1
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Tian Z, Wang X, Chen J. On-chip dielectrophoretic single-cell manipulation. MICROSYSTEMS & NANOENGINEERING 2024; 10:117. [PMID: 39187499 PMCID: PMC11347631 DOI: 10.1038/s41378-024-00750-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/07/2024] [Accepted: 07/07/2024] [Indexed: 08/28/2024]
Abstract
Bioanalysis at a single-cell level has yielded unparalleled insight into the heterogeneity of complex biological samples. Combined with Lab-on-a-Chip concepts, various simultaneous and high-frequency techniques and microfluidic platforms have led to the development of high-throughput platforms for single-cell analysis. Dielectrophoresis (DEP), an electrical approach based on the dielectric property of target cells, makes it possible to efficiently manipulate individual cells without labeling. This review focusses on the engineering designs of recent advanced microfluidic designs that utilize DEP techniques for multiple single-cell analyses. On-chip DEP is primarily effectuated by the induced dipole of dielectric particles, (i.e., cells) in a non-uniform electric field. In addition to simply capturing and releasing particles, DEP can also aid in more complex manipulations, such as rotation and moving along arbitrary predefined routes for numerous applications. Correspondingly, DEP electrodes can be designed with different patterns to achieve different geometric boundaries of the electric fields. Since many single-cell analyses require isolation and compartmentalization of individual cells, specific microstructures can also be incorporated into DEP devices. This article discusses common electrical and physical designs of single-cell DEP microfluidic devices as well as different categories of electrodes and microstructures. In addition, an up-to-date summary of achievements and challenges in current designs, together with prospects for future design direction, is provided.
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Affiliation(s)
- Zuyuan Tian
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada
| | - Xihua Wang
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada
| | - Jie Chen
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada.
- Academy for Engineering & Technology, Fudan University, Shanghai, 200433, China.
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2
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Han J, Zhang H, Li Y, Huang C, Guzman AR, Han A. High-Efficiency Interdigitated Electrode-Based Droplet Merger for Enabling Error-Free Droplet Microfluidic Systems. Anal Chem 2024; 96. [PMID: 39146475 PMCID: PMC11359384 DOI: 10.1021/acs.analchem.4c02376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
Merging two droplets into a droplet to add and mix two contents is one of the common droplet microfluidic functions with droplet generation and sorting, performing broad ranges of biological and chemical assays in droplets. However, traditional droplet-merging techniques often encounter unsynchronized droplets, causing overmerging or mis-merging, and unwanted merging outside of the desired zone. This is more severe when the incoming droplets to be merged are polydisperse in their sizes, often observed in assays that require long-term incubation, elevated-temperature, and/or multiple droplet processing steps. Here, we developed an interdigitated electrode (IDE)-based droplet merger consisting of a droplet autosynchronizing channel and a merging channel. The autosynchronizing channel provides >95% merging efficiency even when 20% polydispersity in the droplet size exists. The highly localized and enhanced dielectrophoretic force generated by the IDEs on the channel bottom allows droplet merging at an extremely low voltage (4.5 V) and only locally at the IDE region. A systematic evaluation of how various design and operation parameters of the IDE merger, such as IDE finger dimensions, dielectric coating layer thickness, droplet size, and droplet flow speed impact the performance was conducted. The optimized device showed consistent performance even when operating for up to 100 h consecutively at high throughput (100 droplets/s). The presented technology has been integrated into a droplet microfluidics workflow to test the lytic activities of bacteriophage on bacterial host cells with 100% merging efficiency. We expect this function to be integrated into droplet microfluidic systems performing broad ranges of high-throughput chemical and biological assays.
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Affiliation(s)
- Jeong
Jae Han
- Department
of Multidisciplinary Engineering, Texas
A&M University, College Station, Texas 77843, United States
| | - Han Zhang
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Yuwen Li
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Can Huang
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Adrian R. Guzman
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Arum Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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3
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Mika T, Kalnins M, Spalvins K. The use of droplet-based microfluidic technologies for accelerated selection of Yarrowia lipolytica and Phaffia rhodozyma yeast mutants. Biol Methods Protoc 2024; 9:bpae049. [PMID: 39114747 PMCID: PMC11303513 DOI: 10.1093/biomethods/bpae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/24/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Microorganisms are widely used for the industrial production of various valuable products, such as pharmaceuticals, food and beverages, biofuels, enzymes, amino acids, vaccines, etc. Research is constantly carried out to improve their properties, mainly to increase their productivity and efficiency and reduce the cost of the processes. The selection of microorganisms with improved qualities takes a lot of time and resources (both human and material); therefore, this process itself needs optimization. In the last two decades, microfluidics technology appeared in bioengineering, which allows for manipulating small particles (from tens of microns to nanometre scale) in the flow of liquid in microchannels. The technology is based on small-volume objects (microdroplets from nano to femtolitres), which are manipulated using a microchip. The chip is made of an optically transparent inert to liquid medium material and contains a series of channels of small size (<1 mm) of certain geometry. Based on the physical and chemical properties of microparticles (like size, weight, optical density, dielectric constant, etc.), they are separated using microsensors. The idea of accelerated selection of microorganisms is the application of microfluidic technologies to separate mutants with improved qualities after mutagenesis. This article discusses the possible application and practical implementation of microfluidic separation of mutants, including yeasts like Yarrowia lipolytica and Phaffia rhodozyma after chemical mutagenesis will be discussed.
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Affiliation(s)
- Taras Mika
- Institute of Energy Systems and Environment, Riga Technical University, 12 – K1 Āzene street, Riga, LV-1048, Latvia
| | - Martins Kalnins
- Institute of Energy Systems and Environment, Riga Technical University, 12 – K1 Āzene street, Riga, LV-1048, Latvia
| | - Kriss Spalvins
- Institute of Energy Systems and Environment, Riga Technical University, 12 – K1 Āzene street, Riga, LV-1048, Latvia
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4
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Thakur R, Weitz D. Manipulating the duration of picoinjection controls the injected volume of individual droplets. BIOMICROFLUIDICS 2024; 18:044102. [PMID: 38966806 PMCID: PMC11221878 DOI: 10.1063/5.0206830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/21/2024] [Indexed: 07/06/2024]
Abstract
The ability to add reagents into droplets is required in many microfluidic workflows. Picoinjection can address this need; however, it is unable to control the injection volume for each individual droplet. Here, we present an improved picoinjection method that can inject controlled volumes into individual droplets. We achieve this by adjusting the injection duration for each picoinjection event. This improved picoinjection method can be used to create complex microfluidic workflows that are able to control the biochemical composition of individual droplets.
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Affiliation(s)
| | - D. Weitz
- Author to whom correspondence should be addressed:
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5
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Jain A, Stavrakis S, deMello A. Droplet-based microfluidics and enzyme evolution. Curr Opin Biotechnol 2024; 87:103097. [PMID: 38430713 DOI: 10.1016/j.copbio.2024.103097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Enzymes are widely used as catalysts in the chemical and pharmaceutical industries. While successful in many situations, they must usually be adapted to operate efficiently under nonnatural conditions. Enzyme engineering allows the creation of novel enzymes that are stable at elevated temperatures or have higher activities and selectivities. Current enzyme engineering techniques require the production and testing of enzyme variant libraries to identify members with desired attributes. Unfortunately, traditional screening methods cannot screen such large mutagenesis libraries in a robust and timely manner. Droplet-based microfluidic systems can produce, process, and sort picoliter droplets at kilohertz rates and have emerged as powerful tools for library screening and thus enzyme engineering. We describe how droplet-based microfluidics has been used to advance directed evolution.
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Affiliation(s)
- Ankit Jain
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
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6
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Verbist W, Breukers J, Sharma S, Rutten I, Gerstmans H, Coelmont L, Dal Dosso F, Dallmeier K, Lammertyn J. SeParate: multiway fluorescence-activated droplet sorting based on integration of serial and parallel triaging concepts. LAB ON A CHIP 2024; 24:2107-2121. [PMID: 38450543 DOI: 10.1039/d3lc01075a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a versatile high-throughput sorting tool that is, unlike most fluorescence-activated cell sorting (FACS) platforms, capable of sorting droplet-compartmentalized cells, cell secretions, entire enzymatic reactions and more. Recently, multiplex FADS platforms have been developed for the sorting of multi-fluorophore populations towards different outlets in addition to the standard, more commonly used, 2-way FADS platform. These multiplex FADS platforms consist of either multiple 2-way junctions one after the other (i.e. serial sorters) or of one junction sorting droplets in more than 2 outlets (i.e. parallel sorters). In this work, we present SeParate, a novel platform based on integrating s̲e̲rial and p̲a̲r̲allel sorting principles for accura̲t̲e̲ multiplex droplet sorting that is able to mitigate limitations of current multiplex sorters. We show the SeParate platform and its capability in highly accurate 4-way sorting of a multi-fluorophore population into four subpopulations with the potential to expand to more. More specifically, the SeParate platform was thoroughly validated using mixed populations of fluorescent beads and picoinjected droplets, yielding sorting accuracies up to 100% and 99.9%, respectively. Finally, transfected HEK-293T cells were sorted employing two different optical setups, resulting in an accuracy up to 99.5%. SeParate's high accuracy for a diverse set of samples, including highly variable biological specimens, together with its scalability beyond the demonstrated 4-way sorting, warrants a broad applicability for multi-fluorophore studies in life sciences, environmental sciences and others.
