1
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Cantwell C, McGrath JS, Smith CA, Whyte G. Image-Based Feedback of Multi-Component Microdroplets for Ultra-Monodispersed Library Preparation. MICROMACHINES 2023; 15:27. [PMID: 38258146 PMCID: PMC10820162 DOI: 10.3390/mi15010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]
Abstract
Using devices with microfluidic channels can allow for precise control over liquids flowing through them. Merging flows of immiscible liquids can create emulsions with highly monodispersed microdroplets within a carrier liquid, which are ideal for miniaturised reaction vessels which can be generated with a high throughput of tens of thousands of droplets per second. Control of the size and composition of these droplets is generally performed by controlling the pumping system pushing the liquids into the device; however, this is an indirect manipulation and inadequate if absolute precision is required in the size or composition of the droplets. In this work, we extend the previous development of image-based closed-loop feedback control over microdroplet generation to allow for the control of not only the size of droplets but also the composition by merging two aqueous flows. The feedback allows direct control over the desired parameters of volume and ratio of the two components over a wide range of ratios and outperforms current techniques in terms of monodispersity in volume and composition. This technique is ideal for situations where precise control over droplets is critical, or where a library of droplets of different concentrations but the same volume is required.
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Affiliation(s)
- Christy Cantwell
- Institute of Biochemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - John S. McGrath
- Institute of Biochemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
- Sphere Fluidics Limited, Granta Centre, Granta Park, Great Abington, Cambridge CB21 6AL, UK
| | - Clive A. Smith
- Sphere Fluidics Limited, Granta Centre, Granta Park, Great Abington, Cambridge CB21 6AL, UK
| | - Graeme Whyte
- Institute of Biochemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
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2
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McCully AL, Loop Yao M, Brower KK, Fordyce PM, Spormann AM. Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes. ISME COMMUNICATIONS 2023; 3:47. [PMID: 37160952 PMCID: PMC10169782 DOI: 10.1038/s43705-023-00241-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.
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Affiliation(s)
- Alexandra L McCully
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - McKenna Loop Yao
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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3
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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4
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Waghchoure AP, Reddy JP, Bhosale RS. Fluorescence based miniaturized microfluidic and nanofluidic systems for biomedical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:217-243. [PMID: 35033286 DOI: 10.1016/bs.pmbts.2021.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the last two decades miniaturized microfluidic and nanofluidic systems with fluorescence setup emerged as a powerful technological platform for diverse biomedical applications. Bio-macromolecules such as nucleic acids and proteins are the core cellular components, their single molecule analysis allow us to understand biological processes, disease creation and progression, and development of novel treatment policies. Design and development of foolproof treatment methods requires rigorously analysis of nucleic acids and proteins such as length quantifications, sequence profiling, sequence mapping, analysis of conformational changes, analysis and recognition of epigenetic changes, and their interactions with other biomolecules. Miniaturized microfluidic and nanofluidic systems with fluorescence spectroscopy enable worldwide researchers to perform nucleic acids and proteins extractions and single molecule analysis from the trace amount of biological samples. In the present chapter we mostly highlighted over one decade applications of microfluidic and nanofluidic systems for single cell micro ribonucleic acid (miRNA) isolation and detection, deoxyribonucleic acid (DNA) mapping, DNA barcoding, identification of epigenetic mark on single DNA molecule, DNA-protein interactions study, protein sensing, protein sequencing, protein binding kinetics and many other applications. We also presented the recently reported microfluidic platform for the preparation of reproducible unisize aggregation induced emission (AIE) active nanomaterials and their biological applications.
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Affiliation(s)
| | - J Prakasha Reddy
- Department of Chemistry, Indrashil University, Rajpur, Mehsana, Gujarat, India.
| | - Rajesh S Bhosale
- Department of Chemistry, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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5
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Nazari H, Heirani-Tabasi A, Ghorbani S, Eyni H, Razavi Bazaz S, Khayati M, Gheidari F, Moradpour K, Kehtari M, Ahmadi Tafti SM, Ahmadi Tafti SH, Ebrahimi Warkiani M. Microfluidic-Based Droplets for Advanced Regenerative Medicine: Current Challenges and Future Trends. BIOSENSORS 2021; 12:20. [PMID: 35049648 PMCID: PMC8773546 DOI: 10.3390/bios12010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
Microfluidics is a promising approach for the facile and large-scale fabrication of monodispersed droplets for various applications in biomedicine. This technology has demonstrated great potential to address the limitations of regenerative medicine. Microfluidics provides safe, accurate, reliable, and cost-effective methods for encapsulating different stem cells, gametes, biomaterials, biomolecules, reagents, genes, and nanoparticles inside picoliter-sized droplets or droplet-derived microgels for different applications. Moreover, microenvironments made using such droplets can mimic niches of stem cells for cell therapy purposes, simulate native extracellular matrix (ECM) for tissue engineering applications, and remove challenges in cell encapsulation and three-dimensional (3D) culture methods. The fabrication of droplets using microfluidics also provides controllable microenvironments for manipulating gametes, fertilization, and embryo cultures for reproductive medicine. This review focuses on the relevant studies, and the latest progress in applying droplets in stem cell therapy, tissue engineering, reproductive biology, and gene therapy are separately evaluated. In the end, we discuss the challenges ahead in the field of microfluidics-based droplets for advanced regenerative medicine.
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Affiliation(s)
- Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
| | - Asieh Heirani-Tabasi
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center Hospital, Tehran University of Medical Sciences, Tehran 14535, Iran; (A.H.-T.); (S.H.A.T.)
- Department of Cell Therapy and Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14535, Iran
| | - Sadegh Ghorbani
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark;
| | - Hossein Eyni
- Cellular and Molecular Research Center, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran;
- Department of Anatomical Sciences, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
| | - Maryam Khayati
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan 45371, Iran;
| | - Fatemeh Gheidari
- Department of Biotechnology, University of Tehran, Tehran 14535, Iran;
| | - Keyvan Moradpour
- Department of Chemical Engineering, Sharif University of Technology, Tehran 14535, Iran;
| | - Mousa Kehtari
- Department of Biology, Faculty of Science, University of Tehran, Tehran 14535, Iran;
| | - Seyed Mohsen Ahmadi Tafti
- Colorectal Surgery Research Center, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran 14535, Iran;
| | - Seyed Hossein Ahmadi Tafti
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center Hospital, Tehran University of Medical Sciences, Tehran 14535, Iran; (A.H.-T.); (S.H.A.T.)
