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Huynh GT, Tunny SS, Frith JE, Meagher L, Corrie SR. Organosilica Nanosensors for Monitoring Spatiotemporal Changes in Oxygen Levels in Bacterial Cultures. ACS Sens 2024; 9:2383-2394. [PMID: 38687178 DOI: 10.1021/acssensors.3c02747] [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] [Indexed: 05/02/2024]
Abstract
Oxygen plays a central role in aerobic metabolism, and while many approaches have been developed to measure oxygen concentration in biological environments over time, monitoring spatiotemporal changes in dissolved oxygen levels remains challenging. To address this, we developed a ratiometric core-shell organosilica nanosensor for continuous, real-time optical monitoring of oxygen levels in biological environments. The nanosensors demonstrate good steady state characteristics (KpSV = 0.40 L/mg, R2 = 0.95) and respond reversibly to changes in oxygen concentration in buffered solutions and report similar oxygen level changes in response to bacterial cell growth (Escherichia coli) in comparison to a commercial bulk optode-based sensing film. We further demonstrated that the oxygen nanosensors could be distributed within a growing culture of E. coli and used to record oxygen levels over time and in different locations within a static culture, opening the possibility of spatiotemporal monitoring in complex biological systems.
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Affiliation(s)
- Gabriel T Huynh
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Manufacturing, Clayton, VIC 3168, Australia
| | - Salma S Tunny
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Jessica E Frith
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- ARC Training Centre for Cell and Tissue Engineering Technologies, Monash University, Clayton, VIC 3800, Australia
| | - Laurence Meagher
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- ARC Training Centre for Cell and Tissue Engineering Technologies, Monash University, Clayton, VIC 3800, Australia
| | - Simon R Corrie
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- ARC Training Centre for Cell and Tissue Engineering Technologies, Monash University, Clayton, VIC 3800, Australia
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Li W, McLeod D, Ketzenberger JT, Kowalik G, Russo R, Li Z, Kay MW, Entcheva E. High-throughput optical sensing of peri-cellular oxygen in cardiac cells: system characterization, calibration, and testing. Front Bioeng Biotechnol 2023; 11:1214493. [PMID: 37397961 PMCID: PMC10313526 DOI: 10.3389/fbioe.2023.1214493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a scalable experimental model relevant to human physiology. Oxygen consumption of hiPSC-CMs has not been studied in high-throughput (HT) format plates used in pre-clinical studies. Here, we provide comprehensive characterization and validation of a system for HT long-term optical measurements of peri-cellular oxygen in cardiac syncytia (human iPSC-CM and human cardiac fibroblasts), grown in glass-bottom 96-well plates. Laser-cut oxygen sensors having a ruthenium dye and an oxygen-insensitive reference dye were used. Ratiometric measurements (409 nm excitation) reflected dynamic changes in oxygen, as validated with simultaneous Clark electrode measurements. Emission ratios (653 nm vs. 510 nm) were calibrated for percent oxygen using two-point calibration. Time-dependent changes in the Stern-Volmer parameter, ksv, were observed during the initial 40-90 min of incubation, likely temperature-related. Effects of pH on oxygen measurements were negligible in the pH range of 4-8, with a small ratio reduction for pH > 10. Time-dependent calibration was implemented, and light exposure time was optimized (0.6-0.8 s) for oxygen measurements inside an incubator. Peri-cellular oxygen dropped to levels <5% within 3-10 h for densely-plated hiPSC-CMs in glass-bottom 96-well plates. After the initial oxygen decrease, samples either settled to low steady-state or exhibited intermittent peri-cellular oxygen dynamics. Cardiac fibroblasts showed slower oxygen depletion and higher steady-state levels without oscillations, compared to hiPSC-CMs. Overall, the system has great utility for long-term HT monitoring of peri-cellular oxygen dynamics in vitro for tracking cellular oxygen consumption, metabolic perturbations, and characterization of the maturation of hiPSC-CMs.
