia coli fed-batch cultivation process was selected to evaluate the performance of the fuzzy-based control algorithm. The investigated control techniques performed similarly when considering the whole process duration. The adaptive PI controller with fuzzy-based parameter adaptation demonstrated advantages over the previously mentioned algorithms—especially when compensating the deviations of the SGR. These deviations usually occur when the equipment malfunctions or process disturbances take place. The fuzzy-based control system was stable within the investigated ranges. It was determined that, regarding control quality, the investigated control algorithms are suited to control the SGR in a fed-batch biotechnological process. However, substrate feeding rate manipulation and limitation needs to be used. Taking into account the time needed to design and tune the controller, the developed controller is suitable for practical applications when expert knowledge is available. The proposed algorithm can be further adapted and developed to control the SGR in other cell cultivations while running the process under substrate limitation conditions.
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Urniezius R, Survyla A. Identification of Functional Bioprocess Model for Recombinant E. Coli Cultivation Process. ENTROPY 2019. [PMCID: PMC7514566 DOI: 10.3390/e21121221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The purpose of this study is to introduce an improved Luedeking–Piret model that represents a structurally simple biomass concentration approach. The developed routine provides acceptable accuracy when fitting experimental data that incorporate the target protein concentration of Escherichia coli culture BL21 (DE3) pET28a in fed-batch processes. This paper presents system identification, biomass, and product parameter fitting routines, starting from their roots of origin to the entropy-related development, characterized by robustness and simplicity. A single tuning coefficient allows for the selection of an optimization criterion that serves equally well for higher and lower biomass concentrations. The idea of the paper is to demonstrate that the use of fundamental knowledge can make the general model more common for technological use compared to a sophisticated artificial neural network. Experimental validation of the proposed model involved data analysis of six cultivation experiments compared to 19 experiments used for model fitting and parameter estimation.
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7
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Adaptive Control of Biomass Specific Growth Rate in Fed-Batch Biotechnological Processes. A Comparative Study. Processes (Basel) 2019. [DOI: 10.3390/pr7110810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This article presents a comparative study on the development and application of two distinct adaptive control algorithms for biomass specific growth rate control in fed-batch biotechnological processes. A typical fed-batch process using Escherichia coli for recombinant protein production was selected for this research. Numerical simulation results show that both developed controllers, an adaptive PI controller based on the gain scheduling technique and a model-free adaptive controller based on the artificial neural network, delivered a comparable control performance and are suitable for application when using the substrate limitation approach and substrate feeding rate manipulation. The controller performance was tested within the realistic ranges of the feedback signal sampling intervals and measurement noise intensities. Considering the efforts for controller design and tuning, including development of the adaptation/learning algorithms, the model-free adaptive control algorithm proves to be more attractive for industrial applications, especially when only limited knowledge of the process and its mathematical model is available. The investigated model-free adaptive controller also tended to deliver better control quality under low specific growth rate conditions that prevail during the recombinant protein production phase. In the investigated simulation runs, the average tracking error did not exceed 0.01 (1/h). The temporary overshoots caused by the maximal disturbances stayed within the range of 0.025–0.11 (1/h). Application of the algorithm can be further extended to specific growth rate control in other bacterial and mammalian cell cultivations that run under substrate limitation conditions.
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Practical Solutions for Specific Growth Rate Control Systems in Industrial Bioreactors. Processes (Basel) 2019. [DOI: 10.3390/pr7100693] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This contribution discusses the main challenges related to successful application of automatic control systems used to control specific growth rate in industrial biotechnological processes. It is emphasized that, after the implementation of basic automatic control systems, primary attention shall be paid to the specific growth rate control systems because this process variable critically affects the physiological state of microbial cultures and the formation of the desired product. Therefore, control of the specific growth rate enables improvement of the quality and reproducibility of the biotechnological processes. The main requirements have been formulated that shall be met to successfully implement the specific growth rate control systems in industrial bioreactors. The relatively easy-to-implement schemes of specific growth rate control systems have been reviewed and discussed. The recommendations for selection of particular control systems for specific biotechnological processes have been provided.
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Pinto J, de Azevedo CR, Oliveira R, von Stosch M. A bootstrap-aggregated hybrid semi-parametric modeling framework for bioprocess development. Bioprocess Biosyst Eng 2019; 42:1853-1865. [DOI: 10.1007/s00449-019-02181-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/23/2019] [Indexed: 12/01/2022]
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von Stosch M, Hamelink JM, Oliveira R. Toward intensifying design of experiments in upstream bioprocess development: An industrialEscherichia colifeasibility study. Biotechnol Prog 2016; 32:1343-1352. [DOI: 10.1002/btpr.2295] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/16/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Moritz von Stosch
- CEAM, Faculty of Science, Agriculture and Engineering; Newcastle University; Newcastle upon Tyne NE1 7RU UK
- REQUIMTE/DQ, Faculty of Science and Technology; University Nova De Lisboa; Campus De Caparica Caparica 2829-516 Portugal
| | | | - Rui Oliveira
- REQUIMTE/DQ, Faculty of Science and Technology; University Nova De Lisboa; Campus De Caparica Caparica 2829-516 Portugal
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Schaepe S, Levisauskas D, Simutis R, Lübbert A. Data-based optimization of protein production processes. Biotechnol Lett 2014; 36:929-35. [PMID: 24557076 DOI: 10.1007/s10529-013-1448-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/23/2013] [Indexed: 11/30/2022]
Abstract
While data-based modeling is possible in various ways, data-based optimization has not been previously described. Here we present such an optimization technique. It is based on dynamic programming principles and uses data directly from exploratory experiments where the influence of the adjustable variables u were tested at various values. Instead of formulating the performance index J as a function of time t within a cultivation process it is formulated as a function of the biomass x. The advantage of this representation is that in most biochemical production processes J(x) only depends of the vector u of the adjustable variables. This given, mathematical programming techniques allow determining the desired optimal paths u(opt)(x) from the x-derivatives of J(x). The resulting u(opt)(x) can easily be transformed back to the u(t) profiles that can then be used in an improved fermentation run. The optimization technique can easily be explained graphically. With numerical experiments the feasibility of the method is demonstrated. Then, two optimization runs for recombinant protein formations in E. coli are discussed and experimental validation results are presented.