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
- Institute of Molecular Medicine, Sechenov University, 119991 Moscow, Russia
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6
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Klaus M, Zurek PJ, Kaminski TS, Pushpanath A, Neufeld K, Hollfelder F. Ultrahigh-Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay. Chembiochem 2021; 22:3292-3299. [PMID: 34643305 PMCID: PMC9291573 DOI: 10.1002/cbic.202100322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Indexed: 12/02/2022]
Abstract
The exploration of large DNA libraries of metagenomic or synthetic origin is greatly facilitated by ultrahigh‐throughput assays that use monodisperse water‐in‐oil emulsion droplets as sequestered reaction compartments. Millions of samples can be generated and analysed in microfluidic devices at kHz speeds, requiring only micrograms of reagents. The scope of this powerful platform for the discovery of new sequence space is, however, hampered by the limited availability of assay substrates, restricting the functions and reaction types that can be investigated. Here, we broaden the scope of detectable biochemical transformations in droplet microfluidics by introducing the first fluorogenic assay for alcohol dehydrogenases (ADHs) in this format. We have synthesized substrates that release a pyranine fluorophore (8‐hydroxy‐1,3,6‐pyrenetrisulfonic acid, HPTS) when enzymatic turnover occurs. Pyranine is well retained in droplets for >6 weeks (i. e. 14‐times longer than fluorescein), avoiding product leakage and ensuring excellent assay sensitivity. Product concentrations as low as 100 nM were successfully detected, corresponding to less than one turnover per enzyme molecule on average. The potential of our substrate design was demonstrated by efficient recovery of a bona fide ADH with an >800‐fold enrichment. The repertoire of droplet screening is enlarged by this sensitive and direct fluorogenic assay to identify dehydrogenases for biocatalytic applications.
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Affiliation(s)
- Miriam Klaus
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Current address: ICB Nuvisan GmbH, Müllerstraße 178, 13353, Berlin, Germany
| | - Paul Jannis Zurek
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Johnson Matthey Plc, 260 Cambridge Science Park, CB4 0WE, Cambridge, UK.,Current address: BioNTech Cell & Gene Therapies GmbH, An der Goldgrube 12, 55131, Mainz, Germany
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Current address: Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Ahir Pushpanath
- Johnson Matthey Plc, 260 Cambridge Science Park, CB4 0WE, Cambridge, UK
| | - Katharina Neufeld
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Johnson Matthey Plc, 260 Cambridge Science Park, CB4 0WE, Cambridge, UK.,Current address: Janssen Pharmaceutica, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK
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7
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Toprakcioglu Z, Knowles TPJ. Sequential storage and release of microdroplets. MICROSYSTEMS & NANOENGINEERING 2021; 7:76. [PMID: 34631144 PMCID: PMC8481565 DOI: 10.1038/s41378-021-00303-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/25/2021] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
Abstract
Droplet microfluidic methods have opened up the possibility of studying a plethora of phenomena ranging from biological to physical or chemical processes at ultra low volumes and high throughput. A key component of such approaches is the ability to trap droplets for observation, and many device architectures for achieving this objective have been developed. A challenge with such approaches is, however, recovering the droplets following their confinement for applications involving further analysis. Here, we present a device capable of generating, confining and releasing microdroplets in a sequential manner. Through a combination of experimental and computational simulations, we shed light on the key features required for successful droplet storage and retrieval. Moreover, we explore the effect of the flow rate of the continuous phase on droplet release, determining that a critical rate is needed to ensure complete droplet deformation through constrictions holding the droplets in place prior to release. Finally, we find that once released, droplets can be retrieved and collected off chip. The ability to generate, store and sequentially release droplets renders such a device particularly promising for future applications where reactions may not only be monitored on-chip, but droplets can also be retrieved for further analysis, facilitating new exploratory avenues in the fields of analytical chemistry and biology.
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Affiliation(s)
- Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE UK
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8
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Gao Y, Zhao CX, Sainsbury F. Droplet shape control using microfluidics and designer biosurfactants. J Colloid Interface Sci 2021; 584:528-538. [PMID: 33129162 DOI: 10.1016/j.jcis.2020.09.126] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/23/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022]
Abstract
Many uses of emulsion droplets require precise control over droplet size and shape. Here we report a 'shape-memorable' micro-droplet formulation stabilized by a polyethylene glycol (PEG)-modified protein -surfactant, the droplets are stable against coalescence for months and can maintain non-spherical shapes for hours, depending on the surface coverage of PEGylated protein. Monodisperse droplets with aspect ratios ranging from 1.0 to 3.4 were controllably synthesized with a flow-focusing microfluidic device. Mechanical properties of the interfacial protein network were explored to elucidate the mechanism behind the droplet shape conservation phenomenon. Characterization of the protein film revealed that the presence of a PEG layer at interfaces alters the mechanical responses of the protein film, resulting in interfacial networks with improved strength. Taking advantage of the prolonged stabilization of non-spherical droplets, we demonstrate functionalization of the droplet interface with accessible biotins. The stabilization of micro-droplet shape with surface-active proteins that also serve as an anchor for integrating functional moieties, provides a tailorable interface for diverse biomimetic applications.
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Affiliation(s)
- Yuan Gao
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Chun-Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Frank Sainsbury
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia; Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia; Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organization (CSIRO), Brisbane, QLD 4001, Australia.
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9
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Hengoju S, Tovar M, Man DKW, Buchheim S, Rosenbaum MA. Droplet Microfluidics for Microbial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:129-157. [PMID: 32888037 DOI: 10.1007/10_2020_140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.
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Affiliation(s)
- Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - DeDe Kwun Wai Man
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - Stefanie Buchheim
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany.
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10
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Neun S, Zurek PJ, Kaminski TS, Hollfelder F. Ultrahigh throughput screening for enzyme function in droplets. Methods Enzymol 2020; 643:317-343. [PMID: 32896286 DOI: 10.1016/bs.mie.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Water-in-oil droplets, made and handled in microfluidic devices, provide a new experimental format, in which ultrahigh throughput experiments can be conducted faster and with minimal reagent consumption. An increasing number of studies have emerged that applied this approach to directed evolution and metagenomic screening of enzyme catalysts. Here, we review the considerations necessary to implement robust workflows, based on choices of device design, detection modes, emulsion formulations and substrates, and scope out which enzyme classes have become amenable to droplet screening.