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Affiliation(s)
- Wannes Verbist
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Jolien Breukers
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Sapna Sharma
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Iene Rutten
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Lotte Coelmont
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Francesco Dal Dosso
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Kai Dallmeier
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
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7
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Nan L, Zhang H, Weitz DA, Shum HC. Development and future of droplet microfluidics. LAB ON A CHIP 2024; 24:1135-1153. [PMID: 38165829 DOI: 10.1039/d3lc00729d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Over the past two decades, advances in droplet-based microfluidics have facilitated new approaches to process and analyze samples with unprecedented levels of precision and throughput. A wide variety of applications has been inspired across multiple disciplines ranging from materials science to biology. Understanding the dynamics of droplets enables optimization of microfluidic operations and design of new techniques tailored to emerging demands. In this review, we discuss the underlying physics behind high-throughput generation and manipulation of droplets. We also summarize the applications in droplet-derived materials and droplet-based lab-on-a-chip biotechnology. In addition, we offer perspectives on future directions to realize wider use of droplet microfluidics in industrial production and biomedical analyses.
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Affiliation(s)
- Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Huidan Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
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8
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Cheng G, Kuan CY, Lou KW, Ho YP. Light-Responsive Materials in Droplet Manipulation for Biochemical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2313935. [PMID: 38379512 DOI: 10.1002/adma.202313935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/31/2024] [Indexed: 02/22/2024]
Abstract
Miniaturized droplets, characterized by well-controlled microenvironments and capability for parallel processing, have significantly advanced the studies on enzymatic evolution, molecular diagnostics, and single-cell analysis. However, manipulation of small-sized droplets, including moving, merging, and trapping of the targeted droplets for complex biochemical assays and subsequent analysis, is not trivial and remains technically demanding. Among various techniques, light-driven methods stand out as a promising candidate for droplet manipulation in a facile and flexible manner, given the features of contactless interaction, high spatiotemporal resolution, and biocompatibility. This review therefore compiles an in-depth discussion of the governing mechanisms underpinning light-driven droplet manipulation. Besides, light-responsive materials, representing the core of light-matter interaction and the key character converting light into different forms of energy, are particularly assessed in this review. Recent advancements in light-responsive materials and the most notable applications are comprehensively archived and evaluated. Continuous innovations and rational engineering of light-responsive materials are expected to propel the development of light-driven droplet manipulation, equip droplets with enhanced functionality, and broaden the applications of droplets for biochemical studies and routine biochemical investigations.
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Affiliation(s)
- Guangyao Cheng
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Chit Yau Kuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Kuan Wen Lou
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, 999077, China
- Centre for Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
- The Ministry of Education Key Laboratory of Regeneration Medicine, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
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9
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Xu Z, Chen Z, Yang S, Chen S, Guo T, Chen H. Passive Focusing of Single Cells Using Microwell Arrays for High-Accuracy Image-Activated Sorting. Anal Chem 2024; 96:347-354. [PMID: 38153415 DOI: 10.1021/acs.analchem.3c04195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Sorting single cells from a population was of critical importance in areas such as cell line development and cell therapy. Image-based sorting is becoming a promising technique for the nonlabeling isolation of cells due to the capability of providing the details of cell morphology. This study reported the focusing of cells using microwell arrays and the following automatic size sorting based on the real-time recognition of cells. The simulation first demonstrated the converged streamlines to the symmetrical plane contributed to the focusing effect. Then, the influence of connecting microchannel, flowing length, particle size, and the sample flow rate on the focusing effect was experimentally analyzed. Both microspheres and cells could be aligned in a straight line at the Reynolds number (Re) of 0.027-0.187 and 0.027-0.08, respectively. The connecting channel was proved to drastically improve the focusing performance. Afterward, a tapered microwell array was utilized to focus sphere/cell spreading in a wide channel to a straight line. Finally, a custom algorithm was employed to identify and sort the size of microspheres/K562 cells with a throughput of 1 event/s and an accuracy of 97.8/97.1%. The proposed technique aligned cells to a straight line at low Reynolds numbers and greatly facilitated the image-activated sorting without the need for a high-speed camera or flow control components with high frequency. Therefore, it is of enormous application potential in the field of nonlabeled separation of single cells.
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Affiliation(s)
- Zheng Xu
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
| | - Zhenlin Chen
- Department of Biomedical Engineering, College of Engineering, Kowloon, City University of Hong Kong, Hong Kong SAR, China
| | - Shiming Yang
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
| | - Siyuan Chen
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
| | - Tianruo Guo
- Graduate School of Biomedical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Huaying Chen
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
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10
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Carpenter AC, Feist AM, Harrison FS, Paulsen IT, Williams TC. Have you tried turning it off and on again? Oscillating selection to enhance fitness-landscape traversal in adaptive laboratory evolution experiments. Metab Eng Commun 2023; 17:e00227. [PMID: 37538933 PMCID: PMC10393799 DOI: 10.1016/j.mec.2023.e00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/05/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023] Open
Abstract
Adaptive Laboratory Evolution (ALE) is a powerful tool for engineering and understanding microbial physiology. ALE relies on the selection and enrichment of mutations that enable survival or faster growth under a selective condition imposed by the experimental setup. Phenotypic fitness landscapes are often underpinned by complex genotypes involving multiple genes, with combinatorial positive and negative effects on fitness. Such genotype relationships result in mutational fitness landscapes with multiple local fitness maxima and valleys. Traversing local maxima to find a global maximum often requires an individual or sub-population of cells to traverse fitness valleys. Traversing involves gaining mutations that are not adaptive for a given local maximum but are necessary to 'peak shift' to another local maximum, or eventually a global maximum. Despite these relatively well understood evolutionary principles, and the combinatorial genotypes that underlie most metabolic phenotypes, the majority of applied ALE experiments are conducted using constant selection pressures. The use of constant pressure can result in populations becoming trapped within local maxima, and often precludes the attainment of optimum phenotypes associated with global maxima. Here, we argue that oscillating selection pressures is an easily accessible mechanism for traversing fitness landscapes in ALE experiments, and provide theoretical and practical frameworks for implementation.
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Affiliation(s)
- Alexander C. Carpenter
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
| | - Adam M. Feist
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Fergus S.M. Harrison
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
| | - Thomas C. Williams
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
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11
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Payne EM, Murray BE, Penabad LI, Abbate E, Kennedy RT. Mass-Activated Droplet Sorting for the Selection of Lysine-Producing Escherichia coli. Anal Chem 2023; 95:15716-15724. [PMID: 37820298 PMCID: PMC11025463 DOI: 10.1021/acs.analchem.3c03080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Synthetic biology relies on engineering cells to have desirable properties, such as the production of select chemicals. A bottleneck in engineering methods is often the need to screen and sort variant libraries for potential activity. Droplet microfluidics is a method for high-throughput sample preparation and analysis which has the potential to improve the engineering of cells, but a limitation has been the reliance on fluorescent analysis. Here, we show the ability to select cell variants grown in 20 nL droplets at 0.5 samples/s using mass-activated droplet sorting (MADS), a method for selecting droplets based on the signal intensity measured by electrospray ionization mass spectrometry (ESI-MS). Escherichia coli variants producing lysine were used to evaluate the applicability of MADS for synthetic biology. E. coli were shown to be effectively grown in droplets, and the lysine produced by these cells was detectable using ESI-MS. Sorting of lysine-producing cells based on the MS signal was shown, yielding 96-98% purity for high-producing variants in the selected pool. Using this technique, cells were recovered after screening, enabling downstream validation via phenotyping. The presented method is translatable to whole-cell engineering for biocatalyst production.