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Affiliation(s)
| | | | | | | | | | - Zhenyu Li
- Correspondence: Zhenyu Li, ; Matthew W. Kay, ; Emilia Entcheva,
| | - Matthew W. Kay
- Correspondence: Zhenyu Li, ; Matthew W. Kay, ; Emilia Entcheva,
| | - Emilia Entcheva
- Correspondence: Zhenyu Li, ; Matthew W. Kay, ; Emilia Entcheva,
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3
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Wang H, Chen D, Chen Y, Liu J, Xu J, Zhu A, Long F. Development of novel handheld optical fiber dissolved oxygen sensor and its applications. Anal Chim Acta 2022; 1200:339587. [DOI: 10.1016/j.aca.2022.339587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 11/01/2022]
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Wei L, Li W, Entcheva E, Li Z. Microfluidics-enabled 96-well perfusion system for high-throughput tissue engineering and long-term all-optical electrophysiology. LAB ON A CHIP 2020; 20:4031-4042. [PMID: 32996969 PMCID: PMC7680692 DOI: 10.1039/d0lc00615g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This work demonstrates a novel high-throughput (HT) microfluidics-enabled uninterrupted perfusion system (HT-μUPS) and validates its use with chronic all-optical electrophysiology in human excitable cells. HT-μUPS consists of a soft multichannel microfluidic plate cover which could button on a commercial HT 96-well plate. Herein, we demonstrate the manufacturing process of the system and its usages in acute and chronic all-optical electrophysiological studies of human induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CM) and engineered excitable (spiking HEK) cells. HT-μUPS perfusion maintained functional voltage and calcium responses in iPSC-CM and spiking HEK cells under spontaneous conditions and under optogenetic pacing. Long-term culture with HT-μUPS improved cell viability and optogenetically-tracked calcium responses in spiking HEK cells. The simplicity of this design and its compatibility with HT all-optical electrophysiology can empower cell-based assays for personalized medicine using patient-derived cells.
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Affiliation(s)
- Lai Wei
- Department of Biomedical Engineering, The George Washington University, Washington DC, USA
- These authors contributed equally: Lai Wei, Weizhen Li
| | - Weizhen Li
- Department of Biomedical Engineering, The George Washington University, Washington DC, USA
- These authors contributed equally: Lai Wei, Weizhen Li
| | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, Washington DC, USA
- ,
| | - Zhenyu Li
- Department of Biomedical Engineering, The George Washington University, Washington DC, USA
- ,
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Ladner T, Flitsch D, Lukacs M, Sieben M, Büchs J. Combined dissolved oxygen tension and online viscosity measurements in shake flask cultivations via infrared fluorescent oxygen-sensitive nanoparticles. Biotechnol Bioeng 2019; 116:3215-3227. [PMID: 31429921 DOI: 10.1002/bit.27145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/07/2019] [Accepted: 08/15/2019] [Indexed: 11/05/2022]
Abstract
Oxygen supply is one of the most critical process parameters in aerobic cultivations. To assure sufficient oxygen supply, shake flasks are usually used in combination with orbital shaking machines. In this study, a measurement technique for the dissolved oxygen tension (DOT) in shake flask cultures with viscosity changes is presented. The movement of the shaker table is monitored by means of a Hall effect sensor. For DOT measurements, infrared fluorescent oxygen-sensitive nanoparticles are added to the culture broth. The position of the rotating bulk liquid needs to be determined to assure measurements inside the liquid. The leading edge of the bulk liquid is detected based on the fluorescence signal intensity of the oxygen-sensitive nanoparticles. Furthermore, online information about the viscosity of the culture broth is acquired due to the detection of the position of the leading edge of the bulk liquid relative to the direction of the centrifugal force, as described by Sieben et al. (2019. Sci. Rep., 9, 8335). The DOT measurement is combined with a respiration activity monitoring system which allows for the determination of the oxygen transfer rate (OTR) in eight parallel shake flasks. Based on DOT and OTR, the volumetric oxygen transfer coefficient (kL a) is calculated during cultivation. The new system was successfully applied in cultivations of Escherichia coli, Bacillus licheniformis, and Xanthomonas campestris.