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Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Paul J Zurek
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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11
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Sesen M, Whyte G. Image-Based Single Cell Sorting Automation in Droplet Microfluidics. Sci Rep 2020; 10:8736. [PMID: 32457421 PMCID: PMC7250914 DOI: 10.1038/s41598-020-65483-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
The recent boom in single-cell omics has brought researchers one step closer to understanding the biological mechanisms associated with cell heterogeneity. Rare cells that have historically been obscured by bulk measurement techniques are being studied by single cell analysis and providing valuable insight into cell function. To support this progress, novel upstream capabilities are required for single cell preparation for analysis. Presented here is a droplet microfluidic, image-based single-cell sorting technique that is flexible and programmable. The automated system performs real-time dual-camera imaging (brightfield & fluorescent), processing, decision making and sorting verification. To demonstrate capabilities, the system was used to overcome the Poisson loading problem by sorting for droplets containing a single red blood cell with 85% purity. Furthermore, fluorescent imaging and machine learning was used to load single K562 cells amongst clusters based on their instantaneous size and circularity. The presented system aspires to replace manual cell handling techniques by translating expert knowledge into cell sorting automation via machine learning algorithms. This powerful technique finds application in the enrichment of single cells based on their micrographs for further downstream processing and analysis.
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Affiliation(s)
- Muhsincan Sesen
- Heriot-Watt University, Institute of Biological Chemistry, Biophysics and Bioengineering, Edinburgh, EH14 4AS, United Kingdom
- Imperial College London, Department of Bioengineering, London, SW7 2AZ, United Kingdom
| | - Graeme Whyte
- Heriot-Watt University, Institute of Biological Chemistry, Biophysics and Bioengineering, Edinburgh, EH14 4AS, United Kingdom.
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12
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Liu L, Chen D, Wang J, Chen J. Advances of Single-Cell Protein Analysis. Cells 2020; 9:E1271. [PMID: 32443882 PMCID: PMC7290353 DOI: 10.3390/cells9051271] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Proteins play a significant role in the key activities of cells. Single-cell protein analysis provides crucial insights in studying cellular heterogeneities. However, the low abundance and enormous complexity of the proteome posit challenges in analyzing protein expressions at the single-cell level. This review summarizes recent advances of various approaches to single-cell protein analysis. We begin by discussing conventional characterization approaches, including fluorescence flow cytometry, mass cytometry, enzyme-linked immunospot assay, and capillary electrophoresis. We then detail the landmark advances of microfluidic approaches for analyzing single-cell protein expressions, including microfluidic fluorescent flow cytometry, droplet-based microfluidics, microwell-based assay (microengraving), microchamber-based assay (barcoding microchips), and single-cell Western blotting, among which the advantages and limitations are compared. Looking forward, we discuss future research opportunities and challenges for multiplexity, analyte, throughput, and sensitivity of the microfluidic approaches, which we believe will prompt the research of single-cell proteins such as the molecular mechanism of cell biology, as well as the clinical applications for tumor treatment and drug development.
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Affiliation(s)
- Lixing Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
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13
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van Tatenhove-Pel RJ, Hernandez-Valdes JA, Teusink B, Kuipers OP, Fischlechner M, Bachmann H. Microdroplet screening and selection for improved microbial production of extracellular compounds. Curr Opin Biotechnol 2020; 61:72-81. [DOI: 10.1016/j.copbio.2019.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/26/2022]
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14
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Chen P, Chen D, Li S, Ou X, Liu BF. Microfluidics towards single cell resolution protein analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Wang X, Sun M, Ferguson SA, Hoff JD, Qin Y, Bailey RC, Meyerhoff ME. Ionophore‐Based Biphasic Chemical Sensing in Droplet Microfluidics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902960] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xuewei Wang
- Department of Chemistry University of Michigan 930 N University Ann Arbor MI 48109 USA
| | - Meng Sun
- Department of Chemistry University of Michigan 930 N University Ann Arbor MI 48109 USA
- Department of Biophysics University of Michigan 930 N University Ann Arbor MI 48109 USA
| | - Stephen A. Ferguson
- Department of Chemistry University of Michigan 930 N University Ann Arbor MI 48109 USA
| | - J. Damon Hoff
- Department of Biophysics University of Michigan 930 N University Ann Arbor MI 48109 USA
| | - Yu Qin
- Department of Chemistry University of Michigan 930 N University Ann Arbor MI 48109 USA
| | - Ryan C. Bailey
- Department of Chemistry University of Michigan 930 N University Ann Arbor MI 48109 USA
| | - Mark E. Meyerhoff
- Department of Chemistry University of Michigan 930 N University Ann Arbor MI 48109 USA
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16
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Ionophore‐Based Biphasic Chemical Sensing in Droplet Microfluidics. Angew Chem Int Ed Engl 2019; 58:8092-8096. [DOI: 10.1002/anie.201902960] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/14/2019] [Indexed: 01/24/2023]
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17
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Shojaeian M, Lehr FX, Göringer HU, Hardt S. On-Demand Production of Femtoliter Drops in Microchannels and Their Use as Biological Reaction Compartments. Anal Chem 2019; 91:3484-3491. [DOI: 10.1021/acs.analchem.8b05063] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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18
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Kleine-Brüggeney H, van Vliet LD, Mulas C, Gielen F, Agley CC, Silva JCR, Smith A, Chalut K, Hollfelder F. Long-Term Perfusion Culture of Monoclonal Embryonic Stem Cells in 3D Hydrogel Beads for Continuous Optical Analysis of Differentiation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804576. [PMID: 30570812 DOI: 10.1002/smll.201804576] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/02/2018] [Indexed: 06/09/2023]
Abstract
Developmental cell biology requires technologies in which the fate of single cells is followed over extended time periods, to monitor and understand the processes of self-renewal, differentiation, and reprogramming. A workflow is presented, in which single cells are encapsulated into droplets (Ø: 80 µm, volume: ≈270 pL) and the droplet compartment is later converted to a hydrogel bead. After on-chip de-emulsification by electrocoalescence, these 3D scaffolds are subsequently arrayed on a chip for long-term perfusion culture to facilitate continuous cell imaging over 68 h. Here, the response of murine embryonic stem cells to different growth media, 2i and N2B27, is studied, showing that the exit from pluripotency can be monitored by fluorescence time-lapse microscopy, by immunostaining and by reverse-transcription and quantitative PCR (RT-qPCR). The defined 3D environment emulates the natural context of cell growth (e.g., in tissue) and enables the study of cell development in various matrices. The large scale of cell cultivation (in 2000 beads in parallel) may reveal infrequent events that remain undetected in lower throughput or ensemble studies. This platform will help to gain qualitative and quantitative mechanistic insight into the role of external factors on cell behavior.
