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Lou C, Yang H, Hou Y, Huang H, Qiu J, Wang C, Sang Y, Liu H, Han L. Microfluidic Platforms for Real-Time In Situ Monitoring of Biomarkers for Cellular Processes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307051. [PMID: 37844125 DOI: 10.1002/adma.202307051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/05/2023] [Indexed: 10/18/2023]
Abstract
Cellular processes are mechanisms carried out at the cellular level that are aimed at guaranteeing the stability of the organism they comprise. The investigation of cellular processes is key to understanding cell fate, understanding pathogenic mechanisms, and developing new therapeutic technologies. Microfluidic platforms are thought to be the most powerful tools among all methodologies for investigating cellular processes because they can integrate almost all types of the existing intracellular and extracellular biomarker-sensing methods and observation approaches for cell behavior, combined with precisely controlled cell culture, manipulation, stimulation, and analysis. Most importantly, microfluidic platforms can realize real-time in situ detection of secreted proteins, exosomes, and other biomarkers produced during cell physiological processes, thereby providing the possibility to draw the whole picture for a cellular process. Owing to their advantages of high throughput, low sample consumption, and precise cell control, microfluidic platforms with real-time in situ monitoring characteristics are widely being used in cell analysis, disease diagnosis, pharmaceutical research, and biological production. This review focuses on the basic concepts, recent progress, and application prospects of microfluidic platforms for real-time in situ monitoring of biomarkers in cellular processes.
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Affiliation(s)
- Chengming Lou
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Hongru Yang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Ying Hou
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Haina Huang
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Jichuan Qiu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Chunhua Wang
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Yuanhua Sang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Hong Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
- Institute for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, 250022, P. R. China
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266000, P. R. China
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Wulandari DA, Tsuru K, Minamihata K, Wakabayashi R, Goto M, Kamiya N. A Functional Hydrogel Bead-Based High-Throughput Screening System for Mammalian Cells with Enhanced Secretion of Therapeutic Antibodies. ACS Biomater Sci Eng 2024; 10:628-636. [PMID: 38048166 DOI: 10.1021/acsbiomaterials.3c01386] [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: 12/06/2023]
Abstract
Droplet-based high-throughput screening systems are an emerging technology that provides a quick test to screen millions of cells with distinctive characteristics. Biopharmaceuticals, specifically therapeutic proteins, are produced by culturing cells that secrete heterologous recombinant proteins with different populations and expression levels; therefore, a technology to discriminate cells that produce more target proteins is needed. Here, we present a droplet-based microfluidic strategy for encapsulating, screening, and selecting target cells with redox-responsive hydrogel beads (HBs). As a proof-of-concept study, we demonstrate the enrichment of hybridoma cells with enhanced capability of antibody secretion using horseradish peroxidase (HRP)-catalyzed hydrogelation of tetra-thiolate poly(ethylene glycol); hybridoma cells were encapsulated in disulfide-bonded HBs. Recombinant protein G or protein M with a C-terminal cysteine residue was installed in the HBs via disulfide bonding to capture antibodies secreted from the cells. HBs were fluorescently stained by adding the protein L-HRP conjugate using a tyramide signal amplification system. HBs were then separated by fluorescence-activated droplet sorting and degraded by reducing the disulfide bonds to recover the target cells. Finally, we succeeded in the selection of hybridoma cells with enhanced antibody secretion, indicating the potential of this system in the therapeutic protein production.