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Affiliation(s)
- Emory M. Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Bridget E. Murray
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Laura I. Penabad
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Eric Abbate
- Applications Development, Inscripta Inc., Pleasanton, CA 94588
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
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12
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Kayirangwa Y, Mohibullah M, Easley CJ. Droplet-based μChopper device with a 3D-printed pneumatic valving layer and a simple photometer for absorbance based fructosamine quantification in human serum. Analyst 2023; 148:4810-4819. [PMID: 37605899 PMCID: PMC10530610 DOI: 10.1039/d3an01149f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The development of microfluidic systems for biological assays presents challenges, particularly in adapting traditional optical absorbance assays to smaller volumes or to microfluidic formats. This often requires assay modification or translation to a fluorescence version, which can be impractical. To address this issue, our group has developed the μChopper device, which uses microfluidic droplet formation as a surrogate for an optical beam chopper, allowing for lock-in analysis and improved limits of detection with both absorbance and fluorescence optics without modifying the optical path length. Here, we have adapted the μChopper to low-cost optics using a light-emitting diode (LED) source and photodiode detector, and we have fabricated the pnuematically valved devices entirely by 3D printing instead of traditional photolithography. Using a hybrid device structure, fluidic channels were made in polydimethylsiloxane (PDMS) by moulding onto a 3D-printed master then bonding to a prefabricated thin layer, and the pneumatic layer was directly made of 3D-printed resin. This hybrid structure allowed an optical slit to be fabricated directly under fluidic channels, with the LED interfaced closely above the channel. Vacuum-operated, normally closed valves provided precise temporal control of droplet formation from 0.6 to 2.0 Hz. The system was validated against the standard plate reader format using a colorimetric fructosamine assay and by quantifying fructosamine in human serum from normal and diabetic patients, where strong correlation was shown. Showing a standard benefit of microfluidics in analysis, the device required 6.4-fold less serum volume for each assay. This μChopper device and lower cost optical system should be applicable to various absorbance based assays in low volumes, and the reliance on inexpensive 3D printers makes it more accessible to users without cleanroom facilities.
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Affiliation(s)
- Yvette Kayirangwa
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA.
| | - Md Mohibullah
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA.
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13
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De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, Kohler TN, Amadei G, Handford CE, Findlay GM, Zernicka-Goetz M, Teichmann SA, Hollfelder F. spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content. Nat Commun 2023; 14:4788. [PMID: 37553326 PMCID: PMC10409775 DOI: 10.1038/s41467-023-40322-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
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Affiliation(s)
- Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - David B Morse
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Gianluca Amadei
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte E Handford
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | | | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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14
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Panwar J, Utharala R, Fennelly L, Frenzel D, Merten CA. iSort enables automated complex microfluidic droplet sorting in an effort to democratize technology. CELL REPORTS METHODS 2023; 3:100478. [PMID: 37323570 PMCID: PMC10261925 DOI: 10.1016/j.crmeth.2023.100478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) is a widely used microfluidic technique for high-throughput screening. However, it requires highly trained specialists to determine optimal sorting parameters, and this results in a large combinatorial space that is challenging to optimize systematically. Additionally, it is currently challenging to track every single droplet within a screen, leading to compromised sorting and "hidden" false-positive events. To overcome these limitations, we have developed a setup in which the droplet frequency, spacing, and trajectory at the sorting junction are monitored in real time using impedance analysis. The resulting data are used to continuously optimize all parameters automatically and to counteract perturbations, resulting in higher throughput, higher reproducibility, increased robustness, and a beginner-friendly character. We believe this provides a missing piece for the spreading of phenotypic single-cell analysis methods, similar to what we have seen for single-cell genomics platforms.
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Affiliation(s)
- Jatin Panwar
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Ramesh Utharala
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Laura Fennelly
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Daniel Frenzel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Christoph A. Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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15
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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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16
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Sun G, Qu L, Azi F, Liu Y, Li J, Lv X, Du G, Chen J, Chen CH, Liu L. Recent progress in high-throughput droplet screening and sorting for bioanalysis. Biosens Bioelectron 2023; 225:115107. [PMID: 36731396 DOI: 10.1016/j.bios.2023.115107] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Owing to its ability to isolate single cells and perform high-throughput sorting, droplet sorting has been widely applied in several research fields. Compared with flow cytometry, droplet allows the encapsulation of single cells for cell secretion or lysate analysis. With the rapid development of this technology in the past decade, various droplet sorting devices with high throughput and accuracy have been developed. A droplet sorter with the highest sorting throughput of 30,000 droplets per second was developed in 2015. Since then, increased attention has been paid to expanding the possibilities of droplet sorting technology and strengthening its advantages over flow cytometry. This review aimed to summarize the recent progress in droplet sorting technology from the perspectives of device design, detection signal, actuating force, and applications. Technical details for improving droplet sorting through various approaches are introduced and discussed. Finally, we discuss the current limitations of droplet sorting for single-cell studies along with the existing gap between the laboratory and industry and provide our insights for future development of droplet sorters.
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Affiliation(s)
- Guoyun Sun
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Lisha Qu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology GTIIT, Shantou, Guangdong, 515063, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, Hong Kong, China.
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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17
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Medcalf EJ, Gantz M, Kaminski TS, Hollfelder F. Ultra-High-Throughput Absorbance-Activated Droplet Sorting for Enzyme Screening at Kilohertz Frequencies. Anal Chem 2023; 95:4597-4604. [PMID: 36848587 PMCID: PMC10018449 DOI: 10.1021/acs.analchem.2c04144] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Droplet microfluidics is a valuable method to "beat the odds" in high throughput screening campaigns such as directed evolution, where valuable hits are infrequent and large library sizes are required. Absorbance-based sorting expands the range of enzyme families that can be subjected to droplet screening by expanding possible assays beyond fluorescence detection. However, absorbance-activated droplet sorting (AADS) is currently ∼10-fold slower than typical fluorescence-activated droplet sorting (FADS), meaning that, in comparison, a larger portion of sequence space is inaccessible due to throughput constraints. Here we improve AADS to reach kHz sorting speeds in an order of magnitude increase over previous designs, with close-to-ideal sorting accuracy. This is achieved by a combination of (i) the use of refractive index matching oil that improves signal quality by removal of side scattering (increasing the sensitivity of absorbance measurements); (ii) a sorting algorithm capable of sorting at this increased frequency with an Arduino Due; and (iii) a chip design that transmits product detection better into sorting decisions without false positives, namely a single-layered inlet to space droplets further apart and injections of "bias oil" providing a fluidic barrier preventing droplets from entering the incorrect sorting channel. The updated ultra-high-throughput absorbance-activated droplet sorter increases the effective sensitivity of absorbance measurements through better signal quality at a speed that matches the more established fluorescence-activated sorting devices.
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Affiliation(s)
- Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom.,Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
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18
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Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting. Nat Protoc 2023; 18:1090-1136. [PMID: 36707723 DOI: 10.1038/s41596-022-00796-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/09/2022] [Indexed: 01/28/2023]
Abstract
Droplet microfluidics has revolutionized quantitative high-throughput bioassays and screening, especially in the field of single-cell analysis where applications include cell characterization, antibody discovery and directed evolution. However, droplet microfluidic platforms capable of phenotypic, fluorescence-based readouts and sorting are still mostly found in specialized labs, because their setup is complex. Complementary to conventional FACS, microfluidic droplet sorters allow the screening of cell libraries for secreted factors, or even for the effects of secreted or surface-displayed factors on a second cell type. Furthermore, they also enable PCR-activated droplet sorting for the isolation of genetic material harboring specific markers. In this protocol, we provide a detailed step-by-step guide for the construction of a high-throughput droplet analyzer and sorter, which can be accomplished in ~45 working hours by nonspecialists. The resulting instrument is equipped with three lasers to excite the fluorophores in droplets and photosensors that acquire fluorescence signals in the blue (425-465 nm), green (505-545 nm) and red (580-630 nm) spectrum. This instrument also allows transmittance-activated droplet sorting by analyzing the brightfield light intensity transmitting through the droplets. The setup is validated by sorting droplets containing fluorescent beads at 200 Hz with 99.4% accuracy. We show results from an experiment where droplets hosting single cells were sorted on the basis of increased matrix metalloprotease activity as an application of our workstation in single-cell molecular biology, e.g., to analyze molecular determinants of cancer metastasis.
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19
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Shao F, Lee PW, Li H, Hsieh K, Wang TH. Emerging platforms for high-throughput enzymatic bioassays. Trends Biotechnol 2023; 41:120-133. [PMID: 35863950 PMCID: PMC9789168 DOI: 10.1016/j.tibtech.2022.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/19/2022] [Accepted: 06/14/2022] [Indexed: 12/27/2022]
Abstract
Enzymes have essential roles in catalyzing biological reactions and maintaining metabolic systems. Many in vitro enzymatic bioassays have been developed for use in industrial and research fields, such as cell biology, enzyme engineering, drug screening, and biofuel production. Of note, many of these require the use of high-throughput platforms. Although the microtiter plate remains the standard for high-throughput enzymatic bioassays, microfluidic arrays and droplet microfluidics represent emerging methods. Each has seen significant advances and offers distinct advantages; however, drawbacks in key performance metrics, including reagent consumption, reaction manipulation, reaction recovery, real-time measurement, concentration gradient range, and multiplexity, remain. Herein, we compare recent high-throughput platforms using the aforementioned metrics as criteria and provide insights into remaining challenges and future research trends.
