1
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Hoshino M, Ota Y, Suyama T, Morishita Y, Tsuneda S, Noda N. Water-in-oil droplet-mediated method for detecting and isolating infectious bacteriophage particles via fluorescent staining. Front Microbiol 2023; 14:1282372. [PMID: 38125569 PMCID: PMC10731258 DOI: 10.3389/fmicb.2023.1282372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Bacteriophages are the most abundant entities on Earth. In contrast with the number of phages considered to be in existence, current phage isolation and screening methods lack throughput. Droplet microfluidic technology has been established as a platform for high-throughput screening of biological and biochemical components. In this study, we developed a proof-of-concept method for isolating phages using water-in-oil droplets (droplets) as individual chambers for phage propagation and co-cultivating T2 phage and their host cell Escherichia coli within droplets. Liquid cultivation of microbes will facilitate the use of microbes that cannot grow on or degrade agar as host cells, ultimately resulting in the acquisition of phages that infect less known bacterial cells. The compartmentalizing characteristic of droplets and the use of a fluorescent dye to stain phages simultaneously enabled the enumeration and isolation of viable phage particles. We successfully recultivated the phages after simultaneously segregating single phage particles into droplets and inoculating them with their host cells within droplets. By recovering individual droplets into 96-well plates, we were able to isolate phage clones derived from single phage particles. The success rate for phage recovery was 35.7%. This study lays the building foundations for techniques yet to be developed that will involve the isolation and rupturing of droplets and provides a robust method for phage enumeration and isolation.
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Affiliation(s)
- Miu Hoshino
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Yuri Ota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
- On-chip Biotechnologies Co., Ltd., Tokyo, Japan
| | - Tetsushi Suyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | | | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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2
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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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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Voci S, Clarke TB, Dick JE. Abiotic microcompartments form when neighbouring droplets fuse: an electrochemiluminescence investigation. Chem Sci 2023; 14:2336-2341. [PMID: 36873831 PMCID: PMC9977408 DOI: 10.1039/d2sc06553c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022] Open
Abstract
Many studies have shown chemistry proceeds differently in small volumes compared to bulk phases. However, few studies exist elucidating spontaneous means by which small volumes can form in Nature. Such studies are critical in understanding the formation of life in microcompartments. In this study, we track in real-time the coalescence of two or more water microdroplets adsorbed on an electrified surface in a 1,2-dichloroethane continuous phase by electrogenerated chemiluminescence (ECL) imaging, uncovering the spontaneous generation of multiple emulsions inside the resulting water droplets. During the fusion of adsorbed water droplets with each other on the electrode surface, volumes of organic and water phases are entrapped in between and detected respectively as ECL not-emitting and emitting regions. The diameter of those confined environments inside the water droplets can be less than a micrometer, as described by scanning electron microscopy data. This study adds a new mechanism for the generation of micro- and nano-emulsions and provides insight into confinement techniques under abiotic conditions as well as new potential strategies in microfluidic devices.
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Affiliation(s)
- Silvia Voci
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
| | - Thomas B Clarke
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
| | - Jeffrey E Dick
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA .,Elmore Family School of Electrical and Computer Engineering, Purdue University West Lafayette IN 47907 USA
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5
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Dong J, Li G, Xia L. Microfluidic Magnetic Spatial Confinement Strategy for the Enrichment and Ultrasensitive Detection of MCF-7 and Escherichia coli O157:H7. Anal Chem 2022; 94:16901-16909. [DOI: 10.1021/acs.analchem.2c04314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Jianwei Dong
- School of Chemistry, Sun Yat-sen University, Guangzhou510006, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou510006, China
| | - Ling Xia
- School of Chemistry, Sun Yat-sen University, Guangzhou510006, China
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6
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Utharala R, Grab A, Vafaizadeh V, Peschke N, Ballinger M, Turei D, Tuechler N, Ma W, Ivanova O, Ortiz AG, Saez-Rodriguez J, Merten CA. A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets. Nat Protoc 2022; 17:2920-2965. [PMID: 36261631 DOI: 10.1038/s41596-022-00740-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Droplet microfluidics is a powerful tool for a variety of biological applications including single-cell genetics, antibody discovery and directed evolution. All these applications make use of genetic libraries, illustrating the difficulty of generating chemically distinct droplets for screening applications. This protocol describes our Braille Display valving platform for on-demand generation of droplets with different chemical contents (16 different reagents and combinations thereof), as well as sorting droplets with different chemical properties, on the basis of fluorescence signals. The Braille Display platform is compact, versatile and cost efficient (only ~US$1,000 on top of a standard droplet microfluidics setup). The procedure includes manufacturing of microfluidic chips, assembly of custom hardware, co-encapsulation of cells and drugs into droplets, fluorescence detection of readout signals and data analysis using shared, freely available LabVIEW and Python packages. As a first application, we demonstrate the complete workflow for screening cancer cell drug sensitivities toward 74 conditions. Furthermore, we describe here an assay enabling the normalization of the observed drug sensitivity to the number of cancer cells per droplet, which additionally increases the robustness of the system. As a second application, we also demonstrate the sorting of droplets according to enzymatic activity. The drug screening application can be completed within 2 d; droplet sorting takes ~1 d; and all preparatory steps for manufacturing molds, chips and setting up the Braille controller can be accomplished within 1 week.
