1
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Zhang P, Liu C, Modavi C, Abate A, Chen H. Printhead on a chip: empowering droplet-based bioprinting with microfluidics. Trends Biotechnol 2024; 42:353-368. [PMID: 37777352 DOI: 10.1016/j.tibtech.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
Droplet-based bioprinting has long struggled with the manipulation and dispensation of individual cells from a printhead, hindering the fabrication of artificial cellular structures with high precision. The integration of modern microfluidic modules into the printhead of a bioprinter is emerging as one approach to overcome this bottleneck. This convergence allows for high-accuracy manipulation and spatial control over placement of cells during printing, and enables the fabrication of cell arrays and hierarchical heterogenous microtissues, opening new applications in bioanalysis and high-throughput screening. In this review, we summarize recent developments in the use of microfluidics in droplet printing systems, with consideration of the working principles; present applications extended through microfluidic features; and discuss the future of this technology.
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Affiliation(s)
- Pengfei Zhang
- School of Mechanical Engineering and Automation, Beihang University, Beijing, China.
| | - Congying Liu
- School of Mechanical Engineering and Automation, Beihang University, Beijing, China
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Huawei Chen
- School of Mechanical Engineering and Automation, Beihang University, Beijing, China
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2
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Strutt R, Xiong B, Abegg VF, Dittrich PS. Open microfluidics: droplet microarrays as next generation multiwell plates for high throughput screening. LAB ON A CHIP 2024; 24:1064-1075. [PMID: 38356285 PMCID: PMC10898417 DOI: 10.1039/d3lc01024d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/04/2024] [Indexed: 02/16/2024]
Abstract
Multiwell plates are prominent in the biological and chemical sciences; however, they face limitations in terms of throughput and deployment in emerging bioengineering fields. Droplet microarrays, as an open microfluidic technology, organise tiny droplets typically in the order of thousands, on an accessible plate. In this perspective, we summarise current approaches for generating droplets, fluid handling on them, and analysis within droplet microarrays. By enabling unique plate engineering opportunities, demonstrating the necessary experimental procedures required for manipulating and interacting with biological cells, and integrating with label-free analytical techniques, droplet microarrays can be deployed across a more extensive experimental domain than what is currently covered by multiwell plates. Droplet microarrays thus offer a solution to the bottlenecks associated with multiwell plates, particularly in the areas of biological cultivation and high-throughput compound screening.
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Affiliation(s)
- Robert Strutt
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Bijing Xiong
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Vanessa Fabienne Abegg
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
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3
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Whitehead J, Leferink NGH, Johannissen LO, Hay S, Scrutton NS. Decoding Catalysis by Terpene Synthases. ACS Catal 2023; 13:12774-12802. [PMID: 37822860 PMCID: PMC10563020 DOI: 10.1021/acscatal.3c03047] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The review by Christianson, published in 2017 on the twentieth anniversary of the emergence of the field, summarizes the foundational discoveries and key advances in terpene synthase/cyclase (TS) biocatalysis (Christianson, D. W. Chem Rev2017, 117 (17), 11570-11648. DOI: 10.1021/acs.chemrev.7b00287). Here, we review the TS literature published since then, bringing the field up to date and looking forward to what could be the near future of TS rational design. Many revealing discoveries have been made in recent years, building on the knowledge and fundamental principles uncovered during those initial two decades of study. We use these to explore TS reaction chemistry and see how a combined experimental and computational approach helps to decipher the complexities of TS catalysis. Revealed are a suite of catalytic motifs which control product outcome in TSs, some obvious, some more subtle. We examine each in detail, using the most recent papers and insights to illustrate how exactly this fascinating class of enzymes takes a single acyclic substrate and turns it into the many thousands of complex terpenoids found in Nature. We then explore some of the recent strategies for TS engineering, including machine learning and other data-driven approaches. From this, rational and predictive engineering of TSs, "designer terpene synthases", will begin to emerge as a realistic goal.