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Affiliation(s)
- Fangchi Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Pei-Wei Lee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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20
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Huang C, Jiang Y, Li Y, Zhang H. Droplet Detection and Sorting System in Microfluidics: A Review. MICROMACHINES 2022; 14:mi14010103. [PMID: 36677164 PMCID: PMC9867185 DOI: 10.3390/mi14010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 05/26/2023]
Abstract
Since being invented, droplet microfluidic technologies have been proven to be perfect tools for high-throughput chemical and biological functional screening applications, and they have been heavily studied and improved through the past two decades. Each droplet can be used as one single bioreactor to compartmentalize a big material or biological population, so millions of droplets can be individually screened based on demand, while the sorting function could extract the droplets of interest to a separate pool from the main droplet library. In this paper, we reviewed droplet detection and active sorting methods that are currently still being widely used for high-through screening applications in microfluidic systems, including the latest updates regarding each technology. We analyze and summarize the merits and drawbacks of each presented technology and conclude, with our perspectives, on future direction of development.
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Affiliation(s)
- Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Yuqian Jiang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuwen Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
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21
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Richter ES, Link A, McGrath JS, Sparrow RW, Gantz M, Medcalf EJ, Hollfelder F, Franke T. Acoustic sorting of microfluidic droplets at kHz rates using optical absorbance. LAB ON A CHIP 2022; 23:195-202. [PMID: 36472476 PMCID: PMC9764809 DOI: 10.1039/d2lc00871h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/28/2022] [Indexed: 05/19/2023]
Abstract
Droplet microfluidics allows one to address the ever-increasing demand to screen large libraries of biological samples. Absorbance spectroscopy complements the golden standard of fluorescence detection by label free target identification and providing more quantifiable data. However, this is limited by speed and sensitivity. In this paper we increase the speed of sorting by including acoustofluidics, achieving sorting rates of target droplets of 1 kHz. We improved the device design for detection of absorbance using fibre-based interrogation of samples with integrated lenses in the microfluidic PDMS device for focusing and collimation of light. This optical improvement reduces the scattering and refraction artefacts, improving the signal quality and sensitivity. The novel design allows us to overcome limitations based on dielectrophoresis sorting, such as droplet size dependency, material and dielectric properties of samples. Our acoustic activated absorbance sorter removes the need for offset dyes or matching oils and sorts about a magnitude faster than current absorbance sorters.
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Affiliation(s)
- Esther S Richter
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, G12 8LT Glasgow, UK.
| | - Andreas Link
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, G12 8LT Glasgow, UK.
| | - John S McGrath
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, G12 8LT Glasgow, UK.
| | - Raymond W Sparrow
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, G12 8LT Glasgow, UK.
| | - Maximilian Gantz
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Thomas Franke
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, G12 8LT Glasgow, UK.
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22
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Philpott DN, Chen K, Atwal RS, Li D, Christie J, Sargent EH, Kelley SO. Ultrathroughput immunomagnetic cell sorting platform. LAB ON A CHIP 2022; 22:4822-4830. [PMID: 36382608 DOI: 10.1039/d2lc00798c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
High-throughput phenotypic cell sorting is critical to the development of cell-based therapies and cell screening discovery platforms. However, current cytometry platforms are limited by throughput, number of fractionated populations that can be isolated, cell viability, and cost. We present an ultrathroughput microfluidic cell sorter capable of processing hundreds of millions of live cells per hour per device based on protein expression. This device, a next-generation microfluidic cell sorter (NG-MICS), combines multiple technologies, including 3D printing, reversible clamp sealing, and superhydrophobic treatments to create a reusable and user-friendly platform ready for deployment. The utility of such a platform is demonstrated through the rapid isolation of mature natural killer cells from peripheral blood mononuclear cells, for use in CAR-NK therapies at clinically-relevant scale.
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Affiliation(s)
- David N Philpott
- Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Kangfu Chen
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Randy S Atwal
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.
| | - Derek Li
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Jessie Christie
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Edward H Sargent
- Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL, USA
| | - Shana O Kelley
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
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23
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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] [MESH Headings] [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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24
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Samlali K, Alves CL, Jezernik M, Shih SCC. Droplet digital microfluidic system for screening filamentous fungi based on enzymatic activity. MICROSYSTEMS & NANOENGINEERING 2022; 8:123. [PMID: 36438986 PMCID: PMC9681769 DOI: 10.1038/s41378-022-00456-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Fungal cell-wall-degrading enzymes have great utility in the agricultural and food industries. These cell-wall-degrading enzymes are known to have functions that can help defend against pathogenic organisms. The existing methods used to discover these enzymes are not well adapted to fungi culture and morphology, which prevents the proper evaluation of these enzymes. We report the first droplet-based microfluidic method capable of long-term incubation and low-voltage conditions to sort filamentous fungi inside nanoliter-sized droplets. The new method was characterized and validated in solid-phase media based on colloidal chitin such that the incubation of single spores in droplets was possible over multiple days (2-4 days) and could be sorted without droplet breakage. With long-term culture, we examined the activity of cell-wall-degrading enzymes produced by fungi during solid-state droplet fermentation using three highly sensitive fluorescein-based substrates. We also used the low-voltage droplet sorter to select clones with highly active cell-wall-degrading enzymes, such as chitinases, β-glucanases, and β-N-acetylgalactosaminidases, from a filamentous fungi droplet library that had been incubated for >4 days. The new system is portable, affordable for any laboratory, and user-friendly compared to classical droplet-based microfluidic systems. We propose that this system will be useful for the growing number of scientists interested in fungal microbiology who are seeking high-throughput methods to incubate and sort a large library of fungal cells.
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Affiliation(s)
- Kenza Samlali
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
| | - Chiara Leal Alves
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
| | - Mara Jezernik
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada
| | - Steve C. C. Shih
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
- Department of Biology, Concordia University, Montréal, QC Canada
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25
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Qu F, Zhao L, Li L, Zhao S, Yang M, Yu J, Ho YP. Thermo-Induced Coalescence of Dual Cores in Double Emulsions for Single-Cell RT-PCR. Anal Chem 2022; 94:11670-11678. [PMID: 35968810 DOI: 10.1021/acs.analchem.2c02294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-cell reverse-transcription polymerase chain reaction (RT-PCR) has shown significant promise for transcriptional profiling of heterogeneous cells. However, currently developed microfluidic droplet-based methodologies for single-cell RT-PCR often require complex chip design to accommodate the associated multistep processes as well as customized detection platforms for high-throughput analysis. Herein, we proposed a dual-core double emulsion (DE)-based method to streamline the single-cell RT-PCR through thermo-induced coalescence of the dual cores. The dual-core DEs were produced by pairing two water-in-oil single emulsions containing a single-cell/lysis buffer and RT-PCR mix, respectively. After complete lysis of single cells in one of the cores, the dual-core DEs were merged by gentle heating, made possible by the optimized glycerol concentration present in the cores. Upon the coalescence of dual cores, the alkaline lysis buffer present in the core of the cell lysate was neutralized by the reaction buffer presented in the RT-PCR core, allowing TaqMan assay-based RT-PCR to occur effectively within the DEs. To demonstrate the potential of this streamlined dual-core platform, AKR1B10-positive A549 cells and AKR1B10-negative HEK293 cells were investigated via the TaqMan assay. Subsequently, specific transcript of AKR1B10 was readily available for quantitative profiling at the single-cell level using a commercially available flow cytometer in a high-throughput manner.
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Affiliation(s)
- Fuyang Qu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Liuyang Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Luoquan Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Shirui Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China.,Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China.,The Ministry of Education Key Laboratory of Regeneration Medicine, Shatin, New Territories, Hong Kong SAR 999077, China.,Centre for Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
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26
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Dannenberg PH, Kang J, Martino N, Kashiparekh A, Forward S, Wu J, Liapis AC, Wang J, Yun SH. Laser particle activated cell sorting in microfluidics. LAB ON A CHIP 2022; 22:2343-2351. [PMID: 35621381 PMCID: PMC9195882 DOI: 10.1039/d2lc00235c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/22/2022] [Indexed: 05/30/2023]
Abstract
Laser particles providing bright, spectrally narrowband emission renders them suitable for use as cellular barcodes. Here, we demonstrate a microfluidic platform integrated with a high-speed spectrometer, capable of reading the emission from laser particles in fluidic channels and routing cells based on their optical barcodes. The sub-nanometer spectral emission of each laser particle enables us to distinguish individual cells labeled with hundreds of different laser colors in the near infrared. Furthermore, cells tagged with laser particles are sorted based on their spectral barcodes at a kilohertz rate by using a real-time field programmable gate array and 2-way electric field switch. We demonstrate several different flavors of sorting, including isolation of barcoded cells, and cells tagged with a specific laser color. We term this novel sorting technique laser particle activated cell sorting (LACS). This flow reading and sorting technology adds to the arsenal of single-cell analysis tools using laser particles.