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Affiliation(s)
- Diah Anggraini Wulandari
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kyosuke Tsuru
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division of Biotechnology, Centre for Future Chemistry, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division of Biotechnology, Centre for Future Chemistry, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
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Ochoa A, Gastélum G, Rocha J, Olguin LF. High-throughput bacterial co-encapsulation in microfluidic gel beads for discovery of antibiotic-producing strains. Analyst 2023; 148:5762-5774. [PMID: 37843562 DOI: 10.1039/d3an01101a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Bacteria with antagonistic activity inhibit the growth of other bacteria through different mechanisms, including the production of antibiotics. As a result, these microorganisms are a prolific source of such compounds. However, searching for antibiotic-producing strains requires high-throughput techniques due to the vast diversity of microorganisms. Here, we screened and isolated bacteria with antagonistic activity against Escherichia coli expressing the green fluorescent protein (E. coli-GFP). We used microfluidics to co-encapsulate and co-culture single cells from different strains within picoliter gel beads and analyzed them using fluorescence-activated cell sorting (FACS). To test the methodology, we used three bacterial isolates obtained from Mexican maize, which exhibit high, moderate, or no antagonistic activity against E. coli-GFP, as determined previously using agar plate assays. Single cells from each strain were separately co-incubated into gel beads with E. coli-GFP. We monitored the development of the maize bacteria microcolonies and tracked the growth or inhibition of E. coli-GFP using bright-field and fluorescent microscopy. We correlated these images with distinctive light scatter and fluorescence signatures of each incubated bead type using FACS. This analysis enabled us to sort gel beads filled with an antagonistic strain, starting from a mixture of the three different types of maize bacteria and E. coli-GFP. Likewise, culturing the FACS-sorted beads on agar plates confirmed the isolation and recovery of the two antagonistic strains. In addition, enrichment assays demonstrated the methodology's effectiveness in isolating rare antibiotic-producer strains (0.01% abundance) present in a mixture of microorganisms. These results show that associating light side scatter and fluorescent flow cytometry signals with microscopy images provides valuable controls to establish successful high-throughput methods for sorting beads in which microbial interaction assays are performed.
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Affiliation(s)
- Abraham Ochoa
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Coyoacán, CDMX 04510, Mexico.
| | - Gabriela Gastélum
- Unidad Regional Hidalgo, Centro de Investigación en Alimentación y Desarrollo A.C., San Agustín Tlaxiaca, Hidalgo 42163, Mexico
| | - Jorge Rocha
- Unidad Regional Hidalgo, Centro de Investigación en Alimentación y Desarrollo A.C., San Agustín Tlaxiaca, Hidalgo 42163, Mexico
- Programa de Agricultura en Zonas Áridas, Centro de Investigaciones Biológicas del Noroeste, La Paz, B.C.S. 23096, Mexico
| | - Luis F Olguin
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Coyoacán, CDMX 04510, Mexico.
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Ito Y, Sasaki R, Asari S, Yasuda T, Ueda H, Kitaguchi T. Efficient Microfluidic Screening Method Using a Fluorescent Immunosensor for Recombinant Protein Secretions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207943. [PMID: 37093208 DOI: 10.1002/smll.202207943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Microbial secretory protein expression is widely used for biopharmaceutical protein production. However, establishing genetically modified industrial strains that secrete large amounts of a protein of interest is time-consuming. In this study, a simple and versatile high-throughput screening method for protein-secreting bacterial strains is developed. Different genotype variants induced by mutagens are encapsulated in microemulsions and cultured to secrete proteins inside the emulsions. The secreted protein of interest is detected as a fluorescence signal by the fluorescent immunosensor quenchbody (Q-body), and a cell sorter is used to select emulsions containing improved protein-secreting strains based on the fluorescence intensity. The concept of the screening method is demonstrated by culturing Corynebacterium glutamicum in emulsions and detecting the secreted proteins. Finally, productive strains of fibroblast growth factor 9 (FGF9) are screened, and the FGF9 secretion increased threefold compared to that of parent strain. This screening method can be applied to a wide range of proteins by fusing a small detection tag. This is a highly simple process that requires only the addition of a Q-body to the medium and does not require the addition of any substrates or chemical treatments. Furthermore, this method shortens the development period of industrial strains for biopharmaceutical protein production.
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Affiliation(s)
- Yoshihiro Ito
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Ryuichi Sasaki
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Sayaka Asari
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Takanobu Yasuda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
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5
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
| | | | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K.