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Affiliation(s)
- Ramesh Utharala
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anna Grab
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Clinical Cooperation Unit Molecular Hematology/Oncology, DKFZ Heidelberg and Translational Myeloma Research Group, Department of Internal Medicine V, University Hospital, Heidelberg, Germany
| | - Vida Vafaizadeh
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nicolas Peschke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martine Ballinger
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Denes Turei
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Nadine Tuechler
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Wenwei Ma
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olga Ivanova
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany.,Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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7
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Geersens É, Vuilleumier S, Ryckelynck M. Growth-Associated Droplet Shrinkage for Bacterial Quantification, Growth Monitoring, and Separation by Ultrahigh-Throughput Microfluidics. ACS OMEGA 2022; 7:12039-12047. [PMID: 35449964 PMCID: PMC9016821 DOI: 10.1021/acsomega.2c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/17/2022] [Indexed: 05/08/2023]
Abstract
Microbiology still relies on en masse cultivation for selection, isolation, and characterization of microorganisms of interest. This constrains the diversity of microbial types and metabolisms that can be investigated in the laboratory also because of intercellular competition during cultivation. Cell individualization by droplet-based microfluidics prior to experimental analysis provides an attractive alternative to access a larger fraction of the microbial biosphere, miniaturizing the required equipment and minimizing reagent use for increased and more efficient analytical throughput. Here, we show that cultivation of a model two-strain bacterial community in droplets significantly reduces representation bias in the grown culture compared to batch cultivation. Further, and based on the droplet shrinkage observed upon cell proliferation, we provide proof-of-concept for a simple strategy that allows absolute quantification of microbial cells in a sample as well as selective recovery of microorganisms of interest for subsequent experimental characterization.
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Affiliation(s)
- Émilie Geersens
- Université
de Strasbourg, CNRS, Architecture
et Réactivité de l’ARN, UPR 9002, 67000 Strasbourg, France
- Université
de Strasbourg, CNRS, Génétique
Moléculaire, Génomique, Microbiologie, UMR 7156, 67000 Strasbourg, France
| | - Stéphane Vuilleumier
- Université
de Strasbourg, CNRS, Génétique
Moléculaire, Génomique, Microbiologie, UMR 7156, 67000 Strasbourg, France
| | - Michael Ryckelynck
- Université
de Strasbourg, CNRS, Architecture
et Réactivité de l’ARN, UPR 9002, 67000 Strasbourg, France
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8
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Nakamura A, Honma N, Tanaka Y, Suzuki Y, Shida Y, Tsuda Y, Hidaka K, Ogasawara W. 7-Aminocoumarin-4-acetic Acid as a Fluorescent Probe for Detecting Bacterial Dipeptidyl Peptidase Activities in Water-in-Oil Droplets and in Bulk. Anal Chem 2021; 94:2416-2424. [PMID: 34963280 PMCID: PMC8886566 DOI: 10.1021/acs.analchem.1c04108] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Droplet-based
microfluidic systems are a powerful tool for biological
assays with high throughput. Water-in-oil droplets (WODLs) are typically
used in droplet-based microfluidic systems to culture microorganisms
and perform enzyme assays. However, because of the oil surrounding
the nanoliter and picoliter volumes of WODLs, availability of suitable
substrates is limited. For instance, although 7-amino-4-methylcoumarin
(AMC) is commonly used as a fluorescent probe of the substrate to
detect peptidase activity, AMC leaks from WODLs to the oil phase due
to its high hydrophobicity. Thus, AMC substrates cannot be used in
droplet-based microfluidic systems with WODLs. In this study, we developed
a peptidase substrate consisting of a dipeptide and 7-aminocoumarin-4-acetic
acid (ACA), an AMC-derived fluorogenic compound. ACA was retained
in the WODL for more than 7 days, and the dipeptidyl ACA substrate
detected dipeptidyl peptidase (DPP) activity in the WODL. Compared
to AMC substrates, the substrate specificity constants of DPPs for
ACA substrates increased up to 4.7-fold. Fluorescence-activated droplet
sorting made high-throughput screening of microorganisms based on
DPP activity using the dipeptidyl ACA substrate possible. Since ACA
could be applied to various substrates as a fluorescent probe, detectable
microbial enzyme activities for droplet-based microfluidic systems
can be largely expanded.
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Affiliation(s)
- Akihiro Nakamura
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Nobuyuki Honma
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuma Tanaka
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yoshiyuki Suzuki
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuko Tsuda
- Faculty of Pharmaceutical Sciences, Cooperative Research Center of Life Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe, Hyogo 650-8586, Japan
| | - Koushi Hidaka
- Graduate School of Health Sciences, Kobe University, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan
| | - Wataru Ogasawara
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.,Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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9
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Das A, Das S, Biswas A, Chattopadhyay N. Exploration of Self-Aggregation of Coumarin 7 and Coumarin 30 in Water: Role of β-Cyclodextrin as a Modulator. J Phys Chem B 2021; 125:13482-13493. [PMID: 34865492 DOI: 10.1021/acs.jpcb.1c07287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Steady-state and time-resolved spectroscopic studies demonstrate that two members of the coumarin class of dyes, coumarin 7 (C7) and coumarin 30 (C30), undergo self-aggregation in water. The development of hypsochromically shifted new absorption bands in addition to the existing monomer bands with an increase in concentration of the dyes in an aqueous medium suggests that the aggregates are of H-type. An absorption-based kinetic study reveals that the rate of aggregation of C30 is an order of magnitude faster than that of C7. Second-order rate kinetics, as obtained from the half-life (t1/2) data, implies that the aggregates are dimeric in nature. Observations of isosbestic points in area-normalized absorption spectra (ANAS) and isoemissive points in area-normalized fluorescence excitation spectra (ANFES) and time-resolved area-normalized emission spectra (TRANES) establish that ground-state monomer ⇌ dimer equilibria for both of the systems are preserved in the photoexcited state. The present study further establishes that β-cyclodextrin is the most efficient of the three common cyclodextrins in shifting the equilibria toward the monomer by encapsulating the monomers within its cavity, making β-CD a convenient modulator to control the self-aggregation process. Dynamic light scattering (DLS), quantum chemical calculations, and molecular docking studies provide further support to our propositions.