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Affiliation(s)
- Joshua
N. Whitehead
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
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4
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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: 5] [Impact Index Per Article: 5.0] [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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5
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Hengoju S, Shvydkiv O, Tovar M, Roth M, Rosenbaum MA. Advantages of optical fibers for facile and enhanced detection in droplet microfluidics. Biosens Bioelectron 2022; 200:113910. [PMID: 34974260 DOI: 10.1016/j.bios.2021.113910] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 11/02/2022]
Abstract
Droplet microfluidics offers a unique opportunity for ultrahigh-throughput experimentation with minimal sample consumption and thus has obtained increasing attention, particularly for biological applications. Detection and measurements of analytes or biomarkers in tiny droplets are essential for proper analysis of biological and chemical assays like single-cell studies, cytometry, nucleic acid detection, protein quantification, environmental monitoring, drug discovery, and point-of-care diagnostics. Current detection setups widely use microscopes as a central device and other free-space optical components. However, microscopic setups are bulky, complicated, not flexible, and expensive. Furthermore, they require precise optical alignments, specialized optical and technical knowledge, and cumbersome maintenance. The establishment of efficient, simple, and cheap detection methods is one of the bottlenecks for adopting microfluidic strategies for diverse bioanalytical applications and widespread laboratory use. Together with great advances in optofluidic components, the integration of optical fibers as a light guiding medium into microfluidic chips has recently revolutionized analytical possibilities. Optical fibers embedded in a microfluidic platform provide a simpler, more flexible, lower-cost, and sensitive setup for the detection of several parameters from biological and chemical samples and enable widespread, hands-on application much beyond thriving point-of-care developments. In this review, we examine recent developments in droplet microfluidic systems using optical fiber as a light guiding medium, primarily focusing on different optical detection methods such as fluorescence, absorbance, light scattering, and Raman scattering and the potential applications in biochemistry and biotechnology that are and will be arising from this.
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Affiliation(s)
- Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Oksana Shvydkiv
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany.
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6
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Fu X, Zhang Y, Xu Q, Sun X, Meng F. Recent Advances on Sorting Methods of High-Throughput Droplet-Based Microfluidics in Enzyme Directed Evolution. Front Chem 2021; 9:666867. [PMID: 33996758 PMCID: PMC8114877 DOI: 10.3389/fchem.2021.666867] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/02/2021] [Indexed: 11/24/2022] Open
Abstract
Droplet-based microfluidics has been widely applied in enzyme directed evolution (DE), in either cell or cell-free system, due to its low cost and high throughput. As the isolation principles are based on the labeled or label-free characteristics in the droplets, sorting method contributes mostly to the efficiency of the whole system. Fluorescence-activated droplet sorting (FADS) is the mostly applied labeled method but faces challenges of target enzyme scope. Label-free sorting methods show potential to greatly broaden the microfluidic application range. Here, we review the developments of droplet sorting methods through a comprehensive literature survey, including labeled detections [FADS and absorbance-activated droplet sorting (AADS)] and label-free detections [electrochemical-based droplet sorting (ECDS), mass-activated droplet sorting (MADS), Raman-activated droplet sorting (RADS), and nuclear magnetic resonance-based droplet sorting (NMR-DS)]. We highlight recent cases in the last 5 years in which novel enzymes or highly efficient variants are generated by microfluidic DE. In addition, the advantages and challenges of different sorting methods are briefly discussed to provide an outlook for future applications in enzyme DE.
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Affiliation(s)
- Xiaozhi Fu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yueying Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Qiang Xu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaomeng Sun
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Fanda Meng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
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7
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Abstract
Microsystem technologies allow a plethora of operations to be achieved for microemulsion- and microdroplet-based assays, providing miniaturized, yet large-throughput capabilities to assist experimentation in analytical chemistry, biology, and synthetic biology. Many of such approaches have been implemented on-chip, using microfluidic and lab-on-a-chip technologies. However, the microfabrication of such devices relies on expensive equipment and time-consuming methods, thus hindering their uptake and use by many research laboratories where microfabrication expertise is not available. Here, we demonstrate how fundamental water-in-oil microdroplet operations, such as droplet trapping, merging, diluting, and splitting, can be obtained using straightforward, inexpensive, and manually fabricated polymeric microtube modules. The modules are based on creating an angled tubing interface at the interconnection between two polymeric microtubes. We have characterized how the geometry and fluid dynamic conditions at this interface enabled different droplet operations to be achieved in a versatile and functional manner. We envisage this approach to be an alternative solution to expensive and laborious microfabrication protocols for droplet microfluidic applications.