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Kim KJ, Lee SJ, Kim DM. The Use of Cell-free Protein Synthesis to Push the Boundaries of Synthetic Biology. BIOTECHNOL BIOPROC E 2023; 28:1-7. [PMID: 36687336 PMCID: PMC9840425 DOI: 10.1007/s12257-022-0279-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/10/2022] [Accepted: 10/23/2022] [Indexed: 01/15/2023]
Abstract
Cell-free protein synthesis is emerging as a powerful tool to accelerate the progress of synthetic biology. Notably, cell-free systems that harness extracted synthetic machinery of cells can address many of the issues associated with the complexity and variability of living systems. In particular, cell-free systems can be programmed with various configurations of genetic information, providing great flexibility and accessibility to the field of synthetic biology. Empowered by recent progress, cell-free systems are now evolving into artificial biological systems that can be tailored for various applications, including on-demand biomanufacturing, diagnostics, and new materials design. Here, we review the key developments related to cell-free protein synthesis systems, and discuss the future directions of these promising technologies.
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Affiliation(s)
- Kyu Jae Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134 Korea
| | - So-Jeong Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134 Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134 Korea
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Loughran ST, Walls D. Tagging Recombinant Proteins to Enhance Solubility and Aid Purification. Methods Mol Biol 2023; 2699:97-123. [PMID: 37646996 DOI: 10.1007/978-1-0716-3362-5_7] [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: 09/01/2023]
Abstract
Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has a long history, and there is a considerable repertoire of these that can be used to address issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. In this chapter, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.
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Affiliation(s)
- Sinéad T Loughran
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Louth, Ireland.
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Dublin, Ireland
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Pan Y, Yang J, Wu J, Yang L, Fang H. Current advances of Pichia pastoris as cell factories for production of recombinant proteins. Front Microbiol 2022; 13:1059777. [PMID: 36504810 PMCID: PMC9730254 DOI: 10.3389/fmicb.2022.1059777] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Pichia pastoris (syn. Komagataella spp.) has attracted extensive attention as an efficient platform for recombinant protein (RP) production. For obtaining a higher protein titer, many researchers have put lots of effort into different areas and made some progress. Here, we summarized the most recent advances of the last 5 years to get a better understanding of its future direction of development. The appearance of innovative genetic tools and methodologies like the CRISPR/Cas9 gene-editing system eases the manipulation of gene expression systems and greatly improves the efficiency of exploring gene functions. The integration of novel pathways in microorganisms has raised more ideas of metabolic engineering for enhancing RP production. In addition, some new opportunities for the manufacture of proteins have been created by the application of novel mathematical models coupled with high-throughput screening to have a better overview of bottlenecks in the biosynthetic process.
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Affiliation(s)
- Yingjie Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiao Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianping Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lirong Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Fang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
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Samlali K, Alves CL, Jezernik M, Shih SCC. Droplet digital microfluidic system for screening filamentous fungi based on enzymatic activity. MICROSYSTEMS & NANOENGINEERING 2022; 8:123. [PMID: 36438986 PMCID: PMC9681769 DOI: 10.1038/s41378-022-00456-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Fungal cell-wall-degrading enzymes have great utility in the agricultural and food industries. These cell-wall-degrading enzymes are known to have functions that can help defend against pathogenic organisms. The existing methods used to discover these enzymes are not well adapted to fungi culture and morphology, which prevents the proper evaluation of these enzymes. We report the first droplet-based microfluidic method capable of long-term incubation and low-voltage conditions to sort filamentous fungi inside nanoliter-sized droplets. The new method was characterized and validated in solid-phase media based on colloidal chitin such that the incubation of single spores in droplets was possible over multiple days (2-4 days) and could be sorted without droplet breakage. With long-term culture, we examined the activity of cell-wall-degrading enzymes produced by fungi during solid-state droplet fermentation using three highly sensitive fluorescein-based substrates. We also used the low-voltage droplet sorter to select clones with highly active cell-wall-degrading enzymes, such as chitinases, β-glucanases, and β-N-acetylgalactosaminidases, from a filamentous fungi droplet library that had been incubated for >4 days. The new system is portable, affordable for any laboratory, and user-friendly compared to classical droplet-based microfluidic systems. We propose that this system will be useful for the growing number of scientists interested in fungal microbiology who are seeking high-throughput methods to incubate and sort a large library of fungal cells.
