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Müller DF, Wibbing D, Herwig C, Kager J. Simultaneous real-time estimation of maximum substrate uptake capacity and yield coefficient in induced microbial cultures. Comput Chem Eng 2023. [DOI: 10.1016/j.compchemeng.2023.108203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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2
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Liu P, Wang S, Li C, Zhuang Y, Xia J, Noorman H. Dynamic response of Aspergillus niger to periodical glucose pulse stimuli in chemostat cultures. Biotechnol Bioeng 2021; 118:2265-2282. [PMID: 33666237 DOI: 10.1002/bit.27739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 12/15/2022]
Abstract
In industrial large-scale bioreactors, microorganisms encounter heterogeneous substrate concentration conditions, which can impact growth or product formation. Here we carried out an extended (12 h) experiment of repeated glucose pulsing with a 10-min period to simulate fluctuating glucose concentrations with Aspergillus niger producing glucoamylase, and investigated its dynamic response by rapid sampling and quantitative metabolomics. The 10-min period represents worst-case conditions, as in industrial bioreactors the average cycling duration is usually in the order of 1 min. We found that cell growth and the glucoamylase productivity were not significantly affected, despite striking metabolomic dynamics. Periodical dynamic responses were found across all central carbon metabolism pathways, with different time scales, and the frequently reported ATP paradox was confirmed for this A. niger strain under the dynamic conditions. A thermodynamics analysis revealed that several reactions of the central carbon metabolism remained in equilibrium even under periodical dynamic conditions. The dynamic response profiles of the intracellular metabolites did not change during the pulse exposure, showing no significant adaptation of the strain to the more than 60 perturbation cycles applied. The apparent high tolerance of the glucoamylase producing A. niger strain for extreme variations in the glucose availability presents valuable information for the design of robust industrial microbial hosts.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands
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3
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Abstract
Pichia pastoris is one of the most important host organisms for the recombinant production of proteins in industrial biotechnology. A prominent promoter system for recombinant protein production in P. pastoris is the promoter of alcohol oxidase (PAOX1) which is induced by methanol, but repressed by several other carbon sources, like glucose and glycerol. Thus, typical cultivation strategies for such P. pastoris strains describe two different phases: growth on a carbon source, like glycerol, to get a high biomass concentration, followed by the induction of recombinant protein production by methanol. However, cells barely grow on methanol resulting in only moderate productivity in such bioprocesses. To enhance productivity, it is common to employ mixed substrate feeding strategies. The knowledge of certain strain-specific parameters is required to be able to set up such mixed feed fed-batch cultivations to avoid methanol accumulation and guarantee highest productivity. Here, we present an efficient strategy comprising only one experiment to determine the settings of such a mixed feed system based on the physiology of the respective yeast strain.
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Recombinant Escherichia coli cultivation in a pressurized airlift bioreactor: assessment of the influence of temperature on oxygen transfer and uptake rates. Bioprocess Biosyst Eng 2017; 40:1621-1633. [DOI: 10.1007/s00449-017-1818-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
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Wurm DJ, Marschall L, Sagmeister P, Herwig C, Spadiut O. Simple monitoring of cell leakiness and viability in Escherichia coli bioprocesses-A case study. Eng Life Sci 2017; 17:598-604. [PMID: 32624805 DOI: 10.1002/elsc.201600204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 09/16/2016] [Accepted: 12/07/2016] [Indexed: 11/10/2022] Open
Abstract
In a recently published study, we developed a simple methodology to monitor Escherichia coli cell integrity and lysis during bioreactor cultivations, where we intentionally triggered leakiness. In this follow-up study, we used this methodology, comprising the measurement of extracellular alkaline phosphatase to monitor leakiness and flow cytometry to follow viability, to investigate the effect of process parameters on a recombinant E. coli strain producing the highly valuable vascular endothelial growth factor A165 (VEGF-A165) in the periplasm. Since the amount of soluble product was very little (<500 μg/g dry cell weight), we directly linked the effect of the three process parameters temperature, specific uptake rate of the inducer arabinose and specific growth rate (μ) to cell integrity and viability. We found that a low temperature and a high μ were beneficial for cell integrity and that an elevated temperature resulted in reduced viability. We concluded that the recombinant E. coli cells producing VEGF-A165 in the periplasm should be cultivated at low temperature and high μ to reduce leakiness and guarantee high viability. Summarizing, in this follow-up study we demonstrate the usefulness of our simple methodology to monitor leakiness and viability of recombinant E. coli cells during bioreactor cultivations.