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Affiliation(s)
- Hans Kleine-Brüggeney
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Carla Mulas
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Chibeza C Agley
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - José C R Silva
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Austin Smith
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Kevin Chalut
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
- Department of Physics, University of Cambridge, 19 J J Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
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19
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Ngara TR, Zhang H. Recent Advances in Function-based Metagenomic Screening. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:405-415. [PMID: 30597257 PMCID: PMC6411959 DOI: 10.1016/j.gpb.2018.01.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/01/2022]
Abstract
Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.
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Affiliation(s)
- Tanyaradzwa Rodgers Ngara
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
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20
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Alam MK, Koomson E, Zou H, Yi C, Li CW, Xu T, Yang M. Recent advances in microfluidic technology for manipulation and analysis of biological cells (2007–2017). Anal Chim Acta 2018; 1044:29-65. [DOI: 10.1016/j.aca.2018.06.054] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022]
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21
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Toprakcioglu Z, Challa PK, Levin A, Knowles TPJ. Observation of molecular self-assembly events in massively parallel microdroplet arrays. LAB ON A CHIP 2018; 18:3303-3309. [PMID: 30270398 DOI: 10.1039/c8lc00862k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The self-assembly of peptide and protein molecules into nanoscale filaments is a process associated with both biological function and malfunction. Microfluidic techniques can provide powerful tools in the study of such aggregation phenomena while providing access to exploring the role of molecular interactions in disease development. Yet, a common challenge encountered in the study of protein aggregation is the difficulty in achieving spatial and temporal control of the underlying processes. Here, we present a planar (2-D) device allowing for both the generation and confinement of 10 000 monodisperse water-in-oil droplets in an array of chambers with a trapping efficiency of 99%. Due to the specific geometry of the device, droplets can be formed and immediately trapped on the same chip, without the need for continuous flow of the oil phase. Furthermore, we demonstrate the capability of this device as a platform to study the aggregation kinetics and determine stochastic molecular nanoscale self-assembly events in a highly parallel manner for the aggregation of the dipeptide, diphenylalanine, the core recognition motif of the Aβ-42 peptide associated with Alzheimer's disease. The ability to reproducibly generate and confine monodisperse water-in-oil droplets with an extremely high trapping efficiency while maintaining entrapment under zero-flow conditions, on timescales compatible with observing molecular self-assembly events, renders it promising for numerous potential further applications in the biological and biophysical fields.
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Affiliation(s)
- Zenon Toprakcioglu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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22
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Negou JT, Hu J, Li X, Easley CJ. Advancement of analytical modes in a multichannel, microfluidic droplet-based sample chopper employing phase-locked detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2018; 10:3436-3443. [PMID: 30505354 PMCID: PMC6258173 DOI: 10.1039/c8ay00947c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In this work, we expand upon our recently developed droplet-based sample chopping concepts by introducing a multiplexed fluidic micro-chopper device (μChopper). Six aqueous input channels were integrated with a single oil input, and each of these seven channels was controlled by a pneumatic valve for automated sampling through software control. This improved design, while maintaining high precision in valve-based droplet generation at bandwidths of 0.03 to 0.05 Hz, enabled a variety of analytical modes to be employed on-chip compared to previous devices limited to sample/reference alternations. The device was analytically validated for real-time, continuous calibration with a single sample and five standards; multiplexed analysis during calibration using a mixed mode; and standard addition through spiking of six sample droplets with varying amounts of standard. Finally, the standard addition mode was applied to protein quantification in human serum samples using on-chip, homogeneous fluorescence immunoassays. Ultimately, with only ~1.2 μL of total analyzed solution volume- representing 100-fold and 75-fold reductions in reagent and serum volumes, respectively-we were able to generate full, six-point standard addition curves in only 1.5 min, and results correlated well with those from standard plate-reader equipment. This work thus exploited microfluidic valves for both their automation and droplet phase-locking capabilities, resulting in a micro-analytical tool capable of complex analytical interrogation modes on sub-microliter sample volumes while also leveraging drastic noise rejection via lock-in detection. The multichannel μChopper device should prove particularly useful in analyzing precious biological samples or for dynamic analyses at small volume scales.
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Affiliation(s)
- Jean T. Negou
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Juan Hu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Xiangpeng Li
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
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23
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Mbanjwa MB, Land KJ, Windvoel T, Papala PM, Fourie L, Korvink JG, Visser D, Brady D. Production of self-immobilised enzyme microspheres using microfluidics. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Ven K, Vanspauwen B, Pérez-Ruiz E, Leirs K, Decrop D, Gerstmans H, Spasic D, Lammertyn J. Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis. ACS Sens 2018; 3:264-284. [PMID: 29363316 DOI: 10.1021/acssensors.7b00873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.
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Affiliation(s)
- Karen Ven
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Bram Vanspauwen
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Karen Leirs
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Deborah Decrop
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Hans Gerstmans
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Department
of Applied biosciences, Ghent University, Valentyn Vaerwyckweg 1 - building
C, 9000 Gent, Belgium
- Department
of Biosystems, KU Leuven - University of Leuven, Kasteelpark Arenberg
21, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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25
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Girault M, Beneyton T, Pekin D, Buisson L, Bichon S, Charbonnier C, del Amo Y, Baret JC. High-Content Screening of Plankton Alkaline Phosphatase Activity in Microfluidics. Anal Chem 2018; 90:4174-4181. [DOI: 10.1021/acs.analchem.8b00234] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mathias Girault
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
| | - Thomas Beneyton
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
| | - Deniz Pekin
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
| | - Lionel Buisson
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
| | - Sabrina Bichon
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
| | - Céline Charbonnier
- Laboratoire d’Environnements et Paléoenvironnements Océaniques et Continentaux, Unité Mixte de Recherche 5805, Centre National de la Recherche Scientifique, 33615 Pessac, France
| | - Yolanda del Amo
- Laboratoire d’Environnements et Paléoenvironnements Océaniques et Continentaux, Unité Mixte de Recherche 5805, Centre National de la Recherche Scientifique, 33615 Pessac, France
| | - Jean-Christophe Baret
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
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26
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Abstract
Quantification of single-cell proteomics provides key insights in the field of cellular heterogeneity. This chapter discusses the emerging techniques that are being used to measure the protein copy numbers at the single-cell level, which includes flow cytometry, mass cytometry, droplet cytometry, microengraving, and single-cell barcoding microchip. The advantages and limitations of each technique are compared, and future research opportunities are highlighted.