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Affiliation(s)
- Kenza Samlali
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
| | - Chiara Leal Alves
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
| | - Mara Jezernik
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada
| | - Steve C. C. Shih
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
- Department of Biology, Concordia University, Montréal, QC Canada
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Shariati FS, Keramati M, Cohan RA. Indirect optimization of staphylokinase expression level in dicistronic auto-inducible system. AMB Express 2022; 12:124. [PMID: 36138332 PMCID: PMC9500143 DOI: 10.1186/s13568-022-01464-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Design of experiment (DOE) is a statistical approach for designing, performing, and interpreting a large set of data with the minimum number of tests. In our previous study, we developed a novel Hsp27 SILEX system for production of recombinant proteins. In the present study, we optimized indirectly the most effective factors including inoculation load, self-induction temperature, and culture media on autoinduction of staphylokinase (SAK) expression using RSM methodology and fluorometry. The expression level of SAK was assayed at different runs after 6 h incubation at 90 rpm. The results indicated all parameters significantly affect the SAK expression level (p < 0.05). The optimum expression condition was obtained with an inoculation load of 0.05, a temperature of 25 °C, and TB culture medium. The analysis of variance with a R2 value of 0.91 showed that a quadratic model well described this prediction (p < 0.05). Applying the optimized condition led to an approximately fourfold increase in the SAK expression level (from 1.3 to 5.2 µg/ml). Moreover, the recombinant protein was purified using immobilized metal affinity chromatography and the activity was also confirmed by semi-quantitative caseinolytic method.
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Affiliation(s)
- Fatemeh Sadat Shariati
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Malihe Keramati
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran.
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran.
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11
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Ai Y, Luo R, Yang D, Ma J, Yu Y, Lu H. Fluorescence lifetime imaging of NAD(P)H upon oxidative stress in Kluyveromyces marxianus. Front Bioeng Biotechnol 2022; 10:998800. [PMID: 36118576 PMCID: PMC9479077 DOI: 10.3389/fbioe.2022.998800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
K. marxianus is a promising cell factory for producing heterologous proteins. Oxidative stresses were raised during overexpression of heterologous proteins, leading to the shift of the redox state. How to measure the redox state of live K. marxianus cells without perturbing their growth remains a big challenge. Here, a fluorescence lifetime imaging (FLIM)-based method was developed in live K. marxianus cells. During the early exponential growth, K. marxianus cells exhibited an increased mean fluorescence lifetime (τ-mean) of NAD(P)H compared with Saccharomyces cerevisiae cells, which was consistent with the preference for respiration in K. marxianus cells and that for fermentation in S. cerevisiae cells. Upon oxidative stresses induced by high temperature or H2O2, K. marxianus cells exhibited an increased τ-mean in company with decreased intracellular NAD(P)H/NAD(P)+, suggesting a correlation between an increased τ-mean and a more oxidized redox state. The relationship between τ-mean and the expression level of a heterologous protein was investigated. There was no difference between the τ-means of K. marxianus strains which were not producing a heterologous protein. The τ-mean of a strain yielding a high level of a heterologous protein was higher than that of a low-yielding strain. The results suggested the potential application of FLIM in the non-invasive screen of high-yielding cells.