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Affiliation(s)
- David J Wurm
- Research Division Biochemical Engineering, Institute of Chemical Engineering Vienna University of Technology Vienna Austria
| | - Lukas Marschall
- Research Division Biochemical Engineering, Institute of Chemical Engineering Vienna University of Technology Vienna Austria
| | - Patrick Sagmeister
- Research Division Biochemical Engineering, Institute of Chemical Engineering Vienna University of Technology Vienna Austria
| | - Christoph Herwig
- Research Division Biochemical Engineering, Institute of Chemical Engineering Vienna University of Technology Vienna Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses Institute of Chemical Engineering Vienna University of Technology Vienna Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical Engineering Vienna University of Technology Vienna Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses Institute of Chemical Engineering Vienna University of Technology Vienna Austria
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Koch C, Posch AE, Herwig C, Lendl B. Comparison of Fiber Optic and Conduit Attenuated Total Reflection (ATR) Fourier Transform Infrared (FT-IR) Setup for In-Line Fermentation Monitoring. APPLIED SPECTROSCOPY 2016; 70:1965-1973. [PMID: 27864445 DOI: 10.1177/0003702816662618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 02/05/2016] [Indexed: 06/06/2023]
Abstract
The performance of a fiber optic and an optical conduit in-line attenuated total reflection mid-infrared (IR) probe during in situ monitoring of Penicillium chrysogenum fermentation were compared. The fiber optic probe was connected to a sealed, portable, Fourier transform infrared (FT-IR) process spectrometer via a plug-and-play interface. The optical conduit, on the other hand, was connected to a FT-IR process spectrometer via a knuckled probe with mirrors that had to be adjusted prior to each fermentation, which were purged with dry air. Penicillin V (PenV) and its precursor phenoxyacetic acid (POX) concentrations were determined by online high-performance liquid chromatography and the obtained concentrations were used as reference to build partial least squares regression models. Cross-validated root-mean-square errors of prediction were found to be 0.2 g L-1 (POX) and 0.19 g L-1 (PenV) for the fiber optic setup and 0.17 g L-1 (both POX and PenV) for the conduit setup. Higher noise-levels and spectrum-to-spectrum variations of the fiber optic setup lead to higher noise of estimated (i.e., unknown) POX and PenV concentrations than was found for the conduit setup. It seems that trade-off has to be made between ease of handling (fiber optic setup) and measurement accuracy (optical conduit setup) when choosing one of these systems for bioprocess monitoring.
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Affiliation(s)
- Cosima Koch
- Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Andreas E Posch
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Vienna, Austria
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Bernhard Lendl
- Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
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Steinwandter V, Zahel T, Sagmeister P, Herwig C. Propagation of measurement accuracy to biomass soft-sensor estimation and control quality. Anal Bioanal Chem 2016; 409:693-706. [PMID: 27376358 PMCID: PMC5233751 DOI: 10.1007/s00216-016-9711-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 12/04/2022]
Abstract
In biopharmaceutical process development and manufacturing, the online measurement of biomass and derived specific turnover rates is a central task to physiologically monitor and control the process. However, hard-type sensors such as dielectric spectroscopy, broth fluorescence, or permittivity measurement harbor various disadvantages. Therefore, soft-sensors, which use measurements of the off-gas stream and substrate feed to reconcile turnover rates and provide an online estimate of the biomass formation, are smart alternatives. For the reconciliation procedure, mass and energy balances are used together with accuracy estimations of measured conversion rates, which were so far arbitrarily chosen and static over the entire process. In this contribution, we present a novel strategy within the soft-sensor framework (named adaptive soft-sensor) to propagate uncertainties from measurements to conversion rates and demonstrate the benefits: For industrially relevant conditions, hereby the error of the resulting estimated biomass formation rate and specific substrate consumption rate could be decreased by 43 and 64 %, respectively, compared to traditional soft-sensor approaches. Moreover, we present a generic workflow to determine the required raw signal accuracy to obtain predefined accuracies of soft-sensor estimations. Thereby, appropriate measurement devices and maintenance intervals can be selected. Furthermore, using this workflow, we demonstrate that the estimation accuracy of the soft-sensor can be additionally and substantially increased.