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Affiliation(s)
- Paul H Dannenberg
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jisoo Kang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicola Martino
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
| | - Anokhi Kashiparekh
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sarah Forward
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jiamin Wu
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Andreas C Liapis
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
| | - Jie Wang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, Jiangsu 210031, China
| | - Seok-Hyun Yun
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA.
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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27
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Characterizing cell interactions at scale with made-to-order droplet ensembles (MODEs). Proc Natl Acad Sci U S A 2022; 119:2110867119. [PMID: 35074872 PMCID: PMC8812558 DOI: 10.1073/pnas.2110867119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 01/22/2023] Open
Abstract
The study of specific cell–cell interactions at scale would be a significant advancement in single-cell biology with clear utility in immuno-oncology. Our development of Droplet Assembly provides a tool for such studies by extending the benefits of single-cell droplet microfluidics to high-order cell analyses. This technology allows for the construction, sorting, and downstream processing of cell–cell interactions and is compatible with single-cell genomic readouts. Cell–cell interactions are important to numerous biological systems, including tissue microenvironments, the immune system, and cancer. However, current methods for studying cell combinations and interactions are limited in scalability, allowing just hundreds to thousands of multicell assays per experiment; this limited throughput makes it difficult to characterize interactions at biologically relevant scales. Here, we describe a paradigm in cell interaction profiling that allows accurate grouping of cells and characterization of their interactions for tens to hundreds of thousands of combinations. Our approach leverages high-throughput droplet microfluidics to construct multicellular combinations in a deterministic process that allows inclusion of programmed reagent mixtures and beads. The combination droplets are compatible with common manipulation and measurement techniques, including imaging, barcode-based genomics, and sorting. We demonstrate the approach by using it to enrich for chimeric antigen receptor (CAR)-T cells that activate upon incubation with target cells, a bottleneck in the therapeutic T cell engineering pipeline. The speed and control of our approach should enable valuable cell interaction studies.
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28
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Hatori MN, Modavi C, Xu P, Weisgerber D, Abate AR. Dual-layered hydrogels allow complete genome recovery with nucleic acid cytometry. Biotechnol J 2022; 17:e2100483. [PMID: 35088927 PMCID: PMC9208836 DOI: 10.1002/biot.202100483] [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: 09/06/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022]
Abstract
Targeting specific cells for sequencing is important for applications in cancer, microbiology, and infectious disease. Nucleic acid cytometry is a powerful approach for accomplishing this because it allows specific cells to be isolated based on sequence biomarkers that are otherwise impossible to detect. However, existing methods require specialized microfluidic devices, limiting adoption. Here, we describe a modified workflow that uses particle-templated emulsification and flow cytometry to conduct the essential steps of cell detection and sorting normally accomplished by microfluidics. Our microfluidic-free workflow allows facile isolation and sequencing of cells, viruses, and nucleic acids and thus provides a powerful enrichment approach for targeted sequencing applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Peng Xu
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Daniel Weisgerber
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
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29
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Pryszlak A, Wenzel T, Seitz KW, Hildebrand F, Kartal E, Cosenza MR, Benes V, Bork P, Merten CA. Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics. CELL REPORTS METHODS 2022; 2:None. [PMID: 35118437 PMCID: PMC8787643 DOI: 10.1016/j.crmeth.2021.100137] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/05/2021] [Accepted: 12/07/2021] [Indexed: 11/25/2022]
Abstract
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low as 1:250 and by successfully enriching endogenous Bacteroides vulgatus to the level required for de novo assembly of high-quality genomes. Although microbiome strains are increasingly demanded for biomedical applications, a vast majority of species and strains are uncultivated and without reference genomes. We address this shortcoming by encapsulating complex microbiome samples directly into microfluidic droplets and amplifying a target-specific genomic fragment using a custom molecular TaqMan probe. We separate those positive droplets by droplet sorting, selectively enriching single target strain cells. Finally, we present a protocol to purify the genomic DNA while specifically removing amplicons and cell debris for high-quality genome sequencing.
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Affiliation(s)
- Anna Pryszlak
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tobias Wenzel
- European Molecular Biology Laboratory, Heidelberg, Germany
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Falk Hildebrand
- European Molecular Biology Laboratory, Heidelberg, Germany
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
- Digital Biology, Earlham Institute, Norwich, UK
| | - Ece Kartal
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Vladimir Benes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- University of Würzburg, Würzburg, Germany
| | - Christoph A. Merten
- European Molecular Biology Laboratory, Heidelberg, Germany
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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30
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Zachos I, Genth R, Sutiono S, Marczynski M, Lieleg O, Sieber V. Hot Flows: Evolving an Archaeal Glucose Dehydrogenase for Ultrastable Carba-NADP+ Using Microfluidics at Elevated Temperatures. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ioannis Zachos
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Robert Genth
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Matthias Marczynski
- TUM School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching 85748, Germany
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Straße 8, Garching 85748, Germany
| | - Oliver Lieleg
- TUM School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching 85748, Germany
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Straße 8, Garching 85748, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, Garching 85748, Germany
- SynBiofoundry@TUM, Technical University of Munich, Straubing 94315, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia 4072, Australia
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31
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Tran TM, Kim SC, Modavi C, Abate AR. Robotic automation of droplet microfluidics. BIOMICROFLUIDICS 2022; 16:014102. [PMID: 35145570 PMCID: PMC8816516 DOI: 10.1063/5.0064265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Droplet microfluidics enables powerful analytic capabilities but often requires workflows involving macro- and microfluidic processing steps that are cumbersome to perform manually. Here, we demonstrate the automation of droplet microfluidics with commercial fluid-handling robotics. The workflows incorporate common microfluidic devices including droplet generators, mergers, and sorters and utilize the robot's native capabilities for thermal control, incubation, and plate scanning. The ability to automate microfluidic devices using commercial fluid handling will speed up the integration of these methods into biological workflows.
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Affiliation(s)
- Tuan M. Tran
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
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32
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Manteca A, Gadea A, Van Assche D, Cossard P, Gillard-Bocquet M, Beneyton T, Innis CA, Baret JC. Directed Evolution in Drops: Molecular Aspects and Applications. ACS Synth Biol 2021; 10:2772-2783. [PMID: 34677942 PMCID: PMC8609573 DOI: 10.1021/acssynbio.1c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 11/29/2022]
Abstract
The process of optimizing the properties of biological molecules is paramount for many industrial and medical applications. Directed evolution is a powerful technique for modifying and improving biomolecules such as proteins or nucleic acids (DNA or RNA). Mimicking the mechanism of natural evolution, one can enhance a desired property by applying a suitable selection pressure and sorting improved variants. Droplet-based microfluidic systems offer a high-throughput solution to this approach by helping to overcome the limiting screening steps and allowing the analysis of variants within increasingly complex libraries. Here, we review cases where successful evolution of biomolecules was achieved using droplet-based microfluidics, focusing on the molecular processes involved and the incorporation of microfluidics to the workflow. We highlight the advantages and limitations of these microfluidic systems compared to low-throughput methods and show how the integration of these systems into directed evolution workflows can open new avenues to discover or improve biomolecules according to user-defined conditions.
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Affiliation(s)
- Aitor Manteca
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Alejandra Gadea
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | | | - Pauline Cossard
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Mélanie Gillard-Bocquet
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thomas Beneyton
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | - C. Axel Innis
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Jean-Christophe Baret
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
- Institut
Universitaire de France, F-75231 Paris, France
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33
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Two-photon fluorescence lifetime for label-free microfluidic droplet sorting. Anal Bioanal Chem 2021; 414:721-730. [PMID: 34792636 PMCID: PMC8748334 DOI: 10.1007/s00216-021-03745-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022]
Abstract
Microfluidic droplet sorting systems facilitate automated selective micromanipulation of compartmentalized micro- and nano-entities in a fluidic stream. Current state-of-the-art droplet sorting systems mainly rely on fluorescence detection in the visible range with the drawback that pre-labeling steps are required. This limits the application range significantly, and there is a high demand for alternative, label-free methods. Therefore, we introduce time-resolved two-photon excitation (TPE) fluorescence detection with excitation at 532 nm as a detection technique in droplet microfluidics. This enables label-free in-droplet detection of small aromatic compounds that only absorb in a deep-UV spectral region. Applying time-correlated single-photon counting, compounds with similar emission spectra can be distinguished due to their fluorescence lifetimes. This information is then used to trigger downstream dielectrophoretic droplet sorting. In this proof-of-concept study, we developed a polydimethylsiloxane-fused silica (FS) hybrid chip that simultaneously provides a very high optical transparency in the deep-UV range and suitable surface properties for droplet microfluidics. The herein developed system incorporating a 532-nm picosecond laser, time-correlated single-photon counting (TCSPC), and a chip-integrated dielectrophoretic pulsed actuator was exemplarily applied to sort droplets containing serotonin or propranolol. Furthermore, yeast cells were screened using the presented platform to show its applicability to study cells based on their protein autofluorescence via TPE fluorescence lifetime at 532 nm.