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Affiliation(s)
- Yu Zhang
- Centre for Microsystems and Photonics, EEE Department, University of Strathclyde, Glasgow G1 1XW, U.K
| | - Ziyun Wang
- Centre for Microsystems and Photonics, EEE Department, University of Strathclyde, Glasgow G1 1XW, U.K
| | - Declan New
- Centre for Microsystems and Photonics, EEE Department, University of Strathclyde, Glasgow G1 1XW, U.K
| | - Michele Zagnoni
- Centre for Microsystems and Photonics, EEE Department, University of Strathclyde, Glasgow G1 1XW, U.K
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8
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High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
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9
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Hengoju S, Tovar M, Man DKW, Buchheim S, Rosenbaum MA. Droplet Microfluidics for Microbial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:129-157. [PMID: 32888037 DOI: 10.1007/10_2020_140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.
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Affiliation(s)
- Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - DeDe Kwun Wai Man
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - Stefanie Buchheim
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany.
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10
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Leavell MD, Singh AH, Kaufmann-Malaga BB. High-throughput screening for improved microbial cell factories, perspective and promise. Curr Opin Biotechnol 2020; 62:22-28. [DOI: 10.1016/j.copbio.2019.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 01/11/2023]
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11
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Zhang JQ, Siltanen CA, Liu L, Chang KC, Gartner ZJ, Abate AR. Linked optical and gene expression profiling of single cells at high-throughput. Genome Biol 2020; 21:49. [PMID: 32093753 PMCID: PMC7041248 DOI: 10.1186/s13059-020-01958-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Single-cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through changes in gene expression. Linking sequencing with optical analysis has provided insight into the molecular basis of cellular function, but current approaches have limited throughput. Here, we present a high-throughput platform for linked optical and gene expression profiling of single cells. We demonstrate accurate fluorescence and gene expression measurements on thousands of cells in a single experiment. We use the platform to characterize DNA and RNA changes through the cell cycle and correlate antibody fluorescence with gene expression. The platform's ability to isolate rare cell subsets and perform multiple measurements, including fluorescence and sequencing-based analysis, holds potential for scalable multi-modal single-cell analysis.
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Affiliation(s)
- Jesse Q Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Christian A Siltanen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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12
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Single-cell assays using integrated continuous-flow microfluidics. Methods Enzymol 2019. [PMID: 31668236 DOI: 10.1016/bs.mie.2019.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The recent maturation of continuous-flow microfluidic technologies has coincided with transformative new methods to profile single cells, including their genetic types, protein expression and enzyme activities. Continuous-flow high-throughput single-cell screening and sorting can reveal relationships across cellular phenotypes (e.g., enzyme activity and secretion) and genetic fingerprints. This technology provides unique opportunities, as well as experimental and computational challenges, for integrative approaches that can process large amounts of single-cell data. In this chapter, we discuss recent advances in integrated continuous-flow microfluidic approaches with a focus on measurements and statistical analysis of single-cell enzyme activity and their applications in quantitative biology, synthetic biology, and diagnosis.
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13
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Droplet Microfluidics-Enabled High-Throughput Screening for Protein Engineering. MICROMACHINES 2019; 10:mi10110734. [PMID: 31671786 PMCID: PMC6915371 DOI: 10.3390/mi10110734] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/19/2022]
Abstract
Protein engineering—the process of developing useful or valuable proteins—has successfully created a wide range of proteins tailored to specific agricultural, industrial, and biomedical applications. Protein engineering may rely on rational techniques informed by structural models, phylogenic information, or computational methods or it may rely upon random techniques such as chemical mutation, DNA shuffling, error prone polymerase chain reaction (PCR), etc. The increasing capabilities of rational protein design coupled to the rapid production of large variant libraries have seriously challenged the capacity of traditional screening and selection techniques. Similarly, random approaches based on directed evolution, which relies on the Darwinian principles of mutation and selection to steer proteins toward desired traits, also requires the screening of very large libraries of mutants to be truly effective. For either rational or random approaches, the highest possible screening throughput facilitates efficient protein engineering strategies. In the last decade, high-throughput screening (HTS) for protein engineering has been leveraging the emerging technologies of droplet microfluidics. Droplet microfluidics, featuring controlled formation and manipulation of nano- to femtoliter droplets of one fluid phase in another, has presented a new paradigm for screening, providing increased throughput, reduced reagent volume, and scalability. We review here the recent droplet microfluidics-based HTS systems developed for protein engineering, particularly directed evolution. The current review can also serve as a tutorial guide for protein engineers and molecular biologists who need a droplet microfluidics-based HTS system for their specific applications but may not have prior knowledge about microfluidics. In the end, several challenges and opportunities are identified to motivate the continued innovation of microfluidics with implications for protein engineering.