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Affiliation(s)
- Tobias Ladner
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - David Flitsch
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Mihaly Lukacs
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Michaela Sieben
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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Hemmerich J, Noack S, Wiechert W, Oldiges M. Microbioreactor Systems for Accelerated Bioprocess Development. Biotechnol J 2018; 13:e1700141. [PMID: 29283217 DOI: 10.1002/biot.201700141] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Indexed: 12/14/2022]
Abstract
In recent years, microbioreactor (MBR) systems have evolved towards versatile bioprocess engineering tools. They provide a unique solution to combine higher experimental throughput with extensive bioprocess monitoring and control, which is indispensable to develop economically and ecologically competitive bioproduction processes. MBR systems are based either on down-scaled stirred tank reactors or on advanced shaken microtiter plate cultivation devices. Importantly, MBR systems make use of optical measurements for non-invasive, online monitoring of important process variables like biomass concentration, dissolved oxygen, pH, and fluorescence. The application range of MBR systems can be further increased by integration into liquid handling robots, enabling automatization and, thus standardization, of various handling and operation procedures. Finally, the tight integration of quantitative strain phenotyping with bioprocess development under industrially relevant conditions greatly increases the probability of finding the right combination of producer strain and bioprocess control strategy. This review will discuss the current state of the art in the field of MBR systems and we can readily conclude that their importance for industrial biotechnology will further increase in the near future.
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Affiliation(s)
- Johannes Hemmerich
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- RWTH Aachen University, Computational Systems Biotechnology (AVT.CSB), Forckenbeckstraße 51, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,RWTH Aachen University, Institute of Biotechnology, Worringer Weg 3, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
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Glauche F, Glazyrina J, Cruz Bournazou MN, Kiesewetter G, Cuda F, Goelling D, Raab A, Lang C, Neubauer P. Detection of growth rate-dependent product formation in miniaturized parallel fed-batch cultivations. Eng Life Sci 2017; 17:1215-1220. [PMID: 32624749 PMCID: PMC6999230 DOI: 10.1002/elsc.201600029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 04/28/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022] Open
Abstract
Saccharomyces cerevisiae is a popular expression system for recombinant proteins. In most cases, production processes are performed as carbon-limited fed-batch cultures to avoid aerobic ethanol formation. Especially for constitutive expression systems, the specific product formation rate depends on the specific growth rate. The development of optimal feeding strategies strongly depends on laboratory-scale cultivations, which are time and resource consuming, especially when continuous experiments are carried out. It is therefore beneficial for accelerated process development to look at alternatives. In this study, S. cerevisiae AH22 secreting a heterologous endo-polygalacturonase (EPG) was characterized in microwell plates with an enzyme-based fed-batch medium. Through variation of the glucose release rate, different growth profiles were established and the impact on EPG secretion was analyzed. Product formation rates of 200-400 U (gx h)-1 were determined. As a reference, bioreactor experiments using the change-stat cultivation technique were performed. The growth-dependent product formation was analyzed over dilution rates of D = 0.01-0.35 with smooth change of D at a rate of 0.003 h-2. EPG production was found to be comparable with a qp of 400 U (gx h)-1 at D = 0.27 h-1. The presented results indicate that parallel miniaturized fed-batch cultures can be applied to determine product formation profiles of putative production strains. With further automation and parallelization of the concept, strain characterization can be performed in shorter time.