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27
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Hammink R, Eggermont LJ, Zisis T, Tel J, Figdor CG, Rowan AE, Blank KG. Affinity-Based Purification of Polyisocyanopeptide Bioconjugates. Bioconjug Chem 2017; 28:2560-2568. [PMID: 28846388 DOI: 10.1021/acs.bioconjchem.7b00398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Water-soluble polyisocyanopeptides (PICs) are a new class of synthetic polymers that mimic natural protein-based filaments. Their unique semiflexible properties combined with a length of several hundred nanometers have recently enabled a number of biomedical applications ranging from tissue engineering to cancer immunotherapy. One crucial step toward the further development of PICs for these applications is the efficient and controlled synthesis and purification of PIC-biomolecule conjugates. Considering the large size of PICs and the biomolecules to be conjugated, conjugation reactions do usually not proceed to completion due to steric effects. As a consequence, purification of the reaction mixture is necessary to separate the obtained bioconjugates from unreacted biomolecules. As a direct result of the semiflexible nature of PICs, standard polymer and protein purification methods based on molecular weight have not been successful. Here, we introduce a new affinity-based purification method utilizing biotin as an affinity tag. PICs decorated with a controlled and tunable density of biotin molecules (biotinPICs) were efficiently bound to and eluted from a monoavidin resin in buffered aqueous solution. Using these biotinPICs, two different protein conjugates were synthesized, one carrying the enzyme alkaline phosphatase (PhoA) and the other T-cell activating anti-CD3 antibodies. The resulting biotinPIC-protein conjugates were successfully obtained in high purity (>90%) and without any loss of protein activity. The high purity greatly simplifies the analysis of biotinPIC bioconjugates, such as the determination of the average number of biomolecules conjugated per biotinPIC chain. Most importantly, it allows for the direct and straightforward application of the obtained bioconjugates in the desired applications. The new method developed may further be adapted for the purification of other advanced bioconjugates that are difficult to obtain in high purity with the available standard methods.
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Affiliation(s)
- Roel Hammink
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands
| | - Loek J Eggermont
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands
| | - Themistoklis Zisis
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jurjen Tel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands.,Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Immunoengineering, Eindhoven University of Technology , De Zaale 15, 5612 AP Eindhoven, The Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands
| | - Alan E Rowan
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kerstin G Blank
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces , Potsdam-Golm Science Park, 14424 Potsdam, Germany
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28
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Crawford DF, Smith CA, Whyte G. Image-based closed-loop feedback for highly mono-dispersed microdroplet production. Sci Rep 2017; 7:10545. [PMID: 28874820 PMCID: PMC5585215 DOI: 10.1038/s41598-017-11254-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/21/2017] [Indexed: 11/19/2022] Open
Abstract
Micron-scale droplets isolated by an immiscible liquid can provide miniaturised reaction vessels which can be manipulated in microfluidic networks, and has seen a rapid growth in development. In many experiments, the precise volume of these microdroplets is a critical parameter which can be influenced by many external factors. In this work, we demonstrate the combination of imaging-based feedback and pressure driven pumping to accurately control the size of microdroplets produced in a microfluidic device. The use of fast-response, pressure-driving pumps allows the microfluidic flow to be quickly and accurately changed, while directly measuring the droplet size allows the user to define the more meaningful parameters of droplet size and generation frequency rather than flow rates or pressures. The feedback loop enables the drift correction of pressure based pumps, and leads to a large increase in the mono-dispersity of the droplets produced over long periods. We also show how this can be extended to control multiple liquid flows, allowing the frequency of droplet formation or the average concentration of living cells per droplet to be controlled and kept constant.
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Affiliation(s)
- D F Crawford
- Institute of Biochemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - C A Smith
- Sphere Fluidics Limited, The Jonas-Webb Building, Babraham Research Campus, Babraham, Cambridge, CB22 3AT, UK
| | - G Whyte
- Institute of Biochemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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29
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Real-time monitoring of hydrophobic aggregation reveals a critical role of cooperativity in hydrophobic effect. Nat Commun 2017; 8:15639. [PMID: 28561067 PMCID: PMC5460034 DOI: 10.1038/ncomms15639] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 04/13/2017] [Indexed: 12/24/2022] Open
Abstract
The hydrophobic interaction drives nonpolar solutes to aggregate in aqueous solution, and hence plays a critical role in many fundamental processes in nature. An important property intrinsic to hydrophobic interaction is its cooperative nature, which is originated from the collective motions of water hydrogen bond networks surrounding hydrophobic solutes. This property is widely believed to enhance the formation of hydrophobic core in proteins. However, cooperativity in hydrophobic interactions has not been successfully characterized by experiments. Here, we quantify cooperativity in hydrophobic interactions by real-time monitoring the aggregation of hydrophobic solute (hexaphenylsilole, HPS) in a microfluidic mixer. We show that association of a HPS molecule to its aggregate in water occurs at sub-microsecond, and the free energy change is −5.8 to −13.6 kcal mol−1. Most strikingly, we discover that cooperativity constitutes up to 40% of this free energy. Our results provide quantitative evidence for the critical role of cooperativity in hydrophobic interactions. Hydrophobic interactions occur between nonpolar molecules in water and their experimental quantification can help the understanding of biological self-assembly. Here Jiang et al. examine the kinetics and thermodynamics of hydrophobic aggregation in a bulk environment and characterize its cooperativity.
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30
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Lu H, Caen O, Vrignon J, Zonta E, El Harrak Z, Nizard P, Baret JC, Taly V. High throughput single cell counting in droplet-based microfluidics. Sci Rep 2017; 7:1366. [PMID: 28465615 PMCID: PMC5431057 DOI: 10.1038/s41598-017-01454-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 03/30/2017] [Indexed: 12/03/2022] Open
Abstract
Droplet-based microfluidics is extensively and increasingly used for high-throughput single-cell studies. However, the accuracy of the cell counting method directly impacts the robustness of such studies. We describe here a simple and precise method to accurately count a large number of adherent and non-adherent human cells as well as bacteria. Our microfluidic hemocytometer provides statistically relevant data on large populations of cells at a high-throughput, used to characterize cell encapsulation and cell viability during incubation in droplets.
