1
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van der Loh M, Schiffmann M, Polack M, Wink K, Belder D. Coupling of droplet-on-demand microfluidcs with ESI/MS to study single-cell catalysis. RSC Adv 2024; 14:25337-25346. [PMID: 39139235 PMCID: PMC11320962 DOI: 10.1039/d4ra04835k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Droplet microfluidics provides an efficient method for analysing reactions within the range of nanoliters to picoliters. However, the sensitive, label-free and versatile detection with ESI/MS poses some difficulties. One challenge is the difficult association of droplets with the MS signal in high-throughput droplet analysis. Hence, a droplet-on-demand system for the generation of a few droplets can address this and other problems such as surfactant concentration or cross-contamination. Accordingly, the system has been further developed for online coupling with ESI/MS. To achieve this, we developed a setup enabling on-demand droplet generation by hydrodynamic gating, with downstream microscopic droplet detection and MS analysis. This facilitated the incorporation of 1-9 yeast cells into individual 1-5 nL droplets and the monitoring of yeast-catalysed transformation from ketoester to ethyl-3-hydroxybutyrate by MS. With our method a mean production rate of 0.035 ± 0.017 fmol per cell per h was observed with a detection limit of 0.30 μM. In conclusion, our droplet-on-demand method is a versatile and advantageous tool for cell encapsulation in droplets, droplet imaging and reaction detection using ESI/MS.
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Affiliation(s)
- Marie van der Loh
- Institute of Analytical Chemistry, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | - Marie Schiffmann
- Institute of Analytical Chemistry, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | - Matthias Polack
- Institute of Analytical Chemistry, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | - Konstantin Wink
- Institute of Analytical Chemistry, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University Linnéstraße 3 04103 Leipzig Germany
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2
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Strutt R, Xiong B, Abegg VF, Dittrich PS. Open microfluidics: droplet microarrays as next generation multiwell plates for high throughput screening. LAB ON A CHIP 2024; 24:1064-1075. [PMID: 38356285 PMCID: PMC10898417 DOI: 10.1039/d3lc01024d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/04/2024] [Indexed: 02/16/2024]
Abstract
Multiwell plates are prominent in the biological and chemical sciences; however, they face limitations in terms of throughput and deployment in emerging bioengineering fields. Droplet microarrays, as an open microfluidic technology, organise tiny droplets typically in the order of thousands, on an accessible plate. In this perspective, we summarise current approaches for generating droplets, fluid handling on them, and analysis within droplet microarrays. By enabling unique plate engineering opportunities, demonstrating the necessary experimental procedures required for manipulating and interacting with biological cells, and integrating with label-free analytical techniques, droplet microarrays can be deployed across a more extensive experimental domain than what is currently covered by multiwell plates. Droplet microarrays thus offer a solution to the bottlenecks associated with multiwell plates, particularly in the areas of biological cultivation and high-throughput compound screening.
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Affiliation(s)
- Robert Strutt
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Bijing Xiong
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Vanessa Fabienne Abegg
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
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3
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Zohouri D, Lienard-Mayor T, Obeid S, Taverna M, Mai TD. A review on hyphenation of droplet microfluidics to separation techniques: From instrumental conception to analytical applications for limited sample volumes. Anal Chim Acta 2024; 1291:342090. [PMID: 38280779 DOI: 10.1016/j.aca.2023.342090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 01/29/2024]
Abstract
In this study, we review various strategies to couple sample processing in microfluidic droplets with different separation techniques, including liquid chromatography, mass spectrometry, and capillary electrophoresis. Separation techniques interfaced with droplet microfluidics represent an emerging trend in analytical chemistry, in which micro to femtoliter droplets serve as microreactors, a bridge between analytical modules, as well as carriers of target analytes between sample treatment and separation/detection steps. This allows to overcome the hurdles encountered in separation science, notably the low degree of module integration, working volume incompatibility, and cross contamination between different operational stages. For this droplet-separation interfacing purpose, this review covers different instrumental designs from all works on this topic up to May 2023, together with our viewpoints on respective advantages and considerations. Demonstration and performance of droplet-interfaced separation strategies for limited sample volumes are also discussed.
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Affiliation(s)
- Delaram Zohouri
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Théo Lienard-Mayor
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Sameh Obeid
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Myriam Taverna
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Thanh Duc Mai
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France.