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Affiliation(s)
- Arindam Das
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Sinjan Das
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Arnab Biswas
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
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10
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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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11
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Geck RC, Boyle G, Amorosi CJ, Fowler DM, Dunham MJ. Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays. Annu Rev Pharmacol Toxicol 2021; 62:531-550. [PMID: 34516287 DOI: 10.1146/annurev-pharmtox-032221-085807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes (ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Gabriel Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; , .,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
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12
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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13
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Chen HM, Nasseri SA, Rahfeld P, Wardman JF, Kohsiek M, Withers SG. Synthesis and evaluation of sensitive coumarin-based fluorogenic substrates for discovery of α-N-acetyl galactosaminidases through droplet-based screening. Org Biomol Chem 2021; 19:789-793. [PMID: 33411870 DOI: 10.1039/d0ob02484h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As part of a search for a substrate for droplet-based microfluidic screening assay of α-N-acetylgalactosaminidases, spectral and physical characteristics of a series of coumarin derivatives were measured. From among these a new coumarin-based fluorophore, Jericho Blue, was selected as having optimal characteristics for our screen. A reliable method for the challenging synthesis of coumarin glycosides of α-GalNAc was then developed and demonstrated with nine examples. The α-GalNAc glycoside of Jericho Blue prepared in this way was shown to function well under screening conditions.
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Affiliation(s)
- Hong-Ming Chen
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, B.C., Canada.
| | | | - Peter Rahfeld
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, B.C., Canada.
| | - Jacob F Wardman
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, B.C., Canada.
| | - Maurits Kohsiek
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, B.C., Canada.
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, B.C., Canada.
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14
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Gargiulo S, Soumillion P. Directed evolution for enzyme development in biocatalysis. Curr Opin Chem Biol 2020; 61:107-113. [PMID: 33385931 DOI: 10.1016/j.cbpa.2020.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
As an important sector of the chemical industry, biocatalysis requires the continuous development of enzymes with tailor-made activity, selectivity, stability, or tolerance to unnatural environments. This is now routinely achieved by directed evolution based on iterative cycles of genetic diversification and activity screening. Here, we highlight its recent developments. First, the design of "smarter" libraries by focused mutagenesis may be a crucial start-up for a fast and successful outcome. Then library assembly and expression are also key steps that benefits from modern molecular biology progresses. Finally, various strategies may be considered for library screening depending on the final objective: while low-throughput direct assays have been very successful in generating enzymes for important biocatalytic processes, even in bringing completely new chemistries to the enzyme world, ultrahigh-throughput screening methods are emerging as powerful approaches for engineering the next generation of industrial enzymes.
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Affiliation(s)
- Serena Gargiulo
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium.
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15
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Boddu RS, Perumal O, K D. Microbial nitroreductases: A versatile tool for biomedical and environmental applications. Biotechnol Appl Biochem 2020; 68:1518-1530. [PMID: 33156534 DOI: 10.1002/bab.2073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022]
Abstract
Nitroreductases, enzymes found mostly in bacteria and also in few eukaryotes, use nicotinamide adenine dinucleotide (NADH) or nicotinamide adenine dinucleotide phosphate (NADPH) as a cofactor for their activity and metabolize an enormous list of a diverse nitro group-containing compounds. Nitroreductases that are capable of metabolizing nitroaromatic and nitro heterocyclic compounds have drawn great attention in recent years owing to their biotechnological, biomedical, environmental, and human impact. These enzymes attracted medicinal chemists and pharmacologists because of their prodrug selectivity for activation/reduction of nitro compounds that wipe out pathogens/cancer cells, leaving the host/normal cells unharmed. It is applied in diverse fields of study like prodrug activation in treating cancer and leishmaniasis, designing fluorescent probes for hypoxia detection, cell imaging, ablation of specific cell types, biodegradation of nitro-pollutants, and interpretation of mutagenicity of nitro compounds. Keeping in view the immense prospects of these enzymes and a large number of research contributions in this area, the present review encompasses the enzymatic reaction mechanism, their role in antibiotic resistance, hypoxia sensing, cell imaging, cancer therapy, reduction of recalcitrant nitro chemicals, enzyme variants, and their specificity to substrates, reaction products, and their applications.
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Affiliation(s)
- Ramya Sree Boddu
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Onkara Perumal
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Divakar K
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur, India
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16
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17
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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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18
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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19
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Droplet Microfluidics-Enabled High-Throughput Screening for Protein Engineering. MICROMACHINES 2019; 10:mi10110734. [PMID: 31671786 PMCID: PMC6915371 DOI: 10.3390/mi10110734] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/19/2022]
Abstract
Protein engineering—the process of developing useful or valuable proteins—has successfully created a wide range of proteins tailored to specific agricultural, industrial, and biomedical applications. Protein engineering may rely on rational techniques informed by structural models, phylogenic information, or computational methods or it may rely upon random techniques such as chemical mutation, DNA shuffling, error prone polymerase chain reaction (PCR), etc. The increasing capabilities of rational protein design coupled to the rapid production of large variant libraries have seriously challenged the capacity of traditional screening and selection techniques. Similarly, random approaches based on directed evolution, which relies on the Darwinian principles of mutation and selection to steer proteins toward desired traits, also requires the screening of very large libraries of mutants to be truly effective. For either rational or random approaches, the highest possible screening throughput facilitates efficient protein engineering strategies. In the last decade, high-throughput screening (HTS) for protein engineering has been leveraging the emerging technologies of droplet microfluidics. Droplet microfluidics, featuring controlled formation and manipulation of nano- to femtoliter droplets of one fluid phase in another, has presented a new paradigm for screening, providing increased throughput, reduced reagent volume, and scalability. We review here the recent droplet microfluidics-based HTS systems developed for protein engineering, particularly directed evolution. The current review can also serve as a tutorial guide for protein engineers and molecular biologists who need a droplet microfluidics-based HTS system for their specific applications but may not have prior knowledge about microfluidics. In the end, several challenges and opportunities are identified to motivate the continued innovation of microfluidics with implications for protein engineering.