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Affiliation(s)
- Heng Lu
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Ouriel Caen
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Jeremy Vrignon
- CNRS, Univ. Bordeaux, CRPP, UPR 8641, 115 Avenue Schweitzer, 33600, Pessac, France
| | - Eleonora Zonta
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Zakaria El Harrak
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Philippe Nizard
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | | | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
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31
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Mair P, Gielen F, Hollfelder F. Exploring sequence space in search of functional enzymes using microfluidic droplets. Curr Opin Chem Biol 2017; 37:137-144. [PMID: 28390246 DOI: 10.1016/j.cbpa.2017.02.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/08/2017] [Accepted: 02/15/2017] [Indexed: 12/21/2022]
Abstract
Screening of enzyme mutants in monodisperse picoliter compartments, generated at kilohertz speed in microfluidic devices, is coming of age. After a decade of proof-of-principle experiments, workflows have emerged that combine existing microfluidic modules to assay reaction progress quantitatively and yield improved enzymes. Recent examples of the screening of libraries of randomised proteins and from metagenomic sources suggest that this approach is not only faster and cheaper, but solves problems beyond the feasibility scope of current methodologies. The establishment of new assays in this format - so far covering hydrolases, aldolases, polymerases and dehydrogenases - will enable the exploration of sequence space for new catalysts of natural and non-natural chemical transformations.
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Affiliation(s)
- Philip Mair
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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32
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Choi A, Seo KD, Kim DW, Kim BC, Kim DS. Recent advances in engineering microparticles and their nascent utilization in biomedical delivery and diagnostic applications. LAB ON A CHIP 2017; 17:591-613. [PMID: 28101538 DOI: 10.1039/c6lc01023g] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Complex microparticles (MPs) bearing unique characteristics such as well-tailored sizes, various morphologies, and multi-compartments have been attempted to be produced by many researchers in the past decades. However, a conventionally used method of fabricating MPs, emulsion polymerization, has a limitation in achieving the aforementioned characteristics and several approaches such as the microfluidics-assisted (droplet-based microfluidics and flow lithography-based microfluidics), electrohydrodynamics (EHD)-based, centrifugation-based, and template-based methods have been recently suggested to overcome this limitation. The outstanding features of complex MPs engineered through these suggested methods have provided new opportunities for MPs to be applied in a wider range of applications including cell carriers, drug delivery agents, active pigments for display, microsensors, interface stabilizers, and catalyst substrates. Overall, the engineered MPs expose their potential particularly in the field of biomedical engineering as the increased complexity in the engineered MPs fulfills well the requirements of the high-end applications. This review outlines the current trends of newly developed techniques used for engineered MPs fabrication and focuses on the current state of engineered MPs in biomedical applications.
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Affiliation(s)
- Andrew Choi
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang City, Gyeongsangbuk-do 37673, South Korea.
| | - Kyoung Duck Seo
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang City, Gyeongsangbuk-do 37673, South Korea.
| | - Do Wan Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang City, Gyeongsangbuk-do 37673, South Korea.
| | - Bum Chang Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang City, Gyeongsangbuk-do 37673, South Korea.
| | - Dong Sung Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang City, Gyeongsangbuk-do 37673, South Korea.
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33
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Gielen F, Butz M, Rees EJ, Erdelyi M, Moschetti T, Hyvönen M, Edel JB, Kaminski CF, Hollfelder F. Quantitative Affinity Determination by Fluorescence Anisotropy Measurements of Individual Nanoliter Droplets. Anal Chem 2017; 89:1092-1101. [PMID: 28192993 PMCID: PMC5287478 DOI: 10.1021/acs.analchem.6b02528] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fluorescence anisotropy measurements of reagents compartmentalized into individual nanoliter droplets are shown to yield high-resolution binding curves from which precise dissociation constants (Kd) for protein-peptide interactions can be inferred. With the current platform, four titrations can be obtained per minute (based on ∼100 data points each), with stoichiometries spanning more than 2 orders of magnitude and requiring only tens of microliters of reagents. In addition to affinity measurements with purified components, Kd values for unpurified proteins in crude cell lysates can be obtained without prior knowledge of the concentration of the expressed protein, so that protein purification can be avoided. Finally, we show how a competition assay can be set up to perform focused library screens, so that compound labeling is not required anymore. These data demonstrate the utility of droplet compartments for the quantitative characterization of biomolecular interactions and establish fluorescence anisotropy imaging as a quantitative technique in a miniaturized droplet format, which is shown to be as reliable as its macroscopic test tube equivalent.
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Affiliation(s)
- Fabrice Gielen
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.,Living Systems Institute, University of Exeter , Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Maren Butz
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Eric J Rees
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom
| | - Miklos Erdelyi
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom.,Department of Optics and Quantum Electronics, University of Szeged , Dom ter 9, Szeged, Hungary
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Joshua B Edel
- Department of Chemistry, Imperial College London , South Kensington, London, SW7 2AZ, United Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, New Museums Site , Pembroke Street, Cambridge, CB2 3RA, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
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34
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Fiedler BL, Van Buskirk S, Carter KP, Qin Y, Carpenter MC, Palmer AE, Jimenez R. Droplet Microfluidic Flow Cytometer For Sorting On Transient Cellular Responses Of Genetically-Encoded Sensors. Anal Chem 2017; 89:711-719. [PMID: 27959493 PMCID: PMC6019271 DOI: 10.1021/acs.analchem.6b03235] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent biosensors are important measurement tools for in vivo quantification of pH, concentrations of metal ions and other analytes, and physical parameters such as membrane potential. Both the development of these sensors and their implementation in examining cellular heterogeneity requires technology for measuring and sorting cells based on the fluorescence levels before and after chemical or physical perturbations. We developed a droplet microfluidic platform for the screening and separation of cell populations on the basis of the in vivo response of expressed fluorescence-based biosensors after addition of an exogenous analyte. We demonstrate the capability to resolve the responses of two genetically encoded Zn2+ sensors at a range of time points spanning several seconds and subsequently sort a mixed-cell population of varying ratios with high accuracy.