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Affiliation(s)
- Florian Glauche
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | - Julia Glazyrina
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | - Fabian Cuda
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | | | - Peter Neubauer
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
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Herold S, Krämer D, Violet N, King R. Rapid process synthesis supported by a unified modular software framework. Eng Life Sci 2017; 17:1202-1214. [PMID: 32624748 DOI: 10.1002/elsc.201600020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 10/12/2016] [Accepted: 01/05/2017] [Indexed: 11/11/2022] Open
Abstract
Although known to be very powerful, the widespread application of model-based techniques is still significantly hampered in the area of bio-processes. Reasons for this situation can be found along the whole chain to set up and implement such approaches. In a time-consuming step, models are typically hand-crafted. Whether alternatives of better models exist to actually fulfill the final goals is undocumented, most often even unknown. In a next step, model-based process control methods are hand-coded in an error-prone procedure. For many of these methods given in the literature, only simulation studies are shown, leaving the interested reader with the unanswered question whether the implementation of a specific method in a real process is viable. As the potentially time-consuming implementation of such a method presents a risk for a rapid process development, promising candidates may be overlooked. To remediate this unsatisfactory situation, a combination of theoretical methods and information technology is proposed here. By an exemplarily realized software tool, it is shown how such an environment helps to promote model-based optimization, supervision, and control of bio-processes and allows for an inexpensive test of new ideas as well in real-life experiments. The contribution concentrates on an overview of a possible software architecture with respect to necessary methods and a meaningful information strategy, highlighting some of the more crucial building blocks. Experimental results exploiting parts of the proposed methods are given for a yeast strain synthesizing a product of industrial interest.
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Affiliation(s)
- Sebastian Herold
- Chair of Measurement and Control Technische Universität Berlin Berlin Germany
| | - Dominik Krämer
- Chair of Measurement and Control Technische Universität Berlin Berlin Germany
| | - Norman Violet
- Department Experimental Toxicology and ZEBET Federal Institute for Risk Assessment Berlin Germany
| | - Rudibert King
- Chair of Measurement and Control Technische Universität Berlin Berlin Germany
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9
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Krause M, Neubauer A, Neubauer P. The fed-batch principle for the molecular biology lab: controlled nutrient diets in ready-made media improve production of recombinant proteins in Escherichia coli. Microb Cell Fact 2016; 15:110. [PMID: 27317421 PMCID: PMC4912726 DOI: 10.1186/s12934-016-0513-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022] Open
Abstract
While the nutrient limited fed-batch technology is the standard of the cultivation of microorganisms and production of heterologous proteins in industry, despite its advantages in view of metabolic control and high cell density growth, shaken batch cultures are still the standard for protein production and expression screening in molecular biology and biochemistry laboratories. This is due to the difficulty and expenses to apply a controlled continuous glucose feed to shaken cultures. New ready-made growth media, e.g. by biocatalytic release of glucose from a polymer, offer a simple solution for the application of the fed-batch principle in shaken plate and flask cultures. Their wider use has shown that the controlled diet not only provides a solution to obtain significantly higher cell yields, but also in many cases folding of the target protein is improved by the applied lower growth rates; i.e. final volumetric yields for the active protein can be a multiple of what is obtained in complex medium cultures. The combination of the conventional optimization approaches with new and easy applicable growth systems has revolutionized recombinant protein production in Escherichia coli in view of product yield, culture robustness as well as significantly increased cell densities. This technical development establishes the basis for successful miniaturization and parallelization which is now an important tool for synthetic biology and protein engineering approaches. This review provides an overview of the recent developments, results and applications of advanced growth systems which use a controlled glucose release as substrate supply.
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Affiliation(s)
- Mirja Krause
- />Laboratory of Bioprocess Engineering, Department of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK 24, 13355 Berlin, Germany
- />Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 5A, 90220 Oulu, Finland
| | | | - Peter Neubauer
- />Laboratory of Bioprocess Engineering, Department of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK 24, 13355 Berlin, Germany
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10
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Affiliation(s)
- Xianting Ding
- School of Biomedical Engineering, Institute for Personalized Medicine, Shanghai Jiao Tong University, Med-X Research Institute, Shanghai, China
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11
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Demuth C, Varonier J, Jossen V, Eibl R, Eibl D. Novel probes for pH and dissolved oxygen measurements in cultivations from millilitre to benchtop scale. Appl Microbiol Biotechnol 2016; 100:3853-63. [DOI: 10.1007/s00253-016-7412-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/31/2022]
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