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20
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Chiu FWY, Stavrakis S. High-throughput droplet-based microfluidics for directed evolution of enzymes. Electrophoresis 2019; 40:2860-2872. [PMID: 31433062 PMCID: PMC6899980 DOI: 10.1002/elps.201900222] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023]
Abstract
Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.
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Affiliation(s)
- Flora W Y Chiu
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
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21
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Etienne G, Ong ILH, Amstad E. Bioinspired Viscoelastic Capsules: Delivery Vehicles and Beyond. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1808233. [PMID: 31081156 DOI: 10.1002/adma.201808233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Microcapsules are often used as individually dispersed carriers of active ingredients to prolong their shelf life or to protect premature reactions with substances contained in the surrounding. This study goes beyond this application and employs microcapsules as principal building blocks of macroscopic 3D materials with well-defined granular structures. To achieve this goal and inspired by nature, capsules are fabricated from block-copolymer surfactants that are functionalized with catechols, a metal-coordinating motive. These surfactants self-assemble at the surface of emulsion drops where they are ionically cross-linked to form viscoelastic capsules that display a low permeability even toward small encapsulants. It is demonstrated that the combination of the mechanical strength, flexibility, and stickiness of the capsules enables their additive manufacturing into macroscopic granular structures. Thereby, they open up new opportunities for 3D printing of soft, self-healing materials composed of individual compartments that can be functionalized with different types of spatially separated reagents.
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Affiliation(s)
- Gianluca Etienne
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Irvine Lian Hao Ong
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Esther Amstad
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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22
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Yin K, Zeng X, Liu W, Xue Y, Li X, Wang W, Song Y, Zhu Z, Yang C. Stable Colloidosomes Formed by Self-Assembly of Colloidal Surfactant for Highly Robust Digital PCR. Anal Chem 2019; 91:6003-6011. [DOI: 10.1021/acs.analchem.9b00470] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kun Yin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xi Zeng
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Weizhi Liu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Yakun Xue
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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23
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Etienne G, Vian A, Biočanin M, Deplancke B, Amstad E. Cross-talk between emulsion drops: how are hydrophilic reagents transported across oil phases? LAB ON A CHIP 2018; 18:3903-3912. [PMID: 30465575 DOI: 10.1039/c8lc01000e] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Emulsion drops are frequently used as vessels, for example, to conduct biochemical reactions in small volumes or to perform screening assays at high throughputs while consuming minimal sample volumes. These applications typically require drops that do not allow exchange of reagents such that no cross-contamination occurs. Unfortunately, in many cases, reagents are exchanged between emulsion drops even if they have a low solubility in the surrounding phase, resulting in cross-contaminations. Here, we investigate the mechanism by which hydrophilic reagents are transported across an oil phase using water-oil-water double emulsion drops as a model system. Remarkably, even large objects, including 11 000 base pair double-stranded circular DNA are transported across oil shells. Importantly, this reagent transport, that is to a large extent caused by aqueous drops that spontaneously form at the water-oil interface, is not limited to double emulsions but also occurs between single emulsion drops. We demonstrate that the uncontrolled reagent transport can be decreased by at least an order of magnitude if appropriate surfactants that lower the interfacial tension only moderately are employed or if the shell thickness of double emulsions is decreased to a few hundreds of nanometers.
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Affiliation(s)
- Gianluca Etienne
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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24
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Zhang R, Jin S, Liu Q, Lin S, Yan Z. Transition Metal-Free Cross-Dehydrogenative Coupling Reaction of Coumarins with Acetonitrile or Acetone. J Org Chem 2018; 83:13030-13035. [DOI: 10.1021/acs.joc.8b01508] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rongxing Zhang
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Shengzhou Jin
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Qian Liu
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Sen Lin
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Zhaohua Yan
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
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25
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Nightingale AM, Hassan SU, Evans GWH, Coleman SM, Niu X. Nitrate measurement in droplet flow: gas-mediated crosstalk and correction. LAB ON A CHIP 2018; 18:1903-1913. [PMID: 29877549 DOI: 10.1039/c8lc00092a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In droplet microfluidics, droplets have traditionally been considered discrete self-contained reaction chambers, however recent work has shown that dissolved solutes can transfer into the oil phase and migrate into neighbouring droplets under certain conditions. The majority of reports on such inter-droplet "crosstalk" have focused on surfactant-driven mechanisms, such as transport within micelles. While trialling a droplet-based system for quantifying nitrate in water, we encountered crosstalk driven by a very different mechanism: conversion of the analyte to a gaseous intermediate which subsequently diffused between droplets. Importantly we found that the crosstalk occurred predictably, could be experimentally quantified, and measurements rationally post-corrected. This showed that droplet microfluidic systems susceptible to crosstalk such as this can nonetheless be used for quantitative analysis.
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Affiliation(s)
- Adrian M Nightingale
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK.
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26
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Abstract
Combinatorial drug treatment strategies perturb biological networks synergistically to achieve therapeutic effects and represent major opportunities to develop advanced treatments across a variety of human disease areas. However, the discovery of new combinatorial treatments is challenged by the sheer scale of combinatorial chemical space. Here, we report a high-throughput system for nanoliter-scale phenotypic screening that formulates a chemical library in nanoliter droplet emulsions and automates the construction of chemical combinations en masse using parallel droplet processing. We applied this system to predict synergy between more than 4,000 investigational and approved drugs and a panel of 10 antibiotics against Escherichia coli, a model gram-negative pathogen. We found a range of drugs not previously indicated for infectious disease that synergize with antibiotics. Our validated hits include drugs that synergize with the antibiotics vancomycin, erythromycin, and novobiocin, which are used against gram-positive bacteria but are not effective by themselves to resolve gram-negative infections.