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Affiliation(s)
- Brett L. Fiedler
- JILA, University of Colorado and NIST, Boulder CO 80309
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
| | | | - Kyle P. Carter
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- BioFrontiers Institute, University of Colorado, Boulder CO 80303
| | - Yan Qin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- Department of Biological Sciences, University of Denver, Denver, CO 80208
| | - Margaret C. Carpenter
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- BioFrontiers Institute, University of Colorado, Boulder CO 80303
| | - Amy E. Palmer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- BioFrontiers Institute, University of Colorado, Boulder CO 80303
| | - Ralph Jimenez
- JILA, University of Colorado and NIST, Boulder CO 80309
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
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35
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Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L. Single-cell barcoding and sequencing using droplet microfluidics. Nat Protoc 2016; 12:44-73. [PMID: 27929523 DOI: 10.1038/nprot.2016.154] [Citation(s) in RCA: 424] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour. A suspension of cells is first encapsulated into nanoliter droplets with hydrogel beads (HBs) bearing barcoding DNA primers. Cells are then lysed and mRNA is barcoded (indexed) by a reverse transcription (RT) reaction. Here we provide details for (i) establishing an inDrops platform (1 d); (ii) performing hydrogel bead synthesis (4 d); (iii) encapsulating and barcoding cells (1 d); and (iv) RNA-seq library preparation (2 d). inDrops is a robust and scalable platform, and it is unique in its ability to capture and profile >75% of cells in even very small samples, on a scale of thousands or tens of thousands of cells.
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Affiliation(s)
- Rapolas Zilionis
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Juozas Nainys
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Adrian Veres
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Virginia Savova
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - David Zemmour
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Linas Mazutis
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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36
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Horka M, Sun S, Ruszczak A, Garstecki P, Mayr T. Lifetime of Phosphorescence from Nanoparticles Yields Accurate Measurement of Concentration of Oxygen in Microdroplets, Allowing One To Monitor the Metabolism of Bacteria. Anal Chem 2016; 88:12006-12012. [DOI: 10.1021/acs.analchem.6b03758] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Michał Horka
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Shiwen Sun
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse9/2, 8010 Graz, Austria
| | - Artur Ruszczak
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Piotr Garstecki
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Torsten Mayr
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse9/2, 8010 Graz, Austria
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37
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Wen N, Zhao Z, Fan B, Chen D, Men D, Wang J, Chen J. Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis. Molecules 2016; 21:E881. [PMID: 27399651 PMCID: PMC6272933 DOI: 10.3390/molecules21070881] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1) prototype demonstration of single-cell encapsulation in microfluidic droplets; (2) technical improvements of single-cell encapsulation in microfluidic droplets; (3) microfluidic droplets enabling single-cell proteomic analysis; (4) microfluidic droplets enabling single-cell genomic analysis; and (5) integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.
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Affiliation(s)
- Na Wen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhan Zhao
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Beiyuan Fan
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Deyong Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dong Men
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Junbo Wang
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jian Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
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38
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Karle M, Vashist SK, Zengerle R, von Stetten F. Microfluidic solutions enabling continuous processing and monitoring of biological samples: A review. Anal Chim Acta 2016; 929:1-22. [DOI: 10.1016/j.aca.2016.04.055] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 04/26/2016] [Accepted: 04/30/2016] [Indexed: 01/25/2023]
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39
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Kaminski TS, Scheler O, Garstecki P. Droplet microfluidics for microbiology: techniques, applications and challenges. LAB ON A CHIP 2016; 16:2168-87. [PMID: 27212581 DOI: 10.1039/c6lc00367b] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.
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Affiliation(s)
- Tomasz S Kaminski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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40
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Jo Y, Shen F, Hahn YK, Park JH, Park JK. Magnetophoretic Sorting of Single Cell-Containing Microdroplets. MICROMACHINES 2016; 7:mi7040056. [PMID: 30407429 PMCID: PMC6190288 DOI: 10.3390/mi7040056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 03/23/2016] [Accepted: 03/28/2016] [Indexed: 11/16/2022]
Abstract
Droplet microfluidics is a promising tool for single-cell analysis since single cell can be comparted inside a tiny volume. However, droplet encapsulation of single cells still remains a challenging issue due to the low ratio of droplets containing single cells. Here, we introduce a simple and robust single cell sorting platform based on a magnetophoretic method using monodisperse magnetic nanoparticles (MNPs) and droplet microfluidics with >94% purity. There is an approximately equal amount of MNPs in the same-sized droplet, which has the same magnetic force under the magnetic field. However, the droplets containing single cells have a reduced number of MNPs, as much as the volume of the cell inside the droplet, resulting in a low magnetic force. Based on this simple principle, this platform enables the separation of single cell-encapsulated droplets from the droplets with no cells. Additionally, this device uses only a permanent magnet without any complex additional apparatus; hence, this new platform can be integrated into a single cell analysis system considering its effectiveness and convenience.
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Affiliation(s)
- Younggeun Jo
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Fengshan Shen
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Young Ki Hahn
- Samsung Electronics, 4 Seocho-daero 74-gil, Seocho-gu, Seoul 06620, Republic of Korea.
| | - Ji-Ho Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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41
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Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization. SENSORS 2016; 16:232. [PMID: 26891303 PMCID: PMC4801608 DOI: 10.3390/s16020232] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
This article reviews recent developments in microfluidic systems enabling high-throughput characterization of single-cell proteins. Four key perspectives of microfluidic platforms are included in this review: (1) microfluidic fluorescent flow cytometry; (2) droplet based microfluidic flow cytometry; (3) large-array micro wells (microengraving); and (4) large-array micro chambers (barcode microchips). We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on three key performance parameters (absolute quantification, sensitivity, and throughput).
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42
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Reply to "Considerations regarding the micromagnetic resonance relaxometry technique for rapid label-free malaria diagnosis". Nat Med 2015; 21:1387-9. [DOI: 10.1038/nm.3959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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43
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Colin PY, Zinchenko A, Hollfelder F. Enzyme engineering in biomimetic compartments. Curr Opin Struct Biol 2015; 33:42-51. [PMID: 26311177 DOI: 10.1016/j.sbi.2015.06.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/12/2015] [Accepted: 06/04/2015] [Indexed: 12/25/2022]
Abstract
The success of a directed evolution approach to creating custom-made enzymes relies in no small part on screening as many clones as possible. The miniaturisation of assays into pico to femtoliter compartments (emulsion droplets, vesicles or gel-shell beads) makes directed evolution campaigns practically more straightforward than current large scale industrial screening that requires liquid handling equipment and much manpower. Several recent experimental formats have established protocols to screen more than 10 million compartments per day, representing unprecedented throughput at low cost. This review introduces the emerging approaches towards making biomimetic man-made compartments that are poised to be adapted by a wider circle of researchers. In addition to cost and time saving, control of selection pressures and conditions, the quantitative readout that reports on every library members and the ability to develop strategies based on these data will increase the degrees of freedom in designing and testing strategies for directed evolution experiments.