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14
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Sesen M, Fakhfouri A, Neild A. Coalescence of Surfactant-Stabilized Adjacent Droplets Using Surface Acoustic Waves. Anal Chem 2019; 91:7538-7545. [DOI: 10.1021/acs.analchem.8b05456] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Muhsincan Sesen
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Armaghan Fakhfouri
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Adrian Neild
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia
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15
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Liu L, Dalal CK, Heineike BM, Abate AR. High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq. LAB ON A CHIP 2019; 19:1838-1849. [PMID: 31020292 PMCID: PMC7909483 DOI: 10.1039/c9lc00084d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Yeast can be engineered into "living foundries" for non-natural chemical production by reprogramming them via a "design-build-test" cycle. While methods for "design" and "build" are relatively scalable and efficient, "test" remains a bottleneck, limiting the effectiveness of the procedure. Here we describe isogenic colony sequencing (ICO-seq), a massively-parallel strategy to assess the gene expression, and thus engineered pathway efficacy, of large numbers of genetically distinct yeast colonies. We use the approach to characterize opaque-white switching in 658 C. albicans colonies. By profiling the transcriptomes of 1642 engineered S. cerevisiae strains, we assess gene expression heterogeneity in a protein mutagenesis library. Our approach will accelerate synthetic biology by allowing facile and cost-effective transcriptional profiling of large numbers of genetically distinct yeast strains.
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Affiliation(s)
- Leqian Liu
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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16
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Eilenberger C, Spitz S, Bachmann BEM, Ehmoser EK, Ertl P, Rothbauer M. The Usual Suspects 2019: of Chips, Droplets, Synthesis, and Artificial Cells. MICROMACHINES 2019; 10:E285. [PMID: 31035574 PMCID: PMC6562886 DOI: 10.3390/mi10050285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/03/2022]
Abstract
Synthetic biology aims to understand fundamental biological processes in more detail than possible for actual living cells. Synthetic biology can combat decomposition and build-up of artificial experimental models under precisely controlled and defined environmental and biochemical conditions. Microfluidic systems can provide the tools to improve and refine existing synthetic systems because they allow control and manipulation of liquids on a micro- and nanoscale. In addition, chip-based approaches are predisposed for synthetic biology applications since they present an opportune technological toolkit capable of fully automated high throughput and content screening under low reagent consumption. This review critically highlights the latest updates in microfluidic cell-free and cell-based protein synthesis as well as the progress on chip-based artificial cells. Even though progress is slow for microfluidic synthetic biology, microfluidic systems are valuable tools for synthetic biology and may one day help to give answers to long asked questions of fundamental cell biology and life itself.
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Affiliation(s)
- Christoph Eilenberger
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Sarah Spitz
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Barbara Eva Maria Bachmann
- Austrian Cluster for Tissue Regeneration, Vienna, Austria; Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Allgemeine Unfallversicherungsanstalt (AUVA) Research Centre, A-1200 Vienna, Austria.
| | - Eva Kathrin Ehmoser
- Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
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Chen K, Sui C, Wu Y, Ao Z, Guo SS, Guo F. A digital acoustofluidic device for on-demand and oil-free droplet generation. NANOTECHNOLOGY 2019; 30:084001. [PMID: 30523921 DOI: 10.1088/1361-6528/aaf3fd] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a digital acoustofluidic device for on-demand and oil-free droplet generation. By applying a programmed radio frequency signal to a circular interdigital transducer, the dynamic focused acoustic pressure profiles generated rise up and dispense sample liquids from a reservoir to dynamically eject the droplets into the air. Our device allows droplets to be dispensed on demand with precisely controlled generation time and sequence, and accurate droplet volume. Moreover, we also demonstrate the generation of a droplet with a volume of 24 pL within 10 ms, as well as the encapsulation of a single cell into droplets. This acoustofluidic droplet generation technique is simple, biocompatible, and enables the on-demand droplet generation and encapsulation of many different biological materials with precise control, which is promising for single cell sampling and analysis applications.
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Affiliation(s)
- Keke Chen
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, People's Republic of China
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Affiliation(s)
- Gongchen Sun
- School of Chemical & Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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