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27
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Exploration of the Fluorescent Properties and the Modulated Activities against Sirtuin Fluorogenic Assays of Chromenone-Derived Natural Products. Molecules 2018; 23:molecules23051063. [PMID: 29724067 PMCID: PMC6100537 DOI: 10.3390/molecules23051063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 02/07/2023] Open
Abstract
Chromenone-derived natural products include chromones (flavone, isoflavone) and coumarins. Chromenone compounds not only exhibit impressive biological activities, but also are an important resource of experimentally used fluorophores, such as, 7-amino-4-methylcoumarin (AMC). Various chromenone compounds have reported to have weak fluorescence, and this has the potential to interfere with the measurements during AMC fluorogenic assays and result in non-robust assay readouts. Several flavones and isoflavones were found as SIRT1 activators, while fluorogenic sirtuin assays utilized AMC labelled peptides as the substrates. In this study we investigated whether the fluorescent properties of chromenone-derived natural products interrupt the measurement of SIRT1/2 modulated activities. We found that the reported SIRT1 activators: flavones were detected with the SIRT1 activation activity, but isoflavones were not detected with SIRT1 activation activity, and instead that they were found to be fluorogenic compounds. Another chromenone compound, osthole, exhibited a moderate SIRT2 inhibitory activity with an IC50 of 10 μM. In conclusion, the fluorescent properties of these chromenone compounds do affect the measurement of the sirtuin activities of both inhibitors and activators. However, if the possible fluorescence properties are mitigated in the assay readout, these fluorogenic assays enable the screening of activity modulators.
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28
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Toor A, Lamb S, Helms BA, Russell TP. Reconfigurable Microfluidic Droplets Stabilized by Nanoparticle Surfactants. ACS NANO 2018; 12:2365-2372. [PMID: 29509400 DOI: 10.1021/acsnano.7b07635] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Interfacial assemblies of nanoparticles can stabilize liquid-liquid interfaces. Due to the interactions between functional groups on nanoparticles dispersed in one liquid and polymers having complementary end-functionality dissolved in a second immiscible fluid, the anchoring of a well-defined number of polymer chains onto the nanoparticles leads to the formation of NP-surfactants that assemble at the interface and reduce the interfacial energy. We have developed droplet interfaces covered with elastic, responsive monolayers of NP-surfactants. Due to the presence of an elastic layer at the interface, the droplets offer a greater resistance to coalescence and can prevent the exchange of materials across interfaces. Our results show the successful encapsulation of nanoparticles, dyes, and proteins with diameters in the 2.4-30 nm range. Further, we show that stable water-in-oil droplets can be generated for various combinations of polymer ligands and nanoparticles bearing complementary functionalities. These NP-surfactant-stabilized microfluidic emulsions would enable applications requiring liquid-liquid interfaces that can adapt and respond to external stimuli and whose mechanical properties can be easily tailored.
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Affiliation(s)
- Anju Toor
- Materials Sciences Division , Lawrence Berkeley National Lab1 , One Cyclotron Road , Berkeley , California 94720 , United States
| | - Sean Lamb
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Brett A Helms
- Materials Sciences Division , Lawrence Berkeley National Lab1 , One Cyclotron Road , Berkeley , California 94720 , United States
- The Molecular Foundry , Lawrence Berkeley National Lab , One Cyclotron Road , Berkeley , California 94720 , United States
| | - Thomas P Russell
- Materials Sciences Division , Lawrence Berkeley National Lab1 , One Cyclotron Road , Berkeley , California 94720 , United States
- Department of Polymer Science and Engineering , University of Massachusetts Amherst , 120 Governors Drive , Amherst , Massachusetts 01003 , United States
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , Beijing 100029 , China
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29
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Fenneteau J, Chauvin D, Griffiths AD, Nizak C, Cossy J. Synthesis of new hydrophilic rhodamine based enzymatic substrates compatible with droplet-based microfluidic assays. Chem Commun (Camb) 2018; 53:5437-5440. [PMID: 28462964 DOI: 10.1039/c7cc01506b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Here we report the conception, synthesis and evaluation of new hydrophilic rhodamine-based enzymatic substrates for detection of peptidase activity compatible with high-throughput screening using droplet-based microfluidics.
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Affiliation(s)
- Johan Fenneteau
- Laboratoire de Chimie Organique, Institute of Chemistry, Biology and Innovation (CBI), UMR 8231, ESPCI Paris/CNRS, PSL Research University, 10 rue Vauquelin, 75231-Paris Cedex 05, France.
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30
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Bunzel HA, Garrabou X, Pott M, Hilvert D. Speeding up enzyme discovery and engineering with ultrahigh-throughput methods. Curr Opin Struct Biol 2018; 48:149-156. [PMID: 29413955 DOI: 10.1016/j.sbi.2017.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/26/2017] [Indexed: 01/24/2023]
Abstract
Exploring the sequence space of enzyme catalysts is ultimately a numbers game. Ultrahigh-throughput screening methods for rapid analysis of millions of variants are therefore increasingly important for investigating sequence-function relationships, searching large metagenomic libraries for interesting activities, and accelerating enzyme evolution in the laboratory. Recent applications of such technologies are reviewed here, with a particular focus on the practical benefits of droplet-based microfluidics for the directed evolution of natural and artificial enzymes. Broader implementation of such rapid, cost-effective screening technologies is likely to redefine the way enzymes are studied and engineered for academic and industrial purposes.
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Affiliation(s)
- Hans Adrian Bunzel
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Xavier Garrabou
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Moritz Pott
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich CH-8093, Switzerland.