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Affiliation(s)
- Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
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44
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Schiller UD, Fleury JB, Seemann R, Gompper G. Collective waves in dense and confined microfluidic droplet arrays. SOFT MATTER 2015; 11:5850-5861. [PMID: 26107262 DOI: 10.1039/c5sm01116g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Excitation mechanisms for collective waves in confined dense one-dimensional microfluidic droplet arrays are investigated by experiments and computer simulations. We demonstrate that distinct modes can be excited by creating specific 'defect' patterns in flowing droplet trains. Excited longitudinal modes exhibit a short-lived cascade of pairs of laterally displacing droplets. Transversely excited modes obey the dispersion relation of microfluidic phonons and induce a coupling between longitudinal and transverse modes, whose origin is the hydrodynamic interaction of the droplets with the confining walls. Moreover, we investigate the long-time behaviour of the oscillations and discuss possible mechanisms for the onset of instabilities. Our findings demonstrate that the collective dynamics of microfluidic droplet ensembles can be studied particularly well in dense and confined systems. Experimentally, the ability to control microfluidic droplets may allow the modulation of the refractive index of optofluidic crystals, which is a promising approach for the production of dynamically programmable metamaterials.
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Affiliation(s)
- Ulf D Schiller
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany.
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45
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van Vliet LD, Colin PY, Hollfelder F. Bioinspired genotype-phenotype linkages: mimicking cellular compartmentalization for the engineering of functional proteins. Interface Focus 2015; 5:20150035. [PMID: 26464791 PMCID: PMC4590426 DOI: 10.1098/rsfs.2015.0035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The idea of compartmentalization of genotype and phenotype in cells is key for enabling Darwinian evolution. This contribution describes bioinspired systems that use in vitro compartments-water-in-oil droplets and gel-shell beads-for the directed evolution of functional proteins. Technologies based on these principles promise to provide easier access to protein-based therapeutics, reagents for processes involving enzyme catalysis, parts for synthetic biology and materials with biological components.
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Affiliation(s)
| | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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46
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Abbaspourrad A, Zhang H, Tao Y, Cui N, Asahara H, Zhou Y, Yue D, Koehler SA, Ung LW, Heyman J, Ren Y, Ziblat R, Chong S, Weitz DA. Label-free single-cell protein quantification using a drop-based mix-and-read system. Sci Rep 2015; 5:12756. [PMID: 26234416 PMCID: PMC4522677 DOI: 10.1038/srep12756] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/22/2015] [Indexed: 12/14/2022] Open
Abstract
Quantitative protein analysis of single cells is rarely achieved due to technical difficulties of detecting minute amounts of proteins present in one cell. We develop a mix-and-read assay for drop-based label-free protein analysis of single cells. This high-throughput method quantifies absolute, rather than relative, amounts of proteins and does not involve antibody labeling or mass spectrometry.
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Affiliation(s)
- Alireza Abbaspourrad
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Huidan Zhang
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
| | - Ye Tao
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Naiwen Cui
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Haruichi Asahara
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Ying Zhou
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Dongxian Yue
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Stephan A Koehler
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Lloyd W Ung
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - John Heyman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Yukun Ren
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Roy Ziblat
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Shaorong Chong
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - David A Weitz
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Physics, Harvard University, Cambridge, MA 02138, USA
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47
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Affiliation(s)
- Hu Zhang
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Xiaolin Cui
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Jingxiu Bi
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Sheng Dai
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Haitao Ye
- School of Engineering and Applied Science; Aston University; Birmingham United Kingdom
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48
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Affiliation(s)
- Jialan Cao
- Department of Physical Chemistry and Microreaction Technology; Institute for Micro and Nanotechnologies/Institute for Chemistry and Biotechnology; Ilmenau University of Technology; Ilmenau Germany
| | - Johann Michael Köhler
- Department of Physical Chemistry and Microreaction Technology; Institute for Micro and Nanotechnologies/Institute for Chemistry and Biotechnology; Ilmenau University of Technology; Ilmenau Germany
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49
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Ng EX, Miller MA, Jing T, Lauffenburger DA, Chen CH. Low-volume multiplexed proteolytic activity assay and inhibitor analysis through a pico-injector array. LAB ON A CHIP 2015; 15:1153-1159. [PMID: 25553996 DOI: 10.1039/c4lc01162g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Secreted active proteases, from families of enzymes such as matrix metalloproteinases (MMPs) and ADAMs (a disintegrin and metalloproteinases), participate in diverse pathological processes. To simultaneously measure multiple specific protease activities, a series of parallel enzyme reactions combined with a series of inhibitor analyses for proteolytic activity matrix analysis (PrAMA) are essential but limited due to the sample quantity requirements and the complexity of performing multiple reactions. To address these issues, we developed a pico-injector array to generate 72 different reactions in picoliter-volume droplets by controlling the sequence of combinational injections, which allowed simultaneous recording of a wide range of multiple enzyme reactions and measurement of inhibitor effects using small sample volumes (~10 μL). Multiple MMP activities were simultaneously determined by 9 different substrates and 2 inhibitors using injections from a pico-injector array. Due to the advantages of inhibitor analysis, the MMP/ADAM activities of MDA-MB-231, a breast cancer cell line, were characterized with high MMP-2, MMP-3 and ADAM-10 activity. This platform could be customized for a wide range of applications that also require multiple reactions with inhibitor analysis to enhance the sensitivity by encapsulating different chemical sensors.
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Affiliation(s)
- Ee Xien Ng
- Department of Biomedical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore.
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Li Y, Yan L, Liu Y, Qian K, Liu B, Yang P, Liu B. High-efficiency nano/micro-reactors for protein analysis. RSC Adv 2015. [DOI: 10.1039/c4ra12333f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This article reviews the recent advances regarding the development of nanomaterial-based nanoreactors and microfluidic droplet reactors and their applications in protein analysis.
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Affiliation(s)
- Yixin Li
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Ling Yan
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Yun Liu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Kun Qian
- Center for Bio-Nano-Chips and Diagnostics in Translational Medicine
- School of Biomedical Engineering and Med-X Research Institute
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Bin Liu
- Center for Bio-Nano-Chips and Diagnostics in Translational Medicine
- School of Biomedical Engineering and Med-X Research Institute
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Baohong Liu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
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