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Affiliation(s)
- Yi Ai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Ruoyu Luo
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Deqiang Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Jiong Ma
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Department of Optical Science and Engineering, School of Information Science and Technology, Fudan University, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
- *Correspondence: Yao Yu, ; Hong Lu,
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
- *Correspondence: Yao Yu, ; Hong Lu,
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12
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Kerk YJ, Jameel A, Xing X, Zhang C. Recent advances of integrated microfluidic suspension cell culture system. ENGINEERING BIOLOGY 2021; 5:103-119. [PMID: 36970555 PMCID: PMC9996741 DOI: 10.1049/enb2.12015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Microfluidic devices with superior microscale fluid manipulation ability and large integration flexibility offer great advantages of high throughput, parallelisation and multifunctional automation. Such features have been extensively utilised to facilitate cell culture processes such as cell capturing and culturing under controllable and monitored conditions for cell-based assays. Incorporating functional components and microfabricated configurations offered different levels of fluid control and cell manipulation strategies to meet diverse culture demands. This review will discuss the advances of single-phase flow and droplet-based integrated microfluidic suspension cell culture systems and their applications for accelerated bioprocess development, high-throughput cell selection, drug screening and scientific research to insight cell biology. Challenges and future prospects for this dynamically developing field are also highlighted.
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Affiliation(s)
- Yi Jing Kerk
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Aysha Jameel
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Xin‐Hui Xing
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
| | - Chong Zhang
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
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13
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Stucki A, Jusková P, Nuti N, Schmitt S, Dittrich PS. Synchronized Reagent Delivery in Double Emulsions for Triggering Chemical Reactions and Gene Expression. SMALL METHODS 2021; 5:e2100331. [PMID: 34927870 DOI: 10.1002/smtd.202100331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/21/2021] [Indexed: 06/14/2023]
Abstract
Microfluidic methods for the formation of single and double emulsion (DE) droplets allow for the encapsulation and isolation of reactants inside nanoliter compartments. Such methods have greatly enhanced the toolbox for high-throughput screening for cell or enzyme engineering and drug discovery. However, remaining challenges in the supply of reagents into these enclosed compartments limit the applicability of droplet microfluidics. Here, a strategy is introduced for on-demand delivery of reactants in DEs. Lipid vesicles are used as reactant carriers, which are co-encapsulated in double emulsions and release their cargo upon addition of an external trigger, here the anionic surfactant sodium dodecyl sulfate (SDS). The reagent present inside the lipid vesicles stays isolated from the remaining content of the DE vessel until SDS enters the DE lumen and solubilizes the vesicles' lipid bilayer. The versatility of the method is demonstrated with two critical applications chosen as representative assays for high-throughput screening: the induction of gene expression in bacteria and the initiation of an enzymatic reaction. This method not only allows for the release of the lipid vesicle content inside DEs to be synchronized for all DEs but also for the release to be triggered at any desired time.
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Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Petra Jusková
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Nicola Nuti
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
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Crosslinking Strategies for the Microfluidic Production of Microgels. Molecules 2021; 26:molecules26123752. [PMID: 34202959 PMCID: PMC8234156 DOI: 10.3390/molecules26123752] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/03/2023] Open
Abstract
This article provides a systematic review of the crosslinking strategies used to produce microgel particles in microfluidic chips. Various ionic crosslinking methods for the gelation of charged polymers are discussed, including external gelation via crosslinkers dissolved or dispersed in the oil phase; internal gelation methods using crosslinkers added to the dispersed phase in their non-active forms, such as chelating agents, photo-acid generators, sparingly soluble or slowly hydrolyzing compounds, and methods involving competitive ligand exchange; rapid mixing of polymer and crosslinking streams; and merging polymer and crosslinker droplets. Covalent crosslinking methods using enzymatic oxidation of modified biopolymers, photo-polymerization of crosslinkable monomers or polymers, and thiol-ene “click” reactions are also discussed, as well as methods based on the sol−gel transitions of stimuli responsive polymers triggered by pH or temperature change. In addition to homogeneous microgel particles, the production of structurally heterogeneous particles such as composite hydrogel particles entrapping droplet interface bilayers, core−shell particles, organoids, and Janus particles are also discussed. Microfluidics offers the ability to precisely tune the chemical composition, size, shape, surface morphology, and internal structure of microgels by bringing multiple fluid streams in contact in a highly controlled fashion using versatile channel geometries and flow configurations, and allowing for controlled crosslinking.
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