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Gielen F, Colin PY, Mair P, Hollfelder F. Ultrahigh-Throughput Screening of Single-Cell Lysates for Directed Evolution and Functional Metagenomics. Methods Mol Biol 2018; 1685:297-309. [PMID: 29086317 DOI: 10.1007/978-1-4939-7366-8_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The success of ultrahigh-throughput screening experiments in directed evolution or functional metagenomics strongly depends on the availability of efficient technologies for the quantitative testing of a large number of variants. With advanced robotics, libraries of up to 105 clones can be screened per day as colonies on agar plates or cell lysates in microwell plates, albeit at high cost of capital, manpower and consumables. These cost considerations and the general need for high-throughput make miniaturization of assay volumes attractive. To provide a general solution to maintain genotype-phenotype linkage, biochemical assays have been compartmentalized into water-in-oil droplets. This chapter presents a microfluidic workflow that translates a frequently used screening procedure consisting of cytoplasmic/periplasmic protein expression and cell lysis to the single cell level in water-in-oil droplet compartments. These droplets are sorted based on reaction progress by fluorescence measurements at the picoliter scale.
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Affiliation(s)
- Fabrice Gielen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Philip Mair
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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Cochrane WG, Hackler AL, Cavett VJ, Price AK, Paegel BM. Integrated, Continuous Emulsion Creamer. Anal Chem 2017; 89:13227-13234. [PMID: 29124927 DOI: 10.1021/acs.analchem.7b03070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Automated and reproducible sample handling is a key requirement for high-throughput compound screening and currently demands heavy reliance on expensive robotics in screening centers. Integrated droplet microfluidic screening processors are poised to replace robotic automation by miniaturizing biochemical reactions to the droplet scale. These processors must generate, incubate, and sort droplets for continuous droplet screening, passively handling millions of droplets with complete uniformity, especially during the key step of sample incubation. Here, we disclose an integrated microfluidic emulsion creamer that packs ("creams") assay droplets by draining away excess oil through microfabricated drain channels. The drained oil coflows with creamed emulsion and then reintroduces the oil to disperse the droplets at the circuit terminus for analysis. Creamed emulsion assay incubation time dispersion was 1.7%, 3-fold less than other reported incubators. The integrated, continuous emulsion creamer (ICEcreamer) was used to miniaturize and optimize measurements of various enzymatic activities (phosphodiesterase, kinase, bacterial translation) under multiple- and single-turnover conditions. Combining the ICEcreamer with current integrated microfluidic DNA-encoded library bead processors eliminates potentially cumbersome instrumentation engineering challenges and is compatible with assays of diverse target class activities commonly investigated in drug discovery.
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Affiliation(s)
- Wesley G Cochrane
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Amber L Hackler
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Valerie J Cavett
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alexander K Price
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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Autour A, Ryckelynck M. Ultrahigh-Throughput Improvement and Discovery of Enzymes Using Droplet-Based Microfluidic Screening. MICROMACHINES 2017. [PMCID: PMC6189954 DOI: 10.3390/mi8040128] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Enzymes are extremely valuable tools for industrial, environmental, and biotechnological applications and there is a constant need for improving existing biological catalysts and for discovering new ones. Screening microbe or gene libraries is an efficient way of identifying new enzymes. In this view, droplet-based microfluidics appears to be one of the most powerful approaches as it allows inexpensive screenings in well-controlled conditions and an ultrahigh-throughput regime. This review aims to introduce the main microfluidic devices and concepts to be considered for such screening before presenting and discussing the latest successful applications of the technology for enzyme discovery.
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Beneyton T, Thomas S, Griffiths AD, Nicaud JM, Drevelle A, Rossignol T. Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica. Microb Cell Fact 2017; 16:18. [PMID: 28143479 PMCID: PMC5282883 DOI: 10.1186/s12934-017-0629-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 01/12/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Droplet-based microfluidics is becoming an increasingly attractive alternative to microtiter plate techniques for enzymatic high-throughput screening (HTS), especially for exploring large diversities with lower time and cost footprint. In this case, the assayed enzyme has to be accessible to the substrate within the water-in-oil droplet by being ideally extracellular or displayed at the cell surface. However, most of the enzymes screened to date are expressed within the cytoplasm of Escherichia coli cells, which means that a lysis step must take place inside the droplets for enzyme activity to be assayed. Here, we take advantage of the excellent secretion abilities of the yeast Yarrowia lipolytica to describe a highly efficient expression system particularly suitable for the droplet-based microfluidic HTS. RESULTS Five hydrolytic genes from Aspergillus niger genome were chosen and the corresponding five Yarrowia lipolytica producing strains were constructed. Each enzyme (endo-β-1,4-xylanase B and C; 1,4-β-cellobiohydrolase A; endoglucanase A; aspartic protease) was successfully overexpressed and secreted in an active form in the crude supernatant. A droplet-based microfluidic HTS system was developed to (a) encapsulate single yeast cells; (b) grow yeast in droplets; (c) inject the relevant enzymatic substrate; (d) incubate droplets on chip; (e) detect enzymatic activity; and (f) sort droplets based on enzymatic activity. Combining this integrated microfluidic platform with gene expression in Y. lipolytica results in remarkably low variability in the enzymatic activity at the single cell level within a given monoclonal population (<5%). Xylanase, cellobiohydrolase and protease activities were successfully assayed using this system. We then used the system to screen for thermostable variants of endo-β-1,4-xylanase C in error-prone PCR libraries. Variants displaying higher thermostable xylanase activities compared to the wild-type were isolated (up to 4.7-fold improvement). CONCLUSIONS Yarrowia lipolytica was used to express fungal genes encoding hydrolytic enzymes of interest. We developed a successful droplet-based microfluidic platform for the high-throughput screening (105 strains/h) of Y. lipolytica based on enzyme secretion and activity. This approach provides highly efficient tools for the HTS of recombinant enzymatic activities. This should be extremely useful for discovering new biocatalysts via directed evolution or protein engineering approaches and should lead to major advances in microbial cell factory development.