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Affiliation(s)
| | | | | | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, Vienna, Austria.
- CD Laboratory on Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna University of Technology, Gumpendorferstrasse 1a, Vienna, Austria.
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Zahel T, Sagmeister P, Suchocki S, Herwig C. Accurate Information from Fermentation Processes - Optimal Rate Calculation by Dynamic Window Adaptation. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201500085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Meitz A, Sagmeister P, Lubitz W, Herwig C, Langemann T. Fed-Batch Production of Bacterial Ghosts Using Dielectric Spectroscopy for Dynamic Process Control. Microorganisms 2016; 4:microorganisms4020018. [PMID: 27681912 PMCID: PMC5029484 DOI: 10.3390/microorganisms4020018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/11/2016] [Accepted: 03/18/2016] [Indexed: 11/17/2022] Open
Abstract
The Bacterial Ghost (BG) platform technology evolved from a microbiological expression system incorporating the ϕX174 lysis gene E. E-lysis generates empty but structurally intact cell envelopes (BGs) from Gram-negative bacteria which have been suggested as candidate vaccines, immunotherapeutic agents or drug delivery vehicles. E-lysis is a highly dynamic and complex biological process that puts exceptional demands towards process understanding and control. The development of a both economic and robust fed-batch production process for BGs required a toolset capable of dealing with rapidly changing concentrations of viable biomass during the E-lysis phase. This challenge was addressed using a transfer function combining dielectric spectroscopy and soft-sensor based biomass estimation for monitoring the rapid decline of viable biomass during the E-lysis phase. The transfer function was implemented to a feed-controller, which followed the permittivity signal closely and was capable of maintaining a constant specific substrate uptake rate during lysis phase. With the described toolset, we were able to increase the yield of BG production processes by a factor of 8–10 when compared to currently used batch procedures reaching lysis efficiencies >98%. This provides elevated potentials for commercial application of the Bacterial Ghost platform technology.
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Affiliation(s)
- Andrea Meitz
- Research Center Pharmaceutical Engineering (RCPE) GmbH, Inffeldgasse 13, Graz A-8010, Austria.
| | - Patrick Sagmeister
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1A 166/4, Vienna A-1060, Austria.
| | - Werner Lubitz
- Biotech Innovation Research Development and Consulting (BIRD-C) GmbH & Co KG, Dr.-Bohr-Gasse 2-8, Vienna A-1030, Austria.
- Center of Molecular Biology, University of Vienna, Dr.-Bohr-Gasse 9, Vienna A-1030, Austria.
| | - Christoph Herwig
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1A 166/4, Vienna A-1060, Austria.
| | - Timo Langemann
- Research Center Pharmaceutical Engineering (RCPE) GmbH, Inffeldgasse 13, Graz A-8010, Austria.
- Biotech Innovation Research Development and Consulting (BIRD-C) GmbH & Co KG, Dr.-Bohr-Gasse 2-8, Vienna A-1030, Austria.
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Abstract
The methylotrophic yeast Pichia pastoris is a widely used host organism for recombinant protein production in biotechnology and pharmaceutical industry. However, if the target product describes a glycoprotein, an α-1,6-mannosyltransferase located in the Golgi apparatus of P. pastoris, called OCH1, triggers hypermannosylation of the recombinant protein which significantly impedes following unit operations and hampers biopharmaceutical product applications. A knockout of the och1 gene allows the production of less-glycosylated proteins-however, morphology and physiology of P. pastoris also change, complicating the upstream process. Here, we describe a controlled and efficient bioprocess based on the specific substrate uptake rate (q s) for a recombinant P. pastoris OCH1 knockout strain expressing a peroxidase as model protein.
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Ex situonline monitoring: application, challenges and opportunities for biopharmaceuticals processes. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.22] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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