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34
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Vyawahare S, Brundage M, Kijac A, Gutierrez M, de Geus M, Sinha S, Homyk A. Sorting droplets into many outlets. LAB ON A CHIP 2021; 21:4262-4273. [PMID: 34617550 DOI: 10.1039/d1lc00493j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Droplet microfluidics is a commercially successful technology, widely used in single cell sequencing and droplet PCR. Combining droplet making with droplet sorting has also been demonstrated, but so far found limited use, partly due to difficulties in scaling manufacture with injection molded plastics. We introduce a droplet sorting system with several new elements, including: 1) an electrode design combining metallic and ionic liquid parts, 2) a modular, multi-sorting fluidic design with features for keeping inter-droplet distances constant, 3) using timing parameters calculated from fluorescence or scatter signal triggers to precisely actuate dozens of sorting electrodes, 4) droplet collection techniques, including ability to collect a single droplet, and 5) a new emulsion breaking method to collect aqueous samples for downstream analysis. We use these technologies to build a fluorescence based cell sorter that can sort with high (>90%) purity. We also show that these microfluidic designs can be translated into injection molded thermoplastic, suitable for industrial production. Finally, we tally the advantages and limitations of these devices.
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Affiliation(s)
- Saurabh Vyawahare
- Verily Life Sciences LLC, 249 E. Grand Avenue, South San Francisco, CA 94080, USA.
| | - Michael Brundage
- Verily Life Sciences LLC, 249 E. Grand Avenue, South San Francisco, CA 94080, USA.
| | - Aleksandra Kijac
- Verily Life Sciences LLC, 249 E. Grand Avenue, South San Francisco, CA 94080, USA.
| | - Michael Gutierrez
- Verily Life Sciences LLC, 249 E. Grand Avenue, South San Francisco, CA 94080, USA.
| | - Martina de Geus
- Verily Life Sciences LLC, 249 E. Grand Avenue, South San Francisco, CA 94080, USA.
| | - Supriyo Sinha
- Verily Life Sciences LLC, 249 E. Grand Avenue, South San Francisco, CA 94080, USA.
| | - Andrew Homyk
- Verily Life Sciences LLC, 249 E. Grand Avenue, South San Francisco, CA 94080, USA.
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35
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Dubay R, Urban JN, Darling EM. Single-Cell Microgels for Diagnostics and Therapeutics. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2009946. [PMID: 36329867 PMCID: PMC9629779 DOI: 10.1002/adfm.202009946] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Indexed: 05/14/2023]
Abstract
Cell encapsulation within hydrogel droplets is transforming what is feasible in multiple fields of biomedical science such as tissue engineering and regenerative medicine, in vitro modeling, and cell-based therapies. Recent advances have allowed researchers to miniaturize material encapsulation complexes down to single-cell scales, where each complex, termed a single-cell microgel, contains only one cell surrounded by a hydrogel matrix while remaining <100 μm in size. With this achievement, studies requiring single-cell resolution are now possible, similar to those done using liquid droplet encapsulation. Of particular note, applications involving long-term in vitro cultures, modular bioinks, high-throughput screenings, and formation of 3D cellular microenvironments can be tuned independently to suit the needs of individual cells and experimental goals. In this progress report, an overview of established materials and techniques used to fabricate single-cell microgels, as well as insight into potential alternatives is provided. This focused review is concluded by discussing applications that have already benefited from single-cell microgel technologies, as well as prospective applications on the cusp of achieving important new capabilities.
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Affiliation(s)
- Ryan Dubay
- Center for Biomedical Engineering, Brown University, 175 Meeting St., Providence, RI 02912, USA
- Draper, 555 Technology Sq., Cambridge, MA 02139, USA
| | - Joseph N Urban
- Center for Biomedical Engineering, Brown University, 175 Meeting St., Providence, RI 02912, USA
| | - Eric M Darling
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Center for Biomedical Engineering, School of Engineering, Department of Orthopaedics, Brown University, 175 Meeting St., Providence, RI 02912, USA
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36
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Loo MH, Nakagawa Y, Kim SH, Isozaki A, Goda K. High-throughput sorting of nanoliter droplets enabled by a sequentially addressable dielectrophoretic array. Electrophoresis 2021; 43:477-486. [PMID: 34599837 DOI: 10.1002/elps.202100057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 11/08/2022]
Abstract
Droplet microfluidics has emerged as a powerful tool for a diverse range of biomedical and industrial applications such as single-cell analysis, directed evolution, and metabolic engineering. In these applications, droplet sorting has been effective for isolating small droplets encapsulating molecules, cells, or crystals of interest. Recently, there is an increased interest in extending the applicability of droplet sorting to larger droplets to utilize their size advantage. However, sorting throughputs of large droplets have been limited, hampering their wide adoption. Here, we report our demonstration of high-throughput fluorescence-activated droplet sorting of 1 nL droplets using an upgraded version of the sequentially addressable dielectrophoretic array (SADA), which we reported previously. The SADA is an array of electrodes that are individually and sequentially activated/deactivated according to the speed and position of a droplet passing nearby the array. We upgraded the SADA by increasing the number of driving electrodes constituting the SADA and incorporating a slanted microchannel. By using a ten-electrode SADA with the slanted microchannel, we achieved fluorescence-activated droplet sorting of 1 nL droplets at a record high throughput of 1752 droplets/s, twice as high as the previously reported maximum sorting throughput of 1 nL droplets.
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Affiliation(s)
- Mun Hong Loo
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Yuta Nakagawa
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Soo Hyeon Kim
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Kanagawa Institute of Industrial Science and Technology, Kanagawa, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Department of Bioengineering, University of California, Los Angeles, CA, USA.,Institute of Technological Sciences, Wuhan University, Hubei, P. R. China
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37
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Van Lent J, Breukers J, Ven K, Ampofo L, Horta S, Pollet F, Imbrechts M, Geukens N, Vanhoorelbeke K, Declerck P, Lammertyn J. Miniaturized single-cell technologies for monoclonal antibody discovery. LAB ON A CHIP 2021; 21:3627-3654. [PMID: 34505611 DOI: 10.1039/d1lc00243k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.
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Affiliation(s)
- Julie Van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Louanne Ampofo
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Maya Imbrechts
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Paul Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
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Nakagawa Y, Ohnuki S, Kondo N, Itto-Nakama K, Ghanegolmohammadi F, Isozaki A, Ohya Y, Goda K. Are droplets really suitable for single-cell analysis? A case study on yeast in droplets. LAB ON A CHIP 2021; 21:3793-3803. [PMID: 34581379 DOI: 10.1039/d1lc00469g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-cell analysis has become one of the main cornerstones of biotechnology, inspiring the advent of various microfluidic compartments for cell cultivation such as microwells, microtrappers, microcapillaries, and droplets. A fundamental assumption for using such microfluidic compartments is that unintended stress or harm to cells derived from the microenvironments is insignificant, which is a crucial condition for carrying out unbiased single-cell studies. Despite the significance of this assumption, simple viability or growth tests have overwhelmingly been the assay of choice for evaluating culture conditions while empirical studies on the sub-lethal effect on cellular functions have been insufficient in many cases. In this work, we assessed the effect of culturing cells in droplets on the cellular function using yeast morphology as an indicator. Quantitative morphological analysis using CalMorph, an image-analysis program, demonstrated that cells cultured in flasks, large droplets, and small droplets significantly differed morphologically. From these differences, we identified that the cell cycle was delayed in droplets during the G1 phase and during the process of bud growth likely due to the checkpoint mechanism and impaired mitochondrial function, respectively. Furthermore, comparing small and large droplets, cells cultured in large droplets were morphologically more similar to those cultured in a flask, highlighting the advantage of increasing the droplet size. These results highlight a potential source of bias in cell analysis using droplets and reinforce the significance of assessing culture conditions of microfluidic cultivation methods for specific study cases.