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Affiliation(s)
- Thomas Beneyton
- Ecole Supérieure de Physique et de Chimie industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231, 10 rue Vauquelin, 75005 Paris, France
- CNRS, University of Bordeaux, CRPP, UPR 8641, 115 Avenue Albert Schweitzer, 33600 Pessac, France
| | - Stéphane Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Andrew D. Griffiths
- Ecole Supérieure de Physique et de Chimie industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231, 10 rue Vauquelin, 75005 Paris, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Antoine Drevelle
- Ets J. Soufflet/CRIS-OSIRIS, Quai Sarrail, BP12, 10400 Nogent-sur-Seine, France
| | - Tristan Rossignol
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
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Glowacka PC, Maindron N, Stephenson GR, Romieu A, Renard PY, da Silva Emery F. Synthesis and photophysical properties of iron-carbonyl complex–coumarin conjugates as potential bimodal IR–fluorescent probes. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Ma F, Fischer M, Han Y, Withers SG, Feng Y, Yang GY. Substrate Engineering Enabling Fluorescence Droplet Entrapment for IVC-FACS-Based Ultrahigh-Throughput Screening. Anal Chem 2016; 88:8587-95. [DOI: 10.1021/acs.analchem.6b01712] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Fuqiang Ma
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Michael Fischer
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yunbin Han
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Stephen G. Withers
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yan Feng
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guang-Yu Yang
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Shanghai
Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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37
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Hümmer D, Kurth F, Naredi-Rainer N, Dittrich PS. Single cells in confined volumes: microchambers and microdroplets. LAB ON A CHIP 2016; 16:447-58. [PMID: 26758781 DOI: 10.1039/c5lc01314c] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Microfluidic devices capable of manipulating and guiding small fluid volumes open new methodical approaches in the fields of biology, pharmacy, and medicine. They have already proven their extraordinary value for cell analysis. The emergence of microfluidic platforms has paved the way to novel analytical strategies for the positioning, treatment and observation of living cells, for the creation of chemically defined liquid environments, and for tailoring biomechanical or physical conditions in small volumes. In this article, we particularly focus on two complementary approaches: (i) the isolation of cells in small chambers defined by microchannels and integrated valves and (ii) the encapsulation of cells in microdroplets. We review the advantages and limitations of both approaches and discuss their potential for single-cell analysis and related fields. Our intention is also to give a recommendation on which platform is most appropriate for a new question, i.e., a guideline to choose the most suitable platform.
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Affiliation(s)
- D Hümmer
- ETH Zurich - Department of Biosystems Science Engineering, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland.
| | - F Kurth
- ETH Zurich - Department of Biosystems Science Engineering, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland.
| | - N Naredi-Rainer
- ETH Zurich - Department of Biosystems Science Engineering, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland.
| | - P S Dittrich
- ETH Zurich - Department of Biosystems Science Engineering, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland.
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38
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Controlling molecular transport in minimal emulsions. Nat Commun 2016; 7:10392. [PMID: 26797564 PMCID: PMC4735829 DOI: 10.1038/ncomms10392] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 12/08/2015] [Indexed: 12/24/2022] Open
Abstract
Emulsions are metastable dispersions in which molecular transport is a major mechanism driving the system towards its state of minimal energy. Determining the underlying mechanisms of molecular transport between droplets is challenging due to the complexity of a typical emulsion system. Here we introduce the concept of ‘minimal emulsions', which are controlled emulsions produced using microfluidic tools, simplifying an emulsion down to its minimal set of relevant parameters. We use these minimal emulsions to unravel the fundamentals of transport of small organic molecules in water-in-fluorinated-oil emulsions, a system of great interest for biotechnological applications. Our results are of practical relevance to guarantee a sustainable compartmentalization of compounds in droplet microreactors and to design new strategies for the dynamic control of droplet compositions. Emulsion droplets have many biotechnological applications, such as parallelized single cell analysis. Here, Gruner et al. introduce the concept of the minimal emulsions in a microfluidic device that allows full control of molecular transport between emulsion droplets.
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39
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Affiliation(s)
- Alexander K. Price
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Brian M. Paegel
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States
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40
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Pan M, Kim M, Blauch L, Tang SKY. Surface-functionalizable amphiphilic nanoparticles for pickering emulsions with designer fluid–fluid interfaces. RSC Adv 2016. [DOI: 10.1039/c6ra03950b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work describes the synthesis of amphiphilic silica nanoparticles with functionalizable surfaces for stabilizing aqueous drops in fluorinated oils, and for enabling the generation of emulsions with tailored interfacial properties.
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Affiliation(s)
- Ming Pan
- Department of Materials Science and Engineering
- Stanford University
- Stanford
- USA
| | - Minkyu Kim
- Department of Mechanical Engineering
- Stanford University
- Stanford
- USA
| | - Lucas Blauch
- Department of Mechanical Engineering
- Stanford University
- Stanford
- USA
| | - Sindy K. Y. Tang
- Department of Mechanical Engineering
- Stanford University
- Stanford
- USA
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41
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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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42
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Pan M, Lyu F, Tang SKY. Fluorinated Pickering Emulsions with Nonadsorbing Interfaces for Droplet-based Enzymatic Assays. Anal Chem 2015; 87:7938-43. [DOI: 10.1021/acs.analchem.5b01753] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ming Pan
- Department
of Material Science and Engineering, Stanford University, Stanford, California 94305-2004, United States
| | - Fengjiao Lyu
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305-2004, United States
| | - Sindy K. Y. Tang
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305-2004, United States
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43
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Gruner P, Riechers B, Chacòn Orellana LA, Brosseau Q, Maes F, Beneyton T, Pekin D, Baret JC. Stabilisers for water-in-fluorinated-oil dispersions: Key properties for microfluidic applications. Curr Opin Colloid Interface Sci 2015. [DOI: 10.1016/j.cocis.2015.07.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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44
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Woronoff G, Ryckelynck M, Wessel J, Schicke O, Griffiths AD, Soumillion P. Activity-Fed Translation (AFT) Assay: A New High-Throughput Screening Strategy for Enzymes in Droplets. Chembiochem 2015; 16:1343-9. [DOI: 10.1002/cbic.201500087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 01/17/2023]
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45
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Abstract
Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation.