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4
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Hu H, Singh AN, Lehnherr D, Mdluli V, Chun SW, Makarewicz AM, Gouker JR, Ukaegbu O, Li S, Wen X, McLaren DG, Velasquez JE, Moore JC, Galanie S, Appiah-Amponsah E, Regalado EL. Accelerating Pharmaceutical Process Development with an Acoustic Droplet Ejection-Multiple Reaction Monitoring-Mass Spectrometry Workflow. Anal Chem 2024; 96:1138-1146. [PMID: 38165811 DOI: 10.1021/acs.analchem.3c04211] [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: 01/04/2024]
Abstract
Fast-paced pharmaceutical process developments (e.g., high-throughput experimentation, directed evolution, and machine learning) involve the introduction of fast, sensitive, and accurate analytical assays using limited sample volumes. In recent years, acoustic droplet ejection (ADE) coupled with an open port interface has been invented as a sampling technology for mass spectrometry, providing high-throughput nanoliter analytical measurements directly from the standard microplates. Herein, we introduce an ADE-multiple reaction monitoring-mass spectrometry (ADE-MRM-MS) workflow to accelerate pharmaceutical process research and development (PR&D). This systematic workflow outlines the selection of MRM transitions and optimization of assay parameters in a data-driven manner using rapid measurements (1 sample/s). The synergy between ADE sampling and MRM analysis enables analytical assays with excellent sensitivity, selectivity, and speed for PR&D reaction screenings. This workflow was utilized to develop new ADE-MRM-MS assays guiding a variety of industrial processes, including (1) screening of Ni-based catalysts for C-N cross-coupling reaction at 1 Hz and (2) high-throughput regioisomer analysis-enabled enzyme library screening for peptide ligation reaction. ADE-MRM-MS assays were demonstrated to deliver accurate results that are comparable to conventional liquid chromatography (LC) experiments while providing >100-fold throughput enhancement.
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Affiliation(s)
- Hang Hu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Andrew N Singh
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dan Lehnherr
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Velabo Mdluli
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie W Chun
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Amanda M Makarewicz
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Joseph R Gouker
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ophelia Ukaegbu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xiujuan Wen
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David G McLaren
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Juan E Velasquez
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie Galanie
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Erik L Regalado
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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5
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He Y, Qiao Y, Ding L, Cheng T, Tu J. Recent advances in droplet sequential monitoring methods for droplet sorting. BIOMICROFLUIDICS 2023; 17:061501. [PMID: 37969470 PMCID: PMC10645479 DOI: 10.1063/5.0173340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 11/17/2023]
Abstract
Droplet microfluidics is an attractive technology to run parallel experiments with high throughput and scalability while maintaining the heterogeneous features of individual samples or reactions. Droplet sorting is utilized to collect the desired droplets based on droplet characterization and in-droplet content evaluation. A proper monitoring method is critical in this process, which governs the accuracy and maximum frequency of droplet handling. Until now, numerous monitoring methods have been integrated in the microfluidic devices for identifying droplets, such as optical spectroscopy, mass spectroscopy, electrochemical monitoring, and nuclear magnetic resonance spectroscopy. In this review, we summarize the features of various monitoring methods integrated into droplet sorting workflow and discuss their suitable condition and potential obstacles in use. We aim to provide a systematic introduction and an application guide for choosing and building a droplet monitoring platform.
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Affiliation(s)
- Yukun He
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yi Qiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lu Ding
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Tianguang Cheng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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6
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Murray BE, Penabad LI, Kennedy RT. Advances in coupling droplet microfluidics to mass spectrometry. Curr Opin Biotechnol 2023; 82:102962. [PMID: 37336080 DOI: 10.1016/j.copbio.2023.102962] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Droplet microfluidics enables development of workflows with low sample consumption and high throughput. Fluorescence-based assays are most used with droplet microfluidics; however, the requirement of a fluorescent reporter restricts applicability of this approach. The coupling of droplets to mass spectrometry (MS) has enabled selective assays on complex mixtures to broaden the analyte scope. Droplet microfluidics has been interfaced to MS via electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). The works reviewed herein outline the development of this nascent field as well as initial exploration of its application in biotechnology and bioanalysis, including synthetic biology, reaction development, and in vivo sensing.
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Affiliation(s)
- Bridget E Murray
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Laura I Penabad
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA.