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Affiliation(s)
- Yuta Nakagawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
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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: 122] [Impact Index Per Article: 40.7] [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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40
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Hyman LB, Christopher CR, Romero PA. Single-cell nucleic acid profiling in droplets (SNAPD) enables high-throughput analysis of heterogeneous cell populations. Nucleic Acids Res 2021; 49:e103. [PMID: 34233007 PMCID: PMC8501953 DOI: 10.1093/nar/gkab577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/03/2022] Open
Abstract
Experimental methods that capture the individual properties of single cells are revealing the key role of cell-to-cell variability in countless biological processes. These single-cell methods are becoming increasingly important across the life sciences in fields such as immunology, regenerative medicine and cancer biology. In addition to high-dimensional transcriptomic techniques such as single-cell RNA sequencing, there is a need for fast, simple and high-throughput assays to enumerate cell samples based on RNA biomarkers. In this work, we present single-cell nucleic acid profiling in droplets (SNAPD) to analyze sets of transcriptional markers in tens of thousands of single mammalian cells. Individual cells are encapsulated in aqueous droplets on a microfluidic chip and the RNA markers in each cell are amplified. Molecular logic circuits then integrate these amplicons to categorize cells based on the transcriptional markers and produce a detectable fluorescence output. SNAPD is capable of analyzing over 100,000 cells per hour and can be used to quantify distinct cell types within heterogeneous populations, detect rare cells at frequencies down to 0.1% and enrich specific cell types using microfluidic sorting. SNAPD provides a simple, rapid, low cost and scalable approach to study complex phenotypes in heterogeneous cell populations.
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Affiliation(s)
- Leland B Hyman
- Graduate Program in Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Clare R Christopher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Philip A Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.,The University of Wisconsin Carbone Cancer Center, Madison, WI 53706, USA
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41
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Li M, Liu H, Zhuang S, Goda K. Droplet flow cytometry for single-cell analysis. RSC Adv 2021; 11:20944-20960. [PMID: 35479393 PMCID: PMC9034116 DOI: 10.1039/d1ra02636d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/06/2021] [Indexed: 01/22/2023] Open
Abstract
The interrogation of single cells has revolutionised biology and medicine by providing crucial unparalleled insights into cell-to-cell heterogeneity. Flow cytometry (including fluorescence-activated cell sorting) is one of the most versatile and high-throughput approaches for single-cell analysis by detecting multiple fluorescence parameters of individual cells in aqueous suspension as they flow past through a focus of excitation lasers. However, this approach relies on the expression of cell surface and intracellular biomarkers, which inevitably lacks spatial and temporal phenotypes and activities of cells, such as secreted proteins, extracellular metabolite production, and proliferation. Droplet microfluidics has recently emerged as a powerful tool for the encapsulation and manipulation of thousands to millions of individual cells within pico-litre microdroplets. Integrating flow cytometry with microdroplet architectures surrounded by aqueous solutions (e.g., water-in-oil-in-water (W/O/W) double emulsion and hydrogel droplets) opens avenues for new cellular assays linking cell phenotypes to genotypes at the single-cell level. In this review, we discuss the capabilities and applications of droplet flow cytometry (DFC). This unique technique uses standard commercially available flow cytometry instruments to characterise or select individual microdroplets containing single cells of interest. We explore current challenges associated with DFC and present our visions for future development.
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Affiliation(s)
- Ming Li
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
- Biomolecular Discovery Research Centre, Macquarie University Sydney NSW 2109 Australia
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University Sydney NSW 2109 Australia
| | - Siyuan Zhuang
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo Tokyo 113-0033 Japan
- Institute of Technological Sciences, Wuhan University 430072 Hubei PR China
- Department of Bioengineering, University of California Los Angeles CA 90095 USA
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42
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White AM, Zhang Y, Shamul JG, Xu J, Kwizera EA, Jiang B, He X. Deep Learning-Enabled Label-Free On-Chip Detection and Selective Extraction of Cell Aggregate-Laden Hydrogel Microcapsules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100491. [PMID: 33899299 PMCID: PMC8203426 DOI: 10.1002/smll.202100491] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/27/2021] [Indexed: 05/05/2023]
Abstract
Microfluidic encapsulation of cells/tissues in hydrogel microcapsules has attracted tremendous attention in the burgeoning field of cell-based medicine. However, when encapsulating rare cells and tissues (e.g., pancreatic islets and ovarian follicles), the majority of the resultant hydrogel microcapsules are empty and should be excluded from the sample. Furthermore, the cell-laden hydrogel microcapsules are usually suspended in an oil phase after microfluidic generation, while the microencapsulated cells require an aqueous phase for further culture/transplantation and long-term suspension in oil may compromise the cells/tissues. Thus, real-time on-chip selective extraction of cell-laden hydrogel microcapsules from oil into aqueous phase is crucial to the further use of the microencapsulated cells/tissues. Contemporary extraction methods either require labeling of cells for their identification along with an expensive detection system or have a low extraction purity (<≈30%). Here, a deep learning-enabled approach for label-free detection and selective extraction of cell-laden microcapsules with high efficiency of detection (≈100%) and extraction (≈97%), high purity of extraction (≈90%), and high cell viability (>95%) is reported. The utilization of deep learning to dynamically analyze images in real time for label-free detection and on-chip selective extraction of cell-laden hydrogel microcapsules is unique and may be valuable to advance the emerging cell-based medicine.
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Affiliation(s)
- Alisa M White
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Yuntian Zhang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - James G Shamul
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Jiangsheng Xu
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Elyahb A Kwizera
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Bin Jiang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Xiaoming He
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, 20742, USA
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, 21201, USA
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43
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Conchouso D, Al-Ma'abadi A, Behzad H, Alarawi M, Hosokawa M, Nishikawa Y, Takeyama H, Mineta K, Gojobori T. Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:504-518. [PMID: 34952209 PMCID: PMC8864243 DOI: 10.1016/j.gpb.2021.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 02/09/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022]
Abstract
Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput. However, their adoption in laboratories studying “-omics” sciences is still irrelevant due to the complex and multidisciplinary nature of the field. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single cells in droplets at a rate of ∼250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers (i.e., 405, 488, 561, and 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability (>50,000 cells/day) for mining and bioprospecting metagenomic data
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Affiliation(s)
- David Conchouso
- Department of Industrial and Mechanical Engineering, Universidad de las Américas Puebla, Puebla 72810, Mexico; Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Amani Al-Ma'abadi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hayedeh Behzad
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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44
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Bouzetos E, Ganar KA, Mastrobattista E, Deshpande S, van der Oost J. (R)evolution-on-a-chip. Trends Biotechnol 2021; 40:60-76. [PMID: 34049723 DOI: 10.1016/j.tibtech.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 01/17/2023]
Abstract
Billions of years of Darwinian evolution has led to the emergence of highly sophisticated and diverse life forms on Earth. Inspired by natural evolution, similar principles have been adopted in laboratory evolution for the fast optimization of genes and proteins for specific applications. In this review, we highlight state-of-the-art laboratory evolution strategies for protein engineering, with a special emphasis on in vitro strategies. We further describe how recent progress in microfluidic technology has allowed the generation and manipulation of artificial compartments for high-throughput laboratory evolution experiments. Expectations for the future are high: we foresee a revolution on-a-chip.
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Affiliation(s)
- Evgenios Bouzetos
- Laboratory of Microbiology, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands
| | - Ketan Ashok Ganar
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands
| | - Enrico Mastrobattista
- Pharmaceutics Division, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Siddharth Deshpande
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands.
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45
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Hu B, Xu P, Ma L, Chen D, Wang J, Dai X, Huang L, Du W. One cell at a time: droplet-based microbial cultivation, screening and sequencing. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:169-188. [PMID: 37073344 PMCID: PMC10077293 DOI: 10.1007/s42995-020-00082-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.
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Affiliation(s)
- Beiyu Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xu
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 USA
| | - Liang Ma
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
| | - Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049 China
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46
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Kasai Y, Leipe C, Saito M, Kitagawa H, Lauterbach S, Brauer A, Tarasov PE, Goslar T, Arai F, Sakuma S. Breakthrough in purification of fossil pollen for dating of sediments by a new large-particle on-chip sorter. SCIENCE ADVANCES 2021; 7:7/16/eabe7327. [PMID: 33853775 PMCID: PMC8046374 DOI: 10.1126/sciadv.abe7327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Particle sorting is a fundamental method in various fields of medical and biological research. However, existing sorting applications are not capable for high-throughput sorting of large-size (>100 micrometers) particles. Here, we present a novel on-chip sorting method using traveling vortices generated by on-demand microjet flows, which locally exceed laminar flow condition, allowing for high-throughput sorting (5 kilohertz) with a record-wide sorting area of 520 micrometers. Using an activation system based on fluorescence detection, the method successfully sorted 160-micrometer microbeads and purified fossil pollen (maximum dimension around 170 micrometers) from lake sediments. Radiocarbon dates of sorting-derived fossil pollen concentrates proved accurate, demonstrating the method's ability to enhance building chronologies for paleoenvironmental records from sedimentary archives. The method is capable to cover urgent needs for high-throughput large-particle sorting in genomics, metabolomics, and regenerative medicine and opens up new opportunities for the use of pollen and other microfossils in geochronology, paleoecology, and paleoclimatology.