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Affiliation(s)
- Evgenia Yu Basova
- Masaryk University
- CEITEC, Central European Institute Technology
- Brno
- Czech Republic
| | - Frantisek Foret
- Masaryk University
- CEITEC, Central European Institute Technology
- Brno
- Czech Republic
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic
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46
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Pan M, Rosenfeld L, Kim M, Xu M, Lin E, Derda R, Tang SKY. Fluorinated pickering emulsions impede interfacial transport and form rigid interface for the growth of anchorage-dependent cells. ACS APPLIED MATERIALS & INTERFACES 2014; 6:21446-53. [PMID: 25347285 DOI: 10.1021/am506443e] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This study describes the design and synthesis of amphiphilic silica nanoparticles for the stabilization of aqueous drops in fluorinated oils for applications in droplet microfluidics. The success of droplet microfluidics has thus far relied on one type of surfactant for the stabilization of drops. However, surfactants are known to have two key limitations: (1) interdrop molecular transport leads to cross-contamination of droplet contents, and (2) the incompatibility with the growth of adherent mammalian cells as the liquid-liquid interface is too soft for cell adhesion. The use of nanoparticles as emulsifiers overcomes these two limitations. Particles are effective in mitigating undesirable interdrop molecular transport as they are irreversibly adsorbed to the liquid-liquid interface. They do not form micelles as surfactants do, and thus, a major pathway for interdrop transport is eliminated. In addition, particles at the droplet interface provide a rigid solid-like interface to which cells could adhere and spread, and are thus compatible with the proliferation of adherent mammalian cells such as fibroblasts and breast cancer cells. The particles described in this work can enable new applications for high-fidelity assays and for the culture of anchorage-dependent cells in droplet microfluidics, and they have the potential to become a competitive alternative to current surfactant systems for the stabilization of drops critical for the success of the technology.
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Affiliation(s)
- Ming Pan
- Department of Material Science and Engineering, Stanford University , Stanford, California 94305-2004, United States
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47
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Roubinet B, Chevalier A, Renard PY, Romieu A. A Synthetic Route to 3-(Heteroaryl)-7-hydroxycoumarins Designed for Biosensing Applications. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403215] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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48
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Sandoz PA, Chung AJ, Weaver WM, Di Carlo D. Sugar additives improve signal fidelity for implementing two-phase resorufin-based enzyme immunoassays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:6637-6643. [PMID: 24870310 DOI: 10.1021/la5004484] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Enzymatic signal amplification based on fluorogenic substrates is commonly used for immunoassays; however, when transitioning these assays to a digital format in water-in-mineral oil emulsions, such amplification methods have been limited by the leakage of small reporting fluorescent probes. In the present study, we used a microfluidic system to study leakage from aqueous droplets in a controlled manner and confirmed that the leakage of fluorescent resorufin derivatives is mostly due to the presence of the lipophilic surfactant Span80, which is commonly used to preserve emulsion stability. This leakage can be overcome by the addition of specific sugars that most strongly interfered with the surfactants ability to form micelles in water. The application of the microfluidic system to the quantitative analysis of droplets and the implementation of the described sugar additives would allow for alternatives to fluorinated surfactant-based platforms and improve the signal fidelity in enzyme immunoassays implemented through multiphase microfluidics.
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Affiliation(s)
- Patrick A Sandoz
- Department of Bioengineering, University of California , Los Angeles, California 90095, United States
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49
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Tjhung KF, Burnham S, Anany H, Griffiths MW, Derda R. Rapid enumeration of phage in monodisperse emulsions. Anal Chem 2014; 86:5642-8. [PMID: 24892245 DOI: 10.1021/ac500244g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Phage-based detection assays have been developed for the detection of viable bacteria for applications in clinical diagnosis, monitoring of water quality, and food safety. The majority of these assays deliver a positive readout in the form of newly generated progeny phages by the bacterial host of interest. Progeny phages are often visualized as plaques, or holes, in a lawn of bacteria on an agar-filled Petri dish; however, this rate-limiting step requires up to 12 h of incubation time. We have previously described an amplification of bacteriophages M13 inside droplets of media suspended in perfluorinated oil; a single phage M13 in a droplet yields 10(7) copies in 3-4 h. Here, we describe that encapsulation of reporter phages, both lytic T4-LacZ and nonlytic M13, in monodisperse droplets can also be used for rapid enumeration of phage. Compartmentalization in droplets accelerated the development of the signal from the reporter enzyme; counting of "positive" droplets yields accurate enumeration of phage particles ranging from 10(2) to 10(6) pfu/mL. For enumeration of T4-LacZ phage, the fluorescent signal appeared in as little as 90 min. Unlike bulk assays, quantification in emulsion is robust and insensitive to fluctuations in environmental conditions (e.g., temperature). Power-free emulsification using gravity-driven flow in the absence of syringe pumps and portable fluorescence imaging solutions makes this technology promising for use at the point of care in low-resource environments. This droplet-based phage enumeration method could accelerate and simplify point-of-care detection of the pathogens for which reporter bacteriophages have been developed.
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Affiliation(s)
- Katrina F Tjhung
- Department of Chemistry, University of Alberta , Edmonton, AB T6G 2G2, Canada
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50
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Yu J, Zhang Y, Liu S. Enzymatic reactivity of glucose oxidase confined in nanochannels. Biosens Bioelectron 2014; 55:307-12. [DOI: 10.1016/j.bios.2013.12.042] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 12/18/2022]
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