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7
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Zeng Y, Khor JW, van Neel TL, Tu WC, Berthier J, Thongpang S, Berthier E, Theberge AB. Miniaturizing chemistry and biology using droplets in open systems. Nat Rev Chem 2023; 7:439-455. [PMID: 37117816 PMCID: PMC10107581 DOI: 10.1038/s41570-023-00483-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2023] [Indexed: 04/30/2023]
Abstract
Open droplet microfluidic systems manipulate droplets on the picolitre-to-microlitre scale in an open environment. They combine the compartmentalization and control offered by traditional droplet-based microfluidics with the accessibility and ease-of-use of open microfluidics, bringing unique advantages to applications such as combinatorial reactions, droplet analysis and cell culture. Open systems provide direct access to droplets and allow on-demand droplet manipulation within the system without needing pumps or tubes, which makes the systems accessible to biologists without sophisticated setups. Furthermore, these systems can be produced with simple manufacturing and assembly steps that allow for manufacturing at scale and the translation of the method into clinical research. This Review introduces the different types of open droplet microfluidic system, presents the physical concepts leveraged by these systems and highlights key applications.
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Affiliation(s)
- Yuting Zeng
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jian Wei Khor
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Tammi L van Neel
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Wan-Chen Tu
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jean Berthier
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Sanitta Thongpang
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakorn Pathom, Thailand
| | - Erwin Berthier
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - Ashleigh B Theberge
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Department of Urology, School of Medicine, University of Washington, Seattle, WA, USA.
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8
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Villarreal J, Kow K, Pham B, Egatz-Gomez A, Sandrin TR, Coleman PD, Ros A. Intracellular Amyloid-β Detection from Human Brain Sections Using a Microfluidic Immunoassay in Tandem with MALDI-MS. Anal Chem 2023; 95:5522-5531. [PMID: 36894164 PMCID: PMC10078609 DOI: 10.1021/acs.analchem.2c03825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
Alzheimer's disease (AD) currently affects more than 30 million people worldwide. The lack of understanding of AD's physiopathology limits the development of therapeutic and diagnostic tools. Soluble amyloid-β peptide (Aβ) oligomers that appear as intermediates along the Aβ aggregation into plaques are considered among the main AD neurotoxic species. Although a wealth of data are available about Aβ from in vitro and animal models, there is little known about intracellular Aβ in human brain cells, mainly due to the lack of technology to assess the intracellular protein content. The elucidation of the Aβ species in specific brain cell subpopulations can provide insight into the role of Aβ in AD and the neurotoxic mechanism involved. Here, we report a microfluidic immunoassay for in situ mass spectrometry analysis of intracellular Aβ species from archived human brain tissue. This approach comprises the selective laser dissection of individual pyramidal cell bodies from tissues, their transfer to the microfluidic platform for sample processing on-chip, and mass spectrometric characterization. As a proof-of-principle, we demonstrate the detection of intracellular Aβ species from as few as 20 human brain cells.
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Affiliation(s)
- Jorvani
Cruz Villarreal
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Keegan Kow
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Brian Pham
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Ana Egatz-Gomez
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Todd R. Sandrin
- School
of Mathematical and Natural Sciences, Arizona
State University, Glendale, Arizona 85306, United States
- Julie
Ann Wrigley Global Futures Laboratory, Arizona
State University, Glendale, Arizona 85306, United States
| | - Paul D. Coleman
- Banner
ASU Neurodegenerative Research Center, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Alexandra Ros
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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9
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Zhou S, Fatma Z, Xue P, Mishra S, Cao M, Zhao H, Sweedler JV. Mass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid Culture. Anal Chem 2023; 95:4067-4076. [PMID: 36790390 DOI: 10.1021/acs.analchem.2c04845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
To meet the ever-increasing need for high-throughput screening in metabolic engineering, information-rich, fast screening methods are needed. Mass spectrometry (MS) provides an efficient and general approach for metabolite screening and offers the capability of characterizing a broad range of analytes in a label-free manner, but often requires a range of sample clean-up and extraction steps. Liquid extraction surface analysis (LESA) coupled MS is an image-guided MS surface analysis approach that directly samples and introduces metabolites from a surface to MS. Here, we combined the advantages of LESA-MS and an acoustic liquid handler with stable isotope-labeled internal standards. This approach provides absolute quantitation of target chemicals from liquid culture-dried droplets and enables high-throughput quantitative screening for microbial metabolites. In this study, LESA-MS was successfully applied to quantify several different metabolites (itaconic acid, triacetic acid lactone, and palmitic acid) from different yeast strains in different mediums, demonstrating its versatility, accuracy, and efficiency across a range of microbial engineering applications.