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Affiliation(s)
- Y Kasai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan
| | - C Leipe
- Institute for Space-Earth Environmental Research, Nagoya University, Aichi 464-8603, Japan.
| | - M Saito
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan
| | - H Kitagawa
- Institute for Space-Earth Environmental Research, Nagoya University, Aichi 464-8603, Japan
| | - S Lauterbach
- Leibniz Laboratory for Radiometric Dating and Stable Isotope Research, Kiel University, Max-Eyth-Str. 11-13, 24118 Kiel, Germany
- Institute of Geosciences, Kiel University, Ludewig-Meyn-Str. 10, 24118 Kiel, Germany
| | - A Brauer
- GFZ German Research Centre for Geosciences, Section 4.3-Climate Dynamics and Landscape Evolution, Telegrafenberg, 14473 Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - P E Tarasov
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74-100, Building D, 12249 Berlin, Germany
| | - T Goslar
- Poznan Radiocarbon Laboratory, Foundation of the Adam Mickiewicz University, Rubiez 46, Poznan, Poland
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan, Poland
| | - F Arai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan
- Department of Mechanical Engineering, The University of Tokyo, Bunkyo-ku 113-8656, Japan
| | - S Sakuma
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan.
- Department of Mechanical Engineering, Kyushu University, Fukuoka 819-0395, Japan
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47
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Kraus D, Kleiber A, Ehrhardt E, Leifheit M, Horbert P, Urban M, Gleichmann N, Mayer G, Popp J, Henkel T. Three step flow focusing enables image-based discrimination and sorting of late stage 1 Haematococcus pluvialis cells. PLoS One 2021; 16:e0249192. [PMID: 33780476 PMCID: PMC8007022 DOI: 10.1371/journal.pone.0249192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
Label-free and gentle separation of cell stages with desired target properties from mixed stage populations are a major research task in modern biotechnological cultivation process and optimization of micro algae. The reported microfluidic sorter system (MSS) allows the subsequent investigation of separated subpopulations. The implementation of a viability preserving MSS is shown for separation of late stage 1 Haematococcus pluvialis (HP) cells form a mixed stage population. The MSS combines a three-step flow focusing unit for aligning the cells in single file transportation mode at the center of the microfluidic channel with a pure hydrodynamic sorter structure for cell sorting. Lateral displacement of the cells into one of the two outlet channels is generated by piezo-actuated pump chambers. In-line decision making for sorting is based on a user-definable set of image features and properties. The reported MSS significantly increased the purity of target cells in the sorted population (94%) in comparison to the initial mixed stage population (19%).
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Affiliation(s)
- Daniel Kraus
- Leibniz Institute of Photonic Technology, Jena, Germany
| | | | - Enrico Ehrhardt
- Gesellschaft zur Förderung von Medizin-, Bio- und Umwelttechnologien e. V. (GMBU), Halle (Saale), Germany
| | - Matthias Leifheit
- Gesellschaft zur Förderung von Medizin-, Bio- und Umwelttechnologien e. V. (GMBU), Halle (Saale), Germany
| | - Peter Horbert
- Leibniz Institute of Photonic Technology, Jena, Germany
| | | | | | - Günter Mayer
- Leibniz Institute of Photonic Technology, Jena, Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Jena, Germany
| | - Thomas Henkel
- Leibniz Institute of Photonic Technology, Jena, Germany
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48
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Pärnamets K, Pardy T, Koel A, Rang T, Scheler O, Le Moullec Y, Afrin F. Optical Detection Methods for High-Throughput Fluorescent Droplet Microflow Cytometry. MICROMACHINES 2021; 12:mi12030345. [PMID: 33807031 PMCID: PMC8004903 DOI: 10.3390/mi12030345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
High-throughput microflow cytometry has become a focal point of research in recent years. In particular, droplet microflow cytometry (DMFC) enables the analysis of cells reacting to different stimuli in chemical isolation due to each droplet acting as an isolated microreactor. Furthermore, at high flow rates, the droplets allow massive parallelization, further increasing the throughput of droplets. However, this novel methodology poses unique challenges related to commonly used fluorometry and fluorescent microscopy techniques. We review the optical sensor technology and light sources applicable to DMFC, as well as analyze the challenges and advantages of each option, primarily focusing on electronics. An analysis of low-cost and/or sufficiently compact systems that can be incorporated into portable devices is also presented.
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Affiliation(s)
- Kaiser Pärnamets
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
- Correspondence:
| | - Tamas Pardy
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086 Tallinn, Estonia; (T.P.); (O.S.)
| | - Ants Koel
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
| | - Toomas Rang
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
| | - Ott Scheler
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086 Tallinn, Estonia; (T.P.); (O.S.)
| | - Yannick Le Moullec
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
| | - Fariha Afrin
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
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49
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Method for Passive Droplet Sorting after Photo-Tagging. MICROMACHINES 2020; 11:mi11110964. [PMID: 33126559 PMCID: PMC7692103 DOI: 10.3390/mi11110964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022]
Abstract
We present a method to photo-tag individual microfluidic droplets for latter selection by passive sorting. The use of a specific surfactant leads to the interfacial tension to be very sensitive to droplet pH. The photoexcitation of droplets containing a photoacid, pyranine, leads to a decrease in droplet pH. The concurrent increase in droplet interfacial tension enables the passive selection of irradiated droplets. The technique is used to select individual droplets within a droplet array as illuminated droplets remain in the wells while other droplets are eluted by the flow of the external oil. This method was used to select droplets in an array containing cells at a specific stage of apoptosis. The technique is also adaptable to continuous-flow sorting. By passing confined droplets over a microfabricated trench positioned diagonally in relation to the direction of flow, photo-tagged droplets were directed toward a different chip exit based on their lateral movement. The technique can be performed on a conventional fluorescence microscope and uncouples the observation and selection of droplets, thus enabling the selection on a large variety of signals, or based on qualitative user-defined features.
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50
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Bacon K, Lavoie A, Rao BM, Daniele M, Menegatti S. Past, Present, and Future of Affinity-based Cell Separation Technologies. Acta Biomater 2020; 112:29-51. [PMID: 32442784 PMCID: PMC10364325 DOI: 10.1016/j.actbio.2020.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023]
Abstract
Progress in cell purification technology is critical to increase the availability of viable cells for therapeutic, diagnostic, and research applications. A variety of techniques are now available for cell separation, ranging from non-affinity methods such as density gradient centrifugation, dielectrophoresis, and filtration, to affinity methods such as chromatography, two-phase partitioning, and magnetic-/fluorescence-assisted cell sorting. For clinical and analytical procedures that require highly purified cells, the choice of cell purification method is crucial, since every method offers a different balance between yield, purity, and bioactivity of the cell product. For most applications, the requisite purity is only achievable through affinity methods, owing to the high target specificity that they grant. In this review, we discuss past and current methods for developing cell-targeting affinity ligands and their application in cell purification, along with the benefits and challenges associated with different purification formats. We further present new technologies, like stimuli-responsive ligands and parallelized microfluidic devices, towards improving the viability and throughput of cell products for tissue engineering and regenerative medicine. Our comparative analysis provides guidance in the multifarious landscape of cell separation techniques and highlights new technologies that are poised to play a key role in the future of cell purification in clinical settings and the biotech industry. STATEMENT OF SIGNIFICANCE: Technologies for cell purification have served science, medicine, and industrial biotechnology and biomanufacturing for decades. This review presents a comprehensive survey of this field by highlighting the scope and relevance of all known methods for cell isolation, old and new alike. The first section covers the main classes of target cells and compares traditional non-affinity and affinity-based purification techniques, focusing on established ligands and chromatographic formats. The second section presents an excursus of affinity-based pseudo-chromatographic and non-chromatographic technologies, especially focusing on magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS). Finally, the third section presents an overview of new technologies and emerging trends, highlighting how the progress in chemical, material, and microfluidic sciences has opened new exciting avenues towards high-throughput and high-purity cell isolation processes. This review is designed to guide scientists and engineers in their choice of suitable cell purification techniques for research or bioprocessing needs.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Ashton Lavoie
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA
| | - Michael Daniele
- Joint Department of Biomedical Engineering, North Carolina State University - University of North Carolina Chapel Hill, North Carolina, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA.
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