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Affiliation(s)
- Sebastian Schaepe
- Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120, Halle (Saale), Germany,
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Cherdkiatikul T, Suwanwong Y. Production of the α and β Subunits of Spirulina Allophycocyanin and C-Phycocyanin in Escherichia coli : A Comparative Study of Their Antioxidant Activities. ACTA ACUST UNITED AC 2014; 19:959-65. [PMID: 24464435 DOI: 10.1177/1087057113520565] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/28/2013] [Indexed: 12/31/2022]
Abstract
Allophycocyanin and c-phycocyanin have been reported to be potent antioxidants. In this work, the genes encoding the apo-proteins of allophycocyanin α (ApcA), allophycocyanin β (ApcB), c-phycocyanin α (CpcA), and c-phycocyanin β (CpcB) from Spirulina platensis were cloned, and the recombinant proteins were produced in Escherichia coli to study their antioxidant effects. All four recombinant phycocyanins could be produced in the soluble form and purified to more than 97% purity. The results of radical scavenging assays showed that the Trolox equivalent values for peroxyl radical scavenging by the ApcA, ApcB, CpcA, and CpcB proteins were 1.81 ± 0.2 µM, 1.98 ± 0.22 µM, 0.95 ± 0.15 µM, and 1.49 ± 0.15 µM, respectively. The IC50 values for hydroxyl radical scavenging of ApcA, ApcB, CpcA, CpcB, and Trolox were 269 ± 9 µg/mL, 190 ± 5 µg/mL, 129 ± 8 µg/mL, 108 ± 4 µg/mL, and 195 ± 12 µg/mL, respectively. These results indicated that allophycocyanin exhibited higher activity than c-phycocyanin in scavenging peroxyl radicals, whereas c-phycocyanin exhibited higher activity than allophycocyanin in scavenging hydroxyl radicals. All of the apo-phycocyanin subunits possessed strong antioxidant activities and can be further developed and applied to the food and drug industries. However, the selection of the most useful antioxidant should depend on the type of targeted free radical to obtain the highest efficiency.
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Affiliation(s)
- Thiti Cherdkiatikul
- Graduate Program of Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Yaneenart Suwanwong
- Center for Research and Development in Molecular Hematology Sciences, Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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Galvanauskas V, Grigs O, Vanags J, Dubencovs K, Stepanova V. Model-based optimization and pO2control of fed-batchEscherichia coliandSaccharomyces cerevisiaecultivation processes. Eng Life Sci 2012. [DOI: 10.1002/elsc.201200012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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14
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Yan X, Hu S, Guan YX, Yao SJ. Coexpression of chaperonin GroEL/GroES markedly enhanced soluble and functional expression of recombinant human interferon-gamma in Escherichia coli. Appl Microbiol Biotechnol 2011; 93:1065-74. [DOI: 10.1007/s00253-011-3599-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/25/2011] [Accepted: 09/20/2011] [Indexed: 11/29/2022]
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15
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Schaepe S, Kuprijanov A, Aehle M, Simutis R, Lübbert A. Simple control of fed-batch processes for recombinant protein production with E. coli. Biotechnol Lett 2011; 33:1781-8. [DOI: 10.1007/s10529-011-0648-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 05/17/2011] [Indexed: 11/29/2022]
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16
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Gnoth S, Simutis R, Lübbert A. Fermentation process supervision and strategies for fail-safe operation: A practical approach. Eng Life Sci 2011. [DOI: 10.1002/elsc.201000114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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17
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Aehle M, Kuprijanov A, Schaepe S, Simutis R, Lübbert A. Increasing batch-to-batch reproducibility of CHO cultures by robust open-loop control. Cytotechnology 2010; 63:41-7. [PMID: 21057872 DOI: 10.1007/s10616-010-9320-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022] Open
Abstract
In order to guarantee the quality of recombinant therapeutic proteins produced in mammalian cell systems, the straightforward approach in industry is to run the processes as reproducible as possible. It is first shown that considerable distortions in the currently operated processes appear when the initial cell density deviates from its nominal value. Small deviations in the initial cell mass may lead to severe deviations from the desired biomass trajectory. Next, it is shown how to design a fed-batch production process in such a way that it is robust with respect to variations in the viable cell density. A simple open loop strategy is proposed for that purpose. Here we show for the first time at animal cell cultures (CHO cells) that by means of an appropriate glutamine feed rate profile F(t), which keeps the specific growth rate of the cells on a predefined value below its maximal value while maintaining the viabilities on a high level, the diverging viable cell count profiles change over into a robust converging set of profiles. The CHO cells used to validate the procedure could be focused to any specific growth rates below μ(max).
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Affiliation(s)
- M Aehle
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120, Halle (Saale), Germany
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