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Affiliation(s)
- Shuaizhen Zhou
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zia Fatma
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shekhar Mishra
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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10
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Recent advances of integrated microfluidic systems for fungal and bacterial analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Jayan H, Pu H, Sun DW. Analyzing macromolecular composition of E. Coli O157:H7 using Raman-stable isotope probing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 276:121217. [PMID: 35427921 DOI: 10.1016/j.saa.2022.121217] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Metabolic dynamics of bacterial cells is needed for understanding the correlation between changes in environmental conditions and cell metabolic activity. In this study, Raman spectroscopy combined with deuterium labelling was used to analyze the metabolic activity of a single Escherichia coli O157:H7 cell. The incorporation of deuterium from heavy water into cellular biomolecules resulted in the formation of carbon-deuterium (CD) peaks in the Raman spectra, indicating the cell metabolic activity. The broad vibrational peaks corresponding to CD and CH peaks encompassed different specific shifts of macromolecules such as protein, lipids, and nucleic acid. The utilization of tryptophan and oleic acid by the cell as the sole carbon source led to changes in cell lipid composition, as indicated by new peaks in the second derivative spectra. Thus, the proposed method could semi-quantitatively determine total metabolic activity, macromolecule specific identification, and lipid and protein metabolism in a single cell.
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Affiliation(s)
- Heera Jayan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin 4, Ireland.
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12
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Wink K, van der Loh M, Hartner N, Polack M, Dusny C, Schmid A, Belder D. Quantification of Biocatalytic Transformations by Single Microbial Cells Enabled by Tailored Integration of Droplet Microfluidics and Mass Spectrometry. Angew Chem Int Ed Engl 2022; 61:e202204098. [PMID: 35511505 PMCID: PMC9401594 DOI: 10.1002/anie.202204098] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Indexed: 12/23/2022]
Abstract
Improving the performance of chemical transformations catalysed by microbial biocatalysts requires a deep understanding of cellular processes. While the cellular heterogeneity of cellular characteristics, such as the concentration of high abundant cellular content, is well studied, little is known about the reactivity of individual cells and its impact on the chemical identity, quantity, and purity of excreted products. Biocatalytic transformations were monitored chemically specific and quantifiable at the single-cell level by integrating droplet microfluidics, cell imaging, and mass spectrometry. Product formation rates for individual Saccharomyces cerevisiae cells were obtained by i) incubating nanolitre-sized droplets for product accumulation in microfluidic devices, ii) an imaging setup to determine the number of cells in the droplets, and iii) electrospray ionisation mass spectrometry for reading the chemical contents of individual droplets. These findings now enable the study of whole-cell biocatalysis at single-cell resolution.
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Affiliation(s)
- Konstantin Wink
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Marie van der Loh
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Nora Hartner
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Matthias Polack
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Christian Dusny
- Department Solar MaterialsHelmholtz Centre for Environmental Research (UFZ)04318LeipzigGermany
| | - Andreas Schmid
- Department Solar MaterialsHelmholtz Centre for Environmental Research (UFZ)04318LeipzigGermany
| | - Detlev Belder
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
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13
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Wink K, Loh M, Hartner N, Polack M, Dusny C, Schmid A, Belder D. Quantifizierung biokatalytischer Umwandlungen durch einzelne mikrobielle Zellen mittels maßgeschneiderter Integration von Tröpfchenmikrofluidik und Massenspektrometrie. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Konstantin Wink
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Marie Loh
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Nora Hartner
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Matthias Polack
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Christian Dusny
- Department Solare Materialien Helmholtz-Zentrum für Umweltforschung (UFZ) 04318 Leipzig Deutschland
| | - Andreas Schmid
- Department Solare Materialien Helmholtz-Zentrum für Umweltforschung (UFZ) 04318 Leipzig Deutschland
| | - Detlev Belder
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
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14
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Towards one sample per second for mass spectrometric screening of engineered microbial strains. Curr Opin Biotechnol 2022; 76:102725. [PMID: 35489307 DOI: 10.1016/j.copbio.2022.102725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/03/2022] [Accepted: 03/20/2022] [Indexed: 12/11/2022]
Abstract
Microbial cell factories convert renewable feedstocks into desirable chemicals and materials. Due to the lack of predictive modeling, high-throughput screening remains essential for microbial strain engineering. Mass spectrometry (MS) is a label-free modality with superior sensitivity and chemical specificity. Critical advances in improving the throughput of MS assays on complex microbial samples include massively parallel cultivation, robotic sample preparation, and chromatography-free instrumentation. Here, we review the recent development and application of rapid MS assays in screening microbial libraries, achieving or approaching a rate of one sample per second. We conclude with unique challenges associated with MS screening of strain libraries and discuss future solutions.
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15
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Cruz Villarreal J, Kruithoff R, Egatz-Gomez A, Coleman PD, Ros R, Sandrin TR, Ros A. MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. Anal Bioanal Chem 2022; 414:3945-3958. [PMID: 35385983 PMCID: PMC9188328 DOI: 10.1007/s00216-022-04038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/26/2022]
Abstract
Understanding cell-to-cell variation at the molecular level provides relevant information about biological phenomena and is critical for clinical and biological research. Proteins carry important information not available from single-cell genomics and transcriptomics studies; however, due to the minute amount of proteins in single cells and the complexity of the proteome, quantitative protein analysis at the single-cell level remains challenging. Here, we report an integrated microfluidic platform in tandem with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for the detection and quantification of targeted proteins from small cell ensembles (> 10 cells). All necessary steps for the assay are integrated on-chip including cell lysis, protein immunocapture, tryptic digestion, and co-crystallization with the matrix solution for MALDI-MS analysis. We demonstrate that our approach is suitable for protein quantification by assessing the apoptotic protein Bcl-2 released from MCF-7 breast cancer cells, ranging from 26 to 223 cells lysed on-chip (8.75 nL wells). A limit of detection (LOD) of 11.22 nM was determined, equivalent to 5.91 × 107 protein molecules per well. Additionally, the microfluidic platform design was further improved, establishing the successful quantification of Bcl-2 protein from MCF-7 cell ensembles ranging from 8 to 19 cells in 4 nL wells. The LOD in the smaller well designs for Bcl-2 resulted in 14.85 nM, equivalent to 3.57 × 107 protein molecules per well. This work shows the capability of our approach to quantitatively assess proteins from cell lysate on the MIMAS platform for the first time. These results demonstrate our approach constitutes a promising tool for quantitative targeted protein analysis from small cell ensembles down to single cells, with the capability for multiplexing through parallelization and automation.
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Affiliation(s)
- Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paul D Coleman
- School of Life Sciences, Arizona State University, Temple, AZ, USA
- ASU-Banner Neurodegenerative Research Center, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Robert Ros
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Temple, AZ, USA
| | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, USA
- Julie Ann Wrigley Global Futures Laboratory, Arizona State University, Tempe, AZ, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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16
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Wang XN, Li B. Monolithic Gold Nanoparticles/Thiol-β-cyclodextrin-Functionalized TiO 2 Nanowires for Enhanced SALDI MS Detection and Imaging of Natural Products. Anal Chem 2021; 94:952-959. [PMID: 34932904 DOI: 10.1021/acs.analchem.1c03764] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Surface-assisted laser desorption/ionization mass spectrometry (SALDI MS) has been successfully applied in the analysis of various small molecules. In this work, gold nanoparticles/thiol-β-cyclodextrin-functionalized TiO2 nanowires (AuNPs/SH-β-CD-TiO2 NWs) were prepared to enhance the performance of SALDI MS and mass spectrometry imaging (MSI). A monolithic TiO2 film was first grown on an indium tin oxide (ITO) glass slide via a modified sol-gel method and treated in an alkaline environment to form nanowires. TiO2 NWs were chemically modified by SH-β-CD for immobilizing AuNPs densely and strongly. Compared with the conventional organic matrix 2,5-dihydroxybenzoic acid (DHB), the prepared AuNPs/SH-β-CD-TiO2 NWs showed superior performances on detection sensitivity, repeatability, and analyte coverage. Analytes typically detectable with negative-ion matrix-assisted laser desorption/ionization (MALDI) MS could also be observed using AuNPs/SH-β-CD-TiO2 NWs in the positive ion mode. Its successful usage efficiently enhanced the SALDI MS detection of various small molecules such as carbohydrates, fatty acids, and bile acids in the positive ion mode. The developed SALDI substrate was further used to characterize and discriminate the natural and in vitro cultured Calculus Bovis, as well as natural and artificial Moschus. Furthermore, the spatial distribution of several natural products in spearmint leaves and potato tubers was explored by tissue imprinting and deposition on the AuNPs/SH-β-CD-TiO2 NW surface for SALDI MSI in dual-polarity mode, respectively. The wide application and satisfied detection sensitivity make AuNPs/SH-β-CD-TiO2 NWs ideal for SALDI MS and MSI of various natural products.
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Affiliation(s)
- Xian-Na Wang
- State Key Laboratory of Natural Medicines and School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Li
- State Key Laboratory of Natural Medicines and School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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17
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Hartner NT, Wink K, Raddatz CR, Thoben C, Schirmer M, Zimmermann S, Belder D. Coupling Droplet Microfluidics with Ion Mobility Spectrometry for Monitoring Chemical Conversions at Nanoliter Scale. Anal Chem 2021; 93:13615-13623. [PMID: 34592821 DOI: 10.1021/acs.analchem.1c02883] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce the coupling of droplet microfluidics and ion mobility spectrometry (IMS) to address the challenges of label-free and chemical-specific detection of compounds in individual droplets. In analogy to the established use of mass spectrometry, droplet-IMS coupling can be also achieved via electrospray ionization but with significantly less instrumental effort. Because IMS instruments do not require high-vacuum systems, they are very compact, cost-effective, and robust, making them an ideal candidate as a chemical-specific end-of-line detector for segmented flow experiments. Herein, we demonstrate the successful coupling of droplet microfluidics with a custom-built high-resolution drift tube IMS system for monitoring chemical reactions in nL-sized droplets in an oil phase. The analytes contained in each droplet were assigned according to their characteristic ion mobility with limit of detections down to 200 nM to 1 μM and droplet frequencies ranging from 0.1 to 0.5 Hz. Using a custom sheath flow electrospray interface, we have further achieved the chemical-specific monitoring of a biochemical transformation catalyzed by a few hundred yeast cells, at single droplet level.
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Affiliation(s)
- Nora T Hartner
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Konstantin Wink
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Christian-Robert Raddatz
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Christian Thoben
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Martin Schirmer
- Helmholtz Centre for Environmental Research - UFZ Leipzig, Leipzig 04318, Germany
| | - Stefan Zimmermann
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
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18
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Ha NS, de Raad M, Han LZ, Golini A, Petzold CJ, Northen TR. Faster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnology. RSC Chem Biol 2021; 2:1331-1351. [PMID: 34704041 PMCID: PMC8496484 DOI: 10.1039/d1cb00112d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
High-throughput screening technologies are widely used for elucidating biological activities. These typically require trade-offs in assay specificity and sensitivity to achieve higher throughput. Microfluidic approaches enable rapid manipulation of small volumes and have found a wide range of applications in biotechnology providing improved control of reaction conditions, faster assays, and reduced reagent consumption. The integration of mass spectrometry with microfluidics has the potential to create high-throughput, sensitivity, and specificity assays. This review introduces the widely-used mass spectrometry ionization techniques that have been successfully integrated with microfluidics approaches such as continuous-flow system, microchip electrophoresis, droplet microfluidics, digital microfluidics, centrifugal microfluidics, and paper microfluidics. In addition, we discuss recent applications of microfluidics integrated with mass spectrometry in single-cell analysis, compound screening, and the study of microorganisms. Lastly, we provide future outlooks towards online coupling, improving the sensitivity and integration of multi-omics into a single platform.
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Affiliation(s)
- Noel S Ha
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
| | - La Zhen Han
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Amber Golini
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Trent R Northen
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
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19
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Yu Z, Jin J, Shui L, Chen H, Zhu Y. Recent advances in microdroplet techniques for single-cell protein analysis. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Chen K, Rong N, Wang S, Luo C. A novel two-layer-integrated microfluidic device for high-throughput yeast proteomic dynamics analysis at the single-cell level. Integr Biol (Camb) 2021; 12:241-249. [PMID: 32995887 DOI: 10.1093/intbio/zyaa018] [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: 04/20/2020] [Revised: 08/12/2020] [Accepted: 08/31/2020] [Indexed: 11/14/2022]
Abstract
Current microfluidic methods for studying multicell strains (e.g., m-types) with multienvironments (e.g., n-types) require large numbers of inlets/outlets (m*n), a complicated procedure or expensive machinery. Here, we developed a novel two-layer-integrated method to combine different PDMS microchannel layers with different functions into one chip by a PDMS through-hole array, which improved the design of a PDMS-based microfluidic system. Using this method, we succeeded in converting 2 × m × n inlets/outlets into m + n inlets/outlets and reduced the time cost of loading processing (from m × n to m) of the device for studying multicell strains (e.g., m-types) in varied multitemporal environments (i.e., n-types). Using this device, the dynamic behavior of the cell-stress-response proteins was studied when the glucose concentration decreased from 2% to a series of lower concentrations. Our device could also be widely used in high-throughput studies of various stress responses, and the new concept of a multilayer-integrated fabrication method could greatly improve the design of PDMS-based microfluidic systems.
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Affiliation(s)
- Kaiyue Chen
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Shujing Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
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21
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Li L, Wu E, Jia K, Yang K. Temperature field regulation of a droplet using an acoustothermal heater. LAB ON A CHIP 2021; 21:3184-3194. [PMID: 34195725 DOI: 10.1039/d1lc00267h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Heating a droplet without contamination is desired for the emerging applications of microfluidic devices in life science and materials science, especially in the form of controllable temperature distribution. Microfluidic heaters using surface acoustic waves have been recently demonstrated, which highlights an urgent need for an insight into the detailed heating mechanism to guide the development of temperature regulation methodologies. Here, we show that the temperature field of a droplet on the path of a travelling wave can be regulated by modulating the heat source distribution and thermal conduction inside the target. We model the acoustothermal process of the droplet including the effects of electric dissipation, acoustic dissipation, and acoustic-induced steady flow. The electric-mechanical-acoustic coupling contributes to the dominant heat source, and we call it acoustic heat source. The nonlinear effects of incident waves generate acoustic vortexes with a velocity of up to 20 mm s-1, inducing forced convection inside the droplet to enhance heat transfer. The equilibrium temperature field of a droplet is determined by a synergy of dissipative acoustic attenuation and acoustic streaming. We demonstrate that the distribution of the acoustic heat source and the patterns of acoustic streaming can be modulated by fluid viscosity and droplet size. Various spatial combinations of the acoustic heat source and steady streaming make different temperature fields in the droplet. We also propose a phase diagram of the temperature distribution in the droplet. This methodology enables opportunities for temperature-related processing inside a droplet bioparticle carrier or microreactor.
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Affiliation(s)
- Liqiang Li
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, P. R. China
| | - Eryong Wu
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, P. R. China
| | - Kun Jia
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace, Xi'an Jiaotong University, No. 28 West Xianning Road, 710049, Xi'an, P. R. China.
| | - Keji Yang
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, P. R. China
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22
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Yang M, Villarreal JC, Ariyasinghe N, Kruithoff R, Ros R, Ros A. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry. Anal Chem 2021; 93:6053-6061. [PMID: 33819014 PMCID: PMC8128341 DOI: 10.1021/acs.analchem.0c04112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing evidence has demonstrated that cells are individually heterogeneous. Advancing the technologies for single-cell analysis will improve our ability to characterize cells, study cell biology, design and screen drugs, and aid cancer diagnosis and treatment. Most current single-cell protein analysis approaches are based on fluorescent antibody-binding technology. However, this technology is limited by high background and cross-talk of multiple tags introduced by fluorescent labels. Stable isotope labels used in mass cytometry can overcome the spectral overlap of fluorophores. Nevertheless, the specificity of each antibody and heavy-metal-tagged antibody combination must be carefully validated to ensure detection of the intended target. Thus, novel single-cell protein analysis methods without using labels are urgently needed. Moreover, the labeling approach targets already known motifs, hampering the discovery of new biomarkers relevant to single-cell population variation. Here, we report a combined microfluidic and matrix-assisted laser desorption and ionization (MALDI) mass spectrometric approach for the analysis of protein biomarkers suitable for small cell ensembles. All necessary steps for cell analysis including cell lysis, protein capture, and digestion as well as MALDI matrix deposition are integrated on a microfluidic chip prior to the downstream MALDI-time-of-flight (TOF) detection. For proof of principle, this combined method is used to assess the amount of Bcl-2, an apoptosis regulator, in metastatic breast cancer cells (MCF-7) by using an isotope-labeled peptide as an internal standard. The proposed approach will eventually provide a new means for proteome studies in small cell ensembles with the potential for single-cell analysis and improve our ability in disease diagnosis, drug discovery, and personalized therapy.
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Affiliation(s)
- Mian Yang
- Department of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan City, Hubei Province, 430081, P.R.China
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
| | - Nethmi Ariyasinghe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
| | - Robert Ros
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
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23
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Napiorkowska M, Pestalozzi L, Panke S, Held M, Schmitt S. High-Throughput Optimization of Recombinant Protein Production in Microfluidic Gel Beads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005523. [PMID: 33325637 DOI: 10.1002/smll.202005523] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/31/2020] [Indexed: 06/12/2023]
Abstract
Efficient production hosts are a key requirement for bringing biopharmaceutical and biotechnological innovations to the market. In this work, a truly universal high-throughput platform for optimization of microbial protein production is described. Using droplet microfluidics, large genetic libraries of strains are encapsulated into biocompatible gel beads that are engineered to selectively retain any protein of interest. Bead-retained products are then fluorescently labeled and strains with superior production titers are isolated using flow cytometry. The broad applicability of the platform is demonstrated by successfully culturing several industrially relevant bacterial and yeast strains and detecting peptides or proteins of interest that are secreted or released from the cell via autolysis. Lastly, the platform is applied to optimize cutinase secretion in Komagataella phaffii (Pichia pastoris) and a strain with 5.7-fold improvement is isolated. The platform permits the analysis of >106 genotypes per day and is readily applicable to any protein that can be equipped with a His6 -tag. It is envisioned that the platform will be useful for large screening campaigns that aim to identify improved hosts for large-scale production of biotechnologically relevant proteins, thereby accelerating the costly and time-consuming process of strain engineering.
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Affiliation(s)
- Marta Napiorkowska
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Luzius Pestalozzi
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Martin Held
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
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24
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Wright NR, Rønnest NP, Sonnenschein N. Single-Cell Technologies to Understand the Mechanisms of Cellular Adaptation in Chemostats. Front Bioeng Biotechnol 2020; 8:579841. [PMID: 33392163 PMCID: PMC7775484 DOI: 10.3389/fbioe.2020.579841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
There is a growing interest in continuous manufacturing within the bioprocessing community. In this context, the chemostat process is an important unit operation. The current application of chemostat processes in industry is limited although many high yielding processes are reported in literature. In order to reach the full potential of the chemostat in continuous manufacture, the output should be constant. However, adaptation is often observed resulting in changed productivities over time. The observed adaptation can be coupled to the selective pressure of the nutrient-limited environment in the chemostat. We argue that population heterogeneity should be taken into account when studying adaptation in the chemostat. We propose to investigate adaptation at the single-cell level and discuss the potential of different single-cell technologies, which could be used to increase the understanding of the phenomena. Currently, none of the discussed single-cell technologies fulfill all our criteria but in combination they may reveal important information, which can be used to understand and potentially control the adaptation.
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Affiliation(s)
- Naia Risager Wright
- Novo Nordisk A/S, Bagsvaerd, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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25
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Peretzki AJ, Schmidt S, Flachowsky E, Das A, Gerhardt RF, Belder D. How electrospray potentials can disrupt droplet microfluidics and how to prevent this. LAB ON A CHIP 2020; 20:4456-4465. [PMID: 33103684 DOI: 10.1039/d0lc00936a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A pressure-resistant microfluidic glass chip that integrates a packed-bed HPLC column, a droplet generator and a monolithic electrospray emitter is presented. This approach enables a seamless coupling of chip-HPLC and droplet microfluidics with ESI-MS detection. For the electrical contacting of the emitter, an electrode was integrated into the channel, which reaches up to the emitter tip. The incidental finding that under certain circumstances, the electrospray potential can strongly disturb the droplet microfluidics by electrowetting, was investigated in detail. Strategies to avoid this are evaluated and include electrical shielding and/or chip layouts, where the droplet generator is positioned at a long distance from the emitter.
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Affiliation(s)
- Andrea J Peretzki
- Institute of Analytical Chemistry, Leipzig University, Johannisallee 29, D-04103 Leipzig, Germany.
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26
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Berlanda SF, Breitfeld M, Dietsche CL, Dittrich PS. Recent Advances in Microfluidic Technology for Bioanalysis and Diagnostics. Anal Chem 2020; 93:311-331. [DOI: 10.1021/acs.analchem.0c04366] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon F. Berlanda
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Maximilian Breitfeld
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Claudius L. Dietsche
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
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27
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Microfluidic Single-Cell Analytics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:159-189. [PMID: 32737554 DOI: 10.1007/10_2020_134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
What is the impact of cellular heterogeneity on process performance? How do individual cells contribute to averaged process productivity? Single-cell analysis is a key technology for answering such key questions of biotechnology, beyond bulky measurements with populations. The analysis of cellular individuality, its origins, and the dependency of process performance on cellular heterogeneity has tremendous potential for optimizing biotechnological processes in terms of metabolic, reaction, and process engineering. Microfluidics offer unmatched environmental control of the cellular environment and allow massively parallelized cultivation of single cells. However, the analytical accessibility to a cell's physiology is of crucial importance for obtaining the desired information on the single-cell production phenotype. Highly sensitive analytics are required to detect and quantify the minute amounts of target analytes and small physiological changes in a single cell. For their application to biotechnological questions, single-cell analytics must evolve toward the measurement of kinetics and specific rates of the smallest catalytic unit, the single cell. In this chapter, we focus on an introduction to the latest single-cell analytics and their application for obtaining physiological parameters in a biotechnological context from single cells. We present and discuss recent advancements in single-cell analytics that enable the analysis of cell-specific growth, uptake, and production kinetics, as well as the gene expression and regulatory mechanisms at a single-cell level.
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